classdef us_phantom < handle %-- Class defining a standard way to generate numerical phantom in %-- ultrasound %-- Authors: Olivier Bernard (olivier.bernard@creatis.insa-lyon.fr) %-- Alfonso Rodriguez-Molares (alfonso.r.molares@ntnu.no) %------------------------------------------------------ %------------------------------------------------------ %-- Class attributes properties (SetAccess = public) %-- administration name %-- String containing the name of the us_field_simulation author %-- String containing the name of the author(s) of the beamformed image affiliation %-- String containing the affiliation of the author(s) of the beamformed image creation_date %-- String containing the date the reconstruction was created %-- Common attributes N_scatterers amp sca xLimits zLimits bckDensity %-- Occlusion attributes occlusionCenterX occlusionCenterZ occlusionDiameter %-- Region to check speckle attributes RoiCenterX RoiCenterZ RoiPsfTimeX RoiPsfTimeZ %-- Point scatterers xPts zPts %-- system resolution (needed to fix the number of scatterers) axialResolution lateralResolution end %-- data properties (SetAccess = private) mode end %------------------------------------------------------ %------------------------------------------------------ %-- Class methods %-- Constructor methods (Access = public) function h = us_phantom(input_name) %-- Constructor of the US_PHANTOM class. %-- Syntax: %-- US_PHANTOM(name) %-- name: Name of the reconstruction if exist('input_name') h.name= input_name; else h.name = ' '; end h.creation_date = sprintf('%d/%02d/%d %02d:%02d:%02.2f',clock); h.author = ' '; h.affiliation = ' '; h.xLimits = 0; h.zLimits = 0; h.bckDensity = 20; h.occlusionCenterX = 0; h.occlusionCenterZ = 0; h.occlusionDiameter = 0; h.RoiCenterX = 0; h.RoiCenterZ = 0; h.RoiPsfTimeX = 0; h.RoiPsfTimeZ = 0; h.mode = 0; h.xPts = 0; h.zPts = 20e-3; h.axialResolution = 0.45e-3; h.lateralResolution = 0.45e-3; end end %-- set methods, input format check methods %-- name function set.name(h,input) assert(isstr(input), 'Wrong format of the beamformed data name. It should be a string.'); h.name = input; end %-- author function set.author(h,input) assert(isstr(input), 'Wrong format of the author. It should be a string.'); h.author = input; end %-- affiliation function set.affiliation(h,input) assert(isstr(input), 'Wrong format of the affiliation. It should be a string.'); h.affiliation = input; end %-- creation_date function set.creation_date(h,input_date) assert(isstr(input_date), 'Wrong format of the creation date. It should be a string.'); h.creation_date = input_date; end %-- xPts function set.xPts(h,input_xPts) assert(isnumeric(input_xPts), 'Wrong format of the x-axis point scatterers xPts. It should be a numeric vector in (m)'); h.xPts = input_xPts; end %-- zPts function set.zPts(h,input_zPts) assert(isnumeric(input_zPts), 'Wrong format of the x-axis point scatterers zPts. It should be a numeric vector in (m)'); h.zPts = input_zPts; end %-- xLimits function set.xLimits(h,input_xLimits) assert(isnumeric(input_xLimits), 'Wrong format of the x-axis limits xLimits. It should be a numeric vector in (m)'); h.xLimits = input_xLimits; end %-- zLimits function set.zLimits(h,input_zLimits) assert(isnumeric(input_zLimits), 'Wrong format of the z-axis limits xLimits. It should be a numeric vector in (m)'); h.zLimits = input_zLimits; end %-- background density function set.bckDensity(h,input_bckDensity) assert(numel(input_bckDensity)==1&&isnumeric(input_bckDensity), 'Wrong format of the background density bckDensity. It should be a numeric scalar'); h.bckDensity = input_bckDensity; end %-- occlusion center X function set.occlusionCenterX(h,input) assert(isnumeric(input), 'Wrong format of the