Volume Help

The Volume Display Widget

This widget is only needed if image data has been read in (-I on the dave command line). If more than two images have been read in, see also the Series widget (from the Stuff menu on the Master widget).

The brightness sliders are the primary way one controls how the image data appears. This is similar to the way "edmap" controls the appearance of images displayed with "play". The "Color Square" menu option in the "Edit Volume Display" menu displays a color square which graphically shows how these sliders are affecting the display. This is similar to an "edmap" color bar, but it includes opacity effects and can handle dual wavelength images (hence a square - two dimensions). By default, any voxels which are mapped to 0 by the brightness sliders are transparent, and the brighter the voxel (after being intensity mapped based upon the brightness slider) the more opaque it is. You can change the default opacity mapping by going to the Edit Volume Options widget (from the Edit Volume Display Menu) if you desire. You can also specify a subset of the volume data using the Volume Clipping widget. Alternatively, for sparse images you may want to try Render Cubes, since it has a speedup when less than 50,000 voxels are visible. See below for an explanation of these actions.

RS Slider

This slider controls the relative scale of the red and green images (assuming two images have been specified). Moving the slider towards the red end de-emphasizes the green (thus making things look redder). The CTR button on top centers the slider so the two images are weighted exactly equally. If you want this you should use the CTR button, since when the slider is centered exactly no performance penalty is incurred (since no rescaling is necessary). Note: all slider rescaling occurs AFTER the rescaling performed upon reading in the image data.Thus, once you use the slider to find a good balance between the two images you should probably use that infomation to restart DAVE using the appropriate scale factors (so that extra brightness information won't be thrown away). Note: Since the slider works by de-emphasizing (i.e, making values smaller) it may also change the opacity of the voxel (making it more transparent).

Brightness Sliders

Changes how the image data values are mapped to the display colorscale (like what edmap does). Note: making data values appear brighter will make them more opaque (in the default opacity mode). See the Edit Volume Options widget (gotten from this widget's menu) for more information on opacity. See "Map - Rescale" below for how the remapping of brightness is performed. The arrows on either side of the sliders move the sliders by 1 unit or by 5 units (these are units after the image intensity range has been rescaled 0-255). The "LOCK" button will lock the two sliders together so that the distance between them remains constant (so when one is moved the other moves also). Use "Volume Threshold" from the menu if you want to eliminate bright voxels from the display (rather than settting bright voxels to white).

Res Sliders

The left RES slider selects the resolution at which the volume is drawn when the object is moving. The right RES slider selects the resolution at which the volume is drawn when the image is paused. Zero is the highest resolution and each resolution level is one-half the resolution of the previous level. Level 0 typically can take 10-60 seconds to draw, so you may want to set the right slider to 1 except when you need a nice static image. Note: while a level 0 resolution image is being calculated a "Percent Done" information bar is highlighted in yellow near the top of the Edit Volume widget.

Image 1/Image 2/Image 3 Buttons

These buttons control which image data volumes will be displayed. If more than one mages was read in (eg, -I image1 -I image2 on the command line) then they can all (up to 3) be displayed simultaneously. If an image is selected for display then the circle just to the left of the button text will be filled. The color of the images (either red/green/blue pseudocolor or gray) can be changed via the "False Color" menu toggle in the Edit Volume Options widget. These images can be swapped using the Series widget (from the Stuff menu on the Master widget). When two images are displayed, the third color at each pixel is set to the minimum of the two colors. This prevents new colors from appearing (eg, red+green doesn't produce yellow, but rather a reddish or greenish color depending upon with value is larger. Equal values will produce a gray or white pixel). When all three images are displayed the intensity at each voxel is based upon the brighter two values. These values are displayed the same as when just two images are active. This makes images easier to interpret, but you must remember that you are not seeing any information about the weakest of the 3 colors when all three images are on.

Show Vol. Button

This button must be pressed (which will highlight it) for the volume to be displayed.

HELP Button

The HELP button brings up this help message.

HALT DRAW

Pressing this button will halt the drawing of the current image. This is useful if it seems as if it will take a long time to draw and you decide you don't want to wait, or want to change drawing parameters.

