Renaming: MATLAB names → Python names¶

The upstream MATLAB functions are prefixed with their author’s initials (bm for Bastien Milani, mle for Mauro Leidi, dh for Dominik Helbing). In Python they are named after what they do, following PEP 8:

the author prefix is removed (bmMathilda → mathilda, mleSiemensReader → SiemensReader);
functions are in snake_case (bmCoilSense_nonCart_data → coil_sense_non_cart_data), classes in CapWords (bmSparseMat → SparseMat), methods too (readRawData → read_raw_data);
a 2 between words means to (bmTraj2SparseMat → traj_to_sparse_mat); in n2u (non-uniform to uniform) and in dimensions (bmDFT2, _demons23) it stays;
the reconstruction methods keep their Monalisa names (mathilda, sensa, teva_morphosia_chain).

The names that depart from these rules are explained in the Note column. Functions live in subpackages by topic (monalisa.recon, monalisa.io, …) and are all available from the top-level package: monalisa.recon.mathilda is also monalisa.mathilda. In code, monalisa.find_function("bmMathilda") returns the Python function of a MATLAB name.

Not renamed, on purpose:

arguments, struct fields and object properties keep the MATLAB names (N_u, dK_u, nCh, acquisitionParams.nShot_off): they are the notation of the Monalisa papers and documentation, N_u and n_u are different quantities, and the fields are compared with the MATLAB recordings;
option values that MATLAB scripts pass as strings (sparseType='bmSparseMat', class_type='bmMriAcquisitionParam');
MATLAB recordings (fixtures/matlab/<scenario>/<MATLAB name>/) and the parity tolerances, which refer to the MATLAB functions.

Python-only public functions (no MATLAB counterpart in src/): monalisa.display.roipoly and poly2mask (as in MATLAB’s Image Processing Toolbox), monalisa.io.loadmat73 and savemat73 (MATLAB v7.3 files).

141 functions and classes:

`monalisa.array`¶

MATLAB	Upstream file	Python	Note
`bmBlockReshape`	src/arrayUtility/bmBlockReshape.m	`block_reshape`
`bmCell2Array`	src/arrayUtility/bmCell2Array.m	`cell_to_array`
`bmCol`	src/arrayUtility/bmCol.m	`col`
`bmColReshape`	src/arrayUtility/bmColReshape.m	`col_reshape`
`bmIndex2MultiIndex`	src/arrayUtility/bmIndex2MultiIndex.m	`index_to_multi_index`
`bmIsBlockShape`	src/arrayUtility/bmIsBlockShape.m	`is_block_shape`
`bmIsColShape`	src/arrayUtility/bmIsColShape.m	`is_col_shape`
`bmIsScalar`	src/arrayUtility/bmIsScalar.m	`is_scalar`
`bmPermuteToCol`	src/arrayUtility/bmPermuteToCol.m	`permute_to_col`
`bmPermuteToPoint`	src/arrayUtility/bmPermuteToPoint.m	`permute_to_point`
`bmPointReshape`	src/arrayUtility/bmPointReshape.m	`point_reshape`
`bmSingle`	src/arrayUtility/bmSingle.m	`to_single`	`single` would read as the NumPy type
`bmZero`	src/arrayUtility/bmZero.m	`zero`

`monalisa.binning`¶

MATLAB	Upstream file	Python
`bmMitosis`	src/arrayUtility/bmMitosis.m	`mitosis`
`bmMitosius_create`	src/mitosius/bmMitosius_create.m	`mitosius_create`
`bmMitosius_load`	src/mitosius/bmMitosius_load.m	`mitosius_load`

`monalisa.coil`¶

MATLAB	Upstream file	Python
`bmCoilSense_nonCart_data`	src/coilSense/nonCart/bmCoilSense_nonCart_data.m	`coil_sense_non_cart_data`
`bmCoilSense_nonCart_mask_automatic`	src/coilSense/nonCart/bmCoilSense_nonCart_mask_automatic.m	`coil_sense_non_cart_mask_automatic`
`bmCoilSense_nonCart_primary`	src/coilSense/nonCart/bmCoilSense_nonCart_primary.m	`coil_sense_non_cart_primary`
`bmCoilSense_nonCart_ref`	src/coilSense/nonCart/bmCoilSense_nonCart_ref.m	`coil_sense_non_cart_ref`
`bmCoilSense_nonCart_secondary`	src/coilSense/nonCart/bmCoilSense_nonCart_secondary.m	`coil_sense_non_cart_secondary`
`bmCoilSense_pinv`	src/coilSense/map/bmCoilSense_pinv.m	`coil_sense_pinv`
`detectROI`	src/coilSense/automatic/detectROI.m	`detect_roi`
`selectROI`	src/coilSense/automatic/selectROI.m	`select_roi`
`thresholdRMS_MIP`	src/coilSense/automatic/thresholdRMS_MIP.m	`threshold_rms_mip`

