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%% TEMPLATE FOR AUTOMATIC TOMOGRAPHY CODE TESTS
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% perform tests on measured dataset stored in /das/work/p16/p16812/
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cd(fullfile( fileparts(mfilename('fullpath')), '..'))
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addpath('tests')
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addpath('utils')
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addpath('./')
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addpath(find_base_package)
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clearvars -except par0 tested_templates scratch_path GPU_id base_path test_simulated_data test_real_data base_path
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%%%%%%%%%%%%%%%%%%%%%%%%%
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%%% Edit this section %%%
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%%%%%%%%%%%%%%%%%%%%%%%%%
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datasets = 1:5; % 1-nature chip, 2-FFC particle, 3-retina, 4-local tomo, 5-lamni chip
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verbose_level = -1; % -1 = keep very quiet the reconstructions
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scratch_path = '/das/work/p16/p16812/'; % path to the cSAXS scratch p-folder where are saved the test datasets
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if ~exist('GPU_id', 'var'); GPU_id = [1]; end
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if ~exist('base_path', 'var'); base_path = '../'; end
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%%%%%%%%%%%%%%%%%%%%%%%%%
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%%%%%%%%%%%%%%%%%%%%%%%%%
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utils.verbose(verbose_level)
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setenv('TMP',[base_path,'/tmp']) % TEMP for matlab scripts
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utils.verbose(-1, '=== Searching for data in %s ====', scratch_path)
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for dataset = datasets
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par0 = struct();
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par0.GPU_list = GPU_id;
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switch dataset
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case 1
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%% Nature chip 2016
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% test: large projections, phase residua/errors from sharp transitions
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tested_templates ={'template_tomo_recons'} ;
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par0.tomo_id = [];
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par0.scanstomo = [2718:3925];
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par0.fileprefix='online_'; % string at the beginning of the filename, related to reconstruction name
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par0.filesuffix = '_600x600_wrap_1_c'; % string searched at the end of the data filenames, No need to add _c or _recons, it will look for it
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par0.file_extension = 'mat';
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par0.analysis_path = fullfile(scratch_path, 'data/e16622_tomo_nature_chip_2016/analysis/');
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par0.surface_calib_file = [];
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par0.omnyposfile = fullfile(scratch_path, 'data/e16622_tomo_nature_chip_2016/specES1/scan_positions/scan_%05d.dat'); %Filename pattern for Orchestra interferometer position files
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par0.OMNY_angle_file = fullfile(scratch_path, 'data/e16622_tomo_nature_chip_2016/specES1/dat-files/tomography_scannumbers.txt'); % Filename with angles
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par0.max_residua_limit = inf; % limit used to determine which projection have failed
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case 2
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%% johanness FCC catalyst
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% test: large projections, low freq. errors, periodic artefacts, vertically asymmetric sample
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tested_templates ={'template_tomo_recons'} ;
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par0.tomo_id = [];
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par0.scanstomo = [500:1349];
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par0.fileprefix='offline_'; % string at the beginning of the filename, related to reconstruction name
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par0.filesuffix = '500x500_run_1_recons'; % string searched at the end of the data filenames, No need to add _c or _recons, it will look for it
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par0.file_extension = 'mat';
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par0.analysis_path = fullfile(scratch_path, 'data/e16410_tomo_FCC_particle/analysis/');
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par0.surface_calib_file = [];
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par0.omnyposfile = fullfile(scratch_path, 'data/e16410_tomo_FCC_particle/specES1/scan_positions/scan_%05d.dat'); %Filename pattern for Orchestra interferometer position files
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par0.OMNY_angle_file = fullfile(scratch_path, 'data/e16410_tomo_FCC_particle/specES1/dat-files/tomography_scannumbers.txt'); % Filename with angles
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% solve in lower resolution
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par0.downsample_projections = 1;
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case 3
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%% retina from OMNY
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% test: large projections, low freq. errors, huge phase jumps
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tested_templates ={'template_tomo_recons'} ;
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par0.tomo_id = [];
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par0.scanstomo = [1925:2384];
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par0.fileprefix='online_wrap_'; % string at the beginning of the filename, related to reconstruction name
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par0.filesuffix = '_452x452_run_1_c'; % string searched at the end of the data filenames, No need to add _c or _recons, it will look for it
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par0.file_extension = 'mat';
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par0.analysis_path = fullfile(scratch_path, 'data/e15634_retina_2015_OMNY/analysis/');
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par0.surface_calib_file = [];
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par0.omnyposfile = fullfile(scratch_path, 'data/e15634_retina_2015_OMNY/specES1/omny_recontruct/scan_%05d.dat'); %Filename pattern for Orchestra interferometer position files
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par0.OMNY_angle_file = fullfile(scratch_path, 'data/e15634_retina_2015_OMNY/specES1/dat-files/omny_scannumbers.txt'); % Filename with angles
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par0.downsample_projections = 1; % downsample projections by factor of 2^x, set 0 to do nothing and 1,2,.. for different levels of projection binning
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par0.auto_alignment = false;
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par0.get_auto_calibration = false;
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case 4
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%% local tomo dataset !! THIS TEST TAKES ~1 HOUR and requires 200GB of RAM !!
