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Feat/rt cetsa #541
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Feat/rt cetsa #541
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feat: containerized plate extraction and run with cwl.
…original intensities.
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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 line needs another column
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
Add two new tools :