occlusion center occlusionCenterX. It should be a numeric vector in (m)'); h.occlusionCenterX = input; end %-- occlusion center Z function set.occlusionCenterZ(h,input) assert(isnumeric(input), 'Wrong format of the occlusion center occlusionCenterZ. It should be a numeric vector in (m)'); h.occlusionCenterZ = input; end %-- occlusion diameter function set.occlusionDiameter(h,input) assert(isnumeric(input), 'Wrong format of the occlusion diameter occlusion. It should be a numeric vector in (m)'); h.occlusionDiameter = input; end %-- RoiCenterX function set.RoiCenterX(h,input) assert(isnumeric(input), 'Wrong format of the ROI center RoiCenterX. It should be a numeric vector in (m)'); h.RoiCenterX = input; end %-- RoiCenterZ function set.RoiCenterZ(h,input) assert(isnumeric(input), 'Wrong format of the ROI center RoiCenterZ. It should be a numeric vector in (m)'); h.RoiCenterZ = input; end %-- RoiPsfTimeX function set.RoiPsfTimeX(h,input) assert(isnumeric(input), 'Wrong format of the ROI psf times RoiPsfTimeX. It should be a numeric vector in (m)'); h.RoiPsfTimeX = input; end %-- RoiPsfTimeZ function set.RoiPsfTimeZ(h,input) assert(isnumeric(input), 'Wrong format of the ROI psf times RoiPsfTimeZ. It should be a numeric vector in (m)'); h.RoiPsfTimeZ = input; end %-- axial resolution of the system function set.axialResolution(h,input) assert(numel(input)==1&&isnumeric(input), 'Wrong format of the axial resolution value. It should be a numeric scalar in (m)'); h.axialResolution = input; end %-- lateral resolution of the system function set.lateralResolution(h,input) assert(numel(input)==1&&isnumeric(input), 'Wrong format of the lateral resolution value. It should be a numeric scalar in (m)'); h.lateralResolution = input; end end %-- Main method call to generate phantom methods (Access = public) function setPtsScatterersMode(h) h.mode = 0; end function setOcclusionMode(h) h.mode = 1; end function generate(h) switch (h.mode) case 0 h.generatePtsScatterersPht(); case 1 h.generateOcclusionPht(); end end function read_file(h,filename) %-- Reads all the information from a mat or hdf5 file %-- Syntax: %-- read_file(file_name) %-- file_name: Name of the mat or hdf5 file [pathstr, name, ext] = fileparts(filename); switch ext case '.mat' h.read_file_mat(filename); case '.hdf5' h.read_file_hdf5(filename); otherwise error('Unknown signal format!'); end end function write_file(h,filename) %-- Write all the information into a mat or hdf5 file %-- Syntax: %-- write_file(file_name) %-- file_name: Name of the mat or hdf5 file [pathstr, name, ext] = fileparts(filename); switch ext case '.mat' h.write_file_mat(filename); case '.hdf5' h.write_file_hdf5(filename); otherwise error('Unknown signal format!'); end end %-- HDF5 Ultrasound File Format function write_file_hdf5(h,filename) %-- write HDF5 version in the root group attr_details.Name = 'version'; attr_details.AttachedTo = '/'; attr_details.AttachType = 'group'; hdf5write(filename, attr_details, 'v.0.0.39'); %-- We create the /US metagroup in case it is not there try h5info(filename,'/US') catch fid = H5F.open(filename,'H5F_ACC_RDWR','H5P_DEFAULT'); gid = H5G.create(fid,'US','H5P_DEFAULT','H5P_DEFAULT','H5P_DEFAULT'); H5G.close(gid); H5F.close(fid); end %-- We create a unique us_dataset group group_name='US_DATASET0000'; fid = H5F.open(filename,'H5F_ACC_RDWR','H5P_DEFAULT'); gid = H5G.open(fid,'/US'); s_gid = H5G.create(gid,group_name,'H5P_DEFAULT','H5P_DEFAULT','H5P_DEFAULT'); H5G.close(s_gid); H5G.close(gid); H5F.close(fid); location = ['/US/' group_name]; %-- Attributes %-- Dataset type file = H5F.open(filename,'H5F_ACC_RDWR','H5P_DEFAULT'); filetype = H5T.enum_create ('H5T_NATIVE_INT'); H5T.enum_insert (filetype, 'US', 0); H5T.enum_insert (filetype, 'SR', 1); gid = H5G.open(file,location); space = H5S.create_simple (1,1,[]); attr = H5A.create (gid, 'type', filetype, space, 'H5P_DEFAULT'); H5A.write(attr, filetype, uint32(0)); % <--- US H5A.close(attr); H5G.close(gid); H5S.close(space); H5T.close(filetype); H5F.close(file); %-- us_dataset subtype file = H5F.open(filename,'H5F_ACC_RDWR','H5P_DEFAULT'); filetype = H5T.enum_create ('H5T_NATIVE_INT'); H5T.enum_insert(filetype, 'STA', 0); H5T.enum_insert(filetype, 'CPW', 1); H5T.enum_insert(filetype, 'VS', 2); H5T.enum_insert(filetype, 'BS', 3); gid = H5G.open(file,location); space = H5S.create_simple (1,1,[]); attr = H5A.create(gid, 'subtype', filetype, space, 'H5P_DEFAULT'); H5A.write(attr, filetype, uint32(1)); % <---- TYPE CPWC %-- Signal format file = H5F.open(filename,'H5F_ACC_RDWR','H5P_DEFAULT'); filetype = H5T.enum_create ('H5T_NATIVE_INT'); H5T.enum_insert (filetype, 'RF', 0); H5T.enum_insert (filetype, 'IQ', 1); gid = H5G.open(file,location); space = H5S.create_simple (1,1,[]); attr = H5A.create (gid, 'signal_format', filetype, space, 'H5P_DEFAULT'); H5A.write(attr, filetype, uint32(1)); % <--- IQ H5A.close(attr); H5G.close(gid); H5S.close(space); H5T.close(filetype); H5F.close(file); %-- add name attr_details.Name = 'name'; attr_details.AttachedTo = location; attr_details.AttachType = 'group'; hdf5write(filename, attr_details, h.name, 'WriteMode', 'append'); %-- add author attr_details.Name = 'author'; attr_details.AttachedTo = location; attr_details.AttachType = 'group'; hdf5write(filename, attr_details, h.author, 'WriteMode', 'append'); %-- add affiliation attr_details.Name = 'affiliation'; attr_details.AttachedTo = location; attr_details.AttachType = 'group'; hdf5write(filename, attr_details, h.affiliation, 'WriteMode', 'append'); %-- add date attr_details.Name = 'creation_date'; attr_details.AttachedTo = location; attr_details.AttachType = 'group'; hdf5write(filename, attr_details, h.creation_date, 'WriteMode', 'append'); %-- Data %-- Common attributes dset_details.Location = location; dset_details.Name = 'nb_scatterers'; hdf5write(filename, dset_details, single(h.N_scatterers), 'WriteMode', 'append'); %-- dset_details.Location = location; dset_details.Name = 'scatterers_amplitude'; hdf5write(filename, dset_details, single(h.amp), 'WriteMode', 'append'); %-- dset_details.Location = location; dset_details.Name = 'scatterers_positions'; hdf5write(filename, dset_details, single(h.sca), 'WriteMode', 'append'); %-- dset_details.Location = location; dset_details.Name = 'phantom_xLimits'; hdf5write(filename, dset_details, single(h.xLimits), 'WriteMode', 'append'); %-- dset_details.Location = location; dset_details.Name = 'phantom_zLimits'; hdf5write(filename, dset_details, single(h.zLimits), 'WriteMode', 'append'); %-- dset_details.Location = location; dset_details.Name = 'phantom_bckDensity'; hdf5write(filename, dset_details, single(h.bckDensity), 'WriteMode', 'append'); %-- Occlusion attributes dset_details.Location = location; dset_details.Name = 'phantom_occlusionCenterX'; hdf5write(filename, dset_details, single(h.occlusionCenterX), 'WriteMode', 'append'); %-- dset_details.Location = location; dset_details.Name = 'phantom_occlusionCenterZ'; hdf5write(filename, dset_details, single(h.occlusionCenterZ), 'WriteMode', 'append'); %-- dset_details.Location = location; dset_details.Name = 'phantom_occlusionDiameter'; hdf5write(filename, dset_details, single(h.occlusionDiameter), 'WriteMode', 'append'); %-- Roi attributes dset_details.Location = location; dset_details.Name = 'phantom_RoiCenterX'; hdf5write(filename, dset_details, single(h.RoiCenterX), 'WriteMode', 'append'); %-- dset_details.Location = location; dset_details.Name = 