Merge pull request #328 from mgxd/new/reports

ENH: Use nireports report generation

Author: mgxd

nibabies/cli/run.py

@@ -139,8 +139,6 @@ def main():
                 config.execution.unique_labels,
                 config.execution.nibabies_dir,
                 config.execution.run_uuid,
-                config=pkgrf("nibabies", "data/reports-spec.yml"),
-                packagename="nibabies",
             )
             write_derivative_description(config.execution.bids_dir, config.execution.nibabies_dir)
             write_bidsignore(config.execution.nibabies_dir)

nibabies/cli/workflow.py

@@ -55,8 +55,6 @@ def build_workflow(config_file):
             config.execution.unique_labels,
             nibabies_dir,
             config.execution.run_uuid,
-            config=pkgrf("nibabies", "data/reports-spec.yml"),
-            packagename="nibabies",
         )
         return retval
 

nibabies/data/reports-spec.yml

@@ -23,9 +23,17 @@ sections:
     static: false
     subtitle: Spatial normalization of the anatomical T1w reference
   - bids: {datatype: figures, 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
+  - bids: {datatype: figures, desc: infantfs, suffix: T1w}
     caption: Surfaces (white and pial) reconstructed with FreeSurfer (<code>infant_recon_all</code>)
       overlaid on the participant's T1w template.
     subtitle: Surface reconstruction
+  - bids: {datatype: figures, desc: mcribs, suffix: T2w}
+    caption: Surfaces (white and pial) reconstructed with M-CRIB-S (<code>MCRIBReconAll</code>)
+      overlaid on the participant's T2w template.
+    subtitle: Surface reconstruction
 
 - name: <em>B<sub>0</sub></em> field mapping
   ordering: session,acquisition,run,fmapid

nibabies/reports/core.py

@@ -1,74 +1,16 @@
-from itertools import product
 from pathlib import Path
 
-from niworkflows.reports.core import Report as _Report
-from pkg_resources import resource_filename as pkgrf
+from nireports.assembler.report import Report
 
-
-class Report(_Report):
-    # niworkflows patch to preserve `out_filename` even if subject_id is present
-    def __init__(
-        self,
-        out_dir,
-        run_uuid,
-        config=None,
-        out_filename=None,
-        packagename=None,
-        reportlets_dir=None,
-        subject_id=None,
-    ):
-        self.root = Path(reportlets_dir or out_dir)
-
-        # Initialize structuring elements
-        self.sections = []
-        self.errors = []
-        self.out_dir = Path(out_dir)
-        self.run_uuid = run_uuid
-        self.packagename = packagename
-        self.subject_id = subject_id
-        if subject_id is not None:
-            self.subject_id = subject_id[4:] if subject_id.startswith("sub-") else subject_id
-            # ensure set output filename is preserved
-            if not out_filename:
-                out_filename = f"sub-{self.subject_id}.html"
-
-        self.out_filename = out_filename or "report.html"
-
-        # Default template from niworkflows
-        self.template_path = Path(pkgrf("niworkflows", "reports/report.tpl"))
-        self._load_config(Path(config or pkgrf("niworkflows", "reports/default.yml")))
-        assert self.template_path.exists()
-
-    # TODO: Upstream ``Report._load_config`` to niworkflows
-    def _load_config(self, config):
-        from yaml import safe_load as load
-
-        settings = load(config.read_text())
-        self.packagename = self.packagename or settings.get("package", None)
-
-        # Removed from here: Appending self.packagename to self.root and self.out_dir
-        # In this version, pass reportlets_dir and out_dir with nibabies in the path.
-
-        if self.subject_id is not None:
-            self.root = self.root / "sub-{}".format(self.subject_id)
-
-        if "template_path" in settings:
-            self.template_path = config.parent / settings["template_path"]
-
-        self.index(settings["sections"])
-
-
-#
-# The following are the interface used directly by NiBabies
-#
+from nibabies.data import load_resource
 
 
 def run_reports(
     out_dir,
-    subject_label,
+    subject,
     run_uuid,
-    config=None,
-    out_filename='report.html',
+    session=None,
+    out_filename=None,
     reportlets_dir=None,
     packagename=None,
 ):
@@ -78,10 +20,9 @@ def run_reports(
     return Report(
         out_dir,
         run_uuid,
-        config=config,
-        out_filename=out_filename,
-        subject_id=subject_label,
-        packagename=packagename,
+        subject=subject,
+        session=session,
+        bootstrap_file=load_resource('reports-spec.yml'),
         reportlets_dir=reportlets_dir,
     ).generate_report()
 
@@ -90,7 +31,6 @@ def generate_reports(
     sub_ses_list,
     output_dir,
     run_uuid,
-    config=None,
     work_dir=None,
     packagename=None,
 ):
@@ -100,17 +40,13 @@ def generate_reports(
         reportlets_dir = Path(work_dir) / "reportlets"
 
     report_errors = []
-    for subject_label, session in sub_ses_list:
-        html_report = ''.join(
-            [f"sub-{subject_label}", f"_ses-{session}" if session else "", ".html"]
-        )
+    for subject, session in sub_ses_list:
         report_errors.append(
             run_reports(
                 output_dir,
-                subject_label,
+                subject,
                 run_uuid,
-                config=config,
-                out_filename=html_report,
+                session=session,
                 packagename=packagename,
                 reportlets_dir=reportlets_dir,
             )

nibabies/workflows/anatomical/outputs.py

@@ -233,25 +233,29 @@ def init_anat_reports_wf(
     if not surface_recon:
         return workflow
 
-    # TODO: Separate report for MCRIBS?
     from smriprep.interfaces.reports import FSSurfaceReport
 
     recon_report = pe.Node(FSSurfaceReport(), name="recon_report")
     recon_report.interface._always_run = True
 
+    if surface_recon == "freesurfer":
+        recon_desc = "reconall"
+    elif surface_recon == "infantfs":
+        recon_desc = "infantfs"
+    elif surface_recon == "mcribs":
+        recon_desc = "mcribs"
+
     ds_recon_report = pe.Node(
-        DerivativesDataSink(base_directory=output_dir, desc="reconall", datatype="figures"),
+        DerivativesDataSink(base_directory=output_dir, desc=recon_desc, datatype="figures"),
         name="ds_recon_report",
         run_without_submitting=True,
     )
-    # fmt: off
     workflow.connect([
         (inputnode, recon_report, [('subjects_dir', 'subjects_dir'),
                                    ('subject_id', 'subject_id')]),
         (recon_report, ds_recon_report, [('out_report', 'in_file')]),
         (inputnode, ds_recon_report, [('source_file', 'source_file')])
-    ])
-    # fmt: on
+    ])  # fmt: skip
 
     return workflow
 

pyproject.toml

@@ -22,6 +22,7 @@ dependencies = [
     'importlib_resources; python_version < "3.9"',
     "nibabel >= 5.0.0",
     "nipype >= 1.8.5",
+    "nireports >= 23.2.0",
     "nitime",
     "nitransforms >= 23.0.1",
     "niworkflows >= 1.9.0",