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302 lines
8.9 KiB
Matlab
302 lines
8.9 KiB
Matlab
%LOAD_PTYCHO_ML_RECONS Load ML reconstructions from h5 or mat file and return it as
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% structure, single dataset or directly into the workspace.
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% An additional argument can be passed to select subsections of the data.
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% Loading single datasets is only supported for at least 2 output
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% arguments.
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% Created by YJ based on PSI's function.
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%
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function [object, probe, dx_spec] = load_aps_ML_recons( filename_with_path)
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if ~ischar(filename_with_path)
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error('First argument has to be string')
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end
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filename_with_path = utils.abspath(filename_with_path);
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%disp(filename_with_path)
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if ~exist(filename_with_path, 'file')
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error('Could not find reconstruction file %s', filename_with_path)
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end
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object = load(filename_with_path,'object');
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object = object.object;
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probe = load(filename_with_path,'probe');
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probe = probe.probe;
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parameter = load(filename_with_path,'p');
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dx_spec = parameter.p.dx_spec; %pixel size
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%% legacy code: read recon from processed h5 files
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%{
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object_r = h5read(filename_with_path,'/object_r');
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object_i = h5read(filename_with_path,'/object_i');
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object = object_r + 1i*object_i;
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probe_r = h5read(filename_with_path,'/probe_r');
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probe_i = h5read(filename_with_path,'/probe_i');
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probe = probe_r + 1i*probe_i;
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% load pixel size
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dx_spec = h5read(filename_with_path,'/dx_spec');
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% load projection angle
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%ang = h5read(filename_with_path,'/angle');
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%}
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end
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%% old PSI code, too complex for APS data
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%{
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function varargout = load_ptycho_ML_recons( filename_with_path, varargin )
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import io.HDF.hdf5_load
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varargout = {};
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if ~ischar(filename_with_path)
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error('First argument has to be string')
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end
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filename_with_path = utils.abspath(filename_with_path);
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if ~exist(filename_with_path, 'file')
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error('Could not find reconstruction file %s', filename_with_path)
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end
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if nargin > 1
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switch varargin{1}
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case {'pr'; 'probe'; 'probes'}
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section = 'probe';
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case {'ob'; 'obj'; 'objects'}
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section = 'object';
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otherwise
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section = varargin{1};
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end
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else
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section = 'full';
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end
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if ~nargout
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output = 0;
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elseif nargout >=2
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output = 2;
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else
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output = 1;
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end
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function assign_struct(val, val_name)
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switch output
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case 1
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varargout{1}.(val_name) = val;
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case 2
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varargout{end+1} = val;
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otherwise
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assignin('base', val_name, val);
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end
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end
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function assign_val(struc)
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switch output
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case 1
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varargout{1} = struc;
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case 2
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if isfield(struc, 'object')
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varargout{end+1} = struc.object;
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end
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if isfield(struc, 'probe')
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varargout{end+1} = struc.probe;
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end
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if isfield(struc, 'p')
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varargout{end+1} = struc.p;
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end
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otherwise
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fn = fieldnames(struc);
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for ii=1:length(fn)
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assignin('base', fn{ii}, struc.(fn{ii}))
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end
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end
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end
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% check if it is a .mat file or a .cxs file
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[~, ~, ext] = fileparts(filename_with_path);
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switch ext
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%{
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case '.mat'
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switch section
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case 'recon'
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S = load(filename_with_path, 'object', 'probe');
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assign_val(S);
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case 'full'
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S = load(filename_with_path);
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assign_val(S);
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case 'object'
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S = load(filename_with_path, 'object');
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assign_val(S);
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case 'probe'
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S = load(filename_with_path, 'probe');
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size(S)
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assign_val(S);
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case 'p'
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S = load(filename_with_path, 'p');
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assign_val(S);
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otherwise
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error('Unknown data section %s', section);
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end
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%}
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case {'.cxs','.h5'}
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%{
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if io.HDF.hdf5_dset_exists(filename_with_path, 'object', '/reconstruction', true)
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h5_path = '/reconstruction';
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else
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h5_path = '';
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end
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%}
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% reconstruction
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switch section
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%{
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case 'recon'
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% load object
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h = hdf5_load(filename_with_path, [h5_path '/object']);
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assign_struct(load_data_cell(h), 'object');
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% load probe
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h = hdf5_load(filename_with_path, [h5_path '/probes']);
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assign_struct(load_data_cell(h), 'probe');
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case 'full'
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% load object
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h = hdf5_load(filename_with_path, [h5_path '/object']);
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assign_struct(load_data_cell(h), 'object');
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% load probe
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h = hdf5_load(filename_with_path, [h5_path '/probes']);
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assign_struct(load_data_cell(h), 'probe');
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% load p
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p = convert2p(hdf5_load(filename_with_path, '/reconstruction/p', '-c'));
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if io.HDF.hdf5_dset_exists(filename_with_path, 'meta_all', '/measurement', true)
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p.meta = hdf5_load(filename_with_path, '/measurement/meta_all', '-c');
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elseif io.HDF.hdf5_dset_exists(filename_with_path, 'spec_all', '/measurement', true)
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p.meta = hdf5_load(filename_with_path, '/measurement/spec_all', '-c');
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end
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assign_struct(p, 'p');
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%}
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case 'object'
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% load object
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%h = hdf5_load(filename_with_path, [h5_path '/object']);
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%assign_struct(load_data_cell(h), 'object');
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object_r = h5read(filename_with_path,'/object_r');
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object_i = h5read(filename_with_path,'/object_i');
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object = object_r + 1i*object_i;
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assign_struct(object, 'object');
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case 'probe'
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% load probe
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%h = hdf5_load(filename_with_path, [h5_path '/probes']);
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%assign_struct(load_data_cell(h), 'probe');
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probe_r = h5read(filename_with_path,'/probe_r');
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probe_i = h5read(filename_with_path,'/probe_i');
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probe = probe_r + 1i*probe_i;
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assign_struct(probe, 'probe');
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case 'p'
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% load p
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p = convert2p(hdf5_load(filename_with_path, '/reconstruction/p', '-c'));
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if io.HDF.hdf5_dset_exists(filename_with_path, 'meta_all', '/measurement', true)
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p.meta = hdf5_load(filename_with_path, '/measurement/meta_all', '-c');
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elseif io.HDF.hdf5_dset_exists(filename_with_path, 'spec_all', '/measurement', true)
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p.meta = hdf5_load(filename_with_path, '/measurement/spec_all', '-c');
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end
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assign_struct(p, 'p');
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otherwise
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error('Unknown data section %s', section);
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end
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otherwise
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error('Unknown ptycho datatype %s.', ext)
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end
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end
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function tmp = load_data_cell(h)
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fn = fieldnames(h);
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num_end = str2double(subsref(strsplit(fn{1}, '_'), struct('type', '{}', 'subs',{{length(strsplit(fn{1},'_'))}})));
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if length(fn)==2 && (strcmpi(fn{1}, 'i') || strcmpi(fn{1}, 'r'))
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tmp = permute(h.r + 1i*h.i, [2,1,3,4]);
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elseif isnumeric(num_end) && ~isnan(num_end)
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for ii=1:length(fn)
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if isstruct(h.(fn{ii}))
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tmp{ii} = load_data_cell(h.(fn{ii}));
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else
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if isnumeric(h.(fn{ii}))
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tmp{ii} = double(h.(fn{ii}));
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else
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tmp{ii} = h.(fn{ii});
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end
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end
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end
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% tmp = h;
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else
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for ii=1:length(fn)
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if isstruct(h.(fn{ii}))
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tmp.(fn{ii}) = load_data_cell(h.(fn{ii}));
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else
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if isnumeric(h.(fn{ii}))
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tmp.(fn{ii}) = double(h.(fn{ii}));
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else
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tmp.(fn{ii}) = h.(fn{ii});
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end
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end
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end
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end
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end
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function tmp = convert2p(h)
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fn = fieldnames(h);
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for ii=1:length(fn)
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if isstruct(h.(fn{ii}))
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h.(fn{ii}) = load_data_cell(h.(fn{ii}));
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elseif isnumeric(h.(fn{ii}))
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h.(fn{ii}) = double(h.(fn{ii}));
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else
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continue;
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end
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end
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tmp = h;
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% object
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for ii=1:length(h.objects)
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tmp.object{ii} = permute(h.objects{ii}, [2 1 3 4]);
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end
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tmp = rmfield(tmp, 'objects');
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% probes
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pr = tmp.probes;
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tmp.probes = [];
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for ii=1:length(pr)
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tmp.probes(:,:,ii,:) = permute(pr{ii}, [2 1 3 4]);
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end
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% positions
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tmp.positions = transpose(tmp.positions);
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tmp.positions_real = transpose(tmp.positions_real);
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tmp.positions_orig = transpose(tmp.positions_orig);
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% ctr
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tmp.ctr = transpose(tmp.ctr);
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end
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%}
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