Merge branch 'develop'

Mouse-Imaging-Centre · Oct 25, 2016 · cfe58aa · cfe58aa
2 parents ea6251a + 2a68afd
commit cfe58aa
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Showing 4 changed files with 16 additions and 7 deletions.
diff --git a/NEWS b/NEWS
@@ -1,3 +1,8 @@
+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

diff --git a/m4/smr_WITH_BUILD_PATH.m4 b/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
     ])
 ])
diff --git a/python/TFCE b/python/TFCE
@@ -7,7 +7,7 @@ from numpy import *
 import operator
 
 
-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"
 
@@ -43,7 +43,11 @@ def tfce(invol, outvol, dh=0.1, E=0.5, H=2.0):
                      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;
             }}}}
             """
@@ -52,7 +56,7 @@ 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')
 
@@ -101,8 +105,8 @@ 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()
-
+
diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 import sys
 
 setup(name="python-stuffs",
-      version='0.1.16',
+      version='0.1.17',
       scripts=["python/TFCE",
                "python/smooth_vector",
                "python/measure_xcorr",