`monalisa.display`¶

MATLAB	Upstream file	Python	Note
`bmImage`	src/imDisp/bmImage.m	`show_image`	`image` is the subpackage `monalisa.image`; the function opens a viewer

`monalisa.fourier`¶

MATLAB	Upstream file	Python	Note
`bmK`	src/fourier123/prep_function/bmK.m	`deapodization`	one-letter name; K is the deapodization in the Monalisa notation
`bmDFT1`	src/fourier1/bmDFT1.m	`dft1`
`bmDFT1_conjTrans`	src/fourier1/bmDFT1_conjTrans.m	`dft1_conj_trans`
`bmDFT2`	src/fourier2/bmDFT2.m	`dft2`
`bmDFT2_conjTrans`	src/fourier2/bmDFT2_conjTrans.m	`dft2_conj_trans`
`bmDFT3`	src/fourier3/bmDFT3.m	`dft3`
`bmDFT3_conjTrans`	src/fourier3/bmDFT3_conjTrans.m	`dft3_conj_trans`
`bmFC`	src/fourier123/prep_function/bmFC.m	`fc`
`bmFC_conj`	src/fourier123/prep_function/bmFC_conj.m	`fc_conj`
`bmIDF`	src/fourierN/bmIDF.m	`idf`
`bmIDF1`	src/fourier1/bmIDF1.m	`idf1`
`bmIDF1_conjTrans`	src/fourier1/bmIDF1_conjTrans.m	`idf1_conj_trans`
`bmIDF2`	src/fourier2/bmIDF2.m	`idf2`
`bmIDF2_conjTrans`	src/fourier2/bmIDF2_conjTrans.m	`idf2_conj_trans`
`bmIDF3`	src/fourier3/bmIDF3.m	`idf3`
`bmIDF3_conjTrans`	src/fourier3/bmIDF3_conjTrans.m	`idf3_conj_trans`
`bmKF`	src/fourier123/prep_function/bmKF.m	`kf`
`bmKF_conj`	src/fourier123/prep_function/bmKF_conj.m	`kf_conj`
`bmNakatsha`	src/fourier123/map_function/nonCartesian/bmNakatsha.m	`nakatsha`
`bmNakatsha_MATLAB`	src/fourier123/map_function/nonCartesian/bmNakatsha_MATLAB.m	`nakatsha_matlab`
`bmShanna`	src/fourier123/map_function/nonCartesian/bmShanna.m	`shanna`
`bmShanna_MATLAB`	src/fourier123/map_function/nonCartesian/bmShanna_MATLAB.m	`shanna_matlab`

`monalisa.geometry`¶

MATLAB	Upstream file	Python
`bmVolumeElement`	src/geom123/bmVolumeElement.m	`volume_element`
`bmVolumeElement1`	src/geom1/bmVolumeElement1.m	`volume_element1`
`bmVolumeElement_cartesian2`	src/geom2/bmVolumeElement_cartesian2.m	`volume_element_cartesian2`
`bmVolumeElement_center_out_radial3`	src/geom3/bmVolumeElement_center_out_radial3.m	`volume_element_center_out_radial3`
`bmVolumeElement_full_radial3`	src/geom3/bmVolumeElement_full_radial3.m	`volume_element_full_radial3`
`bmVolumeElement_randomPartialCartesian2_x`	src/geom2/bmVolumeElement_randomPartialCartesian2_x.m	`volume_element_random_partial_cartesian2_x`
`bmVolumeElement_randomPartialCartesian3_x`	src/geom3/bmVolumeElement_randomPartialCartesian3_x.m	`volume_element_random_partial_cartesian3_x`
`bmVolumeElement_voronoi_box2`	src/geom2/bmVolumeElement_voronoi_box2.m	`volume_element_voronoi_box2`
`bmVolumeElement_voronoi_center_out_radial2`	src/geom2/bmVolumeElement_voronoi_center_out_radial2.m	`volume_element_voronoi_center_out_radial2`
`bmVolumeElement_voronoi_full_radial2`	src/geom2/bmVolumeElement_voronoi_full_radial2.m	`volume_element_voronoi_full_radial2`
`bmVolumeElement_voronoi_full_radial3`	src/geom3/bmVolumeElement_voronoi_full_radial3.m	`volume_element_voronoi_full_radial3`
`bmVoronoi`	src/geom123/bmVoronoi.m	`voronoi`

