Difference between revisions of "Software2"

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  /home/lml/krypton/bin/em -h  
 
  /home/lml/krypton/bin/em -h  
  
−
== Statistics ==
+
===  makebeads2 ===
−
===  cluster_distances.pl ===
+
/home/lml/krypton/bin/makebeads2
  
−
  Takes output from channel_current2 (after 11/24/09) and pulls out statistics about
+
randomly distributes beads within a volume.  created to let Jack simulate
−
  mean distance to each BK cluster.  Then produces average stats from all the files
+
distribution of glut4 labels vesicles in the TIRF field of a microscope.
−
  analyzed. Output to stdout.
+
A bead has a constant value between its inner and outer diameters. This value
 +
falls to zero 3 standard deviations inside the inner diameter and 3 sd outside
 +
the outer diameter. Beads are not allowed to intersect each other.
 +
Writes info about beads created or moved to stdout (can be read back in with -b option).
 +
note: coords written out are zero indexed (not 1-indexed like addlines and play) in pixels.
 +
usage:
 +
makebeads2 [options] outimage.i2i
 +
options:
 +
-d x y z: image dimensions in pixels, default = (256,256,64)
 +
-D # #: bead inner and outer diameters in microns, default = 0.200000 and 0.200000
 +
  -R #: inner rise standard deviation (in microns), default = 0.012500
 +
-F #: outer fall standard deviation (in microns), default = 0.012500
 +
-S x y z: x, y, and z pixel dimensions (in microns), default = (0.040000,0.040000,0.010000)
 +
  -c x y z: x, y, and z pixel dimensions for new image size.  If you are planning on taking the
 +
image produced by makebeads2 and using chres to change pixel size, put the new
 +
pixel sizes here. This is used when calculating the intensity of the brightest pixel
 +
from each bead. This output info can be useful for signal to noise ratio tests.
 +
  -X #: number of subpixels per pixels, default = 10
 +
-p # val: set z plane # (0 indexed) to val (modelling diffuse fluorescence on the plasma membrane)
 +
If val is < 1 it is interpreted as a fraction of total light in the image.
 +
For example: val = .2 means set the z plane to the intensity necessary so that the total
 +
light in that plane is 2012f the total in the final image (i.e., after exponential if -e or -E)
 +
  -e dist: apply an exponential scale factor exp(-z/dist) to each zslice; like a TIRF excitation intensity
 +
dist is the 1/e distance in microns (.1 is a good value)
 +
This exponential also get applied to z plane value set via "-p # val" if val >= 1. It does
 +
NOT apply to that if val < 1.
 +
-E amp2 dist2:apply a second an exponential scale factor amp2*exp(-z/dist2) to each zslice
 +
must also use -e option.  Each intensity will be scaled by (amp1*exp(-z/dist)+amp2*exp(-z/dist2)).
 +
amp1 + amp2 = 1 and is automatically set when -E is used (amp1 = 1-amp2).
  
 +
options related to output:
 +
-i #: outimage.i2i should be scaled by # before writing it.  Format is short int (our default format).
 +
-f #: outimage.i2i should be scaled by # before writing it.  Format is float.
 +
-v: verbose.
 +
-A: don't create outimage.i2i (still need a dummy name on command line though).
 +
-B: don't even simulate voxels (just prints beads centers, amplitudes, sizes).  Automatically sets -A.
 +
-u file.objs: create file, which has a list of bead objects created, in the same format countobjs produces.
 +
this lets utilities written to analyze files in that format to then be used
 +
(e.g., objs2dist.pl, objs2bb.pl). COM field is the bead center even if part of it is outside
 +
the image. Size field is in pixels (only counting what is within the image).
 +
IOD is the total bead light in the image after exponential weighting (if -e or -E) and scaling (-i, -f).
 +
AVG = IOD/size.  MAX is the max pixel (after -e,-E,-i,-f) . Some file header info may be wrong.
 +
-U file.objs: like -u, but all z coords are replaced by 1, and coordinates are for the new resolution specified
 +
by -c option. MAX value and max coord come from a sum projection in z at the new resolution.
 +
(after -e,-E,-i,-f).
 +
-W: print some warning messages to stderr if appropriate.  note: This will mess up the output in the file
 +
if you are running it as:  makebeads2 -W .... >& file.out
  
−
  usage:
+
options controlling randomization (of a uniform random distribution unless otherwise noted):
 +
-s min max: mininum and maximum range of allowed bead sizes. This number scales the
 +
bead inner and outer diameters (does not change sd). default = 1.000000 and 1.000000
 +
-G mean sd:  make bead sizes (scales) a Gaussian variable with specified mean and sd (instead of -s).
 +
note: since beads can't intersect, if you place beads densely you will tend to get more
 +
small beads (since the program generates a new random bead if one doesn't fit), and hence
 +
the size distribution will no longer match the parameters specified here.
 +
-g mean sd shell: like -G, but also specify bead shell thickness in microns.  mean doesn't scale the shell thickness.
 +
mean is the diameter to midway between the inner and outer diameters (so don't use -D option).
 +
-a min max: min and max amplitude (brightness) of bead, default = 1000.000000 and 1000.000000
 +
a pixel which is entirely covered by the shell of the bead (between -D numbers) will have this value.
 +
So this is like specifying a fluorescent concentration.
 +
-P lambda scale:  make amplitude a Poisson variable with the specified mean (lambda) value (instead of -a option).
 +
this value then gets multiplied by scale.  Amplitudes of 0 get ignored (a new amplitude is calculated).
 +
note: this is still just the amplitude of a covered pixel, not of the entire bead unless -T used too.
 +
-T: The amplitude specified with -a or -P option is the total light in the bead, not the light
 +
of one fully covered pixel.  Takes about double the time to run.
 +
note: if the amplitude isn't large compared to number of pixels in the bead's shell, then
 +
individual pixel intensities will be small and truncation may effect total intensity.
 +
-x min max:  allowed position of beads, in pixels, zero indexed, inclusive. The entire bead must fit in this region
 +
unless -o option also specified.
 +
-y min max:  allowed position of beads, in pixels, zero indexed (default = anywhere within image)
 +
-z min max:  allowed position of beads, in pixels, zero indexed (default = anywhere within image)
 +
-o: allow bead centers to fall outside the image volume (except in low z direction, i.e. coverslip).
 +
This is a more accurate way to represent a small view of a large cell.
 +
This option is ignored if -b option used.
 +
-O: like -o, but beads in low z direction outside the volume reflect back inside the volume (i.e. get
 +
moved back inside volume instead of thrown away).
 +
note: if bead density is too high, reflecting a bead inside may cause it to intersect with a previous
 +
bead, in which case the reflecting bead will be thrown away and a new randomly placed bead created.
 +
-w #: use # as the seed for random number generator, so can reproduce exact runs. must be negative.
 +
-b file xyspeed zspeed:  read initial bead params (e.g., size, position) from file, just add random position to this.
 +
the random position uses the speeds (in microns) as the max the vesicle can move in each direction
 +
in this time period (i.e., dx = ran(0 to 1)*xyspeed, etc).
 +
Set xyspeed and zspeed = 0 if you don't want to move the beads.
 +
  -j #: long int starting seed for random number generator. specify the same number (not 0) each time you run this
 +
program if you want to exactly repeat the random numbers generated. The default is to use a different
 +
starting seed each time based upon the process id when you run the program.
 +
  -n #: number of beads to make, default = 100, max = 10000
  
−
  -files:file1:file2:...:filen       which files to analyze. Defaults are files named 2_*.currents in cwd.
+
Examples:
−
  -numBKvsProb       also prints numBK vs prob data suitable for xmgrace
+
#create 200 beads, with a 50 nm (5 z plane) gap before the pm, which has an
 +
#intensity of 50. Apply a TIRF exponential excitation scale to it.
 +
makebeads2 -e .1 -z 5 63 -p 5 50 -n 200 beads1.i2i > beads1.info
 +
# apply microscope psf
 +
blur3d -P -N 256 256 128 beads1.i2i empiricalpsf_seg_40nm_seg.i2i beads1_blur3d.i2i
 +
# bin (averge) to 100/160 nm resolution
 +
reduceima -A -X 1 256 4 -Y 1 256 4 beads1_blur3d.i2i beads1_blur3d4x4.i2i
 +
# extract infocus plane
 +
segment -Z 16 16 1 beads1_blur3d4x4.i2i beads1_blur2d4x4.i2i
 +
# add ScratchNG camera noise
 +
noise -e 1.4 -n 8 beads1_blur2d4x4.i2i beads1_blur2d4x4N.i2i
 +
histima -size 10 -bins 100 beads1_blur2d4x4N.i2i > beads1_blur2d4x4N.hist
  
 +
#creates beads, move them, look at the results
 +
makebeads2 -z 5 63 beads1.i2i > beads1.info
 +
#read those beads in and move them. but still must stay outside the first 50 nm.
 +
makebeads2 -z 5 63 -b beads1.info .05 .05 beads2.i2i > beads2.info
 +
concateima beads1.i2i beads2.i2i beads.i2i
 +
imsets beads.i2i 2
 +
dave -tdim 2 -4 -I beads.i2i
  
−
example:
+
#just create scripts (very fast) with positions of beads, and move them around.
−
  (channel_current2  .... > file.channel_current) >& file1.currents
+
makebeads -z 5 63 -n 200 -A dummy.i2i > beads1.info
−
  (channel_current2  .... > file2.channel_current) >& file2.currents
+
makebeads -b beads1.info .05 .05 -z 5 63 -A dummy.i2i > beads2.info
−
  cluster_distances.pl -numBKvsProb -files=file1.currents:file2.currents > avg_distances.txt
+
makebeads -b beads2.info .05 .05 -z 5 63 -A dummy.i2i > beads3.info
−
  fgrep -v clusters avg_distances.txt |xmgrace -pipe
+
#now create the images
 +
makebeads -b beads1.info 0 0  beads1.i2i > beads1.info2
 +
makebeads -b beads2.info 0 0  beads2.i2i > beads2.info2
 +
makebeads -b beads3.info 0 0  beads3.i2i > beads3.info2
  
−
  note: mean distances to clusters are not always increasing (e.g., mean distance to 10th
+
see also: makebead, readbeads.pl, blur3d, project, /storage/big1/sh/simul
−
      cluster could be SMALLER than the mean distance to the 9th cluster).  I think this
 
−
      has to do with limiting my maximum distance (see comments in this file).
 
  
 +
source code in ~lml/krypton/facil
 
   
 
   
−
  see also:
+
=== oxygen  ===
−
  channel_current2
+
Calculates steady state partial oxygen pressure (P) as a function of distance from a blood vessel (r).
−
  /home/lml/krypton/Zhuge/BKandRyr/analysis6/run12
+
The blood vessel has a radius of R1 (5.0 um) and Oxygen at the vessel is Ps (52.0 mm Hg).
−
  /home/lml/krypton/Huang/Kth_pt.m
+
The default is to print partial Oxygen pressure (mm Hg) as a function of distance (um) as columns to stdout.
−
  p. 637 of Cressie.  
+
All models set P at R1 (and r<R1) to Ps. All models clamp P at R1 to be Ps for all time (vessels stay oxygenated).
 +
 
 +
The line source model (-m 1) implements equation 17 from KroghOxygenDiffusionModel1.pdf
 +
  Modeling pO2 Distributions in the Bone Marrow Hematopoietic Compartment.
 +
  I. Krogh's Model  by D.C.Chow, L. A. Wenning, W. M. Miller, and E.T. Papoutsakis
 +
  Biophysical Journal, vol. 81, August 2001, pp. 675-684.
 +
This models O2 assuming a constant oxygen consumption by the tissue and constant O2 (Ps) at the blood vessel.
 +
They claim results don't change by more than a few percent using proportional (or other) O2 consumption models.
 +
The value of dP/dr at R2 is forced to 0.
 +
note: this is an implmentation of O2 from a line source (e.g., blood vessel), not a point source.
 +
So it is not appropriate to convolve (in 3D) this with a 3D image of blood vessels.
 +
But -p (or -m 2) will produce a point source image.
 +
 
 +
The point source model (-m 2) implements equation 14 from HeatConduction.pdf
 +
  Steady Heat Conduction in Layered Mediums: The Half-Space and Sphere, by Henry N. Pollack
 +
  J. of Geophysical Research, vol. 70(22), Nov. 15, 1965, pp. 5645-5648
 +
This models O2 assuming a constant oxygen consumption by the tissue and constant O2 (Ps) at the blood vessel.
 +
note: The value of dP/dr at R2 is forced to 0 unless -b # is specified.
 +
note: Since O2 consumption is constant, it might not make sense to use this in a convolution, since it isn't
 +
      linear.
  
−
+
Model 3 is a point source model, but O2 consumption by the tissue is proportional to the O2 level in the tissue.
−
===  coloc.pl  ===
+
  I derived it from Crank's equations 6.60 (infinite hollow sphere model) and 14.13 (see below).
 +
  It requires the specification of an initial O2 level in the tissue (P0, which is the same everywhere).
 +
  R2 is used only to determine how far out to plot the graph (and dP/dr at R2 is not used either).
 +
  See my paper notes or ~/krypton/Corvera/Olga/SteadyStatePointDiffusion.pdf
 +
  Not only is proportional O2 consumption more biological, but I think this should be linear and therefore
 +
  it makes more sense to use in a convolution with a (binarized?) blood vessel image.
  
−
calls coloc3way with a bunch of different thresholds. Creates an output file which can be
+
note: because R2 really should vary in an image, depending upon the distance between nearby blood vessels
−
graphed with VennDiagram.m.
+
        and because Ps is not just a scale factor (so, eg, brighter blood vessels in an image, if brightness is
 +
        proportional to Ps, do NOT just cause a scale factor in the P(r) values), it may NOT be appropriate
 +
to take the image produced by this program and convolve it with an image of blood vessels to get
 +
estimates of oxygenation of tissue. This comment may apply to all three models (definitely to -m 1)
  
−
coloc.pl im1.i2i im2.i2i im3.i2i  > out.coloc3way
+
Usage: oxygen -m # [options] 
 +
    required:
 +
  -m # which model to use.  
 +
        -m 1 :line source model with constant O2 consumption
 +
-m 2: point source model with constant O2 consumption.
 +
        -m 3 :point source model with O2 consumption proportional to O2 concentration.
 +
Use point source models if planning on convolving resulting image with a blood vessel image.
  
−
options:
+
    options for all models:
−
-time_vs_thresh just generate a file which shows which times correspond to which thresholds. images can be dummy names.
+
Although these options can be used in all models, different models have different sensitivities to them.
 +
  -R1 # vessel radius (um). Changes to this can change P a lot (if -m 1), and may require R2 to change (see -c).
 +
default = 5.00
 +
  -R2 # max distance any tissue is from a vessel (um). This changes the solution a lot for some models
 +
but for the -m 3 model it only affects how far out data is graphed, default = 2268.00
 +
More precisely, for -m 1 and -m 2 it is the distance at which dP/dr = 0 (ie, a b.c. on the pde).
 +
  -Ps # partial pressure of Oxygen at the blood vessel (mm Hg). Default = 52.00
 +
40 is typical of veins, 95 of arteries. This is held constant over time in all the models right now.
 +
For -m 1, this will affect the O2 value at R1, but how P changes RELATIVE to P(at R1) (as r increases)
 +
will not be affected (ie, it does NOT just scale everything).
 +
    model 1 options:
 +
  -c use with -R1 to automatically calculate R2 based on the specified R1 (since R2 affects the solution).
 +
(this also sets -m 1 as a convenience)
 +
    model 2 options:
 +
  -b # changes the 2nd boundary condition to be P at R2 = # mm Hg
 +
instead of dP/dr = 0 at R2 (this also sets -m 2 as a convenience)
 +
    model 3 options:
 +
  -P0 # the initial oxygenation level of the tissue (mm Hg). Default = 0.000000
 +
This will change the solution a lot, since it is also the level that O2, in steady state, approaches as r->infinity.
 +
Therefore, nonzero P0 may also make convolution with a blood vessel image inappropriate.
 +
-P0 0 seems to produce the same results as -r. (-P0 also sets -m 3 as a convenience)
  
−
-t1=#:#:# threshold one should go from # to # by #. default = 800:1200:50
+
    output graph options:
−
-t2=#:#:# threshold two should go from # to # by #. default = 800:1200:50
+
  -n normalize output (doesn't affect -i image.i2i), ie, print r/R1  vs P/Ps  rather than r vs. P
−
-t3=#:#:# threshold three should go from # to # by #. default = 2000:4000:200
+
  -r add a third reference column which is the "simple" diffusion solution (goes as 1/r)
−
-numthresh=#1:#2:#3  ignore the third number in the -t1, -t2, and -t3 options (or in the default) and instead calculate a
+
This is for a point source in 3D (not a line source), and ignores O2 consumption.
−
  threshold step size so that #1 thresholds are applied to im1.i2i (dat image)
+
graph as: oxygen_krogh -r | xmgr -nxy stdin
−
  #2 thresholds are applied to im2.i2i (ctx image), #3 thresholds are applied to im3.i2i (rin image).
+
 
−
  e.g., -numthresh=5:10:10 will apply 5 different thresholds to im1.i2i, and 10 thresholds to im2.i2i and im3.i2i.
+
    output image options:
−
  Using this option lets me insure that each call to coloc.pl will produce exactly the same number of data points;
+
  -i image.i2i xdim ydim zdim: create an image of the values, to use with blur3d to find
−
  this may make the statistical comparison between cells easier.
+
O2 everywhere in an image as a function of distance from blood vessels.
 +
If you are planning on convolving you should probably specify -m 3 .
 +
  -d x y z if -i is specified. pixel dimensions in um. default = 0.60 0.60 10.00
 +
  -s # if -i is specified. scale output intensities by #. Otherwise max is 52.0 mm Hg
 +
  -o xorig yorig zorig: location of the blood vessel in the image (zero indexed, floating point)
 +
blur3d may care about this, depending upon options. default = (0.00,0.00,0.00)
 +
(maybe I should change this to define a line in the image when -m 1 is specified?)
 +
-p the output image should be for the simple 1/r point source (see -r explanation) rather
 +
for the line source (-m 1) or point source with O2 consumption (-m 2 or -m 3).
  
−
-Melikian=file in addition to creating output for VennDiagram, create text file with the coloc percentages
+
    other options:
−
Dr. Melikian is interested in. Graph via xmgr -nxy. See header in file for coloc info.
+
  -v verbose. stuff to stderr.
−
For this to work the three image files MUST be specified in the order 405  594  488 (i.e., rin.i2i ctx.i2i dat.i2i)
+
  -V more verbose. stuff to stderr. debugging info.
−
-Melikian2=file Same as -Melikian, but dat (488) is image 1, ctx (594) image 2, and rin (405) image 3
+
  -h print this help
−
-area=file.xyr also print out Melikian data as xyr where r is proportional to the number of pixels involved
 
−
(i.e., the denominator used when calculating the percent colocalized).
 
−
prints to "file.xyr".  Must also specify either -Melikian or -Melikian2
 
−
xmgrace -graphtype fixed -settype xyr file.xyr
 
−
-matlab=file:#  like -area but as columns so easy to read into matlab: t p1 n1 p2 n2 p3 n3 p4 n4
 
−
# is the max n value (ie, all n values are scaled so the max over n1,n2,n3,n4 is #).
 
−
Since p1,p2,p3,p4 are percent, # is typically set to a small part of that, e.g. .05.
 
−
If # is negative then abs(#) is just used as a scale factor (so -1 would just keep the
 
−
n values as the number of voxels). Graph in matlab with line width of 2*n1:
 
−
matlab  # import data=(tdim,9)
 
−
>> lowy = data(:,2) - data(:,3); hiy = data(:,2) + data(:,3);  x = data(:,1);
 
−
>> area(x,hiy,'FaceColor',[1 0 0],'EdgeColor','r','LineWidth',1); hold on;
 
−
>> area(x,lowy,'FaceColor',[1 1 1],'EdgeColor','r','LineWidth',1);
 
−
Must also specify -Melikian or -Melikian2.
 
  
−
-debug
+
Examples:
−
-verbose
+
      # create a binary image of blood vessels (maybe use BestPath3D_ellipse instead? Maybe thin3D afterwards?):
 +
    mask_image -m 2700 -r 1 G03_x_1_2_r4.i2i G03_x_1_2_r4.i2i G03_x_1_2_r4_binaryvessels.i2i
 +
      # create a psf of blood oxygenation:
 +
    oxygen -s 500 -i O2ptsource.i2i 50 50 21 -d 2.58 2.58 10 -o 25 25 10 -m 3 -r > O2ptsource.xy
 +
    blur3d -S .002 -Z -d -v G03_x_1_2_r4_binaryvessels.i2i O2ptsource.i2i G03_x_1_2_r4_O2.i2i
  
−
example:
+
see also: /home/lml/krypton/Corvera/Olga/README, SteadyStatePointDiffusion.pdf (my notes)
 +
        Random Walks in Biology (New, expanded edition) by Berg p. 23 eq. 2.11;
 +
The Mathematics of Diffusion (2nd Ed) by Crank p. 32 eq  3.5b; p. 89 eq 6.5; p. 102 eq 6.60; p. 330 eq 14.13
 +
source code in:  /home/lml/krypton/facil
 +
error: A model must be specified, i.e., -m # must be specified.
  
−
coloc.pl im1.i2i im2.i2i im3.i2i > coloc.data
 
−
coloc.pl -time_vs_thresh im1.i2i im2.i2i im3.i2i > coloc.times
 
−
matlab
 
−
>> VennDiagram('coloc.data','percent')  # and manually look at coloc.times while doing this to convert times to thresholds.
 
  
−
see also:
+
===  sparkspread  ===
−
~/krypton/packages/fiji/Fiji.app/plugins/jacob_.jar  - more traditional colocalization measures
+
 
−
coloc_tseries2
+
Calculates the spread of spark event amplitudes given that two events occur at the same
−
colocalizeL
+
spark site and compares it to the spread of amplitudes given that two events occur at
 +
different spark sites. A spark site has a unique (x,y) position.
 +
Prints mean and stddev to stdout. Also prints out histograms and cumulative distributions.
 +
 
 +
A valid datafile has either blank lines, comments (start with #) or a data line (spark event).
 +
A data line has 8 or 11 fields. 11 if a stoc is associated with the spark event
 +
A valid stoc (last 3 fields) must have a nonzero stoc amplitude (1st of 3 fields)
 +
See /usr/people/lml/vision/Rhonghua/Sparks/singlesitev2 for a valid file format.
  
