oct-to-tiff 0.5.0__py3-none-any.whl → 0.6.0__py3-none-any.whl

oct_to_tiff/cli.py

@@ -6,24 +6,25 @@ from typing import Any
 
 import defusedxml.ElementTree as DET
 import numpy as np
+import numpy.typing as npt
 import tifffile
-from numpy.typing import NDArray
+from roifile import ROI_TYPE, ImagejRoi, roiwrite
 
 logger = logging.getLogger(__name__)
 
 
 def reshape_volume(
-    volume: NDArray[Any],
+    volume: npt.NDArray[Any],
     frames_per_data_group: int,
     total_data_groups: int,
     oct_window_height: int,
     xy_scan_length: int,
-) -> NDArray[Any]:
+) -> npt.NDArray[Any]:
     """Reshape a 1-dimensional array to a 3-dimensional array.
 
     Parameters
     ----------
-    volume : NDArray[Any]
+    volume : npt.NDArray[Any]
         A 1-dimensional array.
     frames_per_data_group : int
         The number of frames per data group.
@@ -36,7 +37,7 @@ def reshape_volume(
 
     Returns
     -------
-    volume : NDArray[Any]
+    volume : npt.NDArray[Any]
         A 3-dimensional array.
 
     """
@@ -51,29 +52,9 @@ def reshape_volume(
     return volume
 
 
-def rotate_volume(
-    volume: NDArray[Any],
-) -> NDArray[Any]:
-    """Rotate a 3-dimensional array 90 degrees left (anti-clockwise) about the z-axis.
-
-    Parameters
-    ----------
-    volume : NDArray[Any]
-        A 3-dimensional array.
-
-    Returns
-    -------
-    volume : NDArray[Any]
-        A rotated version of the input volume.
-
-    """
-    volume = np.rot90(volume, k=1, axes=(1, 2))
-    return volume
-
-
 def write_volume(
     output_path: Path,
-    volume: NDArray[Any],
+    volume: npt.NDArray[Any],
     pixel_size_x: float,
     pixel_size_y: float,
     pixel_size_z: float,
@@ -84,7 +65,7 @@ def write_volume(
     ----------
     output_path : Path
         The specified output path.
-    volume : NDArray[Any]
+    volume : npt.NDArray[Any]
         A 3-dimensional array.
     pixel_size_x : float
         The pixel (voxel) width in mm.
@@ -110,7 +91,7 @@ def write_volume(
     )
 
 
-def extract_boundaries(input_path: str | Path) -> None:
+def boundaries_to_arrays(input_path: str | Path) -> list[npt.NDArray[np.int_]]:
     """Extract segmentation lines.
 
     Parameters
@@ -118,6 +99,10 @@ def extract_boundaries(input_path: str | Path) -> None:
     input_path : str | Path
         The specified input path.
 
+    Returns
+    -------
+    arrays : list[npt.NDArray[np.int_]]
+        A list of 2-dimensional arrays.
     """
     input_path = Path(input_path)
     tree = DET.parse(input_path)
@@ -128,14 +113,36 @@ def extract_boundaries(input_path: str | Path) -> None:
         int(point.text) if point.text else 0
         for point in root.findall("./Curve_Set/Image/Curve/D")
     ]
-    scan_length = np.arange(len(data_points))
-    num_files = len(data_points) // array_size
-    for i in range(num_files):
+    num_arrays = len(data_points) // array_size
+
+    arrays = []
+    for i in range(num_arrays):
         start = i * array_size
         end = start + array_size
-        table = np.column_stack([scan_length[start:end], data_points[start:end]])
-        table_path = f"{input_path.parent}/{input_path.stem}_{i+1}.txt"
-        np.savetxt(table_path, table, delimiter="\t", fmt="%d")
+        array = np.column_stack([np.arange(array_size), data_points[start:end]])
+        arrays.append(array)
+
+    return arrays
+
+
+def arrays_to_rois(arrays: list[npt.NDArray[np.int_]], output_path: Path) -> None:
+    """
+    Convert a list of 2-dimensional arrays to ImageJ ROIs (ZIP file).
+
+    Parameters
+    ----------
+    arrays : list[npt.NDArray[np.int_]]
+        A list of 2-dimensional arrays.
+    output_path : Path
+        The specified output path.
+    """
+    rois = []
+    for array in arrays:
+        roi = ImagejRoi.frompoints(array)
+        roi.roitype = ROI_TYPE(4)  # FREELINE
+        rois.append(roi)
+
+    roiwrite(output_path, rois, mode="w")
 
 
 def main() -> None:
@@ -202,18 +209,22 @@ def main() -> None:
     else:
         dir_name = input_path.parent
     file_name = input_path.stem
-    file_extension = ".ome.tif"
+    if args.boundaries:
+        file_extension = "_rois.zip"
+    else:
+        file_extension = ".ome.tif"
     output_path = dir_name / (file_name + file_extension)
 
     if Path.is_file(output_path):
         if args.overwrite:
-            pass
+            logger.warning(f"Overwriting {output_path}")
         else:
             logger.error(f"{output_path} already exists.")
             return
 
     if args.boundaries:
-        extract_boundaries(input_path)
+        arrays = boundaries_to_arrays(input_path)
+        arrays_to_rois(arrays, output_path)
         return
 