`monalisa.gridding`¶

MATLAB	Upstream file	Python
`bmGridder_n2u_leight`	src/gridding123/m/bmGridder_n2u_leight.m	`gridder_n2u_leight`
`bmImDeformField2SparseMat`	src/gridding123/m/bmImDeformField2SparseMat.m	`im_deform_field_to_sparse_mat`
`bmImDeformField2sparseMat_ind_weight`	src/gridding123/m/bmImDeformField2sparseMat_ind_weight.m	`im_deform_field_to_sparse_mat_ind_weight`
`bmTraj2SparseMat`	src/gridding123/m/bmTraj2SparseMat.m	`traj_to_sparse_mat`

`monalisa.image`¶

MATLAB	Upstream file	Python	Note
`bmImCrope`	src/image123/bmImCrope.m	`im_crop`	spelling
`bmImDeform`	src/image123/bmImDeform.m	`im_deform`
`bmImDeformField_hardThresholding2`	src/image2/m/bmImDeformField_hardThresholding2.m	`im_deform_field_hard_thresholding2`
`bmImDeformT`	src/image123/bmImDeformT.m	`im_deform_t`
`bmImDim`	src/imageN/bmImDim.m	`im_dim`
`bmImLaplaceEquationSolver`	src/image123/bmImLaplaceEquationSolver.m	`im_laplace_equation_solver`
`bmImLaplaceIterator`	src/image123/bmImLaplaceIterator.m	`im_laplace_iterator`
`bmImLaplacian`	src/image123/bmImLaplacian.m	`im_laplacian`
`bmImPseudoDiffusion`	src/image123/bmImPseudoDiffusion.m	`im_pseudo_diffusion`
`bmImPseudoDiffusion_inMask`	src/image123/bmImPseudoDiffusion_inMask.m	`im_pseudo_diffusion_in_mask`
`bmImReshape`	src/image123/bmImReshape.m	`im_reshape`
`bmImResize`	src/image123/bmImResize.m	`im_resize`
`bmImZeroFill`	src/image123/bmImZeroFill.m	`im_zero_fill`
`bmMIP`	src/imageN/bmMIP.m	`mip`
`bmRMS`	src/imageN/bmRMS.m	`rms`

`monalisa.io`¶

MATLAB	Upstream file	Python
`bmCheckDir`	src/readWrite/bmCheckDir.m	`check_dir`
`checkMetadataInteractive`	src/rawDataReader/checkMetadataInteractive.m	`check_metadata_interactive`
`correctMetadataInteractive`	src/rawDataReader/correctMetadataInteractive.m	`correct_metadata_interactive`
`bmCreateDir`	src/readWrite/bmCreateDir.m	`create_dir`
`createRawDataReader`	src/rawDataReader/createRawDataReader.m	`create_raw_data_reader`
`dhIsmrmrdReadMetaData`	src/rawDataReader/ismrmrd/dhIsmrmrdReadMetaData.m	`ismrmrd_read_meta_data`
`dhIsmrmrdReadRawData`	src/rawDataReader/ismrmrd/dhIsmrmrdReadRawData.m	`ismrmrd_read_raw_data`
`mleIsmrmrdReader`	src/rawDataReader/ismrmrd/mleIsmrmrdReader.m	`IsmrmrdReader`
`bmMriAcquisitionParam`	src/mriRecon/class/bmMriAcquisitionParam.m	`MriAcquisitionParam`
`mleRawDataReader`	src/rawDataReader/mleRawDataReader.m	`RawDataReader`
`dhSiemensReadMetaData`	src/rawDataReader/siemens/dhSiemensReadMetaData.m	`siemens_read_meta_data`
`bmSiemensReadRawData`	src/rawDataReader/siemens/bmSiemensReadRawData.m	`siemens_read_raw_data`
`mleSiemensReader`	src/rawDataReader/siemens/mleSiemensReader.m	`SiemensReader`