 +
Usage: sparkspread [options] datafile
 +
options:
 +
  -h: do NOT print histogram for intraspark data.
 +
  -H: do NOT print histogram for interspark data.
 +
  -c: do NOT print cumulative distribution for intraspark data.
 +
  -C: do NOT print cumulative distribution for interspark data.
 +
  -b #: number of bins for histogram, default = 20
 +
  -n: normalize the histograms so their maximum is 1
 +
  -k: also print ks statistic showing if two distributions are different.
 +
 +
===  spot_diffusion  ===
 +
#/home/lml/krypton/bin/spot_diffusion
 +
0.001  15918.5
 +
0.002  16550.4
 +
0.003  16831.4
 +
0.004  16999.1
 +
0.005  17113.6
 +
0.006  17198.2
 +
0.007  17264
 +
0.008  17317
 +
0.009  17360.9
 +
0.01  17398.1
 +
0.011  17430.1
 +
0.012  17458
 +
0.013  17482.6
 +
0.014  17504.5
 +
0.015  17524.2
 +
0.016  17542.1
 +
0.017  17558.3
 +
0.018  17573.1
 +
0.019  17586.8
 +
0.02  17599.4
 +
0.021  17611.2
 +
0.022  17622.1
 +
0.023  17632.3
 +
0.024  17641.8
 +
0.025  17650.8
 +
0.026  17659.2
 +
0.027  17667.2
 +
0.028  17674.7
 +
0.029  17681.9
 +
0.03  17688.7
 +
0.031  17695.1
 +
0.032  17701.3
 +
0.033  17707.1
 +
0.034  17712.7
 +
0.035  17718.1
 +
0.036  17723.3
 +
0.037  17728.2
 +
0.038  17732.9
 +
0.039  17737.5
 +
0.04  17741.9
 +
0.041  17746.1
 +
0.042  17750.1
 +
0.043  17754.1
 +
0.044  17757.9
 +
0.045  17761.5
 +
0.046  17765.1
 +
0.047  17768.5
 +
0.048  17771.8
 +
0.049  17775
 +
0.05  17778.2
 +
0.051  17781.2
 +
0.052  17784.1
 +
0.053  17787
 +
0.054  17789.8
 +
0.055  17792.5
 +
0.056  17795.1
 +
0.057  17797.7
 +
0.058  17800.2
 +
0.059  17802.6
 +
0.06  17805
 +
0.061  17807.3
 +
0.062  17809.5
 +
0.0629999  17811.7
 +
0.064  17813.9
 +
0.065  17816
 +
0.066  17818
 +
0.067  17820
 +
0.068  17822
 +
0.069  17823.9
 +
0.07  17825.8
 +
0.071  17827.6
 +
0.072  17829.4
 +
0.073  17831.2
 +
0.074  17832.9
 +
0.075  17834.6
 +
0.076  17836.3
 +
0.077  17837.9
 +
0.078  17839.5
 +
0.079  17841
 +
0.08  17842.6
 +
0.081  17844.1
 +
0.082  17845.6
 +
0.083  17847
 +
0.084  17848.4
 +
0.085  17849.8
 +
0.086  17851.2
 +
0.087  17852.6
 +
0.088  17853.9
 +
0.089  17855.2
 +
0.09  17856.5
 +
0.091  17857.8
 +
0.092  17859
 +
0.093  17860.2
 +
0.094  17861.4
 +
0.095  17862.6
 +
0.096  17863.8
 +
0.097  17864.9
 +
0.098  17866
 +
0.099  17867.2
 +
0.1  17868.3
 +
0.101  17869.3
 +
0.102  17870.4
 +
0.103  17871.4
 +
0.104  17872.5
 +
0.105  17873.5
 +
0.106  17874.5
 +
0.107  17875.5
 +
0.108  17876.5
 +
0.109  17877.4
 +
0.11  17878.4
 +
0.111  17879.3
 +
0.112  17880.2
 +
0.113  17881.1
 +
0.114  17882
 +
0.115  17882.9
 +
0.116  17883.8
 +
0.117  17884.7
 +
0.118  17885.5
 +
0.119  17886.4
 +
0.12  17887.2
 +
0.121  17888
 +
0.122  17888.8
 +
0.123  17889.6
 +
0.124  17890.4
 +
0.125  17891.2
 +
0.126  17892
 +
0.127  17892.8
 +
0.128  17893.5
 +
0.129  17894.3
 +
0.13  17895
 +
0.131  17895.7
 +
0.132  17896.4
 +
0.133  17897.2
 +
0.134  17897.9
 +
0.135  17898.6
 +
0.136  17899.3
 +
0.137  17899.9
 +
0.138  17900.6
 +
0.139  17901.3
 +
0.14  17901.9
 +
0.141  17902.6
 +
0.142  17903.2
 +
0.143  17903.9
 +
0.144  17904.5
 +
0.145  17905.1
 +
0.146  17905.8
 +
0.147  17906.4
 +
0.148  17907
 +
0.149  17907.6
 +
0.15  17908.2
 +
0.151  17908.8
 +
0.152  17909.3
 +
0.153  17909.9
 +
0.154  17910.5
 +
0.155  17911.1
 +
0.156  17911.6
 +
0.157  17912.2
 +
0.158  17912.7
 +
0.159  17913.3
 +
0.16  17913.8
 +
0.161  17914.3
 +
0.162  17914.9
 +
0.163  17915.4
 +
0.164  17915.9
 +
0.165  17916.4
 +
0.166  17916.9
 +
0.167  17917.5
 +
0.168  17918
 +
0.169  17918.5
 +
0.17  17918.9
 +
0.171  17919.4
 +
0.172  17919.9
 +
0.173  17920.4
 +
0.174  17920.9
 +
0.175  17921.3
 +
0.176  17921.8
 +
0.177  17922.3
 +
0.178  17922.7
 +
0.179  17923.2
 +
0.18  17923.6
 +
0.181  17924.1
 +
0.182  17924.5
 +
0.183  17925
 +
0.184  17925.4
 +
0.185  17925.9
 +
0.186  17926.3
 +
0.187  17926.7
 +
0.188  17927.1
 +
0.189  17927.6
 +
0.19  17928
 +
0.191  17928.4
 +
0.192  17928.8
 +
0.193  17929.2
 +
0.194  17929.6
 +
0.195  17930
 +
0.196  17930.4
 +
0.197  17930.8
 +
0.198  17931.2
 +
0.199  17931.6
 +
0.2  17932
 +
0.201  17932.3
 +
0.202  17932.7
 +
0.203  17933.1
 +
0.204  17933.5
 +
0.205  17933.9
 +
0.206  17934.2
 +
0.207  17934.6
 +
0.208  17935
 +
0.209  17935.3
 +
0.21  17935.7
 +
0.211  17936
 +
0.212  17936.4
 +
0.213  17936.7
 +
0.214  17937.1
 +
0.215  17937.4
 +
0.216  17937.8
 +
0.217  17938.1
 +
0.218  17938.5
 +
0.219  17938.8
 +
0.22  17939.1
 +
0.221  17939.5
 +
0.222  17939.8
 +
0.223  17940.1
 +
0.224  17940.4
 +
0.225  17940.8
 +
0.226  17941.1
 +
0.227  17941.4
 +
0.228  17941.7
 +
0.229  17942
 +
0.23  17942.3
 +
0.231  17942.7
 +
0.232  17943
 +
0.233  17943.3
 +
0.234  17943.6
 +
0.235  17943.9
 +
0.236  17944.2
 +
0.237  17944.5
 +
0.238  17944.8
 +
0.239  17945.1
 +
0.24  17945.4
 +
0.241  17945.7
 +
0.242  17945.9
 +
0.243  17946.2
 +
0.244  17946.5
 +
0.245  17946.8
 +
0.246  17947.1
 +
0.247  17947.4
 +
0.248  17947.7
 +
0.249  17947.9
 +
0.25  17948.2
 +
0.251  17948.5
 +
0.252  17948.8
 +
0.253  17949
 +
0.254  17949.3
 +
0.255  17949.6
 +
0.256  17949.8
 +
0.257  17950.1
 +
0.258  17950.4
 +
0.259  17950.6
 +
0.26  17950.9
 +
0.261  17951.1
 +
0.262  17951.4
 +
0.263  17951.6
 +
0.264  17951.9
 +
0.265  17952.2
 +
0.266  17952.4
 +
0.267  17952.7
 +
0.268  17952.9
 +
0.269  17953.2
 +
0.27  17953.4
 +
0.271  17953.6
 +
0.272  17953.9
 +
0.273  17954.1
 +
0.274  17954.4
 +
0.275  17954.6
 +
0.276  17954.8
 +
0.277  17955.1
 +
0.278  17955.3
 +
0.279  17955.6
 +
0.28  17955.8
 +
0.281  17956
 +
0.282  17956.2
 +
0.283  17956.5
 +
0.284  17956.7
 +
0.285  17956.9
 +
0.286  17957.2
 +
0.287  17957.4
 +
0.288  17957.6
 +
0.289  17957.8
 +
0.29  17958
 +
0.291  17958.3
 +
0.292  17958.5
 +
0.293  17958.7
 +
0.294  17958.9
 +
0.295  17959.1
 +
0.296  17959.3
 +
0.297  17959.6
 +
0.298  17959.8
 +
0.299  17960
 +
0.3  17960.2
 +
0.301  17960.4
 +
0.302  17960.6
 +
0.303  17960.8
 +
0.304  17961
 +
0.305  17961.2
 +
0.306  17961.4
 +
0.307  17961.6
 +
0.308  17961.8
 +
0.309  17962
 +
0.31  17962.2
 +
0.311  17962.4
 +
0.312  17962.6
 +
0.313  17962.8
 +
0.314  17963
 +
0.314999  17963.2
 +
0.315999  17963.4
 +
0.316999  17963.6
 +
0.317999  17963.8
 +
0.318999  17964
 +
0.319999  17964.2
 +
0.320999  17964.4
 +
0.321999  17964.6
 +
0.322999  17964.7
 +
0.323999  17964.9
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0.324999  17965.1
 +
0.325999  17965.3
 +
0.326999  17965.5
 +
0.327999  17965.7
 +
0.328999  17965.9
 +
0.329999  17966
 +
0.330999  17966.2
 +
0.331999  17966.4
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0.332999  17966.6
 +
0.333999  17966.8
 +
0.334999  17966.9
 +
0.335999  17967.1
 +
0.336999  17967.3
 +
0.337999  17967.5
 +
0.338999  17967.6
 +
0.339999  17967.8
 +
0.340999  17968
 +
0.341999  17968.2
 +
0.342999  17968.3
 +
0.343999  17968.5
 +
0.344999  17968.7
 +
0.345999  17968.8
 +
0.346999  17969
 +
0.347999  17969.2
 +
0.348999  17969.3
 +
0.349999  17969.5
 +
0.350999  17969.7
 +
0.351999  17969.8
 +
0.352999  17970
 +
0.353999  17970.2
 +
0.354999  17970.3
 +
0.355999  17970.5
 +
0.356999  17970.7
 +
0.357999  17970.8
 +
0.358999  17971
 +
0.359999  17971.1
 +
0.360999  17971.3
 +
0.361999  17971.5
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0.362999  17971.6
 +
0.363999  17971.8
 +
0.364999  17971.9
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0.365999  17972.1
 +
0.366999  17972.2
 +
0.367999  17972.4
 +
0.368999  17972.5
 +
0.369999  17972.7
 +
0.370999  17972.8
 +
0.371999  17973
 +
0.372999  17973.2
 +
0.373999  17973.3
 +
0.374999  17973.5
 +
0.375999  17973.6
 +
0.376999  17973.8
 +
0.377999  17973.9
 +
0.378999  17974
 +
0.379999  17974.2
 +
0.380999  17974.3
 +
0.381999  17974.5
 +
0.382999  17974.6
 +
0.383999  17974.8
 +
0.384999  17974.9
 +
0.385999  17975.1
 +
0.386999  17975.2
 +
0.387999  17975.3
 +
0.388999  17975.5
 +
0.389999  17975.6
 +
0.390999  17975.8
 +
0.391998  17975.9
 +
0.392998  17976.1
 +
0.393998  17976.2
 +
0.394998  17976.3
 +
0.395998  17976.5
 +
0.396998  17976.6
 +
0.397998  17976.7
 +
0.398998  17976.9
 +
0.399998  17977
 +
0.400998  17977.2
 +
0.401998  17977.3
 +
0.402998  17977.4
 +
0.403998  17977.6
 +
0.404998  17977.7
 +
0.405998  17977.8
 +
0.406998  17978
 +
0.407998  17978.1
 +
0.408998  17978.2
 +
0.409998  17978.4
 +
0.410998  17978.5
 +
0.411998  17978.6
 +
0.412998  17978.7
 +
0.413998  17978.9
 +
0.414998  17979
 +
0.415998  17979.1
 +
0.416998  17979.3
 +
0.417998  17979.4
 +
0.418998  17979.5
 +
0.419998  17979.6
 +
0.420998  17979.8
 +
0.421998  17979.9
 +
0.422998  17980
 +
0.423998  17980.1
 +
0.424998  17980.3
 +
0.425998  17980.4
 +
0.426998  17980.5
 +
0.427998  17980.6
 +
0.428998  17980.8
 +
0.429998  17980.9
 +
0.430998  17981
 +
0.431998  17981.1
 +
0.432998  17981.2
 +
0.433998  17981.4
 +
0.434998  17981.5
 +
0.435998  17981.6
 +
0.436998  17981.7
 +
0.437998  17981.8
 +
0.438998  17982
 +
0.439998  17982.1
 +
0.440998  17982.2
 +
0.441998  17982.3
 +
0.442998  17982.4
 +
0.443998  17982.5
 +
0.444998  17982.7
 +
0.445998  17982.8
 +
0.446998  17982.9
 +
0.447998  17983
 +
0.448998  17983.1
 +
0.449998  17983.2
 +
0.450998  17983.4
 +
0.451998  17983.5
 +
0.452998  17983.6
 +
0.453998  17983.7
 +
0.454998  17983.8
 +
0.455998  17983.9
 +
0.456998  17984
 +
0.457998  17984.1
 +
0.458998  17984.2
 +
0.459998  17984.4
 +
0.460998  17984.5
 +
0.461998  17984.6
 +
0.462998  17984.7
 +
0.463998  17984.8
 +
0.464998  17984.9
 +
0.465998  17985
 +
0.466998  17985.1
 +
0.467998  17985.2
 +
0.468998  17985.3
 +
0.469997  17985.4
 +
0.470997  17985.6
 +
0.471997  17985.7
 +
0.472997  17985.8
 +
0.473997  17985.9
 +
0.474997  17986
 +
0.475997  17986.1
 +
0.476997  17986.2
 +
0.477997  17986.3
 +
0.478997  17986.4
 +
0.479997  17986.5
 +
0.480997  17986.6
 +
0.481997  17986.7
 +
0.482997  17986.8
 +
0.483997  17986.9
 +
0.484997  17987
 +
0.485997  17987.1
 +
0.486997  17987.2
 +
0.487997  17987.3
 +
0.488997  17987.4
 +
0.489997  17987.5
 +
0.490997  17987.6
 +
0.491997  17987.7
 +
0.492997  17987.8
 +
0.493997  17987.9
 +
0.494997  17988
 +
0.495997  17988.1
 +
0.496997  17988.2
 +
0.497997  17988.3
 +
0.498997  17988.4
 +
0.499997  17988.5
 +
0.500997  17988.6
 +
0.501997  17988.7
 +
0.502997  17988.8
 +
0.503997  17988.9
 +
0.504997  17989
 +
0.505997  17989.1
 +
0.506997  17989.2
 +
0.507997  17989.3
 +
0.508997  17989.4
 +
0.509997  17989.5
 +
0.510997  17989.6
 +
0.511997  17989.6
 +
0.512997  17989.7
 +
0.513997  17989.8
 +
0.514997  17989.9
 +
0.515997  17990
 +
0.516997  17990.1
 +
0.517997  17990.2
 +
0.518997  17990.3
 +
0.519997  17990.4
 +
0.520997  17990.5
 +
0.521997  17990.6
 +
0.522997  17990.7
 +
0.523997  17990.8
 +
0.524997  17990.8
 +
0.525997  17990.9
 +
0.526997  17991
 +
0.527997  17991.1
 +
0.528997  17991.2
 +
0.529997  17991.3
 +
0.530997  17991.4
 +
0.531997  17991.5
 +
0.532997  17991.6
 +
0.533997  17991.7
 +
0.534997  17991.7
 +
0.535997  17991.8
 +
0.536997  17991.9
 +
0.537997  17992
 +
0.538997  17992.1
 +
0.539997  17992.2
 +
0.540997  17992.3
 +
0.541997  17992.3
 +
0.542997  17992.4
 +
0.543997  17992.5
 +
0.544997  17992.6
 +
0.545997  17992.7
 +
0.546997  17992.8
 +
0.547997  17992.9
 +
0.548997  17992.9
 +
0.549996  17993
 +
0.550996  17993.1
 +
0.551996  17993.2
 +
0.552996  17993.3
 +
0.553996  17993.4
 +
0.554996  17993.4
 +
0.555996  17993.5
 +
0.556996  17993.6
 +
0.557996  17993.7
 +
0.558996  17993.8
 +
0.559996  17993.9
 +
0.560996  17993.9
 +
0.561996  17994
 +
0.562996  17994.1
 +
0.563996  17994.2
 +
0.564996  17994.3
 +
0.565996  17994.3
 +
0.566996  17994.4
 +
0.567996  17994.5
 +
0.568996  17994.6
 +
0.569996  17994.7
 +
0.570996  17994.8
 +
0.571996  17994.8
 +
0.572996  17994.9
 +
0.573996  17995
 +
0.574996  17995.1
 +
0.575996  17995.1
 +
0.576996  17995.2
 +
0.577996  17995.3
 +
0.578996  17995.4
 +
0.579996  17995.5
 +
0.580996  17995.5
 +
0.581996  17995.6
 +
0.582996  17995.7
 +
0.583996  17995.8
 +
0.584996  17995.8
 +
0.585996  17995.9
 +
0.586996  17996
 +
0.587996  17996.1
 +
0.588996  17996.2
 +
0.589996  17996.2
 +
0.590996  17996.3
 +
0.591996  17996.4
 +
0.592996  17996.5
 +
0.593996  17996.5
 +
0.594996  17996.6
 +
0.595996  17996.7
 +
0.596996  17996.8
 +
0.597996  17996.8
 +
0.598996  17996.9
 +
0.599996  17997
 +
0.600996  17997.1
 +
0.601996  17997.1
 +
0.602996  17997.2
 +
0.603996  17997.3
 +
0.604996  17997.3
 +
0.605996  17997.4
 +
0.606996  17997.5
 +
0.607996  17997.6
 +
0.608996  17997.6
 +
0.609996  17997.7
 +
0.610996  17997.8
 +
0.611996  17997.9
 +
0.612996  17997.9
 +
0.613996  17998
 +
0.614996  17998.1
 +
0.615996  17998.1
 +
0.616996  17998.2
 +
0.617996  17998.3
 +
0.618996  17998.4
 +
0.619996  17998.4
 +
0.620996  17998.5
 +
0.621996  17998.6
 +
0.622996  17998.6
 +
0.623996  17998.7
 +
0.624996  17998.8
 +
0.625996  17998.8
 +
0.626996  17998.9
 +
0.627995  17999
 +
0.628995  17999.1
 +
0.629995  17999.1
 +
0.630995  17999.2
 +
0.631995  17999.3
 +
0.632995  17999.3
 +
0.633995  17999.4
 +
0.634995  17999.5
 +
0.635995  17999.5
 +
0.636995  17999.6
 +
0.637995  17999.7
 +
0.638995  17999.7
 +
0.639995  17999.8
 +
0.640995  17999.9
 +
0.641995  17999.9
 +
0.642995  18000
 +
0.643995  18000.1
 +
0.644995  18000.1
 +
0.645995  18000.2
 +
0.646995  18000.3
 +
0.647995  18000.3
 +
0.648995  18000.4
 +
0.649995  18000.5
 +
0.650995  18000.5
 +
0.651995  18000.6
 +
0.652995  18000.7
 +
0.653995  18000.7
 +
0.654995  18000.8
 +
0.655995  18000.9
 +
0.656995  18000.9
 +
0.657995  18001
 +
0.658995  18001
 +
0.659995  18001.1
 +
0.660995  18001.2
 +
0.661995  18001.2
 +
0.662995  18001.3
 +
0.663995  18001.4
 +
0.664995  18001.4
 +
0.665995  18001.5
 +
0.666995  18001.6
 +
0.667995  18001.6
 +
0.668995  18001.7
 +
0.669995  18001.7
 +
0.670995  18001.8
 +
0.671995  18001.9
 +
0.672995  18001.9
 +
0.673995  18002
 +
0.674995  18002.1
 +
0.675995  18002.1
 +
0.676995  18002.2
 +
0.677995  18002.2
 +
0.678995  18002.3
 +
0.679995  18002.4
 +
0.680995  18002.4
 +
0.681995  18002.5
 +
0.682995  18002.6
 +
0.683995  18002.6
 +
0.684995  18002.7
 +
0.685995  18002.7
 +
0.686995  18002.8
 +
0.687995  18002.9
 +
0.688995  18002.9
 +
0.689995  18003
 +
0.690995  18003
 +
0.691995  18003.1
 +
0.692995  18003.2
 +
0.693995  18003.2
 +
0.694995  18003.3
 +
0.695995  18003.3
 +
0.696995  18003.4
 +
0.697995  18003.4
 +
0.698995  18003.5
 +
0.699995  18003.6
 +
0.700995  18003.6
 +
0.701995  18003.7
 +
0.702995  18003.7
 +
0.703995  18003.8
 +
0.704994  18003.9
 +
0.705994  18003.9
 +
0.706994  18004
 +
0.707994  18004
 +
0.708994  18004.1
 +
0.709994  18004.1
 +
0.710994  18004.2
 +
0.711994  18004.3
 +
0.712994  18004.3
 +
0.713994  18004.4
 +
0.714994  18004.4
 +
0.715994  18004.5
 +
0.716994  18004.5
 +
0.717994  18004.6
 +
0.718994  18004.7
 +
0.719994  18004.7
 +
0.720994  18004.8
 +
0.721994  18004.8
 +
0.722994  18004.9
 +
0.723994  18004.9
 +
0.724994  18005
 +
0.725994  18005.1
 +
0.726994  18005.1
 +
0.727994  18005.2
 +
0.728994  18005.2
 +
0.729994  18005.3
 +
0.730994  18005.3
 +
0.731994  18005.4
 +
0.732994  18005.4
 +
0.733994  18005.5
 +
0.734994  18005.5
 +
0.735994  18005.6
 +
0.736994  18005.7
 +
0.737994  18005.7
 +
0.738994  18005.8
 +
0.739994  18005.8
 +
0.740994  18005.9
 +
0.741994  18005.9
 +
0.742994  18006
 +
0.743994  18006
 +
0.744994  18006.1
 +
0.745994  18006.1
 +
0.746994  18006.2
 +
0.747994  18006.2
 +
0.748994  18006.3
 +
0.749994  18006.4
 +
0.750994  18006.4
 +
0.751994  18006.5
 +
0.752994  18006.5
 +
0.753994  18006.6
 +
0.754994  18006.6
 +
0.755994  18006.7
 +
0.756994  18006.7
 +
0.757994  18006.8
 +
0.758994  18006.8
 +
0.759994  18006.9
 +
0.760994  18006.9
 +
0.761994  18007
 +
0.762994  18007
 +
0.763994  18007.1
 +
0.764994  18007.1
 +
0.765994  18007.2
 +
0.766994  18007.2
 +
0.767994  18007.3
 +
0.768994  18007.3
 +
0.769994  18007.4
 +
0.770994  18007.4
 +
0.771994  18007.5
 +
0.772994  18007.5
 +
0.773994  18007.6
 +
0.774994  18007.6
 +
0.775994  18007.7
 +
0.776994  18007.7
 +
0.777994  18007.8
 +
0.778994  18007.8
 +
0.779994  18007.9
 +
0.780994  18007.9
 +
0.781994  18008
 +
0.782993  18008
 +
0.783993  18008.1
 +
0.784993  18008.1
 +
0.785993  18008.2
 +
0.786993  18008.2
 +
0.787993  18008.3
 +
0.788993  18008.3
 +
0.789993  18008.4
 +
0.790993  18008.4
 +
0.791993  18008.5
 +
0.792993  18008.5
 +
0.793993  18008.6
 +
0.794993  18008.6
 +
0.795993  18008.7
 +
0.796993  18008.7
 +
0.797993  18008.8
 +
0.798993  18008.8
 +
0.799993  18008.9
 +
0.800993  18008.9
 +
0.801993  18009
 +
0.802993  18009
 +
0.803993  18009.1
 +
0.804993  18009.1
 +
0.805993  18009.2
 +
0.806993  18009.2
 +
0.807993  18009.3
 +
0.808993  18009.3
 +
0.809993  18009.4
 +
0.810993  18009.4
 +
0.811993  18009.4
 +
0.812993  18009.5
 +
0.813993  18009.5
 +
0.814993  18009.6
 +
0.815993  18009.6
 +
0.816993  18009.7
 +
0.817993  18009.7
 +
0.818993  18009.8
 +
0.819993  18009.8
 +
0.820993  18009.9
 +
0.821993  18009.9
 +
0.822993  18010
 +
0.823993  18010
 +
0.824993  18010.1
 +
0.825993  18010.1
 +
0.826993  18010.1
 +
0.827993  18010.2
 +
0.828993  18010.2
 +
0.829993  18010.3
 +
0.830993  18010.3
 +
0.831993  18010.4
 +
0.832993  18010.4
 +
0.833993  18010.5
 +
0.834993  18010.5
 +
0.835993  18010.6
 +
0.836993  18010.6
 +
0.837993  18010.6
 +
0.838993  18010.7
 +
0.839993  18010.7
 +
0.840993  18010.8
 +
0.841993  18010.8
 +
0.842993  18010.9
 +
0.843993  18010.9
 +
0.844993  18011
 +
0.845993  18011
 +
0.846993  18011
 +
0.847993  18011.1
 +
0.848993  18011.1
 +
0.849993  18011.2
 +
0.850993  18011.2
 +
0.851993  18011.3
 +
0.852993  18011.3
 +
0.853993  18011.3
 +
0.854993  18011.4
 +
0.855993  18011.4
 +
0.856993  18011.5
 +
0.857993  18011.5
 +
0.858993  18011.6
 +
0.859993  18011.6
 +
0.860992  18011.7
 +
0.861992  18011.7
 +
0.862992  18011.7
 +
0.863992  18011.8
 +
0.864992  18011.8
 +
0.865992  18011.9
 +
0.866992  18011.9
 +
0.867992  18012
 +
0.868992  18012
 +
0.869992  18012
 +
0.870992  18012.1
 +
0.871992  18012.1
 +
0.872992  18012.2
 +
0.873992  18012.2
 +
0.874992  18012.2
 +
0.875992  18012.3
 +
0.876992  18012.3
 +
0.877992  18012.4
 +
0.878992  18012.4
 +
0.879992  18012.5
 +
0.880992  18012.5
 +
0.881992  18012.5
 +
0.882992  18012.6
 +
0.883992  18012.6
 +
0.884992  18012.7
 +
0.885992  18012.7
 +
0.886992  18012.7
 +
0.887992  18012.8
 +
0.888992  18012.8
 +
0.889992  18012.9
 +
0.890992  18012.9
 +
0.891992  18013
 +
0.892992  18013
 +
0.893992  18013
 +
0.894992  18013.1
 +
0.895992  18013.1
 +
0.896992  18013.2
 +
0.897992  18013.2
 +
0.898992  18013.2
 +
0.899992  18013.3
 +
0.900992  18013.3
 +
0.901992  18013.4
 +
0.902992  18013.4
 +
0.903992  18013.4
 +
0.904992  18013.5
 +
0.905992  18013.5
 +
0.906992  18013.6
 +
0.907992  18013.6
 +
0.908992  18013.6
 +
0.909992  18013.7
 +
0.910992  18013.7
 +
0.911992  18013.8
 +
0.912992  18013.8
 +
0.913992  18013.8
 +
0.914992  18013.9
 +
0.915992  18013.9
 +
0.916992  18014
 +
0.917992  18014
 +
0.918992  18014
 +
0.919992  18014.1
 +
0.920992  18014.1
 +
0.921992  18014.1
 +
0.922992  18014.2
 +
0.923992  18014.2
 +
0.924992  18014.3
 +
0.925992  18014.3
 +
0.926992  18014.3
 +
0.927992  18014.4
 +
0.928992  18014.4
 +
0.929992  18014.5
 +
0.930992  18014.5
 +
0.931992  18014.5
 +
0.932992  18014.6
 +
0.933992  18014.6
 +
0.934992  18014.6
 +
0.935992  18014.7
 +
0.936992  18014.7
 +
0.937991  18014.8
 +
0.938991  18014.8
 +
0.939991  18014.8
 +
0.940991  18014.9
 +
0.941991  18014.9
 +
0.942991  18014.9
 +
0.943991  18015
 +
0.944991  18015
 +
0.945991  18015.1
 +
0.946991  18015.1
 +
0.947991  18015.1
 +
0.948991  18015.2
 +
0.949991  18015.2
 +
0.950991  18015.2
 +
0.951991  18015.3
 +
0.952991  18015.3
 +
0.953991  18015.4
 +
0.954991  18015.4
 +
0.955991  18015.4
 +
0.956991  18015.5
 +
0.957991  18015.5
 +
0.958991  18015.5
 +
0.959991  18015.6
 +
0.960991  18015.6
 +
0.961991  18015.7
 +
0.962991  18015.7
 +
0.963991  18015.7
 +
0.964991  18015.8
 +
0.965991  18015.8
 +
0.966991  18015.8
 +
0.967991  18015.9
 +
0.968991  18015.9
 +
0.969991  18015.9
 +
0.970991  18016
 +
0.971991  18016
 +
0.972991  18016
 +
0.973991  18016.1
 +
0.974991  18016.1
 +
0.975991  18016.2
 +
0.976991  18016.2
 +
0.977991  18016.2
 +
0.978991  18016.3
 +
0.979991  18016.3
 +
0.980991  18016.3
 +
0.981991  18016.4
 +
0.982991  18016.4
 +
0.983991  18016.4
 +
0.984991  18016.5
 +
0.985991  18016.5
 +
0.986991  18016.5
 +
0.987991  18016.6
 +
0.988991  18016.6
 +
0.989991  18016.7
 +
0.990991  18016.7
 +
0.991991  18016.7
 +
0.992991  18016.8
 +
0.993991  18016.8
 +
0.994991  18016.8
 +
0.995991  18016.9
 +
0.996991  18016.9
 +
0.997991  18016.9
 +
0.998991  18017
 +
0.999991  18017
 +
%
 
   
 
   
−
===  probcircle.pl ===
+
===  total_ca ===
−
  given a sphere of diameter D, what is the prob of oberving a disk of radius r when a random plane intersects it?
+
#/home/lml/krypton/bin/total_ca
−
  prints to stdout: r  prob(r) 1/prob(r)
 
  
−
  usage:
+
Reads in a floating point image or short int image as produced by simulation (i.e., cylindrical coords), calculates
−
      probcircle.pl [options]  
+
the total calcium change (i.e., [ca](r)*pi*r*r - t(0)) as a function of distance from the calcium entry site.
 +
Output is printed to stdout.
 +
All input concentrations should be in nM
 +
Each z slice is analyzed separately (i.e., z is assumed to be time) unless image is rectangular and 3D (-R).
  
−
  options:
+
Usage: total_ca [options] ca.i2i
−
-D=# default = 1
+
      options for printing graphs of calcium (not concentration) vs. distance from ca entry location:
−
-just_prob don't print the third column
+
the units for the graph are nM*um^3, but 1nM = .6ions/um^3 , so multiply be .6 to get ions
 +
                      (and 1pA = 3,000 ions/msec if you want to convert to pA-msec).
 +
        -n: normalize calcium distance graph for each z slice (so sum of amplitudes = 1),
 +
                      (otherwise when graph spacing is changed, -g option, the height of the graph will change).
 +
  -a:    print absolute calcium, not delta calcium (the default).
 +
                      when this is applied to a uniform image it should produce a 4pi*r*r distribution.
 +
            The default, delta calcium, prints the delta (i.e., change) from slice 0 (regardless -z option)
 +
        (but delta calcium not calculated if 3D rectangular, i.e., -R specified).
  
−
  examples:
+
  -p # #: pixel size in microns in the radial (x) and lengthwise (y) directions,
−
       probcircle.pl | xmgrace -free -pipe -nxy -
+
default =  0.10 and  0.10
 +
  -P # # #: pixel size in microns in x,y,z directions (rectangular not cylindrical coords),
 +
default = ( 0.10, 0.10, 0.10)
 +
  -r: data is rectangular, not cylindrical coords (-P sets this too)
 +
(e.g., already passed through cyl2cart).
 +
  -R: data is 3D rectangular (not 2D+time), not cylindrical coords.
 +
  -e x y:       0-indexed coords of calcium entry location (default: x= 0, y = ydim/2)
 +
  -E x y x:    0-indexed coords of calcium entry location for 3D rectangular data
 +
(i.e., z direction is not time). sets -R option.
 +
        -g #: graph spacing. default is the pixel size.
 +
        -s #:        subsample each voxel this number of times in the x (radial) and y (longitudinal) directions,
 +
                      (and z if 3D and not 2D+time) default = 3 (anything less tends to introduce errors).
 +
        -z low hi dz: only look at z slices low to hi (0-indexed, inclusive), stepping by dz.
  
−
  see also: p. 249 stereology_book.pdf
+
see also:
−
    /home/lml/krypton/packages/fiji/stereology_lml.template
+
    printvals, float2int, in matlab: readxmgr, acurves (see ~lml/krypton/JSinger for an example)
−
    /home/lml/krypton/Corvera/Raz/stereology/plot_results.pl
 
−
    /home/lml/krypton/facil/cross_sections_of_sphere
 
  
 +
source code in ~lml/krypton/Walsh directory.
 
   
 
   
−
===  compare2dist ===
+
===  vcspat-models ===
 +
argc = 1
  
−
This program calculates whether two amplitude distributions are the same.
+
This program creates a volume image with objects randomly placed
−
It was written to examine Rhonghua's STOCS data to determine whether the increase
+
within it. The mask image defines where an object is allowed to be placed.
−
in observed STOC frequency could be explained by an increase in STOC amplitude
+
The mask value can be changed with the -M option.  Objects can either be individual
−
(since then more events above threshold would be observed).   
+
voxels (the default) or tiny images (-o option) or connected voxels in an image (-O).
−
datafile2 should be the one with larger amplitudes (so we hypothesize it has fewer missing
 
−
events if it is just a version of datafile1 shifted higher).  It will get shifted down
 
−
by a range of shifts (-s option) and compared with datafile1.
 
−
This routine also compares the temporal interarrival time distribution of each datafile with
 
−
that predicted by a poisson process and with the other datafile; the temporal calculations
 
−
ignore all missing data issues and shifting issues for now.
 
  
−
This program reads data in the form:
+
Usage:
−
     time calcium prior_baseline post_baseline amplitude
+
  vcspat-models [options] mask.i2i out.i2i
−
      where the values are
+
 
−
      time:           time of STOC
+
Options:
−
      calcium:         SR calcium level
+
  -m #     : model number (default 0).
−
      prior_baseline: amplitude just prior to STOC
+
            0 - grid pattern
−
      post_baseline:  amplitude just after STOC
+
            1 - random pattern
−
      amplitude:       amplitude amplitude of STOC (not relative to baseline)
+
  -M #    : value of mask pixels (default 1).
−
Data is expected to already be sorted by time (smallest to largest).
+
  -r #    : number of random points to use in random pattern (default 25000)
−
comment lines must begin with a #
+
  -o name  : image to use at point in pattern (default just turns on a pixel)
 +
(can use up to 256 images - image will be randomly chosen)
 +
  -a : if objects overlap, add their pixel values instead of just replacing
 +
 
 +
Options related to objects:
 +
   -O thresh name.i2i: threshold an image to use for objects. Extracts as an object each
 +
            connected set of voxels above threshold.  Places these  objects randomly
 +
            into the output image (uses each object once). Use with the
 +
            -m 1 option. Do not use the -r option
 +
  -P name.i2i id.i2i: similar to -O option, extracts as an object each of the
 +
    the objects in name.i2i based upon their pixel values (object id) in id.i2i
 +
(e.g., id.i2i was produced via objs_via_ascent). This option preserves the
 +
distinction between objects in name.i2i which may be touching - since simple thresholding is not used.
 +
If only an id.i2i is available (no name.i2i), you can specify -P id.i2i id.i2i
 +
  -v: replace objects (after fitting them into the image) with just the single voxel
 +
at the brightest location in the object.  Only use with -O and -e options.
 +
  -S # #:  minimum and maximum object sizes to allow (use with -O option).
 +
  -e: do not allow (exclude) objects to be placed so that they overlap with each
 +
other, go outside the image, or go outside the mask.  The default is to allow
 +
overlaps and to just zero out that part of an object which goes outside the
 +
image volume or mask.
 +
  -n: number the objects in out.i2i (use with -O or -P options). Rather than all
 +
the pixels in an object being their original values, all the pixels in object 1
 +
will be labeled 1, all those in object 2 labeled 2, etc.  If -e not specied and
 +
objects overlap the first object placed (usually the largest) will prevail.
 +
Can also be used with -v, then output will have the brightest voxel set to object id, others to 0.
 +
The output of this can be analyzed by object_overlap program.
 +
  -N out2.i2i:  create a second output file, number the objects in out2.i2i (like -n).
 +
 
 +
OtherOptions
 +
  -s #    : seed for random number generator (default pid)
 +
  -x #    : x increment for grid pattern (default 3)
 +
  -y #    : y increment for grid pattern (default 3)
 +
  -z #     : z increment for grid pattern (default 3)
 +
  -V: verbose
 +
 
 +
note: entire image name (with extension) is required.
 +
note: a - in place of an image name means stdin or stdout.
 +
Examples:
 +
  objs_via_ascent in1.i2i inid1.i2i
 +
  objs_via_ascent in2.i2i inid2.i2i
 +
  vcspat-models-new -m 1 -M 1 -P in1.i2i inid1.i2i -N outid1.i2i  mask.i2i out1.i2i
 +
  vcspat-models-new -m 1 -M 1 -P in2.i2i inid2.i2i -N outid2.i2i  mask.i2i out2.i2i
 +
  object_overlap outid1.i2i outid2.i2i  > obj_overlap
 +
  overlapL out1.i2i out2.i2i > coloc
 +
 
 +
See also:  krypton/Qiong/run1,  vcspat, randompuncs, spatial_stats2, objs_via_ascent, countobjs
 +
 
 +
Source code in /storage/big1/lml/jac/was_invitro/Projects/cspat-volume
 +
 
 +
== Statistics ==
 +
===  cluster_distances.pl  ===
  
−
Usage: compare2dist [options] datafile1 datafile2
+
Takes output from channel_current2 (after 11/24/09) and pulls out statistics about
−
options:
+
mean distance to each BK cluster. Then produces average stats from all the files
−
    -t #: only include data with an amplitude > #. The default
+
analyzed. Output to stdout.
−
is to assume a 0 threshold. If you have acquired the data
+
 
−
using some thresholding criterium (eg, only peaks above
+
 
−
10picoamps are counted) then you should provide that number
+
  usage:
−
here, even if all your data is above this (ie, you've applied
 
−
the threshold in your identification phase). This is because
 
−
we need to know it when we shift amplitudes of the second
 
−
distribution to see if it could match the first distribution.
 
−
    -b: subtract average baseline from amplitude prior to use (ie, prior
 
−
to any thresholding or intensity shifting of data).
 
−
    -s delta max: shift datafile2 amplitudes down by a maximum of max, in
 
−
increments of delta, to see if it will then match datafile1.
 
−
  -p #: our guess of the percentage of data missing from datafile2 because it was
 
−
below our threshold/detection criteria (a # from 0 to 1).
 
−
This plus the amount of datafile2 shifted below threshold determines
 
−
our estimate of the amount of data missing from the shifted datafile2 and
 
−
the unshifted datafile1. The larger this number is, the more likely
 
−
the two curves will appear similar (since differences in actual data
 
−
examined will be proportionally smaller differences, and we are assuming
 
−
all missing data matches exactly, but see -m below). Default = 0.000000
 
−
    -m: assume all missing data maximally MISmatches, this would probably be
 
−
a worst case scenario, so that if the KS statistic says the distributions
 
−
could be the same even with the -m option, its probably true.  But I'm
 
−
not certain of this, since it really depends how this affects the
 
−
relative spacing between the cumulative distributions. I'd have to
 
−
think about it some more.
 
  
−
see also:test_distr, poisson
+
  -files:file1:file2:...:filen       which files to analyze. Defaults are files named 2_*.currents in cwd.
−
This code is in ~lml/vision/Rhonghua/STOCS
+
  -numBKvsProb       also prints numBK vs prob data suitable for xmgrace
−
#/home/lml/krypton/bin/compare2dist
 
  
−
===  compare2gaussian  ===
 
−
incorrect command line, need 1 data files.
 
