fix: run stardist cli with mind docker image #290
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Codecov Report
@@ Coverage Diff @@
## dev #290 +/- ##
==========================================
- Coverage 76.18% 75.99% -0.19%
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Files 52 53 +1
Lines 3552 3566 +14
==========================================
+ Hits 2706 2710 +4
- Misses 846 856 +10
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aauker
approved these changes
Mar 25, 2022
| run_stardist_cell_detection 10001.svs | ||
| -cs 8 -it -it BRIGHTFIELD_H_DAB -nc 8 | ||
| -o 10001/cells | ||
| run_stardist_cell_detection /absolute/path/to/10001.svs |
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A much nicer documentation!
aauker
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Apr 14, 2022
* chore: merge updated release version to dev 0.1.1 (#264) Automatically generated by python-semantic-release Co-authored-by: Andy Aukerman <ataukerman@gmail.com> Co-authored-by: github-actions <action@github.com> * feat: New CLIs from lung project (#261) All new CLI tools for radiology/pathology work from the lung project. Co-authored-by: Aukerman <aukermaa@pllimsksparky3.mskcc.org> * fix: Save size as list, not a tuple (safe for yaml) Co-authored-by: Aukerman <aukermaa@pllimsksparky3.mskcc.org> * feat: radiology - generate scan table cli (#265) * 1074 final tutorial qc (#267) chore: streamline docker-compose build and execution * chore: 1074 final tutorial qc (#267) chore: streamline docker-compose build and execution * perf: Further refinements to pathology CLI calls (#269) * feat: Stardist and Spatial Statistics (#270) * feat: pathology - adding model trainer, samplers for tile classifiers (#268) * 0.1.1 Automatically generated by python-semantic-release * feat: pathology - adding model trainer, samplers for tile classifiers * Update setup.cfg sklearn dep * fix: added ability to pass modules via yaml, resolved issue with parameterized types * fix: removed custom StratifiedGroupKfold, small changes to get_group_stratified_sampler * feat: adding cli for model training with ray * fix: adding cli, dependencies for model training cli * fix: adding updated dependencies to docker * fix: fixing sklearn import * fix: fixing mistake in Dataset * Fix: changes to type system/param parsing for model training Co-authored-by: Andy Aukerman <ataukerman@gmail.com> Co-authored-by: github-actions <action@github.com> * test: pathology - extract feature vector example (#273) * docs: pathology - extract feature vector example * update docstring * perf: save tile data in h5 (#272) * feat: New slide ETL (#271) * fix: Imports for slide_etl (#274) * fix: Imports for slide_etl * Some fixes to generate tile to match conventions * Fixing coordinates, updating test * refactor * row.tile_size * schema check * Updating tests * -o * ds test * ds test * new otsu tiles * 10x * Remove address assert * Better warning with scale factor business * spacing cleanup * close hf file * minor fix * add subset test * typo fix Co-authored-by: Aukerman <aukermaa@pllimsksparky3.mskcc.org> Co-authored-by: doori <doori.rose@gmail.com> * fix: Inference Model (#275) Refactoring and improvement of inference CLI * feat: adding CLI for generating tile label masks (#276) * fix: removing explicit support for jsons, treat them like dict objects instead * fix: fixing dict param in test cases * fix: changing radiomic params from json to dict * feat: adding CLI for generating tile mask from labels * feat: Update tile schema, add save_tiles (#280) * refactor: dsa visualization and upload tool (#281) * docs: contribution guide (#278) * Update Makefile * feat: adding CLI for shape feature extraction (#282) * test: adding test data for mask generation * feat: adding cli for hif extraction * test: adding test for feature extractor * doc: update docstrings * doc: update docstring with more details * fix: Updated DSA annotation (#279) More complete ETL * fix: Fixes on slide ingestion (#283) * Fixes on slide ingestion * Update adapters.py Co-authored-by: Aukerman <aukermaa@pllimsksparky3.mskcc.org> * feat: precommit w/ black and flake8 (#277) * chore: adding pre-commit w. black/flake8 * sty: testing precommit * chore: adding pre-commit to requirements * docs: adding black badge * fix: fixing flake8 config * sty: remove comments * fix: nifti scan orientation (#284) * feat: pathology - dsa visualize bmps (#285) * fix: Fixes from end-to-end tests (#286) * Fixes from end-to-end tests + goodbye to preprocess.py Co-authored-by: Aukerman <aukermaa@pllimsksparky3.mskcc.org> * test: pathology - unit tests (#287) * test: circleci config (#288) * chore: reorganize and clean up pathology (#289) * fix: run stardist cli with mind docker image (#290) * Init post CLI tool * feat: PET Pre-processing (SUVs) (#292) * PET Processing * Fix indent level * Only propagate keys from non-aliases * Reference origin Co-authored-by: Aukerman <aukermaa@pllimsksparky3.mskcc.org> * feat: Add dataset addition to eligible CLI tools (#293) * Make other tools dataset enabled * add dataset post as part of CLI runner * Add dataset ID options * Revert uncomment * Move to parquet * More parquet migration * Further migrate to parquet * Parquet migration tests pass * Forgot about run detection * Combine ifs * Better loggin * Set language * Better detect url scheme * Docs post_to_dataset * documentation * Last few changes * Fix tests * PNG parquet fix Co-authored-by: Aukerman <aukermaa@pllimsksparky3.mskcc.org> * docs: inference,viz,dsa notebook updates (#294) * docs: update inference tutorial * docs: update dsa tools, add examples, remove configs * docs: dsa annotation nb Co-authored-by: armaan <kohli@cooper.edu> Co-authored-by: doori <doori.rose@gmail.com> Co-authored-by: github-actions <action@github.com> Co-authored-by: Aukerman <aukermaa@pllimsksparky3.mskcc.org> Co-authored-by: arfathpasha <arfathpasha@gmail.com> Co-authored-by: armaan <kohli@cooper.edu>
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added notes in dockerhub: https://hub.docker.com/r/mskmind/qupath-stardist
some bug with nbconvert from the new release. jupyter/nbconvert#1736