TissueImageAnalytics/tiatoolbox issues and pull requests

#656 - [skip ci] :rotating_light: Add linter checks to `01-wsi-reading.ipynb`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 2 comments

#655 - :arrow_up: Upgrade `ruff` to Version `0.0.280`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment

#654 - :rotating_light: Add "NPY" `NumPy-specific rules` Checks

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment

#653 - 🚨 Add `Perflint`, `flake8-simplify`, `flake8-raise`, `flake8-implicit-str-concat`, `flake8-fixme`, `pandas-vet`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: code readability

#652 - 🚨 Add `bugbear`. `pep8-naming`, `flake8-commas`, `flake8-print`, `mccabe`, `pycodestyle-Error` and `pyupgrade` Checks

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: code readability

#651 - 🐛 Parse JP2 Boxes By ID Not Position

Pull Request - State: closed - Opened by John-P over 1 year ago - 9 comments
Labels: bug, enhancement

#650 - :rotating_light: Replace `flake8` with `ruff` with Base Settings

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: code readability

#649 - 🚨 Fix Linter Error in `tools`, `utils` and `pre-commit`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: code readability

#648 - :rotating_light: Fix Linter Error in `cli`, `annotation` and `visualization`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: code readability

#647 - :rotating_light: Fix Linter Errors

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: code readability

#646 - :adhesive_bandage: Add `imwrite` Check

Pull Request - State: closed - Opened by blaginin over 1 year ago - 1 comment
Labels: enhancement

#645 - Add check for Phase correlation transform

Pull Request - State: closed - Opened by ruqayya over 1 year ago - 3 comments

#644 - 💚 Add CI Cache

Pull Request - State: closed - Opened by blaginin over 1 year ago - 3 comments
Labels: dev tools

#643 - :recycle: Small tests improvements

Pull Request - State: closed - Opened by blaginin over 1 year ago - 1 comment
Labels: dev tools

#642 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#641 - ✅ Reuse models and datasets in tests

Pull Request - State: closed - Opened by blaginin over 1 year ago - 2 comments
Labels: dev tools

#640 - :white_check_mark: Upgrade remote sample fixtures

Pull Request - State: closed - Opened by blaginin over 1 year ago - 4 comments
Labels: dev tools

#639 - ✨ Extend Annotation to Support Init from WKB

Pull Request - State: closed - Opened by John-P over 1 year ago - 4 comments
Labels: enhancement

#638 - :technologist: Use `poetry` for Version Updates

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: dev tools

#637 - :recycle: Move Dataset Classes to `dataset_abc.py`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: code readability

#636 - :recycle: Move `WSIStreamDataset` to `dataset_abc.py`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago

#635 - :art: New `EngineABC` Design for `Patches`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 4 comments
Labels: enhancement

#634 - Shifted patches when merging patch predictions!

Issue - State: open - Opened by mrahimpour over 1 year ago - 2 comments
Labels: bug

#633 - Issue generating WSI thumbnails from CLI

Issue - State: closed - Opened by Abdol over 1 year ago - 3 comments
Labels: bug

#632 - ✨ Feature: `wkb` Decoding via `numpy`

Pull Request - State: closed - Opened by measty over 1 year ago - 4 comments
Labels: enhancement

#631 - :white_check_mark: Improve Tests for `save_tiles` to Reduce Runtime

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: dev tools

#630 - :test_tube: Improve `micronet` Tests

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: dev tools

#629 - :technologist: Reduce Test runtime for JP2

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 3 comments
Labels: dev tools

#628 - Issue in reading WSI with missing mpp information.

Issue - State: closed - Opened by engrodawood over 1 year ago - 2 comments

#627 - :white_check_mark: Reduce run time for Mapde test

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment

#626 - :bug: Fix `dictionary changed size` Error

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 5 comments
Labels: documentation

#625 - ✨ Use `ruff` for Linting

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 10 comments
Labels: dev tools

#624 - :memo: Fix docstrings

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: documentation

#623 - :art: Add typehints for `env_detection.py` and `exceptions.py`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: code readability

#622 - :wastebasket: Remove `shapely.speedups`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: invalid

#621 - :recycle: Replace deprecated input `pretrained` with `weights`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: refactoring