−
This program calculates whether a given set of data could be samples from a known mixture of Gaussians.
 
−
datafile should have one data point per line. comment lines begin with #.
 
−
Output statistics to stdout.
 
  
−
Usage: compare2gaussian [options] datafile
+
example:
−
options:
+
  (channel_current2  .... > file.channel_current) >& file1.currents
−
      -t #: only include data with an amplitude > #. The default is to include all data.
+
  (channel_current2  .... > file2.channel_current) >& file2.currents
−
  -g # amp1 mean1 sd1 ... :
+
  cluster_distances.pl -numBKvsProb -files=file1.currents:file2.currents > avg_distances.txt
−
The Gaussian mixture model the data should be compared against (using a KS statistic).
+
  fgrep -v clusters avg_distances.txt |xmgrace -pipe
−
# is the number of Gaussians, this is followed by the amplitude, mean, and sd of
 
−
each Gaussian. The default is one Gaussian with mean = 0 and sd = 1.
 
−
You can get these values using the fitgaussians2 program.
 
−
  -v: verbose. Also prints the observed (first) and theoretical (second) curves to stdout.
 
−
  -T: test. runs through x = 0 to 10 and prints out cumulative prob. exits.
 
  
−
See Also: fitgaussians2, fit2gaussians, fit3gaussians
+
note: mean distances to clusters are not always increasing (e.g., mean distance to 10th
 +
      cluster could be SMALLER than the mean distance to the 9th cluster).  I think this
 +
      has to do with limiting my maximum distance (see comments in this file).
  
−
Source code is in ~lml/krypton/Lefkowitz
+
−
#/home/lml/krypton/bin/compare2gaussian
+
see also:
 +
  channel_current2
 +
  /home/lml/krypton/Zhuge/BKandRyr/analysis6/run12
 +
  /home/lml/krypton/Huang/Kth_pt.m
 +
  p. 637 of Cressie.
  
−
===  compare_dist2 ===
+
 +
===  coloc.pl ===
  
−
This program calculates whether two distributions are the same using chi-square test (unless -k).
+
calls coloc3way with a bunch of different thresholds. Creates an output file which can be
−
It was written to examine the distribution of sizes of Ryanodine Receptor objects
+
graphed with VennDiagram.m.  
−
to determine if they are randomly distributed. datafile1 should be the reference
 
−
data (gotten from many simulations or from a theoretical formula), datafile2
 
−
should be the real data (max number of data values = 100000).
 
  
−
This program reads data which is just a list of sizes of objects seen (one per line).
+
coloc.pl im1.i2i im2.i2i im3.i2i  > out.coloc3way
−
Comment lines must begin with a #
+
 
−
Floating pt numbers are truncated to integers for bin number (max bin number = 50000).
+
options:
 +
-time_vs_thresh just generate a file which shows which times correspond to which thresholds. images can be dummy names.
 +
 
 +
-t1=#:#:# threshold one should go from # to # by #. default = 800:1200:50
 +
-t2=#:#:# threshold two should go from # to # by #. default = 800:1200:50
 +
-t3=#:#:# threshold three should go from # to # by #. default = 2000:4000:200
 +
-numthresh=#1:#2:#3  ignore the third number in the -t1, -t2, and -t3 options (or in the default) and instead calculate a  
 +
  threshold step size so that #1 thresholds are applied to im1.i2i (dat image)
 +
  #2 thresholds are applied to im2.i2i (ctx image), #3 thresholds are applied to im3.i2i (rin image).
 +
  e.g., -numthresh=5:10:10 will apply 5 different thresholds to im1.i2i, and 10 thresholds to im2.i2i and im3.i2i.
 +
  Using this option lets me insure that each call to coloc.pl will produce exactly the same number of data points;
 +
  this may make the statistical comparison between cells easier.
 +
 
 +
-Melikian=file in addition to creating output for VennDiagram, create text file with the coloc percentages
 +
Dr. Melikian is interested in. Graph via xmgr -nxy. See header in file for coloc info.
 +
For this to work the three image files MUST be specified in the order 405  594  488 (i.e., rin.i2i ctx.i2i dat.i2i)
 +
-Melikian2=file Same as -Melikian, but dat (488) is image 1, ctx (594) image 2, and rin (405) image 3
 +
-area=file.xyr also print out Melikian data as xyr where r is proportional to the number of pixels involved
 +
(i.e., the denominator used when calculating the percent colocalized).
 +
prints to "file.xyr".  Must also specify either -Melikian or -Melikian2
 +
xmgrace -graphtype fixed -settype xyr file.xyr
 +
-matlab=file:#  like -area but as columns so easy to read into matlab: t p1 n1 p2 n2 p3 n3 p4 n4
 +
# is the max n value (ie, all n values are scaled so the max over n1,n2,n3,n4 is #).
 +
Since p1,p2,p3,p4 are percent, # is typically set to a small part of that, e.g. .05.
 +
If # is negative then abs(#) is just used as a scale factor (so -1 would just keep the
 +
n values as the number of voxels). Graph in matlab with line width of 2*n1:
 +
matlab  # import data=(tdim,9)
 +
>> lowy = data(:,2) - data(:,3); hiy = data(:,2) + data(:,3);  x = data(:,1);
 +
>> area(x,hiy,'FaceColor',[1 0 0],'EdgeColor','r','LineWidth',1); hold on;
 +
>> area(x,lowy,'FaceColor',[1 1 1],'EdgeColor','r','LineWidth',1);
 +
Must also specify -Melikian or -Melikian2.
 +
 
 +
-debug
 +
-verbose
  
−
Usage: compare_dist2 [options] datafile1 datafile2
 
−
options:
 
−
  -k perform K-S test instead (I'm not certain the numbins I use to calculate this is correct).
 
−
  -a also print the histograms produced
 
−
  -b also print the normalized histograms (total count datafile2 scaled to the same count as in datafile1,
 
−
  bins with 0 removed), this is only done if -k not specified (ie, only if performing chi-square test).
 
−
  -c also print the cumulative prob distributions (only done if -k also specified)
 
−
  -r # #: only analyze sizes within the specified range (inclusive)
 
−
  -m #: cap the maximum number of counts for any size in datafile1 to #
 
−
  -M #: cap the maximum number of counts for any size in datafile2 to #
 
−
  -z: for chi-square keep zero entry bins (chi square only correct if this option is NOT used)
 
−
so why is this option here?  if you just really want to use this program to do
 
−
histogram normalization (-b), and don't care about the stat.  xmgrace running avg
 
−
will produce strange results if you don't use -z, ie, if data not equally spaced.
 
−
  -v verbose
 
−
  -V very verbose
 
 
example:
 
example:
−
      create a simulated distribution and compare it with real restored data (real_ryrr.i2i, run5 does this 100 times):
 
−
  cluster -wsize 10 43 25 -cylinder 0.001 3 -psize 0.08 0.08 0.25 -mindist 0.030 -numryr 500 -image ryr.i2i
 
−
  blur3d -S 40000 -P ryr.i2i psf.i2i ryr_b.i2i
 
−
  noise -c RCA ryr_b.i2i ryr_bn.i2i
 
−
  setenv myloc /home/lml/krypton/Zhuge/Ryr_clusters
 
−
  setenv eprloc /storage/big1/epr/queues
 
−
  echo "  /storage/big1/epr/run_epr -V -log -NSC 4 -sm 1e-05 -it 5000 -sc 0.025 -co 0.001
 
−
-psf ${myloc}/psf.i2i ${myloc}/ryr_bn.i2i ${myloc}/ryr_bnr.i2i " > /storage/big1/epr/queues/standard/lml.0
 
−
  while (1==1)  if ( ( ! -e ${eprloc}/standard/lml.0 ) && ( ! -e ${eprloc}/running/lml.0 ) ) then break endif sleep 60s end
 
−
  countobjs -k -s 5 300 -t 4500 4500 sim_ryr.objs ryr_bnr.i2i
 
−
  cull -s -c -2 < sim_ryr.objs > sim_ryr.stats
 
−
  countobjs -k -s 5 300 -t 4500 4500 real_ryr.objs real_ryrr.i2i
 
−
  cull -s -c -2 < real_ryr.objs > real_ryr.stats
 
−
  compare_dist2 -b sim_ryr.stats real_ryr.stats  >& chi_ryr
 
−
  compare_dist2 -k -b sim_ryr.stats real_ryr.stats  >& ks_ryr
 
−
  tail chi_ryr ks_ryr
 
−
  xmgrace chi_ryr; xmgrace ks_ryr
 
  
−
see also: cluster, run5
+
coloc.pl im1.i2i im2.i2i im3.i2i > coloc.data
−
This code is in /home/lml/krypton/Zhuge/Ryr_clusters/
+
coloc.pl -time_vs_thresh im1.i2i im2.i2i im3.i2i > coloc.times
−
#/home/lml/krypton/bin/compare_dist2
+
matlab
 +
>> VennDiagram('coloc.data','percent')  # and manually look at coloc.times while doing this to convert times to thresholds.
 +
 
 +
see also:
 +
~/krypton/packages/fiji/Fiji.app/plugins/jacob_.jar  - more traditional colocalization measures
 +
coloc_tseries2
 +
colocalizeL
  
−
===  correlationL ===
+
−
/home/lml/krypton/bin/correlationL
+
===  probcircle.pl ===
 +
  given a sphere of diameter D, what is the prob of oberving a disk of radius r when a random plane intersects it?
 +
  prints to stdout: r  prob(r) 1/prob(r)
  
−
This program plots intensities from image1 vs intensities from
+
  usage:
−
image2. image1 on the x axis, image 2 on the y axis. Intensities
+
      probcircle.pl [options]
−
in both images are rescaled 0 to the size of the output image
 
−
(default = 512).  The intensity at each pixel in the output
 
−
image is the number of (image1,image2) voxels with that particular
 
−
intensity combination.
 
−
The intent is to be able to look at the output image and get a sense
 
−
for whether there is a correlation between intensities
 
−
in the two images.  If so, perhaps a least squares line
 
−
fit should be done to see how well one images correlates with the
 
−
other, or -s option can be specified.
 
−
The minimum, maximum, and scale factors are printed to stdout.
 
−
Version 1.1
 
  
−
Usage: correlation [options] im1.i2i im2.i2i out.i2i
+
  options:
−
options:
+
-D=# default = 1
−
  -d xdim ydim: output dimensions of new image
+
-just_prob don't print the third column
−
(default = 512,512).
 
−
  -S im1scale im2scale: scale intensities with these scale factors. newval = (intens-min_intens)*scale
 
−
  -B b1 b2:    force min_intens (black level) to specified value.  newval1 = (intens-b1)*scale1
 
−
  -i val1 val2: Ignore any voxels in image1 <= val1 and
 
−
any voxels in image2 <= val2.
 
  
−
  -h val1 val2: Ignore any voxels in image1 >= val1 and
+
  examples:
−
any voxels in image2 >= val2.
+
      probcircle.pl | xmgrace -free -pipe -nxy -
  
−
  -r: instead of intensities, use the rank
+
  see also: p. 249 stereology_book.pdf
−
order of the intensities.
+
    /home/lml/krypton/packages/fiji/stereology_lml.template
−
  -a: automatically calculate the size of the
+
    /home/lml/krypton/Corvera/Raz/stereology/plot_results.pl
−
output image. attempts to make the scale
+
    /home/lml/krypton/facil/cross_sections_of_sphere
−
factor = 1.
 
−
  -b: keep the xdim and ydim scale factors the same.
 
−
  -s: calculate Spearman rank-order correlation
 
−
coefficients. print results to stdout.
 
−
  -z zslice:    only examine the specified z slice (the first
 
−
slice is considered slice 0).
 
−
note: entire image name is NOT required.
 
−
note: a - in place of an image name means stdin or stdout.
 
  
−
examples:
 
−
    # to apply this to a set of 3D images, using the same scales and size images for easy comparison
 
−
correlationL -S s1 s2 -d 512 512 -B 0 0 image1.i2i corr1.i2i    (and same for other images)
 
 
   
 
   
−
===  create_imagesL ===
+
===  compare2dist ===
  
−
This program takes output from many runs of "overlap" and
+
This program calculates whether two amplitude distributions are the same.
−
produces two images. One image is a percent colocalization image
+
It was written to examine Rhonghua's STOCS data to determine whether the increase
−
and the other is a probability image.  The overlap program MUST be
+
in observed STOC frequency could be explained by an increase in STOC amplitude
−
run via the "many_overlaps" command.  The probability calculations
+
(since then more events above threshold would be observed).   
−
are the same as those performed by "probcolocal", but only -n
+
datafile2 should be the one with larger amplitudes (so we hypothesize it has fewer missing
−
needs to be specified since the other values are automatically
+
events if it is just a version of datafile1 shifted higher).  It will get shifted down
−
extracted from the file produced by "many_overlaps".
+
by a range of shifts (-s option) and compared with datafile1.
 +
This routine also compares the temporal interarrival time distribution of each datafile with
 +
that predicted by a poisson process and with the other datafile; the temporal calculations
 +
ignore all missing data issues and shifting issues for now.
  
−
The percent image is the percent of voxels above threshold in image1
+
This program reads data in the form:
−
(as originally specified to "many_overlaps") which overlap with
+
    time calcium prior_baseline post_baseline amplitude
−
voxels above threshold in image2. A 100 in the output image = 100 percent.
+
      where the values are
−
The probability of observing as much (or more) overlap as we did due to
+
      time:            time of STOC
−
random chance is the prob.i2i image.  Probabilities are mulitplied by 100.
+
      calcium:        SR calcium level
 +
      prior_baseline:  amplitude just prior to STOC
 +
      post_baseline:  amplitude just after STOC
 +
      amplitude:      amplitude amplitude of STOC (not relative to baseline)
 +
Data is expected to already be sorted by time (smallest to largest).
 +
comment lines must begin with a #
  
−
Position along the y-axis (vertical axis) of the image, corresponds to
+
Usage: compare2dist [options] datafile1 datafile2
−
thresholds for image2. The x-axis represents image1 thresholds. The
+
options:
−
lowest threshold is the bottom left corner.  See the first line in  
+
    -t #: only include data with an amplitude > #. The default
−
your datafile for the range of thresholds this represents.
+
is to assume a 0 threshold. If you have acquired the data
−
Overlap produces statistics for a range of allowed overlaps.
+
using some thresholding criterium (eg, only peaks above
−
Create_images, by default, chooses an overlap within 1 voxel.
+
10picoamps are counted) then you should provide that number
−
If you want to use a different overlap distance use the -o option.
+
here, even if all your data is above this (ie, you've applied
 +
the threshold in your identification phase). This is because
 +
we need to know it when we shift amplitudes of the second
 +
distribution to see if it could match the first distribution.
 +
    -b: subtract average baseline from amplitude prior to use (ie, prior
 +
to any thresholding or intensity shifting of data).
 +
    -s delta max: shift datafile2 amplitudes down by a maximum of max, in
 +
increments of delta, to see if it will then match datafile1.
 +
  -p #: our guess of the percentage of data missing from datafile2 because it was
 +
below our threshold/detection criteria (a # from 0 to 1).
 +
This plus the amount of datafile2 shifted below threshold determines
 +
our estimate of the amount of data missing from the shifted datafile2 and
 +
the unshifted datafile1.  The larger this number is, the more likely
 +
the two curves will appear similar (since differences in actual data
 +
examined will be proportionally smaller differences, and we are assuming
 +
all missing data matches exactly, but see -m below). Default = 0.000000
 +
    -m: assume all missing data maximally MISmatches, this would probably be
 +
a worst case scenario, so that if the KS statistic says the distributions
 +
could be the same even with the -m option, its probably true.  But I'm
 +
not certain of this, since it really depends how this affects the
 +
relative spacing between the cumulative distributions. I'd have to
 +
think about it some more.
  
−
See also: overlap, probcolocal, many_overlaps
+
see also:test_distr, poisson
 +
This code is in ~lml/vision/Rhonghua/STOCS
 +
#/home/lml/krypton/bin/compare2dist
  
−
Usage:
+
===  compare2gaussian  ===
−
create_images [options] datafile percent.i2i prob.i2i
+
incorrect command line, need 1 data files.
−
options:
+
This program calculates whether a given set of data could be samples from a known mixture of Gaussians.
−
  -o distance:    voxels within this distance count as overlapped.
+
datafile should have one data point per line. comment lines begin with #.
−
  -n number:    number of voxels (1000000 default), see probcolocal.
+
Output statistics to stdout.
  
−
Examples:
+
Usage: compare2gaussian [options] datafile
−
  many_overlaps -t 100 1000 100 -T 100 1000 100 alpha_T.i2i beta_T.i2i tmp_output
+
options:
−
  create_images -n 363264 tmp_output percent.i2i prob.i2i
+
      -t #: only include data with an amplitude > #. The default is to include all data.
−
+
  -g # amp1 mean1 sd1 ... :
−
== Analysis of Points ==
+
The Gaussian mixture model the data should be compared against (using a KS statistic).
−
===  components.pl  ===
+
# is the number of Gaussians, this is followed by the amplitude, mean, and sd of  
 +
each Gaussian. The default is one Gaussian with mean = 0 and sd = 1.
 +
You can get these values using the fitgaussians2 program.
 +
  -v: verbose. Also prints the observed (first) and theoretical (second) curves to stdout.
 +
  -T: test. runs through x = 0 to 10 and prints out cumulative prob. exits.
  
−
Calculates the number of connected components resolved over a range of point densities.
+
See Also: fitgaussians2, fit2gaussians, fit3gaussians
  
−
components.pl [options]
+
Source code is in ~lml/krypton/Lefkowitz
 +
#/home/lml/krypton/bin/compare2gaussian
  
−
options:
+
===  compare_dist2  ===
  
−
-numpts=low:hi:delta
+
This program calculates whether two distributions are the same using chi-square test (unless -k).
−
-repeat=# number of times to repeat at each point density
+
It was written to examine the distribution of sizes of Ryanodine Receptor objects
−
-res=# in microns
+
to determine if they are randomly distributed. datafile1 should be the reference
−
-outfile=name name of output file. otherwise to _tmp. always need write permission in current directory.
+
data (gotten from many simulations or from a theoretical formula), datafile2
 +
should be the real data (max number of data values = 100000).
  
−
+
This program reads data which is just a list of sizes of objects seen (one per line).
−
===  convex_hull.pl  ===
+
Comment lines must begin with a #
 +
Floating pt numbers are truncated to integers for bin number (max bin number = 50000).
  
−
This program takes an object outputfile (unless -rptsin or -tripletsin) produced by countobjs (or maskobjs) and finds the minimal
+
Usage: compare_dist2 [options] datafile1 datafile2
−
spanning tree connecting the center of mass of the objects, and the convex hull. Writes out connections as an rpts file to stdout.
+
options:
−
It also loops through 20 thresholds  for the pts, and prints to stderr some stats about the minimal spanning tree and
+
  -k perform K-S test instead (I'm not certain the numbins I use to calculate this is correct).
−
convex hull of the points above each of these thresholds.
+
  -a also print the histograms produced
−
 
+
  -b also print the normalized histograms (total count datafile2 scaled to the same count as in datafile1,
−
Options can be used to only selected a subset of the objects and to constrain the maximum distance (-maxdist).  
+
  bins with 0 removed), this is only done if -k not specified (ie, only if performing chi-square test).
−
 
+
  -c also print the cumulative prob distributions (only done if -k also specified)
−
It was written with the hope that triplets (maxima in an image which has a cell in the center) will show a pattern in their
+
  -r # #: only analyze sizes within the specified range (inclusive)
−
convex hull area, so that when the threshold rises high enough, only maxima inside the cell will still be present and hence
+
  -m #: cap the maximum number of counts for any size in datafile1 to #
−
the convex hull will be stable and of much smaller area.
+
  -M #: cap the maximum number of counts for any size in datafile2 to #
−
 
+
  -z: for chi-square keep zero entry bins (chi square only correct if this option is NOT used)
−
This program requires perl modules Graph::Kruskal and Math::Geometry::Planar, use cpanp to install these:
+
so why is this option here?  if you just really want to use this program to do
−
    yum install perl-CPANPLUS-0.91.3-202.fc16.noarch  - for cpanp
+
histogram normalization (-b), and don't care about the stat. xmgrace running avg
−
    cpanp -i Graph::Kruskal
+
will produce strange results if you don't use -z, ie, if data not equally spaced.
−
    cpanp i Math::Geometry::Planar
+
  -v verbose
 +
  -V very verbose
 +
example:
 +
      create a simulated distribution and compare it with real restored data (real_ryrr.i2i, run5 does this 100 times):
 +
  cluster -wsize 10 43 25 -cylinder 0.001 3 -psize 0.08 0.08 0.25 -mindist 0.030 -numryr 500 -image ryr.i2i
 +
  blur3d -S 40000 -P ryr.i2i psf.i2i ryr_b.i2i
 +
  noise -c RCA ryr_b.i2i ryr_bn.i2i
 +
  setenv myloc /home/lml/krypton/Zhuge/Ryr_clusters
 +
  setenv eprloc /storage/big1/epr/queues
 +
  echo "  /storage/big1/epr/run_epr -V -log -NSC 4 -sm 1e-05 -it 5000 -sc 0.025 -co 0.001
 +
-psf ${myloc}/psf.i2i ${myloc}/ryr_bn.i2i ${myloc}/ryr_bnr.i2i " > /storage/big1/epr/queues/standard/lml.0
 +
  while (1==1)  if ( ( ! -e ${eprloc}/standard/lml.0 ) && ( ! -e ${eprloc}/running/lml.0 ) ) then break endif sleep 60s end
 +
  countobjs -k -s 5 300 -t 4500 4500 sim_ryr.objs ryr_bnr.i2i
 +
  cull -s -c -2 < sim_ryr.objs > sim_ryr.stats
 +
  countobjs -k -s 5 300 -t 4500 4500 real_ryr.objs real_ryrr.i2i
 +
  cull -s -c -2 < real_ryr.objs > real_ryr.stats
 +
  compare_dist2 -b sim_ryr.stats real_ryr.stats  >& chi_ryr
 +
  compare_dist2 -k -b sim_ryr.stats real_ryr.stats  >& ks_ryr
 +
  tail chi_ryr ks_ryr
 +
  xmgrace chi_ryr; xmgrace ks_ryr
  
−
usage:
+
see also: cluster, run5
−
  convex_hull.pl -tripletsin file1.triplets > file1_mst.rpts
+
This code is in /home/lml/krypton/Zhuge/Ryr_clusters/
 +
  #/home/lml/krypton/bin/compare_dist2
  
−
  input options:
+
=== correlationL  ===
−
    -dx=#   spacing in the x direction, default = 1
+
/home/lml/krypton/bin/correlationL
−
    -dy=#   spacing in the y direction, default = 1
 
−
    -dz=#   spacing in the z direction, default = 1
 
−
    -rptsin     instead of file1.objs, read file1.rpts where file1.rpts was produced by max2d.
 
−
      -size1 and -iod1 are ignored when this option is specified.
 
−
    -tripletsin   instead of file1.objs read in file1.xyi,  triplets of x y and intensity.
 
  
−
  analysis options:
+
This program plots intensities from image1 vs intensities from
−
    -size1=min:max     min and max object size allowed for file1.objs in pixels (inclusive)
+
image2. image1 on the x axis, image 2 on the y axis. Intensities
−
    -iod1=min:max   min and max object iod allowed for file1.objs (inclusive), or intensity if -tripletsin was specified.
+
in both images are rescaled 0 to the size of the output image
−
    -maxdist=#: :  don't allow connections between pts further apart than this distance (after applying dx, dy, dz spacing factors).
+
(default = 512). The intensity at each pixel in the output
−
  warning: if the distance is too small, then all the pts will not be connected to begin with;
+
image is the number of (image1,image2) voxels with that particular
−
    this may cause the minimal spanning tree algorithm to fail.
+
intensity combination.
−
    default maxdist is  3000
+
The intent is to be able to look at the output image and get a sense
 +
for whether there is a correlation between intensities
 +
in the two images.  If so, perhaps a least squares line
 +
fit should be done to see how well one images correlates with the
 +
other, or -s option can be specified.
 +
The minimum, maximum, and scale factors are printed to stdout.
 +
Version 1.1
  
−
  output options:
+
Usage: correlation [options] im1.i2i im2.i2i out.i2i
−
    -addlines : output rpts format which addlines is more likely to be happy with (may not work in dave?)
+
options:
−
    -hist :  calculate histogram of distances (hist[int(dist)]++, where int just truncates to integer). obsolete.
+
  -d xdim ydim: output dimensions of new image
−
    -sizehist : calculate histogram of object sizes (in voxels) in file1.out. (hist[int(size)]++, where int just
+
(default = 512,512).
−
        truncates to integer). If you don't care about distances between two files (ie, only want -sizehist)
+
  -S im1scale im2scale: scale intensities with these scale factors. newval = (intens-min_intens)*scale
−
        put the same file name for both files on the command line.  obsolete.
+
  -B b1 b2:     force min_intens (black level) to specified value.  newval1 = (intens-b1)*scale1
−
    -rpts=file.rpts : put bounding boxes around objects found and lines between closest objects (similar to objs2bb.pl)
+
  -i val1 val2: Ignore any voxels in image1 <= val1 and
−
  display this in dave eg:  dave -n 0 -u -I file.i2i file.rpts (use the -n 0 and -u options)
+
any voxels in image2 <= val2.
−
  note: may not show up in dave until you click on "scale" to force a rescale (or draw?).
 
−
    -jack=max.rpts:# :  create an rpts file with the maxima in each object displayed as a small jack.
 
−
    # controls the size of the jack. 1=1 pixel in size, 2 = 2 pixels, etc.
 
−
-twod   add this (in addition to -jack) if you want 2D jacks rather than 3D jacks.
 
−
    -strlim=# :  limit length of names of objects in rpts files to # characters.  dave sometimes crashes if the
 
−
        names are too long.
 
−
    -tyz :  transpose coords in yz before writing them to the rpts (must specify -rpts option)
 
−
    -color=# : for the w value (color) use the specified value (use -P in play to see this as a color). default = none.
 
−
        if you have no color (no w value), addlines can put one in (-P option in addlines).
 
  
−
  diagnostics:
+
  -h val1 val2: Ignore any voxels in image1 >= val1 and
−
    -silent :  suppress warning messages.
+
any voxels in image2 >= val2.
−
    -verbose
 
−
-debug
 
  
−
example:
+
  -r: instead of intensities, use the rank
−
  convex_hull2.pl -tripletsin -jack=jack.rpts:5 -addlines -twod -maxdist=100 file1.triplets  > file1_mst.rpts
+
order of the intensities.
−
  addlines2 -P -1 image.i2i file1_mst.rpts - | addlines2 -P -2 - jack.rpts - | reduceima -bin 3 3 -L - -| play -P -1 R  -P -1 G -
+
  -a: automatically calculate the size of the
−
 
+
output image. attempts to make the scale
−
 
+
factor = 1.
−
see also:
+
  -b: keep the xdim and ydim scale factors the same.
−
  convex_hull, objs2mst.pl
+
  -s: calculate Spearman rank-order correlation
−
  objs2bb.pl, objs2dist.pl, objs2dist121.pl, closest_object, closest_voxel, countobjs, maskobjs, objs_via_ascent
+
coefficients. print results to stdout.
−
  resolve_pts
+
  -z zslice:   only examine the specified z slice (the first
 +
slice is considered slice 0).
 +
note: entire image name is NOT required.
 +
note: a - in place of an image name means stdin or stdout.
  
 +
examples:
 +
    # to apply this to a set of 3D images, using the same scales and size images for easy comparison
 +
correlationL -S s1 s2 -d 512 512 -B 0 0 image1.i2i corr1.i2i    (and same for other images)
 
   
 
   
−
===  objs2alldists.pl ===
+
===  create_imagesL ===
−
Like obs2disp.pl but calculates the distance to ALL the objects (within -maxdist), not just the closest.
 
−
See ~/krypton/Zhuge/grants/AsthmaRO1/README for 5/27/11 and /home/lml/krypton/Zhuge/BKandRyr/analysis6/run18
 
−
  (which did NOT use this).
 
  
−
This program takes 2 object outputfiles produced by countobjs (or maskobjs) and finds the shortest distance
+
This program takes output from many runs of "overlap" and
−
from the center of mass of objects in file1.out to the center of mass of objects in file2.out.
+
produces two images. One image is a percent colocalization image
 +
and the other is a probability image.  The overlap program MUST be
 +
run via the "many_overlaps" command. The probability calculations
 +
are the same as those performed by "probcolocal", but only -n
 +
needs to be specified since the other values are automatically
 +
extracted from the file produced by "many_overlaps".
  
−
If both file arguments are the same (e.g., objs2dist.pl file1.out file1.out >file.dist), you can use this
+
The percent image is the percent of voxels above threshold in image1
−
routine to find the distances between objects within an image (an object match with the same id is automatically
+
(as originally specified to "many_overlaps") which overlap with
−
ignored in this case so objects don't match to themselves). See also the option -skipsame.
+
voxels above threshold in image2. A 100 in the output image = 100 percent.
 +
The probability of observing as much (or more) overlap as we did due to
 +
random chance is the prob.i2i image. Probabilities are mulitplied by 100.
  
−
(modified from /storage/big1/lml/was_voxel/Corvera/track/objs2bb.pl)
+
Position along the y-axis (vertical axis) of the image, corresponds to
 +
thresholds for image2. The x-axis represents image1 thresholds.  The
 +
lowest threshold is the bottom left corner.  See the first line in
 +
your datafile for the range of thresholds this represents.
 +
Overlap produces statistics for a range of allowed overlaps.
 +
Create_images, by default, chooses an overlap within 1 voxel.
 +
If you want to use a different overlap distance use the -o option.
  
−
usage:
+
See also: overlap, probcolocal, many_overlaps
−
  objs2alldists.pl file1.out file2.out >file.dist 
 
  
 +
Usage:
 +
create_images [options] datafile percent.i2i prob.i2i
 
options:
 
options:
−
  -dx=# : spacing in the x direction ,default = 1
+
  -o distance:   voxels within this distance count as overlapped.
−
  -dy=# : spacing in the y direction ,default = 1
+
  -n number:     number of voxels (1000000 default), see probcolocal.
−
  -dz=# : spacing in the z direction ,default = 1
+
 
−
  -size1=min:max :  min and max object size allowed for file 1 in pixels (inclusive)
+
Examples:
−
  -size2=min:max : min and max object size allowed for file 2 in pixels (inclusive)
+
  many_overlaps -t 100 1000 100 -T 100 1000 100 alpha_T.i2i beta_T.i2i tmp_output
−
  -iod1=min:max :  min and max object iod allowed for file 1 (inclusive)
+
  create_images -n 363264 tmp_output percent.i2i prob.i2i
−
  -iod2=min:max :  min and max object iod allowed for file 2 (inclusive)
+
   
−
  -maxdist=#: : don't allow matches further away than this distance (after applying dx, dy, dz spacing factors).
+
===  makeGmixtures ===
−
  default maxdist is ~ 3000.
+
This program creates a set of data which is sampled from a known mixture of Gaussians.
−
  -hist :  calculate histogram of distances (hist[int(dist)]++, where int just truncates to integer).
+
Output statistics to stdout. This can be used to test the compare2gaussian program.
−
  -sizehist :  calculate histogram of object sizes (in voxels) in file1.out. (hist[int(size)]++, where int just
+
 
−
  truncates to integer). If you don't care about distances between two files (ie, only want -sizehist)
+
Usage: makeGmixtures [options]
−
  put the same file name for both files on the command line.  
+
options:
−
  -rpts=file.rpts :  put bounding boxes around objects found and lines between closest objects (similar to objs2bb.pl)
+
  -n #: number of data points to calculate, default = 100
−
  display this in dave eg: dave -n 0 -u -I file.i2i file.rpts (use the -n 0 and -u options)
+
  -g # amp1 mean1 sd1 ... :
−
  note: may not show up in dave until you click on "scale" to force a rescale (or draw?).
+
The Gaussian mixture model the data drawn from.
−
  -jack=max.rpts:# : create an rpts file with the maxima in each object displayed as a small jack.
+
# is the number of Gaussians, this is followed by the amplitude, mean, and sd of
−
  # controls the size of the jack. 1=1 pixel in size, 2 = 2 pixels, etc.
+
each Gaussian. The default is one Gaussian with mean = 0 and sd = 1.
−
  -strlim=# :  limit length of names of objects in rpts files to # characters. dave sometimes crashes if the
+
Really only the relative amplitudes matter, not their absolute value since they
−
  names are too long.
+
determine the relative probability of drawing from each distribution.
−
  -tyz : transpose coords in yz before writing them to the rpts (must specify -rpts option)
+
  -v: verbose. prints extra info to stdout, each point is labeled with which Gaussian
−
  -skipsame :  don't match an object in file1.out to an object with the same id in file2.out
+
it is from. Use,e.g.,: fgrep G1 output|cull -2 > tmp.dat    to then graph it.
−
  This is set automatically if file1.out = file2.out.
+
 
−
  -silent :  don't print the distances (sets -hist)
+
See Also: compare2gaussian, fitgaussians2, fit2gaussians, fit3gaussians
−
  -simpleprint :  when printing distances, just print distance, one per line, nothing else. to be read in
 
−
  by ~/Zhuge/grants/AsthmaRO1/distance_distribution.m. note: that program assumes distances
 
−
  are in pixels and pixels are 80 nm, unless you specify pixelsize=somethingelse.
 
−
  -simpleprint2 :  like simpleprint, but the first column is id of the Ryr to which this BK is closest.
 
−
  -onelineprint :  like objs2alldists.pl  but prints the distance to ALL the objects (within -maxdist),  
 
−
  not just the closest on one line, so we can keep track of which BK are near which Ryr.
 
−
  see comdists3.pl (which uses this option).
 
−
  -verbose
 
  
−
example:
+
Source code is in ~lml/krypton/Lefkowitz
−
  countobjs -k -t 2000 2000 wave1.objs wave1.i2i
+
#/home/lml/krypton/bin/makeGmixtures -h
−
  countobjs -k -t 2000 2000 wave2.objs wave2.i2i
 
−
  objs2dist.pl wave1.objs wave2.objs > wave1and2.dist
 
  
−
see also:
+
===  mpoisson  ===
−
  objs2dist121.pl, closest_object, closest_voxel, countobjs, maskobjs, objs_via_ascent, pt_distances
+
Generate the inter-arrival distribution seen from 10 independent poisson processes
 +
(eg, spark sites), to check that it is equivalent to 1 process whose lambda is the
 +
sum of the independent processes
  
 +
Usage: mpoisson
 +
options:
 +
  -t #:  total time (in seconds) to count number of arrivals, default = 1000.000000
 +
  -l #:  lambda of each poisson process (mean number of events per second), default = 10.000000
 +
  -p #:  number of processed, default = 10
 +
  -d dur sep:  drop intervals of specified duration, sep seconds between the start of one dropped
 +
                  interval and the next. This is to test if the resulting process is still Poisson.
 +
                  It mimics how Rhongua acquired the data (a series of disconnected 2 second intervals).
 +
  -i dt:  print histogram of inter-arrival times instead.  bin width is dt (in seconds)
 
   
 
   
−
===  objs2dist2.pl ===
+
===  probcolocalL ===
−
objs2dist2.pl: like objs2dist.pl but when -rpts specified prints out lines to ALL objects
 
−
      within -maxdist (which now defaults to 20), rather than just the closest. 
 
−
      So we can see all the BK clusters which are close enough
 
−
      to a Ryr to be activated. see /home/lml/krypton/Zhuge/paper2010/README for 5/20/10.
 
  
−
This program takes 2 object outputfiles produced by countobjs (or maskobjs) and finds the shortest distance
+
This program calculates the probability of an event occurring
−
from the center of mass of objects in file1.out to the center of mass of objects in file2.out.
+
k or more times in n trials if the probability of an event is
 +
p and events are independent (see p.182 of Numerical Recipies)
  
−
If both file arguments are the same (e.g., objs2dist.pl file1.out file1.out >file.dist), you can use this
+
It is intended as one way to determine if an observed level of
−
routine to find the distances between objects within an image (an object match with the same id is automatically
+
volume colocalization is due to random chance or not. To use it
−
ignored in this case so objects don't match to themselves). See also the option -skipsame.
+
in this manner, first find the fraction of voxels in each image
 +
which are used to calculate colocalization (e.g., those above
 +
threshold). Call these fractions f1 and f2.  Then, if these
 +
voxels were randomly placed, the probability that identical voxels
 +
are turned on in both images is f1*f2. An "event" is just such
 +
a coincidence, so p = f1*f2. n = number of voxels in one image.
 +
k= number of voxels which are observed to colocalize.
 +
This program then returns the probability that this amount of
 +
colocalization or more would have occurred merely due to chance.
 +
Note: if only an annulus (i.e., a subset of the total image volume)
 +
    is really being analyzed, then f1 and f2 and n should probably be
 +
    derived based on the volume subset, not the entire image.
 +
 
 +
Usage: probcolocal [options]
 +
Output (to standard out): the probability of this or greater occuring randomly.
 +
options:
 +
  -n number:    number of trials (100 default)
 +
  -k occurrences: number of occurrences (50 default).
 +
  -p probability: prob of an event (0.500000 default).
 +
  -h:   print this help message.
 +
 +
===  roc  ===
 +
/home/lml/krypton/bin/roc
 +
This program reads two images. It attempts to use voxel values in
 +
image1 as a predictor of voxel values in image2; ie, as a type of
 +
measure of colocalization.  Both images are first rescaled to be
 +
between 0 and max (100).Then image2 is thresholded. Image1
 +
is then set,sequentially, to all integer thresholds between 0 and
 +
and max (unless -r is used to restrict the range).  If a voxel
 +
in image1 is above threshold then we guess
 +
that the same voxel is above threshold in image2.
 +
It also does the reverse, ie, use image2 to predict image1.
 +
The default cost function is:  1- 255*prob(detection)*(1-prob(false alarm)).
 +
 
 +
OUTPUT: 
 +
TO STDOUT:
 +
  The best thresholds, lowest cost and probability of detection,
 +
  prob of failure, prob of miss and prob of saying nothing when
 +
  there is nothing.
 +
TO A FILE:
 +
  6 images get created, they are the costs and probability of
 +
  detection and false alarm (3 separate images) when im1 is ussed
 +
  to predict im2, and another 3 for when im2 is used to predict im1.
 +
  By default these will be named:
 +
    im1predictingim2_c.i2i, im1predictingim2_pd.i2i, im1predictingim2_pf.i2i
 +
    im2predictingim1_c.i2i, im2predictingim1_pd.i2i, im2predictingim1_pf.i2i
 +
  The -p option changes the prefix (eg,the "im1predictingim2").
 +
  The images all have thresh1 on x axis, thresh2 on y axis.
 +
  The cost images are always scaled 0-255.
 +
  The pd and pf images are scaled 0-100.
 +
  Additional output files can be created with the -c option.
 +
SEE ALSO: playims . This program quickly puts up all 6 images
 +
  created by roc.  It can take arguments.
 +
 
 +
Usage: roc [options] image1 image2
 +
      options:
 +
-m max:    max of intensity range to rescale data to
 +
    the default is 0 to 100.
 +
-b val1 val2: ignore all background voxels. A voxel will be
 +
  ignored in both images if the voxel in image1
 +
  is <= val1 and the voxel in image2<= val2.
 +
-r low hi: range of intensity threshold values to check
 +
          in image1 (in original image intensity units),
 +
  default is entire intensity range.
 +
-R low hi: range of intensity threshold values to check
 +
          in image2 (in original image intensity units),
 +
  default is entire intensity range.
 +
-t thresh: only examine this threshold value for image1.
 +
-T thresh: only examine this threshold value for image2.
 +
  I am not sure -t and -T work completely correctly.
 +
-c file1 file2:
 +
  Creates 2 roc curve data files for graph and plot.
 +
    The probability of false alarm (x coord) and
 +
  detection (y coord) and cost (intensity) for all
 +
  thresholds in image1 for a threshold in image2
 +
  is written file1. A text string
 +
    indicating the image2 threshold level is written out.
 +
  This is then repeated for other image2 threshold levels.
 +
 
 +
  file2 is the same, but for image2 predicting im1.
 +
  Use: graph -f 1 -b <file1 |plot  to display these roc curves.
 +
-C d f m n: d is the "cost" of a correct detection, ie
 +
  a voxel in image1 is above threshold the same time
 +
  that the equivalent voxel is above thresh2 in
 +
  image2.
 +
  f is the cost of a false alarm (voxel in
 +
  image1 > thresh1 but voxel in image2 is < thresh2).
 +
  m is cost of a miss (im 1 <t1, im 2 > t2) and
 +
  n is cost of nothing present ( both im 1 and im 2
 +
  less than threshold, ie correctly predicting that
 +
  nothing is there).
 +
  Given these costs the program will print to stderr
 +
  the thresh1 and thresh2 values which minimize the
 +
  total cost. It will also print the total cost.
 +
  Total cost = d*pd + m*pm + f*pf + n*pn 
 +
  where pd = probability of detection, etc.
 +
  Typically, d = n = 0 and f = m = 1.
 +
-p pre1 pre2: prefixes for the names of the saved images
 +
  which show the sensitivity analysis. 6 images
 +
  get created (regardless of whether the p option
 +
  is specified), they are the costs and prob. of
 +
  detection and false alarm (3 separate images)
 +
  when im1 is used to predict im2, and another 3
 +
  for when im2 is used to predict im1.
 +
  By default these will be named:
 +
  im1predictingim2c.i2i, im1predictingim2pd.i2i,
 +
  im1predictingim2pf.i2i, im2predictingim1c.i2i, etc.
 +
  This option changes the prefix (ie, what comes
 +
  before the "c","pd",and "pf") for the
 +
  images saved. pre1 will be for im1 predicting im2,
 +
  and pre2 will be vis versa.
 +
-s file:  save roc data as an array of floats to "file".
 +
  Once this file is saved, any particular values
 +
  of costs can be examined very
 +
  quickly. In other words, this is the data that
 +
  the roc program is really taking a long time to
 +
  calculate. So if you want to examine the same
 +
  pair of images under different cost
 +
  scenarios, save the data file during the 1st
 +
  scenario, and run the others using the saved data.
 +
  NOT IMPLEMENTED YET.
 +
-f file:  read in a saved array (see -s above). When this
 +
  option is specified the args image1 and image2 are
 +
  not specified on the command line.
 +
  NOT IMPLEMENTED YET.
 +
note: entire image name is NOT required.
 +
note: a - in place of an image name means stdin.
 +
 
 +
 
 +
Typical examples:
 +
1). roc  im1.i2i im2.i2i > roc.info
 +
    playims dummy
 +
2). roc -p 1to2 2to1 -b 0 0 im1.i2i im2.i2i > roc.info
 +
3). roc -C 0 1 1 0  -b 0 0 im1.i2i im2.i2i > roc.info
 +
4). roc -r 20 80 -R 50 200 im1.i2i im2.i2i > roc.info
 +
5). roc -b 5 5 -c roc1to2.dat roc2to1.dat im1.i2i im2.i2i > roc.info
 +
    graph -f 1 -b <roc1to2.dat |plot
 +
    graph -f 1 -b <roc2to1.dat |plot
 +
    playims dummy
 +
 +
 
 +
===  sparkstats5  ===
 +
#/home/lml/krypton/bin/sparkstats5
 +
 
 +
sparkstats5 is similar to sparkstats3 (only examines the first 10 seconds of data from any cell
 +
and ignores cells which don't have 10 seconds of data).
 +
 
 +
It eliminates from any 2 second interval multiple events at the same site, since we guess that is
 +
due to a second "bursting" process which we want to ignore.
 +
All events in the same cell, at the same x,y are considered events from the same spark
 +
 
 +
Usage: sparkstats5 [options] datafile
 +
options:
 +
  -N #: spark events considered the same site if <= # pixels in x and y from first event and
 +
also in the same cell and 2 second interval (note: histogram produced does not compensate for
 +
the longer time some cells were under observation).
 +
  -O #: like -N. in addition, sparks with 0 events in a 2 second interval are added for
 +
each spark that exists in  an interval but does not exhibit spark events
 +
in some other interval in the same cell.
 +
  -i: spark events condidered the same "site" if in same cell and same 2 second interval
 +
this is the default.
 +
  -I: an extra spark id field does NOT precede the spark data (ie, test.data, not bestdata.data).
 +
  -J: datafile is just one cell; data format: x y amp; just calculate spark sites (use specify -N)
 +
 
 +
[source code in /usr/people/lml/vision/Rhonghua/Sparks/sparkstats5.c]
 +
 +
== Analysis of Points ==
 +
===  components.pl  ===
  
−
(modified from /storage/big1/lml/was_voxel/Corvera/track/objs2bb.pl)
+
Calculates the number of connected components resolved over a range of point densities.
  
−
usage:
+
components.pl [options]
−
  objs2dist2.pl file1.out file2.out >file.dist 
 
  
 
options:
 
options:
−
  -dx=# :  spacing in the x direction ,default = 1
+
 
−
  -dy=# : spacing in the y direction ,default = 1
+
-numpts=low:hi:delta
−
  -dz=# : spacing in the z direction ,default = 1
+
-repeat=# number of times to repeat at each point density
−
  -size1=min:max :  min and max object size allowed for file 1 in pixels (inclusive)
+
-res=# in microns
−
  -size2=min:max :  min and max object size allowed for file 2 in pixels (inclusive)
+
-outfile=name name of output file. otherwise to _tmp. always need write permission in current directory.
−
  -iod1=min:max :  min and max object iod allowed for file 1 (inclusive)
 
−
  -iod2=min:max :  min and max object iod allowed for file 2 (inclusive)
 
−
  -maxdist=#: :  don't allow matches further away than this distance (after applying dx, dy, dz spacing factors).
 
−
  default maxdist is 20.
 
−
  -hist :  calculate histogram of distances (hist[int(dist)]++, where int just truncates to integer).
 
−
  -sizehist :  calculate histogram of object sizes (in voxels) in file1.out. (hist[int(size)]++, where int just
 
−
  truncates to integer). If you don't care about distances between two files (ie, only want -sizehist)
 
−
  put the same file name for both files on the command line.
 
−
  -rpts=file.rpts :  put bounding boxes around objects found and lines from objects in file1.out to all objects
 
−
  in file2.out that are <= maxdist away (these lines will become an object named "near_to_file1.out").
 
−
  display this in dave eg:  dave -n 0 -u -I file.i2i file.rpts (use the -n 0 and -u options)
 
−
  note: may not show up in dave until you click on "scale" to force a rescale (or draw?).
 
−
  -jack=max.rpts:# :  create an rpts file with the maxima in each object displayed as a small jack.
 
−
  # controls the size of the jack. 1=1 pixel in size, 2 = 2 pixels, etc.
 
−
  -strlim=# :  limit length of names of objects in rpts files to # characters. dave sometimes crashes if the
 
−
  names are too long.
 
−
  -tyz :  transpose coords in yz before writing them to the rpts (must specify -rpts option)
 
−
  -skipsame :  don't match an object in file1.out to an object with the same id in file2.out
 
−
  This is set automatically if file1.out = file2.out.
 
−
  -silent :  don't print the shortest distances (sets -hist)
 
−
  -verbose
 
−
 
 
−
example:
 
−
  countobjs -k -t 2000 2000 wave1.objs wave1.i2i
 
−
  countobjs -k -t 2000 2000 wave2.objs wave2.i2i
 
−
  objs2dist2.pl wave1.objs wave2.objs > wave1and2.dist
 
−
 
 
−
see also:
 
−
  objs2dist121.pl, objs2dist.pl, closest_object, closest_voxel, countobjs, maskobjs, objs_via_ascent, pt_distances
 
  
 
   
 
   
−
===  objs2mst.pl  ===
+
===  convex_hull.pl  ===
  
−
This program takes an object outputfiles (unless -rptsin) produced by countobjs (or maskobjs) and finds the minimal
+
This program takes an object outputfile (unless -rptsin or -tripletsin) produced by countobjs (or maskobjs) and finds the minimal
−
spanning tree connecting the center of mass of the objects. Writes out connections as an rpts file to stdout.
+
spanning tree connecting the center of mass of the objects, and the convex hull. Writes out connections as an rpts file to stdout.
−
Options can be used to only selected a subset of the objects and to constrain max distance (so multiple
+
It also loops through 20 thresholds  for the pts, and prints to stderr some stats about the minimal spanning tree and
−
trees can be produced).
+
convex hull of the points above each of these thresholds.
 +
 
 +
Options can be used to only selected a subset of the objects and to constrain the maximum distance (-maxdist).
 +
 
 +
It was written with the hope that triplets (maxima in an image which has a cell in the center) will show a pattern in their
 +
convex hull area, so that when the threshold rises high enough, only maxima inside the cell will still be present and hence
 +
the convex hull will be stable and of much smaller area.
 +
 
 +
This program requires perl modules Graph::Kruskal and Math::Geometry::Planar, use cpanp to install these:
 +
    yum install perl-CPANPLUS-0.91.3-202.fc16.noarch  - for cpanp
 +
    cpanp -i Graph::Kruskal
 +
    cpanp i Math::Geometry::Planar
  
 
usage:
 
usage:
−
   objs2mst.pl file1.objs > file1_mst.rpts
+
   convex_hull.pl -tripletsin file1.triplets > file1_mst.rpts
 +
 
 +
  input options:
 +
    -dx=#   spacing in the x direction, default = 1
 +
    -dy=#   spacing in the y direction, default = 1
 +
    -dz=#   spacing in the z direction, default = 1
 +
    -rptsin     instead of file1.objs, read file1.rpts where file1.rpts was produced by max2d.
 +
      -size1 and -iod1 are ignored when this option is specified.
 +
    -tripletsin   instead of file1.objs read in file1.xyi,  triplets of x y and intensity.
  
−
options:
+
  analysis options:
−
  -dx=# :  spacing in the x direction, default = 1
+
    -size1=min:max     min and max object size allowed for file1.objs in pixels (inclusive)
−
  -dy=# :  spacing in the y direction, default = 1
+
    -iod1=min:max   min and max object iod allowed for file1.objs (inclusive), or intensity if -tripletsin was specified.
−
  -dz=# :  spacing in the z direction, default = 1
+
    -maxdist=#: :  don't allow connections between pts further apart than this distance (after applying dx, dy, dz spacing factors).
−
  -size1=min:max :  min and max object size allowed for file1.objs in pixels (inclusive)
+
  warning: if the distance is too small, then all the pts will not be connected to begin with;
−
  -iod1=min:max :  min and max object iod allowed for file1.objs (inclusive)
+
    this may cause the minimal spanning tree algorithm to fail.
−
  -rptsin :  instead of file1.objs, read file1.rpts where file1.rpts was produced by max2d.
+
    default maxdist is  3000
−
  -size1 and -iod1 are ignored when this option is specified.
+
 
−
  -addlines :  output rpts format which addlines is more likely to be happy with (may not work in dave?)
+
   output options:
−
  -maxdist=#: :  don't allow matches further away than this distance (after applying dx, dy, dz spacing factors).
+
    -addlines :  output rpts format which addlines is more likely to be happy with (may not work in dave?)
−
  default maxdist is ~ 3000.
+
    -hist :  calculate histogram of distances (hist[int(dist)]++, where int just truncates to integer). obsolete.
−
   -hist :  calculate histogram of distances (hist[int(dist)]++, where int just truncates to integer).
+
    -sizehist :  calculate histogram of object sizes (in voxels) in file1.out. (hist[int(size)]++, where int just  
−
  -sizehist :  calculate histogram of object sizes (in voxels) in file1.out. (hist[int(size)]++, where int just  
+
        truncates to integer). If you don't care about distances between two files (ie, only want -sizehist)
−
  truncates to integer). If you don't care about distances between two files (ie, only want -sizehist)
+
        put the same file name for both files on the command line.  obsolete.
−
  put the same file name for both files on the command line.  
+
    -rpts=file.rpts :  put bounding boxes around objects found and lines between closest objects (similar to objs2bb.pl)
−
  -rpts=file.rpts :  put bounding boxes around objects found and lines between closest objects (similar to objs2bb.pl)
 
 
  display this in dave eg:  dave -n 0 -u -I file.i2i file.rpts (use the -n 0 and -u options)
 
  display this in dave eg:  dave -n 0 -u -I file.i2i file.rpts (use the -n 0 and -u options)
 
  note: may not show up in dave until you click on "scale" to force a rescale (or draw?).
 
  note: may not show up in dave until you click on "scale" to force a rescale (or draw?).
−
  -jack=max.rpts:# :  create an rpts file with the maxima in each object displayed as a small jack.  
+
    -jack=max.rpts:# :  create an rpts file with the maxima in each object displayed as a small jack.  
−
  # controls the size of the jack. 1=1 pixel in size, 2 = 2 pixels, etc.
+
    # controls the size of the jack. 1=1 pixel in size, 2 = 2 pixels, etc.
−
  -strlim=# :  limit length of names of objects in rpts files to # characters.  dave sometimes crashes if the
+
-twod   add this (in addition to -jack) if you want 2D jacks rather than 3D jacks.
−
  names are too long.
+
    -strlim=# :  limit length of names of objects in rpts files to # characters.  dave sometimes crashes if the
−
  -tyz :  transpose coords in yz before writing them to the rpts (must specify -rpts option)
+
        names are too long.
−
  -color=# :  for the w value (color) use the specified value (use -P in play to see this as a color). default = none.
+
    -tyz :  transpose coords in yz before writing them to the rpts (must specify -rpts option)
−
  if you have no color (no w value), addlines can put one in (-P option in addlines).
+
    -color=# :  for the w value (color) use the specified value (use -P in play to see this as a color). default = none.
−
   -silent : don't print the shortest distances (sets -hist)
+
        if you have no color (no w value), addlines can put one in (-P option in addlines).
−
  -verbose
+
 
 +
   diagnostics:
 +
    -silent :   suppress warning messages.
 +
    -verbose
 +
-debug
  
 
example:
 
example:
−
   countobjs -k -t 2000 2000 wave1.objs wave1.i2i
+
   convex_hull2.pl -tripletsin -jack=jack.rpts:5 -addlines -twod -maxdist=100 file1.triplets > file1_mst.rpts
−
  objs2mst.pl wave1.objs > wave1mst.rpts
+
   addlines2 -P -1 image.i2i file1_mst.rpts - | addlines2 -P -2 - jack.rpts - | reduceima -bin 3 3 -L - -| play -P -1 R  -P -1 G -
−
   dave -I wave1.i2i -n 0 -u wave1mst.rpts
+
 
  
 
see also:
 
see also:
 +
  convex_hull, objs2mst.pl
 
   objs2bb.pl, objs2dist.pl, objs2dist121.pl, closest_object, closest_voxel, countobjs, maskobjs, objs_via_ascent
 
   objs2bb.pl, objs2dist.pl, objs2dist121.pl, closest_object, closest_voxel, countobjs, maskobjs, objs_via_ascent
 
   resolve_pts
 
   resolve_pts
  
 
   
 
   
−
===  objs_within_dist.pl  ===
+
===  objs2alldists.pl  ===
 +
Like obs2disp.pl but calculates the distance to ALL the objects (within -maxdist), not just the closest.
 +
See ~/krypton/Zhuge/grants/AsthmaRO1/README for 5/27/11 and /home/lml/krypton/Zhuge/BKandRyr/analysis6/run18
 +
  (which did NOT use this).
  
−
This program takes 2 object outputfiles produced by countobjs (or maskobjs) and finds the number of objects
+
This program takes 2 object outputfiles produced by countobjs (or maskobjs) and finds the shortest distance  
−
in the second file which are within a given distance of each object in the first file.  A histogram is
+
from the center of mass of objects in file1.out to the center of mass of objects in file2.out.
−
printed out.
 
−
Distances are from the center of mass of objects in file1.out to the center of mass of objects in file2.out.
 
−
(modified from objs2dist.pl)
 
  
−
usage:
+
If both file arguments are the same (e.g., objs2dist.pl file1.out file1.out >file.dist), you can use this
−
   objs_within_dist.pl file1.out file2.out >file.dist   
+
routine to find the distances between objects within an image (an object match with the same id is automatically
 +
ignored in this case so objects don't match to themselves). See also the option -skipsame.
 +
 
 +
(modified from /storage/big1/lml/was_voxel/Corvera/track/objs2bb.pl)
 +
 
 +
usage:
 +
   objs2alldists.pl file1.out file2.out >file.dist   
  
 
options:
 
options:
Line 1,591: Line 3,012:
 
   -maxdist=#: :  don't allow matches further away than this distance (after applying dx, dy, dz spacing factors).
 
   -maxdist=#: :  don't allow matches further away than this distance (after applying dx, dy, dz spacing factors).
 
  default maxdist is ~  3000.
 
  default maxdist is ~  3000.
−
   -rpts :  read in file in rpts format
+
   -hist :  calculate histogram of distances (hist[int(dist)]++, where int just truncates to integer).
−
   -verbose :  extra info written to stderr
+
  -sizehist :  calculate histogram of object sizes (in voxels) in file1.out. (hist[int(size)]++, where int just
−
   -vverbose :  print other info. can be combined with -verbose.
+
  truncates to integer). If you don't care about distances between two files (ie, only want -sizehist)
 +
  put the same file name for both files on the command line.
 +
  -rpts=file.rpts :  put bounding boxes around objects found and lines between closest objects (similar to objs2bb.pl)
 +
  display this in dave eg:  dave -n 0 -u -I file.i2i file.rpts (use the -n 0 and -u options)
 +
  note: may not show up in dave until you click on "scale" to force a rescale (or draw?).
 +
  -jack=max.rpts:# :  create an rpts file with the maxima in each object displayed as a small jack.
 +
  # controls the size of the jack. 1=1 pixel in size, 2 = 2 pixels, etc.
 +
   -strlim=# :  limit length of names of objects in rpts files to # characters.  dave sometimes crashes if the
 +
  names are too long.
 +
  -tyz :  transpose coords in yz before writing them to the rpts (must specify -rpts option)
 +
  -skipsame :  don't match an object in file1.out to an object with the same id in file2.out
 +
  This is set automatically if file1.out = file2.out.
 +
  -silent :  don't print the distances (sets -hist)
 +
   -simpleprint :  when printing distances, just print distance, one per line, nothing else. to be read in
 +
  by ~/Zhuge/grants/AsthmaRO1/distance_distribution.m. note: that program assumes distances
 +
  are in pixels and pixels are 80 nm, unless you specify pixelsize=somethingelse.
 +
  -simpleprint2 :  like simpleprint, but the first column is id of the Ryr to which this BK is closest.
 +
  -onelineprint :  like objs2alldists.pl  but prints the distance to ALL the objects (within -maxdist),
 +
  not just the closest on one line, so we can keep track of which BK are near which Ryr.
 +
  see comdists3.pl (which uses this option).
 +
  -verbose
  
 
example:
 
example:
 
   countobjs -k -t 2000 2000 wave1.objs wave1.i2i
 
   countobjs -k -t 2000 2000 wave1.objs wave1.i2i
 
   countobjs -k -t 2000 2000 wave2.objs wave2.i2i
 
   countobjs -k -t 2000 2000 wave2.objs wave2.i2i
−
   objs_within_dist.pl wave1.objs wave2.objs > wave1and2.dist
+
   objs2dist.pl wave1.objs wave2.objs > wave1and2.dist
  
 
see also:
 
see also:
Line 1,604: Line 3,045:
  
 
   
 
   
−
===  connected_random_pts ===
+
===  objs2dist2.pl ===
−
Generates random pts in a planar region, calculates how many connected components are created
+
objs2dist2.pl: like objs2dist.pl but when -rpts specified prints out lines to ALL objects
−
if a pt is connected to all other pts within a given radius.
+
      within -maxdist (which now defaults to 20), rather than just the closest. 
 +
      So we can see all the BK clusters which are close enough
 +
      to a Ryr to be activated. see /home/lml/krypton/Zhuge/paper2010/README for 5/20/10.
  
−
Usage:
+
This program takes 2 object outputfiles produced by countobjs (or maskobjs) and finds the shortest distance
−
connected_random_pts [options]
+
from the center of mass of objects in file1.out to the center of mass of objects in file2.out.
−
Options:
 
−
-x lowx hix:         pts have xcoords within this range, default = (0.0,100.0)
 
−
-y lowy hiy:         pts have ycoords within this range, default = (0.0,100.0)
 
−
-r #: radius (in pixels), default = 5.0
 
−
-s #: long int starting seed for random number generator. default = process id.
 
−
-n #: number of pts to create, default = 1000
 
−
  -h: help
 
−
  -v: verbose
 
  
−
See also:
+
If both file arguments are the same (e.g., objs2dist.pl file1.out file1.out >file.dist), you can use this
−
krypton/Huang/README, components.pl, Kth_pt.m, num_observed.m, mean_minimum_distance.m,objs2mst.pl
+
routine to find the distances between objects within an image (an object match with the same id is automatically
 +
ignored in this case so objects don't match to themselves). See also the option -skipsame.
  
−
Source code in ~krypton/lml/facil 
+
(modified from /storage/big1/lml/was_voxel/Corvera/track/objs2bb.pl)
−
 
−
== Image Manipulation ==
 
−
===  align_quadrants.pl ===
 
−
This program displays the four quadrant images of a well.  The user then saves 3 pairs of points
 
−
(s when middle mouse is pressed). Each pair of points should be points that match in two
 
−
neighboring quadrants.  When done, each quadrant must have one (or two) points specified.
 
−
Points must be in pair order (see recalc_quadrant2.pl).  When done, the use must write them out
 
−
via z (when middle mouse is also pressed, no confimation is given in play). 
 
−
The quadrant images are then aligned based on these points and newimage.i2i is created.
 
  
−
It will also create a file with the output from play, for future reference.
+
usage:
−
It will be named, eg, G02_combined_play.pts. It can be passed manually to recalc_quadrant2.pl to redo
+
  objs2dist2.pl file1.out file2.out >file.dist 
−
the alignment if necessary.
 
