Eliminate toarray() for spectral/spatial metrics#1719
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* Webapp docs initial setup * Fixed docs deploy tasks * gitignore for vitepress * Add Vitepress configuration * Add docs markdown * Add screenshot images * [docs] commented unused references * Few text modifications * Add "what's new" * [Header] Added link to docs --------- Co-authored-by: Bishoy Wadie <bwadie298@gmail.com>
…1706) Bumps [picomatch](https://github.com/micromatch/picomatch) from 2.3.1 to 2.3.2. - [Release notes](https://github.com/micromatch/picomatch/releases) - [Changelog](https://github.com/micromatch/picomatch/blob/master/CHANGELOG.md) - [Commits](micromatch/picomatch@2.3.1...2.3.2) --- updated-dependencies: - dependency-name: picomatch dependency-version: 2.3.2 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [requests](https://github.com/psf/requests) from 2.32.4 to 2.33.0. - [Release notes](https://github.com/psf/requests/releases) - [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md) - [Commits](psf/requests@v2.32.4...v2.33.0) --- updated-dependencies: - dependency-name: requests dependency-version: 2.33.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…pp (#1709) Bumps [lodash-es](https://github.com/lodash/lodash) from 4.17.23 to 4.18.1. - [Release notes](https://github.com/lodash/lodash/releases) - [Commits](lodash/lodash@4.17.23...4.18.1) --- updated-dependencies: - dependency-name: lodash-es dependency-version: 4.18.1 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…#1710) Bumps [picomatch](https://github.com/micromatch/picomatch) from 2.2.2 to 2.3.2. - [Release notes](https://github.com/micromatch/picomatch/releases) - [Changelog](https://github.com/micromatch/picomatch/blob/master/CHANGELOG.md) - [Commits](micromatch/picomatch@2.2.2...2.3.2) --- updated-dependencies: - dependency-name: picomatch dependency-version: 2.3.2 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…1712) Bumps [lodash](https://github.com/lodash/lodash) from 4.17.23 to 4.18.1. - [Release notes](https://github.com/lodash/lodash/releases) - [Commits](lodash/lodash@4.17.23...4.18.1) --- updated-dependencies: - dependency-name: lodash dependency-version: 4.18.1 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…#1713) Bumps [lodash](https://github.com/lodash/lodash) from 4.17.23 to 4.18.1. - [Release notes](https://github.com/lodash/lodash/releases) - [Commits](lodash/lodash@4.17.23...4.18.1) --- updated-dependencies: - dependency-name: lodash dependency-version: 4.18.1 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [follow-redirects](https://github.com/follow-redirects/follow-redirects) from 1.15.3 to 1.16.0. - [Release notes](https://github.com/follow-redirects/follow-redirects/releases) - [Commits](follow-redirects/follow-redirects@v1.15.3...v1.16.0) --- updated-dependencies: - dependency-name: follow-redirects dependency-version: 1.16.0 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…1717) Bumps [dompurify](https://github.com/cure53/DOMPurify) from 3.3.2 to 3.4.0. - [Release notes](https://github.com/cure53/DOMPurify/releases) - [Commits](cure53/DOMPurify@3.3.2...3.4.0) --- updated-dependencies: - dependency-name: dompurify dependency-version: 3.4.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [brace-expansion](https://github.com/juliangruber/brace-expansion) from 1.1.12 to 1.1.14. - [Release notes](https://github.com/juliangruber/brace-expansion/releases) - [Commits](juliangruber/brace-expansion@v1.1.12...v1.1.14) --- updated-dependencies: - dependency-name: brace-expansion dependency-version: 1.1.14 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…1711) Bumps [vite](https://github.com/vitejs/vite/tree/HEAD/packages/vite) from 5.4.21 to 6.4.2. - [Release notes](https://github.com/vitejs/vite/releases) - [Changelog](https://github.com/vitejs/vite/blob/v6.4.2/packages/vite/CHANGELOG.md) - [Commits](https://github.com/vitejs/vite/commits/v6.4.2/packages/vite) --- updated-dependencies: - dependency-name: vite dependency-version: 6.4.2 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Add image_segmentation postprocessing python package as a new service * Add docker, requirements and app for image segmentation service * Add segmentation_wrapper.py and sm/rest/segmentation.py * Add segmentation to update_daemon, dataset manager, and daemon actions * Mount segmentation app * Graphql for segmentation * Add image segmentation docker config to docker compose and modify .env * Add segmentation_data_loader from inside engine * Modify S3 I/O and update diagnostics * Update graphql schema and model.ts * Update docker * Update config and add config to postprocessing upstream * Add migration and update db_schema * Fix isoimage bug * Remove anndata and metaspace_converter dependancy * Implement callback and update segmentation app * Fix image_segmentation docker * Update segmentation config.json * fixed tests * fixed pytest * Add assignment confidence histogram * [Segmentation] added segmentation dialog and fixed back to run with docker * [SegmentationPage] started segmentation resul page * [SegmentationPage] added segment markers component * [SegmentationPage] started segnebtatuib diagnostics component * [SegmentationPage] added optical image and opacity controls * [SegmentationPage] updated diagnostics charts * [Segmentation] starter deploy setup * [Segmentation] optimized tables * [Segmentation] fixed callback default value * [Segmentation] Compatibility with python 3.8 * simplified segmentation supervisor * [Segmentation] adjusts backend to se database id and segmentation manager * [Added segment name] * updated db schema * [Segmentation] Segmentation table and better logger * [Postprocessing] added detailed logs * [Segmentation] added feature as feature flagged * [Segmentation] added error on job mail * [segmentation] enabled admin access * Use AUC instead of FE for segmentation profiles * fixed actions test * [Segmentation] restart pending jobs on seg service restart * [Segmentation] waiting for api to request pending processing * fixed linting issues * [Segmentation] fixed Cluster name * [Graphql] Added segmentation tests --------- Co-authored-by: Bishoy Wadie <bwadie298@gmail.com>
…020/metaspace into Fix/eliminate-toarray
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Problem
Follow-up to #1718 . The annotation pipeline sometimes crashes with OOM on datasets where spectra form isolated blobs inside a large bounding box. After #1718 fixed
chaos_metric, the remaining crash point isformula_validator.pywhich still materialises the full h×w dense array for every peak of every formula when building iso_imgs_flat.Change
imzml_readergets apixel_to_flat_idxlookup table built once at init — maps any pixel coordinate directly to its position in themasked-flat metrics array.
formula_validator.pyuses it to scatter sparsecoovalues directly into a 1D array of sizen_spectra, removing thetoarray()call and the intermediate denseiso_imgslist entirely.pipeline.pylogs a warning when pixel density is below 5% so blob datasets are visible in logs.