Set which atlases are following the Allen ccfv3 convention

BIOP · Oct 31, 2024 · 4f5101d · 4f5101d
1 parent 665ed5e
commit 4f5101d
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Showing 3 changed files with 39 additions and 37 deletions.
diff --git a/examples/demo_gui.py b/examples/demo_gui.py
@@ -6,6 +6,10 @@
 
 
 def main():
+
+    # if you want to change the atlas that are using the ccfv3 convention
+    # abba.atlases_using_allen_ccfv3_convention = []
+
     # To enable Java debugging:
 
     attach_java_debugger = False

diff --git a/src/abba_python/abba.py b/src/abba_python/abba.py
@@ -21,6 +21,33 @@
 
 LogLevel = Literal['OFF', 'DEBUG', 'INFO']
 
+atlases_using_allen_ccfv3_convention = [
+        'example_mouse_100um',
+        'allen_mouse_10um',
+        'allen_mouse_25um',
+        'allen_mouse_50um',
+        'allen_mouse_100um',
+        'kim_mouse_10um',
+        'kim_mouse_25um',
+        'kim_mouse_50um',
+        'kim_mouse_100um',
+        'osten_mouse_10um',
+        'osten_mouse_25um',
+        'osten_mouse_50um',
+        'osten_mouse_100um',
+        'perens_lsfm_mouse_20um',
+        'kim_dev_mouse_stp_10um',
+        'kim_dev_mouse_idisco_10um',
+        'kim_dev_mouse_mri_a0_10um',
+        'kim_dev_mouse_mri_adc_10um',
+        'kim_dev_mouse_mri_dwi_10um',
+        'kim_dev_mouse_mri_fa_10um',
+        'kim_dev_mouse_mri_mtr_10um',
+        'kim_dev_mouse_mri_t2_10um',
+        'allen_mouse_bluebrain_barrels_10um',
+        'allen_mouse_bluebrain_barrels_25um',
+        'princeton_mouse_20um'
+    ]
 
 def get_java_dependencies():
     """
@@ -31,7 +58,7 @@ def get_java_dependencies():
     """
     return ['net.imagej:imagej:2.15.0',
             'net.imagej:imagej-legacy:1.2.2',
-            'ch.epfl.biop:ImageToAtlasRegister:0.9.6',
+            'ch.epfl.biop:ImageToAtlasRegister:0.9.7',
             'ch.epfl.biop:bigdataviewer-biop-tools:0.10.6',
             'sc.fiji:bigdataviewer-playground:0.10.5',
             'sc.fiji:bigwarp_fiji:9.1.2',
@@ -142,35 +169,10 @@ def get(self):
 
     # Specify which atlases are compatible with DeepSlice Mouse and Rat models - this only affects the GUI
     DeepSliceHelper = jimport('ch.epfl.biop.atlas.aligner.DeepSliceHelper')
-    mouse_compatible_atlases = [  # Not sure thew all work!
-        'example_mouse_100um',
-        'allen_mouse_10um',
-        'allen_mouse_25um',
-        'allen_mouse_50um',
-        'allen_mouse_100um',
-        'kim_mouse_10um',
-        'kim_mouse_25um',
-        'kim_mouse_50um',
-        'kim_mouse_100um',
-        'osten_mouse_10um',
-        'osten_mouse_25um',
-        'osten_mouse_50um',
-        'osten_mouse_100um',
-        'perens_lsfm_mouse_20um',
-        'kim_dev_mouse_stp_10um',
-        'kim_dev_mouse_idisco_10um',
-        'kim_dev_mouse_mri_a0_10um',
-        'kim_dev_mouse_mri_adc_10um',
-        'kim_dev_mouse_mri_dwi_10um',
-        'kim_dev_mouse_mri_fa_10um',
-        'kim_dev_mouse_mri_mtr_10um',
-        'kim_dev_mouse_mri_t2_10um',
-        'allen_mouse_bluebrain_barrels_10um',
-        'allen_mouse_bluebrain_barrels_25um',
-        'princeton_mouse_20um'
-    ]
-    for atlas_name in mouse_compatible_atlases:
+
+    for atlas_name in atlases_using_allen_ccfv3_convention:
         DeepSliceHelper.addMouseCompatibleAtlas(JString(atlas_name))
+
     DeepSliceHelper.addRatCompatibleAtlas(JString('whs_sd_rat_39um'))
 
 

diff --git a/src/abba_python/abba_map.py b/src/abba_python/abba_map.py
@@ -4,6 +4,8 @@
 
 import numpy as np
 
+import abba
+
 AffineTransform3D = jimport('net.imglib2.realtransform.AffineTransform3D')
 ArrayList = jimport('java.util.ArrayList')
 AtlasHelper = jimport('ch.epfl.biop.atlas.struct.AtlasHelper')
@@ -25,12 +27,6 @@ def array_to_source(ij, array, name, transform=AffineTransform3D()):
     rai_source = RandomAccessibleIntervalSource(img, pixel_type, transform, name_java_str)
     return SourceAndConverterHelper.createSourceAndConverter(rai_source)
 
-
-def is_mouse_ccfv3_compatible(atlas_name: str):
-    # Assume that if it is deepslice compatible, it is ccfv3 compatible
-    DeepSliceHelper  = jimport('ch.epfl.biop.atlas.aligner.DeepSliceHelper')
-    return DeepSliceHelper.isDeepSliceMouseCompatible(JString(atlas_name))
-
 @JImplements(AtlasMap)
 class AbbaMap(object):
     """This python class is part of the translation mechanism between the underlying Java ABBA API:
@@ -68,7 +64,7 @@ def initialize(self, atlasName):
         affine_transform = AffineTransform3D()
         affine_transform.scale(JDouble(vox_x_mm), JDouble(vox_y_mm), JDouble(vox_z_mm))
 
-        if is_mouse_ccfv3_compatible(atlasName):
+        if atlasName in abba.atlases_using_allen_ccfv3_convention:
             transform_to_ccfv3 = AffineTransform3D()
             transform_to_ccfv3.set(
                 JDouble(0), JDouble(0), JDouble(1), JDouble(0),
@@ -144,7 +140,7 @@ def getAtlasPrecisionInMillimeter(self):
 
     @JOverride
     def getCoronalTransform(self):
-        if is_mouse_ccfv3_compatible(self.atlasName):
+        if self.atlasName in abba.atlases_using_allen_ccfv3_convention:
             coronal_transform = AffineTransform3D()
             coronal_transform.set(
                 JDouble(0), JDouble(0), JDouble(1), JDouble(0),