Mercurial > repos > mvdbeek > incucyte_stack_and_upload_omero_debug

annotate stack_buildXml.groovy @ 0:a599551e800d draft

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author mvdbeek
date Tue, 06 Aug 2024 15:28:26 +0000
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mvdbeek
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1 /*
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mvdbeek
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2 ****************************************************
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mvdbeek
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3 * Relative to the generation of the .companion.ome *
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mvdbeek
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4 ****************************************************
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mvdbeek
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5 * #%L
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6 * BSD implementations of Bio-Formats readers and writers
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mvdbeek
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7 * %%
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mvdbeek
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8 * The functions buildXML, makeImage, makePlate, postProcess and asString has been modified and adapted from
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9 * https://github.com/ome/bioformats/blob/master/components/formats-bsd/test/loci/formats/utests/SPWModelMock.java
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mvdbeek
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10 *
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mvdbeek
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11 * Copyright (C) 2005 - 2015 Open Microscopy Environment:
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mvdbeek
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12 * - Board of Regents of the University of Wisconsin-Madison
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mvdbeek
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13 * - Glencoe Software, Inc.
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mvdbeek
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14 * - University of Dundee
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mvdbeek
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15 *
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mvdbeek
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16 * @author Chris Allan <callan at blackcat dot ca>
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mvdbeek
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17 * %%
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mvdbeek
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18 *
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mvdbeek
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19 ****************************************************
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mvdbeek
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20 * Relative to the rest of the script *
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mvdbeek
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21 ****************************************************
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mvdbeek
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22 *
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mvdbeek
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23 * * = AUTHOR INFORMATION =
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mvdbeek
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24 * Code written by Rémy Dornier, EPFL - SV - PTECH - BIOP
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mvdbeek
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25 * and Romain Guiet, EPFL - SV - PTECH - BIOP
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mvdbeek
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26 * and Lucille Delisle, EPFL - SV - UPDUB
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mvdbeek
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27 * and Pierre Osteil, EPFL - SV - UPDUB
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mvdbeek
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28 *
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mvdbeek
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29 * Last modification: 2023-12-19
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mvdbeek
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30 *
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mvdbeek
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31 * = COPYRIGHT =
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mvdbeek
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32 * © All rights reserved. ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, BioImaging And Optics Platform (BIOP), 2023
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mvdbeek
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33 *
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mvdbeek
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34 * Licensed under the BSD-3-Clause License:
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mvdbeek
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35 * Redistribution and use in source and binary forms, with or without modification, are permitted provided
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mvdbeek
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36 * that the following conditions are met:
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mvdbeek
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37 * 1. Redistributions of source code must retain the above copyright notice,
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mvdbeek
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38 * this list of conditions and the following disclaimer.
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mvdbeek
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39 * 2. Redistributions in binary form must reproduce the above copyright notice,
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mvdbeek
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40 * this list of conditions and the following disclaimer
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mvdbeek
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41 * in the documentation and/or other materials provided with the distribution.
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mvdbeek
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42 * 3. Neither the name of the copyright holder nor the names of its contributors
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mvdbeek
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43 * may be used to endorse or promote products
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mvdbeek
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44 * derived from this software without specific prior written permission.
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mvdbeek
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45 *
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mvdbeek
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46 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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mvdbeek
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47 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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mvdbeek
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48 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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mvdbeek
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49 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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mvdbeek
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50 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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mvdbeek
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51 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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mvdbeek
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52 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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mvdbeek
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53 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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mvdbeek
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54 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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mvdbeek
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55 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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mvdbeek
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56 * POSSIBILITY OF SUCH DAMAGE.
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57 *
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58 */
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59
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60 /**
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mvdbeek
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61 *
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mvdbeek
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62 * The purpose of this script is to combine a series of time-lapse images into
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63 * one file per well/field with possibly multiple channels and multiple time points
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mvdbeek
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64 * and in addition create a .companion.ome file to create an OMERO plate object,
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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65 * with a single image per well/field. This .companion.ome file can be directly uploaded on OMERO via
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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66 * OMERO.insight software or CLI, with screen import option.
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mvdbeek
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67 *
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mvdbeek
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68 * To make the script run
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mvdbeek
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69 * 1. Create a parent folder (base_dir) and a output folder (output_dir)
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mvdbeek
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70 * 2. Create a dir *Phase, *Green, *Red with the corresponding channels
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71 * 3. The image names must contains a prefix followed by '_', the name of the well (no 0-pad) followed by '_', followed by the field id followed by '_', the date of the acquisition in YYYYyMMmDDdHHhMMm and the extension '.tif'
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mvdbeek
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72 * 4. The images can be either regular tif or the raw tif from Incucyte which contains multiple series.
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mvdbeek
parents:
diff changeset
73 * 5. You must provide the path of the Incucyte XML file to populate key values
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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74 *
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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75 * The expected outputs are:
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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76 * 1. In the output_dir one tiff per well/field (multi-T and potentially multi-C)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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77 * 2. In the output_dir a .companion.ome
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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78 */
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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79
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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80 #@ File(style="directory", label="Directory with up to 3 subdirectories ending by Green, Phase and/or Red") base_dir
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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81 #@ File(label="Incucyte XML File (plateMap)") incucyteXMLFile
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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82 #@ File(style="directory", label="Output directory (must exist)") output_dir
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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83 #@ String(label="Final XML file name", value="Test") xmlName
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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84 #@ String(label="Number of well in plate", choices={"96", "384"}, value="96") nWells
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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85 #@ Integer(label="Maximum number of images per well", value=1, min=1) n_images_per_well
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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86 #@ String(label="Objective", choices={"4x","10x","20x"}) objectiveChoice
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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87 #@ String(label="Plate name", value="Experiment:0") plateName
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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88 #@ String(label="common Key Values formatted as key1=value1;key2=value2", value="") commonKeyValues
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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89 #@ Boolean(label="Ignore Compound concentration from plateMap", value=true) ignoreConcentration
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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90 #@ Boolean(label="Ignore Cell passage number from plateMap", value=true) ignorePassage
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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91 #@ Boolean(label="Ignore Cell seeding concentration from plateMap", value=true) ignoreSeeding
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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92
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93
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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94 /**
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95 * *****************************************************************************************************************
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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96 * ********************************************* Final Variables **************************************************
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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97 * ********************************************* DO NOT MODIFY ****************************************************
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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98 * ****************************************************************************************************************
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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99 */
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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100
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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101 /** objectives and respective pixel sizes */
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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102 objective = 0
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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103 objectives = new String[]{"4x", "10x", "20x"}
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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104 pixelSizes = new double[]{2.82, 1.24, 0.62}
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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105
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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106 /** pattern for date */
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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107 REGEX_FOR_DATE = ".*_([0-9]{4})y([0-9]{2})m([0-9]{2})d_([0-9]{2})h([0-9]{2})m.tif"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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108
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109 ALTERNATIVE_REGEX_FOR_DATE = ".*_([0-9]{2})d([0-9]{2})h([0-9]{2})m.tif"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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110
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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111 /** Image properties keys */
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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112 DIMENSION_ORDER = "dimension_order"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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113 FILE_NAME = "file_name"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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114 IMG_POS_IN_WELL = "img_pos_in_well"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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115 FIRST_ACQUISITION_DATE = "acquisition_date"
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116 FIRST_ACQUISITION_TIME = "acquisition_time"
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117 RELATIVE_ACQUISITION_HOUR = "relative_acquisition_hour"
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118
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119 /** global variable for index to letter conversion */
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120 LETTERS = new String("ABCDEFGHIJKLMNOP")
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121
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122 // Version number = date of last modif
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123 VERSION = "20231219"
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124
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125 /** Key-Value pairs namespace */
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126 GENERAL_ANNOTATION_NAMESPACE = "openmicroscopy.org/omero/client/mapAnnotation"
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127 annotations = new StructuredAnnotations()
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128
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129 /** Plate details and conventions */
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130 PLATE_ID = "Plate:0"
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131 PLATE_NAME = plateName
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132
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133 if (nWells == "96") {
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134 nRows = 8
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135 nCols = 12
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136 } else if (nWells == "384") {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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137 nRows = 16
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138 nCols = 24
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139 }
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140
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141 WELL_ROWS = new PositiveInteger(nRows)
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142 WELL_COLS = new PositiveInteger(nCols)
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143 WELL_ROW = NamingConvention.LETTER
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144 WELL_COL = NamingConvention.NUMBER
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145
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146 /** XML namespace. */
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147 XML_NS = "http://www.openmicroscopy.org/Schemas/OME/2010-06"
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148
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149 /** XSI namespace. */
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150 XSI_NS = "http://www.w3.org/2001/XMLSchema-instance"
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151
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152 /** XML schema location. */
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153 SCHEMA_LOCATION = "http://www.openmicroscopy.org/Schemas/OME/2010-06/ome.xsd"
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154
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155
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156 /**
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mvdbeek
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157 * *****************************************************************************************************************
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mvdbeek
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158 * **************************************** Beginning of the script ***********************************************
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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159 * ****************************************************************************************************************
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160 */
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161
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162 try {
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163
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164 println "Beginning of the script"
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165
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166 /**
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167 * Prepare list of wells name
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168 */
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169 String[] well = []
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170
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171 well = [(0..(nRows - 1)),(0..(nCols - 1))].combinations().collect{ r,c -> LETTERS.substring(r, r + 1) +""+ (c+ 1).toString() }
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172
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173 IJ.run("Close All", "")
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174
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175 // loop for all the wells
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176
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177 // Store all merged ImagePlus into a HashMap where
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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178 // keys are well name (A1, A10)
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179 // values are a list of ImagePlus corresponding to different field of view
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180 Map<String, List<ImagePlus>> wellSamplesMap = new HashMap<>()
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181
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182 well.each{ input ->
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183 IJ.run("Close All", "")
