Merge branch 'fix/osf-templates' into enh/3dvolreg

oesteban · oesteban · commit 1d772473488d · 2018-10-18T09:09:23.000-07:00
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -165,8 +165,8 @@ jobs:
     steps:
       - restore_cache:
           keys:
-            - regression-v0-{{ epoch }}
-            - regression-v0-
+            - regression-v2-{{ epoch }}
+            - regression-v2-
       - run:
           name: Get truncated BOLD series
           command: |
@@ -193,7 +193,7 @@ jobs:
           paths:
             - data
       - save_cache:
-         key: regression-v0-{{ epoch }}
+         key: regression-v2-{{ epoch }}
          paths:
             - /tmp/data
 
@@ -227,10 +227,6 @@ jobs:
             fi
       - attach_workspace:
           at: /tmp
-      - restore_cache:
-          keys:
-            - regression-v0-{{ epoch }}
-            - regression-v0-
       - run:
           name: Check PyPi preconditions
           command: |
@@ -260,7 +256,13 @@ jobs:
               -e FMRIPREP_REGRESSION_REPORTS=/tmp/data/reports \
               --entrypoint="py.test" poldracklab/fmriprep:latest \
               /root/src/fmriprep/ \
-              --doctest-modules --ignore=/root/src/fmriprep/docs --ignore=setup.py
+              -svx --doctest-modules --ignore=/root/src/fmriprep/docs --ignore=setup.py
+      - run:
+          name: Package new masks
+          no_output_timeout: 10m
+          working_directory: /tmp/data/reports
+          command: |
+            tar cfz fmriprep_bold_mask.tar.gz fmriprep_bold_mask/*/*.nii.gz
       - run:
           name: Test fmriprep-wrapper (Python 2)
           command: |
@@ -719,7 +721,9 @@ workflows:
       - get_data:
           filters:
             branches:
-              ignore: /docs?\/.*/
+              ignore:
+                - /docs?\/.*/
+                - /tests?\/.*/
             tags:
               only: /.*/
 
@@ -732,6 +736,8 @@ workflows:
           requires:
             - build
           filters:
+            branches:
+              ignore: /tests?\/.*/
             tags:
               only: /.*/
 
@@ -740,7 +746,9 @@ workflows:
             - build
           filters:
             branches:
-              ignore: /docs?\/.*/
+              ignore:
+                - /docs?\/.*/
+                - /tests?\/.*/
             tags:
               only: /.*/
 
@@ -760,7 +768,9 @@ workflows:
             - build
           filters:
             branches:
-              ignore: /docs?\/.*/
+              ignore:
+                - /docs?\/.*/
+                - /tests?\/.*/
             tags:
               only: /.*/
 
@@ -770,7 +780,9 @@ workflows:
             - build
           filters:
             branches:
-              ignore: /docs?\/.*/
+              ignore:
+                - /docs?\/.*/
+                - /tests?\/.*/
             tags:
               only: /.*/
 
@@ -781,7 +793,9 @@ workflows:
           filters:
             branches:
               # only: /meepi.*/
-              ignore: /docs?\/.*/
+              ignore:
+                - /docs?\/.*/
+                - /tests?\/.*/
             tags:
               only: /.*/
 
diff --git a/fmriprep/__about__.py b/fmriprep/__about__.py
@@ -98,7 +98,7 @@
     'pybids==0.6.5',
     'nitime',
     'nipype>=1.1.3',
-    'niworkflows>=0.4.3',
+    'niworkflows>=0.4.4',
     'statsmodels',
     'seaborn',
     'indexed_gzip>=0.8.2',
diff --git a/fmriprep/interfaces/cifti.py b/fmriprep/interfaces/cifti.py
@@ -130,10 +130,9 @@ def _fetch_data(self):
             raise IOError("Freesurfer annotations for %s not found in %s" % (
                           self.inputs.surface_target, self.inputs.subjects_dir))
 
