Add rotate3D implementation

[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.

[mcencini]

I would use scipy's Rotation from_quat() method instead of a custom function - scipy is already a pypulseq dependency - see e.g., @fzimmermann89 gist for the import syntax.

[mcencini]

Currently, pypyulseq styling for optional args is Union[actual-data-type, None].

[mcencini]

I would add a Numpy styled docstring:

Parameters
------------
arg1 : type
    Description.
optional_arg2 : type, default=default_value.
     Description.

Return
-------
output : type
     Description.

Notes
-------
Optional notes section if required.

Example
---------
Optional usage example as
>>> import mypackage
>>> out = mypackage.func(inputs)

[fzimmermann89]

why do the gradients need to be realigned after scaling?

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

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
/home/runner/.local/lib/python3.12/site-packages/pypulseq
add_gradients.py	137	60	56%	44, 52, 58, 61, 75–86, 92, 125–128, 135–136, 155, 162, 167–263
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	116	116	0%	1–228
rotate.py	69	14	80%	15, 55, 66–69, 85–90, 112, 119–120
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	5238	1721	67%

Tests	Skipped	Failures	Errors	Time
1441	24 💤	0 ❌	0 🔥	4m 58s ⏱️

[Moji3h]

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

[mcencini]

There are missing dashes for correct rendering:

Parameters
------------

same for the other sections of the docstring

[mcencini]

@Moji3h, do you have any comment regarding @fzimmermann89 concern?

[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!