oct-to-tiff 0.3.0__tar.gz → 0.5.0__tar.gz

oct_to_tiff-0.5.0/PKG-INFO

@@ -0,0 +1,217 @@
+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)
+[![PyPI Downloads](https://static.pepy.tech/badge/oct-to-tiff)](https://pepy.tech/projects/oct-to-tiff)
+
+
+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-0.3.0 → oct_to_tiff-0.5.0}/README.md

@@ -1,6 +1,10 @@
 # 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)
+[![PyPI Downloads](https://static.pepy.tech/badge/oct-to-tiff)](https://pepy.tech/projects/oct-to-tiff)
+
 
 A command line tool for converting optical coherence tomography angiography (OCTA) data.
 
@@ -9,9 +13,9 @@ via pip:
 
     pip install oct-to-tiff
 
-via conda:
+via mamba:
 
-    conda install -c conda-forge oct-to-tiff
+    mamba install -c conda-forge oct-to-tiff
 
 ## Getting started
     oct-to-tiff /path/to/image.OCT
@@ -27,6 +31,12 @@ By default, the output file will be written with the same name as the input file
 
 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.
@@ -89,6 +99,13 @@ Sets the correct voxel size for scan patterns with adjustable length.
 
     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.
 
@@ -96,7 +113,7 @@ Sets the correct voxel size for scan patterns with adjustable length.
 
     oct-to-tiff --version
 
-#### The following options are currently experimental:
+#### The following options are mutually exclusive:
     
 #### `--angio`
 **Description**: convert extracted OCTA data. 
@@ -123,10 +140,17 @@ Requires `--size SIZE`.
 
     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 [black](https://github.com/psf/black) for formatting and [isort](https://github.com/PyCQA/isort) for sorting imports.
+This project uses [Ruff](https://github.com/astral-sh/ruff) for linting and formatting.
 
 ## Requirements
 
-Requires Python 3.7 or higher.
+Requires Python 3.10 or higher.

oct_to_tiff-0.5.0/pyproject.toml

@@ -0,0 +1,55 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "oct-to-tiff"
+version = "0.5.0"
+dependencies = [
+    "defusedxml",
+    "numpy",
+    "tifffile",
+]
+requires-python = ">=3.10"
+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"}
+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",
+]
+
+[project.optional-dependencies]
+dev = [
+    "mypy",
+    "ruff",
+    "types-defusedxml"
+]
+
+[project.urls]
+Homepage = "https://github.com/camlloyd/oct-to-tiff"
+"Bug Tracker" = "https://github.com/camlloyd/oct-to-tiff/issues"
+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.ruff.lint]
+select = [
+    "I", # isort
+    "S", # flake8-bandit
+]

oct_to_tiff-0.5.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

{oct_to_tiff-0.3.0 → oct_to_tiff-0.5.0}/src/oct_to_tiff/cli.py

@@ -1,17 +1,221 @@
 import argparse
 import logging
+from importlib.metadata import version
 from pathlib import Path
+from typing import Any
 
+import defusedxml.ElementTree as DET
 import numpy as np
 import tifffile
+from numpy.typing import NDArray
 
-logging.basicConfig(
-    format="%(asctime)s %(name)s:%(funcName)s %(levelname)s - %(message)s"
-)
 logger = logging.getLogger(__name__)
 