-        label_space = 'tpl-OASISTRT20'
-        label_dir = getters.get_oasis_dkt31_mni152()
-        label_file = os.path.join(label_dir,
-                                  'tpl-OASISTRT20_variant-DKT31_space-MNI152NLin2009cAsym.nii.gz')
+        label_space = 'OASISTRT20'
+        label_file = str(getters.get_template(label_space) /
+                         'tpl-OASISTRT20_variant-DKT31_space-MNI152NLin2009cAsym.nii.gz')
 
         download_link = getters.OSF_PROJECT_URL + getters.OSF_RESOURCES[label_space][0]
         return annotation_files, label_file, download_link
diff --git a/fmriprep/viz/config.json b/fmriprep/viz/config.json
@@ -100,7 +100,7 @@
             },
             {
                 "name": "epi_mean_t1_registration/flirt",
-                "file_pattern": "func/.*_flirt",
+                "file_pattern": "func/.*_flirtnobbr",
                 "title": "EPI to T1 registration",
                 "description": "FSL <code>flirt</code> was used to generate transformations from EPI space to T1 Space - BBR refinement rejected"
             },
diff --git a/fmriprep/viz/reports.py b/fmriprep/viz/reports.py
@@ -145,7 +145,7 @@ def _read_pkl(path):
 
     @staticmethod
     def _read_txt(path):
-        lines = path.read_text().splitlines()
+        lines = path.read_text(encoding='UTF-8').splitlines()
         data = {'file': str(path)}
         traceback_start = 0
         if lines[0].startswith('Node'):
@@ -170,27 +170,27 @@ def generate_report(self):
         boiler_idx = 0
 
         if (logs_path / 'CITATION.html').exists():
-            text = (logs_path / 'CITATION.html').read_text()
+            text = (logs_path / 'CITATION.html').read_text(encoding='UTF-8')
             text = '<div class="boiler-html">%s</div>' % re.compile(
                 '<body>(.*?)</body>',
                 re.DOTALL | re.IGNORECASE).findall(text)[0].strip()
             boilerplate.append((boiler_idx, 'HTML', text))
             boiler_idx += 1
 
         if (logs_path / 'CITATION.md').exists():
-            text = '<pre>%s</pre>\n' % (logs_path / 'CITATION.md').read_text()
+            text = '<pre>%s</pre>\n' % (logs_path / 'CITATION.md').read_text(encoding='UTF-8')
             boilerplate.append((boiler_idx, 'Markdown', text))
             boiler_idx += 1
 
         if (logs_path / 'CITATION.tex').exists():
-            text = (logs_path / 'CITATION.tex').read_text()
+            text = (logs_path / 'CITATION.tex').read_text(encoding='UTF-8')
             text = re.compile(
                 r'\\begin{document}(.*?)\\end{document}',
                 re.DOTALL | re.IGNORECASE).findall(text)[0].strip()
             text = '<pre>%s</pre>\n' % text
             text += '<h3>Bibliography</h3>\n'
             text += '<pre>%s</pre>\n' % Path(
-                pkgrf('fmriprep', 'data/boilerplate.bib')).read_text()
+                pkgrf('fmriprep', 'data/boilerplate.bib')).read_text(encoding='UTF-8')
             boilerplate.append((boiler_idx, 'LaTeX', text))
             boiler_idx += 1
 
@@ -204,7 +204,7 @@ def generate_report(self):
                                           boilerplate=boilerplate)
 
         # Write out report
-        (self.out_dir / 'fmriprep' / self.out_filename).write_text(report_render)
+        (self.out_dir / 'fmriprep' / self.out_filename).write_text(report_render, encoding='UTF-8')
         return len(self.errors)
 
 
diff --git a/fmriprep/workflows/bold/registration.py b/fmriprep/workflows/bold/registration.py
@@ -157,7 +157,7 @@ def init_bold_reg_wf(freesurfer, use_bbr, bold2t1w_dof, mem_gb, omp_nthreads,
 
         def _bold_reg_suffix(fallback, freesurfer):
             if fallback:
-                return 'coreg' if freesurfer else 'flirt'
+                return 'coreg' if freesurfer else 'flirtnobbr'
             return 'bbregister' if freesurfer else 'flirtbbr'
 
         workflow.connect([
diff --git a/fmriprep/workflows/bold/tests/test_util.py b/fmriprep/workflows/bold/tests/test_util.py
@@ -1,10 +1,11 @@
 ''' Testing module for fmriprep.workflows.bold.util '''
 import pytest
 import os
+from pathlib import Path
 
