Bugfixes and updates to save functionality.
This commit is contained in:
Karthik
parent
93210fb5e6
commit
7d196f4bb0
@ -38,7 +38,7 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
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% --- Save OD images to disk if requested ---
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if ~options.skipSaveProcessedOD
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saveOD(od_imgs, options);
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saveProcessedOD(od_imgs, options);
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end
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return; % ✅ bypass cropping/background subtraction
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@ -51,14 +51,13 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
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if isfield(options, 'FullODImagesFolder') && ...
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~isempty(options.FullODImagesFolder) && ...
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isfolder(options.FullODImagesFolder)
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% User-specified parent folder
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fullodimage_folders = dir(fullfile(options.FullODImagesFolder, 'FullODImages_*'));
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full_od_image_parent_folder = dir(fullfile(options.FullODImagesFolder, 'FullODImages_*'));
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elseif isfield(options, 'saveDirectory') && isfolder(options.saveDirectory)
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full_od_image_parent_folder = dir(fullfile(options.saveDirectory, 'FullODImages_*'));
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else
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% Default to saveDirectory
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fullodimage_folders = dir(fullfile(options.saveDirectory, 'FullODImages_*'));
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full_od_image_parent_folder = '';
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end
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% --- Specific sequence, data and run ---
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dataSource = makeDataSourceStruct(options.folderPath);
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@ -73,88 +72,143 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
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[options.SAVE_TO_WORKSPACE, ~] = Helper.estimateDatasetMemory(dataSource, options);
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end
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fullodimage_folder = [];
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full_od_image_subfolder = [];
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% --- Prepare full_od_imgs, full_bkg_imgs, scan values, file list ---
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if fullDataExists
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% --- Case 1: Already in workspace ---
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fprintf('\n[INFO] Reusing full OD image dataset and scan parameters from memory.\n');
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full_od_imgs = evalin('base', 'full_od_imgs');
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full_bkg_imgs = evalin('base', 'full_bkg_imgs');
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raw_scan_parameter_values = evalin('base', 'raw_scan_parameter_values');
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raw_file_list = evalin('base', 'raw_file_list');
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full_od_imgs = evalin('base','full_od_imgs');
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full_bkg_imgs = evalin('base','full_bkg_imgs');
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raw_scan_parameter_values = evalin('base','raw_scan_parameter_values');
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raw_file_list = evalin('base','raw_file_list');
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nFiles = size(full_od_imgs,3);
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fprintf('\n[INFO] Cropping and subtracting background from images...\n');
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elseif ~options.SAVE_TO_WORKSPACE || (~isempty(fullodimage_folders) || (isfield(options,'selectedPath') && isfolder(options.selectedPath)))
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else
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matched = false;
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full_od_image_subfolder = [];
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useFullODFolders = ~isfield(options,'skipFullODImagesFolderUse') || ~options.skipFullODImagesFolderUse;
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% --- Use selectedPath directly if it exists and full OD usage is enabled ---
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if isfield(options, 'selectedPath') && isfolder(options.selectedPath) ...
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&& (~isfield(options, 'skipFullODImagesFolderUse') || ~options.skipFullODImagesFolderUse)
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fullodimage_folder = options.selectedPath;
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matched = true;
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fprintf('\n[INFO] Using selected full OD images subfolder: %s\n', fullodimage_folder);
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else
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% --- Otherwise, search among available full OD image folders ---
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for r = 1:numel(fullodimage_folders)
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metaPath = fullfile(fullodimage_folders(r).folder, fullodimage_folders(r).name, 'metadata.mat');
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if ~isfile(metaPath), continue; end
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S = load(metaPath,'metadata');
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% --- If user provided selectedPath and it is a folder, disambiguate its meaning ---
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if isfield(options,'selectedPath') && isfolder(options.selectedPath)
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selPath = options.selectedPath;
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% Compare only measurementName and folder path via dataSource struct
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mdDataSource = makeDataSourceStruct(S.metadata.options.folderPath);
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currentDataSource = makeDataSourceStruct(options.folderPath);
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% --- Determine if selectedPath looks like a FullODImages folder ---
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selIsFullOD = false;
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if isfile(fullfile(selPath,'metadata.mat'))
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selIsFullOD = true;
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else
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% exact match to any discovered fullodimage_folders entry
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if ~isempty(full_od_image_parent_folder)
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for r = 1:numel(full_od_image_parent_folder)
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cand = fullfile(full_od_image_parent_folder(r).folder, full_od_image_parent_folder(r).name);
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if strcmp(cand, selPath)
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selIsFullOD = true;
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break;
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end
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end
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end
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end
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if isfield(S.metadata.options,'measurementName') && isfield(options,'measurementName') && ...
