classdef us_image < handle %-- Class containing the beamformed data %-- Authors: Alfonso Rodriguez-Molares (alfonso.r.molares@ntnu.no) %-- Olivier Bernard (olivier.bernard@creatis.insa-lyon.fr) properties (SetAccess = public) %-- administration name %-- String containing the name of the beamformed image 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 algorithm %-- String containing the name of the algorithm used to create the beamformed image creation_date %-- String containing the date the reconstruction was created %-- input data scan %-- SCAN class defining the scan area %-- output data number_plane_waves %-- Vector containing number of plane waves used in each reconstructed frame data %-- Matrix containing the envelope of the reconstructed signal %- information transmit_f_number %-- Scalar of the F-number used on transmit transmit_apodization_window %-- String describing the transmit apodization window receive_f_number %-- Scalar of the F-number used on receive receive_apodization_window %-- String describing the receive apodization window end %-- version properties (SetAccess = private) version %-- version of this us_image class, needed for back compatibility end %-- constructor methods (Access = public) function h = us_image(name) %-- Constructor of the US_IMAGE class. %-- Syntax: %-- US_IMAGE(name) %-- name: Name of the reconstruction h.creation_date = sprintf('%d/%02d/%d %02d:%02d:%02.2f',clock); h.version = 'v0.10'; if exist('name') h.name=name; else h.name=''; end author = ''; affiliation = ''; algorithm = ''; creation_date = ''; number_plane_waves = NaN; transmit_f_number = NaN; transmit_apodization_window = ''; receive_f_number = NaN; receive_apodization_window = ''; 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 %-- algorithm function set.algorithm(h,input) assert(isstr(input), 'Wrong format of the algorithm name. It should be a string.'); h.algorithm = 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 %-- set scan function set.scan(h,input) assert(isa(input,'linear_scan'), 'Wrong format of the scan. It should be a LINEAR_SCAN class.'); h.scan = input; end %-- data function set.data(h,input_data) assert(isnumeric(input_data)&&ndims(input_data)>1&&ndims(input_data)<4, 'Wrong format of the data. It should be a numeric array of dimensions [z_axis, x_axis, frames].'); %-- scan if(~isempty(h.scan)) if(size(input_data,1)~=length(h.scan.z_axis)) error('The data size in the z-axis does not match the size of the scan area');end if(size(input_data,2)~=length(h.scan.x_axis)) error('The data size in the x-axis does not match the size of the scan area');end end %-- number of plane waves used assert(~any(isnan(h.number_plane_waves)),'The number of plane waves must be set before assigning the data'); if(size(input_data,3)~=length(h.number_plane_waves)) error('The number of images size(data,3) should match the number of elements in the vector number_plane_waves');end %-- data h.data = input_data; %-- data check assert(isreal(h.data)&~any(h.data(:)<0),'Data provided must be the envelope of the beamformed signal, i.e. the magnitude of the beamformed IQ signal or the magnitude of the Hilbert transform of a RF beamformed signal. Do not apply compression to the signal envelope.'); end end %-- presentation methods methods (Access = public) function im = show(h,dynamic_range,frame_list) %-- Plots the envelope of the beamformed data and returns a copy of the image %-- Syntax: %-- image = show(dynamic_range) %-- image: Matrix with the output signal %-- dynamic_range: Desired dynamic range of the displayed images in dB %-- frame_list: List of frames to be displayed if ~exist('dynamic_range') dynamic_range=60; end %-- setting axis limits (mm) x_lim = [min(h.scan.x_matrix(:)) max(h.scan.x_matrix(:))]*1e3; z_lim = [min(h.scan.z_matrix(:)) max(h.scan.z_matrix(:))]*1e3; %-- ploting image reconstruction figure; set(gca,'fontsize',16); if ~exist('frame_list') || isempty(frame_list) frame_list = 1:size(h.data,3); end for f=frame_list %-- compute dB values env = h.data(:,:,f); im = 20*log10(env./max(env(:))); vrange = [-dynamic_range 0]; %-- display image imagesc((h.scan.x_axis)*1e3,(h.scan.z_axis)*1e3,im); shading