Add summary reportlets to HTML report

pyproject.toml

@@ -28,7 +28,7 @@ dependencies = [
     "nibabel <= 5.2.0",
     "nilearn == 0.10.1",
     "nipype == 1.8.6",
-    "nireports",
+    "nireports ~= 23.2.2",
     "niworkflows >=1.9,<= 1.10",
     "numpy <= 1.26.3",
     "pandas < 2.0.0",

qsirecon/cli/run.py

@@ -171,7 +171,6 @@ def main():
     finally:
 
         from ..reports.core import generate_reports
-        from ..workflows.base import _load_recon_spec
         from .workflow import copy_boilerplate
 
         # Generate reports phase
@@ -184,15 +183,8 @@ def main():
         )
         write_bidsignore(config.execution.output_dir)
 
-        workflow_spec = _load_recon_spec()
         # Compile list of output folders
-        # TODO: Retain QSIRecon pipeline names in the config object
-        qsirecon_suffixes = []
-        for node_spec in workflow_spec["nodes"]:
-            qsirecon_suffix = node_spec.get("qsirecon_suffix", None)
-            qsirecon_suffixes += [qsirecon_suffix] if qsirecon_suffix else []
-
-        qsirecon_suffixes = sorted(list(set(qsirecon_suffixes)))
+        qsirecon_suffixes = config.workflow.qsirecon_suffixes
         config.loggers.cli.info(f"QSIRecon pipeline suffixes: {qsirecon_suffixes}")
         failed_reports = []
         for qsirecon_suffix in qsirecon_suffixes:

qsirecon/config.py

@@ -553,6 +553,20 @@ class workflow(_Config):
     """Recon workflow specification."""
     output_resolution = None
     """Isotropic voxel size for outputs."""
+    qsirecon_suffixes = []
+    """List of reconstruction workflow names, derived from the recon_spec."""
+
+    @classmethod
+    def init(cls):
+        from .workflows.base import _load_recon_spec
+
+        workflow_spec = _load_recon_spec(cls.recon_spec)
+        qsirecon_suffixes = []
+        for node_spec in workflow_spec["nodes"]:
+            qsirecon_suffix = node_spec.get("qsirecon_suffix", None)
+            qsirecon_suffixes += [qsirecon_suffix] if qsirecon_suffix else []
+
+        cls.qsirecon_suffixes = sorted(list(set(qsirecon_suffixes)))
 
 
 class loggers:

qsirecon/data/io_spec.json

@@ -52,7 +52,7 @@
         "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<mu>}.{extension<txt|json>|txt}",
         "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<exemplarbundles>}.{extension<zip|json>|zip}",
         "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<connectivity>}.{extension<mat|json>|mat}",
-        "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<dwi>}.{extension<html|svg|png|json>}",
+        "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<dwi|T1w|T2w>}.{extension<html|svg|png|json>}",
         "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<peaks>}.{extension<html|svg|png|json>}",
         "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_atlas-{atlas}][_model-{model}][_bundles-{bundles}][_fit-{fit}][_mdp-{mdp}][_mfp-{mfp}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<odfs|matrices>}.{extension<html|svg|png|json>}"
     ]

qsirecon/interfaces/reports.py

@@ -23,6 +23,7 @@
     CommandLineInputSpec,
     Directory,
     File,
+    InputMultiObject,
     InputMultiPath,
     SimpleInterface,
     Str,
@@ -35,45 +36,25 @@
 
 from .qc import createB0_ColorFA_Mask_Sprites, createSprite4D
 
-SUBJECT_TEMPLATE = """\t<ul class="elem-desc">
+SUBJECT_TEMPLATE = """\
+\t<ul class="elem-desc">
 \t\t<li>Subject ID: {subject_id}</li>
-\t\t<li>Structural images: {n_t1s:d} T1-weighted {t2w}</li>
-\t\t<li>Diffusion-weighted series: inputs {n_dwis:d}, outputs {n_outputs:d}</li>
-{groupings}
-\t\t<li>Resampling targets: T1wACPC
+\t\t<li>Structural images: {n_t1w:d} T1-weighted {t2w}</li>
+\t\t<li>Diffusion-weighted series: {n_dwi:d}</li>
+\t\t<li>Standard output spaces: {std_spaces}</li>
+\t\t<li>Non-standard output spaces: {nstd_spaces}</li>
+\t\t<li>FreeSurfer reconstruction: {freesurfer_status}</li>
 \t</ul>
 """
 
-DIFFUSION_TEMPLATE = """\t\t<h3 class="elem-title">Summary</h3>
-\t\t<ul class="elem-desc">
-\t\t\t<li>Phase-encoding (PE) direction: {pedir}</li>
-\t\t\t<li>Susceptibility distortion correction: {sdc}</li>
-\t\t\t<li>Coregistration Transform: {coregistration}</li>
-\t\t\t<li>Denoising Method: {denoise_method}</li>
-\t\t\t<li>Denoising Window: {denoise_window}</li>
-\t\t\t<li>HMC Transform: {hmc_transform}</li>
-\t\t\t<li>HMC Model: {hmc_model}</li>
-\t\t\t<li>DWI series resampled to spaces: T1wACPC</li>
-\t\t\t<li>Confounds collected: {confounds}</li>
-\t\t\t<li>Impute slice threshold: {impute_slice_threshold}</li>
-\t\t</ul>
-{validation_reports}
-"""
-
 ABOUT_TEMPLATE = """\t<ul>
 \t\t<li>QSIRecon version: {version}</li>
 \t\t<li>QSIRecon command: <code>{command}</code></li>
-\t\t<li>Date preprocessed: {date}</li>
+\t\t<li>Date postprocessed: {date}</li>
 \t</ul>
 </div>
 """
 