#620 - 🎨 Add Typehints for `misc.py`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: enhancement

#619 - ✨ Add `tiatoolbox.typing` for TypeHints

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: enhancement

#618 - :recycle: Refactor base code from `IOSegmentorConfig` to `ModelIOConfigABC`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 2 comments
Labels: enhancement

#617 - :construction_worker: Add notebooks tests

Pull Request - State: closed - Opened by blaginin over 1 year ago - 4 comments
Labels: dev tools

#616 - ✨ File Magic Detection & NGFF SQLite3 Support

Pull Request - State: closed - Opened by John-P over 1 year ago - 1 comment
Labels: enhancement

#615 - Reading a very large region using WSIReader.read_rect results in crash

Issue - State: closed - Opened by gafaua over 1 year ago - 5 comments

#614 - :recycle: Use `all` for High Level Imports

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment

#613 - ✏️ Update `README.md`

Pull Request - State: closed - Opened by John-P over 1 year ago - 1 comment
Labels: documentation

#612 - 🐛 Fix Errors with `glymur` Update to `0.12.6`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: dependencies

#611 - 🐛 Tests fail with `glymur>=0.12.6`

Issue - State: closed - Opened by shaneahmed over 1 year ago
Labels: bug, dependencies

#610 - Issue in patch extraction from images with more than 3 channels

Issue - State: closed - Opened by Arwa-AlRubaian over 1 year ago - 3 comments
Labels: enhancement

#609 - :monocle_face: Rename `VirtualWSIReader` Modes

Issue - State: closed - Opened by blaginin over 1 year ago - 1 comment
Labels: code readability

#608 - :bug: Fix Errors in the `slidegraph` Example Notebook

Pull Request - State: closed - Opened by measty over 1 year ago - 3 comments
Labels: bug, documentation

#607 - :recycle: High Level `engines` Import

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 2 comments
Labels: refactoring

#606 - :recycle: High Level `misc` functions Import

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 2 comments
Labels: refactoring

#605 - 🐛 Segmentation engines produce dictionary changed size during iteration error

Issue - State: closed - Opened by shaneahmed over 1 year ago - 3 comments
Labels: bug

#604 - [skip ci] :adhesive_bandage: Update notebooks for Google Colab runs

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment

#603 - 🐌 Slow tests

Issue - State: open - Opened by blaginin over 1 year ago - 4 comments
Labels: enhancement, dev tools

#602 - Issues with reproducing the result in examples/inference-pipelines/slide-graph.ipynb

Issue - State: closed - Opened by mohsuliman over 1 year ago - 21 comments

#601 - [skip ci] :bug: Fix `pixman` Incompatibility Error on Google Colab

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment

#600 - 🔖 Release 1.4.0

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 2 comments
Labels: release

#599 - 🔖 Release 1.4.0

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 2 comments
Labels: release

#598 - :recycle: Refactor `Resolution` and `Units`

Pull Request - State: closed - Opened by blaginin over 1 year ago - 4 comments
Labels: refactoring

#597 - 🐛 Fix `MultiTaskSegmentor` Example

Pull Request - State: closed - Opened by blaginin over 1 year ago - 1 comment
Labels: documentation

#596 - :pencil2: Fix Typo `stain_norm_target`

Pull Request - State: closed - Opened by blaginin over 1 year ago - 2 comments
Labels: documentation

#595 - Issue in ImageFont.py

Issue - State: closed - Opened by MyYo over 1 year ago - 1 comment

#594 - 🐛 Fix `deepsource` Errors

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: bug, dev tools

#593 - [skip ci] :bug: Fix Docstring and License Badge

Pull Request - State: closed - Opened by shaneahmed over 1 year ago
Labels: documentation

#592 - :page_facing_up: Update Documentation for License on Model Weights

Pull Request - State: closed - Opened by simongraham over 1 year ago - 1 comment
Labels: documentation

#591 - ✅ Add Tests For Lazy Import

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: dev tools

#590 - 🚨 Use `logger` Instead Of `warnings` for `pyramid.py` and `storage.py`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: enhancement

#589 - 🚨 Use `logger` Instead Of `warnings` for `patchextraction.py`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: enhancement

