fixed CT to structure registration

drmichaeldouglass · Apr 27, 2024 · 5e821ec · 5e821ec
1 parent 8da53a4
commit 5e821ec
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Showing 4 changed files with 22 additions and 5 deletions.
diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,4 @@ __pycache__/proton.cpython-310.pyc
 __pycache__/constants.cpython-310.pyc
 __pycache__/__init__.cpython-310.pyc
 __pycache__/node_groups.cpython-310.pyc
+test.py
diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023 Michael Douglass
+Copyright (c) 2024 Michael Douglass
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/__init__.py b/__init__.py
@@ -151,7 +151,7 @@ def execute(self, context):
 
             # Sort those filtered DICOM CT slices by their instance number using sort_by_instance_number function
             sorted_images = sort_by_instance_number(filtered_images)
-            CT_volume, spacing, slice_position, slice_spacing, image_origin = extract_dicom_data(sorted_images)
+            CT_volume, spacing, slice_position, slice_spacing, image_origin, image_orientation, image_columns = extract_dicom_data(sorted_images)
 
             #If spacing is invalid, set to slice spacing of 1 mm
             if slice_spacing == 0:
@@ -164,6 +164,10 @@ def execute(self, context):
             origin = np.asarray(origin)
             volume_dim = np.shape(CT_volume)
 
+            print('Origin:', origin)
+            print('Volume Dimensions:', volume_dim)
+            print('Spacing:', spacing)
+
             # Print out some information about your sorted slices
             #print(f"Number of slices: {len(sorted_images)}")
             #print(f"First slice instance number: {sorted_images[0].InstanceNumber}")
@@ -191,7 +195,7 @@ def execute(self, context):
 
             # Add the volume to the scene
             bpy.ops.object.volume_import(filepath=str(dir_path.joinpath("CT.vdb")), files=[])
-            bpy.context.active_object.location = origin/1000
+            #bpy.context.active_object.location = origin/1000
 
 
             #DICOM_object = easybpy.get_selected_object()

diff --git a/dicom_util.py b/dicom_util.py
@@ -1,9 +1,19 @@
 # dicom_utilities.py
 
 import os
-import pydicom
+
 import numpy as np
 
+try:
+
+    import pydicom
+
+except ImportError:
+
+        print("pydicom is not installed. Please install it using the command 'pip install pydicom'")
+
+        pydicom = None
+
 
 #Checks if the DICOM file is a RTDose file.
 def is_dose_file(ds):
@@ -122,10 +132,12 @@ def extract_dicom_data(images):
         slice_position.append(images[i].ImagePositionPatient)
         slice_spacing = images[i].SliceThickness
         image_origin = images[i].ImagePositionPatient
+        image_orientation = images[i].ImageOrientationPatient
+        image_columns = images[i].Columns
         print(slice_spacing)
     dicom_3d_array = np.asarray(dicom_3d_array)   
     dicom_3d_array = np.flipud(dicom_3d_array)
-    return dicom_3d_array, spacing, slice_position, slice_spacing, image_origin
+    return dicom_3d_array, images[0].PixelSpacing, slice_position, images[0].SliceThickness, images[0].ImagePositionPatient, images[0].ImageOrientationPatient, images[0].Columns
 
 
 def filter_by_series_uid(images, series_uid):