From b4094a195dbbed1f5c5b4e8939c5a4379706038e Mon Sep 17 00:00:00 2001 From: Hamdah Shafqat Abbasi Date: Tue, 1 Oct 2024 12:23:08 -0400 Subject: [PATCH] updated dependencies & added CLT & ICT --- .../.bumpversion.cfg | 2 +- .../CHANGELOG.md | 6 +++ .../Dockerfile | 2 +- .../KaggleNucleiSegmentation.cwl | 32 +++++++++++ .../kaggle-nuclei-segmentation-tool/README.md | 2 +- .../kaggle-nuclei-segmentation-tool/VERSION | 2 +- .../kaggle-nuclei-segmentation-tool/ict.yaml | 54 +++++++++++++++++++ .../plugin.json | 6 +-- .../pyproject.toml | 7 +-- .../kaggle_nuclei_segmentation/__init__.py | 2 +- 10 files changed, 104 insertions(+), 11 deletions(-) create mode 100644 segmentation/kaggle-nuclei-segmentation-tool/KaggleNucleiSegmentation.cwl create mode 100644 segmentation/kaggle-nuclei-segmentation-tool/ict.yaml diff --git a/segmentation/kaggle-nuclei-segmentation-tool/.bumpversion.cfg b/segmentation/kaggle-nuclei-segmentation-tool/.bumpversion.cfg index 09848330b..6f5dbc619 100644 --- a/segmentation/kaggle-nuclei-segmentation-tool/.bumpversion.cfg +++ b/segmentation/kaggle-nuclei-segmentation-tool/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.1.5-dev1 +current_version = 0.1.5-dev2 commit = False tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/segmentation/kaggle-nuclei-segmentation-tool/CHANGELOG.md b/segmentation/kaggle-nuclei-segmentation-tool/CHANGELOG.md index a61528bcf..ea1144e90 100644 --- a/segmentation/kaggle-nuclei-segmentation-tool/CHANGELOG.md +++ b/segmentation/kaggle-nuclei-segmentation-tool/CHANGELOG.md @@ -3,3 +3,9 @@ ## 0.1.5-dev1 Initial release. + +## 0.1.5-dev2 + +Updated the bfio package. +Pinned the TensorFlow version. +Created ICT and CLT for this plugin. diff --git a/segmentation/kaggle-nuclei-segmentation-tool/Dockerfile b/segmentation/kaggle-nuclei-segmentation-tool/Dockerfile index e7dcb37a0..59f1134d1 100644 --- a/segmentation/kaggle-nuclei-segmentation-tool/Dockerfile +++ b/segmentation/kaggle-nuclei-segmentation-tool/Dockerfile @@ -1,4 +1,4 @@ -FROM polusai/bfio:2.1.9 +FROM polusai/bfio:2.4.4 # environment variables defined in polusai/bfio ENV EXEC_DIR="/opt/executables" diff --git a/segmentation/kaggle-nuclei-segmentation-tool/KaggleNucleiSegmentation.cwl b/segmentation/kaggle-nuclei-segmentation-tool/KaggleNucleiSegmentation.cwl new file mode 100644 index 000000000..37fc7869f --- /dev/null +++ b/segmentation/kaggle-nuclei-segmentation-tool/KaggleNucleiSegmentation.cwl @@ -0,0 +1,32 @@ +class: CommandLineTool +cwlVersion: v1.2 +inputs: + filePattern: + inputBinding: + prefix: --filePattern + type: string? + inpDir: + inputBinding: + prefix: --inpDir + type: Directory + outDir: + inputBinding: + prefix: --outDir + type: Directory + preview: + inputBinding: + prefix: --preview + type: boolean? +outputs: + outDir: + outputBinding: + glob: $(inputs.outDir.basename) + type: Directory +requirements: + DockerRequirement: + dockerPull: polusai/kaggle-nuclei-segmentation-tool:0.1.5-dev2 + InitialWorkDirRequirement: + listing: + - entry: $(inputs.outDir) + writable: true + InlineJavascriptRequirement: {} diff --git a/segmentation/kaggle-nuclei-segmentation-tool/README.md b/segmentation/kaggle-nuclei-segmentation-tool/README.md index 48d888c50..c21248852 100644 --- a/segmentation/kaggle-nuclei-segmentation-tool/README.md +++ b/segmentation/kaggle-nuclei-segmentation-tool/README.md @@ -1,4 +1,4 @@ -# Kaggle Nuclei Segmentation (v0.1.5-dev1) +# Kaggle Nuclei Segmentation (v0.1.5-dev2) Segments cell nuclei using U-Net in Tensorflow. diff --git a/segmentation/kaggle-nuclei-segmentation-tool/VERSION b/segmentation/kaggle-nuclei-segmentation-tool/VERSION index db5b6f8a0..ff4552239 100644 --- a/segmentation/kaggle-nuclei-segmentation-tool/VERSION +++ b/segmentation/kaggle-nuclei-segmentation-tool/VERSION @@ -1 +1 @@ -0.1.5-dev1 +0.1.5-dev2 diff --git a/segmentation/kaggle-nuclei-segmentation-tool/ict.yaml b/segmentation/kaggle-nuclei-segmentation-tool/ict.yaml new file mode 100644 index 000000000..6f451f0dd --- /dev/null +++ b/segmentation/kaggle-nuclei-segmentation-tool/ict.yaml @@ -0,0 +1,54 @@ +author: +- Gauhar Bains +- Konstantin Taletskiy +- Nick Schaub +- Hamdah Shafqat +contact: gauhar.bains@labshare.org +container: polusai/kaggle-nuclei-segmentation-tool:0.1.5-dev2 +description: Segments cell nuclei using U-Net in Tensorflow. Neural net architecture + and pretrained