 
-def convert_oct_file(args, file_name, input_path, output_path):
+def reshape_volume(
+    volume: NDArray[Any],
+    frames_per_data_group: int,
+    total_data_groups: int,
+    oct_window_height: int,
+    xy_scan_length: int,
+) -> NDArray[Any]:
+    """Reshape a 1-dimensional array to a 3-dimensional array.
+
+    Parameters
+    ----------
+    volume : NDArray[Any]
+        A 1-dimensional array.
+    frames_per_data_group : int
+        The number of frames per data group.
+    total_data_groups : int
+        The total number of data groups.
+    oct_window_height : int
+        The OCT window height.
+    xy_scan_length : int
+        The XY scan length.
+
+    Returns
+    -------
+    volume : NDArray[Any]
+        A 3-dimensional array.
+
+    """
+    volume = np.reshape(
+        volume,
+        (
+            frames_per_data_group * total_data_groups,
+            xy_scan_length,
+            oct_window_height,
+        ),
+    )
+    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],
+    pixel_size_x: float,
+    pixel_size_y: float,
+    pixel_size_z: float,
+) -> None:
+    """Write a 3-dimensional array to the output path as an OME-TIFF file, including voxel size in the metadata.
+
+    Parameters
+    ----------
+    output_path : Path
+        The specified output path.
+    volume : NDArray[Any]
+        A 3-dimensional array.
+    pixel_size_x : float
+        The pixel (voxel) width in mm.
+    pixel_size_y : float
+        The pixel (voxel) height in mm.
+    pixel_size_z : float
+        The pixel (voxel) depth in mm.
+
+    """
+    tifffile.imwrite(
+        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",
+        },
+    )
+
+
+def extract_boundaries(input_path: str | Path) -> None:
+    """Extract segmentation lines.
+
+    Parameters
+    ----------
+    input_path : str | Path
+        The specified input path.
+
+    """
+    input_path = Path(input_path)
+    tree = DET.parse(input_path)
+    root = tree.getroot()
+
+    array_size = int(root.findtext("./Curve_Set/Image/Curve/ARRAY", 0))
+    data_points = [
+        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):
+        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")
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser(
+        description="Convert optical coherence tomography angiography (OCTA) data."
+    )
+    parser.add_argument("input", type=Path, help="OCT file to convert")
+    parser.add_argument("--output", type=Path, help="specify a custom output directory")
+    parser.add_argument(
+        "--overwrite",
+        default=False,
+        action="store_true",
+        help="overwrite output file if it exists",
+    )
+    parser.add_argument("--size", type=float, help="scan size in mm")
+    group = parser.add_mutually_exclusive_group()
+    group.add_argument(
+        "--angio",
+        default=False,
+        action="store_true",
+        help="convert extracted OCTA data",
+    )
+    group.add_argument(
+        "--en-face",
+        default=False,
+        action="store_true",
+        help="convert extracted en face image",
+    )
+    group.add_argument(
+        "--seg-curve",
+        default=False,
+        action="store_true",
+        help="convert extracted segmentation data",
+    )
+    group.add_argument(
+        "--boundaries",
+        default=False,
+        action="store_true",
+        help="extract segmentation lines",
+    )
+    parser.add_argument(
+        "--log-level",
+        default="WARNING",
+        metavar="LEVEL",
+        help="sets the logging level (default: %(default)s)",
+    )
+    parser.add_argument(
+        "--version", action="version", version="%(prog)s " + version("oct_to_tiff")
+    )
+    args = parser.parse_args()
+
+    numeric_level = getattr(logging, args.log_level.upper(), None)
+    if not isinstance(numeric_level, int):
+        raise ValueError(f"Invalid log level: {args.log_level}")
+    logging.basicConfig(
+        level=numeric_level,
+        format="%(asctime)s %(name)s:%(funcName)s %(levelname)s - %(message)s",
+    )
+
+    input_path = args.input
+    if args.output:
+        dir_name = args.output
+        dir_name.mkdir(parents=True, exist_ok=True)
+    else:
+        dir_name = input_path.parent
+    file_name = input_path.stem
+    file_extension = ".ome.tif"
+    output_path = dir_name / (file_name + file_extension)
+
+    if Path.is_file(output_path):
+        if args.overwrite:
+            pass
+        else:
+            logger.error(f"{output_path} already exists.")
+            return
+
+    if args.boundaries:
+        extract_boundaries(input_path)
+        return
+
     with open(input_path, "rb") as f:
         if args.angio and args.size:
             volume = np.frombuffer(f.read(), dtype=np.uint16)
@@ -266,144 +470,5 @@ def convert_oct_file(args, file_name, input_path, output_path):
         write_volume(output_path, volume, pixel_size_x, pixel_size_y, pixel_size_z)
 
