[v1.5.x] Implemented rotate3D

[mcencini]

@schuenke @FrankZijlstra this PR re-open #244, which was closed because apparently @BenWilhelmUniklinikFreiburg GitHub profile does not exists anymore.

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
/home/runner/.local/lib/python3.12/site-packages/pypulseq
add_gradients.py	137	29	79%	44, 52, 61, 85, 92, 125–128, 135–136, 155, 162, 177, 187–190, 194–225, 230, 261
add_ramps.py	36	36	0%	1–92
align.py	35	4	89%	41, 45, 69, 73
calc_duration.py	25	1	96%	37
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	14	85%	6–9, 48–51, 70–71, 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%	204–208, 228–232, 240–241, 264, 270, 339–358, 462–471, 509–517
make_arbitrary_grad.py	53	15	72%	71, 74, 77, 80, 96–98, 107, 109, 117–121, 130
make_arbitrary_rf.py	75	63	16%	95–179
make_block_pulse.py	48	3	94%	121–125, 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	93	3	97%	52, 227, 230
make_gauss_pulse.py	73	20	73%	139–143, 146–170, 177, 180
make_label.py	22	4	82%	64, 66, 68, 75
make_sigpy_pulse.py	119	30	75%	12–13, 121, 124, 128, 165–169, 173, 176–177, 180–181, 196, 203, 208, 220, 223, 248–258, 272, 275, 305–315
make_sinc_pulse.py	70	10	86%	102, 108, 136–140, 144, 147–148, 151–152, 174
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
rotate3D.py	54	6	89%	44, 54, 57, 59, 93–94
rotate.py	76	5	93%	59, 83, 126, 133–134
scale_grad.py	30	1	97%	65
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	469	79	83%	63, 66, 74, 80, 95, 103, 109, 120, 123, 126, 134, 139, 148, 159, 167, 207, 209, 213, 225, 274, 278, 294, 319–345, 382–385, 421–429, 436, 466–470, 512, 518, 551, 587–594, 611, 621, 647, 685, 703, 706, 724, 738, 765, 844, 881, 905
calc_grad_spectrum.py	81	76	6%	68–190
calc_pns.py	40	31	22%	45–96
ext_test_report.py	144	11	92%	61, 138, 149–150, 237–243
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	400	39	90%	44–45, 110, 117, 130, 133–134, 138, 184, 228, 401, 422–439, 502, 505, 590, 614, 654, 685, 701–705, 712, 823, 834
sequence.py	631	128	80%	10–13, 105–115, 136–149, 196, 261–264, 311, 355, 431, 458–463, 500, 528–531, 622, 650–659, 671, 693, 734–737, 791, 829, 840–841, 847, 858, 864, 866, 874, 907–915, 1045, 1135, 1141, 1144, 1147, 1184, 1309–1322, 1380, 1402–1404, 1425, 1488, 1496, 1563, 1574–1587, 1656–1657, 1668–1686, 1710, 1740–1748, 1784, 1798–1808
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%	47–130
safe_pns_prediction.py	126	113	10%	50–87, 102–189, 197–214, 222, 244–250, 279–286, 310–336, 344–383, 396–411, 415
seq_plot.py	389	190	51%	20, 98, 130–131, 150, 167–169, 174–216, 226–233, 240–305, 309–315, 319–327, 349, 351, 354, 379–401, 446–447, 450–453, 476–485, 497, 512–522, 531–533, 551–553, 555–556, 558–559, 592–604, 619–620, 636–653, 694–698
tracing.py	16	6	62%	33–34, 42, 54–55, 75
/home/runner/.local/lib/python3.12/site-packages/pypulseq/utils/siemens
asc_to_hw.py	58	53	9%	21–28, 48–106
readasc.py	48	45	6%	25–100
TOTAL	5184	1571	70%

Tests	Skipped	Failures	Errors	Time
1480	24 💤	0 ❌	0 🔥	2m 16s ⏱️

[mcencini]

This is just a friendly reminder about this issue - apologies if it is already under the radar. I just wanted to point out that this feature would be required both by rotation extension (e.g., for plotting) and new 1.5.1 FOV (e.g., here) - unless we want to write custom rotation functions for both applications, which would probably harder to maintain. It would be great if someone wants to review this when they have time.

[mcencini]

@m-a-x-i-m-z I think the initial BenWilhelmUniklinikFreiburg commits were done before license change - did Ben Wilhelm work with you and do you have any way to ask him if it is ok to keep his changes under MIT license? Or being the changes a port of your MATLAB code, does that fall under MATLAB pulseq copyright anyway (MIT)?

[m-a-x-i-m-z]

Hi Matteo,

as mentioned before, we have another version of rotate3D in our lab, which we will push in the coming days. It then will not be affected by the GLP problem as well.

Best regards,
Maxim

[mcencini]

@m-a-x-i-m-z sweet, thank you so much! I am keeping this open for the moment as it contains some commits I did which may be useful for the tests and we may cherry pick if needed.

[fzimmermann89]

I have also a similair function here under MIT.
https://gist.github.com/fzimmermann89/6c27a2a4bf27354857e8451274e8b23b
without tests, and using scipy Rotation instead of a naked numpy array for the rotation matrix