fix: Numpy stopped accepting b-strings as savetxt args

Author: effigies

nipype/algorithms/confounds.py

@@ -188,7 +188,7 @@ def _run_interface(self, runtime):
 
         if self.inputs.save_std:
             out_file = self._gen_fname("dvars_std", ext="tsv")
-            np.savetxt(out_file, dvars[0], fmt=b"%0.6f")
+            np.savetxt(out_file, dvars[0], fmt="%0.6f")
             self._results["out_std"] = out_file
 
             if self.inputs.save_plot:
@@ -228,7 +228,7 @@ def _run_interface(self, runtime):
 
         if self.inputs.save_vxstd:
             out_file = self._gen_fname("dvars_vxstd", ext="tsv")
-            np.savetxt(out_file, dvars[2], fmt=b"%0.6f")
+            np.savetxt(out_file, dvars[2], fmt="%0.6f")
             self._results["out_vxstd"] = out_file
 
             if self.inputs.save_plot:
@@ -251,8 +251,8 @@ def _run_interface(self, runtime):
             np.savetxt(
                 out_file,
                 np.vstack(dvars).T,
-                fmt=b"%0.8f",
-                delimiter=b"\t",
+                fmt="%0.8f",
+                delimiter="\t",
                 header="std DVARS\tnon-std DVARS\tvx-wise std DVARS",
                 comments="",
             )
@@ -689,7 +689,7 @@ def _run_interface(self, runtime):
         np.savetxt(
             components_file,
             components,
-            fmt=b"%.10f",
+            fmt="%.10f",
             delimiter="\t",
             header="\t".join(components_header),
             comments="",
@@ -729,7 +729,7 @@ def _run_interface(self, runtime):
             np.savetxt(
                 self._results["pre_filter_file"],
                 filter_basis,
-                fmt=b"%.10f",
+                fmt="%.10f",
                 delimiter="\t",
                 header="\t".join(header),
                 comments="",

nipype/algorithms/rapidart.py

@@ -600,10 +600,10 @@ 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=b"%d", delimiter=" ")
-        np.savetxt(intensityfile, g, fmt=b"%.2f", delimiter=" ")
+        np.savetxt(artifactfile, outliers, fmt="%d", delimiter=" ")
+        np.savetxt(intensityfile, g, fmt="%.2f", delimiter=" ")
         if self.inputs.use_norm:
-            np.savetxt(normfile, normval, fmt=b"%.4f", delimiter=" ")
+            np.savetxt(normfile, normval, fmt="%.4f", delimiter=" ")
 
         if isdefined(self.inputs.save_plot) and self.inputs.save_plot:
             import matplotlib

nipype/interfaces/fsl/epi.py

@@ -417,7 +417,7 @@ def _generate_encfile(self):
                 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=b"%d %d %d %.8f")
+        np.savetxt(out_file, np.array(lines), fmt="%d %d %d %.8f")
         return out_file
 
     def _overload_extension(self, value, name=None):

nipype/interfaces/nilearn.py

@@ -105,7 +105,7 @@ def _run_interface(self, runtime):
 
         # save output
         self._results["out_file"] = os.path.join(runtime.cwd, self.inputs.out_file)
-        np.savetxt(self._results["out_file"], output, fmt=b"%s", delimiter="\t")
+        np.savetxt(self._results["out_file"], output, fmt="%s", delimiter="\t")
         return runtime
 
     def _process_inputs(self):