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RawDataAccess.m
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RawDataAccess.m
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% Copyright (C) 2011-2014 University of Dundee & Open Microscopy Environment.
% All rights reserved.
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License along
% with this program; if not, write to the Free Software Foundation, Inc.,
% 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
% Raw Data access
try
%%
% start-code
%%
% Initialize a client and a session using the ice.config file
% See ConnectToOMERO for alternative ways to initialize a session
[client, session] = loadOmero();
p = parseOmeroProperties(client);
eventContext = session.getAdminService().getEventContext();
fprintf(1, 'Created connection to %s\n', p.hostname);
msg = 'Created session for user %s (id: %g) using group %s (id: %g)\n';
fprintf(1, msg, char(eventContext.userName), eventContext.userId,...
char(eventContext.groupName), eventContext.groupId);
% Information to edit
imageId = p.imageid;
% First retrieve the image.
image = getImages(session, imageId);
assert(~isempty(image), 'OMERO:RawDataAccess', 'Image Id not valid');
% you should only have one pixels set per image.
fprintf(1, 'Reading image %g\n', image.getId.getValue);
pixels = image.getPrimaryPixels();
sizeX = pixels.getSizeX().getValue(); % The number of pixels along the X-axis.
sizeY = pixels.getSizeY().getValue(); % The number of pixels along the Y-axis.
sizeZ = pixels.getSizeZ().getValue(); % The number of z-sections.
sizeC = pixels.getSizeC().getValue(); % The number of channels.
sizeT = pixels.getSizeT().getValue(); % The number of timepoints.
fprintf(1, 'Size X: %g\n', sizeX);
fprintf(1, 'Size Y: %g\n', sizeY);
fprintf(1, 'Size Z: %g\n', sizeZ);
fprintf(1, 'Size C: %g\n', sizeC);
fprintf(1, 'Size T: %g\n', sizeT);
% Plane
% =====
% The following loop initializes a raw pixels store, reads the pixels
% data and closes the store for each method call
disp('Reading planes with raw pixels store re-initialization');
tic
for z = 0:sizeZ-1,
for t = 0:sizeT-1,
for c = 0:sizeC-1,
fprintf(1, ' Plane Z: %g, C: %g, T: %g\n', z, c, t);
plane = getPlane(session, image, z, c, t);
end
end
end
toc
% The following loop initializes a raw pixels store which is re-used in
% each method call. The store must be closed manually at the end of the
% loop.
disp('Reading planes with raw pixels store recycling');
tic
[store, pixels] = getRawPixelsStore(session, image);
for z = 0:sizeZ-1,
for t = 0:sizeT-1,
for c = 0:sizeC-1,
fprintf(1, ' Plane Z: %g, C: %g, T: %g\n', z, c, t);
plane = getPlane(pixels, store, z, c, t);
end
end
end
store.close();
toc
% Tile
% ====
% The following loop initializes a raw pixels store, reads the pixels
% data and closes the store for each method call
disp('Reading tiles with raw pixels store re-initialization');
x = 0;
y = 0;
width = sizeX/2;
height = sizeY/2;
tic
for z = 0:sizeZ-1,
for t = 0:sizeT-1,
for c = 0:sizeC-1,
fprintf(1, ' Tile Z: %g, C: %g, T: %g\n', z, c, t);
tile = getTile(session, image, z, c, t, x, y, width, height);
end
end
end
toc
% The following loop initializes a raw pixels store which is re-used in
% each method call. The store must be closed manually at the end of the
% loop.
disp('Reading tiles with raw pixels store recycling');
tic
[store, pixels] = getRawPixelsStore(session, image);
for z = 0:sizeZ-1,
for t = 0:sizeT-1,
for c = 0:sizeC-1,
fprintf(1, ' Tile Z: %g, C: %g, T: %g\n', z, c, t);
plane = getTile(pixels, store, z, c, t, x, y, width, height);
end
end
end
store.close();
toc
% Stack
% =====
% The following loop initializes a raw pixels store, reads the pixels
% data and closes the store for each method call
disp('Reading stacks with raw pixels store re-initialization');
tic
for t = 0:sizeT-1,
for c = 0:sizeC-1,
fprintf(1, ' Stack C: %g, T: %g\n', c, t);
stack = getStack(session, image, c, t);
end
end
toc
% The following loop initializes a raw pixels store which is re-used in
% each method call. The store must be closed manually at the end of the
% loop.
disp('Reading stacks with raw pixels store recycling');
tic
[store, pixels] = getRawPixelsStore(session, image);
for t = 0:sizeT-1,
for c = 0:sizeC-1,
fprintf(1, ' Stack C: %g, T: %g\n', c, t);
stack = getStack(pixels, store, c, t);
end
end
store.close();
toc
% Hypercube
% =========
disp('Reading hypercube');
%Create the store to load the stack
[store, pixels] = getRawPixelsStore(session, image);
% offset values in each dimension XYZCT
offset = toJavaList(zeros(1,5), 'java.lang.Integer');
% offset values in each dimension XYZCT
size = toJavaList([sizeX/2 sizeY/2 sizeZ sizeC sizeT],...
'java.lang.Integer');
% indicate the step in each direction, step = 1, will return values at index 0, 1, 2.
% step = 2, values at index 0, 2, 4 etc.
step = toJavaList(ones(1,5), 'java.lang.Integer');
% Retrieve the data
store.getHypercube(offset, size, step);
% close the store
store.close();
%%
% end-code
%%
catch err
client.closeSession();
throw(err);
end
% Close the session
client.closeSession();