weights are taken from Data Science Bowl 2018 entry by Muhammad Asim +entrypoint: python3 -m polus.images.segmentation.kaggle_nuclei_segmentation +inputs: +- description: Input image collection to be processed by this plugin + format: + - collection + name: inpDir + required: true + type: path +- description: Filename pattern used to separate data + format: + - string + name: filePattern + required: false + type: string +- description: Generate an output preview. + format: + - boolean + name: preview + required: false + type: boolean +name: polusai/KaggleNucleiSegmentation +outputs: +- description: Output collection + format: + - collection + name: outDir + required: true + type: path +repository: https://github.com/PolusAI/image-tools +specVersion: 1.0.0 +title: Kaggle Nuclei Segmentation +ui: +- description: Input image collection to be processed by this plugin + key: inputs.inpDir + title: Input collection + type: path +- description: Filename pattern used to separate data + key: inputs.filePattern + title: Filename pattern + type: text +- description: Generate an output preview. + key: inputs.preview + title: preview + type: checkbox +version: 0.1.5-dev2 diff --git a/segmentation/kaggle-nuclei-segmentation-tool/plugin.json b/segmentation/kaggle-nuclei-segmentation-tool/plugin.json index c672c8eae..d15e014d8 100644 --- a/segmentation/kaggle-nuclei-segmentation-tool/plugin.json +++ b/segmentation/kaggle-nuclei-segmentation-tool/plugin.json @@ -1,14 +1,14 @@ { "name": "Kaggle Nuclei Segmentation", - "version": "0.1.5-dev1", + "version": "0.1.5-dev2", "title": "Kaggle Nuclei Segmentation", "description": "Segments cell nuclei using U-Net in Tensorflow. Neural net architecture and pretrained weights are taken from Data Science Bowl 2018 entry by Muhammad Asim", - "author": "Gauhar Bains, Konstantin Taletskiy,Nick Schaub , Hamdah Shafqat Abbasi (gauhar.bains@labshare.org, Konstantin.Taletskiy@labshare.org, nick.schaub@nih.gov, hamdahshafqat.abbasi@nih.gov)", + "author": "Gauhar Bains (gauhar.bains@labshare.org), Konstantin Taletskiy (Konstantin.Taletskiy@labshare.org), Nick Schaub (nick.schaub@nih.gov) , Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)", "institution": "National Center for Advancing Translational Sciences, National Institutes of Health", "repository": "https://github.com/PolusAI/image-tools", "website": "https://ncats.nih.gov/preclinical/core/informatics", "citation": "", - "containerId": "polusai/kaggle-nuclei-segmentation-tool:0.1.5-dev1", + "containerId": "polusai/kaggle-nuclei-segmentation-tool:0.1.5-dev2", "baseCommand": [ "python3", "-m", diff --git a/segmentation/kaggle-nuclei-segmentation-tool/pyproject.toml b/segmentation/kaggle-nuclei-segmentation-tool/pyproject.toml index ac5e07131..ce6b274a7 100644 --- a/segmentation/kaggle-nuclei-segmentation-tool/pyproject.toml +++ b/segmentation/kaggle-nuclei-segmentation-tool/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "polus-images-segmentation-kaggle-nuclei-segmentation" -version = "0.1.5-dev1" +version = "0.1.5-dev2" description = "Segments cell nuclei using U-Net in Tensorflow. Neural net architecture and pretrained weights are taken from Data Science Bowl 2018 entry by Muhammad Asim" authors = ["Gauhar Bains, Konstantin Taletskiy,Nick Schaub , Hamdah Shafqat Abbasi "] readme = "README.md" @@ -8,11 +8,12 @@ packages = [{include = "polus", from = "src"}] [tool.poetry.dependencies] python = ">=3.9,<3.12" -bfio = {version = "2.1.9", extras = ["all"]} +bfio = {version = "^2.4.4", extras = ["all"]} filepattern = ">=2.0.4,<3.0" typer = "^0.7.0" -tensorflow = "^2.15.0" +tensorflow = "2.15.0" opencv-python-headless = "^4.9.0.80" +numpy ="<2.0.0" [tool.poetry.group.dev.dependencies] bump2version = "^1.0.1" diff --git a/segmentation/kaggle-nuclei-segmentation-tool/src/polus/images/segmentation/kaggle_nuclei_segmentation/__init__.py b/segmentation/kaggle-nuclei-segmentation-tool/src/polus/images/segmentation/kaggle_nuclei_segmentation/__init__.py index a877b5090..14d042a64 100644 --- a/segmentation/kaggle-nuclei-segmentation-tool/src/polus/images/segmentation/kaggle_nuclei_segmentation/__init__.py +++ b/segmentation/kaggle-nuclei-segmentation-tool/src/polus/images/segmentation/kaggle_nuclei_segmentation/__init__.py @@ -1,3 +1,3 @@ """Kaggle Nuclei Segmentation.""" -__version__ = "0.1.5-dev" +__version__ = "0.1.5-dev2"