| Name | oct-to-tiff JSON |
| Version |
0.5.0
JSON |
| download |
| home_page | None |
| Summary | A command line tool for converting optical coherence tomography angiography (OCTA) data. |
| upload_time | 2024-12-06 13:26:30 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| 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. |
| keywords |
angiography
cli
oct
octa
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
defusedxml
numpy
tifffile
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# oct-to-tiff
[](https://zenodo.org/badge/latestdoi/382486199)
[](https://pypi.org/project/oct-to-tiff)
[](https://github.com/camlloyd/oct-to-tiff/blob/main/LICENSE.txt)
[](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.
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"description": "# oct-to-tiff\n\n[](https://zenodo.org/badge/latestdoi/382486199)\n[](https://pypi.org/project/oct-to-tiff)\n[](https://github.com/camlloyd/oct-to-tiff/blob/main/LICENSE.txt)\n[](https://pepy.tech/projects/oct-to-tiff)\n\n\nA command line tool for converting optical coherence tomography angiography (OCTA) data.\n\n## Installation\nvia pip:\n\n pip install oct-to-tiff\n\nvia mamba:\n\n mamba install -c conda-forge oct-to-tiff\n\n## Getting started\n oct-to-tiff /path/to/image.OCT\n \nwill read an OCT volume and write to a single OME-TIFF file, including voxel size in the metadata.\n\nBy default, the output file will be written with the same name as the input file and to the same directory:\n\n\n tree /path/to/images\n \u251c\u2500\u2500 image.OCT\n \u2514\u2500\u2500 image.ome.tif\n\nTo specify a custom output directory, see [Optional arguments](#optional-arguments) below.\n\n## Batch processing\n``` bash\nfor file in *.OCT; do oct-to-tiff \"${file}\"; done\n```\nwill convert all OCT volumes in the current directory to OME-TIFF files, including voxel size in the metadata.\n\n## Supported scan patterns\n\nThis tool has been developed by reverse engineering data from the Optovue RTVue XR Avanti System.\n\nDue to limited test data, only the following scan patterns are currently supported:\n\n### Structural OCT\n- 3D Cornea\n- 3D Disc\n- 3D Retina\n- 3D Widefield\n- 3D Widefield MCT\n- Angle\n- Cornea Cross Line\n- Cornea Line\n- Cross Line\n- Enhanced HD Line\n- GCC\n- Grid\n- Line\n- ONH (Partial)\n- Pachymetry Wide\n- Radial Lines\n- Raster\n- Retina Map (Partial)\n\n### OCT Angiography\n- Angio Disc\n- Angio Retina\n- HD Angio Disc\n- HD Angio Retina\n\n\n## Optional arguments\n\nTo view these options at any time, run `oct-to-tiff --help`.\n\n#### `--output OUTPUT`\n**Description**: specify a custom output directory. \n\nIf the path to the output directory does not exist, a new directory (and parent directories) will be created.\n\n**Usage**: \n \n oct-to-tiff /path/to/image.OCT --output /path/to/output/directory\n \n#### `--overwrite`\n**Description**: overwrite output file if it exists.\n\n**Usage**: \n \n oct-to-tiff /path/to/image.OCT --overwrite\n \n#### `--size SIZE`\n**Description**: scan size in mm.\n\nSets the correct voxel size for scan patterns with adjustable length.\n\n**Usage**:\n\n oct-to-tiff /path/to/image.OCT --size 4.5\n\n#### `--log-level LEVEL`\n**Description**: sets the logging level (default: `WARNING`)\n\n**Usage**:\n\n oct-to-tiff /path/to/image.OCT --log-level INFO\n\n#### `--version`\n**Description**: show program's version number and exit.\n\n**Usage**:\n\n oct-to-tiff --version\n\n#### The following options are mutually exclusive:\n \n#### `--angio`\n**Description**: convert extracted OCTA data. \n\nRequires `--size SIZE`.\n\n**Usage**:\n\n oct-to-tiff /path/to/data --angio --size 4.5\n \n#### `--en-face`\n**Description**: convert extracted en face data.\n\nRequires `--size SIZE`.\n\n**Usage**:\n\n oct-to-tiff /path/to/data --en-face --size 4.5\n \n#### `--seg-curve`\n**Description**: convert extracted segmentation data.\n\n**Usage**:\n\n oct-to-tiff /path/to/data --seg-curve\n\n#### `--boundaries`\n**Description**: extract segmentation lines.\n\n**Usage**:\n\n oct-to-tiff /path/to/curve.xml --boundaries\n\n## Contributing\n\nThis project uses [Ruff](https://github.com/astral-sh/ruff) for linting and formatting.\n\n## Requirements\n\nRequires Python 3.10 or higher.\n",
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