     with open(input_path, "rb") as f:
@@ -257,6 +268,32 @@ def main() -> None:
             pixel_size_x = 0.007797
             pixel_size_y = 0.003071
             pixel_size_z = 0.040000
+
+            volume = reshape_volume(
+                volume,
+                frames_per_data_group,
+                total_data_groups,
+                oct_window_height,
+                xy_scan_length,
+            )
+            volume = np.rot90(volume, k=1, axes=(1, 2))
+            volume_main = volume[:101]
+            volume_align = volume[101:frames_per_data_group]
+            align_path = dir_name / (file_name + "_Align.ome.tif")
+            pixel_size_x_align = 0.003899
+            pixel_size_y_align = 0.003071
+            pixel_size_z_align = 0.040000
+            write_volume(
+                output_path, volume_main, pixel_size_x, pixel_size_y, pixel_size_z
+            )
+            write_volume(
+                align_path,
+                volume_align,
+                pixel_size_x_align,
+                pixel_size_y_align,
+                pixel_size_z_align,
+            )
+            return
         elif "3D Disc" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 106
@@ -465,7 +502,7 @@ def main() -> None:
         )
 
         if not args.en_face and not args.seg_curve:
-            volume = rotate_volume(volume)
+            volume = np.rot90(volume, k=1, axes=(1, 2))
 
         write_volume(output_path, volume, pixel_size_x, pixel_size_y, pixel_size_z)
 

{oct_to_tiff-0.5.0.dist-info → oct_to_tiff-0.6.0.dist-info}/METADATA

@@ -1,63 +1,35 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: oct-to-tiff
-Version: 0.5.0
+Version: 0.6.0
 Summary: A command line tool for converting optical coherence tomography angiography (OCTA) data.
 Author-email: Cameron Lloyd <lloyd@med.unideb.hu>
 Maintainer-email: Cameron Lloyd <lloyd@med.unideb.hu>
-License: BSD 3-Clause License
-        
-        Copyright (c) 2021, Cameron Lloyd
-        All rights reserved.
-        
-        Redistribution and use in source and binary forms, with or without
-        modification, are permitted provided that the following conditions are met:
-        
-        1. Redistributions of source code must retain the above copyright notice, this
-           list of conditions and the following disclaimer.
-        
-        2. Redistributions in binary form must reproduce the above copyright notice,
-           this list of conditions and the following disclaimer in the documentation
-           and/or other materials provided with the distribution.
-        
-        3. Neither the name of the copyright holder nor the names of its
-           contributors may be used to endorse or promote products derived from
-           this software without specific prior written permission.
-        
-        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-        
+License-Expression: BSD-3-Clause
 Project-URL: Homepage, https://github.com/camlloyd/oct-to-tiff
 Project-URL: Bug Tracker, https://github.com/camlloyd/oct-to-tiff/issues
 Project-URL: Changelog, https://github.com/camlloyd/oct-to-tiff/blob/main/CHANGELOG.md
 Keywords: angiography,cli,oct,octa
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: BSD License
 Classifier: Natural Language :: English
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Python: >=3.10
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 Requires-Dist: defusedxml
 Requires-Dist: numpy
+Requires-Dist: roifile
 Requires-Dist: tifffile
 Provides-Extra: dev
 Requires-Dist: mypy; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 Requires-Dist: types-defusedxml; extra == "dev"
+Dynamic: license-file
 
 # oct-to-tiff
 
@@ -214,4 +186,4 @@ This project uses [Ruff](https://github.com/astral-sh/ruff) for linting and form
 
 ## Requirements
 
-Requires Python 3.10 or higher.
+Requires Python 3.11 or higher.

oct_to_tiff-0.6.0.dist-info/RECORD

@@ -0,0 +1,8 @@
+oct_to_tiff/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+oct_to_tiff/cli.py,sha256=GmIMXLuNfAEZaijX2_93XB95V0Mdr1yb73Q_j8eBiEI,17232
+oct_to_tiff-0.6.0.dist-info/licenses/LICENSE.txt,sha256=8KO0dluzLStmIF0HM18BOP9T2miIcX8q-GOfMOw6Ngk,1521
+oct_to_tiff-0.6.0.dist-info/METADATA,sha256=7atS8U7OhVhVpU48NjbGzqMtbGhlA_l4Dh6jZUiu010,4913
+oct_to_tiff-0.6.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+oct_to_tiff-0.6.0.dist-info/entry_points.txt,sha256=mKWNdkTThZm2JKtLwp4PGMpXkvAWk-xnQDAOyRsCo9Y,53
+oct_to_tiff-0.6.0.dist-info/top_level.txt,sha256=_ovqm7f48yb_IAiVqWzB3VPnHXwzkkEqQQ_ZJz_McSY,12
+oct_to_tiff-0.6.0.dist-info/RECORD,,

{oct_to_tiff-0.5.0.dist-info → oct_to_tiff-0.6.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

oct_to_tiff-0.5.0.dist-info/RECORD

@@ -1,8 +0,0 @@
-oct_to_tiff/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-oct_to_tiff/cli.py,sha256=tHRUNBff0TTTtc0pnecF_t5mLWyoGG0kNKNVopyL4Sw,15934
-oct_to_tiff-0.5.0.dist-info/LICENSE.txt,sha256=8KO0dluzLStmIF0HM18BOP9T2miIcX8q-GOfMOw6Ngk,1521
-oct_to_tiff-0.5.0.dist-info/METADATA,sha256=8-nIJ6Pg_vvfxovcjIHgax-D1nMQaWYZ_9cJLT7lq2g,6649
-oct_to_tiff-0.5.0.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-oct_to_tiff-0.5.0.dist-info/entry_points.txt,sha256=mKWNdkTThZm2JKtLwp4PGMpXkvAWk-xnQDAOyRsCo9Y,53
-oct_to_tiff-0.5.0.dist-info/top_level.txt,sha256=_ovqm7f48yb_IAiVqWzB3VPnHXwzkkEqQQ_ZJz_McSY,12
-oct_to_tiff-0.5.0.dist-info/RECORD,,