Merge pull request #12 from jh-mipc/flexible_surface_qa

Flexible surface qa features
jh-mipc · May 23, 2024 · eef76be · eef76be
2 parents b850a3a + 907a36c
commit eef76be
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Showing 2 changed files with 12 additions and 3 deletions.
diff --git a/radifox/qa/create.py b/radifox/qa/create.py
@@ -292,11 +292,19 @@ def create_surface_qa_image(
     surf_file,
     img_file,
     output_file,
+    color="red",
     axial_slices=(0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65, 0.7),
     coronal_slices=(0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65, 0.7),
     sagittal_slices=(0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65, 0.7),
-    color="red",
 ):
+    linewidth = 0.5
+    if color == "binary":
+        linecolor = "red"
+    if isinstance(color, (list, tuple)):
+        linecolor = color[0]
+        linewidth = color[1]
+    else:
+        linecolor = color
     img_obj = nib.Nifti1Image.load(img_file)
     img_data = img_obj.get_fdata()
     # noinspection PyUnresolvedReferences
@@ -381,7 +389,7 @@ def create_surface_qa_image(
                             points[:, 0] = img_data.shape[0] - points[:, 0]
                     else:
                         points[:, 1] = img_data.shape[1] - points[:, 1]
-                    ax.plot(*points.T, color=color, linewidth=0.5)
+                    ax.plot(*points.T, color=linecolor, linewidth=linewidth)
             buf = io.BytesIO()
             fig.savefig(buf, format="png")
             buf.seek(0)

diff --git a/radifox/records/processing.py b/radifox/records/processing.py
@@ -262,7 +262,8 @@ def create_qa(
                 create_surface_qa_image(
                     overlay,
                     bg_image,
-                    out_dir / out_name
+                    out_dir / out_name,
+                    color=lut,
                 )
             else:
                 create_qa_image(