fix: Use the image loader for dicom-seg to allow compressed images#2611
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wayfarer3130 wants to merge 75 commits intomainfrom
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fix: Use the image loader for dicom-seg to allow compressed images#2611wayfarer3130 wants to merge 75 commits intomainfrom
wayfarer3130 wants to merge 75 commits intomainfrom
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* fix(security): Update lodash to 4.17.23 using a resolution to address CVE-2025-13465. * Removed lodash from the dev dependencies since it is in the resolutions now. * Update lodash to 4.17.23 in the docs package. --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Joe Boccanfuso <joe.boccanfuso@radicalimaging.com>
* refactor: replace string literals with OrientationAxis enums for better type safety and clarity in BaseVolumeViewport and getCameraVectors * feat(rendering): Add function to calculate acquisition plane reformat orientation based on image orientation patient values * feat: enhance reformat orientation handling in VolumeViewport and BaseVolumeViewport, allowing for specific axial, sagittal, and coronal reformats while maintaining base orientation references * feat: add buttons for setting viewport orientations to non-reformat, reformat, and acquisition types, enhancing user control over viewport display * fix: suppress events during camera reset in VolumeViewport to prevent premature rendering * fix(getCameraVectors): import OrientationVectors type * fix(tests): update button text in MPR Reformat visual tests * fix(tests): update MPR Reformat screenshots for Chromium and WebKit --------- Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>
--------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Joe Boccanfuso <joe.boccanfuso@radicalimaging.com>
* refactor the solution given * fix fetch color tables * important refactors to optimize worker functionality * refactor fetch palette data * fix clearly wrong test values * refactor as reviewer suggestions * fix: Convert 16 bit declared as 8 palette color data * fix: or condition on setting 16 bit palette data --------- Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>
…eehandROI open U-shape contours (#2615) * feat(tools): implement orthogonalT and lineSegment modes for PlanarFreehandROI open U-shape contours Add two new rendering modes for the open U-shaped contour T-overlay: - 'orthogonalT': computes the T-line endpoint as the perpendicular ray-contour intersection from the chord midpoint, instead of the farthest point. Useful for LA cardiac workflows where the T must be perpendicular to the chord. - 'lineSegment': draws only the dashed chord connecting endpoints without any T-line, closing the contour visually. Also adds optional shaded fill for the enclosed region (contour + chord) when fillOpacity > 0, and centralizes variant dispatch into a single resolveVectorToPeak function to eliminate duplicated branching across drawLoop, openContourEditLoop, and renderMethods. * fix(tools): address PR review for PlanarFreehandROI U-shape modes - Use vec2.sub instead of create+set for chord vector - Replace double-loop ray intersection with single-pass dot-product approach for orthogonalT peak finding - Return null with console.warn instead of falling back to farthestT when no orthogonal intersection is found - Add 'none' option to U-shape dropdown to remove U-shape rendering - Auto-apply U-shape mode on dropdown change, remove separate button - Apply configured U-shape mode to newly drawn open contours - Add fill opacity dropdown using tool configuration - Read fillOpacity from tool config in renderMethods * refactor(tools): use vec2.dot for orthogonal T dot product calculation * Move open u shaped to utils helper --------- Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>
* fix(security): Various dependency updates as a result of CVE-2026-26996. Ultimately the vulnerability was ignored because it is only exposed in itk-wasm via CLI and it is limited to build/dev environments.