-GROUPING_TEMPLATE = """\t<ul>
-\t\t<li>Output Name: {output_name}</li>
-{input_files}
-</ul>
-"""
-
 INTERACTIVE_TEMPLATE = """
 <script src="https://unpkg.com/vue"></script>
 <script src="https://nipreps.github.io/dmriprep-viewer/dmriprepReport.umd.min.js"></script>
@@ -128,11 +109,18 @@ def _run_interface(self, runtime):
 class SubjectSummaryInputSpec(BaseInterfaceInputSpec):
     t1w = InputMultiPath(File(exists=True), desc="T1w structural images")
     t2w = InputMultiPath(File(exists=True), desc="T2w structural images")
-    subjects_dir = Directory(desc="FreeSurfer subjects directory")
+    subjects_dir = traits.Either(
+        Directory,
+        None,
+        desc="FreeSurfer subjects directory",
+    )
     subject_id = Str(desc="Subject ID")
-    dwi_groupings = traits.Dict(desc="groupings of DWI files and their output names")
-    output_spaces = traits.List(desc="Target spaces")
-    template = traits.Enum("MNI152NLin2009cAsym", desc="Template space")
+    dwi = InputMultiObject(
+        traits.Either(File(exists=True), traits.List(File(exists=True))),
+        desc="Preprocessed DWI series",
+    )
+    std_spaces = traits.List(Str, desc="list of standard spaces")
+    nstd_spaces = traits.List(Str, desc="list of non-standard spaces")
 
 
 class SubjectSummaryOutputSpec(SummaryOutputSpec):
@@ -148,49 +136,30 @@ class SubjectSummary(SummaryInterface):
     def _run_interface(self, runtime):
         if isdefined(self.inputs.subject_id):
             self._results["subject_id"] = self.inputs.subject_id
-        return super(SubjectSummary, self)._run_interface(runtime)
+        return super()._run_interface(runtime)
 
     def _generate_segment(self):
+        if not isdefined(self.inputs.subjects_dir):
+            freesurfer_status = "Not run"
+        else:
+            freesurfer_status = "Pre-existing directory"
+
         t2w_seg = ""
         if self.inputs.t2w:
-            t2w_seg = "(+ {:d} T2-weighted)".format(len(self.inputs.t2w))
-
-        # Add text for how the dwis are grouped
-        n_dwis = 0
-        n_outputs = 0
-        groupings = ""
-        if isdefined(self.inputs.dwi_groupings):
-            for output_fname, group_info in self.inputs.dwi_groupings.items():
-                n_outputs += 1
-                files_desc = []
-                files_desc.append(
-                    "\t\t\t<li>Scan group: %s (PE Dir %s)</li><ul>"
-                    % (output_fname, group_info["dwi_series_pedir"])
-                )
-                files_desc.append("\t\t\t\t<li>DWI Files: </li>")
-                for dwi_file in group_info["dwi_series"]:
-                    files_desc.append("\t\t\t\t\t<li> %s </li>" % dwi_file)
-                    n_dwis += 1
-                fieldmap_type = group_info["fieldmap_info"]["suffix"]
-                if fieldmap_type is not None:
-                    files_desc.append("\t\t\t\t<li>Fieldmap type: %s </li>" % fieldmap_type)
-
-                    for key, value in group_info["fieldmap_info"].items():
-                        files_desc.append("\t\t\t\t\t<li> %s: %s </li>" % (key, str(value)))
-                        n_dwis += 1
-                files_desc.append("</ul>")
-                groupings += GROUPING_TEMPLATE.format(
-                    output_name=output_fname, input_files="\n".join(files_desc)
-                )
+            t2w_seg = f"(+ {len(self.inputs.t2w):d} T2-weighted)"
+
+        # Add list of tasks with number of runs
+        dwi_series = self.inputs.dwi if isdefined(self.inputs.dwi) else []
+        dwi_series = [s[0] if isinstance(s, list) else s for s in dwi_series]
 
         return SUBJECT_TEMPLATE.format(
             subject_id=self.inputs.subject_id,
-            n_t1s=len(self.inputs.t1w),
+            n_t1w=len(self.inputs.t1w),
             t2w=t2w_seg,
-            n_dwis=n_dwis,
-            n_outputs=n_outputs,
-            groupings=groupings,
-            output_spaces="T1wACPC",
+            n_dwi=len(dwi_series),
+            std_spaces=", ".join(self.inputs.std_spaces),
+            nstd_spaces=", ".join(self.inputs.nstd_spaces),
+            freesurfer_status=freesurfer_status,
         )
 
 

qsirecon/interfaces/utils.py

@@ -97,6 +97,25 @@ def _run_interface(self, runtime):
         return runtime
 
 
+class _GetUniqueInputSpec(BaseInterfaceInputSpec):
+    inlist = traits.List(mandatory=True, desc="list of things")
+
+
+class _GetUniqueOutputSpec(TraitedSpec):
+    outlist = traits.List()
+
+
+class GetUnique(SimpleInterface):
+    input_spec = _GetUniqueInputSpec
+    output_spec = _GetUniqueOutputSpec
+
+    def _run_interface(self, runtime):
+        in_list = self.inputs.inlist
+        in_list = [x for x in in_list if isdefined(x)]
+        self._results["outlist"] = sorted(list(set(in_list)))
+        return runtime
+
+
 def _resample_atlas(input_atlas, output_atlas, transform, ref_image):
     xform = ants.ApplyTransforms(
         transforms=[transform],