Merge branch 'release-0.1.19'

NEWS

@@ -1,3 +1,22 @@
+New in Version 0.1.19
+=====================
+* added script: make_xfm_for_grid.pl which creates an xfm file for a provided deformation grid
+  (vector file)
+
+New in Version 0.1.18
+=====================
+* 2to3 fixes
+* fix `install_requires` in setup.py
+
+New in Version 0.1.17
+=====================
+* fix bug in TFCE implementation
+* fix linking on OS X
+
+New in Version 0.1.16
+=====================
+* fix compilation against static HDF5 libs
+
 New in Version 0.1.15
 =====================
 * fairly big overhaul of rotational_minctracc.py: it turns out that the centre of gravity (cog)

m4/mni_REQUIRE_MNILIBS.m4

@@ -8,6 +8,7 @@ AC_DEFUN([mni_REQUIRE_MINC],
     mni_REQUIRE_LIB(netcdf,[#include <netcdf.h>],[int i = ncopen("",0);])
     if test "$with_minc2" = "yes"; then
         mni_REQUIRE_LIB(z,[#include <zlib.h>],[int f = compress2;])
+        mni_REQUIRE_LIB(dl,[#include <dlfcn.h>],[int f = dlopen("",0)])
         mni_REQUIRE_LIB(hdf5,[#include <hdf5.h>],[int f = H5Fopen("",0,H5P_DEFAULT);])
         mni_REQUIRE_LIB(minc2,[#include <minc.h>],[int i = miicv_create();])
         AC_DEFINE([MINC2], 1, [Define if should build with MINC 2.0])

m4/smr_WITH_BUILD_PATH.m4

@@ -22,7 +22,7 @@ AC_DEFUN([smr_WITH_BUILD_PATH],
 	for d in `echo $withval | tr : ' '`; do
             test -d $d || AC_MSG_ERROR([build path $d not found.])
 	    test -d $d/include && CPPFLAGS="$CPPFLAGS -I$d/include"
-	    test -d $d/lib && LDFLAGS="$LDFLAGS -L$d/lib"
+	    test -d $d/lib && LDFLAGS="$LDFLAGS -L$d/lib -Wl,-rpath,$d/lib"
 	done
     ])
 ])

perl/make_xfm_for_grid.pl

@@ -0,0 +1,47 @@
+#!/usr/bin/perl
+
+# generates an xfm file for a provided grid file
+
+use strict;
+use warnings;
+
+use File::Spec;
+use MNI::Startup;
+use Getopt::Tabular;
+use MNI::Spawn;
+use MNI::FileUtilities qw(test_file check_output_dirs);
+
+my $usage = "
+
+$0 [options] deformation_grid.mnc output_xfm_for_grid.xfm\n";
+
+
+# handle arguments
+my @left_over_args;
+my @arg_table = 
+    ( @DefaultArgs,
+    );
+
+GetOptions(\@arg_table, \@ARGV, \@left_over_args) or die "\n";
+
+
+my $deformation_grid = shift @left_over_args or die $usage;
+my $output_xfm = shift @left_over_args or die $usage;
+
+if(-f $output_xfm and not $Clobber) {
+  die "Error: output xfm file already exists and -clobber not specified: $output_xfm.\n";
+}
+
+if(not -f $deformation_grid){
+  die "Error: deformation grid does not exist: $deformation_grid.\n";
+}
+
+# save the realpath to the grid, otherwise it won't necessarily work
+my $deformation_grid_abs_path = File::Spec->rel2abs( $deformation_grid );
+
+# write to the output
+open(OUTPUT, "> $output_xfm");
+print OUTPUT "MNI Transform File\n";
+print OUTPUT "% created by $0 with grid $deformation_grid\n";
+print OUTPUT "Transform_Type = Grid_Transform;\n";
+print OUTPUT "Displacement_Volume = $deformation_grid_abs_path;\n";

python/TFCE

@@ -5,9 +5,10 @@ from pyminc.volumes.factory import *
 from scipy import ndimage, weave
 from numpy import *
 import operator
+from functools import reduce
 
 
-def tfce(invol, outvol, dh=0.1, E=0.5, H=2.0):
+def tfce(invol, outvol, dh=0.1, E=0.5, H=2.0, negative = False):
     #infile = "1.mnc"
     #out = "1-tfce.mnc"
 
@@ -26,24 +27,28 @@ def tfce(invol, outvol, dh=0.1, E=0.5, H=2.0):
 
         # connected components labelling
         l = ndimage.label(thresh)
-        print "L:", l[1]
+        print("L:", l[1])
         # compute the size of each label
-        sizes = array(ndimage.sum(thresh, l[0], range(l[1]+1)))
+        sizes = array(ndimage.sum(thresh, l[0], list(range(l[1]+1))))
         # modulate label size by voxel volume
         sizes = sizes * reduce(operator.mul, invol.separations)
-        print "sizes", sizes.shape
+        print("sizes", sizes.shape)
 
