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Velocity: Read Data

1. Getting Started
2. The Bottle
3. The Pelvis
4. Creating Data Files
5. Creating Info Files

Getting Started

Copy the workshop data files to the local scratch disk on i7 by entering the following at the % prompt:

cd /scratch.i7
mkdir username
cd username
cp /usr/velocity/images/Bottle/* .
cp /usr/velocity/images/Pelvis/* .

Three windows will open: a control panel, an image display window, and a filmstrip window. You will first use the Image program to process the water bottle image files.

The Bottle

The water bottle image data have x, y pixel dimensions of 0.234 x 0.234 inches. These values, and the Z-values of each image that are specified in the data sets info file, ultimately determine the x, y, z scaling of the 3D model.

Select the Open item from the File menu, or click on the Open folder icon to pop-up the File Chooser dialog.
 

The Pelvis

A set of CT scan data of the pelvic bones in a young individual who has congenital hip dysplasia. The data illustrate some of the difficulties that can be encountered with medical scans: (1) There are artifacts present, including in this case a table pad, that must be eliminated; and, (2) Average gray values slowly vary across the image set.

Run the Image program and open the file pelvis. info file in the directory /scratch.i7/username.  Scroll through the image set using the filmstrip and examine each image. There should be 46 image slices.

Creating Data Files

1.  TIFF Format Images

TIFF format images are available with several applications.  If your data is in this format, then you are done.  If your data is in another image format, then use an application like photoshop or xv to convert your images to tiff.

As an example, I can grab part of my desk top background using snapshot on an SGI workstation.

snapshot

xv snap.rgb

Save the image as a TIFF format image.

2. Binary Files

For binary files containing more than one slice, or slices with header information, this header information must be removed and the slices seperated.  The following command is used for this purpose:

/usr/velocity/bin/vunpack -x 512 -y 512 -n 1 -e 2 -s -o 512 -v file f

vunpack

Synopsis:

vunpack -x xsize -y ysize [-b image] [-n number] [-d delta] ...
... [-e esize] [-s] [-i] [-o offset] [-v] input output

where:

-x xsize X-dimension (number of samples per line) of a single image slice.
-y ysize Y-dimension (number of lines) of a single image slice.
-b image Beginning image number, 1 being first (Default is 1).
-n number Number of images to extract (Default is 1).
-d delta Number of images to skip. If delta is greater than 1 then delta images are skipped between sampled images beginning after the first sampled image. This option is provided to sample data such as seismic data which has repeating images. (Default is 0).
-e esize Size of the data value, 1 = byte, 2 = short integer, 4 = long integer (Default is 1).
-s Swap input data bytes (Default is no swapping).
-i Optionally resample output image to 512x512 using bicubic interpolation.
-o offset Byte offset into input file to first slice (Default is 0).
-v Turns on verbose mode.

Files:

input Name of the input file.
output Prefix name for the output file(s). Images are written to headerless files with names of the form prefix001, prefix002, etc.

To then transfer the binary file into an image file Velocity can read, use the following command:

/usr/velocity/bin/bin2v -h 0 -s 512 -l 512 -x 18.0 -y 18.0 -b 8 -z 14400.0 -f 0 f001 b001.img

bin2v

Converts fixed format, image data to Velocity 2 Pro .img image format. Any size of gray level image having a fixed-length header and pixel depth of 8, 16 or 32 bits can be accommodated.  bin2v also has a special feature for extracting even and odd fields from interlaced video images, such as might be derived from videotape data. This is useful when the image data are of moving objects and helps to reduce motion blur.

Synopsis:

bin2v [-h size -s samples -l lines -x pixel_x -y pixel y
-b pixel_depth -z zvalue -f field] [-i] [-r] input output

where the options are:

-h size Size of any preexisting header. The preexisting header will be removed and replaced with a .img format header.
-s samples Number of samples per line in the input.
-l lines Total number of lines in the input.
-x pixel_x X-dimension of a pixel.
-y pixel_y Y-dimension of a pixel.
-b pixel_depth Number of bits per pixel. Must be one of 8, 16 or 32. Default is 8.
-z zvalue Z value of the image.
-f field Field number. This option applies to interlaced video image data. A field number of 1 selects all the odd lines for output while a field number of
2 selects the even lines. The resultant output image will have one-half the number of input lines unless image resampling is elected (option -i).  Default is to convert entire image.
-i Optionally resample image to 512x512 using bicubic interpolation.
-r Optionally remove the input image file after conversion.

If any of the options hslxybz are missing, the program prompts for input.

Files:

input Name of the fixed format input image file.
output Name for the .img format output image file.

Creating Info Files

Example:

i000.tif        0
i001.tif        5
i002.tif        10
i003.tif        15
i004.tif        20
i005.tif        25
i006.tif        30
i007.tif        35
i008.tif        40
i009.tif        45
i010.tif        50
i011.tif        55
i012.tif        60
i013.tif        65
i014.tif        70
i015.tif        75
i016.tif        80
i017.tif        85
i018.tif        90
i019.tif        95
i020.tif        100