oct-to-tiff 0.5.0__tar.gz → 0.6.1__tar.gz

{oct_to_tiff-0.5.0/src/oct_to_tiff.egg-info → oct_to_tiff-0.6.1}/PKG-INFO

@@ -1,63 +1,36 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: oct-to-tiff
-Version: 0.5.0
+Version: 0.6.1
 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.
-        
-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
+Author: Cameron Lloyd
+Author-email: Cameron Lloyd <lloyd@med.unideb.hu>
+License-Expression: BSD-3-Clause
+License-File: LICENSE.txt
 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
-Description-Content-Type: text/markdown
-License-File: LICENSE.txt
+Classifier: Programming Language :: Python :: 3.14
 Requires-Dist: defusedxml
 Requires-Dist: numpy
+Requires-Dist: roifile
 Requires-Dist: tifffile
+Requires-Dist: mypy ; extra == 'dev'
+Requires-Dist: ruff ; extra == 'dev'
+Requires-Dist: types-defusedxml ; extra == 'dev'
+Maintainer: Cameron Lloyd
+Maintainer-email: Cameron Lloyd <lloyd@med.unideb.hu>
+Requires-Python: >=3.11
+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
 Provides-Extra: dev
-Requires-Dist: mypy; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
-Requires-Dist: types-defusedxml; extra == "dev"
+Description-Content-Type: text/markdown
 
 # oct-to-tiff
 
@@ -74,9 +47,9 @@ via pip:
 
     pip install oct-to-tiff
 
-via mamba:
+via conda:
 
-    mamba install -c conda-forge oct-to-tiff
+    conda install conda-forge::oct-to-tiff
 
 ## Getting started
     oct-to-tiff /path/to/image.OCT
@@ -214,4 +187,4 @@ 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-0.5.0 → oct_to_tiff-0.6.1}/README.md

@@ -13,9 +13,9 @@ via pip:
 
     pip install oct-to-tiff
 
-via mamba:
+via conda:
 
-    mamba install -c conda-forge oct-to-tiff
+    conda install conda-forge::oct-to-tiff
 
 ## Getting started
     oct-to-tiff /path/to/image.OCT
@@ -153,4 +153,4 @@ 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-0.5.0 → oct_to_tiff-0.6.1}/pyproject.toml

@@ -1,33 +1,34 @@
 [build-system]
-requires = ["setuptools>=61.0"]
-build-backend = "setuptools.build_meta"
+requires = ["uv_build>=0.9.26,<0.10.0"]
+build-backend = "uv_build"
 
 [project]
 name = "oct-to-tiff"
-version = "0.5.0"
+version = "0.6.1"
 dependencies = [
     "defusedxml",
     "numpy",
+    "roifile",
     "tifffile",
 ]
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 authors = [{name = "Cameron Lloyd", email = "lloyd@med.unideb.hu"}]
 maintainers = [{name = "Cameron Lloyd", email = "lloyd@med.unideb.hu"}]
 description = "A command line tool for converting optical coherence tomography angiography (OCTA) data."
 readme = "README.md"
-license = {file = "LICENSE.txt"}
+license = "BSD-3-Clause"
+license-files = ["LICEN[CS]E.*"]
 keywords = ["angiography", "cli", "oct", "octa"]
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: BSD License",
     "Natural Language :: English",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
 ]
 
 [project.optional-dependencies]
@@ -45,11 +46,12 @@ Changelog = "https://github.com/camlloyd/oct-to-tiff/blob/main/CHANGELOG.md"
 [project.scripts]
 oct-to-tiff = "oct_to_tiff.cli:main"
 
-[tool.setuptools.packages.find]
-where = ["src"]
+[tool.semantic_release]
+allow_zero_version = "true"
+version_toml = ["pyproject.toml:project.version"]
 
 [tool.ruff.lint]
 select = [
     "I", # isort
     "S", # flake8-bandit
-]
+]

{oct_to_tiff-0.5.0 → oct_to_tiff-0.6.1}/src/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.
 