         # compute TFCE
         if l[1] > 0:
-            print "inside", h, l[1]
+            print("inside", h, l[1])
             code = """
             for (int x=0; x < nx; ++x) {
                for (int y=0; y < ny; ++y) {
                   for (int z=0; z < nz; ++z) {
                      if (labeled(x,y,z) > 0) {
                         int e = labeled(x,y,z);
                         //std::cout << data(x,y,z) << " " << h << " " << sizes(e) << std::endl;
-                        data(x,y,z) = data(x,y,z) + (pow(h, H) * pow(sizes(e), E) * dh);
+                        if(negative == 1){
+                          data(x,y,z) = data(x,y,z) - (pow(h, H) * pow(sizes(e), E) * dh);
+                        } else {
+                          data(x,y,z) = data(x,y,z) + (pow(h, H) * pow(sizes(e), E) * dh);
+                        }
                         //data(x,y,z) = n;
             }}}}
             """
@@ -52,11 +57,11 @@ def tfce(invol, outvol, dh=0.1, E=0.5, H=2.0):
             labeled = l[0]
 
             weave.inline(code, ['data', 'nx', 'ny', 'nz', 'labeled', 'h',
-                                'H', 'E', 'sizes', 'dh'],
+                                'H', 'E', 'sizes', 'dh', 'negative'],
                          type_converters=weave.converters.blitz,
                          compiler='gcc')
 
-        print h
+        print(h)
     #outvol.writeFile()
     #outvol.closeVolume()
 
@@ -101,8 +106,8 @@ Smith and Nichols. Threshold-free cluster enhancement: addressing problems of sm
         tfce(invol, outvol, options.dh, options.E, options.H)
     if options.pos_and_neg == "both" or options.pos_and_neg == "neg":
         invol.data = invol.data * -1
-        tfce(invol, outvol, options.dh, options.E, options.H)
+        tfce(invol, outvol, options.dh, options.E, options.H, negative = True)
 
     outvol.writeFile()
     outvol.closeVolume()
-
+

python/measure_xcorr

@@ -46,7 +46,7 @@ if __name__ == "__main__":
 
     result = compute_xcorr(sourcevol, targetvol, options.mask)
 
-    print result
+    print(result)
 
 
 

python/rotational_minctracc.py

@@ -11,6 +11,7 @@
 import shutil
 import subprocess
 import sys
+import math
 
 
 def get_tempfile(suffix):
@@ -115,6 +116,23 @@ def compute_xcorr(sourcefile, targetvol, maskvol):
     f3 = 0
 
     if maskvol is not None:
+        # we've had issues with mask files that after 
+        # running autocrop on them, only contain "nan"
+        # values. This seems to happen when the original
+        # mask has a valid image range indicated as:
+        # image: unsigned short 1 to 1
+        # when that happens, all following calculations 
+        # fail, so we should quit:
+        if math.isnan(maskvol.data.sum()):
+            # clean up...
+            shutil.rmtree("%s/rot_%s" % (os.environ["TMPDIR"], os.getpid()))
+            raise ValueError("\n\n* * * * * * * * * *\n"
+                  "Error: the mask volume is corrupted. No values are found inside the mask.\n"
+                  "probably you are using a mask with only the value 1 in it, but which at the same\n"
+                  "time has a valid range of 1 to 1 . You can check this using mincinfo.\n"
+                  "You need to generate a new mask. To produce a full field of view mask for file.mnc\n"
+                  "run:\n\nminccalc -expression if(true){out = 1;} file.mnc file_mask.mnc\n"
+                  "* * * * * * * * * *\n")
         f1 = sum(sourcevol.data[maskvol.data > 0.5] * \
              targetvol.data[maskvol.data > 0.5])
         f2 = sum(sourcevol.data[maskvol.data > 0.5] ** 2)

python/volumes_from_labels_only

@@ -23,7 +23,7 @@ if __name__ == "__main__":
 
     for l in labels:
         voxelsPerLabel = len(atlas.data[atlas.data == l])
-	volumePerLabel = volumePerVoxel*voxelsPerLabel
+        volumePerLabel = volumePerVoxel*voxelsPerLabel
         output.write(str(int(l)) + ", " + str(volumePerLabel) +  "\n")
 
     atlas.closeVolume()

setup.py

@@ -5,7 +5,8 @@
 import sys
 
 setup(name="python-stuffs",
-      version='0.1.15',
+      version='0.1.19',
+      install_requires=['numpy', 'scipy', 'pyminc'],
       scripts=["python/TFCE",
                "python/smooth_vector",
                "python/measure_xcorr",