fix: update workflows with new NiReports API

nipreps · Mar 10, 2023 · cb688e5 · cb688e5
1 parent d3608d5
commit cb688e5
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Showing 2 changed files with 30 additions and 22 deletions.
diff --git a/mriqc/workflows/anatomical.py b/mriqc/workflows/anatomical.py
@@ -536,7 +536,6 @@ def individual_reports(name="ReportsWorkflow"):
         PlotMosaic(
             out_file="plot_anat_mosaic1_zoomed.svg",
             cmap="Greys_r",
-            species=config.workflow.species.lower()
         ),
         name="PlotMosaicZoomed",
     )
@@ -546,10 +545,12 @@ def individual_reports(name="ReportsWorkflow"):
             out_file="plot_anat_mosaic2_noise.svg",
             only_noise=True,
             cmap="viridis_r",
-            species=config.workflow.species.lower(),
         ),
         name="PlotMosaicNoise",
     )
+    if config.workflow.species.lower() in ("rat", "mouse"):
+        mosaic_zoom.inputs.view = ("coronal", "axial")
+        mosaic_noise.inputs.view = ("coronal", "axial")
 
     mplots = pe.Node(niu.Merge(pages + extra_pages), name="MergePlots")
     rnode = pe.Node(IndividualReport(), name="GenerateReport")
@@ -582,9 +583,10 @@ def individual_reports(name="ReportsWorkflow"):
 
     from nireports.interfaces import PlotContours
 
+    display_mode = "y" if config.workflow.species.lower() in ("rat", "mouse") else "z"
     plot_segm = pe.Node(
         PlotContours(
-            display_mode="y" if config.workflow.species.lower() == "rat" else "z",
+            display_mode=display_mode,
             levels=[0.5, 1.5, 2.5],
             cut_coords=10,
             colors=["r", "g", "b"],
@@ -594,17 +596,32 @@ def individual_reports(name="ReportsWorkflow"):
 
     plot_bmask = pe.Node(
         PlotContours(
-            display_mode="y" if config.workflow.species.lower() == "rat" else "z",
+            display_mode=display_mode,
             levels=[0.5],
             colors=["r"],
             cut_coords=10,
             out_file="bmask",
         ),
         name="PlotBrainmask",
     )
+
+    plot_artmask = pe.Node(
+        PlotContours(
+            display_mode=display_mode,
+            levels=[0.5],
+            colors=["r"],
+            cut_coords=10,
+            out_file="artmask",
+            saturate=True,
+        ),
+        name="PlotArtmask",
+    )
+
+    # NOTE: humans switch on these two to coronal view.
+    display_mode = "y" if config.workflow.species.lower() in ("rat", "mouse") else "x"
     plot_airmask = pe.Node(
         PlotContours(
-            display_mode="y" if config.workflow.species.lower() == "rat" else "x",
+            display_mode=display_mode,
             levels=[0.5],
             colors=["r"],
             cut_coords=6,
@@ -614,25 +631,14 @@ def individual_reports(name="ReportsWorkflow"):
     )
     plot_headmask = pe.Node(
         PlotContours(
-            display_mode="y" if config.workflow.species.lower() == "rat" else "x",
+            display_mode=display_mode,
             levels=[0.5],
             colors=["r"],
             cut_coords=6,
             out_file="headmask",
         ),
         name="PlotHeadmask",
     )
-    plot_artmask = pe.Node(
-        PlotContours(
-            display_mode="y" if config.workflow.species.lower() == "rat" else "z",
-            levels=[0.5],
-            colors=["r"],
-            cut_coords=10,
-            out_file="artmask",
-            saturate=True,
-        ),
-        name="PlotArtmask",
-    )
 
     # fmt: off
     workflow.connect([

diff --git a/mriqc/workflows/functional.py b/mriqc/workflows/functional.py
@@ -532,7 +532,6 @@ def individual_reports(name="ReportsWorkflow"):
         PlotMosaic(
             out_file="plot_func_mean_mosaic1.svg",
             cmap="Greys_r",
-            species=config.workflow.species.lower(),
         ),
         name="PlotMosaicMean",
     )
@@ -541,7 +540,6 @@ def individual_reports(name="ReportsWorkflow"):
         PlotMosaic(
             out_file="plot_func_stddev_mosaic2_stddev.svg",
             cmap="viridis",
-            species=config.workflow.species.lower(),
         ),
         name="PlotMosaicSD",
     )
@@ -614,7 +612,6 @@ def individual_reports(name="ReportsWorkflow"):
         PlotMosaic(
             out_file="plot_anat_mosaic1_zoomed.svg",
             cmap="Greys_r",
-            species=config.workflow.species.lower(),
         ),
         name="PlotMosaicZoomed",
     )
@@ -624,17 +621,22 @@ def individual_reports(name="ReportsWorkflow"):
             out_file="plot_anat_mosaic2_noise.svg",
             only_noise=True,
             cmap="viridis_r",
-            species=config.workflow.species.lower(),
         ),
         name="PlotMosaicNoise",
     )
 
+    if config.workflow.species.lower() in ("rat", "mouse"):
+        mosaic_mean.inputs.view = ("coronal", "axial")
+        mosaic_stddev.inputs.view = ("coronal", "axial")
+        mosaic_zoom.inputs.view = ("coronal", "axial")
+        mosaic_noise.inputs.view = ("coronal", "axial")
+
     # Verbose-reporting goes here
     from nireports.interfaces import PlotContours
 
     plot_bmask = pe.Node(
         PlotContours(
-            display_mode="y" if config.workflow.species.lower() == "rat" else "z",
+            display_mode="y" if config.workflow.species.lower() in ("rat", "mouse") else "z",
             levels=[0.5],
             colors=["r"],
             cut_coords=10,