−
 
 
−
usage:
 
−
  align_quadrants.pl [options] well newimage.i2i
 
−
 
 
−
 
 
−
examples:
 
−
  align_quadrants.pl [options] G02 G02_combined.i2i
 
  
 
options:
 
options:
−
-no_pts_output don't produce the pts file
+
  -dx=# :  spacing in the x direction ,default = 1
−
-noblend by default the quadrant images are blended together where
+
  -dy=# :  spacing in the y direction ,default = 1
−
they overlap.  use this option to turn that off.
+
  -dz=# :  spacing in the z direction ,default = 1
−
-print_overlap also print the amount of overlap to stderr
+
  -size1=min:max :  min and max object size allowed for file 1 in pixels (inclusive)
−
-debug
+
  -size2=min:max :  min and max object size allowed for file 2 in pixels (inclusive)
−
-debug_all
+
  -iod1=min:max :  min and max object iod allowed for file 1 (inclusive)
−
 
+
  -iod2=min:max :  min and max object iod allowed for file 2 (inclusive)
−
 
+
  -maxdist=#: :  don't allow matches further away than this distance (after applying dx, dy, dz spacing factors).
−
see also:
+
  default maxdist is 20.
−
combine_images
+
  -hist :  calculate histogram of distances (hist[int(dist)]++, where int just truncates to integer).
−
recalc_quadrant2.pl
+
  -sizehist :  calculate histogram of object sizes (in voxels) in file1.out. (hist[int(size)]++, where int just
−
/home/lml/krypton/Corvera/Raz/README 5/16/14
+
  truncates to integer). If you don't care about distances between two files (ie, only want -sizehist)
−
http://wiki.imagej.net/Grid/Collection_Stitching_Plugin
+
  put the same file name for both files on the command line.
 +
  -rpts=file.rpts : put bounding boxes around objects found and lines from objects in file1.out to all objects
 +
  in file2.out that are <= maxdist away (these lines will become an object named "near_to_file1.out").
 +
  display this in dave eg:  dave -n 0 -u -I file.i2i file.rpts (use the -n 0 and -u options)
 +
  note: may not show up in dave until you click on "scale" to force a rescale (or draw?).
 +
  -jack=max.rpts:# :  create an rpts file with the maxima in each object displayed as a small jack.
 +
  # controls the size of the jack. 1=1 pixel in size, 2 = 2 pixels, etc.
 +
  -strlim=# :  limit length of names of objects in rpts files to # characters.  dave sometimes crashes if the
 +
  names are too long.
 +
  -tyz : transpose coords in yz before writing them to the rpts (must specify -rpts option)
 +
  -skipsame :  don't match an object in file1.out to an object with the same id in file2.out
 +
  This is set automatically if file1.out = file2.out.
 +
  -silent :  don't print the shortest distances (sets -hist)
 +
  -verbose
 +
 
 +
example:
 +
  countobjs -k -t 2000 2000 wave1.objs wave1.i2i
 +
  countobjs -k -t 2000 2000 wave2.objs wave2.i2i
 +
  objs2dist2.pl wave1.objs wave2.objs > wave1and2.dist
  
 +
see also:
 +
  objs2dist121.pl, objs2dist.pl, closest_object, closest_voxel, countobjs, maskobjs, objs_via_ascent, pt_distances
  
 
   
 
   
−
===  combine_images.pl  ===
+
===  objs2mst.pl  ===
  
−
This program runs combine_images on all the images in the current directory.  All images which have names
+
This program takes an object outputfiles (unless -rptsin) produced by countobjs (or maskobjs) and finds the minimal
−
like L##_morestuff.i2i (where L is any letter and # is any digit) will be combined;
+
spanning tree connecting the center of mass of the objects. Writes out connections as an rpts file to stdout.
−
all the A02 will be combined (to produce A02_comb.i2i), all the A03, etc.
+
Options can be used to only selected a subset of the objects and to constrain max distance (so multiple
−
The resulting image for the combination of the A02 images will be A02_tag.i2i (see -newtag option, e.g. A02_comb.i2i).
+
trees can be produced).
−
Any images already existing in the current directory with a name like L##_stuff_oldtag.i2i will be ignored.
 
  
 
usage:
 
usage:
−
combine_images.pl [options]
+
  objs2mst.pl file1.objs  > file1_mst.rpts
  
 
options:
 
options:
−
-newtag=something The output filename for L##*.i2i will be L##_newtag.i2i. Default = comb
+
  -dx=# : spacing in the x direction, default = 1
−
-oldtag=something Any files of the form L##*_oldtag.i2i will be ignored. Default = comb
+
  -dy=# :  spacing in the y direction, default = 1
−
-pixsize=# pass this as -p # to combine_images program (pixel size).
+
  -dz=# :  spacing in the z direction, default = 1
−
Specify -pixsize=2.41 (um/pixel) for the 2.5X objective.
+
  -size1=min:max :  min and max object size allowed for file1.objs in pixels (inclusive)
−
-reduceima=#:#:tag After creating output image, apply reduceima to it  
+
  -iod1=min:max :  min and max object iod allowed for file1.objs (inclusive)
−
with -bin # # and the specified output tag on the name.
+
  -rptsin :  instead of file1.objs, read file1.rpts where file1.rpts was produced by max2d.
−
So, e.g., A02_comb.i2i will become A02_tag.i2i
+
  -size1 and -iod1 are ignored when this option is specified.
−
-flipx flip images in X prior to combining them
+
  -addlines :  output rpts format which addlines is more likely to be happy with (may not work in dave?)
−
-flipy flip images in Y prior to combining them (can be used at the same time as -flipx)
+
  -maxdist=#: : don't allow matches further away than this distance (after applying dx, dy, dz spacing factors).
−
-x=#:#:#:# manually specified picture offsets. see combine images
+
  default maxdist is ~  3000.
−
-y=#:#:#:# manually specified picture offsets. see combine images
+
  -hist :  calculate histogram of distances (hist[int(dist)]++, where int just truncates to integer).
−
-o=# number of pixels the images overlap (ignores info in image headers). see combine_images
+
  -sizehist :  calculate histogram of object sizes (in voxels) in file1.out. (hist[int(size)]++, where int just
−
-f do MOT pad images at border (as of 2/3/14). see combine_images.
+
  truncates to integer). If you don't care about distances between two files (ie, only want -sizehist)
−
-remove Remove the full-size combined image (e.g., A02_comb.i2i) when done (use with -reduceima).
+
  put the same file name for both files on the command line.
−
-dummy Just echo what would be done, but don't do anything
+
  -rpts=file.rpts :  put bounding boxes around objects found and lines between closest objects (similar to objs2bb.pl)
−
-verbose Echo as things are done.
+
  display this in dave eg:  dave -n 0 -u -I file.i2i file.rpts (use the -n 0 and -u options)
−
-debug
+
  note: may not show up in dave until you click on "scale" to force a rescale (or draw?).
−
 
+
  -jack=max.rpts:# :  create an rpts file with the maxima in each object displayed as a small jack.
−
note:
+
  # controls the size of the jack. 1=1 pixel in size, 2 = 2 pixels, etc.
−
combine_images (in /storage/big1/lml/Linux/bin) and reduceima (in /storage/big1/kef/Linuxbin) must be in your
+
  -strlim=# :  limit length of names of objects in rpts files to # characters.  dave sometimes crashes if the
−
path for this perl script to work. You can check this by just typing: which combine_images  and  which reduceima;
+
  names are too long.
−
if they are not found you need to add their directory to your PATH environment variable (echo $PATH will show you
+
  -tyz : transpose coords in yz before writing them to the rpts (must specify -rpts option)
−
what it is currently). How this is done varies depending upon which shell you are running. Under tcsh it would
+
  -color=# :  for the w value (color) use the specified value (use -P in play to see this as a color). default = none.
−
be   setenv PATH $PATH:/storage/big1/kef/Linuxbin:/storage/big1/lml/Linux/bin .
+
  if you have no color (no w value), addlines can put one in (-P option in addlines).
 +
  -silent :  don't print the shortest distances (sets -hist)
 +
   -verbose
  
 
example:
 
example:
−
      cd /storage/big3/kdb/Zeiss/20130326/GEDMAT_002_PRO_SQ2_DAY14
+
  countobjs -k -t 2000 2000 wave1.objs wave1.i2i
−
# Combine all images in each well. The combined image will be L##_combined (-newtag=combined).
+
  objs2mst.pl wave1.objs > wave1mst.rpts
−
# Then reduce the combined size back down to the size of one original image;
+
  dave -I wave1.i2i -n 0 -u wave1mst.rpts
−
# call the new image L##_combined_reduc.i2i (-reduceima=2:2:reduc).
 
−
# Finally, remove the big (unreduced) combined image (-remove).   
 
−
# First do a dummy run (-dummy) to see if it is going to do what we want:
 
−
      combine_images.pl -newtag=combined -reduceima=2:2:reduc -pixsize=2.41 -remove -dummy   
 
−
# ok, now the real thing (just leave off -dummy):
 
−
      combine_images.pl -newtag=combined -reduceima=2:2:reduc -pixsize=2.41 -remove
 
  
 
see also:
 
see also:
−
combine_images
+
  objs2bb.pl, objs2dist.pl, objs2dist121.pl, closest_object, closest_voxel, countobjs, maskobjs, objs_via_ascent
−
/storage/big1/raz/GEDMAT
+
  resolve_pts
−
mask_gedmat_images.pl
 
  
 
   
 
   
−
===  overlap_images.pl  ===
+
===  objs_within_dist.pl  ===
  
−
  Takes output from parsepos.pl  and calculates how the images overlap so they can then be combined easily (-create option).
+
This program takes 2 object outputfiles produced by countobjs (or maskobjs) and finds the number of objects
 +
in the second file which are within a given distance of each object in the first file. A histogram is
 +
printed out.
 +
Distances are from the center of mass of objects in file1.out to the center of mass of objects in file2.out.
 +
(modified from objs2dist.pl)
  
−
overlap_images.pl [options]
+
usage:
 +
  objs_within_dist.pl file1.out file2.out >file.dist 
  
−
options:
+
options:
−
-xdim=# xdim of image in pixels, default = 1392
+
  -dx=# :  spacing in the x direction ,default = 1
−
-ydim=# ydim of image in pixels, default = 1040
+
  -dy=# :  spacing in the y direction ,default = 1
−
-zdim=# zdim of image in pixels, default = 25
+
  -dz=# :  spacing in the z direction ,default = 1
−
-pixsize=# size of pixels in um, default = 0.645
+
  -size1=min:max :  min and max object size allowed for file 1 in pixels (inclusive)
−
-create=file.i2i actually combine the images into one big image
+
  -size2=min:max :  min and max object size allowed for file 2 in pixels (inclusive)
−
-flipx flip each image around its x-axis prior to inserting it into the new image (if -create is specified)
+
  -iod1=min:max :  min and max object iod allowed for file 1 (inclusive)
−
-flipy flip each image around its y-axis prior to inserting it into the new image (if -create is specified)
+
  -iod2=min:max :  min and max object iod allowed for file 2 (inclusive)
−
-verbose
+
  -maxdist=#: :  don't allow matches further away than this distance (after applying dx, dy, dz spacing factors).
−
-dummy just echo what would be done, but don't do anything (nothing normally done anyway unless -create specified).
+
  default maxdist is ~  3000.
 +
  -rpts :  read in file in rpts format
 +
  -verbose :  extra info written to stderr
 +
  -vverbose :  print other info. can be combined with -verbose.
  
−
see also:
+
example:
−
parsepos.pl
+
  countobjs -k -t 2000 2000 wave1.objs wave1.i2i
−
insert_image called by this program if -create is specified.
+
  countobjs -k -t 2000 2000 wave2.objs wave2.i2i
−
reduceima if -create is used, this may be needed to make the image small enough to see via play.
+
  objs_within_dist.pl wave1.objs wave2.objs > wave1and2.dist
−
 
−
example:
 
−
        parsepos.pl -pre=/storage/big3/kdb/Zeiss/20121004/LectinExp3/ -post=_1_1_20121004_LectinExp3.i2i \
 
−
                /storage/big3/kdb/Zeiss/20121004/LectinExp3/LextinExp3.pos | overlap_images.pl -create=newimage.i2i
 
−
reduceima -A -bin 4 4 newimage.i2i newimage_reduced.i2i
 
  
−
note: you may need /storage/big1/lml/Linux/bin and /storage/big1/kef/Linux/bin in your path
+
see also:
−
 
+
  objs2dist121.pl, closest_object, closest_voxel, countobjs, maskobjs, objs_via_ascent, pt_distances
−
source code in /storage/big1/lml/Corvera/Olga/data/ptrs
 
−
see also: insert_image
 
−
  http://bigwww.epfl.ch/algorithms.html -> MosaicJ (which may already exist in Fiji)
 
  
 
   
 
   
−
===  parsepos.pl ===
+
===  connected_random_pts ===
−
Parse a position file produced by Zeiss system to pull out x y coords for each of the images taken in well C09.
+
Generates random pts in a planar region, calculates how many connected components are created
−
Output triples (well_id x y) written to stdout.
+
if a pt is connected to all other pts within a given radius.
−
Position may be in microns, x increasing to the right, y increasing down.
 
  
−
parsepos.pl filename.pos
+
Usage:
 +
connected_random_pts [options]
 +
Options:
 +
-x lowx hix:         pts have xcoords within this range, default = (0.0,100.0)
 +
-y lowy hiy:         pts have ycoords within this range, default = (0.0,100.0)
 +
-r #: radius (in pixels), default = 5.0
 +
-s #: long int starting seed for random number generator. default = process id.
 +
-n #: number of pts to create, default = 1000
 +
  -h: help
 +
  -v: verbose
  
−
options:
+
See also:
−
-well=string well to analyze. default = C09
+
krypton/Huang/README, components.pl, Kth_pt.m, num_observed.m, mean_minimum_distance.m,objs2mst.pl
−
-pre=prestring add this string in front of the well_id
+
 
−
-post=postring add this string after the well_id
+
Source code in ~krypton/lml/facil 
−
these two options are needed if you want to pass this output to
+
−
overlap_image.pl -create=newimage.i2i, since that will need to be able
+
===  pt_distances  ===
−
to find the image associated with each well_id.
+
#/home/lml/krypton/bin/pt_distances
−
-verbose additional output to stderr
 
−
-vverbose additional output to stderr
 
  
−
example:
+
Takes output from 2 runs of max2d_simple -p file.rpts and calculates minimum distance between pts.
−
parsepos.pl -pre=/storage/big3/kdb/Zeiss/20121004/LectinExp3/ -post=_1_1_20121004_LectinExp3.i2i \
+
See comments printed to stdout when the program runs to explain the fields in the output data.
−
/storage/big3/kdb/Zeiss/20121004/LectinExp3/LextinExp3.pos | overlap_images.pl -create=newimage.i2i
 
−
 
  
 +
Usage:
 +
pt_distances [options] file1.rpts file2.rpts
 +
Options:
 +
-h: print histograms of distances. entry for pt at dist d:  histogram[int((d+tiny)/binsize)]++
 +
-t #: set tiny to #, default = 0.000010 . Points at exactly 1 pixel seem to be put into the .9 bin
 +
perhaps due to slight roundoff error. By adding tiny, they go into the next bin.
 +
      -b #: set binsize to # pixels, default = 0.100000
 +
      -m #: set maximum distance histogram will go out to (distances > this get put in last bin)
 +
default = 50.000000 pixels
 +
-a #: the area (in pixels) of the region used to generate file1.rpts and file2.rpts
 +
this is used to compare observed rates with theoretical rates if randomly distributed.
 +
NOTE: the theoretical calculations for image1 vs. image2 (and vice versa) are probably WRONG.
 +
default = 10000.000000
 +
-M #: the minimum distance allowed between maxima, for theoretical calculations. This might be
 +
1 (pixel) since maxima normally can't be next to each other. Or it might be the
 +
resolution of the microscope (since objects closer than that will appear as one maxima).
 +
by default M from 0.0 to 3.0 by 1.0 is calculated. if you want an additional value use this option.
 +
  -v: verbose
  
−
see also:
+
See also: max2d_simple read_hist.pl
−
overlap_images.pl
 
−
insert_image
 
  
−
note: you may need /storage/big1/lml/Linux/bin and /storage/big1/kef/Linux/bin in your path.
+
Example:
 +
  max2d_simple -t 10 -d .5 clathrin.i2i > clathrin.pts
 +
  max2d_simple -t 10 -d .5 glut.i2i > glut.pts
 +
  pt_distances -h -a 26443 -M 1.5 clathrin.pts glut.pts > both.dat
 +
  fgrep "image1 only" both.dat | fgrep mean_min | cull -n -15 -21 -24 -30 > clathrin_mindist.xy
 +
  xmgrace -nxy clathrin_mindist.xy &
 +
  read_hist.pl -im1 -norm=1 -nummax=26443 -avg=5 -nozero < clathrin_mindist.dat > clathrin_histo.xy
 +
  xmgrace clathrin_histo.xy &
  
 +
Source code in ~krypton/lml/facil 
 
   
 
   
−
===  prep_and_restore.pl ===
+
===  resolve_pts ===
 +
 
 +
Takes minimimal spanning tree rpts file (just an rpts file with each pair of pts which are to be compared specified
 +
as a line segment, i.e., two pts and a "break") as produced by objs2mst.pl and finds which connected
 +
pts are resolved and which are not.  Resolved pts are those which have at least the specified
 +
intensity dip along the minimum cost (roughly: brightest) path connecting those pts. note: if there is no path between the two
 +
pts such that all voxels are greater than the threshold, the pts are also considered to be resolved.
 +
If a pair of pts is resolved, both are written to out.rpts (but not more than once).  If a pair of pts is not resolved
 +
then the brighter of the two (voxel intensity) is written to out.rpts.
 +
The intensity dip is the max amount the intensity goes below the dimmer of the two endpts (anywhere along the minimum cost path).
 +
Each pair of lines (i.e., pair of coordinates) in mst.rpts defines ends of a minimum cost path
 +
along which an intensity dip will be searched for. 
  
−
Restores all the i2i files in the current directory. Skips any files with  _.i2i or _r.i2i in their name.
+
Usage: resolve_pts [options] image.i2i mst.rpts out.rpts
−
  Also ignores any files which do not have dat or ctx in their name.
+
options:
 +
  -t #: threshold, default = 0.000000
 +
  -f : normally a pt is discarded if it does not resolve against at least one other pt it is connected to in the input rpts file.
 +
Thus, AXXXXBXXXXC if A and B resolve, but B doesn't resolve against C, and B is smaller than C
 +
B will normally be discarded (even though it resolves against A, it fails against C). If you specify -f
 +
then maxima which fail will be kept as long as they resolve against some other pt.
 +
  -d #: intensity dip required to be resolved. default = 10.000000
 +
  -p #: the percentage dip required relative to the dimmer endpt (e.g. 26 is 26 percent dip)
 +
  -l: instead of dip being the maximum amount below the dimmer of the two pts, dip
 +
is the max amount below a linearly interpolated intensity between the two endpoints.
 +
  -i: truncate coords written to out.rpts to integers (addlines prefers this I think).
 +
  -v: verbose.
 +
  -V: very verbose.  
  
−
options:
+
Examples:
−
-dummy just print what would be done
+
countobs image.i2i > image.objs
−
-bkgnd=# pass this through to find_bkgnd as the -a option. eg, -bkgnd=-.10 will lower the bkgnd value
+
obs2mst.pl -maxdist=10 image.objs > image_mst.rpts
−
which is subtracted off by 10 percent.  
+
resolve_pts -d 100 -i image.i2i image_mst.rpts image_maxima.rpts
−
        -smooth=#      smoothness factor (smaller is less smoothing). default = .00002
+
See also:  BestPath, objs2mst.pl, krypton/Huang/TIRF4/README
−
        -iterations=#  maximum number of iterations, default = 999
+
Source code in krypton/facil
−
        -scale=#:#      GFP and RFP output scaling for restoration (respectively). default = 1.0 and 1.0.
+
−
-verbose echo what is being done
+
== Image Manipulation ==
−
        -maxfiles=# only analyze this many files. primarily for debugging
+
=== align_quadrants.pl  ===
−
-twod during background subtraction, vary the background value for each 2D slice, instead of
+
This program displays the four quadrant images of a well. The user then saves 3 pairs of points
−
just using the same value for all z slices.
+
(s when middle mouse is pressed). Each pair of points should be points that match in two
−
-files=:file.i2i:...:filen.i2i  just restore these files. and do it even if _.i2i or _r.i2i exists.
+
neighboring quadrants. When done, each quadrant must have one (or two) points specified.
−
-dont_restore  do the data prep (filename_.i2i and filename__.i2i produced), but don't do the restoration (but not filename__r.i2i).
+
Points must be in pair order (see recalc_quadrant2.pl). When done, the use must write them out
−
-beowulf queue the restorations to run on our beowulf (dispatched via qsub, using pbs (torque), from a daemon running on m13)
+
via z (when middle mouse is also pressed, no confimation is given in play).   
−
rather than immediately on the localhost.
+
The quadrant images are then aligned based on these points and newimage.i2i is created.
−
see also: pbsnodes (on m13, only servers running fc16 or fc17 are on the allowed list right now)
 
−
          qstat -f (on m13) will show lots of info on each job.
 
−
If this is not specified, each restoration is run sequentially, with this script blocking while waiting for each one.
 
−
-gpu only use this if you are logged into zirconium. It will run the restoration on zirconium using the GPU version
 
−
of the restoration.
 
−
-outdir=dir    rather than place the results in the current directory, place it in the fully qualified specified directory.
 
−
leave off the last /
 
−
      -GFPpsf=file    fully qualified path to GPFpsf (used when file name is *_#_#_1*.i2i, eg,  file_0_1_1.i2i)
 
−
default = /storage/big1/lml/Corvera/Olga/data/GFPpsf_segxyz_.i2i
 
−
note: psf should have background values of ~0, otherwise 0-padding will produce blocking artifacts.
 
−
      -RFPpsf=file    fully qualified path to RPFpsf (used when file name is *_#_#_2*.i2i, eg, file_0_1_2.i2i)
 
−
default = /storage/big1/lml/Corvera/Olga/data/RFPpsf_segxyz_.i2i
 
−
note: psf should have background values of ~0, otherwise 0-padding will produce blocking artifacts.
 
−
-silent print less info
 
  
 +
It will also create a file with the output from play, for future reference.
 +
It will be named, eg, G02_combined_play.pts. It can be passed manually to recalc_quadrant2.pl to redo
 +
the alignment if necessary.
  
−
  examples:
+
usage:
−
cd /storage/big3/kdb/Zeiss/20121004/LectinExp3
+
  align_quadrants.pl [options] well newimage.i2i
−
        /home/lml/krypton/Corvera/Olga/prep_and_restore.pl -files=G11_0_1_1_20121004_LectinExp3.i2i:G03_0_1_2_20121004_LectinExp3.i2i  
 
−
      -beowulf -outdir=/storage/big1/lml/Corvera/Olga/data
 
−
 
 
−
  see also:
 
−
epr_beowulf    a GUI front end for submitting individual restoration jobs to the beowulf queue
 
−
/storage/big1/epr/bin/cuda/epr_gpu -cuda 1  if logged into zirconium, will run a single job on the graphics card (like -gpu option).
 
−
prepdata
 
−
preppsf
 
  
−
  note: /storage/big1/lml/Linux/bin /storage/big1/lml/Linux/bin64 and /storage/big1/kef/Linux/bin probably need to be in your
 
−
path to successfully run this script.
 
  
−
+
examples:
−
===  prepfiles.pl  ===
+
  align_quadrants.pl [options] G02 G02_combined.i2i
−
prepfiles.pl [options]
 
−
 
 
−
Takes a dual-wavelength image and splits it into two separate images (segim_huge), applies scratchng, and prepdata.
 
−
Run this from a directory. It will be applied to all images in the directory.  There must be
 
−
a file called dark.i2i in the directory too. Removes all intermediate files and original 2wavelength image.
 
  
 
options:
 
options:
−
  -safe : don't delete the original dual-wavelength image
+
-no_pts_output don't produce the pts file
−
  -echo : echo what is being done
+
-noblend by default the quadrant images are blended together where
 +
they overlap.  use this option to turn that off.
 +
-print_overlap also print the amount of overlap to stderr
 +
-debug
 +
-debug_all
  
−
 
−
===  recalc_quadrant2.pl  ===
 
−
align_quadrants.pl calls this program.  It is easier to use it than to call recalc_quadrant2.pl manually.
 
  
−
This program converts from pts printed by play (so in the coordinate system gotten from combining the four quadrant images of a well (with no overlap))
+
see also:
−
to one used by register_images.pl (ie, each pt is in the coordinate system of its own individual image).
+
combine_images
−
It also pairs the points up and orders them the way that register_images.pl requires.
+
recalc_quadrant2.pl
−
It assumes the user picked matching pairs of pts in order when using play.  Eg, first a pt was picked (s key while holding down middle mouse button),
+
/home/lml/krypton/Corvera/Raz/README 5/16/14
−
then its matching point in a neighboring quadrant was picked. This was then repeated 3 times (so 3 pairs of points are present).
+
http://wiki.imagej.net/Grid/Collection_Stitching_Plugin
−
note: the file names for the files associated with each quadrant are not stored in the output by default, just the quadrant number,
+
 
−
      use -qnames to change this; they are needed if you want to subsequently have register_images.pl use chained.txt to actually combine the images.
 
  
 +
 +
===  combine_images.pl  ===
  
−
recalc_quadrant2.pl [options] < pts.txt > chained.txt
+
This program runs combine_images on all the images in the current directory.  All images which have names
 +
like L##_morestuff.i2i (where L is any letter and # is any digit) will be combined;
 +
all the A02 will be combined (to produce A02_comb.i2i), all the A03, etc.
 +
The resulting image for the combination of the A02 images will be A02_tag.i2i (see -newtag option, e.g. A02_comb.i2i).
 +
Any images already existing in the current directory with a name like L##_stuff_oldtag.i2i will be ignored. 
 +
 
 +
usage:
 +
combine_images.pl [options]
  
 
options:
 
options:
−
-res=# resolution the display was downsampled by prior to getting coords (ie, what was used in chres, see below).
+
-newtag=something The output filename for L##*.i2i will be L##_newtag.i2i.  Default = comb
−
if chres was .5, then -res=2, ie, 1/chres value. default = 2.
+
-oldtag=something Any files of the form L##*_oldtag.i2i will be ignored. Default = comb
−
-xdim=# default = 1392
+
-pixsize=# pass this as -p # to combine_images program (pixel size).  
−
-ydim=# default = 1040
+
Specify -pixsize=2.41 (um/pixel) for the 2.5X objective.
−
-qnames=name0:name1:name2:name3    file names associated with the images used to produce each of the 4 quadrants.
+
-reduceima=#:#:tag After creating output image, apply reduceima to it 
−
  they must be in this order. If not specified, then the output will not be
+
with -bin # # and the specified output tag on the name.
−
  usable by register_images.pl (unless -root is implemented there).
+
So, e.g., A02_comb.i2i will become A02_tag.i2i
−
-outimage=image.i2i also produce an output combined image (ie, call register_images.pl, see below).
+
-flipx flip images in X prior to combining them
−
-qnames required for this option.
+
-flipy flip images in Y prior to combining them (can be used at the same time as -flipx)
−
-blend if -outimage is specified, then blend the overlapping images to produce the output image.
+
-x=#:#:#:# manually specified picture offsets. see combine images
−
-verbose print overlap info to stderr. maybe to use in -o option to combine_images.
+
-y=#:#:#:# manually specified picture offsets. see combine images
−
-debug stuff to stderr
+
-o=# number of pixels the images overlap (ignores info in image headers). see combine_images
 +
-f do MOT pad images at border (as of 2/3/14). see combine_images.
 +
-remove Remove the full-size combined image (e.g., A02_comb.i2i) when done (use with -reduceima).
 +
-dummy Just echo what would be done, but don't do anything
 +
-verbose Echo as things are done.
 +
-debug
  
−
more info. the quadrants in the combined image (see combine_images below) are numbered as follows:
+
note:
−
quadrant 1 |  quadrant 3
+
combine_images (in /storage/big1/lml/Linux/bin) and reduceima (in /storage/big1/kef/Linuxbin) must be in your
−
quadrant 0   |   quadrant 2
+
path for this perl script to work. You can check this by just typing: which combine_images   and   which reduceima;
−
    where x increases to the right, y increases up
+
if they are not found you need to add their directory to your PATH environment variable (echo $PATH will show you
 +
what it is currently). How this is done varies depending upon which shell you are running. Under tcsh it would
 +
be  setenv PATH $PATH:/storage/big1/kef/Linuxbin:/storage/big1/lml/Linux/bin .
  
 
example:
 
example:
−
 
+
      cd /storage/big3/kdb/Zeiss/20130326/GEDMAT_002_PRO_SQ2_DAY14
−
# combine the 4 well images without overlap to see what pts might match between quadrants:
+
# Combine all images in each well. The combined image will be L##_combined (-newtag=combined).
−
    combine_images -o 0 F06_0_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i F06_1_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i 
+
# Then reduce the combined size back down to the size of one original image;
−
          F06_2_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i F06_3_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i tmp.i2i
+
# call the new image L##_combined_reduc.i2i (-reduceima=2:2:reduc).   
−
 
+
# Finally, remove the big (unreduced) combined image (-remove).
−
# look at the resulting image and identify matching pts:
+
# First do a dummy run (-dummy) to see if it is going to do what we want:
−
    chres -S .5 .5 1 tmp.i2i - |play -    # save (s) pairs of pts which match between the quadrants. print them using z.  create file F06_pts.txt:
+
      combine_images.pl -newtag=combined -reduceima=2:2:reduc -pixsize=2.41 -remove -dummy   
−
marked points
+
# ok, now the real thing (just leave off -dummy):
−
x= 769 y= 497 z=  1 set=  1 value=    3099
+
      combine_images.pl -newtag=combined -reduceima=2:2:reduc -pixsize=2.41 -remove
−
x= 799 y= 525 z=  1 set=  1 value=    3684
 
−
x= 709 y= 819 z=  1 set=  1 value=    4039
 
−
x= 682 y= 854 z=  1 set=  1 value=    3974
 
−
x= 518 y= 497 z=  1 set=  1 value=    3257
 
−
x= 543 y= 524 z=  1 set=  1 value=    3436
 
−
 
 
−
# now use this program to multiply by 2, subtract xdim (1392) and/or ydim (1040) as appropriate, pair and order pts.
 
−
    recalc_quadrant2.pl -outimage=F06_combined.i2i -qnames=F06_0_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i:F06_1_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i:F06_2_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i:F06_3_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i  < F06_pts.txt > F06_chained.txt
 
−
 
 
−
# same thing, but in two steps.
 
−
    recalc_quadrant2.pl -qnames=F06_0_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i:F06_1_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i:F06_2_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i:F06_3_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i  < F06_pts.txt > F06_chained.txt
 
−
    register_images.pl -zdim=5 -xscale=1 -yscale=1 -post= -debug -out=F06_combined.i2i F06_chained.txt
 
−
 
 
  
 
see also:
 
see also:
−
/home/lml/krypton/Corvera/Raz/README  5/15/14
 
−
align_quadrants.pl
 
−
recalc_quadrant.pl
 
 
combine_images
 
combine_images
−
combine_images.pl
+
/storage/big1/raz/GEDMAT
−
register_images.pl
+
mask_gedmat_images.pl
−
insert_image2
 
  
 
   
 
   
−
===  register_images.pl  ===
+
===  overlap_images.pl  ===
  
−
Takes a bunch of images taken in one well on the microscope, translates them
+
Takes output from parsepos.pl  and calculates how the images overlap so they can then be combined easily (-create option).
−
based on ChainedTrans.txt and combines them into one big image.
+
 
 +
overlap_images.pl [options]
  
−
ChainedTrans.txt should be a partially ordered file with entries like
+
options:
−
X02:X03    (685,282):(736,287)
+
-xdim=# xdim of image in pixels, default = 1392
−
This means that location (685,282) in file X02 is the same as location (736,287) in file X03.
+
-ydim=# ydim of image in pixels, default = 1040
−
By partially ordered I mean that for file1:file2  file1 should already have been the
+
-zdim=# zdim of image in pixels, default = 25
−
right hand side of a similar line previously (so its position is already defined relative to
+
-pixsize=# size of pixels in um, default = 0.645
−
the file on the left hand side), unless it is the very first line in
+
-create=file.i2i actually combine the images into one big image
−
the file. So every right hand side is relative to a left hand side which has already
+
-flipx flip each image around its x-axis prior to inserting it into the new image (if -create is specified)
−
had its position defined.
+
-flipy flip each image around its y-axis prior to inserting it into the new image (if -create is specified)
−
Output goes to new_trans.i2i
+
-verbose
 +
-dummy just echo what would be done, but don't do anything (nothing normally done anyway unless -create specified).
  
