Blobs: added mask creation and loading for difblobs

Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>

2_difspot/gtConvertRawImages2Blobs.m

-function gtConvertRawImages2Blobs(acq_name, first, last)
+function gtConvertRawImages2Blobs(parameters, first, last)
+    if (~exist('parameters', 'var'))
+        parameters = gtMATVolReader('parameters.mat:parameters');
+    end
+
     if (~exist('first', 'var'))
         first = 1;
     end
-    difblob_num = mym(['select count(*) from ' acq_name 'difblob']);
+    difblob_num = mym(['select count(*) from ' parameters.acq.name 'difblob']);
     if (~exist('last', 'var'))
         last = difblob_num;
     end
@@ -11,10 +15,11 @@ function gtConvertRawImages2Blobs(acq_name, first, last)
 
     stats = GtTasksStatistics();
     stats.add_task('load_blob', 'Time to load from DB');
+    stats.add_task('load_mask', 'Time to load mask');
     stats.add_task('save_blob', 'Time to save to HDF5');
     stats.add_task('convert_blob', 'Time for converting from DB to HDF5')
 
-    table_difspot = sprintf('%sdifspot', acq_name);
+    table_difspot = sprintf('%sdifspot', parameters.acq.name);
 
     fprintf('Progress: ')
     c = tic();
@@ -27,8 +32,13 @@ function gtConvertRawImages2Blobs(acq_name, first, last)
         blob(blob < 0) = 0;
         stats.toc('load_blob')
 
+        stats.tic('load_mask')
+        mask = get_mask('2_difspot', ii, size(blob, 3), parameters);
+        mask(mask < 0) = 0;
+        stats.toc('load_mask')
+
         stats.tic('save_blob')
-        gtWriteBlobToHDF5('2_difblob', ii, blob, bb);
+        gtWriteBlobToHDF5('2_difblob', ii, blob, bb, mask);
         stats.toc('save_blob')
         stats.toc('convert_blob')
 
@@ -58,3 +68,18 @@ function [blob, bb] = get_blob(table_difspot, difspotID, info)
         blob(:, :, s_ii) = edf_read(filename, GT_bb, false, info);
     end
 end
+
+function mask = get_mask(spot_dir, blob_id, depth_blob, parameters)
+
+    if (parameters.seg.writeblobs)
+        mask = gtDBBrowseDiffractionVolume(parameters.acq.name, blob_id);
+        mask = mask ~= 0;
+    else
+        sub_dir = fullfile(spot_dir, sprintf('%05d', blob_id - mod(blob_id, 1e4)));
+        filename = fullfile(sub_dir, sprintf('difspot%05d.edf', blob_id));
+        mask = edf_read(filename) ~= 0;
+        mask = mask(:, :, ones(1, depth_blob));
+    end
+end
+
+

2_difspot/gtReadBlobFromHDF5.m

-function [blob_vol, blob_bb] = gtReadBlobFromHDF5(blob_dir, blob_id)
-% [blob_vol, blob_bb] = gtReadBlobFromHDF5(blob_dir, blob_id)
+function [blob_vol, blob_bb, blob_mask] = gtReadBlobFromHDF5(blob_dir, blob_id)
+% [blob_vol, blob_bb, blob_mask] = gtReadBlobFromHDF5(blob_dir, blob_id)
 
+    if (~exist('blob_dir', 'var') || isempty(blob_dir))
+        blob_dir = '2_difblob';
+    end
     sub_dir = fullfile(blob_dir, sprintf('%06d', blob_id - mod(blob_id, 1e4)));
     fnameout = fullfile(sub_dir, sprintf('difblob_%06d.hdf5', blob_id) );
     if (isempty(dir(fnameout)))
@@ -9,9 +12,13 @@ function [blob_vol, blob_bb] = gtReadBlobFromHDF5(blob_dir, blob_id)
     end
 
     blob_vol = h5read(fnameout, '/rawblob');
-    if (nargout == 2)
+    if (nargout >= 2)
         blob_bb = h5readatt(fnameout, '/rawblob', 'bb');
         blob_bb = [blob_bb(2:3:end), blob_bb(1:3:end), blob_bb(3:3:end)];
         blob_bb = double([blob_bb(1, :), blob_bb(2, :)]);
     end
+    if (nargout >= 3)
+        blob_mask = h5read(fnameout, '/mask');
+        blob_mask = logical(blob_mask);
+    end
 end
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2_difspot/gtSegmentationDoubleThreshold.m

@@ -474,7 +474,7 @@ function sfWriteBlob(blob, stack)
         blob_bb = blob.bb;
         % put z into reference of the dataset
         blob_bb(3) = blob_bb(3) + stack.first - 1;
-        gtWriteBlobToHDF5(stack.difblobdir, blob.difblobID, blob.rawgreyvol, blob_bb);
+        gtWriteBlobToHDF5(stack.difblobdir, blob.difblobID, blob.rawgreyvol, blob_bb, blob.greyvol ~= 0);
     end
 
     if (stack.writespots)

2_difspot/gtWriteBlobToHDF5.m

-function gtWriteBlobToHDF5(blob_dir, blob_id, blob_vol, blob_bb)
+function gtWriteBlobToHDF5(blob_dir, blob_id, blob_vol, blob_bb, blob_mask)
     sub_dir = fullfile(blob_dir, sprintf('%06d', blob_id - mod(blob_id, 1e4)));
     if (~exist(sub_dir, 'dir'))
         [status, message, messageid] = mkdir(sub_dir);
@@ -16,8 +16,15 @@ function gtWriteBlobToHDF5(blob_dir, blob_id, blob_vol, blob_bb)
     vol_size = [size(blob_vol, 1) size(blob_vol, 2) size(blob_vol, 3)];
     chunk_size = min([16 16 4], vol_size);
     h5create(fnameout, '/rawblob', vol_size, 'Datatype', 'single', 'Deflate', 1, 'ChunkSize', chunk_size);
-%     h5create(fnameout, '/rawblob', size(blob_vol), 'Datatype', 'single');
 
-    h5write(fnameout, '/rawblob', single(blob_vol))
-    h5writeatt(fnameout, '/rawblob', 'bb', uint32(blob_bb))
+    h5write(fnameout, '/rawblob', single(blob_vol));
+    h5writeatt(fnameout, '/rawblob', 'bb', uint32(blob_bb));
+
+    % Mask comes from segmentation
+    h5create(fnameout, '/mask', vol_size, 'Datatype', 'uint8', 'Deflate', 1, 'ChunkSize', chunk_size);
+    if (~exist('blob_mask', 'var'))
+        h5write(fnameout, '/mask', ones(size(blob_vol), 'uint8'));
+    else
+        h5write(fnameout, '/mask', uint8(blob_mask));
+    end
 end
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