Merge branch 'master' into GDC

python/asl/fslhelpers.py

@@ -67,7 +67,7 @@ def __call__(self, args):
         p = subprocess.Popen(cmd_args, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
         while 1:
             retcode = p.poll() #returns None while subprocess is running
-            line = p.stdout.readline()
+            line = p.stdout.readline().decode('utf-8')
             out += line
             if retcode is not None: break
         if retcode != 0:
@@ -144,4 +144,4 @@ def tmpdir(suffix, debug=False):
     else:
         tmpdir = tempfile.mkdtemp("_%s" % suffix)
     print("Using temporary dir: %s" % tmpdir)
-    return tmpdir
+    return tmpdir

python/asl/fslwrap.py

@@ -11,6 +11,7 @@
 import errno
 import tempfile
 import collections
+from six import string_types
 
 import nibabel as nib
 import numpy as np
@@ -352,7 +353,7 @@ def run(self, prog, args="", expected=[]):
             p = subprocess.Popen(shlex.split(cmd), stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
             while 1:
                 retcode = p.poll() # returns None while subprocess is running
-                stdout_line = p.stdout.readline()
+                stdout_line = p.stdout.readline().decode('utf-8')
                 cmd_stdout += stdout_line
                 self.echo(stdout_line)
                 if retcode is not None: break
@@ -507,7 +508,7 @@ def _input_img(self, img):
         """
         if isinstance(img, Image):
             return img, self.IMAGE
-        elif isinstance(img, basestring):
+        elif isinstance(img, string_types):
             return Image(img), self.FILENAME
         elif isinstance(img, np.ndarray):
             tempf = tempfile.NamedTemporaryFile(dir=self.workdir, prefix="fsl", delete=False)
@@ -526,7 +527,7 @@ def _input_matrix(self, mat):
         Note that care is required with Numpy arrays because they have no
         orientation or grid information which some FSL programs may require.
         """
-        if isinstance(mat, basestring):
+        if isinstance(mat, string_types):
             return mat, self.FILENAME
         elif isinstance(mat, np.ndarray):
             tempf = tempfile.NamedTemporaryFile(dir=self.workdir, prefix="fsl", suffix=".mat", delete=False)
@@ -703,7 +704,7 @@ def _grab_temp_data(data):
 
     We also remove the temporary path from the image file name
     """
-    if isinstance(data, collections.Sequence) and not isinstance(data, basestring):
+    if isinstance(data, collections.Sequence) and not isinstance(data, string_types):
         for d in data:
             _grab_temp_data(d)
     else:

python/asl/gui/run_box.py

@@ -51,7 +51,7 @@ def run(self):
         p = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
         while 1:
             retcode = p.poll() #returns None while subprocess is running
-            line = p.stdout.readline()
+            line = p.stdout.readline().decode('utf-8')
             self.write_output(line)
             if retcode is not None: break
         self.write_output("\nReturn code: %i\n\n" % retcode)
@@ -82,16 +82,16 @@ class AslRun(wx.Frame):
     """
 
     # The options we need to pass to oxford_asl for various data orderings
-    order_opts = {"trp" : "--ibf=tis --iaf=diff", 
-                  "trp,tc" : "--ibf=tis --iaf=tcb", 
-                  "trp,ct" : "--ibf=tis --iaf=ctb",
-                  "rtp" : "--ibf=rpt --iaf=diff",
-                  "rtp,tc" : "--rpt --iaf=tcb",
-                  "rtp,ct" : "--ibf=rpt --iaf=ctb",
-                  "ptr,tc" : "--ibf=tis --iaf=tc",
-                  "ptr,ct" : "--ibf=tis --iaf=ct",
-                  "prt,tc" : "--ibf=rpt --iaf=tc",
-                  "prt,ct" : "--ibf=rpt --iaf=ct"}
+    order_opts = {"trp" : "--ibf=rpt --iaf=diff", 
+                  "trp,tc" : "--ibf=rpt --iaf=tcb", 
+                  "trp,ct" : "--ibf=rpt --iaf=ctb",
+                  "rtp" : "--ibf=tis --iaf=diff",
+                  "rtp,tc" : "--ibf=tis --iaf=tcb",
+                  "rtp,ct" : "--ibf=tis --iaf=ctb",
+                  "ptr,tc" : "--ibf=rpt --iaf=tc",
+                  "ptr,ct" : "--ibf=rpt --iaf=ct",
+                  "prt,tc" : "--ibf=tis --iaf=tc",
+                  "prt,ct" : "--ibf=tis --iaf=ct"}
 
     def __init__(self, parent, run_btn, run_label):
         wx.Frame.__init__(self, parent, title="Run", size=(600, 400), style=wx.DEFAULT_FRAME_STYLE)

python/asl/image.py

@@ -7,6 +7,7 @@
 import sys
 import shutil
 from optparse import OptionParser, OptionGroup
+from six import string_types
 
 import numpy as np
 import nibabel as nib
@@ -82,7 +83,7 @@ def __init__(self, name, order="prt", ntis=None, tis=None, plds=None, nrpts=None
         if ntis is None and tis is None:
             raise RuntimeError("Number of TIs not specified")
         elif tis is not None:
-            if isinstance(tis, basestring): tis = [float(ti) for ti in tis.split(",")]
+            if isinstance(tis, string_types): tis = [float(ti) for ti in tis.split(",")]
             ntis = len(tis)
             if ntis is not None and len(tis) != ntis:
                 raise RuntimeError("Number of TIs: %i, but list of %i TIs given" % (ntis, len(tis)))
@@ -95,14 +96,14 @@ def __init__(self, name, order="prt", ntis=None, tis=None, plds=None, nrpts=None
             # Calculate fixed number of repeats 
             if self.nv % (self.ntc * self.ntis) != 0:
                 raise RuntimeError("Data contains %i volumes, inconsistent with %i TIs and TC pairs" % (self.nv, self.ntis))        
-            rpts = [self.nv / (self.ntc * self.ntis)] * self.ntis
+            rpts = [int(self.nv / (self.ntc * self.ntis))] * self.ntis
         elif nrpts is not None:
             nrpts = int(nrpts)
             if nrpts * self.ntis * self.ntc != self.nv:
                 raise RuntimeError("Data contains %i volumes, inconsistent with %i TIs and %i repeats" % (self.nv, self.ntis, nrpts))
             rpts = [nrpts] * self.ntis
         else:
-            if isinstance(rpts, basestring): rpts = [int(rpt) for rpt in rpts.split(",")]
+            if isinstance(rpts, string_types): rpts = [int(rpt) for rpt in rpts.split(",")]
             if len(rpts) != self.ntis:
                 raise RuntimeError("%i TIs, but only %i variable repeats" % (self.ntis, len(rpts)))        
             elif sum(rpts) * self.ntc != self.nv:
@@ -206,13 +207,13 @@ def diff(self):
             # Already differenced
             output_data = self.data()
         else:
-            output_data = np.zeros(list(self.shape[:3]) + [self.nv/2])
+            output_data = np.zeros(list(self.shape[:3]) + [int(self.nv/2)])
 
             # Re-order so that TC pairs are together with the tag first
             out_order = self.order.replace("p", "").replace("P", "")
             reordered = self.reorder("p" + out_order).data()
 
-            for t in range(self.nv / 2):
+            for t in range(int(self.nv / 2)):
                 tag = 2*t
                 ctrl = tag+1
                 output_data[:,:,:,t] = reordered[:,:,:,ctrl] - reordered[:,:,:,tag]