−
register_images.pl [options] ChainedTrans.txt
+
see also:
−
-out=filename.i2i  name of output file produced. default = newimage.i2i
+
parsepos.pl
−
-post=string the rest of the filename after what is in ChainedTrans.txt, eg, if the file is named
+
insert_image called by this program if -create is specified.
−
X01_0_0_1.i2i, -post=_0_0_1.i2i (this is also the default for post if not specified).
+
reduceima if -create is used, this may be needed to make the image small enough to see via play.
−
-xdim=# size of original each original image (before recaling by maxtrima, see example below). default = 1392.
+
−
-ydim=# default = 1040
+
example:
−
-zdim=# default = 21
+
        parsepos.pl -pre=/storage/big3/kdb/Zeiss/20121004/LectinExp3/ -post=_1_1_20121004_LectinExp3.i2i \
−
-xscale=# binning done by matrixima (see example), coords will be scaled by this. default = 4.
+
                /storage/big3/kdb/Zeiss/20121004/LectinExp3/LextinExp3.pos | overlap_images.pl -create=newimage.i2i
−
-yscale=#
+
reduceima -A -bin 4 4 newimage.i2i newimage_reduced.i2i
−
-blend when combining images, blend the values where they overlap (default is to just replace any previous
+
 
−
value with the new value).
+
note: you may need /storage/big1/lml/Linux/bin and /storage/big1/kef/Linux/bin in your path
−
    -dummy
 
−
-debug
 
−
-h
 
  
 +
source code in /storage/big1/lml/Corvera/Olga/data/ptrs
 +
see also: insert_image
 +
  http://bigwww.epfl.ch/algorithms.html -> MosaicJ (which may already exist in Fiji)
  
−
-shift no circular shift (see tranima). old.  
+
−
note: tranima will pad images with -32768 which play will show in red (I think) and DAVE will be bothered by.
+
===  parsepos.pl  ===
 +
Parse a position file produced by Zeiss system to pull out x y coords for each of the images taken in well C09.
 +
Output triples (well_id x y) written to stdout.
 +
Position may be in microns, x increasing to the right, y increasing down.
  
−
example:
+
  parsepos.pl filename.pos
−
matrixima -row 4 W X Y Z -col 3 01 02 03 -pos 0 -obj 0 -fil 1 new.i2i
 
−
play new.i2i -> ChainedTrans.txt
 
−
        register_images.pl ChainedTrans.txt
 
−
        dave -I new_trans.i2i -K -z 15  # a very big file.
 
  
−
source code: ~/krypton/bin/
+
options:
−
see also:
+
-well=string well to analyze. default = C09
−
combine use this on newer images which have spatial information stored in their header
+
-pre=prestring add this string in front of the well_id
−
parsepos.pl
+
-post=postring add this string after the well_id
−
~/krypton/Corvera/Olga
+
these two options are needed if you want to pass this output to
−
/storage/big1/lml/Corvera/Olga
+
overlap_image.pl -create=newimage.i2i, since that will need to be able
−
recalc_quadrant.pl
+
to find the image associated with each well_id.
−
recalc_quadrant2.pl
+
-verbose additional output to stderr
−
align_quadrants.pl the simplest manual method of aligning the four images in the well
+
-vverbose additional output to stderr
  
−
   
+
  example:
−
===  smooth_gaps.pl ===
+
parsepos.pl -pre=/storage/big3/kdb/Zeiss/20121004/LectinExp3/ -post=_1_1_20121004_LectinExp3.i2i \
−
  This program applies smooth_gaps to all files named *reduced.i2i
+
/storage/big3/kdb/Zeiss/20121004/LectinExp3/LextinExp3.pos | overlap_images.pl -create=newimage.i2i
−
  and produces files named  *reduced_sg.i2i (unless -tag changed it).
+
  
−
  usage:
 
−
smooth_gaps.pl -run [options]
 
  
−
  options:
+
see also:
−
-tag=something    tag to add before the .i2i in the new file name.
+
overlap_images.pl
−
-verbose   print out each filename as it is being smoothed.
+
insert_image
−
-dummy   just echo what would be done, but don't do anything
 
  
−
  see also:
+
note: you may need /storage/big1/lml/Linux/bin and /storage/big1/kef/Linux/bin in your path.
−
smooth_gaps
 
  
 
   
 
   
−
===  trans.pl  ===
+
===  prep_and_restore.pl  ===
  
−
Takes a bunch of images taken in one well on the microscope, translates them
+
Restores all the i2i files in the current directory. Skips any files with  _.i2i or _r.i2i in their name.
−
based on ChainedTrans.txt and combines them into one big image.
+
Also ignores any files which do not have dat or ctx in their name.
  
−
ChainedTrans.txt should be a partially ordered file with entries like
+
options:
−
X02:X03    (685,282):(736,287)  
+
-dummy just print what would be done
−
This means that location (685,282) in file X02 is the same as location (736,287) in file X03.
+
-bkgnd=# pass this through to find_bkgnd as the -a option. eg, -bkgnd=-.10 will lower the bkgnd value
−
By partially ordered I mean that for file1:file2  file1 should already have been the
+
which is subtracted off by 10 percent.
−
right hand side of a similar line previously (so its position is already defined relative to
+
        -smooth=#      smoothness factor (smaller is less smoothing). default = .00002
−
the file on the left hand side), unless it is the very first line in
+
        -iterations=#  maximum number of iterations, default = 999
−
the file. So every right hand side is relative to a left hand side which has already
+
        -scale=#:#      GFP and RFP output scaling for restoration (respectively). default = 1.0 and 1.0.
−
had its position defined.
+
-verbose echo what is being done
−
Output goes to new_trans.i2i
+
        -maxfiles=# only analyze this many files. primarily for debugging
−
 
+
-twod during background subtraction, vary the background value for each 2D slice, instead of
−
register_images.pl [options] ChainedTrans.txt
+
just using the same value for all z slices.
−
-out=filename.i2i name of output file produced. default = newimage.i2i
+
-files=:file.i2i:...:filen.i2i  just restore these files. and do it even if _.i2i or _r.i2i exists.
−
-post=string the rest of the filename after what is in ChainedTrans.txt, eg, if the file is named
+
-dont_restore  do the data prep (filename_.i2i and filename__.i2i produced), but don't do the restoration (but not filename__r.i2i).
−
X01_0_0_1.i2i, -post=_0_0_1.i2i (this is also the default for post if not specified).
+
-beowulf queue the restorations to run on our beowulf (dispatched via qsub, using pbs (torque), from a daemon running on m13)
−
-xdim=# size of original each original image (before recaling by maxtrima, see example below). default = 1392.
+
rather than immediately on the localhost.
−
-ydim=# default = 1040
+
see also: pbsnodes (on m13, only servers running fc16 or fc17 are on the allowed list right now)
−
-zdim=# default = 21
+
          qstat -f (on m13) will show lots of info on each job.
−
-xscale=# binning done by matrixima (see example), coords will be scaled by this. default = 4.
+
If this is not specified, each restoration is run sequentially, with this script blocking while waiting for each one.
−
-yscale=#
+
-gpu only use this if you are logged into zirconium. It will run the restoration on zirconium using the GPU version
−
-blend when combining images, blend the values where they overlap (default is to just replace any previous
+
of the restoration.
−
value with the new value).
+
-outdir=dir    rather than place the results in the current directory, place it in the fully qualified specified directory.
−
    -dummy
+
leave off the last /
−
-debug
+
      -GFPpsf=file    fully qualified path to GPFpsf (used when file name is *_#_#_1*.i2i, eg, file_0_1_1.i2i)
−
-h
+
default = /storage/big1/lml/Corvera/Olga/data/GFPpsf_segxyz_.i2i
 +
note: psf should have background values of ~0, otherwise 0-padding will produce blocking artifacts.
 +
      -RFPpsf=file    fully qualified path to RPFpsf (used when file name is *_#_#_2*.i2i, eg, file_0_1_2.i2i)
 +
default = /storage/big1/lml/Corvera/Olga/data/RFPpsf_segxyz_.i2i
 +
note: psf should have background values of ~0, otherwise 0-padding will produce blocking artifacts.
 +
-silent print less info
  
  
−
-shift no circular shift (see tranima). old.  
+
  examples:
−
note: tranima will pad images with -32768 which play will show in red (I think) and DAVE will be bothered by.
+
cd /storage/big3/kdb/Zeiss/20121004/LectinExp3
 +
        /home/lml/krypton/Corvera/Olga/prep_and_restore.pl -files=G11_0_1_1_20121004_LectinExp3.i2i:G03_0_1_2_20121004_LectinExp3.i2i
 +
      -beowulf -outdir=/storage/big1/lml/Corvera/Olga/data
  
−
example:
+
  see also:
−
matrixima -row 4 W X Y Z -col 3 01 02 03 -pos 0 -obj 0 -fil 1 new.i2i
+
epr_beowulf    a GUI front end for submitting individual restoration jobs to the beowulf queue
−
play new.i2i  -> ChainedTrans.txt
+
/storage/big1/epr/bin/cuda/epr_gpu -cuda 1  if logged into zirconium, will run a single job on the graphics card (like -gpu option).
−
        register_images.pl ChainedTrans.txt
+
prepdata
−
        dave -I new_trans.i2i -K -z 15  # a very big file.
+
preppsf
  
−
source code: ~/krypton/bin/
+
  note: /storage/big1/lml/Linux/bin /storage/big1/lml/Linux/bin64 and /storage/big1/kef/Linux/bin probably need to be in your
−
see also:
+
path to successfully run this script.
−
combine use this on newer images which have spatial information stored in their header
 
−
parsepos.pl
 
−
~/krypton/Corvera/Olga
 
−
/storage/big1/lml/Corvera/Olga
 
−
recalc_quadrant.pl
 
−
recalc_quadrant2.pl
 
−
align_quadrants.pl the simplest manual method of aligning the four images in the well
 
  
 
   
 
   
−
===  blur3d ===
+
===  prepfiles.pl ===
 +
prepfiles.pl [options] 
 +
 
 +
Takes a dual-wavelength image and splits it into two separate images (segim_huge), applies scratchng, and prepdata.
 +
Run this from a directory. It will be applied to all images in the directory.  There must be
 +
a file called dark.i2i in the directory too. Removes all intermediate files and original 2wavelength image.
  
−
Blurs an image by a psf.
+
options:
−
FFTs are done with 4 byte floats, so total space needed will be 4 times the padded image size (in voxels)
+
  -safe : don't delete the original dual-wavelength image
−
plus the size of the two original images (image and psf)
+
  -echo : echo what is being done
−
The input image can be real or short int format. The psf must be short int format.
 
−
note: performs a convolution (not a correlation).
 
−
note: fixed a small bug. 10/17/11
 
  
−
Usage: blur3d [options] image psf newimage
+
−
options:
+
=== recalc_quadrant2.pl  ===
−
  -S #: scale (multiply) output values by # (to prevent underflow or overflow)
+
align_quadrants.pl calls this program.  It is easier to use it than to call recalc_quadrant2.pl manually.
−
  voxels which after scaling are > 32767 are set to 32767. voxels < -32766 are set to -32766.
 
−
    -p # # #: pad the image in x, y, and z by the specified amounts
 
−
by default image is padded (with 0) by 1/4 psf width all around,
 
−
so its size for blurring becomes bigger by psf/2.
 
−
psf is always padded to the same size the image becomes.  
 
−
Padding is stripped off before newimage is written, so it will be the same size as
 
−
the original image.
 
−
    -N # # #: pad so that the image has the specified dimensions after padding (just prior to FFT).
 
−
  -n #: pad with # instead of boundary pixel values.
 
−
  -Z:  pad with zero instead of the boundary pixel values.
 
−
  -c # # #: the center of the psf is at (#,#,#) zero indexed.
 
−
                the default is to take the brightest pixel as its center.
 
−
  -C:  don't center the psf at all (default is to center on the max, unless -c is specified).
 
−
  -P:  normalize the psf so each slice (after padding) averages to 1. -P acts like an optical PSF.
 
−
        the default is to normalize so the entire psf (after padding) has an average pixel value of 1
 
−
              (the default keeps total light constant).
 
−
  -d:  don't normalize at all.
 
−
  -o:  do a cross correlation instead of a blur (convolution)
 
−
  -R:  output image as 4 byte floating point instead of short integer.
 
−
  -v:  verbose. print more info to stderr.
 
  
−
note: entire image name (with extension) is NOT required.
+
This program converts from pts printed by play (so in the coordinate system gotten from combining the four quadrant images of a well (with no overlap))
−
note: can read from stdin or write to stdout (use a dash instead of the file name)
+
to one used by register_images.pl (ie, each pt is in the coordinate system of its own individual image).
−
note: a compressed image will be automatically be uncompressed.
+
It also pairs the points up and orders them the way that register_images.pl requires.
 +
It assumes the user picked matching pairs of pts in order when using play. Eg, first a pt was picked (s key while holding down middle mouse button),
 +
then its matching point in a neighboring quadrant was picked.  This was then repeated 3 times (so 3 pairs of points are present).
 +
note: the file names for the files associated with each quadrant are not stored in the output by default, just the quadrant number,
 +
      use -qnames to change this; they are needed if you want to subsequently have register_images.pl use chained.txt to actually combine the images.
  
−
Copyright 2010 University of Massachusetts Medical School and the Biomedical Imaging Group
 
−
All rights reserved. Explicit permission to use this program must be received prior to use.
 
−
 
−
===  canny  ===
 
  
−
This program reads in a 2 or 3d image and outputs the results
+
recalc_quadrant2.pl [options] < pts.txt > chained.txt
−
of a 2D Canny edge detector on it. Canny is the derivative
 
−
(in the gradient direction) of the magnitude of the first
 
−
derivative (so it is a type of 2nd derivative).
 
−
NOTE: see option -n below for an exact answer.
 
−
Each z slice is treated
 
−
independently of the others.  Its application will often be
 
−
preceded by a Gaussian blur and followed by the calculation
 
−
of zero crossings.
 
−
If an INT type image is input, an INT is output.
 
−
If a REAL type image is input, a REAL is output.
 
  
−
Usage: canny [options] infile outfile
+
options:
−
  options:
+
-res=# resolution the display was downsampled by prior to getting coords (ie, what was used in chres, see below).
−
-d: Debugging flag
+
if chres was .5, then -res=2, ie, 1/chres value. default = 2.
−
-n: normalize the result. This option causes the true 2nd
+
-xdim=# default = 1392
−
derivative to be calculated. Without it, only the sign
+
-ydim=# default = 1040
−
of the second derivative is guaranteed to be correct
+
-qnames=name0:name1:name2:name3    file names associated with the images used to produce each of the 4 quadrants.
−
(which is sufficient if only zero crossings will be
+
  they must be in this order. If not specified, then the output will not be
−
calculated from it). Divides each point by Ix*Ix+Iy*Iy.
+
  usable by register_images.pl (unless -root is implemented there).
−
-s #:  scale factor to multiply all output values by. This is
+
-outimage=image.i2i also produce an output combined image (ie, call register_images.pl, see below).  
−
useful if you are outputing an INTEGER image with a very
+
-qnames required for this option.
−
small range of values which would otherwise all be truncated
+
-blend if -outimage is specified, then blend the overlapping images to produce the output image.
−
to just a few numbers.
+
-verbose print overlap info to stderr. maybe to use in -o option to combine_images.
−
note: entire image name (with extension) is NOT required.
+
-debug stuff to stderr
−
note: a - in place of an image name means stdin or stdout.
 
−
Example usage:
 
−
To create a gradient edge strength image for a shrink wrap run:
 
−
  blur_spatial image.i2i -|canny - -|zerosu - - |blur_spatial - out.i2i
 
−
 
−
===  cblur  ===
 
−
 
−
Usage: cblur [options] arg1.i2i arg2.i2i
 
−
  For every zero valued point in each xz plane, cblur
 
−
  replaces the zero value with the -100 times the distance
 
−
  from the nearest non-zero voxel in the xz plane.
 
−
Options: None at this time.
 
  
−
Note: entire image name (with extension) is required.
+
more info. the quadrants in the combined image (see combine_images below) are numbered as follows:
−
Note: a - in place of an image name means stdin or stdout.
+
quadrant 1  |  quadrant 3
 +
quadrant 0  |  quadrant 2
 +
    where x increases to the right, y increases up
  
 +
example:
  
−
===  center_of_mass  ===
+
# combine the 4 well images without overlap to see what pts might match between quadrants:
 +
    combine_images -o 0 F06_0_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i F06_1_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i 
 +
          F06_2_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i F06_3_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i tmp.i2i
  
−
This program reads in a 4D image and translates each 3D image
+
# look at the resulting image and identify matching pts:
−
so its center of mass is moved to be the center of the image.
+
    chres -S .5 .5 1 tmp.i2i - |play -    # save (s) pairs of pts which match between the quadrants. print them using z.  create file F06_pts.txt:
−
One 3D image is read at a time.
+
marked points
−
 
+
x= 769 y= 497 z=  1 set=  1 value=    3099
−
Usage: center_of_mass [options] inimage.i2i outimage.i2i  
+
x= 799 y= 525 z=  1 set=  1 value=    3684
−
options:
+
x= 709 y= 819 z=  1 set=  1 value=    4039
−
  -t tdim:  number of time points, default = 1. This is NOT read from the header.
+
x= 682 y= 854 z=  1 set=  1 value=    3974
−
  -T #:   threshold inimage.i2i prior to analysis. voxels <= # ignored, default = 0
+
x= 518 y= 497 z=  1 set=  1 value=    3257
−
  -v: verbose
+
x= 543 y= 524 z=  1 set=  1 value=    3436
 +
 
 +
# now use this program to multiply by 2, subtract xdim (1392) and/or ydim (1040) as appropriate, pair and order pts.
 +
    recalc_quadrant2.pl -outimage=F06_combined.i2i -qnames=F06_0_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i:F06_1_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i:F06_2_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i:F06_3_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i < F06_pts.txt > F06_chained.txt
 +
 
 +
# same thing, but in two steps.
 +
    recalc_quadrant2.pl -qnames=F06_0_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i:F06_1_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i:F06_2_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i:F06_3_2_0_20140505_GEDMAT_P025_WES_OM_Day14.i2i  < F06_pts.txt > F06_chained.txt
 +
    register_images.pl -zdim=5 -xscale=1 -yscale=1 -post= -debug -out=F06_combined.i2i F06_chained.txt
 +
 
 +
 
 +
see also:
 +
/home/lml/krypton/Corvera/Raz/README  5/15/14
 +
align_quadrants.pl
 +
recalc_quadrant.pl
 +
combine_images
 +
combine_images.pl
 +
register_images.pl
 +
insert_image2
  
−
note: source code in krypton:/home/lml/krypton/facil directory.
 
 
   
 
   
−
===  combine_images ===
+
===  register_images.pl ===
−
This program reads a bunch of image files which have their xy position within a well stored in their header.
 
−
It then combines the images. Karls acquisition program for the Zeiss microscope should automatically add
 
−
this information to the header. A maximum of 50 images can be combined. Images must all be the same size.
 
−
Images are also assumed to be aligned in z already. Images are added to the output image in the order specified
 
−
on the command line, with later pixel values replacing previous values if there is an overlap of the images.
 
  
−
Usage: combine_images [options] im1.i2i im2.i2i [more input images]  outim.i2i
+
Takes a bunch of images taken in one well on the microscope, translates them
−
options:
+
based on ChainedTrans.txt and combines them into one big image.
−
-d debug. stuff to stderr.
 
−
-f do NOT fill pixel locations which have no data with nearest data value (added 2/3/14)
 
−
Filling is done by default to try to avoid introducing sharp intensity edges into the image.
 
−
-X flip each input image in X before using it (-Y can also be specified at the same time)
 
−
-Y flip each input image in Y before using it
 
−
-p # over-ride the specified pixel size with this one (in um). The 2.5X objective has a  
 
−
pixel size of 2.58 um stored in the image header (for images acquired prior to 4/13/13)
 
−
but it should be 2.41
 
−
-x #:#[:#...]  rather than use the x positions stored in the image header use these x pixel positions.
 
−
these should be the x offset of one image relative to another, in the same order as the
 
−
image names on the command line (there MUST be one number for each image). For example:
 
−
combine_images -x=0:500:0:500 im11.i2i im21.i2i im12.i2i im22.i2i outim.i2i  if im21.i2i and im22.i2i
 
−
are displaced 500 pixels to the right of the other two images.
 
−
-y #:#[:#...]  same, but for displacement in the y direction. Since these are pixels, they should be integers.
 
−
note: many times images are 1392x1040 and overlap by 50 pixels, and image 0 is bottom left
 
−
      image 1 is top left, image 2 is bottom right, and image3 is top right, then:
 
−
      -x 0:0:1342:1342 -y 0:990:0:990  should work
 
−
-o # rather than specifying -x and -y, thus just specifies the overlap (e.g., 50) and figures out
 
−
the rest for you (assumes images ordered BL,TL,BR,TP - as above - and x and y overlap the same
 
−
works for any size image.
 
  
−
note: entire image name (with extension) is NOT required.
+
ChainedTrans.txt should be a partially ordered file with entries like
−
note: a - in place of an image name means stdin or stdout.
+
X02:X03    (685,282):(736,287)
−
note: compressed images are temporarily uncompressed into /usr/tmp.
+
This means that location (685,282) in file X02 is the same as location (736,287) in file X03.
 +
By partially ordered I mean that for file1:file2  file1 should already have been the
 +
right hand side of a similar line previously (so its position is already defined relative to
 +
the file on the left hand side), unless it is the very first line in
 +
the file. So every right hand side is relative to a left hand side which has already
 +
had its position defined.
 +
Output goes to new_trans.i2i
  
−
See also: parsepos.pl (not needed now that Karl fills the image header with this info)
+
register_images.pl [options] ChainedTrans.txt
−
    combine_images.pl    applies combine_images (and, optionally, reduceima) to all files in a directory.
+
-out=filename.i2i  name of output file produced. default = newimage.i2i
−
    register_images.pl
+
-post=string the rest of the filename after what is in ChainedTrans.txt, eg, if the file is named
−
    align_well_images.pl    pre-processor for combine_images if the y-coord in the header is invalid.
+
X01_0_0_1.i2i, -post=_0_0_1.i2i (this is also the default for post if not specified).
−
    insert_image
+
-xdim=# size of original each original image (before recaling by maxtrima, see example below). default = 1392.
 +
-ydim=# default = 1040
 +
-zdim=# default = 21
 +
-xscale=# binning done by matrixima (see example), coords will be scaled by this. default = 4.
 +
-yscale=#
 +
-blend when combining images, blend the values where they overlap (default is to just replace any previous
 +
value with the new value).
 +
    -dummy
 +
-debug
 +
-h
  
−
Source code in ~/krypton/facil/combine_images.c
 
−
combine_images:
 
  
−
== Miscellaneous ==
+
-shift no circular shift (see tranima). old.
−
===  analyze_cross_sections_of_voronoi.pl  ===
+
note: tranima will pad images with -32768 which play will show in red (I think) and DAVE will be bothered by.
  
−
This program reads files produced by cross_sections_of_voronoi (-P)
+
example:
−
Results prints volume (x) vs predicted volume (y) to stdout.
+
matrixima -row 4 W X Y Z -col 3 01 02 03 -pos 0 -obj 0 -fil 1 new.i2i
 +
play new.i2i  -> ChainedTrans.txt
 +
        register_images.pl ChainedTrans.txt
 +
        dave -I new_trans.i2i -K -z 15  # a very big file.
  
−
analyze_cross_sections_of_voronoi.pl [options] file1.txt [... filen.txt]
+
source code: ~/krypton/bin/
−
 
+
see also:
−
options:
+
combine use this on newer images which have spatial information stored in their header
−
-debug info about all fields on each line printed to stderr
+
parsepos.pl
−
-stdout everything to stdout
+
~/krypton/Corvera/Olga
−
-print_avg for each file, just graph mean and std error of the mean, rather than all data pts
+
/storage/big1/lml/Corvera/Olga
 +
recalc_quadrant.pl
 +
recalc_quadrant2.pl
 +
align_quadrants.pl the simplest manual method of aligning the four images in the well
 +
 
 +
 +
===  smooth_gaps.pl  ===
 +
  This program applies smooth_gaps to all files named *reduced.i2i
 +
  and produces files named  *reduced_sg.i2i (unless -tag changed it).
  
 +
  usage:
 +
smooth_gaps.pl -run [options]
  
−
examples:
+
  options:
−
cross_sections_of_voronoi -P voronoi.i2i > filename1.txt
+
-tag=something    tag to add before the .i2i in the new file name.
−
cross_sections_of_voronoi -P voronoi.i2i > filename2.txt
+
-verbose   print out each filename as it is being smoothed.
−
        axnalyze_cross_sections_of_voronoi.pl *.txt
+
-dummy   just echo what would be done, but don't do anything
  
−
see also:
+
  see also:
−
/storage/big1/lml/Raz/voronoi/README, true_vs_predicted.xmgr
+
smooth_gaps
−
/home/lml/krypton/Corvera/Raz/stereology/README, run_voronoi.pl, run_voronoi2.pl, compare_volume_measurements.pl, plot_results.pl
 
−
cross_sections_of_voronoi
 
−
/home/lml/krypton/packages/fiji/Fiji.app/macros/stereology_lml.txt
 
−
/home/lml/krypton/packages/fiji/run_stereology.txt
 
−
/storage/big1/lml/Raz/voronoi/
 
  
 
   
 
   
−
===  neartrack.pl  ===
+
===  trans.pl  ===
−
neartrack.pl
+
 
 +
Takes a bunch of images taken in one well on the microscope, translates them
 +
based on ChainedTrans.txt and combines them into one big image.
  
−
find which track a specified coordinate is near (ie, with dx,dy) (eg, DAVE crosshairs gives us a coord, what track is it?)
+
ChainedTrans.txt should be a partially ordered file with entries like
−
assumes coords passed are zero indexed
+
X02:X03    (685,282):(736,287)
 +
This means that location (685,282) in file X02 is the same as location (736,287) in file X03.
 +
By partially ordered I mean that for file1:file2  file1 should already have been the
 +
right hand side of a similar line previously (so its position is already defined relative to
 +
the file on the left hand side), unless it is the very first line in
 +
the file. So every right hand side is relative to a left hand side which has already
 +
had its position defined.
 +
Output goes to new_trans.i2i
  
−
    usage:  neartrack.pl -x=# -y=# [-z=#] [-dx=#] [-dy=#] [-oneindexed] file.rpts
+
register_images.pl [options] ChainedTrans.txt
 +
-out=filename.i2i  name of output file produced. default = newimage.i2i
 +
-post=string the rest of the filename after what is in ChainedTrans.txt, eg, if the file is named
 +
X01_0_0_1.i2i, -post=_0_0_1.i2i (this is also the default for post if not specified).
 +
-xdim=# size of original each original image (before recaling by maxtrima, see example below). default = 1392.
 +
-ydim=# default = 1040
 +
-zdim=# default = 21
 +
-xscale=# binning done by matrixima (see example), coords will be scaled by this. default = 4.
 +
-yscale=#
 +
-blend when combining images, blend the values where they overlap (default is to just replace any previous
 +
value with the new value).
 +
    -dummy
 +
-debug
 +
-h
  
−
 
−
===  parse_macros4.pl  ===
 
−
Can't use 'defined(%hash)' (Maybe you should just omit the defined()?) at /home/lml/krypton/bin/parse_macros4.pl line 562.
 
  
−
===  path_diff.pl  ===
+
-shift no circular shift (see tranima). old.  
−
compare the differences between the paths found from two different runs of exo5
+
note: tranima will pad images with -32768 which play will show in red (I think) and DAVE will be bothered by.
  
−
path_diff.pl  file1 file2
+
example:
 +
matrixima -row 4 W X Y Z -col 3 01 02 03 -pos 0 -obj 0 -fil 1 new.i2i
 +
play new.i2i  -> ChainedTrans.txt
 +
        register_images.pl ChainedTrans.txt
 +
        dave -I new_trans.i2i -K -z 15 # a very big file.
  
−
options:
+
source code: ~/krypton/bin/
−
  -dx=# x coord at fusion time can differ by this and still be considered same path (default = 0)
+
see also:
−
  -dy=# y coord at fusion time can differ by this and still be considered same path (default = 0)
+
combine use this on newer images which have spatial information stored in their header
−
  -df=# fusion time can differ by this and still be considered same path (default = 0)
+
parsepos.pl
 +
~/krypton/Corvera/Olga
 +
/storage/big1/lml/Corvera/Olga
 +
recalc_quadrant.pl
 +
recalc_quadrant2.pl
 +
align_quadrants.pl the simplest manual method of aligning the four images in the well
  
−
  -debug
 
−
  -Debug
 
 
   
 
   
−
===  trackinfo.pl ===
+
===  blur3d ===
  
−
# analyze output from "track or track -r".
+
Blurs an image by a psf.
−
# assumes coords passed are zero indexed.  
+
FFTs are done with 4 byte floats, so total space needed will be 4 times the padded image size (in voxels)
 +
plus the size of the two original images (image and psf)
 +
The input image can be real or short int format. The psf must be short int format.
 +
note: performs a convolution (not a correlation).
 +
note: fixed a small bug. 10/17/11
  
−
# usage:   trackinfo.pl -x=# -y=# [options] file.rpts
+
Usage: blur3d [options] image psf newimage
 +
options:
 +
  -S #: scale (multiply) output values by # (to prevent underflow or overflow)
 +
  voxels which after scaling are > 32767 are set to 32767. voxels < -32766 are set to -32766.
 +
    -p # # #: pad the image in x, y, and z by the specified amounts
 +
by default image is padded (with 0) by 1/4 psf width all around,
 +
so its size for blurring becomes bigger by psf/2.
 +
psf is always padded to the same size the image becomes.
 +
Padding is stripped off before newimage is written, so it will be the same size as
 +
the original image.
 +
    -N # # #: pad so that the image has the specified dimensions after padding (just prior to FFT).
 +
  -n #: pad with # instead of boundary pixel values.
 +
  -Z:  pad with zero instead of the boundary pixel values.
 +
  -c # # #:  the center of the psf is at (#,#,#) zero indexed.
 +
                the default is to take the brightest pixel as its center.
 +
  -C:  don't center the psf at all (default is to center on the max, unless -c is specified).
 +
  -P:  normalize the psf so each slice (after padding) averages to 1. -P acts like an optical PSF.
 +
        the default is to normalize so the entire psf (after padding) has an average pixel value of 1
 +
              (the default keeps total light constant).
 +
  -d:  don't normalize at all.
 +
  -o:  do a cross correlation instead of a blur (convolution)
 +
  -R:  output image as 4 byte floating point instead of short integer.
 +
  -v:  verbose. print more info to stderr.
  
−
#  options:  
+
note: entire image name (with extension) is NOT required.
 +
note:  can read from stdin or write to stdout (use a dash instead of the file name)
 +
note: a compressed image will be automatically be uncompressed.
  
−
#    -reg=# : just print info about the specified region number
+
Copyright 2010 University of Massachusetts Medical School and the Biomedical Imaging Group
−
#    -track=# : just print info about the specified track
+
All rights reserved. Explicit permission to use this program must be received prior to use.
−
#    -trackcoords=minsize:maxsize:miniod:maxiod:minlife:maxlife
+
−
# : print the coords (rpts format) of all tracks which satisfy
+
===  canny ===
−
#   the criteria (or all its regions satisfy them). lifetime is # of timepts it exists for.
 
−
#    -tdist=mindist:maxdist: use with -trackcoords to specify min and max (xy manhattan) distance track travels
 
−
#    -micro:   print coords of all paths. color code them so if they connect at all
 
−
#   they are the same color (eg, all along the same microtubule)
 
−
#    -x=# -y=# : find which track the specified coordinate is near (eg, DAVE
 
−
#   crosshairs gives us a coord, what track is it?)
 
−
#    -z=# : also include z in distance calculation.
 