     """
@@ -51,32 +52,47 @@ 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.
+def volume_metadata(
+    pixel_size_x: float | None,
+    pixel_size_y: float | None,
+    pixel_size_z: float | None,
+) -> dict[str, Any]:
+    """Build a dictionary of metadata.
 
     Parameters
     ----------
-    volume : NDArray[Any]
-        A 3-dimensional array.
+    pixel_size_x : float | None
+        The pixel (voxel) width in mm.
+    pixel_size_y : float | None
+        The pixel (voxel) height in mm.
+    pixel_size_z : float | None
+        The pixel (voxel) depth in mm.
 
     Returns
     -------
-    volume : NDArray[Any]
-        A rotated version of the input volume.
+    metadata : dict[str, Any]
+        A dictionary of metadata.
 
     """
-    volume = np.rot90(volume, k=1, axes=(1, 2))
-    return volume
+    metadata: dict[str, Any] = {"axes": "ZYX"}
+    if pixel_size_x is not None:
+        metadata["PhysicalSizeX"] = pixel_size_x
+        metadata["PhysicalSizeXUnit"] = "mm"
+    if pixel_size_y is not None:
+        metadata["PhysicalSizeY"] = pixel_size_y
+        metadata["PhysicalSizeYUnit"] = "mm"
+    if pixel_size_z is not None:
+        metadata["PhysicalSizeZ"] = pixel_size_z
+        metadata["PhysicalSizeZUnit"] = "mm"
+    return metadata
 
 
 def write_volume(
     output_path: Path,
-    volume: NDArray[Any],
-    pixel_size_x: float,
-    pixel_size_y: float,
-    pixel_size_z: float,
+    volume: npt.NDArray[Any],
+    pixel_size_x: float | None,
+    pixel_size_y: float | None,
+    pixel_size_z: float | None,
 ) -> None:
     """Write a 3-dimensional array to the output path as an OME-TIFF file, including voxel size in the metadata.
 
@@ -84,7 +100,7 @@ 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.
@@ -98,19 +114,11 @@ def write_volume(
         output_path,
         volume,
         photometric="minisblack",
-        metadata={
-            "axes": "ZYX",
-            "PhysicalSizeX": pixel_size_x,
-            "PhysicalSizeXUnit": "mm",
-            "PhysicalSizeY": pixel_size_y,
-            "PhysicalSizeYUnit": "mm",
-            "PhysicalSizeZ": pixel_size_z,
-            "PhysicalSizeZUnit": "mm",
-        },
+        metadata=volume_metadata(pixel_size_x, pixel_size_y, pixel_size_z),
     )
 
