Mercurial > repos > lldelisle > incucyte_stack_and_upload_omero
changeset 0:e1cba36becb2 draft
planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
| author | lldelisle |
|---|---|
| date | Tue, 19 Dec 2023 15:02:41 +0000 |
| parents | |
| children | 3c942429f610 |
| files | README.md incucyte_stack_and_upload_omero.xml stack_buildXml.groovy upload_omero.sh |
| diffstat | 4 files changed, 1269 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Tue Dec 19 15:02:41 2023 +0000 @@ -0,0 +1,9 @@ +I don't know why but I need to run the macro once on GUI before being able to run it in CLI... +```bash +ssh -Y updubsrv1 +. '/data/galaxy/galaxy/var/dependencies/_conda/bin/activate' /data/galaxy/galaxy/var/dependencies/_conda/envs/mulled-v1-db2fcfa8be636326417c50715ab9fec065adbfde66cca33b4958bee1dd8ad945/ +sudo chmod -R 777 /data/galaxy/galaxy/var/dependencies/_conda/envs/mulled-v1-db2fcfa8be636326417c50715ab9fec065adbfde66cca33b4958bee1dd8ad945/bin/../uprefs/ +ImageJ +# I need to check what changed in uprefs + +```
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/incucyte_stack_and_upload_omero.xml Tue Dec 19 15:02:41 2023 +0000 @@ -0,0 +1,303 @@ +<tool id="incucyte_stack_and_upload_omero" name="Stack Incucyte Plate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="BSD-3"> + <description>And upload to omero</description> + <macros> + <token name="@TOOL_VERSION@">20231219</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <requirements> + <requirement type="package" version="20220414">Fiji</requirement> + <requirement type="package" version="5.13.1">omero-py</requirement> + <requirement type="package" version="5.1.0">gawk</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #import os + ## the user wants to use a non-public OMERO instance + ## check if credentials are set in the user-preferences, if not warn the user and exit + #set $username = $__user__.extra_preferences.get('omero_account|username', "") + #set $password = $__user__.extra_preferences.get('omero_account|password', "") + + #if str($upload_omero.upload_omero_select) == "yes": + #if ($username == "" or $password ==""): + echo "OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" 1>&2 && + exit 1 && + #end if + #set $incucyteXMLFile = str($upload_omero.incucyteXMLFile) + #set $objectiveChoice = str($upload_omero.objectiveChoice) + #set $startStage = str($upload_omero.startStage) + #set $plateName = str($upload_omero.plateName) + #set $ignoreConcentration = str($upload_omero.ignoreConcentration) + #set $ignorePassage = str($upload_omero.ignorePassage) + #set $ignoreSeeding = str($upload_omero.ignoreSeeding) + #else + #set $incucyteXMLFile = "inexisting.plateMap" + #set $objectiveChoice = "4x" + #set $startStage = "72" + #set $plateName = "Experiment:0" + #set $ignoreConcentration = "true" + #set $ignorePassage = "true" + #set $ignoreSeeding = "true" + #end if + + ## Prefix to directories provided by users + #set $prefix = "/data/mount_s3/image_storage/" + ## Prepare input and output directories to match groovy expectations + mkdir input && + mkdir output && + #if str($structure.structure_type) == "directory": + #set $original_file = "" + #if str($structure.phase_dir_s3) != "": + #if not os.path.isdir($prefix + "/" + str($structure.phase_dir_s3)): + echo "'${prefix}/${structure.phase_dir_s3}'" && + echo "Phase dir $structure.phase_dir_s3 does not exists" && + exit 1 && + #end if + mkdir input/Phase/ && + ln -s '${prefix}/${structure.phase_dir_s3}/'*'${structure.pattern}'* input/Phase/ && + #set $original_file = str($structure.phase_dir_s3) + #end if + #if str($structure.green_dir_s3) != "": + #if not os.path.isdir($prefix + "/" + str($structure.green_dir_s3)): + echo "Green dir $structure.green_dir_s3 does not exists" && + exit 1 && + #end if + mkdir input/Green/ && + ln -s '${prefix}/${structure.green_dir_s3}/'*'${structure.pattern}'* input/Green/ && + #set $original_file = $original_file + "," + str($structure.green_dir_s3) + #end if + #if str($structure.red_dir_s3) != "": + #if not os.path.isdir($prefix + "/" + str($structure.red_dir_s3)): + echo "Red dir $structure.red_dir_s3 does not exists" && + exit 1 && + #end if + mkdir input/Red/ && + ln -s '${prefix}/${structure.red_dir_s3}/'*'${structure.pattern}'* input/Red/ && + #set $original_file = $original_file + "," + str($structure.red_dir_s3) + #end if + #else: + #if not os.path.isdir($prefix + "/" + str($structure.base_dir)): + echo "Base dir $structure.base_dir does not exists" && + exit 1 && + #end if + #set $original_file = str($structure.base_dir) + #if str($structure.phase_key) != "": + mkdir input/Phase/ && + ln -s '${prefix}/${structure.base_dir}/'*'${structure.phase_key}'* input/Phase/ && + #end if + #if str($structure.green_key) != "": + mkdir input/Green/ && + ln -s '${prefix}/${structure.base_dir}/'*'${structure.green_key}'* input/Green/ && + #end if + #if str($structure.red_key) != "": + mkdir input/Red/ && + ln -s '${prefix}/${structure.base_dir}/'*'${structure.red_key}'* input/Red/ && + #end if + #end if + ## Run the groovy + ImageJ --ij2 --headless --console --run '$__tool_directory__/'stack_buildXml.groovy + 'base_dir="input/",output_dir="output/",incucyteXMLFile="$incucyteXMLFile",objectiveChoice="$objectiveChoice",nWells="${nWells}",n_images_per_well="${n_images_per_well}",plateName="$plateName",commonKeyValues="original_file=${original_file};start_stage=$startStage",xmlName="$plateName",ignoreConcentration="$ignoreConcentration",ignorePassage="$ignorePassage",ignoreSeeding="$ignoreSeeding"' > output.log + ## Upload to omero + #if str($upload_omero.upload_omero_select) == "yes": + && bash '$__tool_directory__/'upload_omero.sh '$upload_omero.omero_host' '$credentials' '$upload_omero.screen.screen_create' '$upload_omero.screen.screenNameOrID' >> output.log + ## Copy the companion.ome + && cp output/*.companion.ome output.companion.ome + #end if + ]]></command> + <configfiles> + <configfile name="credentials"><![CDATA[ + #set $username = $__user__.extra_preferences.get('omero_account|username', "") + #set $password = $__user__.extra_preferences.get('omero_account|password', "") +$username +$password + ]]></configfile> + </configfiles> + <inputs> + <conditional name="structure"> + <param name="structure_type" type="select" label="How are your data organized?" > + <option value="directory">One directory per channel</option> + <option value="keyword">All channels into the same directory</option> + </param> + <when value="directory"> + <param name="phase_dir_s3" type="text" value="" label="Directory on s3 with Phase images (leave empty if no)" help="For example Pierre/EXP001/My_expe_Phase"/> + <param name="green_dir_s3" type="text" value="" label="Directory on s3 with Green images (leave empty if no)" help="For example Pierre/EXP001/My_expe_Green"/> + <param name="red_dir_s3" type="text" value="" label="Directory on s3 with Red images (leave empty if no)" help="For example Pierre/EXP001/My_expe_Red"/> + <param name="pattern" type="text" value="" label="Pattern to restrict to only some wells" help="For example A2"/> + </when> + <when value="keyword"> + <param name="base_dir" type="text" value="" label="Directory on s3 with all images" help="For example Lucille/MyIncucyte/20230213/"/> + <param name="phase_key" type="text" value="" label="Word that can identify all Phase images (leave empty if no)" help="For example Phase or Brightfield"/> + <param name="green_key" type="text" value="" label="Word that can identify all Green images (leave empty if no)" help="For example Green or green or GFP"/> + <param name="red_key" type="text" value="" label="Word that can identify all Red images (leave empty if no)" help="For example Red or red"/> + </when> + </conditional> + <param name="nWells" type="select" label="Number of wells into your plate" > + <option value="96">96</option> + <option value="384">384</option> + </param> + <param name="n_images_per_well" type="integer" min="1" value="1" label="Maximum number of images per well" /> + <conditional name="upload_omero"> + <param name="upload_omero_select" type="select" label="Upload your images to