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184
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185 List<ImagePlus> final_imp_list = process_well(base_dir, input, n_images_per_well) //, perform_bc, mediaChangeTime )
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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186 if (!final_imp_list.isEmpty()) {
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187 wellSamplesMap.put(input, final_imp_list)
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188 for(ImagePlus final_imp : final_imp_list){
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189 final_imp.setTitle(input+"_"+final_imp.getProperty(IMG_POS_IN_WELL))
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190 //final_imp.show()
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191
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192 def fs = new FileSaver(final_imp)
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193 File output_path = new File (output_dir ,final_imp.getTitle()+"_merge.tif" )
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194 fs.saveAsTiff(output_path.toString() )
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195 final_imp.setProperty(FILE_NAME, output_path.getName())
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196
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197 IJ.run("Close All", "")
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198 }
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199 } else {
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200 println "No match for " + input
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201 }
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202 }
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203
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204
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205 // get folder and xml file path
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206 output_dir_abs = output_dir.getAbsolutePath()
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207 incucyteXMLFilePath = incucyteXMLFile.getAbsolutePath()
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208
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209 if (! new File(incucyteXMLFilePath).exists()) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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210 println "The incucyte file does not exists"
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211 return
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212 }
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213
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214 // select the right objective
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215 switch (objectiveChoice){
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216 case "4x":
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217 objective = 0
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218 break
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219 case "10x":
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220 objective = 1
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221 break
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222 case "20x":
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223 objective = 2
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224 break
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225 }
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226
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227 // get plate scheme as key-values
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228 Map<String, List<MapPair>> keyValuesPerWell = parseIncucyteXML(incucyteXMLFilePath, ignoreConcentration, ignorePassage, ignoreSeeding)
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229
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230 // get global key-values
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231 List<MapPair> globalKeyValues = getGlobalKeyValues(objective, commonKeyValues)
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232 double pixelSize = pixelSizes[objective]
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233
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234 // generate OME-XML metadata file
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235 OME ome = buildXMLFile(wellSamplesMap, keyValuesPerWell, globalKeyValues, pixelSize)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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236
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237 // create XML document
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238 DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance()
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239 DocumentBuilder parser = factory.newDocumentBuilder()
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240 Document document = parser.newDocument()
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241
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242 // Produce a valid OME DOM element hierarchy
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243 Element root = ome.asXMLElement(document)
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244 postProcess(root, document)
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245
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246 // Produce string XML
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247 try(OutputStream outputStream = new FileOutputStream(output_dir_abs + File.separator + xmlName + ".companion.ome")){
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248 outputStream.write(asString(document).getBytes())
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249 } catch(Exception e){
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250 e.printStackTrace()
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251 }
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252 println "End of the script"
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253
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254 } catch (Throwable e) {
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255 println("Something went wrong: " + e)
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256 e.printStackTrace()
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257 throw e
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258
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259 if (GraphicsEnvironment.isHeadless()){
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260 // Force to give exit signal of error
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261 System.exit(1)
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262 }
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263
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264 }
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265
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266 return
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267
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268 /**
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269 * ****************************************************************************************************************
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270 * ******************************************* End of the script **************************************************
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271 *
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272 * ****************************************************************************************************************
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273 *
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274 * *********************************** Helpers and processing methods *********************************************
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275 * ***************************************************************************************************************
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276 */
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277
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278 def process_well(baseDir, input_wellId, n_image_per_well){ //, perform_bc, mediaChangeTime){
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279 File bf_dir = baseDir.listFiles().find{ it =~ /.*Phase.*/}
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280 File green_dir = baseDir.listFiles().find{ it =~ /.*Green.*/}
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281 File red_dir = baseDir.listFiles().find{ it =~ /.*Red.*/}
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282 //if (verbose) println bf_dir
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283 //if (verbose) println green_dir
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284
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285 // The images are stored in a TreeMap where
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286 // keys are wellSampleId = field identifier
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287 // values are a TreeMap that we call channelMap where:
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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288 // keys are colors (Green, Grays, Red)
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289 // values are an ImagePlus (T-stack)
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290 Map<Integer, Map<String, ImagePlus>> sampleToChannelMap = new TreeMap<>()
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291
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292 List<File> folder_list = [bf_dir, green_dir, red_dir]
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293 List<String> channels_list = ["Grays", "Green", "Red"]
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294
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295 // loop over the field and open images
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296 for(int wellSampleId = 1; wellSampleId <= n_image_per_well; wellSampleId++) {
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297 // nT is the number of time-points for the well input_wellId
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298 int nT = 0
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299 String first_channel = ""
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mvdbeek
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diff changeset
300 String first_acq_date = ""
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
301 String first_acq_time = ""
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
302 String rel_acq_hour = ""
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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diff changeset
303
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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diff changeset
304 // Initiate a channel map for the wellSampleId
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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diff changeset
305 Map<String, ImagePlus> channelMap = new TreeMap<>()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
306
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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diff changeset
307 // Checking if there are images in the corresponding dir
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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diff changeset
308 // which corresponds to the input_wellId
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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diff changeset
309 // and to the wellSampleId
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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310 // The image name should be:
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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diff changeset
311 // Prefix + "_" + input_wellId + "_" + wellSampleId + "_" + year (4 digits) + "y" + month (2 digits) + "m" + day + "d_" + hour + "h" + minute + "m.tif"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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312 FileFilter fileFilter = new WildcardFileFilter("*_" + input_wellId + "_" + wellSampleId + "_*")
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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313 for(int i = 0; i < folder_list.size(); i++){
