Feat/rt cetsa

features/rt-cetsa-intensity-extraction-tool/.bumpversion.cfg

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+[bumpversion]
+current_version = 0.2.0-dev0
+commit = True
+tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
+serialize = 
+	{major}.{minor}.{patch}-{release}{dev}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = _
+first_value = dev
+values = 
+	dev
+	_
+
+[bumpversion:part:dev]
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:plugin.json]
+
+[bumpversion:file:VERSION]
+
+[bumpversion:file:README.md]
+
+[bumpversion:file:src/polus/images/features/rt_cetsa_intensity_extraction/__init__.py]
+
+[bumpversion:file:ict.yml]
+
+[bumpversion:file:rt_cetsa_intensity_extraction.cwl]

features/rt-cetsa-intensity-extraction-tool/Dockerfile

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+FROM polusai/bfio:2.1.9
+
+# environment variables defined in polusai/bfio
+ENV EXEC_DIR="/opt/executables"
+ENV POLUS_IMG_EXT=".ome.tif"
+ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
+
+# Work directory defined in the base container
+WORKDIR ${EXEC_DIR}
+
+COPY pyproject.toml ${EXEC_DIR}
+COPY VERSION ${EXEC_DIR}
+COPY README.md ${EXEC_DIR}
+COPY src ${EXEC_DIR}/src
+
+RUN apt-get -y update
+RUN apt-get -y install git
+
+RUN pip3 install ${EXEC_DIR} --no-cache-dir
+
+ENTRYPOINT ["python3", "-m", "polus.images.features.rt_cetsa_intensity_extraction"]
+CMD ["--help"]

features/rt-cetsa-intensity-extraction-tool/README.md

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+# RT_CETSA Intensity Extraction Tool (v0.2.0-dev0)
+
+This tool runs well intensities extraction for the RT-CETSA pipeline.
+
+## Building
+
+To build the Docker image for the conversion plugin, run
+`./build-docker.sh`.
+
+## Install WIPP Plugin
+
+If WIPP is running, navigate to the plugins page and add a new plugin. Paste the contents of `plugin.json` into the pop-up window and submit.
+
+## Options
+
+This plugin takes eight input argument and one output argument:
+
+| Name            | Description                                        | I/O    | Type        |
+|-----------------|----------------------------------------------------|--------|-------------|
+| `--inpDir`      | Input data collection to be processed by this tool | Input  | genericData |
+| `--filePattern` | Pattern to parse input files                       | Input  | string      |
+| `--outDir`      | Output file                                        | Output | genericData |
+| `--preview`     | Generate JSON file with outputs                    | Output | JSON        | Optional
+| `--params`      | Plate params to use                                | Output | JSON        | Optional
+| `--temp`        | Temperature range. Default to [37,90]              | Output | JSON        | Optional

features/rt-cetsa-intensity-extraction-tool/VERSION

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+0.2.0-dev0

features/rt-cetsa-intensity-extraction-tool/build-docker.sh

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+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/rt-cetsa-intensity-extraction-tool:"${version}"

features/rt-cetsa-intensity-extraction-tool/ict.yml

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+author:
+- Nick Schaub
+- Antoine Gerardin
+- Najib Ishaq
+contact: [email protected]
+container: polusai/rt-cetsa-intensity-extraction-tool:0.2.0-dev0
+description: Extract well intensities from RT-CETSA plate images and masks.
+entrypoint: python3 -m polus.images.features.rt_cetsa_intensity_extraction
+inputs:
+- description: Input data collection to be processed by this tool
+  format:
+  - inpDir
+  name: inpDir
+  required: true
+  type: path
+- description: filename of the plate params
+  format:
+  - params
+  name: params
+  required: false
+  type: string
+- description: temp interval on which to collect intensities
+  format:
+  - temp
+  name: temp
+  required: false
+  type: array[int]
+- description: Filepattern to parse input files
+  format:
+  - filePattern
+  name: filePattern
+  required: false
+  type: string
+- description: Generate an output preview.
+  format:
+  - preview
+  name: preview
+  required: false
+  type: boolean
+name: polusai/RTCETSAIntensityExtraction
+outputs:
+- description: Output data
+  format:
+  - outDir
+  name: outDir
+  required: true
+  type: path
+repository: https://github.com/PolusAI/image-tools
+specVersion: 1.0.0
+title: RT-CETSA Intensity Extraction
+ui:
+- description: Input data collection
+  key: inputs.inpDir
+  title: Input data collection
+  type: path
+- description: Filepattern to parse input files
+  key: inputs.pattern
+  title: pattern
+  type: text
+- description: Plate params to use
+  key: inputs.params
+  title: Plate Params
+  type: text
+- description: Temperature interval
+  key: inputs.temp
+  title: Temperature interval
+  type: text
+- description: Generate an output preview.
+  key: inputs.preview
+  title: Preview example output of this plugin
+  type: checkbox
+version: 0.2.0-dev0

