fix np.savetxt with format

Author: oesteban

examples/rsfmri_vol_surface_preprocessing.py

@@ -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=str("%.10f").encode())
+        np.savetxt(filename, out_params2, fmt=b"%.10f")
         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=str("%.10f").encode())
+        np.savetxt(filename, out_params, fmt=b"%.10f")
         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=str("%.10f").encode())
+    np.savetxt(components_file, components, fmt=b"%.10f")
     return components_file
 
 

examples/rsfmri_vol_surface_preprocessing_nipy.py

@@ -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=str("%.10f").encode())
+        np.savetxt(filename, out_params2, fmt=b"%.10f")
         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=str("%.10f").encode())
+        np.savetxt(filename, out_params, fmt=b"%.10f")
         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=str("%.10f").encode())
+    np.savetxt(components_file, components, fmt=b"%.10f")
     return components_file
 
 

nipype/algorithms/modelgen.py

@@ -19,7 +19,7 @@
 
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
-from builtins import range, str, bytes
+from builtins import range, str, bytes, int
 
 from copy import deepcopy
 import os
@@ -541,16 +541,20 @@ def _generate_design(self, infolist=None):
             outliers = [[]]
             for i, filename in enumerate(self.inputs.outlier_files):
                 try:
-                    out = np.loadtxt(filename, dtype=int)
+                    out = np.loadtxt(filename)
                 except IOError:
+                    iflogger.warn('Error reading outliers file %s', filename)
                     out = np.array([])
+
                 if out.size > 0:
+                    iflogger.debug('fname=%s, out=%s, nscans=%s', filename, out, repr(sum(nscans[0:i])))
+                    sumscans = out.astype(int) + sum(nscans[0:i])
+
                     if out.size == 1:
-                        outliers[0].extend([(np.array(out) +
-                                             sum(nscans[0:i])).tolist()])
+                        outliers[0]+= [np.array(sumscans, dtype=int).tolist()]
                     else:
-                        outliers[0].extend((np.array(out) +
-                                            sum(nscans[0:i])).tolist())
+                        outliers[0]+= np.array(sumscans, dtype=int).tolist()
+
         self._sessinfo = self._generate_standard_design(concatlist,
                                                         functional_runs=functional_runs,
                                                         realignment_parameters=realignment_parameters,

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=str('%d').encode(), delimiter=' ')
-        np.savetxt(intensityfile, g, fmt=str('%.2f').encode(), delimiter=' ')
+        np.savetxt(artifactfile, outliers, fmt=b'%d', delimiter=' ')
+        np.savetxt(intensityfile, g, fmt=b'%.2f', delimiter=' ')
         if self.inputs.use_norm:
-            np.savetxt(normfile, normval, fmt=str('%.4f').encode(), delimiter=' ')
+            np.savetxt(normfile, normval, fmt=b'%.4f', delimiter=' ')
 
         if isdefined(self.inputs.save_plot) and self.inputs.save_plot:
             import matplotlib

nipype/interfaces/fsl/epi.py

@@ -296,7 +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=str('%d %d %d %.8f').encode())
+        np.savetxt(out_file, np.array(lines), fmt=b'%d %d %d %.8f')
         return out_file
 
     def _overload_extension(self, value, name=None):

nipype/workflows/dmri/fsl/epi.py

@@ -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=str('%0.15f').encode())
+    np.savetxt(out_file, np.array(new_bvecs).T, fmt=b'%0.15f')
     return out_file
 
 

nipype/workflows/dmri/fsl/utils.py

@@ -499,7 +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=str('%0.15f').encode())
+    np.savetxt(out_file, np.array(new_bvecs).T, fmt=b'%0.15f')
     return out_file
 
 
@@ -549,7 +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=str('%0.15f').encode())
+    np.savetxt(out_file, np.array(new_bvecs).T, fmt=b'%0.15f')
     return out_file
 
 
@@ -711,7 +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=str('%0.15f').encode())
+    np.savetxt(out_file, np.array(new_bvecs).T, fmt=b'%0.15f')
     return out_file
 
 

nipype/workflows/rsfmri/fsl/resting.py

@@ -36,7 +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=str("%.10f").encode())
+    np.savetxt(components_file, components, fmt=b"%.10f")
     return components_file