 
-def reshape_volume(
-    volume, frames_per_data_group, total_data_groups, oct_window_height, xy_scan_length
-):
-    """Reshape a 1-dimensional array to a 3-dimensional array.
-
-    Parameters
-    ----------
-    volume : ndarray
-        A 1-dimensional array.
-    frames_per_data_group : int
-        The number of frames per data group.
-    total_data_groups : int
-        The total number of data groups.
-    oct_window_height : int
-        The OCT window height.
-    xy_scan_length : int
-        The XY scan length.
-
-    Returns
-    -------
-    volume : ndarray
-        A 3-dimensional array.
-
-    """
-    volume = np.reshape(
-        volume,
-        (
-            frames_per_data_group * total_data_groups,
-            xy_scan_length,
-            oct_window_height,
-        ),
-    )
-    return volume
-
-
-def rotate_volume(volume):
-    """Rotate a 3-dimensional array 90 degrees left (anti-clockwise) about the z-axis.
-
-    Parameters
-    ----------
-    volume : ndarray
-        A 3-dimensional array.
-
-    Returns
-    -------
-    volume : ndarray
-        A rotated version of the input volume.
-
-    """
-    volume = np.rot90(volume, k=1, axes=(1, 2))
-    return volume
-
-
-def write_volume(output_path, volume, pixel_size_x, pixel_size_y, pixel_size_z):
-    """Write a 3-dimensional array to the output path as an OME-TIFF file, including voxel size in the metadata.
-
-    Parameters
-    ----------
-    output_path : Path
-        The specified output path.
-    volume : ndarray
-        A 3-dimensional array.
-    pixel_size_x : float
-        The pixel (voxel) width in mm.
-    pixel_size_y : float
-        The pixel (voxel) height in mm.
-    pixel_size_z : float
-        The pixel (voxel) depth in mm.
-
-    """
-    tifffile.imwrite(
-        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",
-        },
-    )
-
-
-def main():
-    parser = argparse.ArgumentParser(
-        description="Convert optical coherence tomography angiography (OCTA) data."
-    )
-    parser.add_argument("input", type=Path, help="OCT file to convert")
-    parser.add_argument("--output", type=Path, help="specify a custom output directory")
-    parser.add_argument(
-        "--overwrite",
-        default=False,
-        action="store_true",
-        help="overwrite output file if it exists",
-    )
-    parser.add_argument("--size", type=float, help="scan size in mm")
-    parser.add_argument(
-        "--angio",
-        default=False,
-        action="store_true",
-        help="convert extracted OCTA data",
-    )
-    parser.add_argument(
-        "--en-face",
-        default=False,
-        action="store_true",
-        help="convert extracted en face image",
-    )
-    parser.add_argument(
-        "--seg-curve",
-        default=False,
-        action="store_true",
-        help="convert extracted segmentation data",
-    )
-    parser.add_argument("--version", action="version", version="%(prog)s 0.3.0")
-    args = parser.parse_args()
-
-    input_path = args.input
-    if args.output:
-        dir_name = args.output
-        dir_name.mkdir(parents=True, exist_ok=True)
-    else:
-        dir_name = input_path.parent
-    file_name = input_path.stem
-    file_extension = ".ome.tif"
-    output_path = dir_name / (file_name + file_extension)
-
-    if Path.is_file(output_path):
-        if args.overwrite:
-            convert_oct_file(args, file_name, input_path, output_path)
-        else:
-            logger.error(f"{output_path} already exists.")
-    else:
-        convert_oct_file(args, file_name, input_path, output_path)
-
-
 if __name__ == "__main__":
     main()

oct_to_tiff-0.5.0/src/oct_to_tiff.egg-info/PKG-INFO

@@ -0,0 +1,217 @@
+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)
+[![PyPI Downloads](https://static.pepy.tech/badge/oct-to-tiff)](https://pepy.tech/projects/oct-to-tiff)
+
+
+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-0.3.0 → oct_to_tiff-0.5.0}/src/oct_to_tiff.egg-info/SOURCES.txt

@@ -1,8 +1,6 @@
 LICENSE.txt
 README.md
 pyproject.toml
-setup.cfg
-setup.py
 src/oct_to_tiff/__init__.py
 src/oct_to_tiff/cli.py
 src/oct_to_tiff.egg-info/PKG-INFO