omero?" > + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param name="incucyteXMLFile" type="data" format="xml" label="Incucyte PlateMap" /> + <param name="objectiveChoice" type="select" label="Select the objective used"> + <option value="4x">4x</option> + <option value="10x">10x</option> + <option value="20x">20x</option> + </param> + <param name="startStage" type="integer" min="0" value="72" label="Stage in hour at first acquisition"/> + <param name="omero_host" type="text" label="OMERO host URL"> + <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator> + <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator> + </param> + <param name="plateName" type="text" value="Experiment:0" label="Name of the plate (on omero)" /> + <conditional name="screen"> + <param name="screen_create" type="select" label="Create the screen on OMERO or use existing one"> + <option value="create">Create a new one</option> + <option value="exists">Use an existing one</option> + </param> + <when value="create"> + <param name="screenNameOrID" type="text" value="MyNewScreen" label="Name of the screen (on omero)" /> + </when> + <when value="exists"> + <param name="screenNameOrID" type="integer" min="0" value="605" label="ID of the screen (on omero)" /> + </when> + </conditional> + <param name="get_stacks_in_galaxy" type="boolean" checked="false" label="Get stacks in galaxy" /> + <param name="ignoreConcentration" type="boolean" checked="true" label="Ignore the concentration of compounds from the plateMap" /> + <param name="ignorePassage" type="boolean" checked="true" label="Ignore the passage number of Cells from the plateMap" /> + <param name="ignoreSeeding" type="boolean" checked="true" label="Ignore the seeding concentration of Cells from the plateMap" /> + </when> + <when value="no"> + <param name="get_stacks_in_galaxy" type="hidden" value="true"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="logfile" format="txt" from_work_dir="output.log" label="${tool.name} on ${on_string}: logfile" /> + <collection name="list_output" type="list" label="${tool.name} on ${on_string}: Stacks"> + <discover_datasets pattern="(?P<designation>.+)\.tif" directory="output/" ext="tiff" /> + <filter>upload_omero['get_stacks_in_galaxy']</filter> + </collection> + <data format="xml" name="companion_ome" from_work_dir="output.companion.ome" label="${tool.name} on ${on_string}: companion.ome" > + <filter>upload_omero['get_stacks_in_galaxy'] and upload_omero['upload_omero_select'] == "yes"</filter> + </data> + </outputs> + <tests> + <test> + <conditional name="structure"> + <param name="structure_type" value="directory"/> + <param name="phase_dir_s3" value="tutu_Phase"/> + <param name="green_dir_s3" value="toto_Green"/> + </conditional> + <conditional name="upload_omero"> + <param name="upload_omero_select" value="no"/> + </conditional> + <output name="logfile"> + <assert_contents> + <has_line line="No match for B1"/> + </assert_contents> + </output> + <output_collection name="list_output" type="list" count="1"> + <element name="A1_1_merge" ftype="tiff"> + <assert_contents> + <has_size value="17574881" delta="1500000"/> + </assert_contents> + </element> + </output_collection> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +It will use images coming from the Incucyte which are on the s3 server to make a "T-stack" per well and upload it to omero with key values in the plateMap. +This wrapper uses ImageJ to combine images (with a groovy) and omero-py to import the images. + +Usage +..... + + +**Input** + +- 3 paths of directories (some can be empty of phase, green and red) or one path of directory and 3 keywords (some of them can be empty) +- plateMap generated with the software coming with Incucyte +- objective used (to correctly set the pixel size) +- number of well in your plate (96 or 384), they don't need to be all in your input directories. +- maximum number of images per well +- URL of omero +- Name of the Plate in omero +- Whether the Screen should be created or use an existing one +- Name of the new screen or id of the existing screen +- Whether the concentration