diff --git a/README.md b/README.md index e7f341c..0af9df3 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,5 @@ # [vsi2tif](https://github.com/andreped/vsi2tif#vsi2tif) -[![CI](https://github.com/andreped/vsi2tif/workflows/Build%20Package/badge.svg)](https://github.com/andreped/vsi2tif/actions) -[![CI](https://github.com/andreped/vsi2tif/workflows/Check%20Linting/badge.svg)](https://github.com/andreped/vsi2tif/actions) [![License](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13745169.svg)](https://doi.org/10.5281/zenodo.13745169) @@ -9,6 +7,14 @@ Tool for converting WSIs from Olympus' cellSens VSI to Generic TIFF. A simple Jupyter Notebook can be seen [here](https://github.com/andreped/vsi2tif/blob/main/notebooks/conversion_tutorial.ipynb) demonstrating how use the tool. +## [Continuous integration](https://github.com/andreped/vsi2tif#continuous-integration) + +| Build Type | Status | +| - | - | +| **Integration Tests** | [![CI](https://github.com/andreped/vsi2tif/workflows/Integration%20Tests/badge.svg)](https://github.com/andreped/vsi2tif/actions) | +| **Unit Tests** | [![CI](https://github.com/andreped/vsi2tif/workflows/Build%20Package/badge.svg)](https://github.com/andreped/vsi2tif/actions) | +| **Linting Checks** | [![CI](https://github.com/andreped/vsi2tif/workflows/Check%20Linting/badge.svg)](https://github.com/andreped/vsi2tif/actions) | + ## [Requirements](https://github.com/andreped/vsi2tif#requirements) To run the tool, you need to configure bftools and vips. To do that, follow the instructions below for the operating system of interest: @@ -97,7 +103,7 @@ vsi2tif -i /path/to/olympus/wsis/ -o /path/to/converted/wsis/directory/ -b /path Comprehensive CLI documentation can be seen below: ``` -usage: vsi2tif [-h] -i INPUT -o OUTPUT -b BFCONVERT [-c COMPRESSION] [-s TILESIZE] [-p PLANE] [-q QUALITY] [-m MAX_MEM] [-v VERBOSE] +usage: vsi2tif [-h] -i INPUT -o OUTPUT -b BFCONVERT [-c COMPRESSION] [-s TILESIZE] [-q QUALITY] [-m MAX_MEM] [-v VERBOSE] [--remove-name-spaces] [-p PLANE] vsi2tif - simple tool for converting images from cellSens VSI to Generic TIFF @@ -110,24 +116,25 @@ options: -b BFCONVERT, --bfconvert BFCONVERT path to bfconvert tool -c COMPRESSION, --compression COMPRESSION - compression technique for final image + compression technique for final image - default 'jpeg' -s TILESIZE, --tilesize TILESIZE - tile size to use during both conversion steps - -p PLANE, --plane PLANE - which image plane to convert image from + tile size to use during both conversion steps - default 1024 -q QUALITY, --quality QUALITY - compression quality used with JPEG compression + compression quality used with JPEG compression - default 87 -m MAX_MEM, --max-mem MAX_MEM - set maximum memory in the java vm + set maximum memory in the java vm - default 32 -v VERBOSE, --verbose VERBOSE - set verbosity level + set verbosity level - default 1 + --remove-name-spaces replace spaces in filename with underscores in batch mode + -p PLANE, --plane PLANE + which image plane to convert image from. If set to -1, all series are converted and the largest is kept - default 0 ``` ## [License](https://github.com/andreped/vsi2tif#license) This project has [MIT license](https://github.com/andreped/vsi2tif/blob/main/LICENSE). -## [How to cite](https://github.com/andreped/vsi2tif#how-to-cite) +## [How to cite](https://github.com/andreped/vsi2tif#how-to-cite) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13745169.svg)](https://doi.org/10.5281/zenodo.13745169) If you found this tool useful in your research, please cite the following: ``` diff --git a/setup.py b/setup.py index bc02389..2dcb22d 100644 --- a/setup.py +++ b/setup.py @@ -6,7 +6,7 @@ setup( name="vsi2tif", - version="0.1.4", + version="0.1.5", author="André Pedersen, Sebastian Krossa, Erik Smistad, David Bouget", author_email="andrped94@gmail.com", license="MIT", diff --git a/vsi2tif/vsi2tif.py b/vsi2tif/vsi2tif.py index 5799bb3..e96b84a 100644 --- a/vsi2tif/vsi2tif.py +++ b/vsi2tif/vsi2tif.py @@ -15,18 +15,25 @@ def main(): parser.add_argument("-i", "--input", help="folder with input files", required=True) parser.add_argument("-o", "--output", help="folder for output files", required=True) parser.add_argument("-b", "--bfconvert", help="path to bfconvert tool", required=True) - parser.add_argument("-c", "--compression", help="compression technique for final image", default="jpeg") - parser.add_argument("-s", "--tilesize", help="tile size to use during both conversion steps", default=1024) - parser.add_argument("-q", "--quality", help="compression quality used with JPEG compression", default=87) - parser.add_argument("-m", "--max-mem", help="set maximum memory in the java vm", default=32) - parser.add_argument("-v", "--verbose", help="set verbosity level", default=1, type=int) + parser.add_argument( + "-c", "--compression", help="compression technique for final image - default 'jpeg'", default="jpeg" + ) + parser.add_argument( + "-s", "--tilesize", help="tile size to use during both conversion steps - default 1024", default=1024 + ) + parser.add_argument( + "-q", "--quality", help="compression quality used with JPEG compression - default 87", default=87 + ) + parser.add_argument("-m", "--max-mem", help="set maximum memory in the java vm - default 32", default=32) + parser.add_argument("-v", "--verbose", help="set verbosity level - default 1", default=1, type=int) parser.add_argument( "--remove-name-spaces", help="replace spaces in filename with underscores in batch mode", action="store_true" ) parser.add_argument( "-p", "--plane", - help="which image plane to convert image from. If set to -1, all series are converted and the largest is kept", + help="image plane to convert image from. If set to -1, all series are converted and " + "the largest is kept - default 0", default=0, type=int, )