Add optional duration parameter to make_extended_trapezoid_area

[JosephGWoods]

Modified make_extended_trapezoid_area to take duration as an optional input parameter. This is so that extended trapezoids for a given duration, area and gradient start and end points can be created. If no duration is provided, or if duration <=0, the existing minimum duration search is performed.

[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	104	4	96%	68, 71, 261, 264
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
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	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	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	633	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, 1047, 1145, 1151, 1154, 1157, 1194, 1319–1332, 1390, 1412–1414, 1435, 1498, 1506, 1604, 1615–1628, 1697–1698, 1709–1727, 1751, 1781–1789, 1825, 1839–1849
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
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	407	186	54%	22, 106, 138–139, 159, 176–178, 183–225, 235–242, 249–314, 318–324, 328–336, 359, 361, 363, 390–412, 457–458, 461–464, 487–496, 508, 523–533, 542–544, 563–565, 567–568, 570–571, 655–656, 672–689, 737–741
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	59	7	88%	103–104, 110–111, 122–124
TOTAL	5187	1564	70%

Tests	Skipped	Failures	Errors	Time
1284	24 💤	0 ❌	0 🔥	4m 50s ⏱️

[schuenke]

I will have a look at the exact changes later. Unfortunately, the changes are not tracked as say are supposed to be.

However, it would definitely be good to have tests for this new feature.

[schuenke]

I will open a PR to fix this automatically, but for future commits here and other repositories, I highly recommend to switch your git configuration to use Unix style instead of Windows style line endings.

As far as I know, you should be able to do so using:
git config --global core.autocrlf true

For the moment, to see the code changes ignoring whitespaces / line endings, just use this link:
https://github.com/imr-framework/pypulseq/pull/351/changes?w=1

[JosephGWoods]

Hi Patrick. I will add some tests, as you asked.

In terms of the line endings, I hadn't realised they would be crlf. I was making these changes on macOS so assumed it would be lf by default. Sorry about that.

[schuenke]

Hi Patrick. I will add some tests, as you asked.

In terms of the line endings, I hadn't realised they would be crlf. I was making these changes on macOS so assumed it would be lf by default. Sorry about that.

Well.... I was wrong. This isn't a EOL issue, but just a confusing diff output due to the additional indentation. Sorry for the confusion.

[mcencini]

Hi Patrick. I will add some tests, as you asked.
In terms of the line endings, I hadn't realised they would be crlf. I was making these changes on macOS so assumed it would be lf by default. Sorry about that.

Well.... I was wrong. This isn't a EOL issue, but just a confusing diff output due to the additional indentation. Sorry for the confusion.

Still, I think #354 is not bad to have anyway :)

[JosephGWoods]

Hi Patrick and Matteo, I've added the requested changes and unit tests. I don't understand why some sequence code test failed or why my changes would have caused the reported changes. Are these changes caused by some other commits that have since been merged in?

[schuenke]

I just re-run the tests in #353, which is up to date and all tests pass there. So the breaking changes are from this PR. See my comment above for the potential source of error.

[schuenke]

@mcencini maybe you want to have a quick look at my changes in 11276dd and 52008b3 before we merge this.

[JosephGWoods]

Hi @schuenke and @mcencini, could you approve the additional changes I made? In particular, the code no longer uses 99% of max_grad or max_slew, bringing it inline with other pypulseq code, with the corresponding seq file unit test being updated accordingly. Additionally, the input parameter ordering has been returned to the original order to preserve previous behavior, with the new input parameters added at the end.

[schuenke]

lgtm now