diff --git a/features/nyxus-tool/.bumpversion.cfg b/features/nyxus-tool/.bumpversion.cfg index f4cf5c255..a8b3022de 100755 --- a/features/nyxus-tool/.bumpversion.cfg +++ b/features/nyxus-tool/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.1.7 +current_version = 0.1.8-dev0 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/features/nyxus-tool/README.md b/features/nyxus-tool/README.md index 50131c6cb..41f9d772e 100755 --- a/features/nyxus-tool/README.md +++ b/features/nyxus-tool/README.md @@ -1,4 +1,4 @@ -# Nyxus-Plugin(v0.1.7) +# Nyxus-Plugin(v0.1.8-dev0) Nyxus plugin uses parallel processing of [Nyxus python package](https://pypi.org/project/nyxus/) to extract nyxus features from intensity-label image data. Especially useful when processing high throughput screens. diff --git a/features/nyxus-tool/VERSION b/features/nyxus-tool/VERSION index 11808190d..84d8d7b2b 100755 --- a/features/nyxus-tool/VERSION +++ b/features/nyxus-tool/VERSION @@ -1 +1 @@ -0.1.7 +0.1.8-dev0 diff --git a/features/nyxus-tool/plugin.json b/features/nyxus-tool/plugin.json index b5e0a709f..d3355af70 100755 --- a/features/nyxus-tool/plugin.json +++ b/features/nyxus-tool/plugin.json @@ -1,7 +1,7 @@ { "name": "Nyxus plugin", - "version": "0.1.7", - "containerId": "polusai/nyxus-tool:0.1.7", + "version": "0.1.8-dev0", + "containerId": "polusai/nyxus-tool:0.1.8-dev0", "title": "Nyxus plugin", "description": "Nyxus plugin allows to make use of parallel pocessing for extracting nyxus features", "author": "Nick Schaub (nick.schaub@nih.gov), Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)", diff --git a/features/nyxus-tool/pyproject.toml b/features/nyxus-tool/pyproject.toml index f38ad24db..5deb5e10b 100644 --- a/features/nyxus-tool/pyproject.toml +++ b/features/nyxus-tool/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "polus-images-features-nyxus-plugin" -version = "0.1.7" +version = "0.1.8-dev0" description = "" authors = [ "Nick Schaub ", @@ -21,6 +21,7 @@ vaex = "^4.17.0" preadator = "0.4.0.dev2" pytest-sugar = "^0.9.7" pytest-xdist = "^3.5.0" +pyarrow = ">=16.0,<17.0" [tool.poetry.group.dev.dependencies] bump2version = "^1.0.1" diff --git a/features/nyxus-tool/src/polus/images/features/nyxus_plugin/__init__.py b/features/nyxus-tool/src/polus/images/features/nyxus_plugin/__init__.py index e16336830..8f5b44c45 100644 --- a/features/nyxus-tool/src/polus/images/features/nyxus_plugin/__init__.py +++ b/features/nyxus-tool/src/polus/images/features/nyxus_plugin/__init__.py @@ -1,2 +1,2 @@ """Nyxus Plugin.""" -__version__ = "0.1.7" +__version__ = "0.1.8-dev0" diff --git a/features/pixel-segmentation-eval-tool/.bumpversion.cfg b/features/pixel-segmentation-eval-tool/.bumpversion.cfg index af8ebbcec..eb93072af 100644 --- a/features/pixel-segmentation-eval-tool/.bumpversion.cfg +++ b/features/pixel-segmentation-eval-tool/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.1.12 +current_version = 0.1.13-dev0 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/features/pixel-segmentation-eval-tool/CHANGELOG.md b/features/pixel-segmentation-eval-tool/CHANGELOG.md index 0b06ce39d..9aba63029 100644 --- a/features/pixel-segmentation-eval-tool/CHANGELOG.md +++ b/features/pixel-segmentation-eval-tool/CHANGELOG.md @@ -1,4 +1,4 @@ -# pixel-segmentation-eval(v0.1.12) +# pixel-segmentation-eval(v0.1.13-dev0) 1. This plugin is updated only to the new plugin standards 2. `csv` python packages is replaced with vaex for adding support for additional tabular file formats `.arrow`, `.feather`. diff --git a/features/pixel-segmentation-eval-tool/README.md b/features/pixel-segmentation-eval-tool/README.md index 0ca55ba96..144d9f640 100644 --- a/features/pixel-segmentation-eval-tool/README.md +++ b/features/pixel-segmentation-eval-tool/README.md @@ -1,4 +1,4 @@ -# Pixel segmentation eval (v0.1.12) +# Pixel segmentation eval (v0.1.13-dev0) Plugin to generate