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strcmp(S.metadata.options.measurementName, options.measurementName) && ...
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isequal(mdDataSource, currentDataSource)
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fullodimage_folder = fullfile(fullodimage_folders(r).folder, fullodimage_folders(r).name);
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if selIsFullOD && useFullODFolders
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% --- selectedPath is explicitly the full OD images folder ---
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full_od_image_subfolder = selPath;
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matched = true;
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fprintf('\n[INFO] Using selected full OD images subfolder: %s\n', full_od_image_subfolder);
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else
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% --- selectedPath appears to be a raw-data folder (not a full-OD folder) ---
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fprintf('\n[INFO] Selected path appears to be raw data: %s\n', selPath);
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% If user forces recompute -> recompute from selected raw path
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if isfield(options,'skipFullODImagesFolderUse') && options.skipFullODImagesFolderUse
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[full_od_imgs, full_bkg_imgs, raw_scan_parameter_values, raw_file_list, full_od_image_subfolder, nFiles] = ...
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recomputeODImages(options, dataSource, selPath);
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matched = true;
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fprintf('\n[INFO] Found matching full OD images subfolder: %s\n', fullodimage_folders(r).name);
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break;
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else
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% Try to find an existing full-OD folder whose metadata references this raw path
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found = false;
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if ~isempty(full_od_image_parent_folder) && useFullODFolders
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for r = 1:numel(full_od_image_parent_folder)
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metaPath = fullfile(full_od_image_parent_folder(r).folder, full_od_image_parent_folder(r).name, 'metadata.mat');
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if ~isfile(metaPath), continue; end
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S = load(metaPath,'metadata');
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% Compare data source from metadata to the selected raw path
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mdDataSource = makeDataSourceStruct(S.metadata.options.folderPath);
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selDataSource = makeDataSourceStruct(selPath);
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if isfield(S.metadata.options,'measurementName') && isfield(options,'measurementName') && ...
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strcmp(S.metadata.options.measurementName, options.measurementName) && ...
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isequal(mdDataSource, selDataSource)
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full_od_image_subfolder = fullfile(full_od_image_parent_folder(r).folder, full_od_image_parent_folder(r).name);
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matched = true;
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found = true;
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fprintf('\n[INFO] Found matching full OD images subfolder for selected raw path: %s\n', full_od_image_parent_folder(r).name);
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break;
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end
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end
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end
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% If no matching full-OD folder found, recompute from the selected raw path
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if ~found
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[full_od_imgs, full_bkg_imgs, raw_scan_parameter_values, raw_file_list, full_od_image_subfolder, nFiles] = ...
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recomputeODImages(options, dataSource, selPath);
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matched = true;
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end
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end
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end
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else
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% --- No selectedPath provided: either force recompute or search among fullodimage_folders ---
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if isfield(options,'skipFullODImagesFolderUse') && options.skipFullODImagesFolderUse
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% forced recompute
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[full_od_imgs, full_bkg_imgs, raw_scan_parameter_values, raw_file_list, full_od_image_subfolder, nFiles] = ...
