Merge branch 'develop' of github.com:mfriedel/minc-stuffs into develop

NEWS

@@ -1,3 +1,16 @@
+New in Version 0.1.14
+=====================
+* completely remove the multiprocessing machinery from pmincaverage since this caused extra processes
+  to be spawned even when running single-threaded, causing large memory usage to be attributed to
+  running pmincaverage instances.  If necessary, this machinery could be reinstated
+  behind some conditional logic.
+* small upgrades to voxel_vote: better help messages and argument parsing, 
+  ability to vote on a single file, small code improvements, --(no-)clobber respected
+* sge_batch has been removed; use pipetone/qbatch instead
+* atlas_to_atlas.pl has been added, though use of Pydpiper's MAGeT.py is recommended in general
+* tagtoxfm and some supporting code have been added to allow their use in environments without
+  a build of the visual tools from minc-toolkit
+
 New in Version 0.1.13
 =====================
 * code changes to ensure python3 compatibility

perl/Makefile.am

@@ -1,4 +1,4 @@
-bin_SCRIPTS = lin_from_nlin scale_voxels add_noise_to_volume grid_object_manipulator ray_trace_crosshair concatenate_tags sge_batch
+bin_SCRIPTS = lin_from_nlin scale_voxels add_noise_to_volume grid_object_manipulator ray_trace_crosshair concatenate_tags
 
 grid_object_manipulator: grid_object_manipulator
 	sed < $< > $@-t \

python/pmincaverage

@@ -5,7 +5,10 @@ from numpy import *
 from argparse import ArgumentParser
 import os.path
 import sys
-import multiprocessing as mp
+try:
+    import queue
+except:
+    import Queue as queue
 
 def getslice(volhandle, slice, q,nslices):
     """collects hyperslabs for a particular volume handle. Designed to
@@ -77,8 +80,6 @@ if __name__ == "__main__":
                              volhandles[0].sizes[3]))
 
     # loop over all slices
-    p = mp.Pool(processes=1)
-    manager = mp.Manager()
     for i in range(0,volhandles[0].sizes[sliceIndex],nslices):
         # last set might have less than n-slices - adjust.
         if (i + nslices) > volhandles[0].sizes[sliceIndex]:
@@ -93,14 +94,12 @@ if __name__ == "__main__":
                                      nslices,
                                      volhandles[0].sizes[2],
                                      volhandles[0].sizes[3]))
-
+
+        # without multiprocessing, this queueing stuff probably doesn't make sense -- simplify
         print("SLICE: %i" % i)
-        # use parallel processing to get the slice data
-        q = manager.Queue()
+        q = queue.Queue()
         for j in range(nfiles):
-            t = p.apply_async(getslice, (j,i,q,nslices))
-
-        t.get() # seems to be necessary as a sort of waitpid call ...
+            t = getslice(j,i,q,nslices)
 
         # retrieve the data from the queue
         while not q.empty():

python/replace_label_with_nearest_valid_label

@@ -3,13 +3,15 @@
 
 from pyminc.volumes.factory import *
 import numpy as np
+import scipy.stats as scipy_stats
 from optparse import OptionParser
 import os
 import os.path
-import cython_functions
 import datetime as datetime
 import sys
 
+SDTYPE = np.uint16
+
 ################################################################################
 ################################################################################
 ################################################################################
@@ -27,6 +29,75 @@ def is_minc_2_file(filename):
 ################################################################################
 ################################################################################
 ################################################################################
+
+#
+# This function takes an input data structure which
+# contains label values and a list of unwanted/undesired
+# labels. The output data structure contains the input
+# labels where the unwanted/undesired labels have been
+# replaced by the closest valid label as follows:
+#
+# For an unwanted label:
+#
+# 1) all 26 neighbors of a voxel are considered to have
+#    the same distance. If 1 or more of these 26 
+#    neighbors has a valid label (not 0, nor one of the
+#    values in the unwanted list), it will be used
+#    to re-label the unwanted label (using the 
+#    most occuring label)
+#
+# Input:  inlabels,       the current set of labels
+#         outlables,      a copy of the current set of labels, to be edited
+#         unwantedlabels, an array containing the labels numbers that need to be replaced
+#
+# Output: the function will return the number of labels that could not be replaced,
+#         and outlabels will be updated as described above
+# 
+def substitute_labels_using_26_nearest_neighbors(labels,
+                                                 outlabels,
+                                                 unwantedlabels):
+
+  # make sure that the input files have the appropriate types:
+  assert inlabels.dtype == SDTYPE and outlabels.dtype == SDTYPE and unwantedlabels.dtype == SDTYPE
+
+  # get dimension information from the minc volume
+  nv0 = inlabels.shape[0]
+  nv1 = inlabels.shape[1]
+  nv2 = inlabels.shape[2]
+
+  # the number of unwanted labels
+  nlabels = unwantedlabels.shape[0]
+
+  # number of unwanted labels that could not be replaced using its 26 neighbors
+  nunresolved = 0
+
+  # from each dimension exclude the first and last element, because these have
+  # a number of undefined neighbors: the ones that fall outside of the file
+  for v0 in range(1, nv0 - 1):
+    for v1 in range(1, nv1 - 1):
+      for v2 in range(1, nv2 - 1):
+        # first check whether this label value should be replaced
+        if( np.rint(inlabels[v0,v1,v2]) in unwantedlabels):
+          # create array of possible substitues
+          possible_labels = []
+          # we can safely look at all 27 voxels in the 3*3 block, because
+          # the voxel in question will not be added to the list of 
+          # possible labels
+          for i0 in (v0-1, v0, v0+1):
+            for i1 in (v1-1, v1, v1+1):
+              for i2 in (v2-1, v2, v2+1):
+                if( not(np.rint(inlabels[i0,i1,i2]) == 0) and not(np.rint(inlabels[i0,i1,i2]) in unwantedlabels)):
+                  possible_labels.append(np.rint(inlabels[i0,i1,i2]))
+          # potentially we did not find any valid substitues
+          if len(possible_labels) == 0:
+            nunresolved += 1
+          else: # we have candidates, simply take the most occuring label number
+            outlabels[v0,v1,v2] = np.rint(scipy_stats.mode(possible_labels)[0])
+
+  return nunresolved
+
+
+
 if __name__ == "__main__":
 
