Merge pull request nipreps#482 from jdkent/maint/1.1.x_fix_ceagent

[FIX] Add CE agent to output figure filename templates

Author: effigies

niworkflows/reports/core.py

@@ -234,7 +234,7 @@ class Report(object):
     >>> robj.generate_report()
     0
     >>> len((testdir / 'out' / 'fmriprep' / 'sub-01.html').read_text())
-    36450
+    36540
 
     .. testcleanup::
 
@@ -311,17 +311,14 @@ def index(self, config):
                 reportlets = []
                 for c in list_combos:
                     # do not display entities with the value None.
-                    c = list(filter(None, c))
-                    ent = list(compress(entities, c))
-                    missing_entities = list(set(entities) - set(ent))
+                    c_filt = list(filter(None, c))
+                    ent_filt = list(compress(entities, c))
                     # Set a common title for this particular combination c
                     title = 'Reports for: %s.' % ', '.join(
-                        ['%s <span class="bids-entity">%s</span>' % (ent[i], c[i])
-                         for i in range(len(c))])
+                        ['%s <span class="bids-entity">%s</span>' % (ent_filt[i], c_filt[i])
+                         for i in range(len(c_filt))])
                     for cfg in subrep_cfg['reportlets']:
-                        for m_e in missing_entities:
-                            cfg['bids'].pop(m_e, None)
-                        cfg['bids'].update({ent[i]: c[i] for i in range(len(c))})
+                        cfg['bids'].update({entities[i]: c[i] for i in range(len(c))})
                         rlet = Reportlet(self.layout, self.out_dir, config=cfg)
                         if not rlet.is_empty():
                             rlet.title = title

niworkflows/reports/figures.json

@@ -21,15 +21,15 @@
             "pattern": "[_/\\\\]acq-([a-zA-Z0-9]+)"
         },
         {
-            "name": "ce",
+            "name": "ceagent",
             "pattern": "[_/\\\\]ce-([a-zA-Z0-9]+)"
         },
         {
             "name": "reconstruction",
             "pattern": "[_/\\\\]rec-([a-zA-Z0-9]+)"
         },
         {
-            "name": "dir",
+            "name": "direction",
             "pattern": "[_/\\\\]dir-([a-zA-Z0-9]+)"
         },
         {
@@ -113,6 +113,6 @@
 
     "default_path_patterns": [
         "sub-{subject}[/ses-{session}]/{datatype<anat|figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{contrast}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask>}.{extension<html|svg>}",
-        "sub-{subject}[/ses-{session}]/{datatype<func|figures>}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_desc-{desc}]_{suffix<bold>}.{extension<html|svg>}"
+        "sub-{subject}[/ses-{session}]/{datatype<func|figures>}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_desc-{desc}]_{suffix<bold>}.{extension<html|svg>}"
     ]
 }

niworkflows/reports/tests/test_core.py

@@ -9,6 +9,7 @@
 
 import matplotlib.pyplot as plt
 from bids.layout.writing import build_path
+from bids.layout import BIDSLayout
 
 import pytest
 
@@ -24,26 +25,28 @@ def bids_sessions(tmpdir_factory):
     pattern = (
         "sub-{subject}[/ses-{session}]/{datatype<anat|func>}/"
         "sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}]"
-        "[_ce-{contrast}][_dir-{direction}][_rec-{reconstruction}]"
+        "[_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}]"
         "[_mod-{modality}][_run-{run}][_echo-{echo}][_space-{space}]"
         "[_desc-{desc}]_{suffix<dseg|T1w|bold>}.{extension<svg>}"
     )
     subjects = ['01']
     tasks = ['t1', 't2', 't3']
     runs = ['01', '02', None]
+    ces = ['none', 'Gd']
     descs = ['aroma', 'bbregister', 'carpetplot', 'rois']
     # create functional data for both sessions
-    ses1_combos = product(subjects, ['1'], tasks, runs, descs)
-    ses2_combos = product(subjects, ['2'], tasks, [None], descs)
+    ses1_combos = product(subjects, ['1'], tasks, [None], runs, descs)
+    ses2_combos = product(subjects, ['2'], tasks, ces, [None], descs)
     # have no runs in the second session (ex: dmriprep test data)
     # https://github.com/nipreps/dmriprep/pull/59
     all_combos = list(ses1_combos) + list(ses2_combos)
 
-    for subject, session, task, run, desc in all_combos:
+    for subject, session, task, ce, run, desc in all_combos:
         entities = {
             'subject': subject,
             'session': session,
             'task': task,
+            'ceagent': ce,
             'run': run,
             'desc': desc,
             'extension': 'svg',
@@ -143,10 +146,10 @@ def test_process_orderings_small(test_report1, orderings,
 @pytest.mark.parametrize(
     "orderings,expected_entities,first_value_combo,last_value_combo",
     [
-        (['session', 'task', 'run'],
-         ['session', 'task', 'run'],
-         ('1', 't1', None),
-         ('2', 't3', None),
+        (['session', 'task', 'ceagent', 'run'],
+         ['session', 'task', 'ceagent', 'run'],
+         ('1', 't1', None, None),
+         ('2', 't3', 'none', None),
          ),
         (['run', 'task', 'session'],
          ['run', 'task', 'session'],
@@ -182,6 +185,7 @@ def test_process_orderings_large(test_report2, orderings,
         ("run"),
         ("session,task"),
         ("session,task,run"),
+        ("session,task,ceagent,run"),
         ("session,task,acquisition,ceagent,reconstruction,direction,run,echo"),
         ("session,task,run,madeupentity"),
     ])
@@ -198,12 +202,15 @@ def test_generated_reportlets(bids_sessions, ordering):
     # expected number of reportlets
     expected_reportlets_num = len(report.layout.get(extension='svg'))
     # bids_session uses these entities
-    needed_entities = ['session', 'task', 'run']
+    needed_entities = ['session', 'task', 'ceagent', 'run']
     # the last section is the most recently run
     reportlets_num = len(report.sections[-1].reportlets)
+    # get the number of figures in the output directory
+    out_layout = BIDSLayout(out_dir, config='figures', validate=False)
+    out_figs = len(out_layout.get())
     # if ordering does not contain all the relevent entities
     # then there should be fewer reportlets than expected
     if all(ent in ordering for ent in needed_entities):
-        assert reportlets_num == expected_reportlets_num
+        assert reportlets_num == expected_reportlets_num == out_figs
     else:
-        assert reportlets_num < expected_reportlets_num
+        assert reportlets_num < expected_reportlets_num == out_figs