unicode fixes, np.savetxt does not take unicode fmt

Author: oesteban

examples/rsfmri_vol_surface_preprocessing.py

@@ -44,7 +44,7 @@
 """
 
 from __future__ import division, unicode_literals
-from builtins import open, range
+from builtins import open, range, str
 
 import os
 
@@ -189,7 +189,7 @@ def motion_regressors(motion_params, order=0, derivatives=1):
         for i in range(2, order + 1):
             out_params2 = np.hstack((out_params2, np.power(out_params, i)))
         filename = os.path.join(os.getcwd(), "motion_regressor%02d.txt" % idx)
-        np.savetxt(filename, out_params2, fmt="%.10f")
+        np.savetxt(filename, out_params2, fmt=str("%.10f").encode())
         out_files.append(filename)
     return out_files
 
@@ -237,7 +237,7 @@ def build_filter1(motion_params, comp_norm, outliers, detrend_poly=None):
                     i + 1)(np.linspace(-1, 1, timepoints))[:, None]))
             out_params = np.hstack((out_params, X))
         filename = os.path.join(os.getcwd(), "filter_regressor%02d.txt" % idx)
-        np.savetxt(filename, out_params, fmt="%.10f")
+        np.savetxt(filename, out_params, fmt=str("%.10f").encode())
         out_files.append(filename)
     return out_files
 
@@ -286,7 +286,7 @@ def extract_noise_components(realigned_file, mask_file, num_components=5,
         regressors = np.genfromtxt(extra_regressors)
         components = np.hstack((components, regressors))
     components_file = os.path.join(os.getcwd(), 'noise_components.txt')
-    np.savetxt(components_file, components, fmt="%.10f")
+    np.savetxt(components_file, components, fmt=str("%.10f").encode())
     return components_file
 
 

examples/rsfmri_vol_surface_preprocessing_nipy.py

@@ -45,7 +45,7 @@
 """
 
 from __future__ import division, unicode_literals
-from builtins import open, range
+from builtins import open, range, str
 
 import os
 
@@ -179,7 +179,7 @@ def motion_regressors(motion_params, order=0, derivatives=1):
         for i in range(2, order + 1):
             out_params2 = np.hstack((out_params2, np.power(out_params, i)))
         filename = os.path.join(os.getcwd(), "motion_regressor%02d.txt" % idx)
-        np.savetxt(filename, out_params2, fmt="%.10f")
+        np.savetxt(filename, out_params2, fmt=str("%.10f").encode())
         out_files.append(filename)
     return out_files
 
@@ -224,7 +224,7 @@ def build_filter1(motion_params, comp_norm, outliers, detrend_poly=None):
                     i + 1)(np.linspace(-1, 1, timepoints))[:, None]))
             out_params = np.hstack((out_params, X))
         filename = os.path.join(os.getcwd(), "filter_regressor%02d.txt" % idx)
-        np.savetxt(filename, out_params, fmt="%.10f")
+        np.savetxt(filename, out_params, fmt=str("%.10f").encode())
         out_files.append(filename)
     return out_files
 
@@ -269,7 +269,7 @@ def extract_noise_components(realigned_file, mask_file, num_components=5,
         regressors = np.genfromtxt(extra_regressors)
         components = np.hstack((components, regressors))
     components_file = os.path.join(os.getcwd(), 'noise_components.txt')
-    np.savetxt(components_file, components, fmt="%.10f")
+    np.savetxt(components_file, components, fmt=str("%.10f").encode())
     return components_file
 
 

nipype/algorithms/rapidart.py

@@ -468,10 +468,10 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None):
         outliers = np.unique(np.union1d(iidx, np.union1d(tidx, ridx)))
 
         # write output to outputfile
-        np.savetxt(artifactfile, outliers, fmt='%d', delimiter=' ')
-        np.savetxt(intensityfile, g, fmt='%.2f', delimiter=' ')
+        np.savetxt(artifactfile, outliers, fmt=str('%d').encode(), delimiter=' ')
+        np.savetxt(intensityfile, g, fmt=str('%.2f').encode(), delimiter=' ')
         if self.inputs.use_norm:
-            np.savetxt(normfile, normval, fmt='%.4f', delimiter=' ')
+            np.savetxt(normfile, normval, fmt=str('%.4f').encode(), delimiter=' ')
 
         if isdefined(self.inputs.save_plot) and self.inputs.save_plot:
             import matplotlib

nipype/interfaces/fsl/epi.py

@@ -13,6 +13,7 @@
     >>> os.chdir(datadir)
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import str
 
 import os
 import numpy as np
@@ -295,7 +296,7 @@ def _generate_encfile(self):
             line = [float(val[0] == encdir[0]) * direction
                     for val in ['x', 'y', 'z']] + [durations[idx]]
             lines.append(line)
-        np.savetxt(out_file, np.array(lines), fmt='%d %d %d %.8f')
+        np.savetxt(out_file, np.array(lines), fmt=str('%d %d %d %.8f').encode())
         return out_file
 
     def _overload_extension(self, value, name=None):

nipype/interfaces/spm/base.py

@@ -36,8 +36,6 @@
 __docformat__ = 'restructuredtext'
 logger = logging.getLogger('interface')
 