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recomputeODImages(options, dataSource);
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matched = true;
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else
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% Search for existing matching full-OD folder based on options.folderPath
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if ~isempty(full_od_image_parent_folder) && useFullODFolders
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for r = 1:numel(full_od_image_parent_folder)
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metaPath = fullfile(full_od_image_parent_folder(r).folder, full_od_image_parent_folder(r).name,'metadata.mat');
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if ~isfile(metaPath), continue; end
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S = load(metaPath,'metadata');
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mdDataSource = makeDataSourceStruct(S.metadata.options.folderPath);
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currentDataSource = makeDataSourceStruct(options.folderPath);
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if isfield(S.metadata.options,'measurementName') && isfield(options,'measurementName') && ...
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strcmp(S.metadata.options.measurementName, options.measurementName) && ...
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isequal(mdDataSource, currentDataSource)
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full_od_image_subfolder = fullfile(full_od_image_parent_folder(r).folder, full_od_image_parent_folder(r).name);
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matched = true;
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fprintf('\n[INFO] Found matching full OD images subfolder: %s\n', full_od_image_parent_folder(r).name);
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break;
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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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% --- If still not matched, recompute from raw (fallback) ---
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if ~matched
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fprintf('\n[INFO] No matching full OD images subfolder for this run found.\n');
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[~, ~, ~, ~] = Helper.processRawData(options);
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fprintf('\n[INFO] Completed computing OD images. Images will be stored on disk for reuse.\n');
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if isempty(full_od_image_parent_folder) && ~useFullODFolders
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fprintf('\n[INFO] No full OD images found in workspace or on disk. Computing from raw...\n');
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else
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fprintf('\n[INFO] No matching full OD images subfolder found. Recomputing from raw...\n');
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end
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[full_od_imgs, full_bkg_imgs, raw_scan_parameter_values, raw_file_list, full_od_image_subfolder, nFiles] = ...
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recomputeODImages(options, dataSource);
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end
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% --- Load mat files from determined folder ---
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mat_files = dir(fullfile(fullodimage_folder,'*.mat'));
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mat_files = mat_files(~strcmp({mat_files.name}, 'metadata.mat')); % Exclude metadata.mat
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nFiles = numel(mat_files);
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raw_scan_parameter_values = zeros(1,nFiles);
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raw_file_list = strings(1,nFiles);
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fprintf('\n[INFO] Cropping and subtracting background from images in full OD images folder on disk...\n');
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else
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fprintf('\n[INFO] No full OD images found in either the workspace or on disk.\n');
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[full_od_imgs, full_bkg_imgs, raw_scan_parameter_values, raw_file_list] = Helper.processRawData(options);
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if options.SAVE_TO_WORKSPACE
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nFiles = size(full_od_imgs,3);
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assignin('base', 'full_od_imgs', full_od_imgs);
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assignin('base', 'full_bkg_imgs', full_bkg_imgs);
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assignin('base', 'raw_scan_parameter_values', raw_scan_parameter_values);
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assignin('base', 'raw_file_list', raw_file_list);
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fprintf('\n[INFO] Completed computing OD images. Images stored in workspace for reuse.\n');
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fprintf('\n[INFO] Cropping and subtracting background from images...\n');
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else
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fprintf('\n[INFO] Completed computing OD images. Images stored on disk for reuse.\n');
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runID = sprintf('%s_%s_Run%04d', ...
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dataSource{1}.sequence, ...
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strrep(dataSource{1}.date,'/','-'), ...
