Lesion candidate extraction from a data set abstracted on a separate …

…function

RedLesionDetection/scripts/script_extract_lesion_candidates.m

@@ -12,40 +12,11 @@
 % prepare dataset path
 dataset_path = fullfile(data_path, datasetName);
 % prepare output path
-if (exist('output_path', 'var') == 0)
-    output_path = fullfile(dataset_path, strcat(type_of_lesion, '_candidates'));
-end
+output_path = fullfile(dataset_path, strcat(type_of_lesion, '_candidates'));
 if (exist(output_path, 'dir') == 0)
     mkdir(output_path);
 end
 
-% get image filenames
-img_names = getMultipleImagesFileNames(fullfile(root_path, 'images'));
-% get masks filenames
-mask_names = getMultipleImagesFileNames(fullfile(root_path, 'masks'));
-
-% For each of the images
-for i = 1 : length(img_names)
-
-    fprintf('Extracting candidates from image %i/%i\n', i, length(img_names));
-
-    % open i-th image and its corresponding FOV mask, OD and vessel
-    % segmentation
-    I = imread(fullfile(root_path, 'images', img_names{i}));
-    mask = imread(fullfile(root_path, 'masks', mask_names{i}));
-
-    % get candidates
-    tic
-    [ current_candidates ] = getLesionCandidates(I, mask, L0, step, L, K, px);
-    toc
-
-    % get only the image name
-    [~, filename, extension] = fileparts(img_names{i});
-    if (~strcmp(extension, '.gif'))
-        filename = strcat(filename, '.gif');
-    end
-
-    % save the image
-    imwrite(current_candidates, fullfile(output_path, strcat(filename)));
-
-end
+% Get all candidates from images
+getLesionCandidatesFromDataset(fullfile(root_path, 'images'), ...
+    fullfile(root_path, 'masks'), output_path, L0, step, L, K, px);

RedLesionDetection/util/candidate_detection/getLesionCandidatesFromDataset.m

@@ -0,0 +1,33 @@
+
+function getLesionCandidatesFromDataset(image_path, masks_path, output_path, L0, step, L, K, px)
+
+% get image filenames
+img_names = getMultipleImagesFileNames(image_path);
+% get masks filenames
+mask_names = getMultipleImagesFileNames(masks_path);
+
+% For each of the images
+for i = 1 : length(img_names)
+
+    fprintf('Extracting candidates from image %i/%i\n', i, length(img_names));
+
+    % open i-th image and its corresponding FOV mask, OD and vessel
+    % segmentation
+    I = imread(fullfile(image_path, img_names{i}));
+    mask = imread(fullfile(masks_path, mask_names{i}));
+
+    % get candidates
+    tic
+    [ current_candidates ] = getLesionCandidates(I, mask, L0, step, L, K, px);
+    toc
+
+    % get only the image name
+    [~, filename, extension] = fileparts(img_names{i});
+    if (~strcmp(extension, '.gif'))
+        filename = strcat(filename, '.gif');
+    end
+
+    % save the image
+    imwrite(current_candidates, fullfile(output_path, strcat(filename)));
+
+end