flat; colormap gray; caxis(vrange); colorbar; hold on; axis equal manual; xlabel('x [mm]'); ylabel('z [mm]'); set(gca,'YDir','reverse'); set(gca,'fontsize',16); axis([x_lim z_lim]); title(sprintf('%s\n %d plane waves',char(h.name),h.number_plane_waves(f))); drawnow; hold off; pause(0.5); end end end %-- HDF5 Ultrasound File Format methods (Access = public) 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 function write_file_hdf5(h,filename) %-- Writes all the information in the us_dataset to a HUFF (HDF5 Ultrasound File Format) file %-- Syntax: %-- write_file(file_name,group_name) %-- file_name: Name of the hdf5 file %-- group_name: Name of the group destination %-- write HDF5 version in the root group attr_details.Name = 'version'; attr_details.AttachedTo = '/'; attr_details.AttachType = 'group'; hdf5write(filename, attr_details, 'v.0.0.41'); %-- 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 %-- 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(1)); % <--- SR H5A.close (attr); H5G.close(gid); H5S.close (space); H5T.close (filetype); H5F.close (file); %-- 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); H5T.enum_insert (filetype, 'ENV', 2); 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(2)); % <--- ENVELOPE 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 algorithm attr_details.Name = 'algorithm'; attr_details.AttachedTo = location; attr_details.AttachType = 'group'; hdf5write(filename, attr_details, h.algorithm, 'WriteMode', 'append'); %-- add version of the us_dataset attr_details.Name = 'version'; attr_details.AttachedTo = location; attr_details.AttachType = 'group'; hdf5write(filename, attr_details, h.version, '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 %-- add linear scan dset_details.Location = [location '/scan']; dset_details.Name = 'x_axis'; hdf5write(filename, dset_details, single(h.scan.x_axis), 'WriteMode', 'append'); dset_details.Location = [location '/scan']; dset_details.Name = 'z_axis'; hdf5write(filename, dset_details, single(h.scan.z_axis), 'WriteMode', 'append'); %-- F number dset_details.Location = location; dset_details.Name = 'transmit_f_number'; hdf5write(filename, dset_details, single(h.transmit_f_number), 'WriteMode', 'append'); dset_details.Location = location; dset_details.Name = 'receive_f_number'; hdf5write(filename, dset_details, single(h.receive_f_number), 'WriteMode', 'append'); %-- apodization windows dset_details.Location = location; dset_details.Name = 'transmit_apodization_window'; hdf5write(filename, dset_details, char(h.transmit_apodization_window), 'WriteMode', 'append'); dset_details.Location = location; dset_details.Name = 'receive_apodization_window'; hdf5write(filename, dset_details, char(h.receive_apodization_window), 'WriteMode', 'append'); %-- add number of plane waves dset_details.Location = location; dset_details.Name = 'number_plane_waves'; hdf5write(filename, dset_details, single(h.number_plane_waves), 'WriteMode', 'append'); %-- add data dset_details.Location = [location '/data']; dset_details.Name = 'real'; hdf5write(filename, dset_details, single(real(h.data)), 'WriteMode', 'append'); dset_details.Name = 'imag'; hdf5write(filename, dset_details, single(imag(h.data)), 'WriteMode', 'append'); end function read_file_hdf5(h,filename) %-- Reads all the information from a HUFF (HDF5 Ultrasound File Format) file %-- Syntax: %-- read_file(file_name,location) %-- file_name Name of the hdf5 file %-- check the version here version_cell = h5readatt(filename,'/','version'); version = version_cell{1}(1:8); switch(version) case 'v.0.0.40' warning('The version of the hdf5 is obsolete. Please generate the image again.'); %-- 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,'SR') %-- read signal format signal_format = h5readatt(filename,location,'signal_format'); switch(signal_format{1}) case 'RF' error('RF format not available!'); case 'IQ' error('RF format not available!'); case 'ENV' ; otherwise error('Unknown signal format!'); end %-- 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 algorithm a = h5readatt(filename,location,'algorithm'); h.algorithm=a{1}(1:end-1); %-- read date