Merge pull request #35 from andreped/readme-ci-update

Added default value to argument description in CLI; improved documentation

README.md

@@ -1,14 +1,20 @@
 # [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)
 
 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:
 ```

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="[email protected]",
     license="MIT",

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,
     )