* refactor: update getTextBoxCoordsCanvas function to accept element and textLines parameters for improved textbox placement across multiple annotation tools * fix: correct bounding box calculations in _drawTextGroup function to accurately reflect text box position and size * feat: implement text box overlap management with registry for improved placement accuracy - Added a text box overlap registry to track rendered text box positions. - Integrated overlap avoidance logic in getTextBoxCoordsCanvas to prevent occlusion of existing text boxes. - Updated draw and drawTextBox functions to clear and register text boxes during rendering. * refactor: enhance overlap detection in getTextBoxCoordsCanvas using AABB intersection - Replaced the previous rectangle overlap logic with a more accurate AABB intersection method. - Introduced a new utility function to convert text box rectangles to AABB format, allowing for better handling of overlap checks. - Updated the overlap detection functions to utilize the new intersection logic for improved accuracy in text box placement. * test: add unit tests for getTextBoxCoordsCanvas to validate positioning logic - Introduced a new test suite for getTextBoxCoordsCanvas to ensure correct coordinate calculations for text boxes. - Added tests for default positioning, overlap handling, and fallback mechanisms when space is limited. - Utilized a mock viewport element to simulate various scenarios for accurate testing. * style: format getTextBoxCoordsCanvas test cases for improved readability - Reformatted the test cases in getTextBoxCoordsCanvas.spec.ts to enhance code clarity. - Adjusted the indentation and line breaks for better visual structure without altering functionality. * refactor: update type assertions in getTextBoxCoordsCanvas tests for better type safety - Changed type assertions from any to unknown in getTextBoxCoordsCanvas test cases to enhance type safety and maintain code quality. - Ensured consistency in type handling across the test suite without altering existing functionality. * refactor: remove unnecessary type assertions in getTextBoxCoordsCanvas tests - Updated test cases in getTextBoxCoordsCanvas.spec.ts to eliminate type assertions from unknown to the actual type for annotationPoints and related variables. - Improved code clarity and type safety without changing the existing functionality of the tests. * chore: update tsconfig.json to exclude test files from compilation - Added an "exclude" property to tsconfig.json to prevent test files from being included in the TypeScript compilation process. - This change helps streamline the build process by omitting unnecessary test files. * refactor: integrate getTextBoxCoordsCanvas into ArrowAnnotateTool for improved text box positioning - Replaced direct canvas coordinate assignment with a call to getTextBoxCoordsCanvas to enhance the accuracy of text box placement. - This change ensures that text box coordinates are calculated based on the current canvas state and element, improving overall annotation functionality. * refactor: streamline text box rendering across annotation tools - Replaced direct text box rendering logic with a unified renderLinkedTextBoxAnnotation method in multiple annotation tools. - This change enhances code maintainability and consistency in text box visibility and positioning logic. - Improved handling of text box state and coordinates, ensuring better integration with existing annotation functionalities. --------- Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>
* fix: Continuous flicker on viewer redraw * fix: Comment on size 0
…kfile changes. (#2629) Disabled all dependabot pull requests for bun and npm version updates.
…install --frozen-lockfile (#2659)
…m validation and testing (#2657) * feat(ohif-downstream): Add CI workflow and scripts for OHIF downstream validation and testing - Introduced a GitHub Actions workflow for validating OHIF builds against pull requests. - Added scripts for local setup, building, and testing of OHIF with linked Cornerstone packages. - Updated .gitignore to exclude the new OHIF downstream directory. * bug * feat(ohif-downstream): Enhance CI workflow for OHIF downstream testing - Renamed job to ohif-downstream for clarity. - Increased timeout for builds from 90 to 180 minutes. - Added unit tests, Playwright browser installation, and end-to-end tests to the workflow. - Implemented artifact upload for Playwright test results and reports. * remove build * some * Add unlink script * Move link script to general scripts, not ci specific * Log commit to demonstrate update * Add docs * Try using fixed OHIF tests for ohif-downstream * docs: About wait time * Try updating branch name * fix ohif-downstream with loggin * fix: Use master for release * Undo console change for release --------- Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>
…wport without segmentation (#2683)
… points for default textbox position and improve corner determination logic (#2686)
…#2673) * fix: move crosshairs implementation to absolute camera instead of delta * refactor(CrosshairsTool): remove unused methods and streamline viewport listener management * refactor(CrosshairsTool): consolidate viewport listener management and deprecate unused methods * refactor(CrosshairsTool): simplify viewport iteration using forEach and improve early returns * feat: crosshairs minimal mode * feat(crosshairs): add passive mouse down callback for modifier-aware clicks * feat(crosshairs): enhance dropdown options and streamline configuration management * feat(crosshairs): add crosshairs binding modes example and update CrosshairsTool configuration
ohif-downstream is now running AND passing * fix: Minimal changes to get linking to work for ohif-downstream * Update to use specific ohif branch for ohif-downstream * Temp change to add log to test that cs3d build works correctly * Lock update * Try newer node/bun version and lower timeout * Update build * Axios fix * fix: Yaml syntax * Timeout 120 minutes to try to load libraries
…erstonejs/cornerstone3D into fix/use-imageLoader-for-seg
wayfarer3130
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Context
The previous version of the segmentation loader claimed to support labelmap, but didn't actually work for loading them. As well, both bitmap and labelmap supposedly had RLE support, but again it didn't quite work.
This change adds storing as either labelmap or bitmap, and allows storing in RLE. The RLE encoder is also fixed to support 1,8,16 bits, and actually does the RLE correctly instead of using a count of 1 for every pixel.
The result of this is far faster loading of seg images from standard back ends supporting the SEG frame retrieve rather than trying to retrieve the entire DICOM file. On storage, the store size is also significantly smaller as RLE compresses extremely well for segmentation images.
ohif_ref: feat/load-seg-images
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