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Merged
merged 7 commits into from
Dec 3, 2017
Merged

[ENH] Strip reportlets out of full report #867

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1d9d2d5
fix --reports-only
oesteban Dec 1, 2017
b679d79
convert all automatic reportlets to svg and strip out of report
oesteban Dec 1, 2017
b1b2678
change css class to svg objects
oesteban Dec 1, 2017
2b33560
a more consistent setting of svg reportlets
oesteban Dec 1, 2017
35912c0
change svg->figures, update outputs
oesteban Dec 1, 2017
5010914
update niworkflows requirement
oesteban Dec 1, 2017
f55110c
update outputs
oesteban Dec 2, 2017
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17 changes: 17 additions & 0 deletions .circle/data/ds005_outputs.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,23 @@ ds005/out/fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_target-T1w_w
ds005/out/fmriprep/sub-01/anat/sub-01_T1w_space-orig_target-T1w_affine.txt
ds005/out/fmriprep/sub-01/anat/sub-01_T1w_target-fsnative_affine.txt
ds005/out/fmriprep/sub-01/anat/sub-01_T1w_target-MNI152NLin2009cAsym_warp.h5
ds005/out/fmriprep/sub-01/figures
ds005/out/fmriprep/sub-01/figures/_scratch_reportlets_fmriprep_sub-01_anat_sub-01_T1w_reconall.svg
ds005/out/fmriprep/sub-01/figures/_scratch_reportlets_fmriprep_sub-01_anat_sub-01_T1w_t1_2_mni.svg
ds005/out/fmriprep/sub-01/figures/_scratch_reportlets_fmriprep_sub-01_anat_sub-01_T1w_t1_seg.svg
ds005/out/fmriprep/sub-01/figures/_scratch_reportlets_fmriprep_sub-01_anat_sub-01_T1w_t1_skull_strip.svg
ds005/out/fmriprep/sub-01/figures/_scratch_reportlets_fmriprep_sub-01_func_sub-01_task-mixedgamblestask_run-01_bold_acompcor.svg
ds005/out/fmriprep/sub-01/figures/_scratch_reportlets_fmriprep_sub-01_func_sub-01_task-mixedgamblestask_run-01_bold_bbr.svg
ds005/out/fmriprep/sub-01/figures/_scratch_reportlets_fmriprep_sub-01_func_sub-01_task-mixedgamblestask_run-01_bold_bold_mask.svg
ds005/out/fmriprep/sub-01/figures/_scratch_reportlets_fmriprep_sub-01_func_sub-01_task-mixedgamblestask_run-01_bold_ica_aroma.svg
ds005/out/fmriprep/sub-01/figures/_scratch_reportlets_fmriprep_sub-01_func_sub-01_task-mixedgamblestask_run-01_bold_syn_sdc.svg
ds005/out/fmriprep/sub-01/figures/_scratch_reportlets_fmriprep_sub-01_func_sub-01_task-mixedgamblestask_run-01_bold_tcompcor.svg
ds005/out/fmriprep/sub-01/figures/_scratch_reportlets_fmriprep_sub-01_func_sub-01_task-mixedgamblestask_run-02_bold_acompcor.svg
ds005/out/fmriprep/sub-01/figures/_scratch_reportlets_fmriprep_sub-01_func_sub-01_task-mixedgamblestask_run-02_bold_bbr.svg
ds005/out/fmriprep/sub-01/figures/_scratch_reportlets_fmriprep_sub-01_func_sub-01_task-mixedgamblestask_run-02_bold_bold_mask.svg
ds005/out/fmriprep/sub-01/figures/_scratch_reportlets_fmriprep_sub-01_func_sub-01_task-mixedgamblestask_run-02_bold_ica_aroma.svg
ds005/out/fmriprep/sub-01/figures/_scratch_reportlets_fmriprep_sub-01_func_sub-01_task-mixedgamblestask_run-02_bold_syn_sdc.svg
ds005/out/fmriprep/sub-01/figures/_scratch_reportlets_fmriprep_sub-01_func_sub-01_task-mixedgamblestask_run-02_bold_tcompcor.svg
ds005/out/fmriprep/sub-01/func
ds005/out/fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_AROMAnoiseICs.csv
ds005/out/fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_confounds.tsv
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21 changes: 21 additions & 0 deletions .circle/data/ds054_outputs.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,27 @@ ds054/out/fmriprep/sub-100185/anat/sub-100185_T1w_space-MNI152NLin2009cAsym_prep
ds054/out/fmriprep/sub-100185/anat/sub-100185_T1w_space-MNI152NLin2009cAsym_target-T1w_warp.h5
ds054/out/fmriprep/sub-100185/anat/sub-100185_T1w_space-orig_target-T1w_affine.txt
ds054/out/fmriprep/sub-100185/anat/sub-100185_T1w_target-MNI152NLin2009cAsym_warp.h5
ds054/out/fmriprep/sub-100185/figures
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_anat_sub-100185_T1w_t1_2_mni.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_anat_sub-100185_T1w_t1_seg.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_anat_sub-100185_T1w_t1_skull_strip.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_fmap_sub-100185_phasediff_fmap_mask.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_func_sub-100185_task-machinegame_run-01_bold_acompcor.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_func_sub-100185_task-machinegame_run-01_bold_bold_mask.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_func_sub-100185_task-machinegame_run-01_bold_flt_bbr.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_func_sub-100185_task-machinegame_run-01_bold_fmap_reg.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_func_sub-100185_task-machinegame_run-01_bold_fmap_reg_vsm.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_func_sub-100185_task-machinegame_run-01_bold_syn_sdc.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_func_sub-100185_task-machinegame_run-01_bold_tcompcor.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_func_sub-100185_task-machinegame_run-01_bold_variant-hmcsdc_preproc.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_func_sub-100185_task-machinegame_run-02_bold_acompcor.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_func_sub-100185_task-machinegame_run-02_bold_bold_mask.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_func_sub-100185_task-machinegame_run-02_bold_flt_bbr.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_func_sub-100185_task-machinegame_run-02_bold_fmap_reg.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_func_sub-100185_task-machinegame_run-02_bold_fmap_reg_vsm.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_func_sub-100185_task-machinegame_run-02_bold_syn_sdc.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_func_sub-100185_task-machinegame_run-02_bold_tcompcor.svg
ds054/out/fmriprep/sub-100185/figures/_scratch_reportlets_fmriprep_sub-100185_func_sub-100185_task-machinegame_run-02_bold_variant-hmcsdc_preproc.svg
ds054/out/fmriprep/sub-100185/func
ds054/out/fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_bold_confounds.tsv
ds054/out/fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
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2 changes: 1 addition & 1 deletion docs/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,4 +28,4 @@ dependencies:
- svgutils
- nitime
- nilearn
- niworkflows>=0.1.11
- niworkflows>=0.2.0
28 changes: 17 additions & 11 deletions fmriprep/cli/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -224,10 +224,14 @@ def main():
work_dir = retval['work_dir']
subject_list = retval['subject_list']
run_uuid = retval['run_uuid']
retcode = retval['return_code']

