4 quantus ceus mp4 analysis gui cannot proceed after roi drawing by OmidChaghaneh · Pull Request #63 · QuantUS-OpenSource/QuantUS

OmidChaghaneh · 2026-03-27T08:59:43Z

#4

…ection

…m-format-reading

…wing view

…ing signal and implementing preview transition

…i.py files

…module

…4-quantus-ceus-mp4-analysis-gui-cannot-proceed-after-roi-drawing

Copilot

Pull request overview

Fixes QuantUS CEUS GUI workflow getting stuck after manual ROI/VOI drawing by wiring the “segmentation saved/loaded” flow through the model/controller and introducing the CEUS analysis-loading screens to allow navigation to continue.

Changes:

Connect manual ROI/VOI save → segmentation load → segmentation confirmed, so the workflow can proceed past ROI drawing (Issue #4).
Add CEUS analysis-loading MVC components and generated PyQt UI modules to support selecting/running analyses.
Add ROI preview enhancements (CLAHE/gamma/width scaling + optional pseudocolor) and improve folder-vs-file validation in CEUS file selection.

Reviewed changes

Copilot reviewed 43 out of 44 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
src/qus/visualization_loading/ui/visualization_preview_2d_ui.py	Adds generated UI for 2D visualization preview screen.
src/qus/seg_loading/ui/seg_type_selection_ui.py	Adds generated UI for segmentation type selection.
src/qus/seg_loading/ui/roi_preview_ui.py	Adds generated UI for ROI preview/confirmation.
src/qus/seg_loading/ui/frame_selection_ui.py	Adds generated UI for frame selection.
src/qus/image_loading/ui/scan_type_ui.py	Adds generated UI for scan/data type selection.
src/qus/export_loading/ui/export_loading_ui.py	Adds generated UI for export configuration/loading.
src/qus/config_loading/ui/config_type_selection_ui.py	Adds generated UI for analysis config type selection.
src/qus/application_model.py	Adds debug prints for NIfTI load details (image/seg).
src/qus/analysis_loading/ui/analysis_params_ui.py	Adds generated UI for analysis params screen.
src/qus/analysis_loading/ui/analysis_function_selection_ui.py	Adds generated UI for analysis function selection.
src/ceus/seg_loading/views/draw_roi_widget.py	Adds enhancement controls + pseudocolor and enhanced-frame caching during ROI drawing.
src/ceus/seg_loading/ui/seg_type_selection_ui.py	Adds generated UI for CEUS segmentation type selection.
src/ceus/seg_loading/seg_loading_view_coordinator.py	Wires manual segmentation save to trigger loading; auto-confirms seg to unblock workflow.
src/ceus/seg_loading/seg_loading_controller.py	Re-enables model signal wiring to update views when segmentation loads.
src/ceus/image_loading/views/file_selection_widget.py	Improves “folder vs file” extension handling/validation.
src/ceus/image_loading/ui/scan_type_ui.py	Adds generated UI for CEUS scan type selection.
src/ceus/image_loading/ui/file_selection_ui.py	Adds generated UI for CEUS scan file selection.
src/ceus/application_model.py	Adds analysis support (worker + signals), preprocessing helpers, loader error-code handling, and NIfTI debug prints.
src/ceus/application_controller.py	Adds navigation into CEUS analysis-loading flow after segmentation confirmed.
src/ceus/analysis_loading/views/analysis_params_widget.py	Introduces CEUS analysis params widget scaffold (currently placeholder).
src/ceus/analysis_loading/views/analysis_function_selection_widget.py	Ports analysis function selection widget to CEUS types/imports.
src/ceus/analysis_loading/views/analysis_execution_widget.py	Ports analysis execution widget to CEUS types/imports.
src/ceus/analysis_loading/ui/analysis_params_ui.py	Adds generated UI for CEUS analysis params screen.
src/ceus/analysis_loading/ui/analysis_function_selection_ui.py	Adds generated UI for CEUS analysis function selection screen.
src/ceus/analysis_loading/ui/analysis_execution_ui.py	Adds generated UI for CEUS analysis execution screen.
src/ceus/analysis_loading/analysis_loading_view_coordinator.py	Ports/adjusts coordinator wiring for CEUS analysis flow and safer error handling.
src/ceus/analysis_loading/analysis_loading_controller.py	Selects an available CEUS analysis type and drives function/params/execution workflow.
.gitignore	Stops ignoring `*_ui.py` so generated UI modules can be committed.

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Copilot · 2026-03-27T09:05:19Z

+
+        # Enhancement parameters
+        self._clahe_clip_limit = 1.2
+        self._gamma = 1.5
+        self._use_philips_ceus = False
+        self._enhanced_cache = None # Cache for enhanced current frame


Duplicate initialization of enhancement fields (_clahe_clip_limit/_gamma) appears twice. This makes it unclear which defaults are intended and increases maintenance risk; remove the redundant block and keep a single source of truth for the default values.

Suggested change

# Enhancement parameters

self._clahe_clip_limit = 1.2

self._gamma = 1.5

self._use_philips_ceus = False

self._enhanced_cache = None # Cache for enhanced current frame

self._use_philips_ceus = False

self._enhanced_cache = None # Cache for enhanced current frame

Copilot · 2026-03-27T09:05:20Z

+
+        # Enhancement parameters
+        self._clahe_clip_limit = 1.2
+        self._gamma = 1.5


This second block redefines enhancement defaults that were already set a few lines above, which can easily lead to accidental divergence. Keep only one initialization block (and include _use_philips_ceus/cache fields there).

