emilroz

# -*- coding: utf-8 -*-
"""
-----------------------------------------------------------------------------
  Copyright (C) 2020 Glencoe Software, Inc. 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

emilroz

#!/bin/bash
#  ./parade.test number_of_datasets number_of_images /ouput/directory /where/is/your/OMERO -s omero.server.address -u user.name -w password

NUMBER_OF_DATASETS=$1
NUMBER_OF_IMAGES=$2
OUTPUT_DIR=$3
OMERO_HOME=$4
OMERO_ARGUMENTS="${@:5}"

PROJECT_NAME="Parade.Test"

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;

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

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 <[email protected]
% Copyright (C) 2015 Glencoe Software, Inc.

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 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 <[email protected]
% Copyright (C) 2014 Glencoe Software, Inc.
% All rights reserved.

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 [global_metadata, series_metadata] = ...
    getOriginalMetadata(client, session, image_id)
% GETORIGINALMETADATA Retrieves the global and the series orignal metadata. 
%
% author: Emil Rozbicki <[email protected]
% 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: