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:
MATLAB
Upstream file
Python
Note
bmBlockReshapesrc/arrayUtility/bmBlockReshape.m
block_reshape
bmCell2Arraysrc/arrayUtility/bmCell2Array.m
cell_to_array
bmColsrc/arrayUtility/bmCol.m
col
bmColReshapesrc/arrayUtility/bmColReshape.m
col_reshape
bmIndex2MultiIndexsrc/arrayUtility/bmIndex2MultiIndex.m
index_to_multi_index
bmIsBlockShapesrc/arrayUtility/bmIsBlockShape.m
is_block_shape
bmIsColShapesrc/arrayUtility/bmIsColShape.m
is_col_shape
bmIsScalarsrc/arrayUtility/bmIsScalar.m
is_scalar
bmPermuteToColsrc/arrayUtility/bmPermuteToCol.m
permute_to_col
bmPermuteToPointsrc/arrayUtility/bmPermuteToPoint.m
permute_to_point
bmPointReshapesrc/arrayUtility/bmPointReshape.m
point_reshape
bmSinglesrc/arrayUtility/bmSingle.m
to_singlesingle would read as the NumPy type
bmZerosrc/arrayUtility/bmZero.m
zero
MATLAB
Upstream file
Python
Note
bmMitosissrc/arrayUtility/bmMitosis.m
mitosis
bmMitosius_createsrc/mitosius/bmMitosius_create.m
mitosius_create
bmMitosius_loadsrc/mitosius/bmMitosius_load.m
mitosius_load
MATLAB
Upstream file
Python
Note
bmCoilSense_nonCart_datasrc/coilSense/nonCart/bmCoilSense_nonCart_data.m
coil_sense_non_cart_data
bmCoilSense_nonCart_mask_automaticsrc/coilSense/nonCart/bmCoilSense_nonCart_mask_automatic.m
coil_sense_non_cart_mask_automatic
bmCoilSense_nonCart_primarysrc/coilSense/nonCart/bmCoilSense_nonCart_primary.m
coil_sense_non_cart_primary
bmCoilSense_nonCart_refsrc/coilSense/nonCart/bmCoilSense_nonCart_ref.m
coil_sense_non_cart_ref
bmCoilSense_nonCart_secondarysrc/coilSense/nonCart/bmCoilSense_nonCart_secondary.m
coil_sense_non_cart_secondary
bmCoilSense_pinvsrc/coilSense/map/bmCoilSense_pinv.m
coil_sense_pinv
detectROIsrc/coilSense/automatic/detectROI.m
detect_roi
selectROIsrc/coilSense/automatic/selectROI.m
select_roi
thresholdRMS_MIPsrc/coilSense/automatic/thresholdRMS_MIP.m
threshold_rms_mip
MATLAB
Upstream file
Python
Note
bmImagesrc/imDisp/bmImage.m
show_imageimage is the subpackage monalisa.image; the function opens a viewer
MATLAB
Upstream file
Python
Note
bmKsrc/fourier123/prep_function/bmK.m
deapodizationone-letter name; K is the deapodization in the Monalisa notation
bmDFT1src/fourier1/bmDFT1.m
dft1
bmDFT1_conjTranssrc/fourier1/bmDFT1_conjTrans.m
dft1_conj_trans
bmDFT2src/fourier2/bmDFT2.m
dft2
bmDFT2_conjTranssrc/fourier2/bmDFT2_conjTrans.m
dft2_conj_trans
bmDFT3src/fourier3/bmDFT3.m
dft3
bmDFT3_conjTranssrc/fourier3/bmDFT3_conjTrans.m
dft3_conj_trans
bmFCsrc/fourier123/prep_function/bmFC.m
fc
bmFC_conjsrc/fourier123/prep_function/bmFC_conj.m
fc_conj
bmIDFsrc/fourierN/bmIDF.m
idf
bmIDF1src/fourier1/bmIDF1.m
idf1
bmIDF1_conjTranssrc/fourier1/bmIDF1_conjTrans.m
idf1_conj_trans
bmIDF2src/fourier2/bmIDF2.m
idf2
bmIDF2_conjTranssrc/fourier2/bmIDF2_conjTrans.m