`monalisa.optim`¶

MATLAB	Upstream file	Python	Note
`bmAxpy`	src/mathOp/bmAxpy.m	`axpy`
`bmBackGradient`	src/optim/bmBackGradient.m	`back_gradient`
`bmBackGradient_n`	src/optim/bmBackGradient_n.m	`back_gradient_n`
`bmBackGradient_nT`	src/optim/bmBackGradient_nT.m	`back_gradient_n_t`
`bmBackGradientT`	src/optim/bmBackGradientT.m	`back_gradient_t`
`bmEuclideProd`	src/mathOp/bmEuclideProd.m	`euclidean_prod`	spelling
`bmInitialWitnessInfo`	src/optim/bmInitialWitnessInfo.m	`initial_witness_info`
`bmMinus`	src/mathOp/bmMinus.m	`minus`
`bmMult`	src/mathOp/bmMult.m	`mult`
`bmPlus`	src/mathOp/bmPlus.m	`plus`
`bmProx_oneNorm`	src/linSpace/bmProx_oneNorm.m	`prox_one_norm`
`bmSquaredNorm`	src/mathOp/bmSquaredNorm.m	`squared_norm`
`bmWitnessInfo`	src/optim/bmWitnessInfo.m	`WitnessInfo`
`bmY_norm`	src/linSpace/bmY_norm.m	`y_norm`
`bmY_ve_reshape`	src/linSpace/bmY_ve_reshape.m	`y_ve_reshape`

`monalisa.recon`¶

MATLAB	Upstream file	Python
`bmMathilda`	src/fourier123/map_function/nonCartesian/bmMathilda.m	`mathilda`
`bmNasha`	src/fourier123/map_function/nonCartesian/bmNasha.m	`nasha`
`bmSensa`	src/fourier123/solver_function/imDim/nonCartesian/bmSensa.m	`sensa`
`bmSensitivaMorphosia_chain`	src/fourier123/solver_function/imDim_morphosia/nonCartesian/bmSensitivaMorphosia_chain.m	`sensitiva_morphosia_chain`
`bmSleva`	src/fourier123/solver_function/imDim/nonCartesian/bmSleva.m	`sleva`
`bmSteva`	src/fourier123/solver_function/imDim/nonCartesian/bmSteva.m	`steva`
`bmTevaDuoMorphosia_chain`	src/fourier123/solver_function/imDim_morphosia/nonCartesian/bmTevaDuoMorphosia_chain.m	`teva_duo_morphosia_chain`
`bmTevaMorphosia_chain`	src/fourier123/solver_function/imDim_morphosia/nonCartesian/bmTevaMorphosia_chain.m	`teva_morphosia_chain`

`monalisa.registration`¶

MATLAB	Upstream file	Python	Note
`bmImDeformFieldChain_imRegDemons23`	src/imReg/m/bmImDeformFieldChain_imRegDemons23.m	`im_deform_field_chain_im_reg_demons23`
`bmImDeformFieldSheet_imRegDemons23`	src/imReg/m/bmImDeformFieldSheet_imRegDemons23.m	`im_deform_field_sheet_im_reg_demons23`

`monalisa.sparse`¶

MATLAB	Upstream file	Python	Note
`bmSparseMat_blockPartition`	src/sparseMat/m/bmSparseMat_blockPartition.m	`sparse_mat_block_partition`
`bmSparseMat_completeMatlabSparse`	src/sparseMat/m/bmSparseMat_completeMatlabSparse.m	`sparse_mat_complete_matlab_sparse`
`bmSparseMat_matlabSparse2bmSparseMat`	src/sparseMat/m/bmSparseMat_matlabSparse2bmSparseMat.m	`sparse_mat_from_matlab_sparse`	shorter, without the inner `bm`
`bmSparseMat_r_nJump2index`	src/sparseMat/m/bmSparseMat_r_nJump2index.m	`sparse_mat_r_n_jump_to_index`
`bmSparseMat_vec`	src/sparseMat/m/bmSparseMat_vec.m	`sparse_mat_vec`
`bmSparseMat`	src/sparseMat/m/bmSparseMat.m	`SparseMat`