−
#    -dx=# : dx, default = 3
 
−
#    -dy=# : dy, default = 3
 
−
#    -dz=# : dy, default = 1000 (ie, essentially ignored)
 
−
#    -oneindexed : otherwise -x, -y, -z assumed to be zero indexed (rpts file is always one indexed)
 
−
#    -t : print additional region and track info (which should be in file.rpts
 
−
#   if -r was specified when running "track") for objects found
 
−
#   (eg, via -x=#,-y=#,or -region=#)
 
−
#    -sf=name : sort field. name of field to sort on when printing out a track.
 
−
#   implies -t. default = time ("set");
 
−
#    -rs : reverse the "sense" of the sort (normally smallest to largest). implies -t.
 
−
#    -pf=field1:field2:field3 : print fields. which fields to print from the region info (implies -t).
 
−
#   default is all fields.  you can put as many fields as you want here,
 
−
#   separated by colons.
 
−
#    -verbose: : print info about progress to stderr
 
  
−
# example:
+
This program reads in a 2 or 3d image and outputs the results
−
#    track -a 3 -n 400 -r -s 0 5 -S -t 25 -v 5 500 -d 15 9 -u .33 .33 .25 5 -h .01 a.vel a.i2i > a.rpts
+
of a 2D Canny edge detector on it. Canny is the derivative
−
#    trackinfo.pl -x=52 -y=28 -t -pf=set:size:nextid a.rpts
+
(in the gradient direction) of the magnitude of the first
−
#    trackinfo.pl -reg=103 -t -pf=set:size:nextid a.rpts
+
derivative (so it is a type of 2nd derivative).
−
 
+
NOTE: see option -n below for an exact answer.
−
   
+
Each z slice is treated
−
== Data Reformatting ==
+
independently of the others. Its application will often be
−
===  chres_rpts.pl  ===
+
preceded by a Gaussian blur and followed by the calculation
−
 
+
of zero crossings.
−
  Reads in some rpts files and rescales their x and y coords so that they will match an image which
+
If an INT type image is input, an INT is output.  
−
  has been similarly rescaled.
+
If a REAL type image is input, a REAL is output.
−
 
 
−
  usage:
 
−
    chres_rpts.pl  [options] infile.rpts > outfile.rpts
 
  
 +
Usage: canny [options] infile outfile
 
   options:
 
   options:
−
-sx=# rescale x -> x*#
+
-d: Debugging flag
−
-sy=# rescale y -> y*#
+
-n: normalize the result. This option causes the true 2nd
−
-truncate  after rescaling, truncate to an integer (newer versions of addlines can handle floating pt)
+
derivative to be calculated. Without it, only the sign
−
-round     after rescaling, round to an integer
+
of the second derivative is guaranteed to be correct
−
-max=#:#    don't let x become > than #1. don't let y become > #2.
+
(which is sufficient if only zero crossings will be
−
-min=#:#    don't let x become < than #1. don't let y become < #2.
+
calculated from it). Divides each point by Ix*Ix+Iy*Iy.
−
 
+
-s #: scale factor to multiply all output values by. This is
−
  example:
+
useful if you are outputing an INTEGER image with a very
−
# suppose you have a floating pt rpts file
+
small range of values which would otherwise all be truncated
−
    find_peaks_inrpts.pl -rpts=QS_H10+1Q_3T3_center_2_peaks.rpts:.15:.033
+
to just a few numbers.
−
Results/mat_quad/QS_H10+1Q_3T3_center_2_control_q_kept.rpts > /dev/null
+
note: entire image name (with extension) is NOT required.
−
# and you want to see it in better spatial detail:
+
note: a - in place of an image name means stdin or stdout.
−
    chres -S 4 4 1 Data/QS/QS_H10+1Q_3T3__center_2_ra7.i2i QS_H10+1Q_3T3__center_2_ra7_ch441.i2i
+
Example usage:
−
    chres_rpts.pl -sx=4 -sy=4 QS_H10+1Q_3T3_center_2_peaks.rpts > QS_H10+1Q_3T3_center_2_peaks_ch441.rpts
+
To create a gradient edge strength image for a shrink wrap run:
−
    addlines2 QS_H10+1Q_3T3__center_2_ra7_ch441.i2i QS_H10+1Q_3T3_center_2_peaks_ch441.rpts - |playc -
+
  blur_spatial image.i2i -|canny - -|zerosu - - |blur_spatial - out.i2i
 +
 +
===  cblur  ===
 +
 +
Usage: cblur [options] arg1.i2i arg2.i2i
 +
  For every zero valued point in each xz plane,  cblur
 +
  replaces the zero value with the -100 times the distance
 +
  from the nearest non-zero voxel in the xz plane.
 +
Options: None at this time.
  
−
  see also:
+
Note: entire image name (with extension) is required.
−
  filter_rptsinz.pl
+
Note: a - in place of an image name means stdin or stdout.
  
−
 
−
===  combine_Raz_and_lml_data.pl  ===
 
  
−
combine data pts from Raz with my data points. results printed to stdout
+
=== center_of_mass  ===
  
−
usage:
+
This program reads in a 4D image and translates each 3D image
−
combine_Raz_and_lml_data.pl [options]  file1 file2
+
so its center of mass is moved to be the center of the image.
 +
One 3D image is read at a time.
  
−
where file1 is find_vesselness_results2.txt (or something else in that format, ie with internal filenames formatted that way)
+
Usage: center_of_mass [options] inimage.i2i outimage.i2i
−
      file2 is raz_results.out (or something else in that format)
+
options:
−
 
+
  -t tdim:  number of time points, default = 1. This is NOT read from the header.
−
options:
+
  -T #:  threshold inimage.i2i prior to analysis. voxels <= # ignored, default = 0
−
      -cond1='xxx'  a perl expression to be evaluated to determine which rows of data to analyze. default is all rows.
+
  -v: verbose
−
                        if it evaluates to > 0 the row will be used.
 
−
                        e.g., -cond='if ($tissue eq "OM") {1;} else {0;}'
 
−
                        e.g., -cond='if ($date == 7) {1;} else {0;}'
 
−
                        note the use of single (not double) quotes to protect this from the shell.
 
−
                        If this is not specified all data lines will produce an x and y value.
 
−
                        Some simple perl info:
 
−
                          use eq (equal) and ne (not equal) for comparing strings (which are in double quotes).  
 
−
                          use ==  !=  >  >=  <= for numeric comparisons. && (logical AND), || (logical OR).
 
−
                          put $ in front of all variables (string variables and numeric variables).
 
−
                          statements are separated by semicolons.  Blocks specified with braces.
 
−
                          if ( ) { }  else { }  where the "else {}" is optional. But don't forget the braces.
 
  
 +
note: source code in krypton:/home/lml/krypton/facil directory.
 +
 +
===  combine_images  ===
 +
This program reads a bunch of image files which have their xy position within a well stored in their header.
 +
It then combines the images. Karls acquisition program for the Zeiss microscope should automatically add
 +
this information to the header. A maximum of 50 images can be combined. Images must all be the same size.
 +
Images are also assumed to be aligned in z already. Images are added to the output image in the order specified
 +
on the command line, with later pixel values replacing previous values if there is an overlap of the images.
  
−
-unique_header1=something string which uniquely exists on the header line of file1 (so it can be identified)
+
Usage: combine_images [options] im1.i2i im2.i2i [more input images]  outim.i2i
−
-data_field1=something which column has the actual data we care about and will graph. default = rate
+
options:
−
        -data_factor1=# multiply data_field value in file 1 by data_factor prior to analyzing (or printing) it.
+
-d debug. stuff to stderr.
−
-group_by1=something  how to match the data, eg, a datapoint in file1 will by matched to a datapt in file2 by this criteria
+
-f do NOT fill pixel locations which have no data with nearest data value (added 2/3/14)
−
 
+
Filling is done by default to try to avoid introducing sharp intensity edges into the image.
−
-cond2 same but for file2, defaults to -cond1
+
-X flip each input image in X before using it (-Y can also be specified at the same time)  
−
-unique_header2=something same but for file2. defaults to -unique_header1
+
-Y flip each input image in Y before using it
−
-data_field2 same but for file2, defaults to -data_field1
+
-p # over-ride the specified pixel size with this one (in um). The 2.5X objective has a
−
-data_factor2 same but for file2, defaults to 1
+
pixel size of 2.58 um stored in the image header (for images acquired prior to 4/13/13)
−
-group_by2 same but for file2, defaults to -group_by1
+
but it should be 2.41
 +
-x #:#[:#...]  rather than use the x positions stored in the image header use these x pixel positions.
 +
these should be the x offset of one image relative to another, in the same order as the
 +
image names on the command line (there MUST be one number for each image). For example:
 +
combine_images -x=0:500:0:500 im11.i2i im21.i2i im12.i2i im22.i2i outim.i2i  if im21.i2i and im22.i2i
 +
are displaced 500 pixels to the right of the other two images.
 +
-y #:#[:#...]  same, but for displacement in the y direction. Since these are pixels, they should be integers.
 +
note: many times images are 1392x1040 and overlap by 50 pixels, and image 0 is bottom left
 +
      image 1 is top left, image 2 is bottom right, and image3 is top right, then:
 +
      -x 0:0:1342:1342 -y 0:990:0:990  should work
 +
-o # rather than specifying -x and -y, thus just specifies the overlap (e.g., 50) and figures out
 +
the rest for you (assumes images ordered BL,TL,BR,TP - as above - and x and y overlap the same
 +
works for any size image. 
  
−
-silent don't print warning to stderr when a data pt in one file does not have a match in the other file.
+
note: entire image name (with extension) is NOT required.
−
+
note: a - in place of an image name means stdin or stdout.
 +
note: compressed images are temporarily uncompressed into /usr/tmp.
  
−
  -debug stuff to stderr
+
See also: parsepos.pl (not needed now that Karl fills the image header with this info)
−
    -Debug other stuff to stdout
+
    combine_images.pl    applies combine_images (and, optionally, reduceima) to all files in a directory.
 +
    register_images.pl
 +
    align_well_images.pl    pre-processor for combine_images if the y-coord in the header is invalid.
 +
    insert_image
  
−
  example:  
+
Source code in ~/krypton/facil/combine_images.c
 +
  combine_images:  
  
−
get_find_vesselness_results.pl  -gdm=014:019  -t2dm=005:020:021 > find_vesselness_results2.txt
+
=== flood3dL  ===
−
get_dir_results.pl -verbose > raz_results.out
+
Usage:
−
combine_Raz_and_lml_data.pl -data_factor1=2 -unique_header1=filename -data_field1=pixels_in_mask -group_by1=filename
+
  flood3d [options] input.i2i output.i2i
−
                      -data_field2=mass -group_by2=imagename find_vesselness_results2.txt raz_results.out > Raz_lml_combined.txt
 
  
−
see also:
+
Description:
 +
  flood3d reads in an image and outputs an image with each region's
 +
  voxels all at the same intensity (intensity = 1 for 1st region, 2 for 2nd
 +
  region, etc.). Regions are 26 connected voxels greater than the threshold.
 +
  If no output image is specified no output image will be produced.
  
−
combine_with_Raz_curated_data.pl
+
Options:
−
compare_data_points.pl
+
  -t #:    Value to threshold image (default 0).
−
boxandwhisker2.pl
+
  -s #:    Value to start numbering objects (default 1).
−
xmgrace --help
+
  -r x y z: Mark the region at x y z (1 indexed).
−
http://plasma-gate.weizmann.ac.il/Grace/doc/UsersGuide.html
+
            this option can be specified up to 5 times.
−
/home/lml/krypton/Corvera/Raz/gedmat_dummyhealthr.data
+
            If z < 0, then starting points x y 1, x y 2, .. x y zdim
−
/home/lml/krypton/Corvera/Raz/README 4/2/14
+
            are used. Use z < 0 in conjunction with -c 4 or -c 8.
−
gedmat_to_xy.pl used to produce gedmat_dummyhealthr.data. can also pull out arbitrary rows and columns
+
            all such regions found are marked with the same region number.
 +
  -c #:     Do # connected flood fill (default 26).
 +
            Options are 4, 8, or 26 connected flood fills.
 +
            4 or 8 connected flood fills are for 2D flood fills
 +
            with the fill being done in x, y for each z plane.
 +
            (each slice will be done, unless -r is specified).
 +
  -m #:    only keep regions whose size in voxels is > #. Default = 0.
 +
  -b:      Output will be binary (regions counted will be 1,
 +
            regions not counted will be 0.
 +
  -q:      Quite mode, fewer messages printed.
  
−
+
Caveats:
−
===  coords2pts.pl  ===
+
  Threshold and number of objects has to be less than 32,000.
−
Converts from coords format produced by track_pts to pts format needed by dave.
 
−
Only handles output from track_pts with one object in it right now.
 
  
−
coords2pts.pl [options] <in.coords  > out.pts
+
Note:
 +
  Entire image name (with extension) is required.
 +
  A - in place of an image name means stdin or stdout.
  
−
options:
+
Keywords:
−
   -one: add 1 to x,y,z coords (e.g, to go from zero indexed to the one-indexed coords dave expects)
+
   count objects, flood fill
−
  -name=trackname    the name of the object created. dave wants different objects to have different names.
 
−
  -w=# for the w coord (intensity) just use the specified number (dave has problems if the number > 255)
 
−
track_pts usually puts the max intensity in the w field.
 
  
−
Example usage:
+
Additional programs:
−
   track_pts -tdim 30  green.i2i green_in.coords green_out.coords
+
   patchstat do_transform
−
  track_pts -tdim 30  red.i2i  red_in.coords  red_out.coords
 
−
  coords2pts.pl -w=1 -one -name=green_track < green_out.coords > green_out.pts
 
−
  coords2pts.pl -w=1 -one -name=red_track < red_out.coords > red_out.pts
 
−
  concateima green.i2i red.i2i both.i2i
 
−
  dave -n 0 -u -O -z 1 -4 -I both.i2i green_out.pts red_out.pts
 
  
  
 
   
 
   
−
===  crosshair2bestpath.pl ===
+
===  gauss_deriv ===
−
  Convert a list of pts produced inside DAVE by using the crosshair and the
+
 
−
   "clear and save stack to file" option, to commandline arguments for
+
This program takes an image, blurs it with a Gaussian of
−
  BestPath3D. May still need to add -t and -f options manually.
+
specified standard deviation and then takes derivatives of the image
−
  Must also change IMAGE.i2i and IMAGE.rpts args in the output.
+
It does all of this in the frequency domain. 
 +
 
 +
Usage: gauss_deriv [options] infile.i2i outfile.i2i
 +
options:
 +
  -a angle:  angle of rotation (in radians) for the x,y axes about z.
 +
default = 0.000000
 +
  -x order:  number of derivatives in the x direction.
 +
default = 0
 +
  -y order:  number of derivatives in the y direction.
 +
default = 0
 +
  -p x y z:  pixel size in microns (zsize ignored for now), default = (0.1,0.1,0.1)
 +
  -s dev:  standard deviation in spatial domain of Gaussian (in microns).
 +
  -S dev:  standard deviation in frequency domain of Gaussian (cycles/um).
 +
default = 1.000000
 +
  -e epsilon:   cutoff for Gaussian intensity calculation.
 +
default = 0.040000
 +
  -r newmax: rescale output 0-newmax. newval = (oldval-min)*newmax/(max-min). This is useful
 +
especially when all the values would otherwise be < 1.
 +
This also prints to stderr the min and max values before rescaling.
 +
  -R scale black: rescale output: newval = (oldval-black)/scale .
 +
  -v: verbose
 +
  -n: no op. just take a forward and inverse transform. For debugging.
 +
note: the entire image name is NOT required.
 +
note: compressed images will be uncompressed.
 +
note: a - in place of an image name means stdin or stdout.
 +
restrictions: only works in 2D. 3D images have each z plane processed separately.  
 +
see also: gauss_deriv_unc, blur_spatial, canny, zerosu.
 +
 +
===  i2i2mhd  ===
 +
 
 +
This program just creates a MetaImage header file (file.mhd) which can be read, in conjunction with the original
 +
i2i file, into a ITK or VTK program. NOTE: you must keep inimage.i2i and inimage.mhd together in the same directory.
 +
If specified with a .mha extension then the resulting image has both the ascii header and the data together
 +
in one file (not done yet).
 +
 
 +
Usage: i2i2mhd inimage.i2i inimage.mhd
 +
i2i2mhd inimage.i2i inimage.mha
  
−
   crosshair2bestpath.pl [options] crosshair.dat > commandline.txt
+
options:
 +
-t # : set output tdim to the specified number. specify 0 if the image has no time dimension.
 +
-l : force output to be designated little endian
 +
-b : force output to be designated big endian
 +
-s dx dy dz   : pixel spacing. Some of the ACME routines may look at these values.
  
−
  options:
+
Examples:
−
    -image=# image name (instead of IMAGE.i2i) written out.
+
  i2i2mhd test.i2i test.mhd
−
    -rpts=# rpts name written out (instead of IMAGE.rpts)
+
    ~/krypton/segmentation/MR-Source/ACME/ACME-Binary/bin/cellPreprocess test.mhd test_proproc.mhd .3
−
    -t=# add -t # to options written out written out for BestPath3D
+
the above will create test_preproc.zraw and test_preproc.mhd, if, instead, you specify
−
    -f=#:# add -f # # to options written out for BestPath3D
+
test_resampled.mha as ouput to cellPreprocess you get all the output in the mha file.
  
 +
See also: mhd2i2i
 +
            http://www.itk.org/Wiki/MetaIO/Documentation, ~/krypton/ITK/README.lml.build-4.3,
 +
    ~/krypton/segmenation/MR-Source/README.lml, /home/lml/krypton/segmentation/MR-Source/ACME/lmltest/README
  
 +
source code in:  /home/lml/krypton/facil
 
   
 
   
−
===  dup_rpts.pl ===
+
===  insert_image2 ===
 +
incorrect command line, too few args.
 +
insert_image2 does a weighted merge of pixels in an original image with overlapping pixels from replacement images.
 +
Pixels which fall outside the original volume will be ignored.
 +
WARNING: the original image is MODIFIED, a NEW image is NOT produced (unless -n is specified).
 +
The weighting function for the blending makes the most sense for kind of usage align_quadrants.pl makes of it;
 +
ie, blending four quadrant images which only overlap a little and are being inserted into an initial blank image.
  
−
Takes an input file with one z slice per object, and, for each
+
Usage: insert_image2 [options] original_image.i2i [replacement_part.i2i xpos ypos zpos] 
−
object named on the command line, duplicates that slice for a
+
replacement_part.i2i xpos ypos zpos: the replacement image and the x,y,z coordinate (0-indexed)
−
range of z slices. rpts file must be in xy (not xyz) format
+
that it should start at. This option can be repeated as many times as desired.
−
 
+
options:
−
dup_rpts.pl -name1=#-# [-name2=#-# ...]  < in.rpts  > out.rpts 
+
  -r # if a pixel in original_image.i2i has this value, REPLACE it with any overlapping pixel (not a weighted avg).
−
or
+
  note: it could still then be modified by subsequent replacement images (they are analyzed in command line order)
−
dup_rpts.pl -name1=#-# [-name2=#-# ...] in1.rpts [in2.rpts ...]  > out.rpts 
+
  -R # if a pixel in a replacement image has this value, use it to REPLACE any overlapped pixel (not a weighted avg).
 +
  note: it could still then be modified by subsequent replacement images (they are analyzed in command line order)
 +
  -k # if a pixel in th original_image.i2i has this value, do NOT replace it.
 +
  -v # same as -k (for backwards compatibility). keep this value.
 +
  -n newim.i2i rather than over-write the original image, create a new image with this name.
 +
  -d debug. some info gets printed to stderr
  
 
example:
 
example:
−
  dup_rptsinterp.pl -foo=1-5 -bar=2-8  < in.rpts  > out.rpts 
+
parsepos.pl -pre=/storage/big3/kdb/Zeiss/20121004/LectinExp3/ -post=_1_1_20121004_LectinExp3.i2i \
 +
/storage/big3/kdb/Zeiss/20121004/LectinExp3/LextinExp3.pos | overlap_images.pl -create=newimage.i2i
  
−
  This will take the zslice associated with the object named
+
see also:  /storage/big1/lml/Corvera/Olga/data/ptrs/README
−
  foo and duplicate it into zslices 1 through 5, and duplicate
+
      insert_image  -the same as insert_image2, but doesn't perform any weighted merging.
−
  object bar into zslices 2-8.
+
      smooth_gaps
 +
      combine
 +
            combine_images.pl
 +
      align_quadrants.pl which calls combine_images and recalc_quadrant2.pl which calls register_images.pl which calls insert_image2
 +
(or insert_image if -noblend was passed to align_quadrants.pl).
  
 +
source code in:  /home/lml/krypton/facil
 
   
 
   
−
===  extract_overlap.pl ===
+
===  mergeimL ===
−
Reformats data from the overlap data produced by closest_object for graphing by xmgrace.
+
 
 +
Merge a bunch of 2 D files of same dimensions.
 +
The first image can be a 3 D image.
 +
If -x and -y are specified then all images are padded (on high x and high y sides) to
 +
the same specified dimensions, so the initial images can be different sizes.
 +
This version can read shorts or floats (but all must be the same)
  
−
extract_overlap.pl [options] *.patchdist2 | xmgrace -source stdin
+
Usage: mergeimL [options] im1 ... imN newimage.i2i
 +
options:
 +
  -r  : remove original files as they are merged.
 +
note: if the program bombs for some reason
 +
during this, data will be lost.
 +
  -b:  merge the images in backwards order from the
 +
list (ie, the last image will be the first
 +
slice). Use with -b in extractslice.
 +
  -x xdim: pad all images to this x dimension.
 +
  -y ydim: pad all images to this y dimension.
 +
  NOTE: this permits images of different sizes
 +
        to be merged by padding to the same size.
 +
  -p #:  when padding (-x and -y options) use this value
 +
  (0 default)
 +
  -d:  print out some debugging information.
 +
note: entire image name (with extension) is required.
 +
note: source in krypton:/home/lml/krypton/facil
 +
 +
===  mhd2i2i  ===
  
−
-mstring=im1_im2: : pull out data for fraction of each object in image1 which overlaps with image2 object, default = im2_im1
+
This program reads a MetaImage file (file.mhd or file.mha) and converts (casts) it into a (short int) i2i image file.
−
  You can also specify im1_im1 and im2_im2, in which case overlap is always 0 and the
 
−
  distance (-distance option) is the distance to the nearest other object in the same image.
 
−
-distance : pull out distance info instead of overlap info
 
−
-size : pull out size info instead of overlap info
 
−
-showhist : print histogram of overlaps (or distances or sizes) instead of just a list of all of them
 
−
-normmax : normalize the histogram to have a max of 1 (sets -showhist)  
 
−
-normsum : normalize the histogram to have a sum of 1 (sets -showhist)
 
−
-normint : normalize the histogram to have an integral (area under curve) of 1 (sets -showhist)
 
−
  this lets xmgr->data transformations->integrate produce a cumlative prob distribution which goes to 1
 
−
  Not quite correct yet.
 
−
-cum : print cumulative histogram. also use -normsum if you want this to be a cdf (approaches 1 as a max).
 
−
-binsize=# : binsize for the histogram (sets -showhist), default = 1
 
−
-verbose
 
  
−
+
Usage: mhd2i2i inimage.mhd outimage.i2i
−
===  filter_rptsinz.pl  ===
 
  
−
Takes simple rpts file and only keeps certain z valued pts (they get renumbered).  This is set up so that if
+
options:
−
you use segment -Z # # # image.i2i, and filter_rptsinz.pl -z=#:#:# where the numbers match in
+
-p      : just print some info about the image and quit. outimage.i2i does not need to be specified in this case.
−
the two commands, then the resulting rpts will match the i2i image. rpts which are not in
+
-s # # : multiply values by the first number and add the second, then cast to a short int.
−
the correct slices are not kept.
+
-d debug
  
−
usage:
+
Examples:
−
   filter_rptsinz.pl -z=#:#:# infile.rpts > outfile.rpts
+
   mhd2i2i test.mhd test.i2i
  
−
options:
+
See also: i2i2mhd, http://www.itk.org/Wiki/MetaIO/Documentation, ~/krypton/ITK/README.lml.build-4.3,
−
  -z=#:#:#    Z axis start, end and increment in pixels (1-indexed).
+
~/krypton/segmenation/MR-Source/README.lml, /home/lml/krypton/segmentation/MR-Source/ACME/lmltest/README
−
  -float keep (or convert) x,y,z values as floats. Otherwise it tries to auto-detect when to output floats.
+
      mayavi2 (which can view .mhd files directly)
  
−
  only works on rpts files which have a z value (e.g. xyz or xyzw format).
+
source code in:  /home/lml/krypton/facil
 +
 +
===  oib2i2i  ===
  
−
  see also:
+
oib2i2i takes an Olympus oib file and converts it into one or three i2i files.
−
   chres_rpts.pl
+
 
 +
note: it should also work with many other file types, including DeltaVision files.
 +
 
 +
java oib2i2i [options] file.oib file.i2i  [z dimension will be the number of channels]
 +
java oib2i2i [options] file.oib file_red.i2i file_green.i2i file_blue.i2i
 +
java oib2i2i [options] file.oib file_red.i2i file_green.i2i file_blue.i2i file_alpha.i2i
 +
 
 +
options:
 +
    -l[ittle]: force interpretation of 2 byte pixel values to be little endian (I may have this backwards)
 +
    -b[ig]:    force interpretation of 2 byte pixel values to be big endian (I may have this backwards)
 +
    -v[erbose]: verbose. prints info about file contents as planes are converted.
 +
    -d[ebug]:  prints debug info to stderr.
 +
    -i[nfo]:    like verbose. but ONLY prints info about file contents, then stops
 +
                must still give it a (dummy) output file argument
 +
 
 +
see also:
 +
   GetMicroscopeImageInfo file.oib      :will produce lots of information about the file
 +
  http://www.loci.wisc.edu/software/bio-formats
  
 +
source in /home/lml/krypton/packages/BioFormats/oib2i2i.java
 
   
 
   
−
===  gedmat_to_xy.pl ===
+
entered main()
 +
 
 +
===  pwarpL ===
 +
pwarp warps an image into a new image based upon a set of
 +
registered points from one image to another. That is, the
 +
transformation necessary to transform one set of registered
 +
points into the other is calculated. Then this transformation
 +
is applied to the image specified, producing a new image.
 +
A line segment can also be specified as an old "pt".  The new
 +
pt will match the best position along this line segment.
 +
The pointfile should contain points in the following format,
 +
new x and y dimensions, number of pts, new pts, oldpts. for
 +
example if 10 pts are given:
 +
  300 240
 +
  10 points
 +
  new_x1        new_y1 
 +
      .   .  
 +
      .   .  
 +
  new_x10      new_y10 
 +
  initial_x1  initial_y1 
 +
      .   .  
 +
      .   .  
 +
  L old_lowx old_lowy old_hix old_hiy  (this is a line segment)
 +
      .          .     
 +
      .          .     
 +
  initial_x10  initial_y10 
 +
the points can be in floating point.
  
−
  Takes files of data produced by mask_gedmat_images.pl (either via stdin or as command line arguments, [filenames])
+
Usage: pwarp [options] oldimage pointfile newimage
−
  and writes x y columns of processed data to stdout (but -unique_header=none will allow it to work on other formats).
+
options:
−
  These files have a line with column names, and can have comment lines (start with #) or blank lines in them.
+
  none.
−
  All other lines should just be columns of ascii text data.  strings are allowed (not quoted, and no spaces in them).
 
−
  The column header line (which can appear on any line and multiple times) must have a word (ie column name) unique
 
−
  to it (since the data can also have strings in them).  By default this word is assumed to be "filename"
 
−
  (-unique_header can change this).
 
  
−
  -cond (or -form if I bother to get that working) specifies a condition which decides which lines
+
Note: the .i2i extension is NOT necessary.
−
  of data to analyze. Any expression which evaluates to something > 0 will be analyzed.
+
 +
===  rawtoi2i2 ===
  
−
  -xcoord and -ycoord are the formula to use to determine what will go in the x or y column (if the -cond test is passed).
+
Converts a "raw" image into our i2i format. The raw image can be alternating red, green
 +
blue values or either 1 byte per color channel or 2 bytes per color channel.
 +
It can also be grayscale (-n 1) and 1,2, or 4 bytes per channel.
  
−
  usage:
+
Usage:
−
        gedmat_to_xy.pl [-form='xxx' | -cond='xxx'] -xcoord='xxx'  -ycoord='xxx' [options] [filenames]
+
rawtoi2i [options] -d xdim ydim zdim inimage.rgb outimage.i2i
 +
Options:
 +
-d xdim ydim zdim: dimensions of inimage.rgb. This MUST be specified.
 +
-b #: 1 or 2 bytes per color channel, default = 1
 +
                if the image is grayscale (-n 1) this can be 4
 +
-c #: which color channel to use (0=r, 1=g, 2=b), default = 0
 +
ignored if grayscale (-n 1).
 +
-n #: 3 if color channels (rgb), or 1 for grayscale.
 +
-S scale black: newval = (oldval-black)/scale.
 +
-m min max: after rescaling, if newval < min, newval = min. defaults = -32765,32765
 +
-s: values in inimage are signed values (not unsigned).
 +
-e: swap bytes (change endian). only make sense if -b 2 or 4
 +
  -v: verbose
 +
Examples:
 +
  identify inimage.tif :get image dimensions (xdim,ydim,zdim)
 +
  /usr/bin/convert inimage.tif -channel Red inimage.rgb
 +
  rawtoi2i -d xdim ydim zdim inimage.rgb outimage.i2i
 +
See Also:
 +
  cstoi2i, zeisstoi2i, convert (man ImageMagick), imformat, imformatb.
 +
Bugs:
 +
  the created image has a strange permission. fix it by doing: chmod 644 outimage.i2i
  
−
        xxx should contain the words (as variables) which are the column names in the output produced by mask_gedmat_images.pl.
+
Source code in ~krypton/lml/facil 
 +
 +
===  replace_slicesL  ===
  
 +
This program reads a 3D image and replaces the specified slices
 +
with a weighted composite of the closest surrounding slices which
 +
are not being replaced.  It is useful for getting rid of bad slices
 +
from an image.  The weights perform a linear interpolation.
  
−
  required:
+
Usage: replace_slices [options] inimage.i2i outimage.i2i
−
        -cond='xxx'  a perl expression to be evaluated to determine whether to print x and y derived from each row of data.
+
options:
−
if it evaluates to > 0 the row will be used.
+
  -r # s1 s2 s3, etc : replace # slices (e,g,. 3 slices);
−
e.g., -cond='if ($date eq "date_sure") {1;} else {0;}'
+
                        the slices to replace are s1, s2, s3, etc.
−
                        e.g., -cond='if ($area > 10) {$area+5;} else {$dist/2;}'
+
                        NOTE: the slices must be sorted (s1<s2<s3).
−
                        note the use of single (not double) quotes to protect this from the shell.
+
                        NOTE: slices are 0-indexed (first slice is 0).
−
If this is not specified all data lines will produce an x and y value.
+
                        NOTE: the first and last slices in the image cannot
−
                        Some simple perl info:
+
                              be replaced.
−
                          use eq (equal) and ne (not equal) for comparing strings (which are in double quotes).  
+
note: entire image name (with extension) is NOT required.
−
                          use ==  !=  >  >=  <=  for numeric comparisons. && (logical AND), || (logical OR).
+
note: a - in place of an image name means stdin or stdout.
−
                          put $ in front of all variables (string variables and numeric variables).
+
note: a compressed image will be automatically be uncompressed.
−
                          statements are separated by semicolons.  Blocks specified with braces.
+
−
                          if ( ) { }  else { }  where the "else {}" is optional. But don't forget the braces.
+
=== rescale  ===
−
note: you can also use variables $exarea  and $exdist to refer to the area and dist fields
 
−
from the day 0 datalines. These values correspond to the explant area and its distance
 
−
from the image (ie, well) center for the same patient, well, and tissue type as the
 
−
current line being processed. Suppose you want to look only at data from day 11 if
 
−
the explant area (ie, day 0 area) was larger than 200,000 pixels:
 
−
-cond='if (($exarea > 200000) && ($day == 11)) {1;} else {0;}'
 
  
−
-xcoord='xxx' like -cond, but used to specify what the xcoord value should be
+
This program linearly rescales image intensities to a new intensity
−
e.g., -xcoord='$farea/$area';    do not specify this if you specify -col#
+
range: 0 (new_min) to 1023 (new_max) by default.
−
-xcoord='$numprinted' will print 1, 2, 3, etc (ie, a count of how many datalines have been printed so far) for x.
 