a = h5readatt(filename,location,'creation_date'); h.creation_date=a{1}(1:end-1); %-- read version a = h5readatt(filename,location,'version'); h.version=a{1}(1:end-1); %-- Data %-- read scan x_axis = h5read(filename,[location '/scan/x_axis']); z_axis = h5read(filename,[location '/scan/z_axis']); h.scan = linear_scan(x_axis,z_axis); %-- F-numbers h.transmit_f_number = h5read(filename,[location '/transmit_f_number']); h.receive_f_number = h5read(filename,[location '/receive_f_number']); %-- Apodization window h.transmit_apodization_window = h5read(filename,[location '/transmit_apodization_window']); h.receive_apodization_window = h5read(filename,[location '/receive_apodization_window']); %-- read data real_part = h5read(filename,[location '/data/real']); imag_part = h5read(filename,[location '/data/imag']); h.number_plane_waves = zeros(1,size(real_part,3)); h.data = real_part+1i*imag_part; end end case 'v.0.0.41' %-- 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,'SR') %-- read signal format signal_format = h5readatt(filename,location,'signal_format'); switch(signal_format{1}) case 'RF' error('RF format not available!'); case 'IQ' error('RF format not available!'); case 'ENV' ; otherwise error('Unknown signal format!'); end %-- 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 algorithm a = h5readatt(filename,location,'algorithm'); h.algorithm=a{1}(1:end-1); %-- read date a = h5readatt(filename,location,'creation_date'); h.creation_date=a{1}(1:end-1); %-- read version a = h5readatt(filename,location,'version'); h.version=a{1}(1:end-1); %-- Data %-- read scan x_axis = h5read(filename,[location '/scan/x_axis']); z_axis = h5read(filename,[location '/scan/z_axis']); h.scan = linear_scan(x_axis,z_axis); %-- F-numbers h.transmit_f_number = h5read(filename,[location '/transmit_f_number']); h.receive_f_number = h5read(filename,[location '/receive_f_number']); %-- Apodization window h.transmit_apodization_window = h5read(filename,[location '/transmit_apodization_window']); h.receive_apodization_window = h5read(filename,[location '/receive_apodization_window']); %-- read number of plane waves h.number_plane_waves = h5read(filename,[location '/number_plane_waves']); %-- read data real_part = h5read(filename,[location '/data/real']); imag_part = h5read(filename,[location '/data/imag']); h.data = real_part+1i*imag_part; end end otherwise error(sprintf('HUFF version %s not supported',version)); end end function read_file_mat(h,filename) %-- Read mat file load(filename); %-- Attributes %-- read name h.name = PARAM.name; %-- read author h.author = PARAM.author; %-- read affiliation h.affiliation = PARAM.affiliation; %-- read algorithm h.algorithm = PARAM.algorithm; %-- read date h.creation_date = PARAM.creation_date; %-- read version h.version = PARAM.version; %-- Data %-- read scan x_axis = PARAM.x_axis; z_axis = PARAM.z_axis; h.scan = linear_scan(x_axis,z_axis); %-- F-numbers h.transmit_f_number = PARAM.transmit_f_number; h.receive_f_number = PARAM.receive_f_number; %-- Apodization window h.transmit_apodization_window = PARAM.transmit_apodization_window; h.receive_apodization_window = PARAM.receive_apodization_window; %-- read number of plane waves h.number_plane_waves = PARAM.number_plane_waves; %-- read data real_part = PARAM.real_part; imag_part = PARAM.imag_part; h.data = real_part+1i*imag_part; 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 algorithm PARAM.algorithm = h.algorithm; %-- add date PARAM.creation_date = h.creation_date; %-- add version PARAM.version = h.version; %-- Data %-- add scan PARAM.x_axis = single(h.scan.x_axis); PARAM.z_axis = single(h.scan.z_axis); %-- F-numbers PARAM.transmit_f_number = single(h.transmit_f_number); PARAM.receive_f_number = single(h.receive_f_number); %-- Apodization window PARAM.transmit_apodization_window = char(h.transmit_apodization_window); PARAM.receive_apodization_window = char(h.receive_apodization_window); %-- read number of plane waves PARAM.number_plane_waves = single(h.number_plane_waves); %-- read data PARAM.real_part = single(real(h.data)); PARAM.imag_part = single(imag(h.data)); %-- write mat file save(filename,'PARAM'); end end end