Revision of the System Settings Usage

[schote]

Before calculating a sequence, it must be loaded to the sequence interpreter. This can be achieved either by using the from_pypulseq method or the read method of the interpreter, which is inherited from the pypulseq Sequence.
When using from_pypulseq, so far the system limits were checked and compared to the system specified in the device configuration, before all the attributes of Sequence were overwritten in SequenceProvider. Thereby also the sequence system was overwritten.

With this PR the system defined in the device configuration is considered to be fixed. A sequence, no matter if it is loaded from file or from an existing pypulseq Sequence should not touch the system configuration.

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
src/console
__init__.py	10	1	90%	11
src/console/interfaces
acquisition_data.py	123	25	80%	96–99, 110–111, 129–130, 145–148, 158–159, 188–189, 193–199, 215–216, 227, 231, 249
acquisition_parameter.py	107	4	96%	126, 163, 178, 213
device_configuration.py	53	2	96%	60, 66
dimensions.py	96	22	77%	45–46, 67–68, 71, 79, 89, 95, 101, 107, 113–115, 125–127, 137–139, 149–151
rx_data.py	86	18	79%	77–81, 89, 101, 105, 107, 122, 130–135, 143, 151, 154, 157
src/console/pulseq_interpreter
sequence_provider.py	230	13	94%	257–258, 351–352, 463, 513–514, 583, 609–610, 626, 635, 639
src/console/spcm_control
abstract_device.py	79	79	0%	2–149
acquisition_control.py	153	153	0%	3–360
rx_device.py	209	209	0%	2–493
tx_device.py	175	175	0%	2–465
src/console/spcm_control/spcm
pyspcm.py	161	161	0%	3–295
tools.py	54	54	0%	3–128
src/console/utilities
json_encoder.py	8	3	62%	22–24
load_configuration.py	20	6	70%	18–20, 28–30
plot.py	53	16	70%	31–32, 80–98
src/console/utilities/data
mrd_helper.py	43	8	81%	37, 43, 49, 52, 60, 63, 68, 71
write_acquisition_to_mrd.py	49	5	90%	43–44, 68, 86, 91
src/console/utilities/sequences/calibration
fid_tx_adjust.py	22	1	95%	66
se_tx_adjust.py	29	2	93%	62–64
src/console/utilities/sequences/spectrometry
fid.py	15	15	0%	2–75
se_spectrum.py	25	2	92%	51, 85
src/console/utilities/sequences/tse
tse_3d.py	242	75	69%	110–111, 113–114, 116–117, 124–125, 127–129, 131–134, 145–148, 153–156, 163–174, 191, 213–220, 226, 257, 320–337, 344–345, 412, 415–427, 535–546
TOTAL	5298	1049	80%

Tests	Skipped	Failures	Errors	Time
192	0 💤	0 ❌	0 🔥	29.294s ⏱️

[h3lg3]

Testing the branch results in

  File "C:\Users\hhert\Git-projects\nexus-console\src\console\pulseq_interpreter\sequence_provider.py", line 534, in _calculate_gradient
    self.system.gamma * 1e-3 * self.gpa_gain[output_channel] * self.grad_eff[output_channel]
  File "C:\Users\hhert\miniconda3\envs\console-env\lib\site-packages\pydantic\main.py", line 1026, in __getattr__
    raise AttributeError(f'{type(self).__name__!r} object has no attribute {item!r}')
AttributeError: 'SystemLimits' object has no attribute 'gamma'

I guess the system.gamma is missing.

system = Opts(
    gamma=42.576e6,
)

[schote]

Testing the branch results in

  File "C:\Users\hhert\Git-projects\nexus-console\src\console\pulseq_interpreter\sequence_provider.py", line 534, in _calculate_gradient
    self.system.gamma * 1e-3 * self.gpa_gain[output_channel] * self.grad_eff[output_channel]
  File "C:\Users\hhert\miniconda3\envs\console-env\lib\site-packages\pydantic\main.py", line 1026, in __getattr__
    raise AttributeError(f'{type(self).__name__!r} object has no attribute {item!r}')
AttributeError: 'SystemLimits' object has no attribute 'gamma'

I guess the system.gamma is missing.

system = Opts(
    gamma=42.576e6,
)

I just tested the branch on the system and was not able to reproduce this issue. Which version of pypulseq have you installed?

[h3lg3]

Could you try

# seq.system.gamma exists
print(seq.system.gamma)

seq_provider.from_pypulseq(seq)
# seq_provider.system.gamma does not exist
print(seq_provider.system.gamma)

# unroll_sequence throws error
unrolled_sequence = seq_provider.unroll_sequence(acquisition_parameter)

[schote]

Could you try

# seq.system.gamma exists
print(seq.system.gamma)

seq_provider.from_pypulseq(seq)
# seq_provider.system.gamma does not exist
print(seq_provider.system.gamma)

# unroll_sequence throws error
unrolled_sequence = seq_provider.unroll_sequence(acquisition_parameter)

Works with pypulseq 1.5.0 and 1.4.2

[h3lg3]

I figured out the problem here. If you initialize the seq_provider with the system_limits from system_limits: SystemLimits = load_system_limits("example_device_config.yaml") like below, then gamma is missing in seq_provider but is present in seq (seq_provider.from_pypulseq(seq)) because system_limits is missing gamma. Thats when the error is provoked.

seq = pp.Sequence(system)


seq_provider = SequenceProvider(
        gradient_efficiency=config.tx.gradient_efficiency,
        gpa_gain=config.tx.gpa_gain,
        gradient_output_limits=config.tx.channel_max_amplitude[1:],
        gradients_50ohms = config.tx.gradients_terminated_50ohm,
        rf_output_limit = config.tx.channel_max_amplitude[0],
        rf_50ohms = config.tx.rf_terminated_50ohm,
        spcm_dwell_time=1/(config.tx.sampling_rate * 1e6),
        rf_to_mvolt=config.tx.rf_to_mvolt,
        system=system_limits,
    )

seq_provider.from_pypulseq(seq)`

However, if you use system_limits.get_opts(), the PyPulseq default B0 = 1.5 is added. Is that the desired behavior? Maybe the system_limits can be extended to contain all Opts parameters?