HIDE Button

Removes the Volume widget. You can get it back by choosing "Edit Volume Display" from the Edit menu on the DAVE master widget.

Percent Done 100

This bar displays how much of the image has been rendered so far. This gives the user feedback to estimate how much longer he or she must wait for the to be completed. This display is only active when the display resolution is at level 0. While an image is being rendered the bar is highlighted in yellow and Percent Done specifies how much of the rendering is done.

Hints for Better Viewing

1). When Paused, the image typically switches into Single Buffer mode (see Goodies Menu). This provides for more dynamic range of intensity values which can be displayed. Sometimes dim voxels will be visible in this mode which are not visible while the image is rotating (even if both Paused and Moving resolutions are set to the same value). You may be able to see the dim voxels while the image is moving by turning Dithering on (see the Goodies Menu on the Master Widget).

Edit Volume Display Menu

Volume Clipping

This item pops up a widget which permits the user to specify which subset of the volume data to display. For instance, the z sliders can be set to the same slice to allow examination of one slice at a time. Z-clipping can also be specified. The speed of image update is directly proportional to the size of the volume subset. See the help on this widget for more information.

Render Planes

This is the default rendering mode. The data volume is split into data planes, each of which is then rendered. In this mode THE REGION BETWEEN VOXELS IN A PLANE IS DISPLAYED AS A TRIANGLE whose 3 vertices are colored based upon the value of the 3 voxels it connects. Thus, linear interpolation is performed between voxel values (which are within a data plane). No interpolation is performed between planes (thus you may see slight gaps between the data planes, depending upon the data values and your z spacing). See also the Render Options widget.

Render Cubes

In this rendering mode EACH VOXEL IS DISPLAYED AS A CONSTANT INTENSITY CUBE centered around the voxel's position. This display mode is slower than rendering in planes mode when many voxels are present. However, when fewer than 50,000 voxels are visible this has a speedup mode which makes it quicker than the planes mode. This mode should be particularly useful if you are zoomed way in on a few voxels (or are looking in the snoops window - see "Snoops" under the Goodies menu). See also the Render Options widget.

Render Options

This pops up a widget which provides more rendering options.

Map - Rescale

This controls the mapping performed by the brightness and opacity sliders. This mode means that all values below the left slider are set to 0, all values above the right slider are set to 255, and all values in between are linearly rescaled to go from 0 to 255 (this is the way the sliders in Edmap work by default). This is useful if you want to emphasize data which is originally in a narrow intensity range since it will rescale that range out to 0-255. For example, moving the left brightness slider up will make more and more voxels turn black (0); but it will also cause all other voxels to get dimmer, since their values are now closer to that of the left slider and therefore during the linear rescaling they will get darker than they were. Similarly for the opacity sliders. You can see the mapping being performed by displaying the color square (see above). If you don't want this remapping, choose Map - Threshold (see below).

Map - Threshold

In this mode, all pixel values (brightness or opacity) less than the left slider are set to 0, and all values greater than the right slider are set to 255, but all the other values are not changed at all (this is the way the threshold function in Play works). Thus, as you raise the left brightness slider more and more voxels should become black, but the ones that don't become black should not change at all in intensity. This is useful if you just want to threshold the image. It has the advantage that voxels just above the left slider will remain more visible than when the Rescale mode is used (since their values don't get rescaled to a number close to zero). You can see the mapping being performed by displaying the color square (see above). If you don't want this remapping, choose Map - Rescale (see above).

Map - maxval black

This mode (which can be set with either of the above modes) sets everything above the right brightness slider to black (transparent). It modifies the operation of Map-Threshold and Map-Rescale. Combining this option with the Map - Threshold option displays just those voxels which are between the values specified by the two brightness sliders.