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

@@ -0,0 +1,8 @@
+defusedxml
+numpy
+tifffile
+
+[dev]
+mypy
+ruff
+types-defusedxml

oct_to_tiff-0.3.0/PKG-INFO

@@ -1,154 +0,0 @@
-Metadata-Version: 2.1
-Name: oct_to_tiff
-Version: 0.3.0
-Summary: A command line tool for converting optical coherence tomography angiography (OCTA) data.
-Home-page: https://github.com/camlloyd/oct-to-tiff
-Author: Cameron Lloyd
-Author-email: lloyd@med.unideb.hu
-Project-URL: Bug Tracker, https://github.com/camlloyd/oct-to-tiff/issues
-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 :: 3.7
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Requires-Python: >=3.7
-Description-Content-Type: text/markdown
-License-File: LICENSE.txt
-
-# oct-to-tiff
-
-[![DOI](https://zenodo.org/badge/382486199.svg)](https://zenodo.org/badge/latestdoi/382486199)
-
-A command line tool for converting optical coherence tomography angiography (OCTA) data.
-
-## Installation
-via pip:
-
-    pip install oct-to-tiff
-
-via conda:
-
-    conda 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.
-
-## 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
-
-#### `--version`
-**Description**: show program's version number and exit.
-
-**Usage**:
-
-    oct-to-tiff --version
-
-#### The following options are currently experimental:
-    
-#### `--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
-
-## Contributing
-
-This project uses [black](https://github.com/psf/black) for formatting and [isort](https://github.com/PyCQA/isort) for sorting imports.
-
-## Requirements
-
-Requires Python 3.7 or higher.

oct_to_tiff-0.3.0/pyproject.toml

@@ -1,6 +0,0 @@
-[build-system]
-requires = [
-    "setuptools>=42",
-    "wheel"
-]
-build-backend = "setuptools.build_meta"

oct_to_tiff-0.3.0/setup.cfg

@@ -1,43 +0,0 @@
-[metadata]
-name = oct_to_tiff
-version = 0.3.0
-author = Cameron Lloyd
-author_email = lloyd@med.unideb.hu
-description = A command line tool for converting optical coherence tomography angiography (OCTA) data.
-long_description = file: README.md
-long_description_content_type = text/markdown
-url = https://github.com/camlloyd/oct-to-tiff
-project_urls = 
-	Bug Tracker = https://github.com/camlloyd/oct-to-tiff/issues
-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 :: 3.7
-	Programming Language :: Python :: 3.8
-	Programming Language :: Python :: 3.9
-	Programming Language :: Python :: 3.10
-
-[options]
-packages = find:
-package_dir = 
-	=src
-python_requires = >=3.7
-install_requires = 
-	numpy
-	tifffile
-
-[options.entry_points]
-console_scripts = 
-	oct-to-tiff = oct_to_tiff.cli:main
-
-[options.packages.find]
-where = src
-
-[egg_info]
-tag_build = 
-tag_date = 0
-

oct_to_tiff-0.3.0/setup.py

@@ -1,3 +0,0 @@
-import setuptools
-
-setuptools.setup()

oct_to_tiff-0.3.0/src/oct_to_tiff.egg-info/PKG-INFO

@@ -1,154 +0,0 @@
-Metadata-Version: 2.1
-Name: oct-to-tiff
-Version: 0.3.0
-Summary: A command line tool for converting optical coherence tomography angiography (OCTA) data.
-Home-page: https://github.com/camlloyd/oct-to-tiff
-Author: Cameron Lloyd
-Author-email: lloyd@med.unideb.hu
-Project-URL: Bug Tracker, https://github.com/camlloyd/oct-to-tiff/issues
-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 :: 3.7
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Requires-Python: >=3.7
-Description-Content-Type: text/markdown
-License-File: LICENSE.txt
-
-# oct-to-tiff
-
-[![DOI](https://zenodo.org/badge/382486199.svg)](https://zenodo.org/badge/latestdoi/382486199)
-
-A command line tool for converting optical coherence tomography angiography (OCTA) data.
-
-## Installation
-via pip:
-
-    pip install oct-to-tiff
-
-via conda:
-
-    conda 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.
-
-## 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
-
-#### `--version`
-**Description**: show program's version number and exit.
-
-**Usage**:
-
-    oct-to-tiff --version
-
-#### The following options are currently experimental:
-    
-#### `--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
-
-## Contributing
-
-This project uses [black](https://github.com/psf/black) for formatting and [isort](https://github.com/PyCQA/isort) for sorting imports.
-
-## Requirements
-
-Requires Python 3.7 or higher.

oct_to_tiff-0.3.0/src/oct_to_tiff.egg-info/requires.txt

@@ -1,2 +0,0 @@
-numpy
-tifffile