idf2_conj_trans
bmIDF3src/fourier3/bmIDF3.m
idf3
bmIDF3_conjTranssrc/fourier3/bmIDF3_conjTrans.m
idf3_conj_trans
bmKFsrc/fourier123/prep_function/bmKF.m
kf
bmKF_conjsrc/fourier123/prep_function/bmKF_conj.m
kf_conj
bmNakatshasrc/fourier123/map_function/nonCartesian/bmNakatsha.m
nakatsha
bmNakatsha_MATLABsrc/fourier123/map_function/nonCartesian/bmNakatsha_MATLAB.m
nakatsha_matlab
bmShannasrc/fourier123/map_function/nonCartesian/bmShanna.m
shanna
bmShanna_MATLABsrc/fourier123/map_function/nonCartesian/bmShanna_MATLAB.m
shanna_matlab
MATLAB
Upstream file
Python
Note
bmVolumeElementsrc/geom123/bmVolumeElement.m
volume_element
bmVolumeElement1src/geom1/bmVolumeElement1.m
volume_element1
bmVolumeElement_cartesian2src/geom2/bmVolumeElement_cartesian2.m
volume_element_cartesian2
bmVolumeElement_center_out_radial3src/geom3/bmVolumeElement_center_out_radial3.m
volume_element_center_out_radial3
bmVolumeElement_full_radial3src/geom3/bmVolumeElement_full_radial3.m
volume_element_full_radial3
bmVolumeElement_randomPartialCartesian2_xsrc/geom2/bmVolumeElement_randomPartialCartesian2_x.m
volume_element_random_partial_cartesian2_x
bmVolumeElement_randomPartialCartesian3_xsrc/geom3/bmVolumeElement_randomPartialCartesian3_x.m
volume_element_random_partial_cartesian3_x
bmVolumeElement_voronoi_box2src/geom2/bmVolumeElement_voronoi_box2.m
volume_element_voronoi_box2
bmVolumeElement_voronoi_center_out_radial2src/geom2/bmVolumeElement_voronoi_center_out_radial2.m
volume_element_voronoi_center_out_radial2
bmVolumeElement_voronoi_full_radial2src/geom2/bmVolumeElement_voronoi_full_radial2.m
volume_element_voronoi_full_radial2
bmVolumeElement_voronoi_full_radial3src/geom3/bmVolumeElement_voronoi_full_radial3.m
volume_element_voronoi_full_radial3
bmVoronoisrc/geom123/bmVoronoi.m
voronoi
MATLAB
Upstream file
Python
Note
bmGridder_n2u_leightsrc/gridding123/m/bmGridder_n2u_leight.m
gridder_n2u_leight
bmImDeformField2SparseMatsrc/gridding123/m/bmImDeformField2SparseMat.m
im_deform_field_to_sparse_mat
bmImDeformField2sparseMat_ind_weightsrc/gridding123/m/bmImDeformField2sparseMat_ind_weight.m
im_deform_field_to_sparse_mat_ind_weight
bmTraj2SparseMatsrc/gridding123/m/bmTraj2SparseMat.m
traj_to_sparse_mat
MATLAB
Upstream file
Python
Note
bmImCropesrc/image123/bmImCrope.m
im_cropspelling
bmImDeformsrc/image123/bmImDeform.m
im_deform
bmImDeformField_hardThresholding2src/image2/m/bmImDeformField_hardThresholding2.m
im_deform_field_hard_thresholding2
bmImDeformTsrc/image123/bmImDeformT.m
im_deform_t
bmImDimsrc/imageN/bmImDim.m
im_dim
bmImLaplaceEquationSolversrc/image123/bmImLaplaceEquationSolver.m
im_laplace_equation_solver
bmImLaplaceIteratorsrc/image123/bmImLaplaceIterator.m
im_laplace_iterator
bmImLaplaciansrc/image123/bmImLaplacian.m
im_laplacian
