Write Image Widget Help

This widget lets you save 2D or 3D images. It lets you save "what you see" into an image file. This means that all of the intensity and opacity transformations done to the volume data are similarly applied before the image is saved. In addition, if the colocalization widget is active, then its transformations apply also. Opacity information is ignored except that voxels which are totally transparent are saved as zero intensity voxels regardless of their current intensity (since you don't see them). The file name to save the image as should include any desired extensions (e.g., i2i). By default a 2D color snapshot of the main window will be saved in Silicon Graphics' rgb format (if on an SGI), or a PPM image (if on a Linux system). If you want a different selection go to the Save Image Menu.

Save Button

Saves the image specified in the format specified to the filename specified. All these things must be specified prior to pressing this button.

Save As.. Button

The same as the Save button but prompts for a filename.

Options available on the Save Image Options Widget

This widget is gotten by choosing "Snapshot Options" from the Save Image Menu. The type of image to save is specified from the first drop-down list and allowed formats for that type of image are specified in the second drop-down list. SGI computers can save in different formats than the Linux computers.

DESCRIPTIONS OF THE TYPES OF IMAGES WHICH CAN BE SAVED

Main Display

This saves the 2D image which is currently seen in the main Display window. If you want to preserve the colors, you must choose an image type which is capable of that (SGI: sgi-rgb or i2i-rgb, Linux: PPM or PNG). Note: if anything is covering up part of the main display window it too will be saved.

Snoops Display

This saves the 2D image which is currently seen in the Snoops window. If you want to preserve the colors, you must choose an image type which is capable of that.

Image 1

Save the values in image 1 as a 3D image. SGI formats cannot be used with this (they are 2D). If i2i-rgb is chosen as the image type the red, green, and blue components are all set to the same value so the image will appear gray (if you want a gray image you should probably pick i2i rather than i2i-rgb). When you save a 3D image, only volume data is saved. Any surfaces or wireframe structures in the image are not saved. Similarly any objects added to the scene (via Edit Other Objects) will not be saved (see Write Objects... to do this). An alternative to saving a 3D image is to use Write Configuration... from the File menu to to save your current orientation and slider settings. This takes much less room than saving an image file and saves your orientation (which this does not do).

Image 2

The same as the Image 1 button except for Image 2 values.

Image 1 and Image 2

This saves a combined images (similar to what you see in DAVE). This should usually be used to save 3D color images in i2i-rgb format.

rescale image/do not rescale image

If Rescale has been set then the image data will be scaled back up into its original data range before it is saved. This approximately reverses the effect of the scale and black level calculations. This usually means that one byte is no longer sufficient to represent the values in each voxel.

DESCRIPTIONS OF THE IMAGE FORMATS

The images can be saved in one of several different image formats.

sgi-rgb

This is a 2D color format. It can be displayed using ipaste. Since it is 2D it can only be used to save the Display or the Snoops Display. It uses 3 bytes per voxel, but it should be doing some run-length encoding (compression) automatically. Silicon Graphics programs should handle sgi-rgb format. Only available on SGI computers.

sgi-bw

This is a 2D grayscale format. It can be displayed using ipaste. Since it is 2D it can only be used to save the Display or the Snoops Display. The color image is turned into grayscale ("black-and-white", hence the bw extension) by weighting the Green component by approximately .6, the Red by .3 and the Blue by .1. There is some pyschophysical justification for this. This uses one byte per voxel and also does run-length encoding automatically. Only available on SGI computers.

i2i - rgb

This is the UMASS rgb "format". A 2D or 3D image can be saved in this format. Not all UMASS programs can handle this image format. play_rgb can display these images. Header information is added to explain how to display these images. This preserves the color information. It is the way to save a 3D color image (alternatively you could save image1 and image2 as separate 3D grayscale images and then recombine them in DAVE to get color again). Choose "Image 1 and 2" in conjunction with this to save color information as shown in DAVE (blue is set to the minimum of the two values, just as it is in DAVE). If only "Image 1" or "Image 2" is chosen, then the same voxel values are stored in red, green, and blue so the picture will look gray and you'll be wasting space (if you want a gray image you should be picking a gray image format). This format "doubles" the x dimension of the image, each voxel is saved as two adjacent (2 byte) values. Red, green, blue, and zero are stored in these four bytes. Only available on SGI computers.

i2i

This is the standard UMASS image format. It can save either a 2D image (if Display or Snoops Display is chosen) or a 3D image - either image 1 or image 2 values. If the image is in color it is converted to grayscale using the same formula as sgi-bw uses. Header information is added to explain how to display these images. This uses 2 bytes to store each voxel value. You might want to use this because most of our programs know how to handle it. Also if you pick "Rescale" you may need the extra space to store the voxel values. Only available on SGI computers.

i2i - 1 byte

This is the UMASS one byte format. Since all data for image1 and image2 is stored internally by DAVE with only one byte per voxel, this format looses no information if you want to save a 3D volume based upon image1 or image2 values. Not all UMASS programs can handle this image format. Playexact can display these images. Header information is added to explain how to display these images. This is not a good choice if you have picked "Rescale" since the values will probably be larger than one byte can hold (255) once they are rescaled. A 2D or 3D image can be saved in this format. Only available on SGI computers.

i2i - float

This is the UMASS float format. A 2D or 3D image can be saved in this format. Not all UMASS programs can handle this image format. Playexact can display these images. Header information is added to explain how to display these images. This format uses 4 bytes per voxel. Only available on SGI computers.

PPM

Portable Pixel Map (?). Available on Linux computers.

PNG

Portable Network Graphics. Available on Linux computers.