Remove melodic report (duplicate of AROMA report).

src/fmripost_aroma/interfaces/reportlets.py

@@ -96,87 +96,74 @@ def _generate_segment(self):
         raise NotImplementedError
 
 
-class _MELODICInputSpecRPT(nrb._SVGReportCapableInputSpec, fsl.model.MELODICInputSpec):
-    out_report = File(
-        'melodic_reportlet.svg',
-        usedefault=True,
-        desc='Filename for the visual report generated by Nipype.',
-    )
-    report_mask = File(
-        desc=(
-            'Mask used to draw the outline on the reportlet. '
-            'If not set the mask will be derived from the data.'
-        ),
+class SubjectSummaryInputSpec(BaseInterfaceInputSpec):
+    subject_id = Str(desc='Subject ID')
+    bold = InputMultiObject(
+        traits.Either(File(exists=True), traits.List(File(exists=True))),
+        desc='BOLD functional series',
     )
+    std_spaces = traits.List(Str, desc='list of standard spaces')
+    nstd_spaces = traits.List(Str, desc='list of non-standard spaces')
 
 
-class _MELODICOutputSpecRPT(
-    reporting.ReportCapableOutputSpec,
-    fsl.model.MELODICOutputSpec,
-):
-    pass
-
-
-class MELODICRPT(fsl.MELODIC):
-    """Create a reportlet for MELODIC outputs."""
-
-    input_spec = _MELODICInputSpecRPT
-    output_spec = _MELODICOutputSpecRPT
-    _out_report = None
-
-    def __init__(self, generate_report=False, **kwargs):
-        """Create the reportlet."""
-        super().__init__(**kwargs)
-        self.generate_report = generate_report
-
-    def _post_run_hook(self, runtime):
-        # Run _post_run_hook of super class
-        runtime = super()._post_run_hook(runtime)
-        # leave early if there's nothing to do
-        if not self.generate_report:
-            return runtime
-
-        NIWORKFLOWS_LOG.info('Generating report for MELODIC.')
-        _melodic_dir = runtime.cwd
-        if isdefined(self.inputs.out_dir):
-            _melodic_dir = self.inputs.out_dir
-        self._melodic_dir = os.path.abspath(_melodic_dir)
-
-        self._out_report = self.inputs.out_report
-        if not os.path.isabs(self._out_report):
-            self._out_report = os.path.abspath(os.path.join(runtime.cwd, self._out_report))
-
-        mix = os.path.join(self._melodic_dir, 'melodic_mix')
-        if not os.path.exists(mix):
-            NIWORKFLOWS_LOG.warning("MELODIC outputs not found, assuming it didn't converge.")
-            self._out_report = self._out_report.replace('.svg', '.html')
-            snippet = '<h4>MELODIC did not converge, no output</h4>'
-            with open(self._out_report, 'w') as fobj:
-                fobj.write(snippet)
-            return runtime
-
-        self._generate_report()
-        return runtime
+class SubjectSummary(SummaryInterface):
+    input_spec = SubjectSummaryInputSpec
+    output_spec = SummaryOutputSpec
 
-    def _list_outputs(self):
-        try:
-            outputs = super()._list_outputs()
-        except NotImplementedError:
-            outputs = {}
-        if self._out_report is not None:
-            outputs['out_report'] = self._out_report
-        return outputs
+    def _generate_segment(self):
+        BIDS_NAME = re.compile(
+            r'^(.*\/)?'
+            '(?P<subject_id>sub-[a-zA-Z0-9]+)'
+            '(_(?P<session_id>ses-[a-zA-Z0-9]+))?'
+            '(_(?P<task_id>task-[a-zA-Z0-9]+))?'
+            '(_(?P<acq_id>acq-[a-zA-Z0-9]+))?'
+            '(_(?P<rec_id>rec-[a-zA-Z0-9]+))?'
+            '(_(?P<run_id>run-[a-zA-Z0-9]+))?'
+        )
 
-    def _generate_report(self):
-        from niworkflows.viz.utils import plot_melodic_components
+        # Add list of tasks with number of runs
+        bold_series = self.inputs.bold if isdefined(self.inputs.bold) else []
+        bold_series = [s[0] if isinstance(s, list) else s for s in bold_series]
 
-        plot_melodic_components(
-            melodic_dir=self._melodic_dir,
-            in_file=self.inputs.in_files[0],
-            tr=self.inputs.tr_sec,
-            out_file=self._out_report,
-            compress=self.inputs.compress_report,
-            report_mask=self.inputs.report_mask,
+        counts = Counter(
+            BIDS_NAME.search(series).groupdict()['task_id'][5:] for series in bold_series
+        )
+
+        tasks = ''
+        if counts:
+            header = '\t\t<ul class="elem-desc">'
+            footer = '\t\t</ul>'
+            lines = [
+                '\t\t\t<li>Task: {task_id} ({n_runs:d} run{s})</li>'.format(
+                    task_id=task_id, n_runs=n_runs, s='' if n_runs == 1 else 's'
+                )
+                for task_id, n_runs in sorted(counts.items())
+            ]
+            tasks = '\n'.join([header] + lines + [footer])
+
+        return SUBJECT_TEMPLATE.format(
+            subject_id=self.inputs.subject_id,
+            n_bold=len(bold_series),
+            tasks=tasks,
+            std_spaces=', '.join(self.inputs.std_spaces),
+            nstd_spaces=', '.join(self.inputs.nstd_spaces),
+        )
+
+
+class AboutSummaryInputSpec(BaseInterfaceInputSpec):
+    version = Str(desc='FMRIPREP version')
+    command = Str(desc='FMRIPREP command')
+    # Date not included - update timestamp only if version or command changes
+
+
+class AboutSummary(SummaryInterface):
+    input_spec = AboutSummaryInputSpec
+
+    def _generate_segment(self):
+        return ABOUT_TEMPLATE.format(
+            version=self.inputs.version,
+            command=self.inputs.command,
+            date=time.strftime('%Y-%m-%d %H:%M:%S %z'),
         )
 