   usage = "usage: %prog [options] input_labels.mnc updated_labels.mnc\n"
@@ -94,13 +165,13 @@ only desired label numbers.\n"""
   array_undesired_labels = np.fromstring(options.undesired_labels, dtype=np.uint16, sep=',')
 
   previous_unresolved = -1
-  current_unresolved = cython_functions.substitute_labels_using_26_nearest_neighbors(inlabels.data, outlabels.data, array_undesired_labels)
+  current_unresolved = substitute_labels_using_26_nearest_neighbors(inlabels.data, outlabels.data, array_undesired_labels)
   if(options.verbose):
     print("Number of unresolved labels: %f \n" % (current_unresolved))
   while( current_unresolved > 0 and not(previous_unresolved == current_unresolved)):
     previous_unresolved = current_unresolved
     copy_of_data = outlabels.data[::]
-    current_unresolved = cython_functions.substitute_labels_using_26_nearest_neighbors(copy_of_data, outlabels.data, array_undesired_labels)
+    current_unresolved = substitute_labels_using_26_nearest_neighbors(copy_of_data, outlabels.data, array_undesired_labels)
     if(options.verbose):
       print("Number of unresolved labels: %f \n" % (current_unresolved))
 
@@ -181,4 +252,4 @@ only desired label numbers.\n"""
       #####ndx = distance.argsort()                                                # indirect sort
       #####print("Current point <%s> " % (point))
       #####print("closest point <%s> " % (label_coordinates[ndx[:1]]))
-    #####label_iterator_main.iternext()
+    #####label_iterator_main.iternext()

setup.py

@@ -1,19 +1,11 @@
 #!/usr/bin/env python
 
 from setuptools import setup
-from distutils.extension import Extension
-from Cython.Distutils import build_ext
-import numpy
 
-# setuptools DWIM monkey-patch madness
-# http://mail.python.org/pipermail/distutils-sig/2007-September/thread.html#8204
 import sys
-if 'setuptools.extension' in sys.modules:
-    m = sys.modules['setuptools.extension']
-    m.Extension.__dict__ = m._Extension.__dict__
 
 setup(name="python-stuffs",
-      version='0.1.13',
+      version='0.1.14',
       scripts=["python/TFCE",
                "python/smooth_vector",
                "python/measure_xcorr",
@@ -23,8 +15,6 @@
                "python/volumes_from_labels_only",
                "python/voxel_vote",
                "python/replace_label_with_nearest_valid_label",
-               "python/rotational_minctracc.py",
-               "minc-scripts-jscholz/vtk_meshconvert.py"],
-      cmdclass = {'build_ext': build_ext},
-      ext_modules = [Extension("cython_functions", ["python/cython_functions.pyx"], include_dirs=[numpy.get_include()])]
+               "python/rotational_minctracc.py"]
+      #         "minc-scripts-jscholz/vtk_meshconvert.py"],
       )

src/Makefile.am

@@ -1,7 +1,9 @@
-bin_PROGRAMS = minc_displacement label_volumes_from_jacobians xfm2tag compute_counts_for_labels
+bin_PROGRAMS = minc_displacement label_volumes_from_jacobians xfm2tag compute_counts_for_labels tagtoxfm
 
 minc_displacement_SOURCES = minc_displacement.c
 label_volumes_from_jacobians_SOURCES = label_volumes_from_jacobians.c
 xfm2tag_SOURCES = xfm2tag.c
 compute_counts_for_labels_SOURCES= compute_counts_for_labels.c
+tagtoxfm_SOURCES = tagtoxfm.c tagtoxfm.h ParseArgv.c ParseArgv.h
+