Add Density Compensation Algorithms #2
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There are some support for density now, using the fork (https://github.com/chaithyagr/finufft), and hopefully will be merged in flatironinstitute/finufft#308 |
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* fix typoes (off_resonnance -> off_resonance) * feat: add field interpolators calculation (#124) This add "get_interpolators_from_fieldmap", supporting both real (B0 map only) and complex (Zmap = R2* + 1j * B0map) fields in arbitrary dimension (2D and 3D). The routine supports both numpy / cupy arrays and torch tensors on CPU and GPU, the latter requiring cupy due to limitations in torch.histogram / torch.histogramdd (pytorch/pytorch#69519). Calculation uses time segmentation with uniform time samples and LS coefficients (using histogram). Based on MIRT (https://github.com/JeffFessler/mirt/blob/main/mri/mri_exp_approx.m) and its Python porting from MIRTORCH (https://github.com/guanhuaw/MIRTorch/blob/master/mirtorch/linear/mri.py) and SigPy (https://github.com/mikgroup/sigpy/blob/main/sigpy/mri/util.py). * feat: field interpolator estimation in MRIFourierCorrected constructor. In addition, add off-resonance example. * feat: set autograd_available based on base FourierOperator * Update test_offres_exp_approx.py Avoid torch cuda test case if cupy is not available. * Update src/mrinufft/operators/off_resonance.py remove deprecated get_grad Co-authored-by: Chaithya G R <[email protected]> * address pr review * remove phantominator * remove duplicated example and replacing subject in example_offres * address PR rev #2 * \!docs_build and fix on \!style * \!docs_build * skip field coefficient gpu test case if cupy not available * \!docs_build fix gpuNUFFT * Update src/mrinufft/operators/off_resonance.py Co-authored-by: Guillaume Daval-Frérot <[email protected]> * Update src/mrinufft/operators/off_resonance.py Co-authored-by: Guillaume Daval-Frérot <[email protected]> * \!docs_build gpunufft * Update src/mrinufft/operators/off_resonance.py Co-authored-by: Guillaume Daval-Frérot <[email protected]> * Update src/mrinufft/operators/off_resonance.py Co-authored-by: Guillaume Daval-Frérot <[email protected]> * address PR rev 3 * Update pyproject.toml * Update src/mrinufft/operators/off_resonance.py Co-authored-by: Guillaume Daval-Frérot <[email protected]> * \![docs_build] * temp, \![docs_build] fix * fix cufinufft, \!docs_build fix --------- Co-authored-by: Chaithya G R <[email protected]> Co-authored-by: Guillaume Daval-Frérot <[email protected]>
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* fix typoes (off_resonnance -> off_resonance) * feat: add field interpolators calculation (#124) This add "get_interpolators_from_fieldmap", supporting both real (B0 map only) and complex (Zmap = R2* + 1j * B0map) fields in arbitrary dimension (2D and 3D). The routine supports both numpy / cupy arrays and torch tensors on CPU and GPU, the latter requiring cupy due to limitations in torch.histogram / torch.histogramdd (pytorch/pytorch#69519). Calculation uses time segmentation with uniform time samples and LS coefficients (using histogram). Based on MIRT (https://github.com/JeffFessler/mirt/blob/main/mri/mri_exp_approx.m) and its Python porting from MIRTORCH (https://github.com/guanhuaw/MIRTorch/blob/master/mirtorch/linear/mri.py) and SigPy (https://github.com/mikgroup/sigpy/blob/main/sigpy/mri/util.py). * feat: field interpolator estimation in MRIFourierCorrected constructor. In addition, add off-resonance example. * feat: set autograd_available based on base FourierOperator * Update test_offres_exp_approx.py Avoid torch cuda test case if cupy is not available. * Update src/mrinufft/operators/off_resonance.py remove deprecated get_grad Co-authored-by: Chaithya G R <[email protected]> * address pr review * remove phantominator * remove duplicated example and replacing subject in example_offres * address PR rev #2 * \!docs_build and fix on \!style * \!docs_build * enhancement: refactor with_* decorator to support standalone functions. * skip field coefficient gpu test case if cupy not available * \!docs_build fix gpuNUFFT * Update src/mrinufft/operators/off_resonance.py Co-authored-by: Guillaume Daval-Frérot <[email protected]> * Update src/mrinufft/operators/off_resonance.py Co-authored-by: Guillaume Daval-Frérot <[email protected]> * \!docs_build gpunufft * Update src/mrinufft/operators/off_resonance.py Co-authored-by: Guillaume Daval-Frérot <[email protected]> * Update src/mrinufft/operators/off_resonance.py Co-authored-by: Guillaume Daval-Frérot <[email protected]> * address PR rev 3 * sync with off_resonance PR rev * feat: handle kwargs only input. * fix: decorators now working if required_grad is True * sync with master * Update src/mrinufft/operators/base.py Co-authored-by: Pierre-Antoine Comby <[email protected]> * refactor: array interface conversion in separate module. * lint tfnufft * remove print statements * Update src/mrinufft/_array_compat.py Co-authored-by: Pierre-Antoine Comby <[email protected]> * Update src/mrinufft/_array_compat.py Co-authored-by: Pierre-Antoine Comby <[email protected]> * Update src/mrinufft/_array_compat.py Co-authored-by: Pierre-Antoine Comby <[email protected]> * enhance: handle kwargs and (nested) tuple/lists of arraylike arguments. * update base.py * Update src/mrinufft/_array_compat.py Co-authored-by: Pierre-Antoine Comby <[email protected]> * apply suggested refactor to each decorator. --------- Co-authored-by: Chaithya G R <[email protected]> Co-authored-by: Guillaume Daval-Frérot <[email protected]> Co-authored-by: Pierre-Antoine Comby <[email protected]>
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The density compensation vector can be estimated using several methods:
A good list of methods is provided by Jeff Fessler: https://web.eecs.umich.edu/~fessler/book/c-four.pdf , section 6.4.2
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