 
@@ -243,74 +230,3 @@ def _run_interface(self, runtime):
         )
         self._results['out_report'] = out_file
         return runtime
-
-
-class SubjectSummaryInputSpec(BaseInterfaceInputSpec):
-    subject_id = Str(desc='Subject ID')
-    bold = InputMultiObject(
-        traits.Either(File(exists=True), traits.List(File(exists=True))),
-        desc='BOLD functional series',
-    )
-    std_spaces = traits.List(Str, desc='list of standard spaces')
-    nstd_spaces = traits.List(Str, desc='list of non-standard spaces')
-
-
-class SubjectSummary(SummaryInterface):
-    input_spec = SubjectSummaryInputSpec
-    output_spec = SummaryOutputSpec
-
-    def _generate_segment(self):
-        BIDS_NAME = re.compile(
-            r'^(.*\/)?'
-            '(?P<subject_id>sub-[a-zA-Z0-9]+)'
-            '(_(?P<session_id>ses-[a-zA-Z0-9]+))?'
-            '(_(?P<task_id>task-[a-zA-Z0-9]+))?'
-            '(_(?P<acq_id>acq-[a-zA-Z0-9]+))?'
-            '(_(?P<rec_id>rec-[a-zA-Z0-9]+))?'
-            '(_(?P<run_id>run-[a-zA-Z0-9]+))?'
-        )
-
-        # Add list of tasks with number of runs
-        bold_series = self.inputs.bold if isdefined(self.inputs.bold) else []
-        bold_series = [s[0] if isinstance(s, list) else s for s in bold_series]
-
-        counts = Counter(
-            BIDS_NAME.search(series).groupdict()['task_id'][5:] for series in bold_series
-        )
-
-        tasks = ''
-        if counts:
-            header = '\t\t<ul class="elem-desc">'
-            footer = '\t\t</ul>'
-            lines = [
-                '\t\t\t<li>Task: {task_id} ({n_runs:d} run{s})</li>'.format(
-                    task_id=task_id, n_runs=n_runs, s='' if n_runs == 1 else 's'
-                )
-                for task_id, n_runs in sorted(counts.items())
-            ]
-            tasks = '\n'.join([header] + lines + [footer])
-
-        return SUBJECT_TEMPLATE.format(
-            subject_id=self.inputs.subject_id,
-            n_bold=len(bold_series),
-            tasks=tasks,
-            std_spaces=', '.join(self.inputs.std_spaces),
-            nstd_spaces=', '.join(self.inputs.nstd_spaces),
-        )
-
-
-class AboutSummaryInputSpec(BaseInterfaceInputSpec):
-    version = Str(desc='FMRIPREP version')
-    command = Str(desc='FMRIPREP command')
-    # Date not included - update timestamp only if version or command changes
-
-
-class AboutSummary(SummaryInterface):
-    input_spec = AboutSummaryInputSpec
-
-    def _generate_segment(self):
-        return ABOUT_TEMPLATE.format(
-            version=self.inputs.version,
-            command=self.inputs.command,
-            date=time.strftime('%Y-%m-%d %H:%M:%S %z'),
-        )

src/fmripost_aroma/workflows/aroma.py

@@ -109,7 +109,7 @@ def init_ica_aroma_wf(
 
     from fmripost_aroma.interfaces.confounds import ICAConfounds
     from fmripost_aroma.interfaces.nilearn import MeanImage, MedianValue
-    from fmripost_aroma.interfaces.reportlets import ICAAROMARPT, MELODICRPT
+    from fmripost_aroma.interfaces.reportlets import ICAAROMARPT
 
     workflow = Workflow(name=_get_wf_name(bold_file, 'aroma'))
     workflow.__postdesc__ = f"""\
@@ -200,7 +200,7 @@ def init_ica_aroma_wf(
 
     # ICA with MELODIC
     melodic = pe.Node(
-        MELODICRPT(
+        fsl.MELODIC(
             no_bet=True,
             tr_sec=float(metadata['RepetitionTime']),
             mm_thresh=0.5,
@@ -214,20 +214,6 @@ def init_ica_aroma_wf(
         (smooth, melodic, [('smoothed_file', 'in_files')]),
     ])  # fmt:skip
 
-    ds_report_melodic = pe.Node(
-        DerivativesDataSink(
-            base_directory=config.execution.fmripost_aroma_dir,
-            source_file=bold_file,
-            datatype='figures',
-            desc='melodic',
-            dismiss_entities=('echo', 'den', 'res'),
-        ),
-        name='ds_report_melodic',
-        run_without_submitting=True,
-        mem_gb=config.DEFAULT_MEMORY_MIN_GB,
-    )
-    workflow.connect([(melodic, ds_report_melodic, [('out_report', 'in_file')])])
-
     select_melodic_files = pe.Node(
         niu.Function(
             function=_select_melodic_files,