Interpolate segmentation image to match ct origin, spacing, and direction

Author: bnmajor

examples/integrations/itk/IDC_Seg_Primer_Examples.ipynb

@@ -33,7 +33,7 @@
    "source": [
     "import sys\n",
     "\n",
-    "!{sys.executable} -m pip install -q pooch itk-io \"itkwidgets[all]>=1.0a33\""
+    "!{sys.executable} -m pip install -q pooch itk-io \"itkwidgets[all]>=1.0a33\" pydicom pydicom-seg numpy"
    ]
   },
   {
@@ -49,7 +49,10 @@
     "import itk\n",
     "import pooch\n",
     "from pathlib import Path\n",
-    "from itkwidgets import view"
+    "from itkwidgets import view\n",
+    "import pydicom\n",
+    "import pydicom_seg # Pydicom-Seg is a layer on top of pydicom that handles DICOM SEG objects.# Read the DICOM SEG object using pydicom and pydicom_seg.\n",
+    "import numpy as np"
    ]
   },
   {
@@ -157,7 +160,15 @@
    },
    "outputs": [],
    "source": [
-    "pred_segthor_image = itk.imread(\"./SEG_DICOM_series/1.nrrd\")"
+    "seg_dicom = pydicom.dcmread(\"./SEG_DICOM_series/6c8744b0-5dd7-4730-bef7-1ab465ec2337.dcm\")\n",
+    "seg_reader = pydicom_seg.MultiClassReader()\n",
+    "seg_obj = seg_reader.read(seg_dicom)\n",
+    "\n",
+    "# Convert the DICOM SEG object into an itk image, with correct voxel origin, spacing, and directions in physical space.\n",
+    "seg_image = itk.image_from_array(seg_obj.data.astype(np.float32))\n",
+    "seg_image.SetOrigin(ct_image.GetOrigin())\n",
+    "seg_image.SetSpacing(ct_image.GetSpacing())\n",
+    "seg_image.SetDirection(ct_image.GetDirection())"
    ]
   },
   {