 
-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 +126,10 @@ 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 +140,36 @@ 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 +236,22 @@ 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:
@@ -234,7 +272,7 @@ def main() -> None:
             xy_scan_length = int(len(volume) ** 0.5)
             pixel_size_x = args.size / oct_window_height
             pixel_size_y = args.size / xy_scan_length
-            pixel_size_z = 1
+            pixel_size_z = None
         elif args.seg_curve:
             volume = np.frombuffer(f.read(), dtype=np.single)
             if len(volume) == 1280000 or len(volume) == 1120000:
@@ -245,9 +283,9 @@ def main() -> None:
                 oct_window_height = 304
             total_data_groups = 1
             xy_scan_length = len(volume) // (frames_per_data_group * oct_window_height)
-            pixel_size_x = 1
-            pixel_size_y = 1
-            pixel_size_z = 1
+            pixel_size_x = None
+            pixel_size_y = None
+            pixel_size_z = None
         elif "3D Cornea" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 106
@@ -257,6 +295,32 @@ 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
@@ -301,7 +365,7 @@ def main() -> None:
             xy_scan_length = 1020
             pixel_size_x = 0.002941
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "Cornea Cross Line" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 2
@@ -310,7 +374,7 @@ def main() -> None:
             xy_scan_length = 941
             pixel_size_x = 0.008502
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "Cornea Line" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 1
@@ -319,7 +383,7 @@ def main() -> None:
             xy_scan_length = 1020
             pixel_size_x = 0.007843
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "Cross Line" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 2
@@ -328,7 +392,7 @@ def main() -> None:
             xy_scan_length = 1020
             pixel_size_x = 0.009804
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "Enhanced HD Line" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 1
@@ -337,7 +401,7 @@ def main() -> None:
             xy_scan_length = 998
             pixel_size_x = 0.012024
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "GCC" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 16
@@ -346,7 +410,7 @@ def main() -> None:
             xy_scan_length = 933
             pixel_size_x = 0.007503
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "Grid" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 10
@@ -355,7 +419,7 @@ def main() -> None:
             xy_scan_length = 1020
             pixel_size_x = 0.005882
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "HD Angio Disc" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 400
@@ -409,7 +473,7 @@ def main() -> None:
             xy_scan_length = 1024
             pixel_size_x = 0.009766
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "Line" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 1
@@ -418,7 +482,7 @@ def main() -> None:
             xy_scan_length = 1020
             pixel_size_x = 0.008824
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "ONH" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single, count=2223360)
             frames_per_data_group = 3
@@ -427,7 +491,7 @@ def main() -> None:
             xy_scan_length = 965
             pixel_size_x = 0.015952
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "PachymetryWide" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 16
@@ -436,7 +500,7 @@ def main() -> None:
             xy_scan_length = 1536
             pixel_size_x = 0.005859
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "Raster" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 21
@@ -445,7 +509,7 @@ def main() -> None:
             xy_scan_length = 1020
             pixel_size_x = 0.011765
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "Retina Map" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single, count=6680960)
             frames_per_data_group = 13
@@ -454,7 +518,7 @@ def main() -> None:
             xy_scan_length = 803
             pixel_size_x = 0.007472
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
 
         volume = reshape_volume(
             volume,
@@ -465,7 +529,7 @@ 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/PKG-INFO

