Add verbose option to ica_reclassify to obtain denoised echo images (#1179)

Author: eurunuela

tedana/io.py

@@ -143,9 +143,9 @@ def __init__(
             del old_registry["root"]
             for k, v in old_registry.items():
                 if isinstance(v, list):
-                    self.registry[k] = [op.join(rel_root, vv) for vv in v]
+                    self.registry[k] = [op.normpath(op.join(rel_root, vv)) for vv in v]
                 else:
-                    self.registry[k] = op.join(rel_root, v)
+                    self.registry[k] = op.normpath(op.join(rel_root, v))
 
         if not op.isdir(self.out_dir):
             LGR.info(f"Generating output directory: {self.out_dir}")
@@ -414,7 +414,10 @@ def get_file_path(self, description):
             Description of the file to get the path for.
         """
         if description in self._registry.keys():
-            return op.join(self._base_dir, self._registry[description])
+            if isinstance(self._registry[description], list):
+                return [op.join(self._base_dir, f) for f in self._registry[description]]
+            else:
+                return op.join(self._base_dir, self._registry[description])
         else:
             return None
 
@@ -429,7 +432,10 @@ def get_file_contents(self, description):
         """
         for ftype, loader in InputHarvester.loaders.items():
             if ftype in description:
-                return loader(self.get_file_path(description))
+                if isinstance(self.get_file_path(description), list):
+                    return [loader(f) for f in self.get_file_path(description)]
+                else:
+                    return loader(self.get_file_path(description))
 
     @property
     def registry(self):

tedana/tests/test_integration.py

@@ -192,6 +192,7 @@ def test_integration_four_echo(skip_integration):
         reject=[4, 5, 6],
         out_dir=out_dir_manual,
         mir=True,
+        verbose=True,
     )
 
     # compare the generated output files

tedana/workflows/ica_reclassify.py

@@ -122,6 +122,13 @@ def _get_parser():
     optional.add_argument(
         "--png-cmap", dest="png_cmap", type=str, help="Colormap for figures", default="coolwarm"
     )
+    optional.add_argument(
+        "--verbose",
+        dest="verbose",
+        action="store_true",
+        help="Generate intermediate and additional files.",
+        default=False,
+    )
     optional.add_argument(
         "--debug",
         dest="debug",
@@ -173,6 +180,7 @@ def _main(argv=None):
         no_reports=args.no_reports,
         png_cmap=args.png_cmap,
         overwrite=args.overwrite,
+        verbose=args.verbose,
         debug=args.debug,
         quiet=args.quiet,
         reclassify_command=reclassify_command,
@@ -242,6 +250,7 @@ def ica_reclassify_workflow(
     mir=False,
     no_reports=False,
     png_cmap="coolwarm",
+    verbose=False,
     overwrite=False,
     debug=False,
     quiet=False,
@@ -273,6 +282,8 @@ def ica_reclassify_workflow(
     png_cmap : obj:'str', optional
         Name of a matplotlib colormap to be used when generating figures.
         Cannot be used with --no-png. Default is 'coolwarm'.
+    verbose : :obj:`bool`, optional
+        Generate intermediate and additional files. Default is False.
     debug : :obj:`bool`, optional
         Whether to run in debugging mode or not. Default is False.
     overwrite : :obj:`bool`, optional
@@ -390,13 +401,19 @@ def ica_reclassify_workflow(
         data_optcom = ioh.get_file_contents("combined img")
         used_gs = False
 
+    if verbose:
+        LGR.debug("Loading input 4D data")
+        data_cat = ioh.get_file_contents("input img")
+        # Extract the data from the nibabel objects
+        data_cat, _ = io.load_data(data_cat, n_echos=len(data_cat))
+
     io_generator = io.OutputGenerator(
         data_optcom,
         convention=convention,
         prefix=prefix,
         config=config,
         overwrite=overwrite,
-        verbose=False,
+        verbose=verbose,
         out_dir=out_dir,
         old_registry=ioh.registry,
     )
@@ -499,6 +516,10 @@ def ica_reclassify_workflow(
         )
         io_generator.overwrite = False
 
+    if verbose:
+        LGR.debug("Writing out verbose data")
+        io.writeresults_echoes(data_cat, mixing, mask_denoise, component_table, io_generator)
+
     # Write out BIDS-compatible description file
     derivative_metadata = {
         "Name": "tedana Outputs",