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More bugfixes

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Karthik 2025-08-30 12:00:46 +02:00
parent 9e03632b4f
commit 40b6a6b66d
3 changed files with 18 additions and 12 deletions
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24
Data-Analyzer/+Helper/collectODImages.m
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@ -133,8 +133,9 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
elseif isfield(options, 'saveDirectory') && isfolder(options.saveDirectory)
parentFolder = dir(fullfile(options.saveDirectory, 'FullODImages_*'));
end
dataSource = makeDataSourceStruct(options.folderPath);
fullodimagesFolder = createFullODImagesFolderPath(parentFolder, dataSource);
[mat_files, ~, ~, nFiles] = prepareData(fullodimagesFolder);
[mat_files, ~, ~, nFiles] = prepareFromOnDiskData(fullodimagesFolder);
else
nFiles = numel(raw_file_list);
end
@ -174,8 +175,9 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
elseif isfield(options, 'saveDirectory') && isfolder(options.saveDirectory)
parentFolder = dir(fullfile(options.saveDirectory, 'FullODImages_*'));
end
dataSource = makeDataSourceStruct(options.folderPath);
fullodimagesFolder = createFullODImagesFolderPath(parentFolder, dataSource);
[mat_files, ~, ~, nFiles] = prepareData(fullodimagesFolder);
[mat_files, ~, ~, nFiles] = prepareFromOnDiskData(fullodimagesFolder);
else
nFiles = numel(raw_file_list);
end
@ -198,8 +200,9 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
elseif isfield(options, 'saveDirectory') && isfolder(options.saveDirectory)
parentFolder = dir(fullfile(options.saveDirectory, 'FullODImages_*'));
end
dataSource = makeDataSourceStruct(options.folderPath);
fullodimagesFolder = createFullODImagesFolderPath(parentFolder, dataSource);
[mat_files, ~, ~, nFiles] = prepareData(fullodimagesFolder);
[mat_files, ~, ~, nFiles] = prepareFromOnDiskData(fullodimagesFolder);
else
nFiles = numel(raw_file_list);
end
@ -245,8 +248,9 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
elseif isfield(options, 'saveDirectory') && isfolder(options.saveDirectory)
parentFolder = dir(fullfile(options.saveDirectory, 'FullODImages_*'));
end
dataSource = makeDataSourceStruct(options.folderPath);
fullodimagesFolder = createFullODImagesFolderPath(parentFolder, dataSource);
[mat_files, ~, ~, nFiles] = prepareData(fullodimagesFolder);
[mat_files, ~, ~, nFiles] = prepareFromOnDiskData(fullodimagesFolder);
else
nFiles = numel(raw_file_list);
end
@ -254,7 +258,7 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
% --- If a folder was determined, load its contents (listing) ---
if ~isempty(full_od_image_subfolder) && useFullODFolders
[mat_files, raw_scan_parameter_values, raw_file_list, nFiles] = prepareData(full_od_image_subfolder);
[mat_files, raw_scan_parameter_values, raw_file_list, nFiles] = prepareFromOnDiskData(full_od_image_subfolder);
fprintf('\n[INFO] Cropping and subtracting background from images in full OD images folder on disk...\n');
end
end
@ -516,15 +520,15 @@ function [full_od_imgs, full_bkg_imgs, raw_scan_parameter_values, raw_file_list]
fprintf('\n[INFO] Cropping and subtracting background from images...\n');
end
function fullodimagesFolder = createFullODImagesFolderPath(parentFolder, dataSource)
function fullodimagesFolder = createFullODImagesFolderPath(parentFolder, dataSourcesStruct)
runID = sprintf('%s_%s_Run%04d', ...
dataSource{1}.sequence, ...
strrep(dataSource{1}.date,'/','-'), ...
dataSource{1}.runs);
dataSourcesStruct{1}.sequence, ...
strrep(dataSourcesStruct{1}.date,'/','-'), ...
dataSourcesStruct{1}.runs);
fullodimagesFolder = fullfile(parentFolder, ['FullODImages_' runID]);
end
function [mat_files, raw_scan_parameter_values, raw_file_list, nFiles] = prepareData(folder)
function [mat_files, raw_scan_parameter_values, raw_file_list, nFiles] = prepareFromOnDiskData(folder)
mat_files = dir(fullfile(folder,'*.mat'));
mat_files = mat_files(~strcmp({mat_files.name},'metadata.mat')); % exclude metadata
nFiles = numel(mat_files);

4
Data-Analyzer/+Helper/processRawData.m
View File

@ -24,7 +24,9 @@ function [full_od_imgs, full_bkg_imgs, raw_scan_parameter_values, raw_file_list]
testFile = fullfile(files(1).folder, files(1).name);
atm_test = double(imrotate(h5read(testFile, append(groupList(options.cam), "/atoms")), options.angle, 'bilinear', 'crop'));
[ny, nx] = size(atm_test);
full_od_imgs = [];
full_bkg_imgs = [];
raw_scan_parameter_values = zeros(1, nFiles);
raw_file_list = string(zeros(1,nFiles)); % always string array

2
Data-Analyzer/+Scripts/BECToDropletsToStripes/plotImages.m
View File

@ -70,7 +70,7 @@ options.skipMasking = true;
options.skipIntensityThresholding = true;
options.skipBinarization = true;
options.skipFullODImagesFolderUse = true;
options.skipFullODImagesFolderUse = false;
options.skipSaveData = false;
options.skipSaveFigures = true;
options.skipSaveProcessedOD = true;