ENH: Convert python notebooks to python scripts (with percent tags to define cells)

data/DirLab-4DCT/Convert4DCTToMHD.py

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+#!/usr/bin/env python
+# %%
+import os
+
+# %%
+sizes = [
+    [256, 256, 94],
+    [256, 256, 112],
+    [256, 256, 104],
+    [256, 256, 99],
+    [256, 256, 106],
+    [512, 512, 128],
+    [512, 512, 136],
+    [512, 512, 128],
+    [512, 512, 128],
+    [512, 512, 120],
+]
+spacings = [
+    [0.97, 0.97, 2.5],
+    [1.16, 1.16, 2.5],
+    [1.15, 1.15, 2.5],
+    [1.13, 1.13, 2.5],
+    [1.10, 1.10, 2.5],
+    [0.97, 0.97, 2.5],
+    [0.97, 0.97, 2.5],
+    [0.97, 0.97, 2.5],
+    [0.97, 0.97, 2.5],
+    [0.97, 0.97, 2.5],
+]
+files = [
+    "Case1Pack",
+    "Case2Pack",
+    "Case3Pack",
+    "Case4Pack",
+    "Case5Pack",
+    "Case6Pack",
+    "Case7Pack",
+    "Case8Deploy",
+    "Case9Pack",
+    "Case10Pack",
+]
+file_suffix = [
+    "_s",
+    "-ssm",
+    "-ssm",
+    "-ssm",
+    "-ssm",
+    "",
+    "",
+    "",
+    "",
+    "",
+]
+
+# %%
+for file_num, file_name in enumerate(files):
+    spacing = f"{spacings[file_num][0]} {spacings[file_num][1]} {spacings[file_num][2]}"
+    size = f"{sizes[file_num][0]} {sizes[file_num][1]} {sizes[file_num][2]}"
+    for phase in range(10):
+        img_path = f"{file_name}/Images/case{file_num + 1}_T{phase * 10:02d}{file_suffix[file_num]}.img"
+        script_dir = os.getcwd()
+        hdr_path = f"{script_dir}/{file_name}_T{phase * 10:02d}.mhd"
+        with open(hdr_path, "w") as f:
+            f.write("ObjectType = Image\n")
+            f.write("NDims = 3\n")
+            f.write(f"DimSize = {size}\n")
+            f.write("HeaderSize = -1\n")
+            f.write("BinaryData = True\n")
+            f.write("BinaryDataByteOrderMSB = False\n")
+            f.write("Orientation = 1 0 0 0 1 0 0 0 -1\n")
+            f.write(f"ElementSpacing = {spacing}\n")
+            f.write("ElementType = MET_SHORT\n")
+            f.write("ElementNumberOfChannels = 1\n")
+            f.write(f"ElementDataFile = {img_path}\n")

data/Slicer-Heart-CT/download_and_convert.py

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+#!/usr/bin/env python
+# %%
+import os
+import shutil
+import urllib
+
+from physiomotion4d.convert_nrrd_4d_to_3d import ConvertNRRD4DTo3D
+
+# %%
+data_dir = "."
+output_dir = "."
+
+if not os.path.exists(data_dir):
+    os.makedirs(data_dir, exist_ok=True)
+
+if not os.path.exists(output_dir):
+    os.makedirs(output_dir, exist_ok=True)
+
+# %%
+input_image_url = "https://github.com/SlicerHeart/SlicerHeart/releases/download/TestingData/TruncalValve_4DCT.seq.nrrd"
+input_image_filename = os.path.join(data_dir, "TruncalValve_4DCT.seq.nrrd")
+
+if not os.path.exists(input_image_filename):
+    urllib.request.urlretrieve(input_image_url, input_image_filename)
+
+# %%
+conv = ConvertNRRD4DTo3D()
+conv.load_nrrd_4d(f"{data_dir}/TruncalValve_4DCT.seq.nrrd")
+conv.save_3d_images(f"{output_dir}/slice")
+
+# Save the mid-stroke slice as the fixed/reference image
+shutil.copyfile(f"{output_dir}/slice_007.mha", f"{output_dir}/slice_fixed.mha")