if opts.write_graph:
fmriprep_wf.write_graph(graph2use="colored", format='svg', simple_form=True)

if opts.reports_only:
sys.exit(int(retcode > 0))

# Clean up master process before running workflow, which may create forks
gc.collect()
try:
Expand Down Expand Up @@ -359,14 +363,21 @@ def build_workflow(opts, retval):
},
})

retval['return_code'] = 0
retval['plugin_settings'] = plugin_settings
retval['output_dir'] = output_dir
retval['work_dir'] = work_dir
retval['subject_list'] = subject_list
retval['run_uuid'] = run_uuid

# Called with reports only
if opts.reports_only:
logger.log(25, 'Running --reports-only on participants %s', ', '.join(subject_list))
if opts.run_uuid is not None:
run_uuid = opts.run_uuid

reports_code = generate_reports(subject_list, output_dir, work_dir, run_uuid)
sys.exit(int(reports_code > 0))
retval['return_code'] = generate_reports(subject_list, output_dir, work_dir, run_uuid)
retval['workflow'] = None
return retval

# Build main workflow
logger.log(25, INIT_MSG(
Expand All @@ -376,7 +387,7 @@ def build_workflow(opts, retval):
uuid=run_uuid)
)

fmriprep_wf = init_fmriprep_wf(
retval['workflow'] = init_fmriprep_wf(
subject_list=subject_list,
task_id=opts.task_id,
run_uuid=run_uuid,
Expand Down Expand Up @@ -405,13 +416,8 @@ def build_workflow(opts, retval):
use_aroma=opts.use_aroma,
ignore_aroma_err=opts.ignore_aroma_denoising_errors,
)

retval['workflow'] = fmriprep_wf
retval['plugin_settings'] = plugin_settings
retval['output_dir'] = output_dir
retval['work_dir'] = work_dir
retval['subject_list'] = subject_list
retval['run_uuid'] = run_uuid
retval['return_code'] = 0
return retval


if __name__ == '__main__':
Expand Down
2 changes: 1 addition & 1 deletion fmriprep/info.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@
'grabbit',
'pybids>=0.4.2',
'nitime',
'niworkflows>=0.1.11',
'niworkflows>=0.2.0',
'statsmodels',
'nipype',
'seaborn',
Expand Down
25 changes: 19 additions & 6 deletions fmriprep/viz/reports.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
import re
import os
import html
import shutil

import jinja2
from niworkflows.nipype.utils.filemanip import loadcrash
Expand Down Expand Up @@ -111,21 +112,33 @@ def _load_config(self, config):
self.index()

def index(self):
fig_dir = 'figures'
subject_dir = self.root.split('/')[-1]
subject = re.search('^(?P<subject_id>sub-[a-zA-Z0-9]+)$', subject_dir).group()
svg_dir = os.path.join(self.out_dir, 'fmriprep', subject, fig_dir)
os.makedirs(svg_dir, exist_ok=True)

for root, directories, filenames in os.walk(self.root):
for f in filenames:
f = os.path.join(root, f)
for sub_report in self.sub_reports:
for element in sub_report.elements:
ext = f.split('.')[-1]
if element.file_pattern.search(f) and (ext == 'svg' or ext == 'html'):
with open(f) as fp:
content = fp.read()
element.files_contents.append((f, content))
if element.file_pattern.search(f) and ext in ('svg', 'html'):
if ext == 'html':
with open(f) as fp:
content = fp.read()
else:
fbase = f.replace('/', '_')
newf = os.path.join(svg_dir, fbase)
shutil.copy(f, newf)
content = """\
<object type="image/svg+xml" data="./{0}" class="reportlet">filename:{0}</object>\
""".format(os.path.join(subject, fig_dir, fbase))
element.files_contents.append((f, content))
for sub_report in self.sub_reports:
sub_report.order_by_run()

subject_dir = self.root.split('/')[-1]
subject = re.search('^(?P<subject_id>sub-[a-zA-Z0-9]+)$', subject_dir).group()
error_dir = os.path.join(self.out_dir, "fmriprep", subject, 'log', self.run_uuid)
if os.path.isdir(error_dir):
self.index_error_dir(error_dir)
Expand Down
2 changes: 1 addition & 1 deletion requirements.txt
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
niworkflows>=0.1.11
niworkflows>=0.2.0