Merge pull request #345 from oesteban/rel/0.9.0-fixes

REL: Synchronization with latest fMRIPrep changes + minor improvements

Author: oesteban

niworkflows/reports/__init__.py

@@ -0,0 +1,6 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+
+from .core import generate_reports
+
+__all__ = ['generate_reports']

niworkflows/viz/reports.py renamed to niworkflows/reports/core.py

@@ -20,7 +20,6 @@
 from nipype.utils.filemanip import copyfile
 
 
-add_config_paths(figures=pkgrf('niworkflows', 'viz/figures.json'))
 PLURAL_SUFFIX = defaultdict(str('s').format, [('echo', 'es')])
 SVG_SNIPPET = """\
 <object class="svg-reportlet" type="image/svg+xml" data="./{0}">
@@ -197,7 +196,7 @@ class Report(object):
     >>> robj.generate_report()
     0
     >>> len((testdir / 'out' / 'niworkflows' / 'sub-01.html').read_text())
-    16988
+    17582
 
     """
 
@@ -207,6 +206,11 @@ def __init__(self, reportlets_dir, out_dir, run_uuid, config=None,
         self.root = reportlets_dir
 
         # Initialize a BIDS layout
+        try:
+            add_config_paths(figures=pkgrf('niworkflows', 'reports/figures.json'))
+        except ValueError as e:
+            if "Configuration 'figures' already exists" != str(e):
+                raise
         self.layout = BIDSLayout(self.root, config='figures', validate=False)
 
         # Initialize structuring elements
@@ -225,7 +229,7 @@ def __init__(self, reportlets_dir, out_dir, run_uuid, config=None,
             self.out_filename = 'sub-{}.html'.format(self.subject_id)
 
         if config is None:
-            config = pkgrf('niworkflows', 'viz/defaultconfig.json')
+            config = pkgrf('niworkflows', 'reports/defaultconfig.json')
         self._load_config(Path(config))
 
     def _load_config(self, config):

niworkflows/viz/defaultconfig.json renamed to niworkflows/reports/defaultconfig.json

@@ -123,13 +123,21 @@
           "caption": "Brain mask calculated on the BOLD signal (red contour), along with the masks used for a/tCompCor.<br />The aCompCor mask (magenta contour) is a conservative CSF and white-matter mask for extracting physiological and movement confounds. <br />The fCompCor mask (blue contour) contains the top 5% most variable voxels within a heavily-eroded brain-mask.",
           "subtitle": "ROIs in BOLD space"
         },
+        {
+          "bids": {
+            "datatype": "func",
+            "desc": "[at]compcor",
+            "suffix": "bold",
+            "extensions": [".html"]
+          }
+        },
         {
           "bids": {
             "datatype": "func",
             "desc": "flirtnobbr",
             "suffix": "bold"
           },
-          "caption": "FSL <code>flirt</code> was used to generate transformations from EPI space to T1 Space - BBR refinement rejected",
+          "caption": "FSL <code>flirt</code> was used to generate transformations from EPI space to T1 Space - BBR refinement rejected. Note that Nearest Neighbor interpolation is used in the reportlets in order to highlight potential spin-history and other artifacts, whereas final images are resampled using Lanczos interpolation.",
           "subtitle": "EPI to T1 registration"
         },
         {
@@ -138,7 +146,7 @@
             "desc": "coreg",
             "suffix": "bold"
           },
-          "caption": "<code>mri_coreg</code> (FreeSurfer) was used to generate transformations from EPI space to T1 Space - <code>bbregister</code> refinement rejected",
+          "caption": "<code>mri_coreg</code> (FreeSurfer) was used to generate transformations from EPI space to T1 Space - <code>bbregister</code> refinement rejected. Note that Nearest Neighbor interpolation is used in the reportlets in order to highlight potential spin-history and other artifacts, whereas final images are resampled using Lanczos interpolation.",
           "subtitle": "EPI to T1 registration"
         },
         {
@@ -147,7 +155,7 @@
             "desc": "flirtbbr",
             "suffix": "bold"
           },
-          "caption": "FSL <code>flirt</code> was used to generate transformations from EPI-space to T1w-space - The white matter mask calculated with FSL <code>fast</code> (brain tissue segmentation) was used for BBR",
+          "caption": "FSL <code>flirt</code> was used to generate transformations from EPI-space to T1w-space - The white matter mask calculated with FSL <code>fast</code> (brain tissue segmentation) was used for BBR. Note that Nearest Neighbor interpolation is used in the reportlets in order to highlight potential spin-history and other artifacts, whereas final images are resampled using Lanczos interpolation.",
           "subtitle": "EPI to T1 registration"
         },
         {
@@ -156,7 +164,7 @@
             "desc": "bbregister",
             "suffix": "bold"
           },
-          "caption": "<code>bbregister</code> was used to generate transformations from EPI-space to T1w-space",
+          "caption": "<code>bbregister</code> was used to generate transformations from EPI-space to T1w-space. Note that Nearest Neighbor interpolation is used in the reportlets in order to highlight potential spin-history and other artifacts, whereas final images are resampled using Lanczos interpolation.",
           "subtitle": "EPI to T1 registration"
         },
         {

niworkflows/viz/figures.json renamed to niworkflows/reports/figures.json

@@ -5,3 +5,5 @@
 
 from .plots import plot_carpet
 from .utils import SVGNS
+
+__all__ = ['plot_carpet', 'SVGNS']

niworkflows/viz/report.tpl renamed to niworkflows/reports/report.tpl

@@ -33,8 +33,9 @@ def main():
         'niworkflows': [
             'data/t1-mni_registration*.json',
             'data/bold-mni_registration*.json',
-            'viz/*.json',
-            'viz/report.tpl',
+            'reports/defaultconfig.json',
+            'reports/figures.json',
+            'reports/report.tpl',
         ]}
 
     root_dir = op.dirname(op.abspath(getfile(currentframe())))