Merge pull request #34 from oesteban/enh/reportlet

ENH: Set up customized report specification

Author: oesteban

MANIFEST.in

@@ -5,3 +5,6 @@ include LICENSE
 # versioneer
 include versioneer.py
 include dmriprep/_version.py
+
+# data
+include dmriprep/config/reports-spec.yml

dmriprep/cli/run.py

@@ -384,7 +384,9 @@ def main():
 
         # Generate reports phase
         failed_reports = generate_reports(
-            subject_list, output_dir, work_dir, run_uuid, packagename='dmriprep')
+            subject_list, output_dir, work_dir, run_uuid,
+            config=pkgrf('dmriprep', 'config/reports-spec.yml'),
+            packagename='dmriprep')
         write_derivative_description(bids_dir, output_dir / 'dmriprep')
 
         if failed_reports and not opts.notrack:
@@ -524,12 +526,14 @@ def build_workflow(opts, retval):
 
     # Called with reports only
     if opts.reports_only:
+        from pkg_resources import resource_filename as pkgrf
         build_log.log(25, 'Running --reports-only on participants %s', ', '.join(subject_list))
         if opts.run_uuid is not None:
             run_uuid = opts.run_uuid
             retval['run_uuid'] = run_uuid
         retval['return_code'] = generate_reports(
             subject_list, output_dir, work_dir, run_uuid,
+            config=pkgrf('dmriprep', 'config/reports-spec.yml'),
             packagename='dmriprep')
         return retval
 

dmriprep/config/reports-spec.yml

@@ -0,0 +1,31 @@
+package: dmriprep
+sections:
+- name: Summary
+  reportlets:
+  - bids: {datatype: anat, desc: summary, suffix: T1w}
+- name: Anatomical
+  reportlets:
+  - bids:
+      datatype: anat
+      desc: conform
+      extension: [.html]
+      suffix: T1w
+  - bids: {datatype: anat, suffix: dseg}
+    caption: This panel shows the template T1-weighted image (if several T1w images
+      were found), with contours delineating the detected brain mask and brain tissue
+      segmentations.
+    subtitle: Brain mask and brain tissue segmentation of the T1w
+  - bids: {datatype: anat, space: .*, suffix: T1w, regex_search: True}
+    caption: Spatial normalization of the T1w image to the <code>{space}</code> template.
+    description: Results of nonlinear alignment of the T1w reference one or more template
+      space(s). Hover on the panels with the mouse pointer to transition between both
+      spaces.
+    static: false
+    subtitle: Spatial normalization of the anatomical T1w reference
+  - bids: {datatype: anat, desc: reconall, suffix: T1w}
+    caption: Surfaces (white and pial) reconstructed with FreeSurfer (<code>recon-all</code>)
+      overlaid on the participant's T1w template.
+    subtitle: Surface reconstruction
+- name: About
+  reportlets:
+  - bids: {datatype: anat, desc: about, suffix: T1w}

dmriprep/workflows/base.py

@@ -10,13 +10,13 @@
 
 import sys
 import os
+from packaging.version import Version
 from collections import OrderedDict
 from copy import deepcopy
 
 from nipype import __version__ as nipype_ver
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu
-from nilearn import __version__ as nilearn_ver
 
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from niworkflows.interfaces.bids import (
@@ -340,12 +340,9 @@ def init_single_subject_wf(
 """.format(dmriprep_ver=__version__, nipype_ver=nipype_ver)
     workflow.__postdesc__ = """
 
-Many internal operations of *dMRIPrep* use
-*Nilearn* {nilearn_ver} [@nilearn, RRID:SCR_001362],
-mostly within the diffusion MRI processing workflow.
 For more details of the pipeline, see [the section corresponding
 to workflows in *dMRIPrep*'s documentation]\
-(https://dmriprep.readthedocs.io/en/latest/workflows.html \
+(https://nipreps.github.io/dmriprep/{dmriprep_ver}/workflows.html \
 "dMRIPrep's documentation").
 
 
@@ -359,7 +356,7 @@ def init_single_subject_wf(
 
 ### References
 
-""".format(nilearn_ver=nilearn_ver)
+""".format(dmriprep_ver=Version(__version__).public)
 
     # Filter out standard spaces to a separate dict
     std_spaces = OrderedDict([

docs/requirements.txt

@@ -6,7 +6,7 @@ niworkflows ~= 1.1.0
 packaging
 pydot>=1.2.3
 pydotplus
-smriprep ~= 0.4.0
+smriprep ~= 0.4.1
 sphinx-argparse
 sphinx>=2.1.2
 sphinx_rtd_theme

setup.cfg

@@ -13,25 +13,23 @@ classifiers =
     Intended Audience :: Science/Research
     Topic :: Scientific/Engineering :: Image Recognition
     License :: OSI Approved :: BSD License
-    Programming Language :: Python :: 3.5
     Programming Language :: Python :: 3.6
     Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
 
 [options]
 python_requires = >=3.5
 install_requires =
-    dipy >= 1.0.0
+    dipy >=1.0.0
     indexed_gzip >=0.8.8
     nibabel ~= 3.0.0rc1
-    nilearn !=0.5.0, !=0.5.1
     nipype ~= 1.3.1
     niworkflows ~= 1.1.0
     numpy
-    psutil >=5.4
     pybids ~= 0.9.2
     pyyaml
     smriprep ~= 0.4.1
-    templateflow ~= 0.4.2rc
+    templateflow ~= 0.4.2rc1
 test_requires =
     codecov
     coverage
@@ -58,7 +56,7 @@ doc =
 docs =
     %(doc)s
 duecredit = duecredit
-resmon =
+resmon = psutil >=5.4
 sentry = sentry-sdk >=0.6.9
 style =
     flake8 >= 3.7.0
@@ -73,13 +71,15 @@ all =
     %(datalad)s
     %(doc)s
     %(duecredit)s
+    %(resmon)s
     %(sentry)s
     %(tests)s
 
 [options.package_data]
 dmriprep =
     VERSION
     data/boilerplate.bib
+    config/reports-spec.yml
 
 [options.entry_points]
 console_scripts =