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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314 if (folder_list.get(i) != null) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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315 File[] files_matching = folder_list.get(i).listFiles(fileFilter as FileFilter).sort()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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316 if (files_matching.size() != 0) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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317 // In order to deal with raw images from Incucyte which are
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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318 // Multi series images
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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319 // We open the first image
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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320 ImagePlus first_imp = Opener.openUsingBioFormats(files_matching[0].getAbsolutePath())
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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321 // We check if we can read the infos
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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322 first_image_infos = Opener.getTiffFileInfo(files_matching[0].getAbsolutePath())
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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diff changeset
323 // We define the imageplus object
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
324 ImagePlus single_channel_imp
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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325 if (first_image_infos == null) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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326 // They are raw from incucyte
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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diff changeset
327 // We need to open images one by one and add them to the stack
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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328 ImageStack stack = new ImageStack(first_imp.width, first_imp.height);
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
329 files_matching.each{
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
330 ImagePlus single_imp = (new Opener()).openUsingBioFormats(it.getAbsolutePath())
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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331 String new_title = single_imp.getTitle().split(" - ")[0]
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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diff changeset
332 stack.addSlice(new_title, single_imp.getProcessor())
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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333 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
334 single_channel_imp = new ImagePlus(FilenameUtils.getBaseName(folder_list.get(i).getAbsolutePath()), stack);
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
335 } else {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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336 // They are regular tif file
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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337 // We can use FolderOpener to create the stack at once
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
338 single_channel_imp = FolderOpener.open(folder_list.get(i).getAbsolutePath(), " filter=_"+ input_wellId + "_"+wellSampleId+"_")
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
339 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
340 // Phase are 8-bit and need to be changed to 16-bit
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
341 // Other are already 16-bit but it does not hurt
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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diff changeset
342 IJ.run(single_channel_imp, "16-bit", "")
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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343
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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344 // check frame size
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
345 if (nT == 0) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
346 // This is the first channel with images
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
347 nT = single_channel_imp.getNSlices()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
348 first_channel = channels_list.get(i)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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349 // Process all dates:
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
350 Pattern date_pattern = Pattern.compile(REGEX_FOR_DATE)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
351 ImageStack stack = single_channel_imp.getStack()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
352 // Go to the first time (which is slice)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
353 single_channel_imp.setSlice(1)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
354 int currentSlice = single_channel_imp.getCurrentSlice()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
355 String label = stack.getSliceLabel(currentSlice)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
356 LocalDateTime dateTime_ref = getDate(label, date_pattern)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
357 if (dateTime_ref == null) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
358 date_pattern = Pattern.compile(ALTERNATIVE_REGEX_FOR_DATE)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
359 dateTime_ref = getDate(label, date_pattern)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
360 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
361 if (dateTime_ref != null) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
362 first_acq_date = dateTime_ref.format(DateTimeFormatter.ofPattern("yyyy-MM-dd"))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
363 first_acq_time = dateTime_ref.format(DateTimeFormatter.ofPattern("HH:mm:ss"))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
364 for (int ti = 2; ti<= nT; ti++) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
365 // Process each frame starting at 2
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
366 single_channel_imp.setSlice(ti)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
367 int hours = getHoursFromImp(single_channel_imp, stack, dateTime_ref, date_pattern)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
368 if (rel_acq_hour == "") {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
369 rel_acq_hour = "" + hours
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
370 } else {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
371 rel_acq_hour += "," + hours
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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diff changeset
372 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
373 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
374 } else {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
375 first_acq_date = "NA"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
376 first_acq_time = "NA"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
377 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
378 } else {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
379 assert single_channel_imp.getNSlices() == nT : "The number of "+channels_list.get(i)+" images for well "+input_wellId+" and field " + wellSampleId + " does not match the number of images in " + first_channel + "."
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
380 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
381 // Set acquisition properties
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
382 single_channel_imp.setProperty(FIRST_ACQUISITION_DATE, first_acq_date)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
383 single_channel_imp.setProperty(FIRST_ACQUISITION_TIME, first_acq_time)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
384 single_channel_imp.setProperty(RELATIVE_ACQUISITION_HOUR, rel_acq_hour)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
385 println single_channel_imp.getProperty(FIRST_ACQUISITION_DATE)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
386 println single_channel_imp.getProperty(FIRST_ACQUISITION_TIME)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
387 // add the image stack to the channel map for the corresponding color
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
388 channelMap.put(channels_list.get(i), single_channel_imp)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
389 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
390 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
391 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
392 if (nT != 0) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
393 // add the channelmap to the sampleToChannelMap using the wellSampleId as key
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
394 sampleToChannelMap.put(wellSampleId, channelMap)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
395 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
396 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
397
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
398 ArrayList<ImagePlus> final_imp_list = []
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
399
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
400 // Now loop over the wellSampleId which have images
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
401 for(Integer wellSampleId : sampleToChannelMap.keySet()){
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
402 // get the channel map
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
403 Map<String, ImagePlus> channelsMap = sampleToChannelMap.get(wellSampleId)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
404 ArrayList<String> channels = []
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
405 ArrayList<ImagePlus> current_images = []
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
406
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
407 for(String channel : channelsMap.keySet()){
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
408 channels.add(channel)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
409 current_images.add(channelsMap.get(channel))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
410 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
411 // Get number of time:
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
412 int nT = current_images[0].nSlices
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
413
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
414 // Merge all
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
415 ImagePlus merged_imps = Concatenator.run(current_images as ImagePlus[])
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
416 // Re-order to make a multi-channel, time-lapse image
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
417 ImagePlus final_imp
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
418 if (channels.size() == 1 && nT == 1) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
419 final_imp = merged_imps
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
420 } else {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
421 final_imp = HyperStackConverter.toHyperStack(merged_imps, channels.size() , 1, nT, "xytcz", "Color")
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
422 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
423 // add properties to the image
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
424 final_imp.setProperty(DIMENSION_ORDER, DimensionOrder.XYCZT)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
425 final_imp.setProperty(IMG_POS_IN_WELL, wellSampleId)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
426 final_imp.setProperty(FIRST_ACQUISITION_DATE, current_images[0].getProperty(FIRST_ACQUISITION_DATE))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
427 final_imp.setProperty(FIRST_ACQUISITION_TIME, current_images[0].getProperty(FIRST_ACQUISITION_TIME))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
428 final_imp.setProperty(RELATIVE_ACQUISITION_HOUR, current_images[0].getProperty(RELATIVE_ACQUISITION_HOUR))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
429
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
430 // set LUTs
