util module

Additional helper functions.

import MRzeroCore as mr0
mr0.util.<function>()

`get_signal_from_real_system`

Wait for scanner TWIX files on the given path, and return if ready. Useful if a shared network folder between scanner and research PC is available.

Note

This is developed for internal use and might not be useful for others.

Parameter	Description
`path`	path to TWIX file
`NRep`	number of repetitions
`NRead`	number of ADC samples per repetition
`ncoils`	number of recieve channels
`heuristic_shift`	needed to remove garbage data from the file

`insert_signal_plot`

Insert a measured signal into a currently open pypulseq plot. This is only supported by newer pulseq versions, which do not show (and close) the figure immediately if plot_now=False.

seq.plot(plot_now=False)  # option doesn't exist for older pulseq versions
mr0.util.insert_signal_plot(seq, signal)
plt.show()

Parameter	Description
`seq`	pulseq sequence, needed to align the signal with the ADC samples
`signal`	signal to insert into the ADC plot
`ax`	optional ADC axes; defaults to the first axes of figure 1

`pulseq_plot`

Wrapper around insert_signal_plot, pulseq_plot_15, pulseq_plot_142 and pulseq_plot_pre14 which selects the appropriate plotting function based on the installed pulseq version.

Defaults to a six-row stacked figure (ADC, RF mag, RF phase, Gx, Gy, Gz) on all pypulseq versions. Pass stacked=False for the older two-figure layout. When stacked, only figid[0] is used.

Parameter	Description
`seq`	sequence object
`type`	ignored
`time_range`	same as for pulseq `plot()`
`time_disp`	same as for pulseq `plot()`
`show_blocks`	same as for pulseq `plot()`
`clear`	clear / reuse figures
`signal`	insert simulated signal into the ADC plot
`figid`	figure IDs `(fig1, fig2)`; stacked uses `fig1` only
`stacked`	one six-row figure (default `True`); `False` restores two figures

Thin wrapper around native pulseq plot(). pypulseq 1.5 already returns figure / axes handles and supports clear and stacked, so this does not copy the plotter. ADC sample times come from seq.adc_times(). Defaults to stacked=True.

Parameter	Description
`seq`	sequence object
`time_range`	same as for pulseq `plot()`
`time_disp`	same as for pulseq `plot()`
`show_blocks`	same as for pulseq `plot()`
`clear`	same as for pulseq `plot()`
`signal`	insert simulated signal into the ADC plot
`figid`	matplotlib figure IDs `(fig1, fig2)`; stacked uses `fig1` only
`plot_now`	show the figures immediately
`stacked`	one six-row figure (default `True`)

`pulseq_plot_142`

Use only with pypulseq versions 1.4.x / tested with 1.4.2

Identical to pulseq plot(), but returns the generated axes! This is needed to insert the signal into the ADC plot. Modified from pypulseq 1.4.2 sequence.py - plot() - see pulseq documentation for details.

Parameter	Description
`seq`	sequence object
`label`	same as for pulseq `plot()`
`show_blocks`	same as for pulseq `plot()`
`save`	same as for pulseq `plot()`
`time_range`	same as for pulseq `plot()`
`time_disp`	same as for pulseq `plot()`
`grad_disp`	same as for pulseq `plot()`
`plot_now`	same as for pulseq `plot()`
`figid`	matplotlib figure IDs `(fig1, fig2)`; stacked uses `fig1` only
`stacked`	one six-row figure (default `True`)
`clear`	clear / reuse figures

`pulseq_plot_pre14`

Use only with pypulseq versions before 1.4

Pulseq sequence plot with some aesthetical changes. Most important, it can insert the simulated signal into the ADC plot. Modified from pypulseq 1.2.0post1 sequence.py - plot() - see pulseq documentation for details.

Parameter	Description
`seq`	sequence object
`type`	same as for pulseq `plot()`
`time_range`	same as for pulseq `plot()`
`time_disp`	same as for pulseq `plot()`
`clear`	clear matplotlib figures before plotting
`signal`	insert simulated signal into the ADC plot
`figid`	use specific figure IDs (to reuse previously created figures); stacked uses `fig1` only
`stacked`	one six-row figure (default `True`)

`imshow`

Modified version of matplotlib imshow(), tailored for showing MR reconstructions. reco is expected to be an array with dimensions [x, y], [x, y, z] or [coil, x, y, z]

plots images in RAS+
- x is left-to-right
- y is bottom-to-top
plots 3d data (z) as a side-by-side grid of its slices
applies quadratic coil-combination for multi-coil data

# Replace
import matplotlib.pyplot as plt
plt.imshow(reco, *args, **kwargs)

# with
import MRzeroCore as mr0
mr0.util.imshow(reco, *args, **kwargs)

`load_phantom`

Download a phantom from the MR-zero repository (or a custom URL) for getting started quickly.

DEFAULT_PHANTOM_URL = "https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/numerical_brain_cropped.mat"

Parameter	Description
`size`	scale phantom if desired
`url`	where to load the phantom from, defaults to `DEFAULT_PHANTOM_URL`
`dB0_fB0`	`(offset, scaling)` floats to modify the \(B_0\) map
`dB1_fB1`	`(offset, scaling)` floats to modify the \(B_1\) map
`B0_polynomial`	optional 2d, 2nd degree polinomial to modify the \(B_0\) map

`simulate`

Helper function to simulate using PDG.

Parameter	Description
`seq`	MR-zero sequence, pulseq sequence or file name
`phantom`	`VoxelGridPhantom`, `CustomVoxelPhantom` or .npz / .mat file name
`sim_size`	scales phantom if set
`accuracy`	sets both `min_emitted_signal` and `min_latent_signal` for the PDG sim
`noise_level`	add normal distributed noise with the given std to the signal

`simulate_2d`

Caution

Deprecated - use load_phantom + simulate instead. For parameter descriptions, look at these functions.

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