emilroz

% Copyright (C) 2014 Glencoe Software, Inc.
% All rights reserved.
%  
% Redistribution and use in source and binary forms, with or without
% modification, are permitted provided that the following conditions are met:
%  
% 1. Redistributions of source code must retain the above copyright notice, this
%    list of conditions and the following disclaimer.
% 2. Redistributions in binary form must reproduce the above copyright notice,
%    this list of conditions and the following disclaimer in the documentation

emilroz

function [original_file_paths, client_file_paths] = ...
    getFilePaths(session, image_id)
% GETFILEPATHS Retrieve the fileset's file paths.
%
%   [original_file_path, client_file_paths] = getFilePaths(session, image_id)
%   returns file paths to the Original Files and Client Paths (recorded on import).
%
% author: Emil Rozbicki <emil@glencoesoftware.com
% Copyright (C) 2014 Glencoe Software, Inc.
% All rights reserved.

emilroz

function [global_metadata, series_metadata] = ...
    getOriginalMetadata(client, session, image_id)
% GETORIGINALMETADATA Retrieves the global and the series orignal metadata. 
%
% author: Emil Rozbicki <emil@glencoesoftware.com
% Copyright (C) 2014 Glencoe Software, Inc.
% All rights reserved.
%
% Redistribution and use in source and binary forms, with or without
% modification, are permitted provided that the following conditions are met:

emilroz

cmake_minimum_required(VERSION 2.8)
project(test_bio)

set(CMAKE_PREFIX_PATH "/usr/local/lib/cmake/;${CMAKE_PREFIX_PATH}")
set(CMAKE_MODULE_PATH "/usr/local/lib/cmake/;${CMAKE_MODULE_PATH}")

find_package(ome-bioformats REQUIRED)
include_directories(${OME_BIOFORMATS_INCLUDE_DIR})

MESSAGE(STATUS "OME BIOFORMATS: " ${OME_BIOFORMATS_INCLUDE_DIR})

emilroz

function downloadedFileList = ...
    downloadOriginalFiles(session, imageId, folder, chunkSize)
% DOWNLOADORIGINALFILES downloaded original files assosiated with the Image.
%
%   downloadedFileList = getFilePaths(session, image_id, folder, chunkSize)
%   returns list of paths to downloaded files.
%
% author: Emil Rozbicki <emil@glencoesoftware.com
% Copyright (C) 2014 Glencoe Software, Inc.
% All rights reserved.

emilroz

'''
Copyright (C) 2014 Glencoe Software, Inc.
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this
   list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,

emilroz

'''
Copyright (C) 2014 Glencoe Software, Inc.
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this
   list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,

emilroz

function well_list_return = ...
    getImageListFromPlate(session, plate_id)
% GETIMAGELISTFROMPLATE retrieves a list of image ids belonging to plate id.
%
%   well_list_return = getImageListFromPlate(session, plate_id)
%   returns 3D array of Image ID of size (# of columns, # of rows, # of
%   fields)
%
% author: Emil Rozbicki <emil@glencoesoftware.com
% Copyright (C) 2015 Glencoe Software, Inc.

emilroz

import omero
from omero.rtypes import rint, rdouble
from omero.gateway import ColorHolder
from omero.gateway import BlitzGateway

import numpy
import struct
import math

emilroz

public void dummyTiledTiff(
        String directory, String imageName)
        throws DependencyException, ServiceException,
        FormatException, IOException
{
    Integer sizeX = 1024;
    Integer sizeY = 1024;
    Integer sizeC = 4;
    Integer bpp = 2;
    Integer tileSizeX = 256;