Feat/rt cetsa #541
Feat/rt cetsa #541
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feat: containerized plate extraction and run with cwl.
…original intensities.
agerardin
requested review from
NHotaling,
Nicholas-Schaub and
hsidky
as code owners
nishaq503
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nishaq503
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The types of certain parameters are different between the README.md, ict.yml, plugin.json and *.cwl files. Other than that, this branhc is ready to merge.
| | `--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 |
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These three lines need an additional column in the table.
| { | ||
| "name": "params", | ||
| "type": "boolean", | ||
| "description": "Plate params to use.", | ||
| "required": false | ||
| }, | ||
| { | ||
| "name": "temp", | ||
| "type": "boolean", | ||
| "description": "Temperature range. Default to [37,90].", | ||
| "required": false | ||
| } |
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The types for these are listed as JSON in the README, string in the ICT and boolean here. What is the actual type?
| 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"} |
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This git link will need to be updated to either use the main repo from polusai and the master branch, or it should be changed to a local path dependency
| | `--inpDir` | Input data collection to be processed by this tool | Input | genericData | | ||
| | `--filePattern` | FilePattern to parse input files | Input | string | | ||
| | `--outDir` | Output dir | Output | genericData | | ||
| | `--preview` | Generate JSON file with outputs | Output | JSON | Optional |
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| This method is degree of magnitude slower than extract_wells_intensity | ||
| and is just provided for convenience. Consider using extract_wells_intensity instead. |
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I am surprised that numpy indexing with a mask is so much slower. I'll have to keep that in mind if we can assume that masks always have a specific shape
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superseded by #575 |
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Add two new tools :