Merge dev into master #231
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bug fix to event_lib.py
sequence.py fix
Fix README.md: latest make_sinc_pulse dont return gradient by default
Replace np.float with np.float64
Fix unit issue.
…ct test reports (e.g. wrong slew rates!) and incorrect k-space trajectory calculation. (#125) Checked test reports for gre, tse, gre_radial, ute, and epi_se_rs to be identical with MATLAB. Additionally made some minor changes that avoid some warnings (bad conditioning in polynomial fit and division by zero). Co-authored-by: Frank Zijlstra <[email protected]>
…114) * Hacky fix for waveforms_and_times rf append floating point issue. * Use rf raster instead of eps
Sequence.waveforms_and_times: - Fixed missing implementation for recompressing trapezoids from arbitrary gradients. Now proceeds without recompressing and added a TODO to implement the MATLAB code. - Fixed issue where rounding errors could create non-monotonically increasing times. Also moved the non-monotonicity check outside the loop. make_trapezoid: - Fixed bug that would give an 'requested area is too large' error when explicitly specifiying a triangular gradient with duration, rise_time, and area. - Fixed check for area == 0, while an unspecified area would be None
- Actually fixed the non-monotonic time problem - Two small fixes in sequence plot() that cut off the start of the sequence when time_range is specified, and coloured labels wrongly.
Changes `shape_pieces` to Python lists, allowing them to be concatenated without a loop. Cleaner code, and slightly faster too.
…nd `rotate` (#132) * Several bug fixes in Sequence, add_gradients, make_trapezoid, and `rotate`: - Bypass code for `restoreAdditionalShapeSamples` did not include `grad.first` and `grad.last` - `make_arbitrary_grad` was not available as `pp.make_arbitrary_grad` - `add_gradients`' detection of arbitrary gradients was incorrect for Python's 0-based indexing - `add_gradients` handling of non-unique times was broken - `make_trapezoid` incorrectly checked and reported the minimum duration for gradients specifying area and duration (also fixed in local upstream MATLAB pulseq) - `rotate` did not have a system parameter - `rotate` used the incorrect channel for gradient on the second rotation axis - Small change in `add_gradients` to accept a single gradient (i.e. for cases where a variable number of gradients are added), which also allowed a minor cleanup in `rotate` * Fixed `test_report` when gradient waveforms are not of equal size
This is a direct translation of the MATLAB Pulseq calcPNS function to python, renamed to calculate_pns. This includes a partial translation of the MATLAB safe_pns_prediction repository (https://github.com/filip-szczepankiewicz/safe_pns_prediction), put into utils/safe_pns_prediction.py. To test the functionality, this adds the pnsTest sequence "example" from MATLAB Pulseq.
- np.floor -> math.floor - np.ceil -> math.ceil - np.abs -> abs (could also be done for array operations with no performance hit) - np.round -> round - np.max -> max Performance improvements range from 10x - 50x
… `test_report` - Changed handling of `next_free_ID` to properly work with used-specified `key_id`
…epeatedly accessed (i.e. `calculate_kspace`, `test_report`, `calculate_pns`, etc.) - Added `use_block_cache` option to sequence to disable the caching to save memory (defaults to True)
- Avoid unnecessary deepcopy's - Improved checks for trapezoid timing (pure-Python instead of np.unique) - Avoid unnecessary computations for adding (extended) trapezoids
…Python instead of `np.cumsum`
…` with `np.concatenate`
Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4.1.7. - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](actions/download-artifact@v3...v4.1.7) --- updated-dependencies: - dependency-name: actions/download-artifact dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]>
…dot-github/workflows/actions/download-artifact-4.1.7
* Removed trailing whitespace in a number of files * Corrected `system == None` checks to `system is None` and fixed `system` type hints * Added warnings where RF and ADC delays were silently increased to the dead time * Fixup: system type hint * Removed silent adjustment of ADC delay to ADC dead time (This should be caught by `make_adc`. If we get here, the user really wants to adjust the delay and just accept it and let `check_timing` report it) * Reworked `check_timing` to provide a structured error report - Added unit test for `check_timing` - The default signature of `seq.check_timing` remains the same, but can pretty-print the report with `print_errors=True` - `seq.write` now checks sequence timing by default - 'TotalDuration' calculation moved from `check_timing` to `seq.write` - Check whether gradients in the last block ramp down to zero removed from `check_timing` * Added optional tracing of where blocks/events were created - Can be enabled/disabled with `pp.enable_trace(limit)` and `pp.disable_trace()` - Added tracing to all blocks and all RF/ADC/gradient events - Added printing of the trace to `check_timing` when it is available * Fixed `check_timing` to not assume `rf_raster_time == adc_raster_time` * Updated expected output for `test_sequence` because it did not include `TotalDuration` in the sequence definitions * Fixed continuity checks for arbitrary gradients - `Sequence.write` now checks whether the last block ramps down to 0 - Fixed gradient continuity checks in `set_block` - Now handles arbitrary block orders properly - Now properly checks the last value of the previous block - Added gradient checks for blocks without gradients - Sequence object now remains valid after gradient errors - Added unit tests for gradient continuity in `test_block` * fix None checks fix some type hints some cleanup * refactor timing error report in test_report --------- Co-authored-by: Patrick Schuenke <[email protected]>
…dded in calc_duration (#206)
* add pre-commit workflow * add pre-commit config including ruff, typos * ruff rules to pyproject.toml * reformat / refactor code to pass checks
* Add `Sequence.install` functionality - The Matlab pulseq implementation for Siemens scanners is included - Custom scanner targets can be added using `pypulseq.Sequence.install.register_scanner` * reformat code to pass pre-commit checks --------- Co-authored-by: Patrick Schuenke <[email protected]>
* * fix: exceed of max slew rate for gradient event if make_trapezoid() is called. * [pre-commit] auto fixes from pre-commit hooks * Update make_trapezoid.py to add slew rate check for the ramp down as well --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: FrankZijlstra <[email protected]>
* * fix: exceed of max slew rate for gradient event if make_trapezoid() is called. * - check that waveform does not exceed max_slew and max_grad * [pre-commit] auto fixes from pre-commit hooks * Update make_extended_trapezoid.py to avoid unnecessary conversion to arbitrary just for the slew rate check * [pre-commit] auto fixes from pre-commit hooks * Changed slew rate and max_grad checks from >= to > with `eps` tolerance --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: FrankZijlstra <[email protected]>
* change to src layout and adjust configs * introduce conftest.py in tests * remove old empty SAR folder from utils * fix include of QGlobal.mat in distribution
updates: - [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](pre-commit/pre-commit-hooks@v4.6.0...v5.0.0) - [github.com/astral-sh/ruff-pre-commit: v0.6.9 → v0.8.6](astral-sh/ruff-pre-commit@v0.6.9...v0.8.6) - [github.com/crate-ci/typos: v1.25.0 → dictgen-v0.3.1](crate-ci/typos@v1.25.0...dictgen-v0.3.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
schuenke
requested review from
FrankZijlstra,
btasdelen,
imr-framework,
sairamgeethanath and
sravan953
Collaborator
Collaborator
Author
|
IMO we should have done it before switching the branches, but at least we should do it now as fast as possible. If ppl install from GitHub, they currently get 2 years old code. This should be fixed asap. |
btasdelen
approved these changes
Jan 9, 2025
Collaborator
Author
|
@FrankZijlstra could you approve this as well? Need 2 approving reviews to merge into master now. |
FrankZijlstra
approved these changes
Jan 9, 2025
Merged
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This PR is needed to update the new default branch (
master) to the old one (dev)