Color Square

This menu item pops up a Color Square window. This color square graphically shows how the Opacity, Brightness, and ABS/REL sliders affect the display. This is similar in concept to an "edmap" color bar. One axis of the color square is for one image and runs from 0 on the bottom to 255 at the top (all image data is rescaled 0-255 when read in). The other axis goes from 0 to 255 from left to right for the second image. Thus any point inside the square shows how a voxel with the specified values for image 1 and image 2 would appear. If the ABS and REL sliders are not at 0 then the color square itself may change in appearance due to fidelity/speed tradeoffs. Also if Dithering is chosen from the Goodies menu on the DAVE master widget then that will change the appearance of the color square in the same manner it will change the view in the viewing window. The display of the color square will slow down the image update rate whenever the Opacity, Brightness, or ABS/REL sliders are changed. As long as they are not changed there is no penalty for leaving the square displayed. The color square MUST be removed by picking the color square menu item again. Do NOT use the "quit" item from the window menu!

Color Square (no border)

The same as above, but no border is present so the color square looks better if you are taking slides.

Edit Volume Options

This pops up a widget which allows additional control of the display. It has a menu options for making voxels totally opaque or for manual control of the opacity mapping function. It lets you display one image (of a dual labelled set) in gray scale. It has a "Play" mode. See it for details of these and other options.

Opacity = Brightness

This is probably the most useful preset. It simply means that the opacity of a voxel will depend upon its visible brightness. Brighter voxels are more opaque. Totally black voxels are totally transparent.

Opaque Data

This is similar to "Opacity = Brightness" except that any voxel which is not totally black will be totally opaque. You should probably only use this when the Map-Threshold option is set (see the menu in the Edit Volume Widget) since otherwise dim (but not totally black) voxels will be totally opaque (and hence you will see a lot of black voxels). Also, the left brightness slider should probably be moved up so that a large fraction of voxels are set to 0 (and hence are totally transparent) since otherwise the image volume won't be very sparse and all of the totally opaque voxels will block your view into the interior of the image.

Max Projection

In this mode, the data is drawn back to front (where "back" is the data furthest from the viewer in the current orientation). If new data at a pixel is brighter than the current value at the pixel the new data value either replaces the current value (if Opaque Data rendering is chosen) or else a weighted combination of the new value and the currently stored value (where the brighter the new value the more it is weighted, i.e. the more opaque it is) replaces the stored value (if Opacity = Brightness is chosen). When Opaque Data is chosen the resulting image is similar to the way view3d normally displays volume data. Note: the background color of window also counts in all of these comparisons, so it should probably be set to black when you are in this mode. Also, we currently seem to get a few black pixels here and there; this may be dependent upon the size and position of the image on the screen. Let us know if this is a problem.

Custom Colormap

If you want to display your voxel data volume using a custom colormap (instead of the gray, green, and red colormaps provided as defaults), choose this option. This option, by default, assumes that you have loaded your custom colormap (using Load Map from the Goodies menu on the Master widget) into colormap 15. If you have loaded your colormap into a different map, you should also pick "Custom Volume Colormap" from the Edit Volume Options menu. It lets you type in a different map number. The custom colormap can be rescaled as usual by moving the brightness sliders. If more than 1 image is being rendered, it is assumed the custom colormap applies to the second image. Voxels which have nonzero values in both images, will be colored as if the first image did not exist. In other words, the custom colormap takes precedence, so the colored objects remain visible. If you want to switch image 1 with image 2 see the Series widget (from the Stuff menu on the Master Widget). If you want the first image to be gray instead of green see the "False Color" menu item from the Edit Volume Options widget.

Volume to Surface

This widget takes the data from Image 1 as currently displayed and converts it into a bunch of objects described by their surfaces (instead of by voxels). So, at the boundary between background and foreground voxels (as specified by the left brightness slider) a surface is created. The volume clipping sliders control which surfaces you will see. These surfaces have "shading". The surfaces can be displayed in a wireframe outline or as a solid surface. Note: if you want to apply this to image 2, you can use the Series widget (see the Stuff menu on the Master Widget) to swap image 1 with image 2.

Volume Debugging

This pops up a widget primarily used for debugging purposes. It gives performance statistics. It also can force particular planes (e.g., XY planes, YZ planes or XZ planes) of the data to be displayed. See it for more details. This widget also allows "z-buffer" images to be written to disk. These images can be converted in single image random dot stereograms for 3D prints from the laser printer.

Volume Threshold...

This pops up a widget to allow you to clip out both dim AND bright voxels from the image display (the Brightness slider on the Edit Volume widget has no way to eliminate structures which are too bright from the display).