`monalisa.trajectory`¶

MATLAB	Upstream file	Python	Note
`bmLowRes`	src/mriRecon/function/bmLowRes.m	`low_res`
`bmPhyllotaxisAngle3`	src/traj3/bmPhyllotaxisAngle3.m	`phyllotaxis_angle3`
`bmTraj`	src/trajN/bmTraj.m	`traj`
`bmTraj_formatTraj`	src/traj123/bmTraj_formatTraj.m	`traj_format`	word repeated
`bmTraj_fullRadial3_phyllotaxis_lineAssym2`	src/traj3/bmTraj_fullRadial3_phyllotaxis_lineAssym2.m	`traj_full_radial3_phyllotaxis_line_assym2`
`bmTraj_N_u_dK_u`	src/traj123/bmTraj_N_u_dK_u.m	`traj_grid`	returns `N_u` and `dK_u`, see the two lines above
`bmTraj_N_u`	src/traj123/bmTraj_N_u.m	`traj_grid_size`	`N_u` (grid size) and `n_u` (image size) differ only by case
`bmTraj_dK_u`	src/traj123/bmTraj_dK_u.m	`traj_grid_step`	`dK_u` (grid step) would become `d_k_u`
`bmTraj_lineDirection`	src/traj123/bmTraj_lineDirection.m	`traj_line_direction`
`bmTraj_lineReshape`	src/traj123/bmTraj_lineReshape.m	`traj_line_reshape`
`bmTraj_nLine`	src/traj123/bmTraj_nLine.m	`traj_n_line`
`bmTraj_norm`	src/traj123/bmTraj_norm.m	`traj_norm`
`bmTraj_squaredNorm`	src/traj123/bmTraj_squaredNorm.m	`traj_squared_norm`

`monalisa.util`¶

MATLAB	Upstream file	Python	Note
`bmVarargin_N_u_dK_u`	src/varargin/bmVarargin_N_u_dK_u.m	`default_grid`	default `N_u` and `dK_u` (guessed from the trajectory)
`bmVarargin_kernelType_nWin_kernelParam`	src/varargin/bmVarargin_kernelType_nWin_kernelParam.m	`default_kernel`	default `kernelType`, `nWin` and `kernelParam`
`bmVarargin_sparseType`	src/varargin/bmVarargin_sparseType.m	`default_sparse_type`	default `sparseType`
`bmTimeInSecond`	src/time/bmTimeInSecond.m	`time_in_second`
`bmVarargin`	src/varargin/bmVarargin.m	`varargin`

Methods¶

MATLAB	Python	Classes
`readMetaData`	`read_meta_data`	`RawDataReader`, `SiemensReader`, `IsmrmrdReader`
`readRawData`	`read_raw_data`	`RawDataReader`, `SiemensReader`, `IsmrmrdReader`

Renaming: MATLAB names → Python names¶

`monalisa.array`¶

`monalisa.binning`¶

`monalisa.coil`¶

`monalisa.display`¶

`monalisa.fourier`¶

`monalisa.geometry`¶

`monalisa.gridding`¶

`monalisa.image`¶

`monalisa.io`¶

`monalisa.optim`¶

`monalisa.recon`¶

`monalisa.registration`¶

`monalisa.sparse`¶

`monalisa.trajectory`¶

`monalisa.util`¶

Methods¶

Monalisa (Python)

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Related Topics

Renaming: MATLAB names → Python names¶

monalisa.array¶

monalisa.binning¶

monalisa.coil¶

monalisa.display¶

monalisa.fourier¶

monalisa.geometry¶

monalisa.gridding¶

monalisa.image¶

monalisa.io¶

monalisa.optim¶

monalisa.recon¶

monalisa.registration¶

monalisa.sparse¶

monalisa.trajectory¶

monalisa.util¶

Methods¶

`monalisa.array`¶

`monalisa.binning`¶

`monalisa.coil`¶

`monalisa.display`¶

`monalisa.fourier`¶

`monalisa.geometry`¶

`monalisa.gridding`¶

`monalisa.image`¶

`monalisa.io`¶

`monalisa.optim`¶

`monalisa.recon`¶

`monalisa.registration`¶

`monalisa.sparse`¶

`monalisa.trajectory`¶

`monalisa.util`¶