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tested_templates ={'template_tomo_interior'} ;
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par0.tomo_id = []; % [68:74]; % Either scan numbers or tomo_id can be given, but not both, if not provided leave tomo_id=[]
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par0.scanstomo = 1700:7690;
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par0.lowres_tomo_path =fullfile(scratch_path, 'data/e17312_localtomo_FCC_particle/tomogram_delta_S00089_to_S01525_ram-lak_freqscl_1.00.mat');
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% IO loading
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par0.fileprefix=''; % string at the beginning of the filename, related to reconstruction name
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par0.filesuffix = '_recons'; % string searched at the end of the data filenames, No need to add _c or _recons, it will look for it
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par0.file_extension = 'h5';
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par0.downsample_projections = 0; % downsample projections by factor of 2^x, set 0 to do nothing and 1,2,.. for different levels of projection binning
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par0.analysis_path = fullfile(scratch_path, 'data/e17312_localtomo_FCC_particle/analysis/');
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par0.clip_amplitude_quantile = 0.95; % clip amplitudes in the loaded projections that are exceeding given quantile, if par0.clip_amplitude_quantile == 1, do nothing
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par0.max_residua_limit = 100; % limit used to determine which projection have failed
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par0.surface_calib_file = [];
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par0.omnyposfile = fullfile(scratch_path, 'data/e17312_localtomo_FCC_particle/specES1/scan_positions/scan_%05d.dat'); %Filename pattern for Orchestra interferometer position files
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par0.OMNY_angle_file = fullfile(scratch_path, 'data/e17312_localtomo_FCC_particle/specES1/dat-files/tomography_scannumbers.txt'); % Filename with angles
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% Other
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par0.save_memory = false; % try to limit use of RAM
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par0.inplace_processing = par0.save_memory; % process object_stack using inplace operations to save memory
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par0.fp16_precision = true; % use 16-bit precision to store the complex-valued projections
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par0.cache_stack_object = par0.save_memory; % store stack_object to disk when no needed
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case 5
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%% lamni chip dataset !! THIS TEST TAKES SEVERAL HOURS and requires full RAM !!
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tested_templates ={'template_tomo_recons_lamino'} ;
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% par0.scanstomo = [984:1850]; %2326]; % smaller angular range
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par0.scanstomo = [984:3717]; % full angular range
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par0.tomo_id = []; % Either scan numbers or tomo_id can be given, but not both, if not provided leave tomo_id=[]
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% IO loading
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par0.fileprefix=''; % string at the beginning of the filename, related to reconstruction name
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par0.filesuffix = 'test_1'; %% string searched at the end of the data filenames, No need to add _c or _recons, it will look for it
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par0.file_extension = 'h5';
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par0.downsample_projections = 0; % downsample projections by factor of 2^x, set 0 to do nothing and 1,2,.. for different levels of projection binning
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par0.analysis_path = fullfile(scratch_path, 'data/e17299_lamni_chip_dataset_2018/analysis/');
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par0.clip_amplitude_quantile = 0.95; % clip amplitudes in the loaded projections that are exceeding given quantile, if par0.clip_amplitude_quantile == 1, do nothing
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par0.max_residua_limit = 100; % limit used to determine which projection have failed
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par0.surface_calib_file = [];
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par0.omnyposfile = fullfile(scratch_path, 'data/e17299_lamni_chip_dataset_2018/specES1/scan_positions/scan_%05d.dat'); %Filename pattern for Orchestra interferometer position files
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par0.OMNY_angle_file = fullfile(scratch_path, 'data/e17299_lamni_chip_dataset_2018/specES1/dat-files/tomography_scannumbers.txt'); % Filename with angles
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% Other
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par0.save_memory = true; % try to limit use of RAM
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par0.inplace_processing = par0.save_memory; % process object_stack using inplace operations to save memory
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par0.fp16_precision = par0.save_memory; % use 16-bit precision to store the complex-valued projections
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par0.cache_stack_object = par0.save_memory; % store stack_object to disk when no needed
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otherwise
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error('Missing dataset')
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end
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for tested_template = tested_templates
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clearvars -except par0 tested_template tested_templates scratch_path GPU_id base_path test_simulated_data test_real_data base_path
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utils.verbose(struct('prefix', 'init'))
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%% test stage 0: load basic configuration parameters
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utils.verbose(-1,'====================================================')
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utils.verbose(-1,'===== Testing template "%s" ============', tested_template{1})
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utils.verbose(-1,'====================================================')
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% set debugging info level and marks
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debug(1)
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warning('off', 'MATLAB:mpath:nameNonexistentOrNotADirectory')
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warning('off', 'MATLAB:dispatcher:pathWarning')
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run(tested_template{1})
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for item = fieldnames(par0)'
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par.(item{1}) = par0.(item{1});
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end
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%% test stage 1: load test data and continue with the remplate
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utils.verbose(-1,'Running template')
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debug(3)
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utils.verbose(struct('prefix', 'template'))
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run(tested_template{1})
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end
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end
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%*-----------------------------------------------------------------------*
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%| |
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%| Except where otherwise noted, this work is licensed under a |
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%| Creative Commons Attribution-NonCommercial-ShareAlike 4.0 |
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%| International (CC BY-NC-SA 4.0) license. |
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%| |
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%| Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch) |
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%| |
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%| Author: CXS group, PSI |
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%*-----------------------------------------------------------------------*
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% You may use this code with the following provisions:
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%
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% If the code is fully or partially redistributed, or rewritten in another
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% computing language this notice should be included in the redistribution.
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%
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% If this code, or subfunctions or parts of it, is used for research in a
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% publication or if it is fully or partially rewritten for another
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% computing language the authors and institution should be acknowledged
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% in written form in the publication: “Data processing was carried out
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% using the “cSAXS matlab package” developed by the CXS group,
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% Paul Scherrer Institut, Switzerland.”
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% Variations on the latter text can be incorporated upon discussion with
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% the CXS group if needed to more specifically reflect the use of the package
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% for the published work.
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%
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% A publication that focuses on describing features, or parameters, that
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% are already existing in the code should be first discussed with the
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% authors.
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%
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% This code and subroutines are part of a continuous development, they
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% are provided “as they are” without guarantees or liability on part
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% of PSI or the authors. It is the user responsibility to ensure its
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% proper use and the correctness of the results.
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