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
431 (0..channels.size()-1).each{
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
432 final_imp.setC(it + 1)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
433 IJ.run(final_imp, channels[it], "")
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
434 final_imp.resetDisplayRange()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
435 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
436
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
437 final_imp_list.add(final_imp)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
438 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
439
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
440 return final_imp_list
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
441 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
442
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
443
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
444 /**
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
445 * create the full XML metadata (plate, images, channels, annotations....)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
446 *
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
447 * @param imagesName
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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448 * @param keyValuesPerWell
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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449 * @param globalKeyValues
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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450 * @param pixelSize
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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451 * @return OME-XML metadata instance
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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452 */
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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diff changeset
453 def buildXMLFile(Map<String,List<ImagePlus>> wellToImagesMap, Map<String, List<MapPair>> keyValuesPerWell, List<MapPair> globalKeyValues, double pixelSize) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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454 // create a new OME-XML metadata instance
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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455 OME ome = new OME()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
456
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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457 Map<String, Integer> imgInWellPosToListMap = new HashMap<>()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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458 int imgCmp = 0
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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459 for (String wellId: wellToImagesMap.keySet()) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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460 // get well position from image name
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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461 List<ImagePlus> imagesWithinWell = wellToImagesMap.get(wellId)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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462
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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463 for (ImagePlus image : imagesWithinWell) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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464 // get KVP corresponding to the current well
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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465 // Initiate a list of keyValues for the wellId
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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466 // (or use the existing one)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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467 List<MapPair> keyValues = []
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
468 if(keyValuesPerWell.containsKey(wellId))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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469 keyValues = keyValuesPerWell.get(wellId)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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470 keyValues.addAll(globalKeyValues)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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471
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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472 // create an Image node in the ome-xml
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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473 imgInWellPosToListMap.put(wellId+ "_" +image.getProperty(IMG_POS_IN_WELL),imgCmp)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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474 ome.addImage(makeImage(imgCmp++, image, keyValues, pixelSize))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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475 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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476 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
477
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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478 // create Plate node
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
479 ome.addPlate(makePlate(wellToImagesMap, imgInWellPosToListMap, pixelSize, ome))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
480
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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481 // add annotation nodes
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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482 ome.setStructuredAnnotations(annotations)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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483
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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484 return ome
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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485 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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486
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
487 /**
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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488 * create an image xml-element, populated with annotations, channel, pixels and path elements
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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489 *
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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490 * @param index image ID
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
491 * @param imageName
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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492 * @param keyValues
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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493 * @param pixelSize
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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494 * @return an image xml-element
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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495 */
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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496 def makeImage(int index, ImagePlus imagePlus, List<MapPair> keyValues, double pixelSize) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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497 // Create <Image/>
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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498 Image image = new Image()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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499 image.setID("Image:" + index)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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500 // The image name is the name of the file without extension
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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diff changeset
501 image.setName(((String)imagePlus.getProperty(FILE_NAME)).split("\\.")[0])
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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502 // Set the acquisitionDate:
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
503 if (imagePlus.getProperty(FIRST_ACQUISITION_DATE) != "NA") {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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diff changeset
504 image.setAcquisitionDate(new Timestamp(imagePlus.getProperty(FIRST_ACQUISITION_DATE) + "T" + imagePlus.getProperty(FIRST_ACQUISITION_TIME)))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
505 // Also add it to the key values:
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
506 keyValues.add(new MapPair("acquisition.day", (String)imagePlus.getProperty(FIRST_ACQUISITION_DATE)))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
507 keyValues.add(new MapPair("acquisition.time", (String)imagePlus.getProperty(FIRST_ACQUISITION_TIME)))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
508 keyValues.add(new MapPair("relative.acquisition.hours", (String)imagePlus.getProperty(RELATIVE_ACQUISITION_HOUR)))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
509 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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510 // Create <MapAnnotations/>
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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511 MapAnnotation mapAnnotation = new MapAnnotation()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
512 mapAnnotation.setID("ImageKeyValueAnnotation:" + index)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
513 mapAnnotation.setNamespace(GENERAL_ANNOTATION_NAMESPACE)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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514 mapAnnotation.setValue(keyValues)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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515 annotations.addMapAnnotation(mapAnnotation); // add the KeyValues to the general structured annotation element
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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516 image.linkAnnotation(mapAnnotation)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
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parents:
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517
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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518 // Create <Pixels/>
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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519 Pixels pixels = new Pixels()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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520 pixels.setID("Pixels:" + index)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
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521 pixels.setSizeX(new PositiveInteger(imagePlus.getWidth()))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
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diff changeset
522 pixels.setSizeY(new PositiveInteger(imagePlus.getHeight()))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
523 pixels.setSizeZ(new PositiveInteger(imagePlus.getNSlices()))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
524 pixels.setSizeC(new PositiveInteger(imagePlus.getNChannels()))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
525 pixels.setSizeT(new PositiveInteger(imagePlus.getNFrames()))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
526 pixels.setDimensionOrder((DimensionOrder) imagePlus.getProperty(DIMENSION_ORDER))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
527 pixels.setType(getPixelType(imagePlus))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
528 pixels.setPhysicalSizeX(new Length(pixelSize, UNITS.MICROMETER))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
529 pixels.setPhysicalSizeY(new Length(pixelSize, UNITS.MICROMETER))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
530
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
531 // Create <TiffData/> under <Pixels/>
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
532 TiffData tiffData = new TiffData()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
533 tiffData.setFirstC(new NonNegativeInteger(0))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
534 tiffData.setFirstT(new NonNegativeInteger(0))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
535 tiffData.setFirstZ(new NonNegativeInteger(0))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
536 tiffData.setPlaneCount(new NonNegativeInteger(imagePlus.getNSlices()*imagePlus.getNChannels()*imagePlus.getNFrames()))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
537
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
538 // Create <UUID/> under <TiffData/>
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
539 UUID uuid = new UUID()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
540 uuid.setFileName((String)imagePlus.getProperty(FILE_NAME))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
541 uuid.setValue(java.util.UUID.randomUUID().toString())
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
542 tiffData.setUUID(uuid)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
543
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
544 // Put <TiffData/> under <Pixels/>
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
545 pixels.addTiffData(tiffData)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
546
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
547 // Create <Channel/> under <Pixels/>
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
548 LUT[] luts = imagePlus.getLuts()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
549 for (int i = 0; i < luts.length; i++) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
550 Channel channel = new Channel()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
551 channel.setID("Channel:" + i)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
552 channel.setColor(new Color(luts[i].getRed(255),luts[i].getGreen(255), luts[i].getBlue(255),255))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
553 pixels.addChannel(channel)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
554 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
555
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
556 // Put <Pixels/> under <Image/>
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
557 image.setPixels(pixels)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
558
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
559 return image
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
560 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
561
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
562
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
563 /**
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
564 * get pixel type based on the imagePlus type
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
565 * @param imp
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
566 * @return pixel type
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
567 */
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
568 def getPixelType(ImagePlus imp){
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
569 switch (imp.getType()) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
570 case ImagePlus.GRAY8:
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
571 return PixelType.UINT8
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
572 case ImagePlus.GRAY16:
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
573 return PixelType.UINT16
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
574 case ImagePlus.GRAY32:
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
575 return PixelType.FLOAT
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
576 default:
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
577 return PixelType.FLOAT
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
578 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
579 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
580
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
581 /**
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
582 * create a Plate xml-element, populated with wells and their attributes
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
583 * @param imagesName
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
584 * @return Plate xml-element
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
585 */
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
586 def makePlate(Map<String, List<ImagePlus>> wellToImagesMap, Map<String, Integer> imgPosInListMap, double pixelSize, OME ome) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
587 // Create <Plate/>
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
588 Plate plate = new Plate()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
589 plate.setName(PLATE_NAME)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
590 plate.setID(PLATE_ID)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
591 plate.setRows(WELL_ROWS)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
592 plate.setColumns(WELL_COLS)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
593 plate.setRowNamingConvention(WELL_ROW)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
594 plate.setColumnNamingConvention(WELL_COL)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
595
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
596 // for each image (one image per well)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
597 for (String wellId: wellToImagesMap.keySet()) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
598 // get well position from image name
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
599 List<ImagePlus> imagesWithinWell = wellToImagesMap.get(wellId)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
600
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
601 // get well position from image name
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
602 int row = convertLetterToNumber(wellId.substring(0, 1))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
603 int col = Integer.parseInt(wellId.substring(1)) - 1
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
604
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
605 // row and col should correspond to a real well
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
606 if(row >= 0 && col >= 0 && col < 12) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
607 // Create <Well/> under <Plate/>
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
608 Well well = new Well()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
609 well.setID(String.format("Well:%d_%d", row, col))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
610 well.setRow(new NonNegativeInteger(row))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
611 well.setColumn(new NonNegativeInteger(col))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
612
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
613 for (ImagePlus imagePlus : imagesWithinWell) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
614 int wellSampleIndex = imgPosInListMap.get(wellId + "_" + imagePlus.getProperty(IMG_POS_IN_WELL))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
615
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
616 // Create <WellSample/> under <Well/>
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
617 WellSample sample = new WellSample()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
618 sample.setID(String.format("WellSample:%d", wellSampleIndex))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
619 sample.setIndex(new NonNegativeInteger(wellSampleIndex))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
620 if (imagePlus.getCalibration() != null) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
621 sample.setPositionX(new Length(imagePlus.getCalibration().xOrigin * pixelSize, UNITS.MICROMETER))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
622 sample.setPositionY(new Length(imagePlus.getCalibration().yOrigin * pixelSize, UNITS.MICROMETER))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
623 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
624 sample.linkImage(ome.getImage(wellSampleIndex))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
625
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
626 // Put <WellSample/> under <Well/>
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
627 well.addWellSample(sample)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
628 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
629
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
630 // Put <Well/> under <Plate/>
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
631 plate.addWell(well)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
632 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
633 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
634 return plate
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
635 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
636
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
637 /**
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
638 * convert the XML metadata document into string
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
639 *
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
640 * @param document
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
641 * @return
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
642 * @throws TransformerException
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
643 * @throws UnsupportedEncodingException
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
644 */
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
645 def asString(Document document) throws TransformerException, UnsupportedEncodingException {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
646 TransformerFactory transformerFactory = TransformerFactory.newInstance()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
647 Transformer transformer = transformerFactory.newTransformer()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
648
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
649 //Setup indenting to "pretty print"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
650 transformer.setOutputProperty(OutputKeys.INDENT, "yes")
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
651 transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4")
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
652
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
653 Source source = new DOMSource(document)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
654 ByteArrayOutputStream os = new ByteArrayOutputStream()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
655 Result result = new StreamResult(new OutputStreamWriter(os, "utf-8"))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
656 transformer.transform(source, result)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
657
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
658 return os.toString()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
659 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
660
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
661 /**
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
662 * add document header
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
663 *
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
664 * @param root
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
665 * @param document
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
666 */
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
667 def postProcess(Element root, Document document) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
668 root.setAttribute("xmlns", XML_NS)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
669 root.setAttribute("xmlns:xsi", XSI_NS)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
670 root.setAttribute("xsi:schemaLocation", XML_NS + " " + SCHEMA_LOCATION)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
671 root.setAttribute("UUID", java.util.UUID.randomUUID().toString())
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
672 document.appendChild(root)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
673 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
674
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
675
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
676 /**
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
677 * read Incucyte plate-scheme XML file, extract attributes per well and convert attributes to OMERO-compatible
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
678 * keys-value pairs XML elements.