#588 - 🚨 Use `logger` Instead Of `warnings` for `models` Package

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: enhancement

#587 - 🚨 Use `logger` Instead Of `warnings` for `wsi_registration.py`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: enhancement

#586 - 🚨 Use `logger` Instead Of `warnings` for `utils` Package

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: enhancement

#585 - :pushpin: Update `black` Version to `23.3.0`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago
Labels: dependencies

#584 - 🚨 Use `logger` Instead Of `warnings` for `wsireader.py`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: enhancement

#583 - 📌 Pin `pandas` Version to `>=2.0.0`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: dependencies

#582 - 📌 Update `pandas` Dependency to `2.0.0`

Issue - State: closed - Opened by shaneahmed over 1 year ago
Labels: dependencies

#581 - ➕ Add `joblib` As Dependency

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: dependencies

#580 - 🐛 Fix for Recent `wsidicom` Update

Pull Request - State: closed - Opened by measty over 1 year ago - 3 comments
Labels: bug

#579 - 🔧 Use `pyproject.toml` for `pytest` Configuration

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: dev tools

#578 - ⚡ Improve `Engine` Performance and Implementation

Pull Request - State: open - Opened by shaneahmed over 1 year ago - 1 comment
Labels: enhancement

#577 - ✨ Return True for `is_ngff` With Warning Above Max NGFF Version

Pull Request - State: closed - Opened by John-P over 1 year ago - 2 comments
Labels: enhancement

#576 - 🩹 Support for `np.ndarray` and WSIReader in `PatchPredictor`

Pull Request - State: closed - Opened by blaginin over 1 year ago - 4 comments
Labels: bug, documentation

#575 - :wrench: Use `pyproject.toml` for `bdist_wheel` Configuration

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: dev tools

#574 - :art: Move Models to Top-Level Import

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment

#573 - 🔧 Use `pyproject.toml` for `pytest` Configuration

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: dev tools

#572 - :wrench: Use `pyproject.toml` for `isort` Configuration

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: dev tools

#571 - ⚡ Faster Filtering in Patch Dataset

Pull Request - State: closed - Opened by measty over 1 year ago - 4 comments
Labels: enhancement

#570 - Hovernet gives background false positive

Issue - State: closed - Opened by OmarAshkar over 1 year ago - 1 comment

#569 - 🐛 BUG: Fix Docker Build for Ubuntu OS(s)

Pull Request - State: closed - Opened by mostafajahanifar over 1 year ago - 1 comment
Labels: bug

#568 - 🩹 BUG: Fix Parsing Missing Omero Version NGFF Metadata

Pull Request - State: closed - Opened by John-P over 1 year ago - 1 comment
Labels: bug

#567 - :memo: DOC: Improve Installation Instructions

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: documentation

#566 - Models Inconsistency

Issue - State: open - Opened by blaginin over 1 year ago - 4 comments
Labels: documentation, enhancement, code readability, refactoring

#565 - :memo: DOC: Improve Annotation Store Documentation + Fix Bug

Pull Request - State: closed - Opened by John-P over 1 year ago - 1 comment
Labels: documentation

#564 - :bug: BUG: Fix Level When Using DICOM `read_region`

Pull Request - State: closed - Opened by measty over 1 year ago - 5 comments
Labels: bug

#563 - :recycle: Move `requirements*.txt` to `requirements` Folder

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: refactoring

#562 - 🚨 DEV: Use logger Instead Of print (`slide_info.py`)

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: refactoring

#561 - :heavy_minus_sign: DEP: Remove `tox` Dependency

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: dev tools

#560 - :art: ENH: Move `WSIReader` and `WSIMeta` import to top-level

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 1 comment
Labels: enhancement

#559 - Add No Deps Pip Install Information To Documentation

Issue - State: closed - Opened by John-P over 1 year ago
Labels: documentation

#558 - Inconsistent API / Broken LSP

Issue - State: closed - Opened by John-P over 1 year ago
Labels: documentation, code readability

#557 - :wrench: DEV: Filter Logger Output to `stdout` and `stderr`

Pull Request - State: closed - Opened by shaneahmed over 1 year ago - 3 comments

GitHub / TissueImageAnalytics/tiatoolbox issues and pull requests