MINC/Tutorials/PythonSliceLoop

A slice loop example using pyminc When you open a volume in pyminc, none of the data is read until you access the .data variable. This means that you can open lots of volumes at the same time, and then selectively get a hyperslab out in order to conserve memory. The example below reads a bunch of volumes to find the mode (most common voxel) at every point - a simplistic voxel voting scheme for segmentation. A few comments are in the text, more explanation follows: #!/usr/bin/env python # all the imports go here from pyminc.volumes.factory import * from numpy import * from scipy.stats import * from optparse import OptionParser if __name__ == "__main__": # some argument handling usage = "Usage text" description = "Description text" parser = OptionParser(usage=usage, description=description) parser.add_option("--clobber", dest="clobber", help="clobber output file", type="string") (options, args) = parser.parse_args() if len(args) < 4: parser.error("Incorrect number of arguments") outfilename = args[-1] propfilename = args[-2] # clobber check should go here # create an array of volume handles volhandles = [] nfiles = len(args)-2 for i in range( nfiles ): volhandles.append(volumeFromFile(args[i], dtype='ubyte')) outfile = volumeFromInstance(volhandles[0], outfilename) proportion = volumeFromInstance(volhandles[0], propfilename) # hold one slice from all volumes sliceArray = zeros( (nfiles, volhandles[0].sizes[1], volhandles[0].sizes[2])) # now loop over the slices to get on slice at a time from all volumes - then take the mode for i in range(volhandles[0].sizes[0]): print "SLICE: %i" % i for j in range(nfiles): t = volhandles[j].getHyperslab((i,0,0), (1,volhandles[0].sizes[1], volhandles[0].sizes[2])) t.shape = (volhandles[0].sizes[1], volhandles[0].sizes[2]) sliceArray[j::] = t # take the mode m = mode(sliceArray) # and write the mode and its proportion to the output files outfile.data[i::] = m[0] proportion.data[i::] = m[1] / nfiles proportion.writeFile() proportion.closeVolume() outfile.writeFile() outfile.closeVolume() The key steps in this slice loop is to create an array of all the MINC volume handles, an an array which holds one slice for all volumes, and then to loop over all slices. At every slice the array is refilled with the current slice from each volume, the stat (mode in this case) is computed, and the results inserted into the output volumes.