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):