of the compounds, the passage and the seeding concentration should be ignored from the plateMap. + +**Output** + +- A log file with info +- Optionally all images as T-stack and the xml to upload to omero +- On OMERO your images all channels combined and all time points combined into a plate. + +**License** + +License text:: + + ************************************************* + Relative to the generation of the .companion.ome * + ************************************************** + #%L + BSD implementations of Bio-Formats readers and writers + %% + The functions buildXML, makeImage, makePlate, postProcess and asString has been modified and adapted from + https://github.com/ome/bioformats/blob/master/components/formats-bsd/test/loci/formats/utests/SPWModelMock.java + + Copyright (C) 2005 - 2015 Open Microscopy Environment: + - Board of Regents of the University of Wisconsin-Madison + - Glencoe Software, Inc. + - University of Dundee + + @author Chris Allan <callan at blackcat dot ca> + %% + + ************************************************** + Relative to the rest of the script * + ************************************************** + + * = AUTHOR INFORMATION = + Code written by Rémy Dornier, EPFL - SV - PTECH - BIOP + and Romain Guiet, EPFL - SV - PTECH - BIOP + and Lucille Delisle, EPFL - SV - UPDUB + and Pierre Osteil, EPFL - SV - UPDUB + + Last modification: 2023-08-24 + + = COPYRIGHT = + © All rights reserved. ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, BioImaging And Optics Platform (BIOP), 2023 + + Licensed under the BSD-3-Clause License: + Redistribution and use in source and binary forms, with or without modification, are permitted provided + that the following conditions are met: + 1. Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + 2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer + in the documentation and/or other materials provided with the distribution. + 3. Neither the name of the copyright holder nor the names of its contributors + may be used to endorse or promote products + derived from this software without specific prior written permission. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE + LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR + CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF + SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS + INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN + CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) + ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE + POSSIBILITY OF SUCH DAMAGE. + ]]></help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/stack_buildXml.groovy Tue Dec 19 15:02:41 2023 +0000 @@ -0,0 +1,940 @@ +/* + **************************************************** + * Relative to the generation of the .companion.ome * + **************************************************** + * #%L + * BSD implementations of Bio-Formats readers and writers + * %% + * The functions buildXML, makeImage, makePlate, postProcess and asString has been modified and adapted from + * https://github.com/ome/bioformats/blob/master/components/formats-bsd/test/loci/formats/utests/SPWModelMock.java + * + * Copyright (C) 2005 - 2015 Open Microscopy Environment: + * - Board of Regents of the University of Wisconsin-Madison + * - Glencoe Software, Inc. + * - University of Dundee + * + * @author Chris Allan <callan at blackcat dot ca> + * %% + * + **************************************************** + * Relative to the rest of the script * + **************************************************** + * + * * = AUTHOR INFORMATION = + * Code written by Rémy Dornier, EPFL - SV - PTECH - BIOP + * and Romain Guiet, EPFL - SV - PTECH - BIOP + * and Lucille Delisle, EPFL - SV - UPDUB + * and Pierre Osteil, EPFL - SV - UPDUB + * + * Last modification: 2023-12-19 + * + * = COPYRIGHT = + * © All rights reserved. ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, BioImaging And Optics Platform (BIOP), 2023 + * + * Licensed under the BSD-3-Clause License: + * Redistribution and use in source and binary forms, with or without modification, are permitted provided + * that the following conditions are met: + * 1. Redistributions of source code must retain the above copyright notice, + * this list of conditions and the following disclaimer. + * 2. Redistributions in binary form must reproduce the above copyright notice, + * this list of conditions and the following disclaimer + * in the documentation and/or other materials provided with the distribution. + * 3. Neither the name of the copyright holder nor the names of its contributors + * may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE + * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR + * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF + * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS + * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN + * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) + * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE + * POSSIBILITY OF SUCH DAMAGE. + * + */ + +/** + * + * The purpose of this script is to combine a series of time-lapse images into + * one file per well/field with possibly multiple channels and multiple time points + * and in addition create a .companion.ome file to create an OMERO plate object, + * with a single image per well/field. This .companion.ome file can be directly uploaded on OMERO via + * OMERO.insight software or CLI, with screen import option. + * + * To make the script run + * 1. Create a parent folder (base_dir) and a output folder (output_dir) + * 2. Create a dir *Phase, *Green, *Red with the corresponding channels + * 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' + * 4. The images can be either regular tif or the raw tif from Incucyte which contains multiple series. + * 5. You must provide the path of the Incucyte XML file to populate key values + * + * The expected outputs are: + * 1. In the output_dir one tiff per well/field (multi-T and potentially multi-C) + * 2. In the output_dir a .companion.ome + */ + +#@ File(style="directory", label="Directory with up to 3 subdirectories ending by Green, Phase and/or Red") base_dir +#@ File(label="Incucyte XML File (plateMap)") incucyteXMLFile +#@ File(style="directory", label="Output directory (must exist)") output_dir +#@ String(label="Final XML file name", value="Test") xmlName +#@ String(label="Number of well in plate", choices={"96", "384"}, value="96") nWells +#@ Integer(label="Maximum number of images per well", value=1, min=1) n_images_per_well +#@ String(label="Objective", choices={"4x","10x","20x"}) objectiveChoice +#@ String(label="Plate name", value="Experiment:0") plateName +#@ String(label="common Key Values formatted as key1=value1;key2=value2", value="") commonKeyValues +#@ Boolean(label="Ignore Compound concentration from plateMap", value=true) ignoreConcentration +#@ Boolean(label="Ignore Cell passage number from plateMap", value=true) ignorePassage +#@ Boolean(label="Ignore Cell seeding concentration from plateMap", value=true) ignoreSeeding + + +/** + * ***************************************************************************************************************** + * ********************************************* Final Variables ************************************************** + * ********************************************* DO NOT MODIFY **************************************************** + * **************************************************************************************************************** + */ + +/** objectives and respective pixel sizes */ +objective = 0 +objectives = new String[]{"4x", "10x", "20x"} +pixelSizes = new double[]{2.82, 1.24, 0.62} + +/** pattern for date */ +REGEX_FOR_DATE = ".*_([0-9]{4})y([0-9]{2})m([0-9]{2})d_([0-9]{2})h([0-9]{2})m.tif" + +ALTERNATIVE_REGEX_FOR_DATE = ".