Merge pull request #62 from PennLINC/fix-bval-bvec

now checking for .tsv .bval and .bvec in renaming

bond/bond.py

@@ -143,9 +143,10 @@ def apply_csv_changes(self, summary_csv, files_csv, new_prefix,
  (files_df[["ParamGroup", "KeyGroup"]] == source_id).all(1)]
 
  # Get a source json file
- source_json = img_to_json(source_files.iloc[0].FilePath)
+ source_json = img_to_new_ext(source_files.iloc[0].FilePath,
+ '.json')
  for dest_nii in dest_files.FilePath:
- dest_json = img_to_json(dest_nii)
+ dest_json = img_to_new_ext(dest_nii, '.json')
  if Path(dest_json).exists() and Path(source_json).exists():
  merge_commands.append(
  'bids-sidecar-merge %s %s'
@@ -253,7 +254,7 @@ def change_filename(self, filepath, entities):
  modality = large.replace(small, '')
 
  # detect the subject/session string and keep it together
- # front_stem is the string of subject/session paris
+ # front_stem is the string of subject/session pairs
  # these two entities don't change with the key group
  front_stem = ""
  cntr = 0
@@ -291,13 +292,21 @@ def change_filename(self, filepath, entities):
  self.old_filenames.append(str(path))
  self.new_filenames.append(new_path)
 
- # now also rename json file
- json_file = img_to_json(filepath)
-
- if Path(json_file).exists():
- new_json_path = new_path_front + "_" + new_filename + ".json"
- self.old_filenames.append(json_file)
- self.new_filenames.append(new_json_path)
+ # now also rename files with same stem diff extension
+ extensions = ['.json', '.bval', '.bvec', '.tsv', '.tsv.gz']
+ for ext in extensions:
+ ext_file = img_to_new_ext(filepath, ext)
+
+ # check if ext_file exists in the bids dir
+ if Path(ext_file).exists():
+ # need to remove suffix for .tsv and .tsv.gz files
+ if ext == '.tsv':
+ new_filename = new_filename.rpartition('_')[0] + '_events'
+ if ext == '.tsv.gz':
+ new_filename = new_filename.rpartition('_')[0] + '_physio'
+ new_ext_path = new_path_front + "_" + new_filename + ext
+ self.old_filenames.append(ext_file)
+ self.new_filenames.append(new_ext_path)
 
  def _cache_fieldmaps(self):
  """Searches all fieldmaps and creates a lookup for each file.
@@ -665,5 +674,12 @@ def _order_columns(df):
  return df[new_columns]
 
 
-def img_to_json(img_path):
- return img_path.replace(".nii.gz", "").replace(".nii", "") + ".json"
+def img_to_new_ext(img_path, new_ext):
+ # handle .tsv edge case
+ if new_ext == '.tsv':
+ # take out suffix
+ return img_path.rpartition('_')[0] + '_events' + new_ext
+ if new_ext == '.tsv.gz':
+ return img_path.rpartition('_')[0] + '_physio' + new_ext
+ else:
+ return img_path.replace(".nii.gz", "").replace(".nii", "") + new_ext

tests/test_bond.py

@@ -7,6 +7,7 @@
 from copy import deepcopy
 import hashlib
 import json
+from pathlib import Path
 from pkg_resources import resource_filename as pkgrf
 import pytest
 from bond import BOnD
@@ -366,6 +367,13 @@ def test_apply_csv_changes(tmp_path):
  # make sure files you wanted to rename exist in the bids dir
 
  data_root = get_data(tmp_path)
+
+ # add extension files
+ path_to_img = str(data_root / "complete/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude1.nii.gz")
+ _add_ext_files(path_to_img)
+ assert Path(data_root /
+ "complete/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_physio.tsv.gz").exists() == True
+
  complete_bond = BOnD(data_root / "complete", use_datalad=True)
  complete_bond.datalad_save()
 
@@ -387,11 +395,24 @@ def test_apply_csv_changes(tmp_path):
  assert og_content == mod1_content
 
  # edit the csv, add a RenameKeyGroup
+ # make sure extension files also get renamed
+
  _edit_csv(str(tmp_path / "originals_summary.csv"))
  complete_bond.apply_csv_changes(str(tmp_path / "originals_summary.csv"),
  str(tmp_path / "originals_files.csv"),
  str(tmp_path / "modified2"))
 
+ # check files df to make sure extension files also got renmaed
+ mod_files = tmp_path / "modified2_files.csv"
+ assert Path(data_root /
+ "complete/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v5_magnitude1.bval").exists() == True
+ assert Path(data_root /
+ "complete/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v5_magnitude1.bvec").exists() == True
+ assert Path(data_root /
+ "complete/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v5_events.tsv").exists() == True
+ assert Path(data_root /
+ "complete/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v5_physio.tsv.gz").exists() == True
+
  mod2_path = tmp_path / "modified2_summary.csv"
  with mod2_path.open("r") as f:
  mod2_content = "".join(f.readlines())
@@ -412,6 +433,7 @@ def test_apply_csv_changes(tmp_path):
  deleted_content = "".join(f.readlines())
  assert deleted_keyparam not in deleted_content
 
+
 def _add_deletion(summary_csv):
  df = pd.read_csv(summary_csv)
  df.loc[3, 'MergeInto'] = 0
@@ -430,6 +452,22 @@ def _edit_csv(summary_csv):
  writer = csv.writer(open(summary_csv, 'w'))
  writer.writerows(lines)
 
+def _add_ext_files(img_path):
+ # add and save extension files in
+ exts = ['.bval', '.bvec', '.tsv', '.tsv.gz']
+ for ext in exts:
+ ext_file = img_path.replace(".nii.gz", "").replace(".nii", "") + ext
+
+ if ext == '.tsv':
+ no_suffix = ext_file.rpartition('_')[0]
+ ext_file = no_suffix + '_events' + ext
+ if ext == '.tsv.gz':
+ no_suffix = ext_file.rpartition('_')[0]
+ ext_file = no_suffix + '_physio' + ext
+ # save ext file in img_path's parent dir
+ Path(ext_file).touch()
+
+
  # add new key group name to RenameKeyGroup column