Update MALP-EM matchers

FNNDSC · Mar 7, 2024 · 39fb0aa · 39fb0aa
1 parent 45285ea
commit 39fb0aa
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Showing 2 changed files with 15 additions and 4 deletions.
diff --git a/visualdataset/__init__.py b/visualdataset/__init__.py
@@ -9,4 +9,4 @@
 |_|
 """
 
-__version__ = '0.3.0'
+__version__ = '0.3.1'
diff --git a/visualdataset/wellknown/malpem.py b/visualdataset/wellknown/malpem.py
@@ -5,12 +5,16 @@
 from visualdataset.options import ChrisViewerFileOptions, NiivueVolumeSettings
 
 MALPEM_MATCHERS: Sequence[Matcher] = [
-    Matcher(key='type', value='T1 MRI', regex=r'.+_N4(_masked)?\.nii\.gz'),
+    Matcher(key='type', value='T1 MRI', regex=r'.+_(no)?N4(_masked)?\.nii\.gz'),
     Matcher(key='type', value='labels', regex=r'.+_MALPEM(_tissues)?\.nii\.gz'),
-    Matcher(key='name', value='Head', regex=r'.+_N4\.nii\.gz'),
-    Matcher(key='name', value='Brain', regex=r'.+_N4_masked\.nii\.gz'),
+    Matcher(key='name', value='Head', regex=r'.+_(no)?N4\.nii\.gz'),
+    Matcher(key='name', value='Brain', regex=r'.+_(no)?N4_masked\.nii\.gz'),
     Matcher(key='name', value='MALP-EM tissue segmentation', regex=r'.+_MALPEM_tissues\.nii\.gz'),
     Matcher(key='name', value='MALP-EM structure segmentation', regex=r'.+_MALPEM\.nii\.gz'),
+
+    # special matcher for Stefan's customized MALP-EM pipeline
+    Matcher(key='type', value='labels', regex=r'.+_MALPEM_corrected\.nii\.gz'),
+    Matcher(key='name', value='Corrected MALP-EM structure segmentation', regex=r'.+_MALPEM_corrected\.nii\.gz'),
 ]
 
 MALPEM_OPTIONS: Sequence[OptionsLink] = [
@@ -50,4 +54,11 @@
             niivue_defaults=NiivueVolumeSettings(colormapLabelFile='MALP-EM.v1.3.json', opacity=0.2)
         )
     ),
+    OptionsLink(
+        match={'name': 'Corrected MALP-EM structure segmentation'},
+        options=ChrisViewerFileOptions(
+            name='Corrected MALP-EM structure segmentation',
+            niivue_defaults=NiivueVolumeSettings(colormapLabelFile='MALP-EM.v1.3.json', opacity=0.2)
+        )
+    ),
 ]