Fixes timing of write_gre sequence.

[h3lg3]

The GRE sequence https://github.com/imr-framework/pypulseq/blob/0398b12bc1d86c1997ed5ad34242a22cc95003bd/examples/scripts/write_gre.py has a small TE/TR timing error if the rf.ringdown_time gets longer than the gz.fall_time. Taking the max() of both fixes the issue which becomes relevant for longer ringdown times or thick slices.

[github-actions[bot]]

Coverage Report

File	Stmts	Miss	Cover	Missing
/home/runner/.local/lib/python3.12/site-packages/pypulseq
add_gradients.py	123	51	59%	44, 52, 58, 61, 75–86, 92, 120–123, 130–131, 150, 157, 162–241
add_ramps.py	36	36	0%	1–89
align.py	35	4	89%	41, 45, 69, 73
calc_duration.py	25	1	96%	37
calc_ramp.py	218	214	2%	45–353
calc_rf_bandwidth.py	27	20	26%	37–59, 63–67
check_timing.py	87	27	69%	72, 76, 101, 194, 201, 211–255
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	92	13	86%	63, 72–76, 79, 128, 131, 135, 141, 145, 184, 186, 188, 196
make_adiabatic_pulse.py	129	39	70%	196–200, 217–221, 229–230, 253, 259, 328–347, 451–460, 498–506
make_arbitrary_grad.py	37	7	81%	68, 71, 74, 77, 81, 83, 103
make_arbitrary_rf.py	66	55	17%	83–160
make_block_pulse.py	46	3	93%	112–116, 119
make_delay.py	9	1	89%	27
make_digital_output_pulse.py	16	2	88%	39, 47
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	69	20	71%	127–131, 134–158, 165, 168
make_label.py	19	3	84%	36, 41, 43
make_sigpy_pulse.py	116	31	73%	12–13, 112, 115, 119, 154, 157–161, 165, 168–169, 172–173, 188, 195, 200, 212, 215, 240–250, 264, 267, 297–307
make_sinc_pulse.py	68	10	85%	94, 100, 127–131, 135, 138–139, 142–143, 165
make_trapezoid.py	111	7	94%	177, 190, 196, 214, 232, 237, 255
make_trigger.py	16	2	88%	44, 52
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	14	4	71%	28–30, 33
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	113	98	13%	33–40, 55–62, 89–108, 129–132, 168–212, 242–246, 264–306
/home/runner/.local/lib/python3.12/site-packages/pypulseq/Sequence
block.py	368	32	91%	59, 62, 70, 76, 91, 99, 105, 116, 119, 122, 130, 135, 144, 196, 245, 249, 265, 305–308, 337–338, 404, 410, 430, 499, 535, 541, 568, 606, 640
calc_grad_spectrum.py	81	76	6%	68–190
calc_pns.py	40	31	22%	45–96
ext_test_report.py	140	11	92%	23, 58, 61, 135, 227–233
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	312	68	78%	42–43, 90, 93, 105, 110, 116, 123, 132, 141, 146, 149, 157–159, 192, 197, 205–254, 284–287, 302–303, 332–349, 412, 415, 450, 458, 532, 574–578
sequence.py	723	217	70%	11–14, 101–111, 132–145, 183, 248–251, 292, 319, 336, 384, 412, 439–444, 481, 497, 588, 610, 651–654, 708, 740, 751–752, 758, 769, 775, 777, 785, 818–826, 847–869, 912, 914, 917, 943–944, 947–950, 986–996, 1034–1035, 1071–1072, 1098, 1104, 1107, 1144, 1265–1278, 1301, 1329, 1351–1353, 1374, 1405, 1416–1429, 1441–1452, 1498–1499, 1508–1526, 1550, 1580–1588, 1620–1730, 1759, 1773–1783, 1795
write_seq.py	172	8	95%	41, 65, 68–75
/home/runner/.local/lib/python3.12/site-packages/pypulseq/utils
cumsum.py	14	1	93%	17
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
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	4358	1489	66%

Tests	Skipped	Failures	Errors	Time
1285	18 :zzz:	0 :x:	0 :fire:	2m 51s :stopwatch:

[FrankZijlstra]

Going from the GRE sequence I wrote for https://github.com/pulseq/MR-Physics-with-Pulseq/, the correct delay calculation should be:

delay_TE = (
    math.ceil(
        (
            TE
            - (pp.calc_duration(gz, rf) - pp.calc_rf_center(rf)[0] - rf.delay)
            - pp.calc_duration(gx_pre)
            - pp.calc_duration(gx) / 2
            - pp.eps
        )
        / seq.grad_raster_time
    )
    * seq.grad_raster_time
)

This should fix your issue, and it does not assume that the center of the RF pulse is in the center of the waveform. seq.test_report() is accurate in reporting TE, so any errors with the nominal TE should show up there.

I had meant to update the example sequences based on the "clean" ones we developed for that course, but I never got around to it. This issue almost certainly exists in other examples.

[h3lg3]

I adopted your proposed change. It seems that previously a rounding issue led to a delay_TE of 82 ms. Now it is 81 ms. Therefore the reference seq file for testing in '\tests\expected_output' needs to be updated.