'phantom_RoiCenterZ'; hdf5write(filename, dset_details, single(h.RoiCenterZ), 'WriteMode', 'append'); %-- dset_details.Location = location; dset_details.Name = 'phantom_RoiPsfTimeX'; hdf5write(filename, dset_details, single(h.RoiPsfTimeX), 'WriteMode', 'append'); %-- dset_details.Location = location; dset_details.Name = 'phantom_RoiPsfTimeZ'; hdf5write(filename, dset_details, single(h.RoiPsfTimeZ), 'WriteMode', 'append'); %-- Point scatterers dset_details.Location = location; dset_details.Name = 'phantom_xPts'; hdf5write(filename, dset_details, single(h.xPts), 'WriteMode', 'append'); %-- dset_details.Location = location; dset_details.Name = 'phantom_zPts'; hdf5write(filename, dset_details, single(h.zPts), 'WriteMode', 'append'); %-- System resolution %-- Axial dset_details.Location = location; dset_details.Name = 'phantom_axialResolution'; hdf5write(filename, dset_details, single(h.axialResolution), 'WriteMode', 'append'); %-- Lateral dset_details.Location = location; dset_details.Name = 'phantom_lateralResolution'; hdf5write(filename, dset_details, single(h.lateralResolution), 'WriteMode', 'append'); end function read_file_hdf5(h,filename) %-- read US metagroup info=h5info(filename,'/US'); %-- read the groups in the metagroup for n=1:length(info.Groups) location=info.Groups(n).Name; dstype=h5readatt(filename,location,'type'); if strcmp(dstype,'US') subtype=h5readatt(filename,location,'subtype'); if strcmp(subtype{1},'CPW') %-- Attributes %-- read name a=h5readatt(filename,location,'name'); h.name = a{1}(1:end-1); %-- read author a = h5readatt(filename,location,'author'); h.author = a{1}(1:end-1); %-- read affiliation a = h5readatt(filename,location,'affiliation'); h.affiliation = a{1}(1:end-1); %-- read date a = h5readatt(filename,location,'creation_date'); h.creation_date = a{1}(1:end-1); %-- Data %-- read N_scatterers h.N_scatterers = h5read(filename,[location '/nb_scatterers']); %-- read scatterers_amplitude h.amp = h5read(filename,[location '/scatterers_amplitude']); h.amp = double(h.amp); %-- read scatterers_amplitude h.sca = h5read(filename,[location '/scatterers_positions']); h.sca = double(h.sca); if ( (size(h.sca,1)==3) && (size(h.sca,2)==1) ) h.sca = h.sca'; end %-- read scatterers_amplitude h.xLimits = h5read(filename,[location '/phantom_xLimits']); %-- read scatterers_amplitude h.zLimits = h5read(filename,[location '/phantom_zLimits']); %-- read scatterers_amplitude h.bckDensity = h5read(filename,[location '/phantom_bckDensity']); %-- read phantom_occlusionCenterX h.occlusionCenterX = h5read(filename,[location '/phantom_occlusionCenterX']); %-- read phantom_occlusionCenterZ h.occlusionCenterZ = h5read(filename,[location '/phantom_occlusionCenterZ']); %-- read phantom_occlusionDiameter h.occlusionDiameter = h5read(filename,[location '/phantom_occlusionDiameter']); %-- read phantom_RoiCenterX h.RoiCenterX = h5read(filename,[location '/phantom_RoiCenterX']); %-- read phantom_RoiCenterZ h.RoiCenterZ = h5read(filename,[location '/phantom_RoiCenterZ']); %-- read phantom_RoiPsfTimeX h.RoiPsfTimeX = h5read(filename,[location '/phantom_RoiPsfTimeX']); %-- read phantom_RoiPsfTimeZ h.RoiPsfTimeZ = h5read(filename,[location '/phantom_RoiPsfTimeZ']); %-- read phantom_xPts h.xPts = h5read(filename,[location '/phantom_xPts']); %-- read phantom_zPts h.zPts = h5read(filename,[location '/phantom_zPts']); %-- read axial resolution h.axialResolution = h5read(filename,[location '/phantom_axialResolution']); %-- read lateral resolution h.lateralResolution = h5read(filename,[location '/phantom_lateralResolution']); end end end end function read_file_mat(h,filename) %-- Load mat file load(filename); %-- Attributes %-- read name h.name = PARAM.name; %-- read author h.author = PARAM.author; %-- read