*_([0-9]{2})d([0-9]{2})h([0-9]{2})m.tif" + +/** Image properties keys */ +DIMENSION_ORDER = "dimension_order" +FILE_NAME = "file_name" +IMG_POS_IN_WELL = "img_pos_in_well" +FIRST_ACQUISITION_DATE = "acquisition_date" +FIRST_ACQUISITION_TIME = "acquisition_time" +RELATIVE_ACQUISITION_HOUR = "relative_acquisition_hour" + +/** global variable for index to letter conversion */ +LETTERS = new String("ABCDEFGHIJKLMNOP") + +// Version number = date of last modif +VERSION = "20231219" + +/** Key-Value pairs namespace */ +GENERAL_ANNOTATION_NAMESPACE = "openmicroscopy.org/omero/client/mapAnnotation" +annotations = new StructuredAnnotations() + +/** Plate details and conventions */ +PLATE_ID = "Plate:0" +PLATE_NAME = plateName + +if (nWells == "96") { + nRows = 8 + nCols = 12 +} else if (nWells == "384") { + nRows = 16 + nCols = 24 +} + +WELL_ROWS = new PositiveInteger(nRows) +WELL_COLS = new PositiveInteger(nCols) +WELL_ROW = NamingConvention.LETTER +WELL_COL = NamingConvention.NUMBER + +/** XML namespace. */ +XML_NS = "http://www.openmicroscopy.org/Schemas/OME/2010-06" + +/** XSI namespace. */ +XSI_NS = "http://www.w3.org/2001/XMLSchema-instance" + +/** XML schema location. */ +SCHEMA_LOCATION = "http://www.openmicroscopy.org/Schemas/OME/2010-06/ome.xsd" + + +/** + * ***************************************************************************************************************** + * **************************************** Beginning of the script *********************************************** + * **************************************************************************************************************** + */ + +try { + + println "Beginning of the script" + + /** + * Prepare list of wells name + */ + String[] well = [] + + well = [(0..(nRows - 1)),(0..(nCols - 1))].combinations().collect{ r,c -> LETTERS.substring(r, r + 1) +""+ (c+ 1).toString() } + + IJ.run("Close All", "") + + // loop for all the wells + + // Store all merged ImagePlus into a HashMap where + // keys are well name (A1, A10) + // values are a list of ImagePlus corresponding to different field of view + Map<String, List<ImagePlus>> wellSamplesMap = new HashMap<>() + + well.each{ input -> + IJ.run("Close All", "") + + List<ImagePlus> final_imp_list = process_well(base_dir, input, n_images_per_well) //, perform_bc, mediaChangeTime ) + if (!final_imp_list.isEmpty()) { + wellSamplesMap.put(input, final_imp_list) + for(ImagePlus final_imp : final_imp_list){ + final_imp.setTitle(input+"_"+final_imp.getProperty(IMG_POS_IN_WELL)) + //final_imp.show() + + def fs = new FileSaver(final_imp) + File output_path = new File (output_dir ,final_imp.getTitle()+"_merge.tif" ) + fs.saveAsTiff(output_path.toString() ) + final_imp.setProperty(FILE_NAME, output_path.getName()) + + IJ.run("Close All", "") + } + } else { + println "No match for " + input + } + } + + + // get folder and xml file path + output_dir_abs = output_dir.getAbsolutePath() + incucyteXMLFilePath = incucyteXMLFile.getAbsolutePath() + + if (! new File(incucyteXMLFilePath).exists()) { + println "The incucyte file does not exists" + return + } + + // select the right objective + switch (objectiveChoice){ + case "4x": + objective = 0 + break + case "10x": + objective = 1 + break + case "20x": + objective = 2 + break + } + + // get plate scheme as key-values + Map<String, List<MapPair>> keyValuesPerWell = parseIncucyteXML(incucyteXMLFilePath, ignoreConcentration, ignorePassage, ignoreSeeding) + + // get global key-values + List<MapPair> globalKeyValues = getGlobalKeyValues(objective, commonKeyValues) + double pixelSize = pixelSizes[objective] + + // generate OME-XML metadata file + OME ome = buildXMLFile(wellSamplesMap, keyValuesPerWell, globalKeyValues, pixelSize) + + // create XML document + DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance() + DocumentBuilder parser = factory.newDocumentBuilder() + Document document = parser.newDocument() + + // Produce a valid OME DOM element hierarchy + Element root = ome.asXMLElement(document) + postProcess(root, document) + + // Produce string XML + try(OutputStream outputStream = new FileOutputStream(output_dir_abs + File.separator + xmlName + ".companion.ome")){ + outputStream.write(asString(document).getBytes()) + } catch(Exception e){ + e.printStackTrace() + } + println "End of the script" + +} catch (Throwable e) { + println("Something