Signal recovery optimizer #429
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… in symmetrical colorbar
…Specificaly, Gz must be calculated at each shimming slices deck (e.g., the target slice and slices before; Do not calculate Gz after concatenating slice-by-slice B0 map to form volumetric B0 maps
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We should find a way to calculate and pass the Gx, Gy, Gz options so that it does not affect the other "criteria". In the current form, the "mse" would unnecessarily calculate the gradients, pass it to the _scipy_minimize() function and crash when trying to call "mse"'s _criteria_func().
Similarly, in the sequencer, there should be a function that handles all the necessary calculation and necessary plots for this new method in a if that gets executed only if it's this optimizer.
The code is looking good :)
shimmingtoolbox/cli/b0shim.py
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| end_time = time.time() | ||
| print("Time taken for shim_sequencer to run is : ", end_time - start_time, "seconds") |
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| end_time = time.time() | |
| print("Time taken for shim_sequencer to run is : ", end_time - start_time, "seconds") |
| coil_Gx_mat = np.reshape(merged_coils_Gx, | ||
| (n_channels, -1)).T[mask_erode_vec != 0, :] # masked points x N | ||
| coil_Gy_mat = np.reshape(merged_coils_Gy, | ||
| (n_channels, -1)).T[mask_erode_vec != 0, :] # masked points x N | ||
| coil_Gz_mat = np.reshape(merged_coils_Gz, | ||
| (n_channels, -1)).T[mask_erode_vec != 0, :] # masked points x N |
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What if the acquisition is oblique? The "z gradient" would be in the slice encoding direction, does that have an impact on your calculation? There is some code in the toolbox (shimmingtoolbox.shim.realtime_shim:realtime_shim()) to calculate the gradient in the "true z" direction.
shimmingtoolbox/shim/sequencer.py
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| @@ -186,10 +204,12 @@ def _eval_static_shim(opt: Optimizer, nii_fieldmap_orig, nii_mask, coef, slices, | |||
| shimmed = np.zeros(unshimmed.shape + (len(slices),)) | |||
| corrections = np.zeros(unshimmed.shape + (len(slices),)) | |||
| masks_fmap = np.zeros(unshimmed.shape + (len(slices),)) | |||
| print('The variable slices is as following: ' + str(slices)) # Currently the code works for --slice sequential shimming, but need to adapt it so that it also works for the --slices volume | |||
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| print('The variable slices is as following: ' + str(slices)) # Currently the code works for --slice sequential shimming, but need to adapt it so that it also works for the --slices volume |
Co-authored-by: Alex Dastous <47249340+po09i@users.noreply.github.com>
Co-authored-by: Alex Dastous <47249340+po09i@users.noreply.github.com>
Co-authored-by: Alex Dastous <47249340+po09i@users.noreply.github.com>
Co-authored-by: Alex Dastous <47249340+po09i@users.noreply.github.com>
Co-authored-by: Alex Dastous <47249340+po09i@users.noreply.github.com>
…ming-toolbox into YM/signal_recovery
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