 import numpy as np
 from nipype.pipeline import engine as pe
-from nipype.utils.filemanip import fname_presuffix
+from nipype.utils.filemanip import fname_presuffix, copyfile
 from nilearn.image import load_img
 
 from niworkflows.interfaces.masks import ROIsPlot
@@ -46,33 +47,49 @@ def symmetric_overlap(img1, img2):
         'ds000216/sub-03_task-rest_echo-4_bold.nii.gz',
         'ds000237/sub-03_task-MemorySpan_acq-multiband_run-01_bold.nii.gz',
         'ds000237/sub-06_task-MemorySpan_acq-multiband_run-01_bold.nii.gz',
-        )
-    ])
+        'ds001240/sub-26_task-localizerimagination_bold.nii.gz',
+        'ds001240/sub-26_task-localizerviewing_bold.nii.gz',
+        'ds001240/sub-26_task-molencoding_run-01_bold.nii.gz',
+        'ds001240/sub-26_task-molencoding_run-02_bold.nii.gz',
+        'ds001240/sub-26_task-molretrieval_run-01_bold.nii.gz',
+        'ds001240/sub-26_task-molretrieval_run-02_bold.nii.gz',
+        'ds001240/sub-26_task-rest_bold.nii.gz',
+        'ds001362/sub-01_task-taskname_run-01_bold.nii.gz',
+    )
+])
 def test_masking(input_fname, expected_fname):
     bold_reference_wf = init_bold_reference_wf(omp_nthreads=1, enhance_t2=True)
     bold_reference_wf.inputs.inputnode.bold_file = input_fname
 
     # Reconstruct base_fname from above
     dirname, basename = os.path.split(input_fname)
-    newpath = os.path.join(os.getenv('FMRIPREP_REGRESSION_REPORTS', '.'),
-                           os.path.basename(dirname))
+    dsname = os.path.basename(dirname)
+    reports_dir = Path(os.getenv('FMRIPREP_REGRESSION_REPORTS', ''))
+    newpath = reports_dir / dsname
     out_fname = fname_presuffix(basename, suffix='_masks.svg', use_ext=False,
-                                newpath=newpath)
-    os.makedirs(newpath, exist_ok=True)
+                                newpath=str(newpath))
+    newpath.mkdir(parents=True, exist_ok=True)
 
     mask_diff_plot = pe.Node(ROIsPlot(), name='mask_diff_plot')
     mask_diff_plot.inputs.in_mask = expected_fname
     mask_diff_plot.inputs.out_report = out_fname
 
+    outputnode = bold_reference_wf.get_node('outputnode')
     bold_reference_wf.connect([
-        (bold_reference_wf.get_node('outputnode'), mask_diff_plot, [
-            ('ref_image', 'in_file'),
-            ('bold_mask', 'in_rois'),
-            ])])
+        (outputnode, mask_diff_plot, [('ref_image', 'in_file'),
+                                      ('bold_mask', 'in_rois')])
+    ])
     res = bold_reference_wf.run(plugin='MultiProc')
 
     combine_masks = [node for node in res.nodes if node.name.endswith('combine_masks')][0]
     overlap = symmetric_overlap(expected_fname,
                                 combine_masks.result.outputs.out_file)
 
+    mask_dir = reports_dir / 'fmriprep_bold_mask' / dsname
+    mask_dir.mkdir(parents=True, exist_ok=True)
+    copyfile(combine_masks.result.outputs.out_file,
+             fname_presuffix(basename, suffix='_mask',
+                             use_ext=True, newpath=str(mask_dir)),
+             copy=True)
+
     assert overlap > 0.95, input_fname
diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
-niworkflows>=0.4.3
+niworkflows>=0.4.4
 grabbit==0.2.3
 pybids==0.6.5
 versioneer

Original file line number	Diff line number	Diff line change
`@@ -100,7 +100,7 @@`
`100`	`100`	`},`
`101`	`101`	`{`
`102`	`102`	`"name": "epi_mean_t1_registration/flirt",`
`103`		`- "file_pattern": "func/.*_flirt",`
	`103`	`+ "file_pattern": "func/.*_flirtnobbr",`
`104`	`104`	`"title": "EPI to T1 registration",`
`105`	`105`	`"description": "FSL <code>flirt</code> was used to generate transformations from EPI space to T1 Space - BBR refinement rejected"`
`106`	`106`	`},`