oct-to-tiff 0.6.0__tar.gz → 0.6.1__tar.gz

{oct_to_tiff-0.6.0/src/oct_to_tiff.egg-info → oct_to_tiff-0.6.1}/PKG-INFO

@@ -1,14 +1,12 @@
 Metadata-Version: 2.4
 Name: oct-to-tiff
-Version: 0.6.0
+Version: 0.6.1
 Summary: A command line tool for converting optical coherence tomography angiography (OCTA) data.
+Keywords: angiography,cli,oct,octa
+Author: Cameron Lloyd
 Author-email: Cameron Lloyd <lloyd@med.unideb.hu>
-Maintainer-email: Cameron Lloyd <lloyd@med.unideb.hu>
 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
+License-File: LICENSE.txt
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Science/Research
 Classifier: Natural Language :: English
@@ -18,18 +16,21 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 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
+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"
-Dynamic: license-file
+Description-Content-Type: text/markdown
 
 # oct-to-tiff
 
@@ -46,9 +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
@@ -186,4 +187,4 @@ This project uses [Ruff](https://github.com/astral-sh/ruff) for linting and form
 
 ## Requirements
 
-Requires Python 3.11 or higher.
+Requires Python 3.11 or higher.

{oct_to_tiff-0.6.0 → 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

{oct_to_tiff-0.6.0 → oct_to_tiff-0.6.1}/pyproject.toml

@@ -1,10 +1,10 @@
 [build-system]
-requires = ["setuptools >= 77.0.3"]
-build-backend = "setuptools.build_meta"
+requires = ["uv_build>=0.9.26,<0.10.0"]
+build-backend = "uv_build"
 
 [project]
 name = "oct-to-tiff"
-version = "0.6.0"
+version = "0.6.1"
 dependencies = [
     "defusedxml",
     "numpy",
@@ -46,8 +46,9 @@ 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 = [

{oct_to_tiff-0.6.0 → oct_to_tiff-0.6.1}/src/oct_to_tiff/cli.py

@@ -52,12 +52,47 @@ def reshape_volume(
     return volume
 
 
+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
+    ----------
+    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
+    -------
+    metadata : dict[str, Any]
+        A dictionary of metadata.
+
+    """
+    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: npt.NDArray[Any],
-    pixel_size_x: float,
-    pixel_size_y: float,
-    pixel_size_z: float,
+    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.
 
@@ -79,15 +114,7 @@ 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),
     )
 
 
@@ -245,7 +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:
@@ -256,9 +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
@@ -338,7 +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
@@ -347,7 +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
@@ -356,7 +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
@@ -365,7 +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
@@ -374,7 +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
@@ -383,7 +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
@@ -392,7 +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
@@ -446,7 +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
@@ -455,7 +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
@@ -464,7 +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
@@ -473,7 +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
@@ -482,7 +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
@@ -491,7 +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,

oct_to_tiff-0.6.0/PKG-INFO

@@ -1,189 +0,0 @@
-Metadata-Version: 2.4
-Name: oct-to-tiff
-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-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: Natural Language :: English
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-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
-
-[![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 3.11 or higher.

oct_to_tiff-0.6.0/setup.cfg

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

oct_to_tiff-0.6.0/src/oct_to_tiff.egg-info/SOURCES.txt

@@ -1,11 +0,0 @@
-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-0.6.0/src/oct_to_tiff.egg-info/dependency_links.txt

@@ -1 +0,0 @@
-

oct_to_tiff-0.6.0/src/oct_to_tiff.egg-info/entry_points.txt

@@ -1,2 +0,0 @@
-[console_scripts]
-oct-to-tiff = oct_to_tiff.cli:main

oct_to_tiff-0.6.0/src/oct_to_tiff.egg-info/requires.txt

@@ -1,9 +0,0 @@
-defusedxml
-numpy
-roifile
-tifffile
-
-[dev]
-mypy
-ruff
-types-defusedxml

oct_to_tiff-0.6.0/src/oct_to_tiff.egg-info/top_level.txt

@@ -1 +0,0 @@
-oct_to_tiff