bmImPseudoDiffusionsrc/image123/bmImPseudoDiffusion.m
im_pseudo_diffusion
bmImPseudoDiffusion_inMasksrc/image123/bmImPseudoDiffusion_inMask.m
im_pseudo_diffusion_in_mask
bmImReshapesrc/image123/bmImReshape.m
im_reshape
bmImResizesrc/image123/bmImResize.m
im_resize
bmImZeroFillsrc/image123/bmImZeroFill.m
im_zero_fill
bmMIPsrc/imageN/bmMIP.m
mip
bmRMSsrc/imageN/bmRMS.m
rms
MATLAB
Upstream file
Python
Note
bmCheckDirsrc/readWrite/bmCheckDir.m
check_dir
checkMetadataInteractivesrc/rawDataReader/checkMetadataInteractive.m
check_metadata_interactive
correctMetadataInteractivesrc/rawDataReader/correctMetadataInteractive.m
correct_metadata_interactive
bmCreateDirsrc/readWrite/bmCreateDir.m
create_dir
createRawDataReadersrc/rawDataReader/createRawDataReader.m
create_raw_data_reader
dhIsmrmrdReadMetaDatasrc/rawDataReader/ismrmrd/dhIsmrmrdReadMetaData.m
ismrmrd_read_meta_data
dhIsmrmrdReadRawDatasrc/rawDataReader/ismrmrd/dhIsmrmrdReadRawData.m
ismrmrd_read_raw_data
mleIsmrmrdReadersrc/rawDataReader/ismrmrd/mleIsmrmrdReader.m
IsmrmrdReader
bmMriAcquisitionParamsrc/mriRecon/class/bmMriAcquisitionParam.m
MriAcquisitionParam
mleRawDataReadersrc/rawDataReader/mleRawDataReader.m
RawDataReader
dhSiemensReadMetaDatasrc/rawDataReader/siemens/dhSiemensReadMetaData.m
siemens_read_meta_data
bmSiemensReadRawDatasrc/rawDataReader/siemens/bmSiemensReadRawData.m
siemens_read_raw_data
mleSiemensReadersrc/rawDataReader/siemens/mleSiemensReader.m
SiemensReader
MATLAB
Upstream file
Python
Note
bmAxpysrc/mathOp/bmAxpy.m
axpy
bmBackGradientsrc/optim/bmBackGradient.m
back_gradient
bmBackGradient_nsrc/optim/bmBackGradient_n.m
back_gradient_n
bmBackGradient_nTsrc/optim/bmBackGradient_nT.m
back_gradient_n_t
bmBackGradientTsrc/optim/bmBackGradientT.m
back_gradient_t
bmEuclideProdsrc/mathOp/bmEuclideProd.m
euclidean_prodspelling
bmInitialWitnessInfosrc/optim/bmInitialWitnessInfo.m
initial_witness_info
bmMinussrc/mathOp/bmMinus.m
minus
bmMultsrc/mathOp/bmMult.m
mult
bmPlussrc/mathOp/bmPlus.m
plus
bmProx_oneNormsrc/linSpace/bmProx_oneNorm.m
prox_one_norm
bmSquaredNormsrc/mathOp/bmSquaredNorm.m
squared_norm
bmWitnessInfosrc/optim/bmWitnessInfo.m
WitnessInfo
bmY_normsrc/linSpace/bmY_norm.m
y_norm
bmY_ve_reshapesrc/linSpace/bmY_ve_reshape.m
y_ve_reshape
MATLAB
Upstream file
Python
Note
bmMathildasrc/fourier123/map_function/nonCartesian/bmMathilda.m
mathilda
bmNashasrc/fourier123/map_function/nonCartesian/bmNasha.m
nasha
bmSensasrc/fourier123/solver_function/imDim/nonCartesian/bmSensa.m
sensa
bmSensitivaMorphosia_chainsrc/fourier123/solver_function/imDim_morphosia/nonCartesian/bmSensitivaMorphosia_chain.m
sensitiva_morphosia_chain
bmSlevasrc/fourier123/solver_function/imDim/nonCartesian/bmSleva.m
sleva
bmStevasrc/fourier123/solver_function/imDim/nonCartesian/bmSteva.m
steva
