teem	/	nrrd	/	Visible Female	Inspection

The individual slices are 2048x1216, with non-interleaved color, and compressed with Unix "compress". Currently, nrrd has no "compress"-compatible encoding; the gzip and bzip2 encodings in nrrd only handle those specific compression methods. Perhaps confusingly, the similarly named command-line tools (gzip, bzip2) automatically detect and handle multiple compression types. However, we can use zcat to uncompress the data, and then pipe this to unu make.

The following sequence can be used to inspect any one of the slices with xv, avf1100a is just an example. The image viewer doesn't have to be xv; it just needs to be able to take PPM images on stdin and display them.

zcat data/avf1100a.raw.Z \
  | unu make -i - -t uchar -s 2048 1216 3 -e raw \
  | unu permute -p 2 0 1 \
  | unu save -f pnm | xv -

• unu make ... The data is raw unsigned chars, so we use "-t uchar" and "-e raw". Because the colors are not interleaved, the image values consist of three 8-bit images in succession, first for red, then green, then blue. That means that the axis ordering is (X,Y,RGB), and this is the ordering of the axis sizes given to "-s".
• unu permute ... Most image formats make the colors the fastest axis, not the slowest axis, so we need to re-arrange the axes. The numbers here give the new ordering of the old axes. What was axis 2 (color, the third axis) is now the first axis, going from (X,Y,RGB) to (RGB,X,Y).
• unu save ... This puts the data into PNM format (instead of the default NRRD format) and passes it on to xv for display.

In many of the following examples, an image will be saved to PNG file with ImageMagick's "convert" program, via

 ... | unu save -f pnm | convert PNM:- blah.png

alias topng "unu save -f pnm | convert PNM:- "

zcat data/avf1100a.raw.Z \
  | unu make -i - -t uchar -s 2048 1216 3 -e raw \
  | unu resample -k cubic:0,0.5 -s x0.2 x0.2 = \
  | unu permute -p 2 0 1 | topng doc/avf1100a.th.png

• unu resample ... This does axis-aligned resampling with the given kernel, "-k cubic:0,0.5", a particular member of the Mitchell/Netravali BC-family of cubic kernels (B=0,C=0.5), better known as the Catmull-Rom kernel. We only want to downsample in the spatial axes X and Y by a factor of 0.2, which is signified to "-s" by "x0.2" for axis 0 and 1. However, we don't want to do anything between the colors; axis 2 should be left just as it is. This is signified to "-s" by "=".

Inspecting slices in this manner allows one to see that the shoulders begin around slice avf1215a:

zcat data/avf1215a.raw.Z \
  | unu make -i - -t uchar -s 2048 1216 3 -e raw \
  | unu resample -k cubic:0,0.5 -s x0.2 x0.2 = \
  | unu permute -p 2 0 1 | topng doc/avf1215a.th.png