evaluation metrics for pixel-wise comparison of ground truth and predicted images. Contact [Vishakha Goyal](mailto:vishakha.goyal@nih.gov) , [Hamdah Shafqat Abbasi](mailto:hamdahshafqat.abbasi@nih.gov) for more information. diff --git a/features/pixel-segmentation-eval-tool/VERSION b/features/pixel-segmentation-eval-tool/VERSION index 0e24a92ff..a1702f0db 100644 --- a/features/pixel-segmentation-eval-tool/VERSION +++ b/features/pixel-segmentation-eval-tool/VERSION @@ -1 +1 @@ -0.1.12 +0.1.13-dev0 diff --git a/features/pixel-segmentation-eval-tool/plugin.json b/features/pixel-segmentation-eval-tool/plugin.json index 218171a1e..5885479f5 100644 --- a/features/pixel-segmentation-eval-tool/plugin.json +++ b/features/pixel-segmentation-eval-tool/plugin.json @@ -1,6 +1,6 @@ { "name": "Pixel Segmentation Eval", - "version": "0.1.12", + "version": "0.1.13-dev0", "title": "Pixel Segmentation Eval", "description": "Plugin to generate evaluation metrics for pixel-wise comparison of ground truth and predicted images.", "author": "Vishakha Goyal (vishakha.goyal@nih.gov)", @@ -8,7 +8,7 @@ "repository": "https://github.com/polusai/polus-plugins", "website": "https://ncats.nih.gov/preclinical/core/informatics", "citation": "", - "containerId": "polusai/pixel-segmentation-eval-tool:0.1.12", + "containerId": "polusai/pixel-segmentation-eval-tool:0.1.13-dev0", "baseCommand": [ "python3", "-m", diff --git a/features/pixel-segmentation-eval-tool/pyproject.toml b/features/pixel-segmentation-eval-tool/pyproject.toml index 92c357eda..f9d232d35 100644 --- a/features/pixel-segmentation-eval-tool/pyproject.toml +++ b/features/pixel-segmentation-eval-tool/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "polus-images-features-pixel-segmentation-eval" -version = "0.1.12" +version = "0.1.13-dev0" description = "" authors = [ "Vishakha Goyal ", @@ -18,6 +18,7 @@ tqdm = "^4.64.1" tifffile="^2020.10.1" vaex = "^4.7.0" scipy = "1.9.3" +pyarrow = ">=16.0,<17.0" [tool.poetry.group.dev.dependencies] bump2version = "^1.0.1" diff --git a/features/pixel-segmentation-eval-tool/src/polus/images/features/pixel_segmentation_eval/__init__.py b/features/pixel-segmentation-eval-tool/src/polus/images/features/pixel_segmentation_eval/__init__.py index c533103b2..2934776f5 100644 --- a/features/pixel-segmentation-eval-tool/src/polus/images/features/pixel_segmentation_eval/__init__.py +++ b/features/pixel-segmentation-eval-tool/src/polus/images/features/pixel_segmentation_eval/__init__.py @@ -1,3 +1,3 @@ """Pixel segmentation eval package.""" -__version__ = "0.1.12" +__version__ = "0.1.13-dev0" diff --git a/features/region-segmentation-eval-tool/.bumpversion.cfg b/features/region-segmentation-eval-tool/.bumpversion.cfg index 763aa298d..4b99d1fcd 100644 --- a/features/region-segmentation-eval-tool/.bumpversion.cfg +++ b/features/region-segmentation-eval-tool/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.2.5 +current_version = 0.2.6-dev0 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/features/region-segmentation-eval-tool/VERSION b/features/region-segmentation-eval-tool/VERSION index 3a4036fb4..fccaf8bba 100644 --- a/features/region-segmentation-eval-tool/VERSION +++ b/features/region-segmentation-eval-tool/VERSION @@ -1 +1 @@ -0.2.5 +0.2.6-dev0 diff --git a/features/region-segmentation-eval-tool/plugin.json b/features/region-segmentation-eval-tool/plugin.json index 08391ce8f..0f75caf1f 100644 --- a/features/region-segmentation-eval-tool/plugin.json +++ b/features/region-segmentation-eval-tool/plugin.json @@ -1,6 +1,6 @@ { "name": "Region Segmentation Eval", - "version": "0.2.5", + "version": "0.2.6-dev0", "title": "Region Segmentation Eval", "description": "Plugin to generate evaluation metrics for region-wise comparison of ground truth and predicted images.", "author": "Vishakha Goyal (vishakha.goyal@nih.gov), Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)", @@ -8,7 +8,7 @@ "repository": "https://github.com/polusai/polus-plugins", "website": "https://ncats.nih.gov/preclinical/core/informatics", "citation": "", - "containerId": "polusai/region-segmentation-eval-tool:0.2.5", + "containerId": "polusai/region-segmentation-eval-tool:0.2.6-dev0", "baseCommand": [ "python3", "-m", diff --git a/features/region-segmentation-eval-tool/pyproject.toml b/features/region-segmentation-eval-tool/pyproject.toml index bde799a5d..34d6f4f69 100644 --- a/features/region-segmentation-eval-tool/pyproject.toml +++ b/features/region-segmentation-eval-tool/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "polus-images-features-region-segmentation-eval" -version = "0.2.5" +version = "0.2.6-dev0" description = "" authors = [ "Vishakha Goyal ", @@ -16,7 +16,6 @@ filepattern = "^2.0.1" typer = "^0.7.0" tqdm = "^4.64.1" scikit-image = "^0.19.3" -scikit-learn="^0.24.2" opencv_python="^4.5.1.48" tifffile="^2020.10.1" blake3 = "^0.3.3" @@ -24,6 +23,8 @@ llvmlite = "^0.39.1" fastapi = "^0.92.0" vaex = "^4.7.0" numpy = "<2.0.0" +pyarrow = ">=16.0,<17.0" +scikit-learn = "^1.5.1" [tool.poetry.group.dev.dependencies] bump2version = "^1.0.1" diff --git a/features/region-segmentation-eval-tool/src/polus/images/features/region_segmentation_eval/__init__.py b/features/region-segmentation-eval-tool/src/polus/images/features/region_segmentation_eval/__init__.py index a74a76bde..c89263bbd 100644 --- a/features/region-segmentation-eval-tool/src/polus/images/features/region_segmentation_eval/__init__.py +++ b/features/region-segmentation-eval-tool/src/polus/images/features/region_segmentation_eval/__init__.py @@ -1,2 +1,2 @@ """Region segmentation eval package.""" -__version__ = "0.2.5" +__version__ = "0.2.6-dev0" diff --git a/visualization/ome-to-microjson-tool/.bumpversion.cfg b/visualization/ome-to-microjson-tool/.bumpversion.cfg index 812d3655a..19c4be1a0 100644 --- a/visualization/ome-to-microjson-tool/.bumpversion.cfg +++ b/visualization/ome-to-microjson-tool/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.1.5 +current_version = 0.1.6-dev0 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/visualization/ome-to-microjson-tool/README.md b/visualization/ome-to-microjson-tool/README.md index 2d7f3afd9..d9f5912f7 100644 --- a/visualization/ome-to-microjson-tool/README.md +++ b/visualization/ome-to-microjson-tool/README.md @@ -1,4 +1,4 @@ -# Ome-to-microjson-plugin(v0.1.5) +# Ome-to-microjson-plugin(v0.1.6-dev0) This plugin generate a microjson of polygon coordinates of binary or label segmentations @@ -50,7 +50,7 @@ This plugin can take four input arguments and one output argument: ### Run the Docker Container ```bash -docker run -v /data:/data polusai/ome-to-microjson-plugin:0.1.5-dev \ +docker run -v /data:/data polusai/ome-to-microjson-plugin:0.1.6-dev0-dev \ --inpDir /data/input \ --filePattern ".*.ome.tif" \ --polygonType "encoding" \ diff --git a/visualization/ome-to-microjson-tool/VERSION b/visualization/ome-to-microjson-tool/VERSION index 9faa1b7a7..951891996 100644 --- a/visualization/ome-to-microjson-tool/VERSION +++ b/visualization/ome-to-microjson-tool/VERSION @@ -1 +1 @@ -0.1.5 +0.1.6-dev0 diff --git a/visualization/ome-to-microjson-tool/plugin.json b/visualization/ome-to-microjson-tool/plugin.json index 7addda29c..91416aba8 100644 --- a/visualization/ome-to-microjson-tool/plugin.json +++ b/visualization/ome-to-microjson-tool/plugin.json @@ -1,6 +1,6 @@ { "name": "Ome_to_microjson", - "version": "0.1.5", + "version": "0.1.6-dev0", "title": "Convert binary segmentations to micojson", "description": "This plugin create a microjson of polygon coordinates (rectangle, encodings) of binary segmentations.", "author": "Hamdah Shafqat abbasi (hamdahshafqat.abbasi@nih.gov)", @@ -8,7 +8,7 @@ "repository": "https://github.com/labshare/polus-plugins", "website": "https://ncats.nih.gov/preclinical/core/informatics", "citation": "", - "containerId": "polusai/ome-to-microjson-tool:0.1.5", + "containerId": "polusai/ome-to-microjson-tool:0.1.6-dev0", "baseCommand": [ "python3", "-m", diff --git a/visualization/ome-to-microjson-tool/pyproject.toml b/visualization/ome-to-microjson-tool/pyproject.toml index c75b218d7..6c5c36ac5 100644 --- a/visualization/ome-to-microjson-tool/pyproject.toml +++ b/visualization/ome-to-microjson-tool/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "polus-images-visualization-ome-to-microjson" -version = "0.1.5" +version = "0.1.6-dev0" description = "This plugin create a microjson of polygon coordinates of binary and label segmentations" authors = ["Hamdah Shafqat abbasi "] readme = "README.md" @@ -19,6 +19,7 @@ llvmlite = "^0.40.1" vaex = "^4.17.0" scikit-image = "^0.20.0" memory-profiler = "^0.61.0" +pyarrow = ">=16.0,<17.0" [tool.poetry.group.dev.dependencies] bump2version = "^1.0.1" diff --git a/visualization/ome-to-microjson-tool/src/polus/images/visualization/ome_to_microjson/__init__.py b/visualization/ome-to-microjson-tool/src/polus/images/visualization/ome_to_microjson/__init__.py index 377d071e6..12c737fc3 100644 --- a/visualization/ome-to-microjson-tool/src/polus/images/visualization/ome_to_microjson/__init__.py +++ b/visualization/ome-to-microjson-tool/src/polus/images/visualization/ome_to_microjson/__init__.py @@ -1,3 +1,3 @@ """Ome micojson package.""" -__version__ = "0.1.5" +__version__ = "0.1.6-dev0" diff --git a/visualization/tabular-to-microjson-tool/.bumpversion.cfg b/visualization/tabular-to-microjson-tool/.bumpversion.cfg index e90f2f6a5..6645e22cf 100644 --- a/visualization/tabular-to-microjson-tool/.bumpversion.cfg +++ b/visualization/tabular-to-microjson-tool/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.1.2 +current_version = 0.1.3-dev0 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/visualization/tabular-to-microjson-tool/VERSION b/visualization/tabular-to-microjson-tool/VERSION index d917d3e26..e40c87666 100644 --- a/visualization/tabular-to-microjson-tool/VERSION +++ b/visualization/tabular-to-microjson-tool/VERSION @@ -1 +1 @@ -0.1.2 +0.1.3-dev0 diff --git a/visualization/tabular-to-microjson-tool/plugin.json b/visualization/tabular-to-microjson-tool/plugin.json index 15e23de78..8f681f797 100644 --- a/visualization/tabular-to-microjson-tool/plugin.json +++ b/visualization/tabular-to-microjson-tool/plugin.json @@ -1,7 +1,7 @@ { "name": "Tabular To Microjson", - "version": "0.1.2", - "containerId": "polusai/tabular-to-microjson-tool:0.1.2", + "version": "0.1.3-dev0", + "containerId": "polusai/tabular-to-microjson-tool:0.1.3-dev0", "title": "Tabular To Microjson", "description": "Generates JSON from tabular data.", "author": "Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)", diff --git a/visualization/tabular-to-microjson-tool/pyproject.toml b/visualization/tabular-to-microjson-tool/pyproject.toml index 10da9abd7..8e1954994 100644 --- a/visualization/tabular-to-microjson-tool/pyproject.toml +++ b/visualization/tabular-to-microjson-tool/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "polus-images-visualization-tabular-to-microjson" -version = "0.1.2" +version = "0.1.3-dev0" description = "" authors = ["Hamdah Shafqat abbasi "] readme = "README.md" @@ -15,6 +15,7 @@ pandas = "^2.0.3" microjson = "^0.1.9" vaex = "^4.17.0" pydantic = "^2.4.2" +pyarrow = ">=16.0,<17.0" [tool.poetry.group.dev.dependencies] diff --git a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__init__.py b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__init__.py index a6a40f6bf..a948488a1 100644 --- a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__init__.py +++ b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__init__.py @@ -1,2 +1,2 @@ """Tabular to microjson package.""" -__version__ = "0.1.2" +__version__ = "0.1.3-dev0"