bmTevaDuoMorphosia_chainsrc/fourier123/solver_function/imDim_morphosia/nonCartesian/bmTevaDuoMorphosia_chain.m
teva_duo_morphosia_chain
bmTevaMorphosia_chainsrc/fourier123/solver_function/imDim_morphosia/nonCartesian/bmTevaMorphosia_chain.m
teva_morphosia_chain
MATLAB
Upstream file
Python
Note
bmImDeformFieldChain_imRegDemons23src/imReg/m/bmImDeformFieldChain_imRegDemons23.m
im_deform_field_chain_im_reg_demons23
bmImDeformFieldSheet_imRegDemons23src/imReg/m/bmImDeformFieldSheet_imRegDemons23.m
im_deform_field_sheet_im_reg_demons23
MATLAB
Upstream file
Python
Note
bmSparseMat_blockPartitionsrc/sparseMat/m/bmSparseMat_blockPartition.m
sparse_mat_block_partition
bmSparseMat_completeMatlabSparsesrc/sparseMat/m/bmSparseMat_completeMatlabSparse.m
sparse_mat_complete_matlab_sparse
bmSparseMat_matlabSparse2bmSparseMatsrc/sparseMat/m/bmSparseMat_matlabSparse2bmSparseMat.m
sparse_mat_from_matlab_sparseshorter, without the inner bm
bmSparseMat_r_nJump2indexsrc/sparseMat/m/bmSparseMat_r_nJump2index.m
sparse_mat_r_n_jump_to_index
bmSparseMat_vecsrc/sparseMat/m/bmSparseMat_vec.m
sparse_mat_vec
bmSparseMatsrc/sparseMat/m/bmSparseMat.m
SparseMat
MATLAB
Upstream file
Python
Note
bmLowRessrc/mriRecon/function/bmLowRes.m
low_res
bmPhyllotaxisAngle3src/traj3/bmPhyllotaxisAngle3.m
phyllotaxis_angle3
bmTrajsrc/trajN/bmTraj.m
traj
bmTraj_formatTrajsrc/traj123/bmTraj_formatTraj.m
traj_formatword repeated
bmTraj_fullRadial3_phyllotaxis_lineAssym2src/traj3/bmTraj_fullRadial3_phyllotaxis_lineAssym2.m
traj_full_radial3_phyllotaxis_line_assym2
bmTraj_N_u_dK_usrc/traj123/bmTraj_N_u_dK_u.m
traj_gridreturns N_u and dK_u, see the two lines above
bmTraj_N_usrc/traj123/bmTraj_N_u.m
traj_grid_sizeN_u (grid size) and n_u (image size) differ only by case
bmTraj_dK_usrc/traj123/bmTraj_dK_u.m
traj_grid_stepdK_u (grid step) would become d_k_u
bmTraj_lineDirectionsrc/traj123/bmTraj_lineDirection.m
traj_line_direction
bmTraj_lineReshapesrc/traj123/bmTraj_lineReshape.m
traj_line_reshape
bmTraj_nLinesrc/traj123/bmTraj_nLine.m
traj_n_line
bmTraj_normsrc/traj123/bmTraj_norm.m
traj_norm
bmTraj_squaredNormsrc/traj123/bmTraj_squaredNorm.m
traj_squared_norm
MATLAB
Upstream file
Python
Note
bmVarargin_N_u_dK_usrc/varargin/bmVarargin_N_u_dK_u.m
default_griddefault N_u and dK_u (guessed from the trajectory)
bmVarargin_kernelType_nWin_kernelParamsrc/varargin/bmVarargin_kernelType_nWin_kernelParam.m
default_kerneldefault kernelType, nWin and kernelParam
bmVarargin_sparseTypesrc/varargin/bmVarargin_sparseType.m
default_sparse_typedefault sparseType
bmTimeInSecondsrc/time/bmTimeInSecond.m
time_in_second
bmVararginsrc/varargin/bmVarargin.m
varargin
MATLAB
Python
Classes
readMetaDataread_meta_dataRawDataReader, SiemensReader, IsmrmrdReader
readRawDataread_raw_dataRawDataReader, SiemensReader, IsmrmrdReader