Improve phantom generator tools

[naegelejd]

Added parallel imaging support to each phantom generator tool and fixed other bugs and discrepancies between each tool.

[Copilot]

Pull Request Overview

This PR refactors and enhances the MRD phantom generation and testing infrastructure. It introduces parallel imaging support, improves test validation, and reorganizes the testing workflow.

• Adds parallel imaging (acceleration) support with calibration modes across C++, Python, and MATLAB implementations
• Introduces new validation scripts for verifying reconstruction accuracy and dataset consistency
• Reorganizes testing from test.sh to a more comprehensive test-all.sh with improved error handling

Reviewed Changes

Copilot reviewed 13 out of 14 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
test/validate_recon.py	New validation script to verify reconstruction accuracy against reference coil images
test/test.sh	Removed old test script in favor of new test-all.sh
test/test-all.sh	New comprehensive end-to-end testing script with better structure and error handling
test/compare_images.py	New script to compare MRD image files for consistency
test/compare_dataset.py	New script to validate equivalence of MRD acquisition datasets
python/setup.py	Updates version handling to use date-based fallback
python/mrd/tools/simulation.py	Adds type hints for return types
python/mrd/tools/phantom.py	Major refactor adding parallel imaging support, coordinate storage, and intermediate file outputs
python/mrd/tools/export_png_images.py	Adds verbose mode and fixes filename formatting
matlab/toolbox/examples/generate_phantom.m	Adds parallel imaging support matching Python implementation
justfile	Updates build and test commands to use new test-all.sh
docker/test-docker-images.sh	Updates filename pattern to match new 5-digit format
cpp/mrd-tools/mrd_phantom.cc	Major refactor adding parallel imaging support and coordinate storage
cpp/mrd-tools/mrd_image_stream_to_png.cc	Adds verbose mode and fixes pixel type handling

Comments suppressed due to low confidence (4)

test/compare_dataset.py:2

• Import of 'subprocess' is not used.

import subprocess

test/compare_dataset.py:5

• Import of 'Any' is not used.

from typing import Any

test/validate_recon.py:2

• Import of 'subprocess' is not used.

import subprocess

test/validate_recon.py:5

• Import of 'Any' is not used.

from typing import Any

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.