enh: add background mosaic

nipreps · May 23, 2023 · 8cb88fb · 8cb88fb
1 parent 05203d3
commit 8cb88fb
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Showing 3 changed files with 23 additions and 7 deletions.
diff --git a/mriqc/data/bootstrap-dwi.yml b/mriqc/data/bootstrap-dwi.yml
@@ -31,11 +31,6 @@ sections:
 - name: Summary
   reportlets:
   - bids: {datatype: figures, desc: summary, extension: [.html]}
-  - bids: {datatype: figures, desc: background}
-    caption: This panel shows a mosaic enhancing the background around the head.
-      Artifacts usually unveil themselves in the air surrounding the head, where no signal
-      sources are present.
-    subtitle: View of the background of the voxel-wise average of the DWI orientations
 - name: DWI shells
   ordering: bval
   reportlets:
@@ -51,6 +46,11 @@ sections:
       such as those intrinsic to SMS parallelization.
     subtitle: Voxel-wise standard deviation calculated across volumes in this <em>DWI shell</em>,
       zoomed-in covering just the brain
+  - bids: {datatype: figures, desc: background}
+    caption: This panel shows a mosaic enhancing the background around the head.
+      Artifacts usually unveil themselves in the air surrounding the head, where no signal
+      sources are present.
+    subtitle: View of the background of the voxel-wise average of this <em>DWI shell</em>
 - name: Extended visual report
   reportlets:
   - bids: {datatype: figures, desc: background}

diff --git a/mriqc/reports/individual.py b/mriqc/reports/individual.py
@@ -78,7 +78,7 @@ def _single_report(in_file):
     prov["Versions_TemplateFlow"] = config.environment.templateflow_version
 
     bids_meta = config.execution.layout.get_file(in_file).get_metadata()
-    bids_meta.pop("global")
+    bids_meta.pop("global", None)
 
     robj = Report(
         config.execution.output_dir,

diff --git a/mriqc/workflows/diffusion/output.py b/mriqc/workflows/diffusion/output.py
@@ -101,7 +101,7 @@ def init_dwi_report_wf(name="dwi_report_wf"):
             only_noise=True,
             cmap="viridis_r",
         ),
-        name="PlotMosaicNoise",
+        name="mosaic_noise",
     )
 
     if config.workflow.species.lower() in ("rat", "mouse"):
@@ -134,6 +134,18 @@ def init_dwi_report_wf(name="dwi_report_wf"):
         iterfield=["in_file", "bval"],
     )
 
+    ds_report_noise = pe.MapNode(
+        DerivativesDataSink(
+            base_directory=reportlets_dir,
+            desc="background",
+            datatype="figures",
+            allowed_entities=("bval",),
+        ),
+        name="ds_report_noise",
+        run_without_submitting=True,
+        iterfield=["in_file", "bval"],
+    )
+
     def _gen_entity(inlist):
         return ["00000"] + [f"{int(round(bval, 0)):05d}" for bval in inlist]
 
@@ -143,12 +155,16 @@ def _gen_entity(inlist):
                                   ("brainmask", "bbox_mask_file")]),
         (inputnode, mosaic_stddev, [("in_stdmap", "in_file"),
                                     ("brainmask", "bbox_mask_file")]),
+        (inputnode, mosaic_noise, [("in_avgmap", "in_file")]),
         (inputnode, ds_report_mean, [("name_source", "source_file"),
                                      (("in_shells", _gen_entity), "bval")]),
         (inputnode, ds_report_stdev, [("name_source", "source_file"),
                                       (("in_shells", _gen_entity), "bval")]),
+        (inputnode, ds_report_noise, [("name_source", "source_file"),
+                                      (("in_shells", _gen_entity), "bval")]),
         (mosaic_mean, ds_report_mean, [("out_file", "in_file")]),
         (mosaic_stddev, ds_report_stdev, [("out_file", "in_file")]),
+        (mosaic_noise, ds_report_mean, [("out_file", "in_file")]),
     ])
     # fmt: on