affiliation h.affiliation = PARAM.affiliation; %-- read date h.creation_date = PARAM.creation_date; %-- Data %-- read N_scatterers h.N_scatterers = PARAM.N_scatterers; %-- read scatterers_amplitude h.amp = PARAM.amp; %-- read scatterers_amplitude h.sca = PARAM.sca; if ( (size(h.sca,1)==3) && (size(h.sca,2)==1) ) h.sca = h.sca'; end %-- read scatterers_amplitude h.xLimits = PARAM.xLimits; %-- read scatterers_amplitude h.zLimits = PARAM.zLimits; %-- read scatterers_amplitude h.bckDensity = PARAM.bckDensity; %-- read phantom_occlusionCenterX h.occlusionCenterX = PARAM.occlusionCenterX; %-- read phantom_occlusionCenterZ h.occlusionCenterZ = PARAM.occlusionCenterZ; %-- read phantom_occlusionDiameter h.occlusionDiameter = PARAM.occlusionDiameter; %-- read phantom_RoiCenterX h.RoiCenterX = PARAM.RoiCenterX; %-- read phantom_RoiCenterZ h.RoiCenterZ = PARAM.RoiCenterZ; %-- read phantom_RoiPsfTimeX h.RoiPsfTimeX = PARAM.RoiPsfTimeX; %-- read phantom_RoiPsfTimeZ h.RoiPsfTimeZ = PARAM.RoiPsfTimeZ; %-- read phantom_xPts h.xPts = PARAM.xPts; %-- read phantom_zPts h.zPts = PARAM.zPts; %-- read axial resolution h.axialResolution = PARAM.axialResolution; %-- read lateral resolution h.lateralResolution = PARAM.lateralResolution; end function write_file_mat(h,filename) %-- Attributes %-- add name PARAM.name = h.name; %-- add author PARAM.author = h.author; %-- add affiliation PARAM.affiliation = h.affiliation; %-- add date PARAM.creation_date = h.creation_date; %-- Data %-- add N_scatterers PARAM.N_scatterers = h.N_scatterers; %-- add scatterers_amplitude PARAM.amp = single(h.amp); %-- add scatterers_amplitude PARAM.sca = single(h.sca); %-- add x limit PARAM.xLimits = single(h.xLimits); %-- add z limit PARAM.zLimits = single(h.zLimits); %-- add scatterers_amplitude PARAM.bckDensity = single(h.bckDensity); %-- add phantom_occlusionCenterX PARAM.occlusionCenterX = single(h.occlusionCenterX); %-- add phantom_occlusionCenterZ PARAM.occlusionCenterZ = single(h.occlusionCenterZ); %-- add phantom_occlusionDiameter PARAM.occlusionDiameter = single(h.occlusionDiameter); %-- add phantom_RoiCenterX PARAM.RoiCenterX = single(h.RoiCenterX); %-- add phantom_RoiCenterZ PARAM.RoiCenterZ = single(h.RoiCenterZ); %-- add phantom_RoiPsfTimeX PARAM.RoiPsfTimeX = single(h.RoiPsfTimeX); %-- add phantom_RoiPsfTimeZ PARAM.RoiPsfTimeZ = single(h.RoiPsfTimeZ); %-- read phantom_xPts PARAM.xPts = single(h.xPts); %-- read phantom_zPts PARAM.zPts = single(h.zPts); %-- read axial resolution PARAM.axialResolution = single(h.axialResolution); %-- read lateral resolution PARAM.lateralResolution = single(h.lateralResolution); %-- Write mat file save(filename,'PARAM'); end end methods (Access = private) function generatePtsScatterersPht(h) if ( size(h.xPts,1)==1 ) xxp = h.xPts'; zzp = h.zPts'; else xxp = h.xPts; zzp = h.zPts; end h.N_scatterers = length(zzp(:)); %-- total number of scatterers h.sca = [xxp(:) zeros(h.N_scatterers,1) zzp(:)]; %-- list with the scatterers coordinates [m] h.amp = ones(h.N_scatterers,1); end function generateOcclusionPht(h) psf_length = h.axialResolution; psf_width = h.lateralResolution; width = h.xLimits(2) - h.xLimits(1); depth = h.zLimits(2) - h.zLimits(1); h.N_scatterers = round( h.bckDensity * depth * width / psf_length / psf_width ); x = width * (rand(h.N_scatterers,1)-0.5); y = zeros(size(x)); z = depth * (rand(h.N_scatterers,1))+h.zLimits(1); amp = randn(h.N_scatterers,1); for k=1:length(h.occlusionDiameter) if (h.occlusionDiameter(k)>0) r = h.occlusionDiameter(k) / 2; xc = h.occlusionCenterX(k); zc = h.occlusionCenterZ(k); outside = ( ((x-xc).^2 + (z-zc).^2) >= r^2); x = x(outside); y = y(outside); z = z(outside); amp = amp(outside); end end h.sca = [x y z]; h.amp = amp; end end end