@@ -1,217 +0,0 @@
-Metadata-Version: 2.1
-Name: oct-to-tiff
-Version: 0.5.0
-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.
-        
-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
-Description-Content-Type: text/markdown
-License-File: LICENSE.txt
-Requires-Dist: defusedxml
-Requires-Dist: numpy
-Requires-Dist: tifffile
-Provides-Extra: dev
-Requires-Dist: mypy; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
-Requires-Dist: types-defusedxml; extra == "dev"
-
-# oct-to-tiff
-
-[![DOI](https://zenodo.org/badge/382486199.svg)](https://zenodo.org/badge/latestdoi/382486199)
-[![PyPI - Version](https://img.shields.io/pypi/v/oct-to-tiff)](https://pypi.org/project/oct-to-tiff)
-[![PyPI - License](https://img.shields.io/pypi/l/oct-to-tiff)](https://github.com/camlloyd/oct-to-tiff/blob/main/LICENSE.txt)
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-
-
-A command line tool for converting optical coherence tomography angiography (OCTA) data.
-
-## Installation
-via pip:
-
-    pip install oct-to-tiff
-
-via mamba:
-
-    mamba install -c conda-forge oct-to-tiff
-
-## Getting started
-    oct-to-tiff /path/to/image.OCT
-    
-will read an OCT volume and write to a single OME-TIFF file, including voxel size in the metadata.
-
-By default, the output file will be written with the same name as the input file and to the same directory:
-
-
-    tree /path/to/images
-        ├── image.OCT
-        └── image.ome.tif
-
-To specify a custom output directory, see [Optional arguments](#optional-arguments) below.
-
-## Batch processing
-``` bash
-for file in *.OCT; do oct-to-tiff "${file}"; done
-```
-will convert all OCT volumes in the current directory to OME-TIFF files, including voxel size in the metadata.
-
-## Supported scan patterns
-
-This tool has been developed by reverse engineering data from the Optovue RTVue XR Avanti System.
-
-Due to limited test data, only the following scan patterns are currently supported:
-
-### Structural OCT
-- 3D Cornea
-- 3D Disc
-- 3D Retina
-- 3D Widefield
-- 3D Widefield MCT
-- Angle
-- Cornea Cross Line
-- Cornea Line
-- Cross Line
-- Enhanced HD Line
-- GCC
-- Grid
-- Line
-- ONH (Partial)
-- Pachymetry Wide
-- Radial Lines
-- Raster
-- Retina Map (Partial)
-
-### OCT Angiography
-- Angio Disc
-- Angio Retina
-- HD Angio Disc
-- HD Angio Retina
-
-
-## Optional arguments
-
-To view these options at any time, run `oct-to-tiff --help`.
-
-#### `--output OUTPUT`
-**Description**: specify a custom output directory. 
-
-If the path to the output directory does not exist, a new directory (and parent directories) will be created.
-
-**Usage**: 
-    
-    oct-to-tiff /path/to/image.OCT --output /path/to/output/directory
-    
-#### `--overwrite`
-**Description**: overwrite output file if it exists.
-
-**Usage**: 
-    
-    oct-to-tiff /path/to/image.OCT --overwrite
-    
-#### `--size SIZE`
-**Description**: scan size in mm.
-
-Sets the correct voxel size for scan patterns with adjustable length.
-
-**Usage**:
-
-    oct-to-tiff /path/to/image.OCT --size 4.5
-
-#### `--log-level LEVEL`
-**Description**: sets the logging level (default: `WARNING`)
-
-**Usage**:
-
-    oct-to-tiff /path/to/image.OCT --log-level INFO
-
-#### `--version`
-**Description**: show program's version number and exit.
-
-**Usage**:
-
-    oct-to-tiff --version
-
-#### The following options are mutually exclusive:
-    
-#### `--angio`
-**Description**: convert extracted OCTA data. 
-
-Requires `--size SIZE`.
-
-**Usage**:
-
-    oct-to-tiff /path/to/data --angio --size 4.5
-    
-#### `--en-face`
-**Description**: convert extracted en face data.
-
-Requires `--size SIZE`.
-
-**Usage**:
-
-    oct-to-tiff /path/to/data --en-face --size 4.5
-    
-#### `--seg-curve`
-**Description**: convert extracted segmentation data.
-
-**Usage**:
-
-    oct-to-tiff /path/to/data --seg-curve
-
-#### `--boundaries`
-**Description**: extract segmentation lines.
-
-**Usage**:
-
-    oct-to-tiff /path/to/curve.xml --boundaries
-
-## Contributing
-
-This project uses [Ruff](https://github.com/astral-sh/ruff) for linting and formatting.
-
-## Requirements
-
-Requires Python 3.10 or higher.

oct_to_tiff-0.5.0/setup.cfg

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-[egg_info]
-tag_build = 
-tag_date = 0
-

oct_to_tiff-0.5.0/src/oct_to_tiff.egg-info/SOURCES.txt

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-LICENSE.txt
-README.md
-pyproject.toml
-src/oct_to_tiff/__init__.py
-src/oct_to_tiff/cli.py
-src/oct_to_tiff.egg-info/PKG-INFO
-src/oct_to_tiff.egg-info/SOURCES.txt
-src/oct_to_tiff.egg-info/dependency_links.txt
-src/oct_to_tiff.egg-info/entry_points.txt
-src/oct_to_tiff.egg-info/requires.txt
-src/oct_to_tiff.egg-info/top_level.txt

oct_to_tiff-0.5.0/src/oct_to_tiff.egg-info/dependency_links.txt

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-

oct_to_tiff-0.5.0/src/oct_to_tiff.egg-info/entry_points.txt

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-[console_scripts]
-oct-to-tiff = oct_to_tiff.cli:main

oct_to_tiff-0.5.0/src/oct_to_tiff.egg-info/requires.txt

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-defusedxml
-numpy
-tifffile
-
-[dev]
-mypy
-ruff
-types-defusedxml

oct_to_tiff-0.5.0/src/oct_to_tiff.egg-info/top_level.txt

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-oct_to_tiff