Repository: bids-standard/pybids

Issue:
Add method to build BIDSReport from list of files
It would be nice to be able to build reports from lists of files, for tools that collect their inputs using custom functions, like fMRIPrep. In these cases, BIDSLayout filters are insufficient to collect the exact files required by the tools.

EDIT: I should also note that I've got working code for this and would be happy to open a PR if others think it would be useful.


Discussion:

Resolving patch:
diff --git a/bids/reports/parsing.py b/bids/reports/parsing.py
--- a/bids/reports/parsing.py
+++ b/bids/reports/parsing.py
@@ -456,6 +456,7 @@ def parse_niftis(layout, niftis, subj, config, **kwargs):
                     n_runs = len(layout.get_runs(subject=subj,
                                                  task=nifti_struct.entities['task'],
                                                  **kwargs))
+                    n_runs = max(n_runs, 1)
                     description_list.append(func_info(nifti_struct.entities['task'],
                                                       n_runs, metadata, img,
                                                       config))
diff --git a/bids/reports/report.py b/bids/reports/report.py
--- a/bids/reports/report.py
+++ b/bids/reports/report.py
@@ -49,6 +49,74 @@ def __init__(self, layout, config=None):
 
         self.config = config
 
+    def generate_from_files(self, files):
+        r"""Generate a methods section from a list of files.
+
+        Parameters
+        ----------
+        files : list of BIDSImageFile objects
+            List of files from which to generate methods description.
+
+        Returns
+        -------
+        counter : :obj:`collections.Counter`
+            A dictionary of unique descriptions across subjects in the file list,
+            along with the number of times each pattern occurred. In cases
+            where all subjects underwent the same protocol, the most common
+            pattern is most likely the most complete. In cases where the
+            file list contains multiple protocols, each pattern will need to be
+            inspected manually.
+
+        Examples
+        --------
+        >>> from os.path import join
+        >>> from bids.layout import BIDSLayout
+        >>> from bids.reports import BIDSReport
+        >>> from bids.tests import get_test_data_path
+        >>> layout = BIDSLayout(join(get_test_data_path(), 'synthetic'))
+        >>> report = BIDSReport(layout)
+        >>> files = layout.get(session='01', extension=['nii.gz', 'nii'])
+        >>> counter = report.generate_from_files(files)
+        Number of patterns detected: 1
+        Remember to double-check everything and to replace <deg> with a degree symbol.
+
+        >>> counter.most_common()[0][0]  # doctest: +ELLIPSIS
+        'For session 01:\n\tMR data were...'
+        """
+        descriptions = []
+
+        subjs = sorted(list(set([f.get_entities().get('subject') for f in files])))
+        sessions = sorted(list(set([f.get_entities().get('session') for f in files])))
+        for sid in subjs:
+            subject_files = [f for f in files if f.get_entities().get('subject') == sid]
+            description_list = []
+            for ses in sessions:
+                niftis = [f for f in subject_files if f.get_entities().get('session') == ses]
+
+                if niftis:
+                    description_list.append('For session {0}:'.format(ses))
+                    description_list += parsing.parse_niftis(self.layout, niftis,
+                                                             sid, self.config,
+                                                             session=ses)
+                    metadata = self.layout.get_metadata(niftis[0].path)
+                else:
+                    raise Exception('No niftis for subject {0}'.format(subject))
+
+            # Assume all data were converted the same way and use the last nifti
+            # file's json for conversion information.
+            if 'metadata' not in vars():
+                raise Exception('No valid jsons found. Cannot generate final '
+                                'paragraph.')
+
+            description = '\n\t'.join(description_list)
+            description = description.replace('\tFor session', '\nFor session')
+            description += '\n\n{0}'.format(parsing.final_paragraph(metadata))
+            descriptions.append(description)
+        counter = Counter(descriptions)
+        print('Number of patterns detected: {0}'.format(len(counter.keys())))
+        print(utils.reminder())
+        return counter
+
     def generate(self, **kwargs):
         r"""Generate the methods section.
 


Test patch:
diff --git a/bids/reports/tests/test_report.py b/bids/reports/tests/test_report.py
--- a/bids/reports/tests/test_report.py
+++ b/bids/reports/tests/test_report.py
@@ -34,6 +34,16 @@ def test_report_gen(testlayout):
     assert isinstance(descriptions, Counter)
 
 
+def test_report_gen_from_files(testlayout):
+    """Report generation from file list should return a counter of unique
+    descriptions in the dataset.
+    """
+    report = BIDSReport(testlayout)
+    files = testlayout.get(extension=['nii.gz', 'nii'])
+    descriptions = report.generate_from_files(files)
+    assert isinstance(descriptions, Counter)
+
+
 def test_report_subject(testlayout):
     """Generating a report for one subject should only return one subject's
     description (i.e., one pattern with a count of one).