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
679 *
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
680 * @param path Incucyte plate-scheme XML file path
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
681 * @return Map of OME-XML compatible key-values per well
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
682 */
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
683 def parseIncucyteXML(String path, Boolean ignoreConcentration, Boolean ignorePassage, Boolean ignoreSeeding) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
684 Map<String, List<MapPair>> keyValuesPerWell = new HashMap<>()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
685
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
686 final String rowAttribute = "row"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
687 final String columnAttribute = "col"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
688
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
689 final String wellNode = "well"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
690 final String itemsNode = "items"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
691 final String wellItemNode = "wellItem"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
692 final String referenceItemNode = "referenceItem"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
693
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
694 // There are 3 types of referenceItem: Compound, CellType, GrowthCondition
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
695 //
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
696 // For the Compound, each well can have a concentration and a concentrationUnits
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
697 // the referenceItem has a displayName
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
698 // The key should be: displayName (concentrationUnits)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
699 // The value should be: concentration
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
700 // However, if ignoreConcentration is set to true:
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
701 // The key should be: displayName (NA)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
702 // The value should be: 1
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
703 //
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
704 // For the CellType, each well can have a passage, a seedingDensity and a seedingDensityUnits
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
705 // the referenceItem has a displayName
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
706 // The passage key should be: displayName_passage
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
707 // The value should be: passage
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
708 // However, if ignorePassage is set to true no key value should be stored for this
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
709 // Then:
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
710 // The seeding key should be: displayName_seedingDensity (seedingDensityUnits)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
711 // The value should be: seedingDensity
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
712 // However, if ignoreSeeding is set to true:
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
713 // The key should be: displayName
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
714 // The value should be: "yes"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
715 //
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
716 // For the GrowthCondition, the referenceItem has a displayName
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
717 // The key should be: displayName
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
718 // The value should be: "yes"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
719
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
720 try {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
721 // create an document
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
722 DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
723 DocumentBuilder dBuilder = dbFactory.newDocumentBuilder()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
724
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
725 // read the xml file
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
726 Document doc = dBuilder.parse(new File(path))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
727 doc.getDocumentElement().normalize()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
728
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
729 // get all "well" nodes
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
730 NodeList wellList = doc.getElementsByTagName(wellNode)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
731
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
732 for(int i = 0; i < wellList.getLength(); i++) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
733 Node well = wellList.item(i)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
734
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
735 // extract well attributes
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
736 String row = well.getAttributes().getNamedItem(rowAttribute).getTextContent()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
737 int r = row as int
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
738 String col = well.getAttributes().getNamedItem(columnAttribute).getTextContent()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
739 String wellNumber = LETTERS.substring(r, r + 1) + (Integer.parseInt(col)+ 1)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
740
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
741 // extract items node, under well node
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
742 Node items = ((Element)well).getElementsByTagName(itemsNode).item(0)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
743 if (items != null) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
744 // get all "wellItem" nodes, under items node
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
745 NodeList wellItemList = ((Element)items).getElementsByTagName(wellItemNode)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
746
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
747 // read referenceItem node's attributes and convert them into key-values
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
748 List<MapPair> keyValues = new ArrayList<>()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
749 for (int j = 0; j < wellItemList.getLength(); j++) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
750 Node wellItem = wellItemList.item(j)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
751 // extract referenceItem node, under wellItem node
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
752 Node referenceItem = ((Element)wellItem).getElementsByTagName(referenceItemNode).item(0)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
753 String wellType = wellItem.getAttributes().getNamedItem("type").getTextContent()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
754
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
755 // select the right key-values
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
756 switch (wellType){
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
757 case "Compound":
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
758 String compound_name = referenceItem.getAttributes().getNamedItem("displayName").getTextContent()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
759 if (ignoreConcentration) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
760 keyValues.add(new MapPair(compound_name + " (NA)", "1"))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
761 } else {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
762 String unit = wellItem.getAttributes().getNamedItem("concentrationUnits").getTextContent()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
763 unit = unit.replace("\u00B5", "u")
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
764 String value = wellItem.getAttributes().getNamedItem("concentration").getTextContent()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
765 keyValues.add(new MapPair(compound_name + " (" + unit + ")", value))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
766 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
767 break
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
768 case "CellType":
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
769 String cell_name = referenceItem.getAttributes().getNamedItem("displayName").getTextContent()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
770 if (!ignorePassage) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
771 String passage = wellItem.getAttributes().getNamedItem("passage").getTextContent()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
772 keyValues.add(new MapPair(cell_name + "_passage", passage))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
773 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
774 if (ignoreSeeding) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
775 keyValues.add(new MapPair(cell_name, "yes"))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
776 } else {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
777 String unit = wellItem.getAttributes().getNamedItem("seedingDensityUnits").getTextContent()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
778 unit = unit.replace("\u00B5", "u")
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
779 String value = wellItem.getAttributes().getNamedItem("seedingDensity").getTextContent()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
780 keyValues.add(new MapPair(cell_name + "_seedingDensity (" + unit + ")", value))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
781 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
782 break
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
783 case "GrowthCondition":
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
784 String growth_condition = referenceItem.getAttributes().getNamedItem("displayName").getTextContent()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
785 keyValues.add(new MapPair(growth_condition, "yes"))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
786 break
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
787 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
788 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
789 keyValuesPerWell.put(wellNumber,keyValues)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
790
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
791 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
792 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
793 return keyValuesPerWell
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
794 } catch (Exception e) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
795 println "XML platemap could not be parsed"
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
796 e.printStackTrace()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
797 return new HashMap<>()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
798 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
799 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
800
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
801 /**
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
802 * make a list of all key-values that are common to all images
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
803 *
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
804 * @param objective
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
805 * @param commonKeyValues (a String with the following format: key1=value1;key2=value2)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
806 * @return a list of OME-XML key-values
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
807 */
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
808 def getGlobalKeyValues(int objective, String commonKeyValues){
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
809 List<MapPair> keyValues = new ArrayList<>()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
810 keyValues.add(new MapPair("groovy_version", VERSION))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
