DOC: Custom interfaces dictionary documentation

Medical-Image-Analysis-Laboratory · Dec 22, 2020 · 8c082cc · 8c082cc
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Showing 3 changed files with 11 additions and 17 deletions.
diff --git a/docker/bidsapp/run.py b/docker/bidsapp/run.py
@@ -259,11 +259,6 @@ def main(bids_dir, output_dir, subject, p_stacks, session, paramTV=None, number_
 
                     dict_custom_interfaces = sr_params['custom_interfaces'] if 'custom_interfaces' in sr_params.keys() else None
 
-                    # skip_svr = sr_params['skip_svr'] if 'skip_svr' in sr_params.keys() else False
-                    # do_refine_hr_mask = sr_params['do_refine_hr_mask'] if 'do_refine_hr_mask' in sr_params.keys() else False
-                    # skip_nlm_denoising = sr_params['skip_nlm_denoising'] if 'skip_nlm_denoising' in sr_params.keys() else False
-                    # skip_stacks_ordering = sr_params['skip_stacks_ordering'] if 'skip_stacks_ordering' in sr_params.keys() else False
-
                     if ("sr-id" not in sr_params.keys()):
                         print('Do not process subjects %s because of missing parameters.' % sub)
                         continue
@@ -278,10 +273,6 @@ def main(bids_dir, output_dir, subject, p_stacks, session, paramTV=None, number_
                                masks_derivatives_dir=args.masks_derivatives_dir,
                                number_of_cores=nipype_nb_of_cores,
                                dict_custom_interfaces = dict_custom_interfaces)
-                               # skip_svr=skip_svr,
-                               # do_refine_hr_mask=do_refine_hr_mask,
-                               # skip_nlm_denoising=skip_nlm_denoising,
-                               # skip_stacks_ordering=skip_stacks_ordering)
 
     else:
         print('ERROR: Processing of all dataset not implemented yet\n At least one participant label should be provided')

diff --git a/documentation/usage.rst b/documentation/usage.rst
@@ -40,9 +40,11 @@ The BIDS App configuration file specified by the input flag `--param_file` adopt
           "paramTV": { 
             "lambdaTV": 0.75, 
             "deltatTV": 0.01 },
-          "skip_svr": true,
-          "do_refine_hr_mask": false,
-          "skip_stacks_ordering": false
+          "custom_interfaces":
+            {
+            "skip_svr": true,
+            "do_refine_hr_mask": false,
+            "skip_stacks_ordering": false }
         }]
       "02": [
         { "sr-id": 1,
@@ -64,13 +66,15 @@ where:
 
     * ``"session"`` (optional) It MUST be specified if you have a BIDS dataset composed of multiple sessions with the *sub-XX/ses-YY* structure.
 
-    * ``"skip_svr"`` (optional) indicates weither the Slice-to-Volume Registration should be skipped in the image reconstruction. (default is False)
+    * ``"custom_interfaces"`` (optional): indicates weither optional interfaces of the pipeline should be performed.
 
-    * ``"do_refine_hr_mask"`` (optional) indicates weither a refinement of the HR mask should be performed. (default is False)
+        * ``"skip_svr"`` (optional) the Slice-to-Volume Registration should be skipped in the image reconstruction. (default is False)
 
-    * ``"skip_nlm_denoising"`` (optional) indicates weither the NLM denoising preprocessing should be skipped. (default is False)
+        * ``"do_refine_hr_mask"`` (optional) indicates weither a refinement of the HR mask should be performed. (default is False)
 
-    * ``"skip_stacks_ordering"`` (optional) indicates weither the order of stacks specified in ``"stacks"`` should be kept or re-computed. (default is False)
+        * ``"skip_nlm_denoising"`` (optional) indicates weither the NLM denoising preprocessing should be skipped. (default is False)
+
+        * ``"skip_stacks_ordering"`` (optional) indicates weither the order of stacks specified in ``"stacks"`` should be kept or re-computed. (default is False)
 
 .. important:: 
     Before using any BIDS App, we highly recommend you to validate your BIDS structured dataset with the free, online `BIDS Validator <http://bids-standard.github.io/bids-validator/>`_.

diff --git a/pymialsrtk/pipelines/anatomical/srr.py b/pymialsrtk/pipelines/anatomical/srr.py
@@ -127,7 +127,6 @@ class AnatomicalPipeline:
     def __init__(self, bids_dir, output_dir, subject, p_stacks=None, sr_id=1,
                  session=None, paramTV=None, p_masks_derivatives_dir=None,
                  p_dict_custom_interfaces = None):
-                 # p_skip_svr=False, p_do_refine_hr_mask=False, p_skip_nlm_denoising=False, p_skip_stacks_ordering=False):
         """Constructor of AnatomicalPipeline class instance."""
 
         # BIDS processing parameters