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dataSource{1}.runs);
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fullodimage_folder = fullfile(options.saveDirectory, ['FullODImages_' runID]);
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mat_files = dir(fullfile(fullodimage_folder,'*.mat'));
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mat_files = mat_files(~strcmp({mat_files.name}, 'metadata.mat')); % Exclude metadata.mat
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nFiles = numel(mat_files);
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raw_scan_parameter_values = zeros(1,nFiles);
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raw_file_list = strings(1,nFiles);
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% --- If a folder was determined, load its contents (listing) ---
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if ~isempty(full_od_image_subfolder) && useFullODFolders
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[raw_scan_parameter_values, raw_file_list, nFiles] = prepareDiskListing(full_od_image_subfolder);
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fprintf('\n[INFO] Cropping and subtracting background from images in full OD images folder on disk...\n');
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end
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end
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% --- Unified cropping & background subtraction ---
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absimages = zeros(options.span(1)+1, options.span(2)+1, nFiles, 'single');
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refimages = zeros(options.span(1)+1, options.span(2)+1, nFiles, 'single');
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@ -166,12 +220,12 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
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end
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for k = 1:nFiles
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if fullDataExists || ~isempty(fullodimage_folder)
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if fullDataExists || ~isempty(full_od_image_subfolder)
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if fullDataExists
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od_mat = full_od_imgs(:,:,k);
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bkg_mat = full_bkg_imgs(:,:,k);
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else
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data = load(fullfile(fullodimage_folder, mat_files(k).name));
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data = load(fullfile(full_od_image_subfolder, mat_files(k).name));
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od_mat = data.OD;
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bkg_mat = data.BKG;
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raw_scan_parameter_values(k) = data.Scan;
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@ -261,7 +315,7 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
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% --- Save OD images to disk if requested ---
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if ~options.skipSaveProcessedOD
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saveOD(od_imgs, options);
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saveProcessedOD(od_imgs, options);
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end
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fprintf('\n[INFO] OD image dataset ready for further analysis.\n');
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@ -283,74 +337,78 @@ function changed = haveOptionsChanged(options, prior_options, critical_fields)
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end
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end
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function saveOD(od_img, options)
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% Saves a cell array of OD images (with metadata) to .mat files
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nImgs = numel(od_img);
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function saveProcessedOD(od_imgs, options)
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% Saves a cell array of processed OD images (with metadata) to .mat files
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% od_imgs is expected to be a cell array of structs with fields: OD, Scan, File
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%
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% Inputs:
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% od_imgs - cell array of structs: OD (2D array), Scan (scalar), File (string)
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% options - struct containing folderPath and either FullODImagesFolder or saveDirectory
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nImgs = numel(od_imgs);
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if nImgs == 0
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error('[ERROR] No images found.');
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end
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% --- Determine image size ---
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[ny, nx] = size(od_img{1}.OD);
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[ny, nx] = size(od_imgs{1}.OD);
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% --- Create uniquely identified full OD image folder ---
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% --- Create unique folder name ---
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dataSource = makeDataSourceStruct(options.folderPath);
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runID = sprintf('%s_%s_Run%04d', ...
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dataSource{1}.sequence, ...
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strrep(dataSource{1}.date,'/','-'), ...
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dataSource{1}.runs);
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% --- Determine parent folder for FullODImages ---
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if isfield(options, 'FullODImagesFoldersPath') && ...
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~isempty(options.FullODImagesFoldersPath) && ...
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isfolder(options.FullODImagesFoldersPath)
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parentFolder = options.FullODImagesFoldersPath;
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else
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% --- Determine parent folder ---
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if isfield(options, 'FullODImagesFolder') && ~isempty(options.FullODImagesFolder) && isfolder(options.FullODImagesFolder)
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parentFolder = options.FullODImagesFolder;
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elseif isfield(options, 'saveDirectory') && isfolder(options.saveDirectory)
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parentFolder = options.saveDirectory;
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else
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parentFolder = pwd; % fallback to current folder
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end
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% --- Create uniquely identified full OD image folder ---
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fullODImageFolder = fullfile(parentFolder, ['FullODImages_' runID]);
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if ~exist(fullODImageFolder,'dir'), mkdir(fullODImageFolder); end
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fprintf('\n[INFO] Creating folder of full OD images on disk: %s\n', fullODImageFolder);
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% --- Create ProcessedODImages folder ---
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processedFolder = fullfile(parentFolder, ['ProcessedODImages_' runID]);
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if ~exist(processedFolder, 'dir')
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mkdir(processedFolder);
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end
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fprintf('\n[INFO] Saving processed OD images in folder: %s\n', processedFolder);
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% --- Check if everything already exists ---
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filesExist = all(arrayfun(@(k) ...
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isfile(fullfile(fullODImageFolder, sprintf('Image_%04d.mat', k))), 1:nImgs)) ...
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&& isfile(fullfile(fullODImageFolder,'metadata.mat'));
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% --- Check if files already exist ---
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filesExist = all(arrayfun(@(k) isfile(fullfile(processedFolder, sprintf('Image_%04d.mat', k))), 1:nImgs)) ...
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&& isfile(fullfile(processedFolder,'metadata.mat'));
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if filesExist
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fprintf('\n[INFO] OD .mat files already exist in %s. Skipping save.\n', fullODImageFolder);
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fprintf('\n[INFO] Processed OD .mat files already exist in %s. Skipping save.\n', processedFolder);
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return;
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end
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% --- Save metadata for this run ---
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% --- Save metadata ---
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metadata.options = options;
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metadata.timestamp = datetime; % record analysis time
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metadata.runID = runID; % traceable to experiment run
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metadata.timestamp = datetime;
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metadata.runID = runID;
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metadata.imageSize = [ny, nx];
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metadata.fileList = string(cellfun(@(c) c.File, od_img, 'UniformOutput', false));
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save(fullfile(fullODImageFolder,'metadata.mat'),'metadata','-v7.3');
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metadata.fileList = string(cellfun(@(c) c.File, od_imgs, 'UniformOutput', false));
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save(fullfile(processedFolder,'metadata.mat'), 'metadata', '-v7.3');
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% --- Save each image ---
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% --- Save each image as a struct with OD, Scan, File ---
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for k = 1:nImgs
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% Expecting od_img{k} to be a struct with fields: OD, BKG, Scan, File
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if ~isstruct(od_img{k}) || ...
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~all(isfield(od_img{k}, {'OD','BKG','Scan','File'}))
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error('od_img{%d} must be a struct with fields OD, BKG, Scan, File.', k);
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imgStruct = od_imgs{k};
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if ~isstruct(imgStruct) || ~all(isfield(imgStruct, {'OD','Scan','File'}))
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error('od_imgs{%d} must be a struct with fields OD, Scan, File.', k);
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end
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OD = single(od_img{k}.OD);
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BKG = single(od_img{k}.BKG);
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Scan = single(od_img{k}.Scan);
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File = string(od_img{k}.File);
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OD = single(imgStruct.OD);
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Scan = single(imgStruct.Scan);
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File = string(imgStruct.File);
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matFilePath = fullfile(fullODImageFolder, sprintf('Image_%04d.mat', k));
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save(matFilePath, 'OD','BKG','Scan','File','-v7.3');
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matFilePath = fullfile(processedFolder, sprintf('Image_%04d.mat', k));
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save(matFilePath, 'OD','Scan','File','-v7.3');
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end
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fprintf('[INFO] OD .mat files and metadata saved successfully.\n');