features/rt-cetsa-intensity-extraction-tool/plugin.json

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+{
+  "name": "RT-CETSA Intensity Extraction",
+  "version": "0.2.0-dev0",
+  "title": "RT-CETSA Intensity Extraction",
+  "description": "Extract well intensities from RT-CETSA images and masks.",
+  "author": "Nicholas Schaub ([email protected]), Antoine Gerardin ([email protected]), Najib Ishaq ([email protected])",
+  "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/rt-cetsa-intensity-extraction-tool:0.2.0-dev0",
+  "baseCommand": [
+    "python3",
+    "-m",
+    "polus.images.features.rt_cetsa_intensity_extraction"
+  ],
+  "inputs": [
+    {
+      "name": "inpDir",
+      "type": "genericData",
+      "description": "RT_Cetsa image collection to be processed by this tool.",
+      "required": true
+    },
+    {
+      "name": "filePattern",
+      "type": "string",
+      "description": "filePattern to parse input files.",
+      "default": ".+",
+      "required": false
+    },
+    {
+      "name": "preview",
+      "type": "boolean",
+      "description": "Generate preview of outputs.",
+      "required": false
+    },
+    {
+      "name": "params",
+      "type": "boolean",
+      "description": "Plate params to use.",
+      "required": false
+    },
+    {
+      "name": "temp",
+      "type": "boolean",
+      "description": "Temperature range. Default to [37,90].",
+      "required": false
+    }
+  ],
+  "outputs": [
+    {
+      "name": "outDir",
+      "type": "genericData",
+      "description": "Output data collection."
+    }
+  ],
+  "ui": [
+    {
+      "key": "inputs.inpDir",
+      "title": "Input collection",
+      "description": "Input data collection to be processed by this plugin."
+    },
+    {
+      "key": "inputs.mask",
+      "title": "Mask",
+      "description": "Mask to process plate image."
+    },
+    {
+      "key": "inputs.filePattern",
+      "title": "FilePattern",
+      "description": "File Pattern to parse input files.",
+      "default": ".+"
+    },
+    {
+      "name": "inputs.params",
+      "title": "Params",
+      "description": "Plate params to use."
+    },
+    {
+      "name": "inputs.temp",
+      "title": "Temp",
+      "description": "Temperature range. Default to [37,90]."
+    }
+  ]
+}