Suggested change

# Enhancement parameters

self._clahe_clip_limit = 1.2

self._gamma = 1.5

Copilot · 2026-03-27T09:05:20Z

+    def _create_parameter_inputs(self) -> None:
+        """Create input fields for each required parameter."""
+        # This implementation is simplified compared to QUS for now
+        # Ideally would dynamically create inputs based on CEUS requirements
+        pass


_create_parameter_inputs() is currently a no-op (pass), so the UI will not render any required parameter inputs even when required_params are provided, and the widget will always emit an empty params dict. Implement this method (or remove required_params plumbing) so analysis functions that require parameters can be configured from the GUI.

davidspector67 · 2026-04-19T06:35:21Z

Hey Omid,

Is the goal for this PR to complete an end-to-end GUI analysis pipeline for CEUS MP4? After merging this branch with main and making some tweaks, it still appears not able to support this. Let me know what you're thinking for this PR and I can push the changes I've made so far if you think they would be helpful.

Thanks,
David

OmidChaghaneh · 2026-04-21T09:26:01Z

Hey David, Yes, the goal is indeed to finalize the end-to-end GUI analysis pipeline for CEUS MP4. Currently, the core pipeline is almost there and largely functional, but there are still a few refinements needed. The primary missing piece is the transition after the analysis menu. Right now, it has been tested until reaching to there. Best

davidspector67 · 2026-05-03T05:56:46Z

@@ -0,0 +1,339 @@
+# Form implementation generated from reading ui file 'src\ceus\image_loading\ui\file_selection.ui'


Hey Omid, in the future, try not to add auto-generated *_ui.py files to your commits as it bloats things, the files are constantly being overwritten, and they don't contain any additional information than the source *.ui files. I'll add back to the .gitignore file to enforce this

…ckend from frontend for enhancement, put back .gitignore, updated ceus engines submodule commit ref

davidspector67 · 2026-05-03T19:05:07Z

Hi Omid,

I just made the view draw_roi_widget.py respect the MVC architecture for image enhancements, just as it's respected for the 3D VOI view. Pseudocoloring also doesn't do anything on RGB images, so I removed that from the GUI in the case where the pixel data is RGB.

It looks like the analysis itself still has an error (specifically, I cannot generate a TIC after hitting run on the GUI without it crashing). Can you address this so that the pipeline works through analysis execution? Also, at the end of the newly implemented capabilities, if you can have a message saying that the rest of the pipeline still needs to be finished, that would be great.

Thank you,
David

OmidChaghaneh · 2026-05-05T08:47:50Z

Hi David,

I’ve resolved the analysis execution error and refined the CEUS pipeline. The TIC crash has been fixed, and I’ve also added UI feedback to support continuation of the analysis and development.

Best regards,
Omid

OmidChaghaneh added 15 commits February 9, 2026 10:38

feat: update FileSelectionWidget and ceus engine for single DICOM sel…

b7c3a77

…ection

Fix frame slider synchronization and frame-based display in CEUS GUI

0eec1da

Merge branch '48-urgent-philips-high-quality-data-loading' into 36-dc…

2a0e661

…m-format-reading

Add compact enhancement controls and pseudo-colouring to CEUS ROI dra…

37911ec

…wing view

Update gitignore to include generated UI files

bef8435

fix(ceus): resolve freeze after loading NIfTI segmentation by connect…

12b8086

…ing signal and implementing preview transition

feat(ceus): connect analysis screen to application workflow

efab415

fix(ceus): standardize imports and fix NameErrors in analysis widgets

049e447

feat(ceus): implement analysis discovery and background execution

513177a

feat(ceus): add missing analysis parameters widget

021226b

fix: update .gitignore to include UI files and add missing .ui and _u…

dc4e9eb

…i.py files

Fix silent hang after segmentation loading and update ceus engine sub…

61af6fd

…module

Merge branch 29-ceus-bug-report-gui-cannot-load-saved-nifti-voi into …

0f92600

…4-quantus-ceus-mp4-analysis-gui-cannot-proceed-after-roi-drawing

Fix ModuleNotFoundError by updating image preprocessing imports in GUI

2c7affe

Fix pkl_roi loader missing and TypeErrors in worker threads

3948282

OmidChaghaneh requested a review from davidspector67 March 27, 2026 08:59

OmidChaghaneh self-assigned this Mar 27, 2026

Copilot AI review requested due to automatic review settings March 27, 2026 08:59

OmidChaghaneh linked an issue Mar 27, 2026 that may be closed by this pull request

Quantus CEUS .mp4 analysis GUI cannot proceed after ROI drawing #4

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OmidChaghaneh added the PR Pull request label Mar 27, 2026

Copilot started reviewing on behalf of OmidChaghaneh March 27, 2026 09:00 View session

Copilot AI reviewed Mar 27, 2026

View reviewed changes

Merge main into branch and resolve conflicts

df216c3

davidspector67 reviewed May 3, 2026

View reviewed changes

davidspector67 added 2 commits May 2, 2026 23:01

removed _ui.py files, updated ceus submodule to commit from merged PR

2f273d0

removed pseudocoloring for RGB images, removed direct reference to ba…

c380f7d

…ckend from frontend for enhancement, put back .gitignore, updated ceus engines submodule commit ref

Fix CEUS analysis execution and handle NIfTI phantom_name AttributeError

c876f6b

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4 quantus ceus mp4 analysis gui cannot proceed after roi drawing#63

4 quantus ceus mp4 analysis gui cannot proceed after roi drawing#63
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		@@ -0,0 +1,339 @@
		# Form implementation generated from reading ui file 'src\ceus\image_loading\ui\file_selection.ui'

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