  
−
-ycoord='xxx' like -cond, but used to specify what the ycoord value should be,
+
Usage: rescale [options] inputimage outputimage
−
e.g., -ycoord='$dist';    do not specify this if you specify -col#
+
options:
−
-ycoord='$numprinted' will print a count of how many datalines have been printed so far for y.
+
-N #: New max should be #.
 +
-n #: New min should be #.
 +
-M #1 #2: any original pixel value greater than # should be
 +
      set to #2 before any rescaling takes place.
 +
-m #1 #2: any original pixel value less than #1 should be
 +
      set to #2 before any rescaling takes place.
 +
      So if you have a few munged values, ie, large negative
 +
      numbers which you don't want to mess up the rescaling
 +
      you can just use -m 0 0 on the command line.
 +
-v old new:  voxels with value old will just be set to value new.
 +
      note: "old" cannot be within the range which other pixels will
 +
    be rescaled to.
 +
-b    write out an i2i byte image (rather than a short). values > 255 will be truncated.
 +
note: entire image name (with extension) is NOT required.
 +
note: a - in place of an image name means stdin or stdout.
 +
note: compressed images are temporarily uncompressed into /usr/tmp.
 +
 +
== Miscellaneous ==
 +
===  analyze_cross_sections_of_voronoi.pl  ===
  
−
  options describing input:
+
This program reads files produced by cross_sections_of_voronoi (-P)
−
-unique_header=something rather than look for "filename" to determine which line contains header names, look for something
+
Results prints volume (x) vs predicted volume (y) to stdout.
−
-unique_header=none if you specify the word "none" then column names will be col1, col2,  ... and no header lines
 
−
should exist
 
  
−
  options describing output:
+
analyze_cross_sections_of_voronoi.pl [options] file1.txt [... filen.txt]
−
-comment include a comment line up front showing the command line used to generate this data.
 
−
-col#='xxx' rather than just two columns, you can specify what to print in up to 20 by repeating this command
 
−
# is the column number (starting with 1). do not specify -xcoord or -ycoord if you use this option.
 
−
It will also cause column names to be printed.
 
  
−
-col#_name='name'  if you don't want the default name for the column (which is just col#_name) specifiy a name here.
+
options:
 +
-debug info about all fields on each line printed to stderr
 +
-stdout everything to stdout
 +
-print_avg for each file, just graph mean and std error of the mean, rather than all data pts
  
−
        -form='xxx'    instead of -cond.  a formula. eg -form='(area/dist+.5)-(area/2)' or -form='myfunc(dist,area)'
 
−
not implemented yet.
 
  
−
-line if -cond is satisfied, print the entire line of data (-xcoord and -ycoord not needed, they are ignored).
+
examples:
−
note: fields will be in the same order than they were in the input files, but formatting may be a bit different.
+
cross_sections_of_voronoi -P voronoi.i2i > filename1.txt
 +
cross_sections_of_voronoi -P voronoi.i2i > filename2.txt
 +
        axnalyze_cross_sections_of_voronoi.pl *.txt
  
−
-xmgr_labels=# add output commands for xmgr which will add a label to each point. # is font size (.5 seems to be a good value). 
+
see also:
−
The command lines all begin with @, so if you have a file produced that way and decide you do not want them
+
/storage/big1/lml/Raz/voronoi/README, true_vs_predicted.xmgr
−
displayed in xmgrace do:
+
/home/lml/krypton/Corvera/Raz/stereology/README, run_voronoi.pl, run_voronoi2.pl, compare_volume_measurements.pl, plot_results.pl
−
gedmat_to_xy.pl -xmgr_labels=1 gedmat.areas  > gedmat.xmgr      # you did this thinking you wanted labels
+
cross_sections_of_voronoi
−
fgrep -v @  gedmat.xmgr |xmgrace -free -pipe # but now you decide you don't want the labels
+
/home/lml/krypton/packages/fiji/Fiji.app/macros/stereology_lml.txt
−
This command cannot be used with the -col or -line options (ie, -xcoord and -ycoord must be specified).
+
/home/lml/krypton/packages/fiji/run_stereology.txt
−
Unless -unique_header is specified, the label is the patient id number (gotten from the filename field)
+
/storage/big1/lml/Raz/voronoi/
−
and the well id (from the well field) - these are produced by mask_gedmat_images.pl.
 
−
If -unique_header is specified the label will be the data line number in the file (excluding blank lines, comments, etc).
 
  
−
health options:
+
 +
===  neartrack.pl  ===
 +
neartrack.pl
  
−
-dummy_health add a dummy field (called dummy_health) for health status (e.g. normal, db1, db2) so I can start testing my stats software.
+
find which track a specified coordinate is near (ie, with dx,dy) (eg, DAVE crosshairs gives us a coord, what track is it?)
−
only use if -col is also specified.
+
  assumes coords passed are zero indexed
−
-seed=# seed for random number generator used if -dummy_health is specified. Specifying a seed lets you repeat this over and
 
−
over and get the same random numbers. The default is to use the time of day (which will change with each running).
 
  
−
-t2dm=id[:...:id] list of patients which are type 2 diabetic (t2dm).  These ids should match the patient id field (the 3 digit number)
+
    usage:  neartrack.pl -x=# -y=# [-z=#] [-dx=#] [-dy=#] [-oneindexed] file.rpts
−
in the *.areas files being analzyed.  For example in 017_VQU_OM.areas:
 
−
    filename              well type day  area      farea  area_mex area_mex_border  dist  date        id   perr aerr bad
 
−
B05_017_VQU_OM_Area.zip  B05 OM  11  2866176  2869698    2563883  1642634        1712.8  date_sure  017  0    0
 
−
So if patient 17 is t2dm  specifiy -t2dm=017
 
−
-gdm=id[:...:id] list of patients which are gestational diabetic (gdm).
 
−
The name should be the (3 digit) id field in the data line, just as in the -t2dm example.
 
−
if either (or both) of -tdm and -gdm are specified, a field called "health" will be added to the output. It will
 
−
have values t2dm, gdm, or normal.
 
  
−
misc options:
+
 +
===  parse_macros4.pl  ===
 +
Can't use 'defined(%hash)' (Maybe you should just omit the defined()?) at /home/lml/krypton/bin/parse_macros4.pl line 562.
  
−
-one_space separate columns by exactly one space so sas can parse it easier (see also: spaces.pl) with proc import.
+
===  path_diff.pl ===
 +
compare the differences between the paths found from two different runs of exo5
  
 +
path_diff.pl  file1 file2
  
−
-silent suppress some messages
+
options:
−
        -debug stuff to stderr
+
  -dx=# x coord at fusion time can differ by this and still be considered same path (default = 0)
−
        -Debug other stuff to stderr
+
  -dy=# y coord at fusion time can differ by this and still be considered same path (default = 0)
−
-debug_print_columns
+
  -df=# fusion time can differ by this and still be considered same path (default = 0)
  
−
   examples:
+
   -debug
−
+
  -Debug
−
# analyze some zip files
+
−
mask_gedmat_images.pl > file.areas
+
===  trackinfo.pl ===
  
−
# compare the area mask_gedmat_images.pl produced with that produced by fiji (these should be very close):
+
# analyze output from "track or track -r".
−
gedmat_to_xy.pl -cond='if ($date eq "date_sure") {1;} else {0;}' -xcoord='$area' -ycoord='$farea' file.areas | xmgrace -free pipe
+
# assumes coords passed are zero indexed.  
  
−
# compare the area mask_gedmat_images.pl produced with area_mex_border (eliminating regions near the well border).
+
# usage:   trackinfo.pl -x=# -y=# [options] file.rpts
−
# This is excluding the explant area.  ignore any lines with uncertain dates or parse errors (perr) or area errors (aerr):
 
−
gedmat_to_xy.pl -cond='if (($date eq "date_sure") && ($perr==0) && ($aerr==0)) {1;} else {0;}'
 
−
-xcoord='$area_mex' -ycoord='$area_mex_border' file.areas | xmgrace -free -pipe
 
  
−
# suppose you just have columns of data produced some other way, and no header line, and you just want to do stuff:
+
#   options:  
−
gedmat_to_xy.pl -cond='if ($col5>0) {1;} else {0;}' -xcoord='$col5' -ycoord='abs($col5-$col6)'
 
−
-unique_header=none yourdatafile | xmgrace -free -pipe
 
  
−
  see also:
+
#    -reg=# : just print info about the specified region number
−
mask_gedmat_images.pl
+
#    -track=# : just print info about the specified track
−
/home/lml/krypton/lml/Corvera/Raz
+
#    -trackcoords=minsize:maxsize:miniod:maxiod:minlife:maxlife
−
 
+
# : print the coords (rpts format) of all tracks which satisfy
−
  source code in /home/lml/krypton/bin
+
#   the criteria (or all its regions satisfy them). lifetime is # of timepts it exists for.
 +
#    -tdist=mindist:maxdist: use with -trackcoords to specify min and max (xy manhattan) distance track travels
 +
#    -micro:   print coords of all paths. color code them so if they connect at all
 +
#   they are the same color (eg, all along the same microtubule)
 +
#    -x=# -y=# : find which track the specified coordinate is near (eg, DAVE
 +
#   crosshairs gives us a coord, what track is it?)
 +
#    -z=# : also include z in distance calculation.
 +
#    -dx=# : dx, default = 3
 +
#    -dy=# : dy, default = 3
 +
#    -dz=# : dy, default = 1000 (ie, essentially ignored)
 +
#    -oneindexed : otherwise -x, -y, -z assumed to be zero indexed (rpts file is always one indexed)
 +
#    -t : print additional region and track info (which should be in file.rpts
 +
#   if -r was specified when running "track") for objects found
 +
#   (eg, via -x=#,-y=#,or  -region=#)
 +
#    -sf=name : sort field. name of field to sort on when printing out a track.
 +
#   implies -t. default = time ("set");
 +
#    -rs : reverse the "sense" of the sort (normally smallest to largest). implies -t.
 +
#    -pf=field1:field2:field3 : print fields. which fields to print from the region info (implies -t).
 +
#   default is all fields.  you can put as many fields as you want here,
 +
#   separated by colons.
 +
#    -verbose: : print info about progress to stderr
 +
 
 +
# example:
 +
#    track -a 3 -n 400 -r -s 0 5 -S -t 25 -v 5 500 -d 15 9 -u .33 .33 .25 5 -h .01 a.vel a.i2i > a.rpts
 +
#    trackinfo.pl -x=52 -y=28 -t -pf=set:size:nextid a.rpts
 +
#    trackinfo.pl -reg=103 -t -pf=set:size:nextid a.rpts
  
 
   
 
   
−
===  get_columns.pl ===
+
===  find_bkgnd ===
 +
 
 +
find_bkgnd takes a 3D image and tries to estimate a background intensity value.
 +
It does this by examing the IOD in each of the four corners of the image, picking
 +
the average pixel value associated with the lowest IOD. IOD is calculated in a square
 +
region whose width (default = 2) can be changed with -r.  The IOD is the total light
 +
in this square region added across all z-planes. The avg pixel value is printed to stdout.
  
−
pulls out specified columns from a file. Ignores comment lines.  Header for the file must be the first non-comment line.
+
Usage: find_bkgnd image1
 +
options:
 +
  -r #:  change width of region examined, default = 2
 +
  -c also print out the x and y coord (1-indexed) of the corner producing the avg value.
 +
  -a # add this fraction to the value. eg: -a -.10 will subtract 10 percent from whatever
 +
avg value would have otherwise been printed out, so we don't subtract quite so aggressively.
  
−
  usage:
+
see also: ~/krypton/Melikian/find_and_restore.pl
−
    get_columns.pl [options] -cols=name:....:name  datafile > out.nxy
+
 
 +
source code in: /home/lml/krypton/facil
 +
 +
===  interp  ===
 +
 
 +
interp takes a list of contours from an rpts file and
 +
interpolates new contours between them at each zslice that
 +
was skipped.
 +
METHOD: By default it does this by taking the fft of
 +
each curve, thereby obtaining fourier coefficients. These
 +
coefficients are then interpolated between the known contours
 +
to get coefficients for the in-between slices, then an inverse
 +
fft is taken to produce the curve for the in-between slices.
 +
 
 +
Usage:
 +
    interp [Options] input.rpts output.pts
  
−
options:
 
−
-linenum precede each line with a linenumber
 
−
-noheader do not print out a header line
 
−
-noinfo do not print an info line
 
−
        -cond='xxx'  a perl expression to be evaluated to determine which rows of data to pull data from. default is all rows.
 
−
                        if it evaluates to > 0 the row will be used.
 
−
                        e.g., -cond='if ($tissue eq "OM") {1;} else {0;}'
 
−
                        e.g., -cond='if ($date == 7) {1;} else {0;}'
 
−
                        note the use of single (not double) quotes to protect this from the shell.
 
−
                        If this is not specified all data lines will produce an x and y value.
 
−
                        Some simple perl info:
 
−
                          use eq (equal) and ne (not equal) for comparing strings (which are in double quotes).
 
−
                          use ==  !=  >  >=  <=  for numeric comparisons. && (logical AND), || (logical OR).
 
−
                          put $ in front of all variables (string variables and numeric variables).
 
−
                          statements are separated by semicolons.  Blocks specified with braces.
 
−
                          if ( ) { }  else { }  where the "else {}" is optional. But don't forget the braces.
 
  
−
-skipvals=#:...:#  list of values (or text), of lines which should be skipped if any fields have one of these values
+
Options:
 +
-f #:  number of positive frequency terms to use,
 +
default = 9
 +
-l: perform linear instead of cubic spline interpolation
 +
on the parameters describing the existing outlines.
 +
-o name: only read object "name" from the rpts file.
 +
-n #: number of pts to resample each slice.
 +
(all #'s  factors must be 2)
 +
-S:    do interpolation in spatial domain. do not take fft.
 +
      this is only a linear spatial interpolation.
 +
-a: angularly interpolate positions (fft not used).
 +
this is used if we are interpolating curves, such
 +
as microtubules. The beginning of the curve is linearly
 +
interpolated (the mtoc location), all other points have
 +
their distance and angle from the mtoc linearly interpolated
 +
between their initial distance/angle and final distance/angle.
 +
NOTE: the angular change must by < 180 between defined curves.
 +
NOTE: only one open curve is allowed per image slice.
 +
-p #: pixel value to be output to rpts file, -3 default.
 +
        -c:   add 1 more point to each contour to ensure it is closed, ie
 +
              that the first point equals the last point. (This is not necessary,
 +
              and ill-advised, for use with min_cylinder or shrink_wrap.)
 +
NOTE: zslices must be in ascending order in rpts file.
 +
NOTE: contours must all be drawn in the same direction
 +
      (i.e., all clockwise or all counter-clockwise).
 +
NOTE: the name of each object is changed to "nuke" if -o is not specified.
 +
NOTE: a maximum of 3000 zslices is allowed
  
−
-replacevals=#=#:...#=# if this value (or text) is seen in any field, replace it with the second value
+
see also: interp_many
−
  example: -replacevals=unk=-1:20=10  replace unk with -1 and replace 20 with 10
+
source code was in: /storage/big1/lml/was_vision/interp
 +
source code now in: /home/lml/krypton/was_big1/was_vision/interp
 +
 +
===  object_overlap  ===
 +
#/home/lml/krypton/bin/object_overlap
  
−
-debug stuff to stderr
+
Takes images produced by countobjs -Q option or vcspat-models -n option and calculates
 +
how many object from each image overlap
 +
with objects from the other image.  Writes to stdout.
  
 +
Usage: object_overlap [options] image1.i2i image2.i2i > overlap.txt
 +
options:
 +
  none yet.
  
−
example:
+
Example:
−
    get_columns.pl -cols=time:mass:growth  datafiles > out.nxy
+
    countobjs -Q im1_obj.i2i im1.count im1.i2i
−
    xmgr -type nxy out.nxy
+
    countobjs -Q im2_obj.i2i im2.count im2.i2i
 +
    object_overlap im1_obj.i2i im2_obj.i2i > im1_im2.overlap
  
−
see also:
+
See also: vcspat-models, vcspat, krypton/Qiong/run1
−
graph_xpp2.pl
 
−
cull
 
  
 +
Source code in krypton/facil
 
   
 
   
−
===  get_dir_results.pl  ===
+
== Data Reformatting ==
−
This program looks in subdirectories, finds files named something_Results.txt and then reads info from them,
+
===  chres_rpts.pl  ===
−
These files can be the result of analyzing a projection of the 3D stack (5 z slices) or the result of
 
−
just analyzing the best slice from the stack.  By default only stack projected results files are extracted.
 
−
Results written to stdout.
 
  
−
usage:
+
  Reads in some rpts files and rescales their x and y coords so that they will match an image which
−
get_dir_results.pl
+
  has been similarly rescaled.
  
−
  options:
+
  usage:
−
-verbose stuff written to stderr
+
    chres_rpts.pl [options] infile.rpts > outfile.rpts
−
-loc=/some/path/here rather than looking in /storage/big1/raz/GEDMAT, look in this location
 
  
−
NOTE: the slice options may be buggy, it is better to use get_dir_slice_results.pl
+
  options:
−
-also_use_slice_data also include Results from single slice data (rather than just stack project data).
+
-sx=# rescale x -> x*#
−
this may cause multiple entries in the output (one for stack results and one for slice results).
+
-sy=# rescale y -> y*#
−
-only_use_slice_data exclude any file which are NOT from slice data.
+
-truncate  after rescaling, truncate to an integer (newer versions of addlines can handle floating pt)
 +
-round     after rescaling, round to an integer
 +
-max=#:#    don't let x become > than #1. don't let y become > #2.
 +
-min=#:#    don't let x become < than #1. don't let y become < #2.
  
−
examples:
+
  example:
−
get_dir_results.pl > all_results.txt
+
# suppose you have a floating pt rpts file
−
 
+
    find_peaks_inrpts.pl -rpts=QS_H10+1Q_3T3_center_2_peaks.rpts:.15:.033
−
see also:
+
Results/mat_quad/QS_H10+1Q_3T3_center_2_control_q_kept.rpts > /dev/null
−
get_dir_slice_results.pl
+
# and you want to see it in better spatial detail:
−
get_find_vesselness_results.pl
+
    chres -S 4 4 1 Data/QS/QS_H10+1Q_3T3__center_2_ra7.i2i QS_H10+1Q_3T3__center_2_ra7_ch441.i2i
−
combine_Raz_and_lml_data.pl
+
    chres_rpts.pl -sx=4 -sy=4 QS_H10+1Q_3T3_center_2_peaks.rpts > QS_H10+1Q_3T3_center_2_peaks_ch441.rpts
−
combine_with_Raz_curated_data.pl
+
    addlines2 QS_H10+1Q_3T3__center_2_ra7_ch441.i2i QS_H10+1Q_3T3_center_2_peaks_ch441.rpts - |playc -
 +
 
 +
  see also:
 +
  filter_rptsinz.pl
  
 
   
 
   
−
===  graph_channel_current.pl  ===
+
===  combine_Raz_and_lml_data.pl  ===
−
Reformats data from the histograms produced by channel_current for graphing by xmgrace.
 
  
−
  graph_channel_current.pl [options] *.channel_current | xmgrace -source stdin
+
combine data pts from Raz with my data points. results printed to stdout
  
−
  -linetype=# : 0=no lines, 1=lines[default]
+
  usage:
−
-symboltype=# : 0=pts[default]   1=circles
+
combine_Raz_and_lml_data.pl [options]  file1 file2
−
-normsum : normalize so sum (area under curve) = 1
 
−
-normmax : normalize so the max of the curve = 1
 
−
-countmax=# : cap each bin count at #. applied before normsum or normmax.
 
−
-binmax=# : group all counts in bins > # into that last bin
 
−
-cum : plot cumulative distribution. applied after all other options.
 
  
−
See also:  /home/lml/krypton/Zhuge/BKandRyr/analysis5/graphall3.csh
+
where file1 is find_vesselness_results2.txt (or something else in that format, ie with internal filenames formatted that way)
 +
      file2 is raz_results.out (or something else in that format)
  
−
   
+
  options:
−
===  makebeads2rpts.pl  ===
+
      -cond1='xxx'  a perl expression to be evaluated to determine which rows of data to analyze. default is all rows.
−
 
+
                        if it evaluates to > 0 the row will be used.
−
This program takes output from makebeads2 and converts it into
+
                        e.g., -cond='if ($tissue eq "OM") {1;} else {0;}'
−
an rpts format.  A coord from [0,1) is considered in the first pixel;
+
                        e.g., -cond='if ($date == 7) {1;} else {0;}'
−
this has a pixel coord 1 since rpts uses 1-indexed values.  A coord from
+
                        note the use of single (not double) quotes to protect this from the shell.
−
[1,2) will have a pixel coord 2, etc.
+
                        If this is not specified all data lines will produce an x and y value.
 +
                        Some simple perl info:
 +
                          use eq (equal) and ne (not equal) for comparing strings (which are in double quotes).  
 +
                          use ==  !=  >  >=  <= for numeric comparisons. && (logical AND), || (logical OR).
 +
                          put $ in front of all variables (string variables and numeric variables).
 +
                          statements are separated by semicolons.  Blocks specified with braces.
 +
                          if ( ) { }  else { }  where the "else {}" is optional. But don't forget the braces.
  
−
usage:
 
−
  makebeads2rpts.pl makebeads2.out > makebeads2.rpts
 
  
−
options:
+
-unique_header1=something string which uniquely exists on the header line of file1 (so it can be identified)
−
  -oldres=#    :  pixel size used to create makebeads2.out. default = 1nm
+
-data_field1=something which column has the actual data we care about and will graph. default = rate
−
  -newres=#     :  pixel size for makebeads2.rpts
+
        -data_factor1=# multiply data_field value in file 1 by data_factor prior to analyzing (or printing) it.
−
  default is the same size as oldres.
+
-group_by1=something how to match the data, eg, a datapoint in file1 will by matched to a datapt in file2 by this criteria
−
  If newres = oldres, the pixel coords won't change (except for
 
−
  being converted to 1-indexed integers).
 
−
  -project : ignore z value, project all pts onto the first plane
 
−
  -jack=# :  instead of just coords of each pt, produce a jack of the specified integer radius (in pixels)
 
−
  -verbose
 
  
−
+
-cond2 same but for file2, defaults to -cond1
−
===  merge_rpts.pl  ===
+
-unique_header2=something same but for file2. defaults to -unique_header1
 +
-data_field2 same but for file2, defaults to -data_field1
 +
-data_factor2 same but for file2, defaults to 1
 +
-group_by2 same but for file2, defaults to -group_by1
  
−
Takes output from runall.m, which produces a series of rpts files for a data set, where each rpts file is for a
+
-silent don't print warning to stderr when a data pt in one file does not have a match in the other file.
−
different range of z values, and concatenates the paths together.  The result can then be analyzed by paths5.pl.
+
−
Assumes the files passed are already sorted in z (ie, the first file has paths from z = 1 to 500, the next has
 
−
paths from z = 501 to 1000, etc.).
 
  
−
usage:
+
  -debug stuff to stderr
−
  merge_rpts.pl [options]  z1_500_tracks.rpts 2_z501_1000_tracks.rpts z1001_1500_tracks.rpts > all_tracks.rpts
+
    -Debug other stuff to stdout
  
−
  options:
+
  example:  
  
−
  -dx=# how close (in pixels) the paths must be in x to merge (be considered the same path), default = 0.5
+
get_find_vesselness_results.pl  -gdm=014:019 -t2dm=005:020:021 > find_vesselness_results2.txt
−
  -dy=# how close (in pixels)the paths must be in y to merge (be considered the same path), default = 0.5
+
get_dir_results.pl -verbose > raz_results.out
−
  -verbose_merging prints merging info to stderr
+
combine_Raz_and_lml_data.pl -data_factor1=2 -unique_header1=filename -data_field1=pixels_in_mask -group_by1=filename
−
  -vverbose_merging very verbose, prints other into about merging.
+
                      -data_field2=mass -group_by2=imagename find_vesselness_results2.txt raz_results.out > Raz_lml_combined.txt
−
  -verbose_paths
 
−
  -verbose_files
 
−
  -silent
 
  
 
  see also:
 
  see also:
−
/home/lml/krypton/Satoshi/runall.m
+
 
−
/home/lml/krypton/Satoshi/Results/
+
combine_with_Raz_curated_data.pl
−
 
+
compare_data_points.pl
−
note:
+
boxandwhisker2.pl
−
this could probably be easily modified to skip over short gaps in z by defining a -dz and taking out
+
xmgrace --help
−
the test that requires a path to end at the maxz of the file. But it would only skip over gaps exactly at
+
http://plasma-gate.weizmann.ac.il/Grace/doc/UsersGuide.html
−
the end of the files, unless the comparisons are extended to also look at other paths in the same file.
+
/home/lml/krypton/Corvera/Raz/gedmat_dummyhealthr.data
 +
/home/lml/krypton/Corvera/Raz/README 4/2/14
 +
gedmat_to_xy.pl used to produce gedmat_dummyhealthr.data. can also pull out arbitrary rows and columns
  
 
   
 
   
−
===  modtracks.pl  ===
+
===  coords2pts.pl  ===
 +
Converts from coords format produced by track_pts to pts format needed by dave.
 +
Only handles output from track_pts with one object in it right now.
  
−
# takes output rpts from track and modifies it so that format is changed to superimpose on a projection image
+
coords2pts.pl [options] <in.coords   > out.pts
−
# where each time pt is represented by a single (projection) z slice. This lets us view the result for huge time series.
 
−
# original format:
 
−
#    xyzw # time
 
−
# new format:
 
−
#    x y t
 
−
# assumes time coords passed are zero indexed.  
 
  
−
# usage:  modtracks.pl [options] file.rpts > newfile.rpts
+
options:
 +
  -one: add 1 to x,y,z coords (e.g, to go from zero indexed to the one-indexed coords dave expects)
 +
   -name=trackname    the name of the object created. dave wants different objects to have different names.
 +
  -w=# for the w coord (intensity) just use the specified number (dave has problems if the number > 255)
 +
track_pts usually puts the max intensity in the w field.
  
−
  options:
+
Example usage:
−
    -everyplane have each track show up on all z planes (all projections), otherwise
+
  track_pts -tdim 30  green.i2i green_in.coords green_out.coords
−
only part of the track will be visible at each time point.
+
  track_pts -tdim 30  red.i2i  red_in.coords  red_out.coords
−
    -dup duplicate points so a line from t1 to (t1+1) is completely visible
+
  coords2pts.pl -w=1 -one -name=green_track < green_out.coords > green_out.pts
−
in t1 and in t1+1 (otherwise half will appear in t1 and half in t1+1).
+
  coords2pts.pl -w=1 -one -name=red_track < red_out.coords > red_out.pts
−
    -color color the tracks (use play with options: -P -1 R -P -2 G -P -3 B -P -4 C -P -5 Y)
+
  concateima green.i2i red.i2i both.i2i
−
    -tshift=# add # to the time (z) coord of all pts.  
+
  dave -n 0 -u -O -z 1 -4 -I both.i2i green_out.pts red_out.pts
  
−
# example (a1.i2i through a3.i2i are each a 4D time series):
 
−
#    track3dg.linux -a 3 -u .33 .33 .25 5 -h .01 a.vel a1.i2i a2.i2i a3.i2i > a.rpts
 
−
#    modtrack.pl  a.rpts  > amod.rpts
 
−
#    reduceima -sets 10 -P a1.i2i aproj1.i2i
 
−
#    reduceima -sets 8 -P a2.i2i aproj2.i2i
 
−
#    reduceima -sets 11 -P a3.i2i aproj3.i2i
 
−
#    concateima aproj1.i2i aproj2.i2i aproj3.i2i aproj.i2i
 
−
#    addlines aproj.i2i amod.rpts - |play -P -1 R -P -2 G -P -3 B -P -4 C -P -5 Y  -
 
−
 
−
see also:
 
−
trackinfo.pl
 
  
 
   
 
   
−
===  objs2bb.pl  ===
+
===  crosshair2bestpath.pl  ===
 +
  Convert a list of pts produced inside DAVE by using the crosshair and the
 +
  "clear and save stack to file" option, to commandline arguments for
 +
  BestPath3D. May still need to add -t and -f options manually.
 +
  Must also change IMAGE.i2i and IMAGE.rpts args in the output.
  
−
#this program takes the object outputfile produced by countobjs and creates a pts file
+
  crosshair2bestpath.pl [options] crosshair.dat > commandline.txt
−
#from it. Each object in the original file gets turned into a wireframe cube of the bounding box.
 
  
−
#usage:
+
  options:
−
# objs2bb.pl <file.objs >file_bb.pts 
+
    -image=# image name (instead of IMAGE.i2i) written out.
 +
    -rpts=# rpts name written out (instead of IMAGE.rpts)
 +
    -t=# add -t # to options written out written out for BestPath3D
 +
    -f=#:# add -f # # to options written out for BestPath3D
  
−
#example:
 
−
#  countobjs -k -t 2000 2000 -O cs1_4c_c_objs2.i2i cs1_4c_c.objects2 cs1_4c_c.i2i
 
−
#  objs2bb.pl < cs1_4c_c.objects2 > cs1_4c_c_bb.pts
 
−
#  dave -n 0 -u -kptcolor -K -I cs1_4c_c.i2i cs1_4c_c_bb.pts
 
  
 
   
 
   
−
===  path2rpts.pl  ===
+
===  dup_rpts.pl  ===
  
−
This program converts path files as produced by gimp to our standard rpts format.
+
Takes an input file with one z slice per object, and, for each
−
Currently only handles one path, and strips off any identifying name.
+
object named on the command line, duplicates that slice for a
 +
range of z slices. rpts file must be in xy (not xyz) format
  
−
path2rpts.pl [options] infile.path > outfile.rpts
+
dup_rpts.pl -name1=#-# [-name2=#-# ...] < in.rpts  > out.rpts 
 +
or
 +
dup_rpts.pl -name1=#-# [-name2=#-# ...]  in1.rpts [in2.rpts ...]  > out.rpts
  
−
options:
+
example:
−
 
+
  dup_rptsinterp.pl -foo=1-5 -bar=2-8  < in.rpts  > out.rpts
−
-xmgr: output xmgr format instead of rpts format
 
  
 +
  This will take the zslice associated with the object named
 +
  foo and duplicate it into zslices 1 through 5, and duplicate
 +
  object bar into zslices 2-8.
  
 
   
 
   
−
===  pgfocus2.pl  ===
+
===  extract_overlap.pl  ===
−
   
+
  Reformats data from the overlap data produced by closest_object for graphing by xmgrace.
−
===  plotdata.pl  ===
 
  
−
Takes sas output from running proc tpsline (see runtest.sas) and graph it.
+
extract_overlap.pl [options] *.patchdist2 | xmgrace -source stdin
  
−
plotdata.pl output.txt > output.xy
+
  -mstring=im1_im2: : pull out data for fraction of each object in image1 which overlaps with image2 object, default = im2_im1
−
 
+
  You can also specify im1_im1 and im2_im2, in which case overlap is always 0 and the
−
options:
+
  distance (-distance option) is the distance to the nearest other object in the same image.
−
-alldata : tspline putting out all the variables it can (so there are more cols in output.txt that must be parsed)
+
-distance : pull out distance info instead of overlap info
−
-numbins=# : number </