811 keyValues.add(new MapPair("objective", objectives[objective]))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
812 if (commonKeyValues != "") {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
813 String[] keyValList = commonKeyValues.split(';')
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
814 for (int i = 0; i < keyValList.size(); i ++) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
815 String keyval = keyValList[i]
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
816 String[] keyvalsplit = keyval.split('=')
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
817 int nPieces = keyvalsplit.size()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
818 String value = keyvalsplit[nPieces - 1]
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
819 String key = keyvalsplit[0]
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
820 // In case there are '=' in key
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
821 for (int j = 1; j < nPieces - 1; j++) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
822 key += '=' + keyvalsplit[j]
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
823 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
824 keyValues.add(new MapPair(key, value))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
825 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
826 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
827 return keyValues
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
828 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
829
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
830 /**
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
831 * convert alphanumeric well position to numeric position
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
832 *
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
833 * @param letter
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
834 * @return
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
835 */
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
836 def convertLetterToNumber(String letter){
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
837 for (int i = 0; i < LETTERS.size(); i++) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
838 if (LETTERS.substring(i, i + 1) == letter) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
839 return i
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
840 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
841 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
842 return -1
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
843 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
844
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
845 // Returns a date from a label and a date_pattern
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
846 def getDate(String label, Pattern date_pattern){
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
847 // println "Trying to get date from " + label
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
848 Matcher date_m = date_pattern.matcher(label)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
849 LocalDateTime dateTime
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
850 if (date_m.matches()) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
851 if (date_m.groupCount() == 5) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
852 dateTime = LocalDateTime.parse(date_m.group(1) + "-" + date_m.group(2) + "-" + date_m.group(3) + "T" + date_m.group(4) + ":" + date_m.group(5))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
853 } else {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
854 dateTime = LocalDateTime.parse("1970-01-" + 1 + (date_m.group(1) as int) + "T" + date_m.group(2) + ":" + date_m.group(3))
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
855 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
856 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
857 // println "Found " + dateTime
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
858 return dateTime
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
859 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
860
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
861 // Returns the number of hours
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
862 def getHoursFromImp(ImagePlus imp, ImageStack stack, LocalDateTime dateTime_ref, Pattern date_pattern){
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
863 int currentSlice = imp.getCurrentSlice()
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
864 String label = stack.getSliceLabel(currentSlice)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
865 LocalDateTime dateTime = getDate(label, date_pattern)
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
866 if (dateTime != null) {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
867 return ChronoUnit.HOURS.between(dateTime_ref, dateTime) as int
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
868 } else {
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
869 return -1
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
870 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
871 }
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
872
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
873
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
874 /**
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
875 * *****************************************************************************************************************
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
876 * ************************************************* Imports ****************************************************
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
877 * ****************************************************************************************************************
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
878 */
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
879
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
880
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
881 import ij.IJ
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
882 import ij.ImagePlus
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
883 import ij.ImageStack
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
884 import ij.io.FileSaver
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
885 import ij.io.Opener
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
886 import ij.plugin.Concatenator
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
887 import ij.plugin.FolderOpener
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
888 import ij.plugin.HyperStackConverter
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
889 import ij.process.LUT
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
890
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
891 import java.awt.GraphicsEnvironment
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
892 import java.io.File
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
893 import java.time.format.DateTimeFormatter
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
894 import java.time.LocalDateTime
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
895 import java.time.temporal.ChronoUnit
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
896 import java.util.stream.Collectors
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
897 import java.util.stream.IntStream
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
898 import java.util.regex.*
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
899
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
900 import javax.xml.parsers.DocumentBuilder
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
901 import javax.xml.parsers.DocumentBuilderFactory
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mvdbeek
parents:
diff changeset
902 import javax.xml.transform.OutputKeys
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mvdbeek
parents:
diff changeset
903 import javax.xml.transform.Result
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mvdbeek
parents:
diff changeset
904 import javax.xml.transform.Source
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mvdbeek
parents:
diff changeset
905 import javax.xml.transform.Transformer
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mvdbeek
parents:
diff changeset
906 import javax.xml.transform.TransformerException
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mvdbeek
parents:
diff changeset
907 import javax.xml.transform.TransformerFactory
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mvdbeek
parents:
diff changeset
908 import javax.xml.transform.dom.DOMSource
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mvdbeek
parents:
diff changeset
909 import javax.xml.transform.stream.StreamResult
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mvdbeek
parents:
diff changeset
910
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mvdbeek
parents:
diff changeset
911 import ome.units.UNITS
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mvdbeek
parents:
diff changeset
912 import ome.units.quantity.Length
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mvdbeek
parents:
diff changeset
913
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mvdbeek
parents:
diff changeset
914 import ome.xml.model.Channel
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mvdbeek
parents:
diff changeset
915 import ome.xml.model.Image
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mvdbeek
parents:
diff changeset
916 import ome.xml.model.MapAnnotation
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mvdbeek
parents:
diff changeset
917 import ome.xml.model.MapPair
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mvdbeek
parents:
diff changeset
918 import ome.xml.model.OME
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mvdbeek
parents:
diff changeset
919 import ome.xml.model.Pixels
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mvdbeek
parents:
diff changeset
920 import ome.xml.model.Plate
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mvdbeek
parents:
diff changeset
921 import ome.xml.model.StructuredAnnotations
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mvdbeek
parents:
diff changeset
922 import ome.xml.model.TiffData
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mvdbeek
parents:
diff changeset
923 import ome.xml.model.UUID
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mvdbeek
parents:
diff changeset
924 import ome.xml.model.Well
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mvdbeek
parents:
diff changeset
925 import ome.xml.model.WellSample
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mvdbeek
parents:
diff changeset
926 import ome.xml.model.enums.DimensionOrder
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mvdbeek
parents:
diff changeset
927 import ome.xml.model.enums.NamingConvention
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mvdbeek
parents:
diff changeset
928 import ome.xml.model.enums.PixelType
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mvdbeek
parents:
diff changeset
929 import ome.xml.model.primitives.Color
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mvdbeek
parents:
diff changeset
930 import ome.xml.model.primitives.NonNegativeInteger
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mvdbeek
parents:
diff changeset
931 import ome.xml.model.primitives.PositiveInteger
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mvdbeek
parents:
diff changeset
932 import ome.xml.model.primitives.Timestamp
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
933
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
934 import org.apache.commons.io.filefilter.WildcardFileFilter
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mvdbeek
parents:
diff changeset
935 import org.apache.commons.io.FilenameUtils
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mvdbeek
parents:
diff changeset
936
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
937 import org.w3c.dom.Document
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
938 import org.w3c.dom.Element
a599551e800d planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364-dirty
mvdbeek
parents:
diff changeset
939 import org.w3c.dom.Node
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mvdbeek
parents:
diff changeset
940 import org.w3c.dom.NodeList