features/rt-cetsa-intensity-extraction-tool/pyproject.toml

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+[tool.poetry]
+name = "polus_images_features_rt_cetsa_intensity_extraction"
+version = "0.2.0-dev0"
+description = "Extract well intensities from RT-CETSA plate images."
+authors = [
+    "Nick Schaub <[email protected]>",
+    "Antoine Gerardin <[email protected]>",
+    "Najib Ishaq <[email protected]>",
+]
+readme = "README.md"
+packages = [{include = "polus", from = "src"}]
+
+[tool.poetry.dependencies]
+python = ">=3.9,<3.12"
+typer = "^0.7.0"
+filepattern = "^2.0.5"
+pandas = "^2.2.2"
+numpy = "^1.26.4"
+bfio = "^2.3.6"
+scikit-image = "^0.22.0"
+imagecodecs = "^2024.1.1"
+polus-images-segmentation-rt-cetsa-plate-extraction = {git = "https://github.com/agerardin/image-tools.git", branch = "feat/rt_cetsa", subdirectory = "segmentation/rt-cetsa-plate-extraction-tool"}
+
+
+[tool.poetry.group.dev.dependencies]
+bump2version = "^1.0.1"
+pre-commit = "^3.1.0"
+pytest = "^7.2.1"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.ruff]
+extend = "../../ruff.toml"
+extend-ignore = [
+    "RET505",  # Unnecessary `else` after `return` statement
+    "E501",  # Line too long
+    "ANN001",  # Missing type annotation
+    "D102",  # Missing docstring in public method
+    "ANN201",  # Missing return type annotation
+    "N806",  # Variable in function should be lowercase
+    "D205",  # 1 blank line required between summary line and description
+    "N803",  # Argument name should be lowercase
+    "PLR0913",  # Too many arguments
+    "D415",  # First line should end with a period, question mark, or exclamation point
+    "PLR2004",  # Magic value used in comparison
+    "B006",  # Do not use mutable default arguments
+    "D107",  # Missing docstring
+    "D101",  # Missing docstring
+    "E731",  # Do not assign a lambda expression, use a def
+    "E402",  # Module level import not at top of file
+    "PTH123",  # `open()` should be replaced with `Path.open()`
+    "PTH118",  # `os.path.join()` should be replaced with `/` operator
+    "PTH100",  # `os.path.abspath()` should be replaced with `Path.resolve()`
+    "PLR0915",  # Too many statements
+    "PLR0912",  # Too many branches
+    "C901",  # Function is too complex
+    "T201",  # `print` used
+    "E722",  # Do not use bare 'except'
+    "B904",  # Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
+    "ANN202",  # Missing return type annotation for private function
+    "ARG002",  # Unused method argument
+    "N802",  # Function name should be lowercase
+    "PTH103",  # `os.makedirs()` should be replaced with `Path.mkdir(parents=True)`
+    "ANN003",  # Missing type annotation for `**kwargs`
+    "B007",  # Loop control variable not used within the loop body
+    "ANN204",  # Missing return type annotation for magic method
+    "D417",  # Missing argument descriptions in the docstring
+    "ANN205",  # Missing return type annotation for static method
+    "PLR5501",  # Use `elif` instead of `else` following `if` condition to avoid unnecessary indentation
+    "EM102",  # Exception must not use an f-string literal
+    "D414",  # Section has no content
+    "RUF012",  # Mutable class attributes should be annotated with `typing.ClassVar`
+    "A001",  # Variable `input` is shadowing a Python builtin
+    "A002",  # Argument `input` is shadowing a Python builtin
+    "E741",  # Ambiguous variable name: `l`
+    "PTH120",  # `os.path.dirname()` should be replaced by `Path.parent`
+    "N816",  # Variable `cfFilename` in global scope should not be mixedCase
+    "PTH109",  # `os.getcwd()` should be replaced by `Path.cwd()`
+    "ARG001",  # Unused function argument
+    "S101",  # Use of assert detected
+    "D103",  # Missing docstring in public function
+    "D100",  # Missing docstring in public module
+]

features/rt-cetsa-intensity-extraction-tool/rt_cetsa_intensity_extraction.cwl

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+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  inpDir:
+    inputBinding:
+      prefix: --inpDir
+    type: Directory
+  mask:
+    inputBinding:
+      prefix: --mask
+    type: string?
+  filePattern:
+    inputBinding:
+      prefix: --filePattern
+    type: string?
+  outDir:
+    inputBinding:
+      prefix: --outDir
+    type: Directory
+  params:
+    inputBinding:
+      prefix: --params
+    type: string?
+  temp:
+    type: int[]?
+    inputBinding:
+      prefix: -temp=
+      itemSeparator: " "
+      separate: false
+  preview:
+    inputBinding:
+      prefix: --preview
+    type: boolean?
+outputs:
+  outDir:
+    outputBinding:
+      glob: $(inputs.outDir.basename)
+    type: Directory
+requirements:
+  DockerRequirement:
+    dockerPull: polusai/rt-cetsa-intensity-extraction-tool:0.2.0-dev0
+  InitialWorkDirRequirement:
+    listing:
+    - entry: $(inputs.outDir)
+      writable: true
+  InlineJavascriptRequirement: {}