[Moji3h]

No description provided.

[Moji3h]

This PR adds the rotate3D function to PyPulseq which enables rotation of gradient waveforms in 3D space.

[mcencini]

Thanks @Moji3h for this PR! I left some comments about styling and a suggestion to avoid a custom quat_to_matrix function.

In addition, I think we should add a test suite for this.

[fzimmermann89]

why do the gradients need to be realigned after scaling?

also there are some strange (llm?) comments left in...

[github-actions]

Coverage Report

Warning: Comment truncated due to GitHub's 65536 character limit

File	Stmts	Miss	Cover	Missing
/home/runner/.local/lib/python3.12/site-packages/pypulseq
add_gradients.py	137	21	85%	44, 52, 61, 85, 92, 125–128, 155, 162, 177, 187–190, 211–218, 225, 230, 261
add_ramps.py	36	36	0%	1–92
align.py	35	4	89%	41, 45, 69, 73
calc_duration.py	33	2	94%	43, 50
calc_ramp.py	220	216	2%	48–359
calc_rf_bandwidth.py	37	28	24%	45–81, 85–89
check_timing.py	96	29	70%	78, 82, 107, 180, 199, 232, 239, 249–293
compress_shape.py	30	1	97%	28
convert.py	40	8	80%	42, 48, 66, 72–73, 82, 88–89
event_lib.py	96	15	84%	6–9, 48–51, 70–71, 185, 205–210
make_adc.py	98	14	86%	77, 80, 90–94, 97, 146, 149, 153, 159, 163, 202, 204, 206, 214
make_adiabatic_pulse.py	132	39	70%	208–212, 232–236, 244–245, 268, 274, 343–362, 466–475, 513–521
make_arbitrary_grad.py	53	4	92%	80, 109, 118, 130
make_arbitrary_rf.py	75	63	16%	95–179
make_block_pulse.py	48	1	98%	128
make_delay.py	9	1	89%	27
make_digital_output_pulse.py	16	2	88%	42, 50
make_extended_trapezoid.py	56	12	79%	67, 70, 76, 82, 85, 88, 91, 94, 116, 134, 136, 139
make_extended_trapezoid_area.py	104	4	96%	68, 71, 261, 264
make_gauss_pulse.py	77	5	94%	171, 179–181, 196
make_label.py	21	2	90%	68, 70
make_sigpy_pulse.py	119	30	75%	12–13, 122, 125, 129, 166–170, 174, 177–178, 181–182, 197, 204, 209, 221, 224, 249–259, 273, 276, 306–316
make_sinc_pulse.py	74	5	93%	110, 175–177, 192
make_soft_delay.py	26	2	92%	107, 125
make_trapezoid.py	111	7	94%	177, 190, 196, 214, 232, 237, 255
make_trigger.py	16	2	88%	47, 55
opts.py	66	9	86%	78, 83, 102, 142, 166–170
points_to_waveform.py	9	1	89%	27
rotate.py	69	5	93%	55, 69, 112, 119–120
rotate_3d.py	78	2	97%	145–146
sigpy_pulse_opts.py	26	7	73%	34–41
split_gradient.py	39	31	21%	46–103
split_gradient_at.py	70	27	61%	63–90, 110, 114, 118–120, 154–156
traj_to_grad.py	13	9	31%	26–40
/home/runner/.local/lib/python3.12/site-packages/pypulseq/SAR
SAR_calc.py	5	1	80%	9
/home/runner/.local/lib/python3.12/site-packages/pypulseq/Sequence
block.py	452	54	88%	64, 67, 75, 81, 96, 104, 110, 121, 124, 127, 135, 140, 149, 160, 168, 208, 210, 214, 329, 333, 336, 357, 372, 382, 393, 402, 434, 438, 447, 460, 471, 480–484, 502, 534–541, 558, 568, 594, 632, 671, 685, 712, 791, 828, 852
calc_grad_spectrum.py	81	76	6%	68–190
calc_pns.py	40	31	22%	45–96
ext_grad_check.py	55	2	96%	51, 53
ext_test_report.py	167	11	93%	79, 156, 167–168, 337–343
install.py	75	42	44%	31, 52, 69, 71, 112–131, 148, 181–184, 200–212, 254–278
parula.py	4	2	50%	19–86
read_seq.py	408	41	90%	44–45, 110, 117, 130, 133–134, 138, 184, 223–224, 242, 415, 436–453, 516, 519, 604, 628, 668, 699, 715–719, 726, 837, 848
sequence.py	641	133	79%	10–13, 107–117, 138–151, 205, 270–273, 320, 364, 440, 467–472, 509, 537–540, 631, 659–668, 680, 702, 743–746, 775, 801–807, 842, 853–854, 860, 871, 877, 879, 887, 920–928, 1060, 1158, 1164, 1167, 1170, 1209, 1334–1347, 1405, 1427–1429, 1450, 1513, 1521, 1619, 1630–1643, 1712–1713, 1724–1742, 1766, 1796–1804, 1840, 1854–1864
write_seq.py	362	7	98%	45, 77–79, 313, 347–349, 499
/home/runner/.local/lib/python3.12/site-packages/pypulseq/utils
cumsum.py	14	1	93%	17
paper_plot.py	63	58	8%	49–132

[Moji3h]

Thanks for the comments. I updated it accordingly and resolved the issues.

[mcencini]

@Moji3h thank you for the review! I still see some issues with the docstring, as well as the remaining issue of post rotation gradient alignment.

In addition, I would strongly advise to add some unit tests, it is important not to decrease the coverage. Thanks again for your support!

[mcencini]

Hi @Moji3h, do you have any updates by any chance? I am happy to help with the coverage if you're ok with me pushing commits on this branch

[schuenke]

based on this PR, #302 and https://github.com/m-a-x-i-m-z/pypulseq-matlab-like/blob/master/src/pypulseq_matlab_like/rotate_3d.py me and my AI coding partner created an updated, documented and tested (96% coverage) version of the rotate_3d function.

I also did a MATLAB cross-check using 7 cases covering all input forms and gradient types. All output gradients match in channel, type, timing and waveform (max |Δ| ≈ 1e-10 Hz/m) and trapezoid amplitudes.

I also adjusted the function name (and filename) to rotate_3d with the following API:

def rotate_3d(
    *args: SimpleNamespace,
    rotation: Union[np.ndarray, list, tuple, float, Rotation],
    system: Union[Opts, None] = None,
) -> List[SimpleNamespace]:

So the overlap with the current code is quite small.

@mcencini I guess you would be the best candidate to review it. Do you prefer a new PR or should I push the changes here?

[mcencini]

@schuenke thanks for looking into this! I will be happy to review it asap. I think it is ok to push the changes here.

[mcencini]

@schuenke looks good to me!