sbesson

import java.io.IOException;

import loci.common.services.DependencyException;

import loci.common.services.ServiceException;
import loci.common.services.ServiceFactory;
import loci.formats.services.OMEXMLService;
import loci.formats.FormatException;

sbesson

<?xml version="1.0" encoding="UTF-8"?>
<OME UUID="urn:uuid:07504f88-7bc3-11e0-b937-2faf67bc00b3"
     xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06"
     xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
     xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06
                         http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
  <Image ID="Image:0" Name="ROI with transforms">
    <Pixels DimensionOrder="XYZCT" ID="Pixels:0:0" Type="uint8" SizeC="1" SizeT="2" SizeX="512" SizeY="512" SizeZ="8">
      <Channel ID="Channel:0" SamplesPerPixel="1"/>
      <TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1">

sbesson

% Check Bio-Formats and initialize logging
bfCheckJavaPath();
bfInitLogging();

% Create a reader
r =  bfGetReader();

values = [true false];
for autostich = values
    for attachments = values 

sbesson

import scc.git

# Login and check the organization
gh = scc.git.get_github(scc.git.get_token())
orgs = gh.get_user().get_orgs()


def is_owner(org):
    owners = [x.login for x in org.get_members(role="admin")]
    return gh.get_login() in owners

sbesson

SELECT ns, discriminator, count(*) from annotation group by ns, discriminator;
SELECT ns, discriminator, count(*) from annotation where ns = '' group by ns, discriminator;
SELECT ns, discriminator, count(*) from annotation where ns is null group by ns, discriminator;

sbesson

#!/usr/bin/env python

# Copyright (C) 2016 Open Microscopy Environment & University of Dundee.
# 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.
#

sbesson

parser = loci.formats.tiff.TiffParser(ometiffpath);
service = loci.formats.services.OMEXMLServiceImpl();
version = char(service.getOMEXMLVersion(parser.getComment()))

sbesson

#! /usr/bin/env python

import scc.git
import time

# Create GitHub connection
token = scc.git.get_token()
gh = scc.git.get_github(token)
username = gh.get_user().login
print "Authenticated as %s" % username

sbesson

% Create OME-XML metadata object
OMEXMLService = loci.formats.services.OMEXMLServiceImpl();
metadata = OMEXMLService.createOMEXMLMetadata();

% Create the root object
metadata.createRoot();

% Set the UUID for the OME-TIFF
ometiff_uuid = char(java.util.UUID.randomUUID);
metadata.setUUID(ometiff_uuid);

sbesson

#! /bin/bash
# Fix test_images_good symlinks post curated renaming

set -u
set -e
set -x


if [ $# -ne 1 ]; then
    echo "not enough arguments"