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fprintf('[INFO] Processed OD .mat files and metadata saved successfully.\n');
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end
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function dataSource = makeDataSourceStruct(folderPath)
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@ -382,3 +440,55 @@ function dataSource = makeDataSourceStruct(folderPath)
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'runs', runNum)
|
||||
};
|
||||
end
|
||||
|
||||
function [full_od_imgs, full_bkg_imgs, raw_scan_parameter_values, raw_file_list, fullodimage_folder, nFiles] = recomputeODImages(options, dataSource, selectedPath)
|
||||
% recomputeODImages: central recompute routine
|
||||
% optional argument selectedPath (if provided) will be used as options.folderPath for processing
|
||||
|
||||
if nargin < 3
|
||||
selectedPath = '';
|
||||
end
|
||||
|
||||
fprintf('\n[INFO] Computing OD images from raw data...\n');
|
||||
|
||||
% make a local copy of options so we can override folderPath if selectedPath supplied
|
||||
opts = options;
|
||||
if ~isempty(selectedPath)
|
||||
% assume the Helper.processRawData uses opts.folderPath (or opts.selectedPath) — override folderPath to selectedPath
|
||||
opts.folderPath = selectedPath;
|
||||
end
|
||||
|
||||
[full_od_imgs, full_bkg_imgs, raw_scan_parameter_values, raw_file_list] = Helper.processRawData(opts);
|
||||
|
||||
if opts.SAVE_TO_WORKSPACE
|
||||
nFiles = size(full_od_imgs,3);
|
||||
assignin('base','full_od_imgs',full_od_imgs);
|
||||
assignin('base','full_bkg_imgs',full_bkg_imgs);
|
||||
assignin('base','raw_scan_parameter_values',raw_scan_parameter_values);
|
||||
assignin('base','raw_file_list',raw_file_list);
|
||||
fullodimage_folder = [];
|
||||
fprintf('\n[INFO] Completed computing OD images. Stored in workspace for reuse.\n');
|
||||
fprintf('\n[INFO] Cropping and subtracting background from images...\n');
|
||||
else
|
||||
% Use dataSource to construct a run-folder (keeps naming consistent)
|
||||
fullodimage_folder = createRunFolder(options, dataSource);
|
||||
[raw_scan_parameter_values, raw_file_list, nFiles] = prepareDiskListing(fullodimage_folder);
|
||||
fprintf('\n[INFO] Completed computing OD images. Stored on disk for reuse.\n');
|
||||
end
|
||||
end
|
||||
|
||||
function fullodimage_folder = createRunFolder(options, dataSource)
|
||||
runID = sprintf('%s_%s_Run%04d', ...
|
||||
dataSource{1}.sequence, ...
|
||||
strrep(dataSource{1}.date,'/','-'), ...
|
||||
dataSource{1}.runs);
|
||||
fullodimage_folder = fullfile(options.saveDirectory, ['FullODImages_' runID]);
|
||||
end
|
||||
|
||||
function [raw_scan_parameter_values, raw_file_list, nFiles] = prepareDiskListing(folder)
|
||||
mat_files = dir(fullfile(folder,'*.mat'));
|
||||
mat_files = mat_files(~strcmp({mat_files.name},'metadata.mat')); % exclude metadata
|
||||
nFiles = numel(mat_files);
|
||||
raw_scan_parameter_values = zeros(1,nFiles);
|
||||
raw_file_list = strings(1,nFiles);
|
||||
end
|
||||
@ -30,10 +30,10 @@ function [SAVE_TO_WORKSPACE, runMemoryGB] = estimateDatasetMemory(dataSources, o
|
||||
|
||||
if runBytes > 0.75 * availableRAM
|
||||
SAVE_TO_WORKSPACE = false;
|
||||
fprintf('[INFO] Selected run %s estimated size %.2f GB exceeds 75%% of available RAM. Saving to disk.\n', ...
|
||||
fprintf('\n[INFO] Selected run %s estimated size %.2f GB exceeds 75%% of available RAM. Saving to disk.\n', ...
|
||||
runFolder, runBytes/1e9);
|
||||
else
|
||||
fprintf('[INFO] Selected run %s estimated size %.2f GB fits in memory.\n', ...
|
||||
fprintf('\n[INFO] Selected run %s estimated size %.2f GB fits in memory.\n', ...
|
||||
runFolder, runBytes/1e9);
|
||||
end
|
||||
end
|
||||
|
||||
@ -3,7 +3,7 @@ function [selectedPath, folderPath] = selectDataSourcePath(dataSources, options)
|
||||
%
|
||||
% Inputs:
|
||||
% dataSources - cell array of structs with fields: sequence, date, runs
|
||||
% options - struct, may contain: baseDataFolder, FullODImagesFolder, skipFullODImagesFolderUse
|
||||
% options - struct, may contain: baseDataFolder, FullODImagesFolder, skipFullODImagesFolderUse, saveDirectory
|
||||
%
|
||||
% Outputs:
|
||||
% selectedPath - actual folder to use (raw or FullOD)
|
||||
@ -26,28 +26,39 @@ function [selectedPath, folderPath] = selectDataSourcePath(dataSources, options)
|
||||
end
|
||||
end
|
||||
|
||||
% --- Resolve FullODImagesFolder parent location ---
|
||||
if isfield(options, 'FullODImagesFolder') && ...
|
||||
~isempty(options.FullODImagesFolder) && ...
|
||||
isfolder(options.FullODImagesFolder)
|
||||
full_od_image_parent_folder = options.FullODImagesFolder;
|
||||
elseif isfield(options, 'saveDirectory') && isfolder(options.saveDirectory)
|
||||
full_od_image_parent_folder = options.saveDirectory;
|
||||
else
|
||||
full_od_image_parent_folder = '';
|
||||
end
|
||||
|
||||
% --- Determine whether FullODImagesFolder should be used ---
|
||||
useFullOD = false;
|
||||
if ~isempty(allPaths)
|
||||
if isfield(options,'FullODImagesFolder') && isfolder(options.FullODImagesFolder)
|
||||
if ~isempty(full_od_image_parent_folder)
|
||||
if ~isfield(options,'skipFullODImagesFolderUse') || ~options.skipFullODImagesFolderUse
|
||||
fprintf('\n[INFO] Both raw data folder (%s) and full OD Images folder (%s) found.\n', ...
|
||||
options.baseDataFolder, options.FullODImagesFolder);
|
||||
options.baseDataFolder, full_od_image_parent_folder);
|
||||
fprintf('[INFO] Prioritizing full OD Images folder (set skipFullODImagesFolderUse=true to override).\n');
|
||||
useFullOD = true;
|
||||
else
|
||||
fprintf('\n[INFO] Both raw data folder (%s) and full OD Images folder (%s) found.\n', ...
|
||||
options.baseDataFolder, options.FullODImagesFolder);
|
||||
options.baseDataFolder, full_od_image_parent_folder);
|
||||
fprintf('[INFO] Prioritizing raw data folder (set skipFullODImagesFolderUse=false to override).\n');
|
||||
end
|
||||
else
|
||||
fprintf('\n[INFO] Using raw data folder(s) since full OD images not found or not specified.\n');
|
||||
fprintf('[INFO] Using raw data folder(s) since full OD images not found or not specified.\n');
|
||||
end
|
||||
elseif isfield(options,'FullODImagesFolder') && isfolder(options.FullODImagesFolder)
|
||||
if ~options.skipFullODImagesFolderUse
|
||||
elseif ~isempty(full_od_image_parent_folder)
|
||||
if ~isfield(options,'skipFullODImagesFolderUse') || ~options.skipFullODImagesFolderUse
|
||||
useFullOD = true;
|
||||
fprintf('\n[INFO] Raw data folder(s) not found but found full OD Images folder which will be used.\n');
|
||||
allPaths{end+1} = options.FullODImagesFolder;
|
||||
allPaths{end+1} = full_od_image_parent_folder;
|
||||
else
|
||||
error('Raw data folder(s) not found, found full OD Images folder which cannot be used (set skipFullODImagesFolderUse=false to override). Aborting.\n');
|
||||
end
|
||||
@ -64,7 +75,7 @@ function [selectedPath, folderPath] = selectDataSourcePath(dataSources, options)
|
||||
ds = dataSources{i};
|
||||
for run = ds.runs
|
||||
expectedName = sprintf('FullODImages_%s_%s_Run%04d', ds.sequence, strrep(ds.date,'/','-'), run);
|
||||
candidateFolder = fullfile(options.FullODImagesFolder, expectedName);
|
||||
candidateFolder = fullfile(full_od_image_parent_folder, expectedName);
|
||||
if isfolder(candidateFolder)
|
||||
matchedPaths{end+1} = candidateFolder;
|
||||
end
|
||||
@ -73,7 +84,7 @@ function [selectedPath, folderPath] = selectDataSourcePath(dataSources, options)
|
||||
if ~isempty(matchedPaths)
|
||||
allPaths = matchedPaths;
|
||||
else
|
||||
error('No valid paths for data found. Aborting.');
|
||||
error('No valid FullODImages_* subfolders found under %s. Aborting.', full_od_image_parent_folder);
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user