MAINT: change parrec2nii volume label output from JSON to CSV

Author: grlee77

bin/parrec2nii

@@ -8,8 +8,7 @@ import numpy as np
 import numpy.linalg as npl
 import sys
 import os
-import json
-from copy import deepcopy
+import csv
 import nibabel
 import nibabel.parrec as pr
 from nibabel.parrec import one_line
@@ -69,16 +68,17 @@ def get_opt_parser():
                    for --dwell-time. The field strength must be supplied
                    because it is not encoded in the PAR/REC format.""")))
     p.add_option(
-        Option("-i", "--dimension-info", action="store_true", dest="dim_info",
+        Option("-i", "--volume-info", action="store_true", dest="vol_info",
                default=False,
                help=one_line(
-                   """Export .PAR dimension labels corresponding to the fourth
+                   """Export .PAR volume labels corresponding to the fourth
                    dimension of the data.  The dimension info will be stored in
-                   JSON format with a filename matching the input .PAR, but
-                   with the extension .ordering.json.  Only labels that vary
-                   along the 4th dimension are exported.  (e.g. for a single
-                   volume structural scan there are no dynamic labels and no
-                   output file will be created)""")))
+                   CSV format with the first row containing dimension labels
+                   and the subsequent rows (one per volume), the corresponding
+                   indices.  Only labels that vary along the 4th dimension are
+                   exported (e.g. for a single volume structural scan there
+                   are no dynamic labels and no output file will be created).
+                   """)))
     p.add_option(
         Option("--origin", action="store", dest="origin", default="scanner",
                help=one_line(
@@ -146,16 +146,6 @@ def error(msg, exit_code):
     sys.exit(exit_code)
 
 
-def convert_arrays_to_lists(input_dict):
-    # convert dictionary of numpy arrays to a dictionary of lists
-    output_dict = deepcopy(input_dict)
-    for key, value in output_dict.items():
-        if not isinstance(value, np.ndarray):
-            raise ValueError("all dictionary entries must be numpy arrays")
-        output_dict[key] = value.tolist()
-    return output_dict
-
-
 def proc_file(infile, opts):
     # figure out the output filename, and see if it exists
     basefilename = splitext_addext(os.path.basename(infile))[0]
@@ -285,13 +275,16 @@ def proc_file(infile, opts):
                         fid.write('%s ' % val)
                     fid.write('\n')
 
-    # export data labels varying along the 4th dimensions
-    if opts.dim_info:
-        labels = pr_img.header.get_dimension_labels(collapse_slices=True)
+    # export data labels varying along the 4th dimensions if requested
+    if opts.vol_info:
+        labels = pr_img.header.get_volume_labels()
         if len(labels) > 0:
-            labels = convert_arrays_to_lists(labels)
-            with open(basefilename + '.ordering.json', 'w') as fid:
-                json.dump(labels, fid, sort_keys=True, indent=4)
+            vol_keys = list(labels.keys())
+            with open(basefilename + '.ordering.csv', 'w') as csvfile:
+                csvwriter = csv.writer(csvfile, delimiter=',')
+                csvwriter.writerow(vol_keys)
+                for vals in zip(*[labels[k] for k in vol_keys]):
+                    csvwriter.writerow(vals)
 
     # write out dwell time if requested
     if opts.dwell_time: