Merge tag '1.1.12'

1.1.12 (March 19, 2020)

Bug-fix release in the 1.1.x series.

* FIX: Update naming patterns in figures.json (nipreps#483)
* FIX: Add CE agent to output figure filename templates (nipreps#482)

Author: effigies

CHANGES.rst

@@ -1,3 +1,16 @@
+1.1.12 (March 19, 2020)
+=======================
+Bug-fix release in the 1.1.x series.
+
+  * FIX: Update naming patterns in figures.json (#483)
+  * FIX: Add CE agent to output figure filename templates (#482)
+
+1.1.11 (March 17, 2020)
+=======================
+Bug-fix release to improve CIFTI compatibility with workbench tools.
+
+  * FIX: Ensure BOLD and label orientations are equal (#477)
+
 1.1.10 (March 11, 2020)
 =======================
 Bug-fix release in the 1.1.x series.

niworkflows/interfaces/cifti.py

@@ -318,6 +318,8 @@ def _create_cifti_image(bold_file, label_file, bold_surfs, annotation_files, tr,
         warnings.warn("Resampling bold volume to match label dimensions")
         bold_img = resample_to_img(bold_img, label_img)
 
+    bold_img = _reorient_image(bold_img, target_img=label_img)
+
     bold_data = bold_img.get_fdata(dtype='float32')
     timepoints = bold_img.shape[3]
     label_data = np.asanyarray(label_img.dataobj).astype('int16')
@@ -422,3 +424,66 @@ def _create_cifti_image(bold_file, label_file, bold_surfs, annotation_files, tr,
     out_file = "{}.dtseries.nii".format(split_filename(bold_file)[1])
     ci.save(img, out_file)
     return Path.cwd() / out_file
+
+
+def _reorient_image(img, *, target_img=None, orientation=None):
+    """
+    Coerce an image to a target orientation.
+
+    .. note::
+        Only RAS -> LAS conversion is currently supported
+
+    Parameters
+    ----------
+    img : :obj:`SpatialImage`
+        image to be reoriented
+    target_img : :obj:`SpatialImage`, optional
+        target in desired orientation
+    orientation : :obj:`str` or :obj:`tuple`, optional
+        desired orientation, if no target image is provided
+
+    .. testsetup::
+    >>> img = nb.load(Path(test_data) / 'testRobustMNINormalizationRPTMovingWarpedImage.nii.gz')
+    >>> las_img = img.as_reoriented([[0, -1], [1, 1], [2, 1]])
+
+    Examples
+    --------
+    >>> nimg = _reorient_image(img, target_img=img)
+    >>> nb.aff2axcodes(nimg.affine)
+    ('R', 'A', 'S')
+
+    >>> nimg = _reorient_image(img, target_img=las_img)
+    >>> nb.aff2axcodes(nimg.affine)
+    ('L', 'A', 'S')
+
+    >>> nimg = _reorient_image(img, orientation='LAS')
+    >>> nb.aff2axcodes(nimg.affine)
+    ('L', 'A', 'S')
+
+    >>> _reorient_image(img, orientation='LPI')
+    Traceback (most recent call last):
+      ...
+    NotImplementedError: Cannot reorient ...
+
+    >>> _reorient_image(img)
+    Traceback (most recent call last):
+      ...
+    RuntimeError: No orientation ...
+
+    """
+    orient0 = nb.aff2axcodes(img.affine)
+    if target_img is not None:
+        orient1 = nb.aff2axcodes(target_img.affine)
+    elif orientation is not None:
+        orient1 = tuple(orientation)
+    else:
+        raise RuntimeError("No orientation to reorient to!")
+
+    if orient0 == orient1:  # already in desired orientation
+        return img
+    elif orient0 == tuple('RAS') and orient1 == tuple('LAS'):  # RAS -> LAS
+        return img.as_reoriented([[0, -1], [1, 1], [2, 1]])
+    else:
+        raise NotImplementedError(
+            "Cannot reorient {0} to {1}.".format(orient0, orient1)
+        )

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]+)"
         },
         {
@@ -47,7 +47,7 @@
         },
         {
             "name": "echo",
-            "pattern": "[_/\\\\]echo-([0-9]+)\\_bold."
+            "pattern": "[_/\\\\]echo-([0-9]+)"
         },
         {
             "name": "recording",
@@ -112,7 +112,7 @@
     ],
 
     "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<anat|figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_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}][_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