chore: add scripts for combining a stack of single images to a volume and reducing the number of projections

Author: lukasbehammer

src/scripts/combine_stack.py

@@ -0,0 +1,73 @@
+#!/usr/bin/python3
+"""Convert image stack to a volume via CLI."""
+
+# Authors
+# -------
+# Author: Lukas Behammer
+# Research Center Wels
+# University of Applied Sciences Upper Austria, 2023
+# CT Research Group
+#
+# Modifications
+# -------------
+# Original code, 2025, Lukas Behammer
+#
+# License
+# -------
+# BSD-3-Clause License
+
+import glob
+import os
+import sys
+
+import numpy as np
+from viqa.utils.loading import _load_binary, _parse_bitdepth
+
+
+def combine_image_stack(input_path, size, bitdepth, file_type="raw"):
+    """Combine a stack of single images to a volume."""
+    files = glob.glob(os.path.join(input_path, f"*.{file_type}"))
+    data_type = _parse_bitdepth(bitdepth)
+
+    if len(files) != 0:
+        vol = []
+        for file in files:
+            vol.append(_load_binary(file, data_type, size))
+
+        vol = np.array(vol)
+        return vol
+
+
+def save_volume(output_path, vol, bitdepth, file_type="raw"):
+    """Save a volume to disk."""
+    data_type = _parse_bitdepth(bitdepth)
+    if not os.path.exists(output_path):
+        os.makedirs(output_path)
+    vol_shape = vol.shape
+    vol = vol.astype(data_type)
+    # save volume
+    vol.tofile(
+        os.path.join(
+            output_path,
+            f"volume_{vol_shape[2]}x{vol_shape[1]}x{vol_shape[0]}_{bitdepth}.{file_type}",
+        )
+    )
+
+
+if __name__ == "__main__":
+    if len(sys.argv) == 9:
+        input_path = sys.argv[1]
+        output_path = sys.argv[2]
+        size = [int(sys.argv[3]), int(sys.argv[4]), int(sys.argv[5])]
+        bitdepth = sys.argv[6]
+        file_type_input = sys.argv[7]
+        file_type_output = sys.argv[8]
+
+        vol = combine_image_stack(input_path, size, bitdepth, file_type_input)
+        save_volume(output_path, vol, bitdepth, file_type_output)
+    else:
+        print(
+            "Usage: combine_raw_stack.py <input_path> <output_path> <size_x> "
+            "<size_y> <size_z> <bitdepth> <file_type_input> <file_type_output>"
+        )
+        sys.exit(1)

src/scripts/reduce_projections.py

@@ -0,0 +1,70 @@
+#!/usr/bin/python3
+"""Reduce the number of projections via CLI."""
+
+# Authors
+# -------
+# Author: Lukas Behammer
+# Research Center Wels
+# University of Applied Sciences Upper Austria, 2023
+# CT Research Group
+#
+# Modifications
+# -------------
+# Original code, 2025, Lukas Behammer
+#
+# License
+# -------
+# BSD-3-Clause License
+
+import os
+import sys
+
+from viqa.utils.loading import _load_binary, _parse_bitdepth
+
+
+def load_projection(file, size, bitdepth):
+    """Load projection images from a binary file."""
+    data_type = _parse_bitdepth(bitdepth)
+    vol = _load_binary(file, data_type, size)
+    vol_shape = vol.shape
+    vol = vol.reshape(*vol_shape[::-1])
+    return vol
+
+
+def get_n_projections(volume, reducing_factor):
+    """Reduce the number of projections."""
+    if reducing_factor == 1:
+        raise ValueError(f"Error: factor must be greater than 1, got {reducing_factor}")
+
+    volume_new = volume[..., ::reducing_factor]
+    return volume_new
+
+
+def save_volume(output, vol, bitdepth):
+    """Save the volume to a binary file."""
+    output_folder = os.path.dirname(output)
+    if not os.path.exists(output_folder):
+        os.makedirs(output_folder)
+    data_type = _parse_bitdepth(bitdepth)
+    vol = vol.astype(data_type)
+    # save volume
+    vol.tofile(output)
+
+
+if __name__ == "__main__":
+    if len(sys.argv) == 8:
+        input_path = sys.argv[1]
+        output_path = sys.argv[2]
+        size = [int(sys.argv[3]), int(sys.argv[4]), int(sys.argv[5])]
+        bitdepth = sys.argv[6]
+        factor = int(sys.argv[7])
+
+        vol = load_projection(input_path, size, bitdepth)
+        vol = get_n_projections(vol, factor)
+        save_volume(output_path, vol, bitdepth)
+    else:
+        print(
+            "Usage: reduce_projections.py <input_path> <output_path> <size_x> "
+            "<size_y> <size_z> <bitdepth> <factor>"
+        )
+        sys.exit(1)