-__docformat__ = 'restructuredtext'
-
 
 def func_is_3d(in_file):
     """Checks if input functional files are 3d."""
@@ -421,8 +419,11 @@ def _generate_job(self, prefix='', contents=None):
                     if isinstance(val, np.ndarray):
                         jobstring += self._generate_job(prefix=None,
                                                         contents=val)
+                    elif isinstance(val, list):
+                        val_format = ', '.join(['\'{}\''] * len(val)).format
+                        jobstring += '[{}];...\n'.format(val_format(*val))
                     elif isinstance(val, (str, bytes)):
-                        jobstring += '\'%s\';...\n' % (val)
+                        jobstring += '\'{}\';...\n'.format(val)
                     else:
                         jobstring += '%s;...\n' % str(val)
                 jobstring += '};\n'

nipype/workflows/dmri/fsl/epi.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 # coding: utf-8
 from __future__ import print_function, division, unicode_literals, absolute_import
-from builtins import open
+from builtins import open, str
 
 import warnings
 
@@ -681,7 +681,7 @@ def _rotate_bvecs(in_bvec, in_matrix):
         bvec = np.matrix(bvecs[:, i])
         rot = np.matrix(np.loadtxt(vol_matrix)[0:3, 0:3])
         new_bvecs[i] = (np.array(rot * bvec.T).T)[0]  # fill each volume with x,y,z as we go along
-    np.savetxt(out_file, np.array(new_bvecs).T, fmt='%0.15f')
+    np.savetxt(out_file, np.array(new_bvecs).T, fmt=str('%0.15f').encode())
     return out_file
 
 

nipype/workflows/dmri/fsl/utils.py

@@ -3,10 +3,8 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 
-from __future__ import division
-from builtins import zip
-from builtins import next
-from builtins import range
+from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import zip, next, range, str
 
 from ....pipeline import engine as pe
 from ....interfaces import utility as niu
@@ -501,7 +499,7 @@ def rotate_bvecs(in_bvec, in_matrix):
             newbvec = invrot.dot(bvec)
             new_bvecs.append((newbvec / np.linalg.norm(newbvec)))
 
-    np.savetxt(out_file, np.array(new_bvecs).T, fmt='%0.15f')
+    np.savetxt(out_file, np.array(new_bvecs).T, fmt=str('%0.15f').encode())
     return out_file
 
 
@@ -551,7 +549,7 @@ def eddy_rotate_bvecs(in_bvec, eddy_params):
             newbvec = invrot.dot(bvec)
             new_bvecs.append(newbvec / np.linalg.norm(newbvec))
 
-    np.savetxt(out_file, np.array(new_bvecs).T, fmt='%0.15f')
+    np.savetxt(out_file, np.array(new_bvecs).T, fmt=str('%0.15f').encode())
     return out_file
 
 
@@ -713,7 +711,7 @@ def reorient_bvecs(in_dwi, old_dwi, in_bvec):
     R = RS / S
 
     new_bvecs = [R.dot(b) for b in bvecs]
-    np.savetxt(out_file, np.array(new_bvecs).T, fmt='%0.15f')
+    np.savetxt(out_file, np.array(new_bvecs).T, fmt=str('%0.15f').encode())
     return out_file
 
 

nipype/workflows/rsfmri/fsl/resting.py

@@ -1,7 +1,8 @@
 # -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-from __future__ import division
+from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import str
 
 from ....interfaces import fsl as fsl          # fsl
 from ....interfaces import utility as util     # utility
@@ -35,7 +36,7 @@ def extract_noise_components(realigned_file, noise_mask_file, num_components):
     else:
         components = np.hstack((components, u[:, :num_components]))
     components_file = os.path.join(os.getcwd(), 'noise_components.txt')
-    np.savetxt(components_file, components, fmt="%.10f")
+    np.savetxt(components_file, components, fmt=str("%.10f").encode())
     return components_file