went wrong: " + e) + e.printStackTrace() + throw e + + if (GraphicsEnvironment.isHeadless()){ + // Force to give exit signal of error + System.exit(1) + } + +} + +return + +/** + * **************************************************************************************************************** + * ******************************************* End of the script ************************************************** + * + * **************************************************************************************************************** + * + * *********************************** Helpers and processing methods ********************************************* + * *************************************************************************************************************** + */ + +def process_well(baseDir, input_wellId, n_image_per_well){ //, perform_bc, mediaChangeTime){ + File bf_dir = baseDir.listFiles().find{ it =~ /.*Phase.*/} + File green_dir = baseDir.listFiles().find{ it =~ /.*Green.*/} + File red_dir = baseDir.listFiles().find{ it =~ /.*Red.*/} + //if (verbose) println bf_dir + //if (verbose) println green_dir + + // The images are stored in a TreeMap where + // keys are wellSampleId = field identifier + // values are a TreeMap that we call channelMap where: + // keys are colors (Green, Grays, Red) + // values are an ImagePlus (T-stack) + Map<Integer, Map<String, ImagePlus>> sampleToChannelMap = new TreeMap<>() + + List<File> folder_list = [bf_dir, green_dir, red_dir] + List<String> channels_list = ["Grays", "Green", "Red"] + + // loop over the field and open images + for(int wellSampleId = 1; wellSampleId <= n_image_per_well; wellSampleId++) { + // nT is the number of time-points for the well input_wellId + int nT = 0 + String first_channel = "" + String first_acq_date = "" + String first_acq_time = "" + String rel_acq_hour = "" + + // Initiate a channel map for the wellSampleId + Map<String, ImagePlus> channelMap = new TreeMap<>() + + // Checking if there are images in the corresponding dir + // which corresponds to the input_wellId + // and to the wellSampleId + // The image name should be: + // Prefix + "_" + input_wellId + "_" + wellSampleId + "_" + year (4 digits) + "y" + month (2 digits) + "m" + day + "d_" + hour + "h" + minute + "m.tif" + FileFilter fileFilter = new WildcardFileFilter("*_" + input_wellId + "_" + wellSampleId + "_*") + for(int i = 0; i < folder_list.size(); i++){ + if (folder_list.get(i) != null) { + File[] files_matching = folder_list.get(i).listFiles(fileFilter as FileFilter).sort() + if (files_matching.size() != 0) { + // In order to deal with raw images from Incucyte which are + // Multi series images + // We open the first image + ImagePlus first_imp = Opener.openUsingBioFormats(files_matching[0].getAbsolutePath()) + // We check if we can read the infos + first_image_infos = Opener.getTiffFileInfo(files_matching[0].getAbsolutePath()) + // We define the imageplus object + ImagePlus single_channel_imp + if (first_image_infos == null) { + // They are raw from incucyte + // We need to open images one by one and add them to the stack + ImageStack stack = new ImageStack(first_imp.width, first_imp.height); + files_matching.each{ + ImagePlus single_imp = (new Opener()).openUsingBioFormats(it.getAbsolutePath()) + String new_title = single_imp.getTitle().split(" - ")[0] + stack.addSlice(new_title, single_imp.getProcessor()) + } + single_channel_imp = new ImagePlus(FilenameUtils.getBaseName(folder_list.get(i).getAbsolutePath()), stack); + } else { + // They are regular tif file + // We can use FolderOpener to create the stack at once + single_channel_imp = FolderOpener.open(folder_list.get(i).getAbsolutePath(), " filter=_"+ input_wellId + "_"+wellSampleId+"_") + } + // Phase are 8-bit and need to be changed to 16-bit + // Other are already 16-bit but it does not hurt + IJ.run(single_channel_imp, "16-bit", "") + + // check frame size + if (nT == 0) { + // This is the first channel with images + nT = single_channel_imp.getNSlices() + first_channel = channels_list.get(i) + // Process all dates: + Pattern date_pattern = Pattern.compile(REGEX_FOR_DATE) + ImageStack stack = single_channel_imp.getStack() + // Go to the first time (which is slice) + single_channel_imp.setSlice(1) + int currentSlice = single_channel_imp.getCurrentSlice() + String label = stack.getSliceLabel(currentSlice) + LocalDateTime dateTime_ref = getDate(label, date_pattern) + if (dateTime_ref == null) { + date_pattern = Pattern.compile(ALTERNATIVE_REGEX_FOR_DATE) + dateTime_ref = getDate(label, date_pattern) + } + if (dateTime_ref != null) { + first_acq_date = dateTime_ref.format(DateTimeFormatter.ofPattern("yyyy-MM-dd")) + first_acq_time = dateTime_ref.format(DateTimeFormatter.ofPattern("HH:mm:ss")) + for (int ti = 2; ti<= nT; ti++) { + // Process each frame starting at 2 + single_channel_imp.setSlice(ti) + int hours = getHoursFromImp(single_channel_imp, stack, dateTime_ref, date_pattern) + if (rel_acq_hour == "") { + rel_acq_hour = "" + hours + } else { + rel_acq_hour += "," + hours + } + } + } else { + first_acq_date = "NA" + first_acq_time = "NA" + } + } else { + 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 + "." + } + // Set acquisition properties + single_channel_imp.setProperty(FIRST_ACQUISITION_DATE, first_acq_date) + single_channel_imp.setProperty(FIRST_ACQUISITION_TIME, first_acq_time) + single_channel_imp.setProperty(RELATIVE_ACQUISITION_HOUR, rel_acq_hour) + println single_channel_imp.getProperty(FIRST_ACQUISITION_DATE) + println single_channel_imp.getProperty(FIRST_ACQUISITION_TIME) + // add the image stack to the channel map for the corresponding color + channelMap.put(channels_list.get(i), single_channel_imp) + } + } + } + if (nT != 0) { + // add the channelmap to the sampleToChannelMap using the wellSampleId as key + sampleToChannelMap.put(wellSampleId, channelMap) + } + } + + ArrayList<ImagePlus> final_imp_list = [] + + // Now loop over the wellSampleId which have images + for(Integer wellSampleId : sampleToChannelMap.keySet()){ + // get the channel map + Map<String, ImagePlus> channelsMap = sampleToChannelMap.get(wellSampleId) + ArrayList<String> channels = [] + ArrayList<ImagePlus> current_images = [] + + for(String channel : channelsMap.keySet()){ + channels.add(channel) + current_images.add(channelsMap.get(channel)) + } + // Get number of time: + int nT = current_images[0].nSlices + + // Merge all + ImagePlus merged_imps = Concatenator.run(current_images as ImagePlus[]) + // Re-order to make a multi-channel, time-lapse image + ImagePlus final_imp + if (channels.size() == 1 && nT == 1) { + final_imp = merged_imps + } else { + final_imp = HyperStackConverter.toHyperStack(merged_imps, channels.size() , 1, nT, "xytcz", "Color") + } + // add properties to the image + final_imp.setProperty(DIMENSION_ORDER, DimensionOrder.XYCZT) + final_imp.setProperty(IMG_POS_IN_WELL, wellSampleId) + final_imp.setProperty(FIRST_ACQUISITION_DATE, current_images[0].getProperty(FIRST_ACQUISITION_DATE)) + final_imp.setProperty(FIRST_ACQUISITION_TIME, current_images[0].getProperty(FIRST_ACQUISITION_TIME)) + final_imp.setProperty(RELATIVE_ACQUISITION_HOUR, current_images[0].getProperty(RELATIVE_ACQUISITION_HOUR)) + + // set LUTs + (0..channels.size()-1).each{ + final_imp.setC(it + 1) + IJ.run(final_imp, channels[it], "") + final_imp.resetDisplayRange() + } + + final_imp_list.add(final_imp) + } + + return final_imp_list +} + + +/** + * create the full XML metadata (plate, images, channels, annotations....) + * + * @param imagesName + * @param keyValuesPerWell + * @param globalKeyValues + * @param pixelSize + * @return OME-XML metadata instance + */ +def buildXMLFile(Map<String,List<ImagePlus>> wellToImagesMap, Map<String, List<MapPair>> keyValuesPerWell, List<MapPair> globalKeyValues, double pixelSize) { + // create a new OME-XML metadata instance + OME ome = new OME() + + Map<String, Integer> imgInWellPosToListMap = new HashMap<>() + int imgCmp = 0 + for (String wellId: wellToImagesMap.keySet()) { + // get well position from image name + List<ImagePlus> imagesWithinWell = wellToImagesMap.get(wellId) + + for (ImagePlus image : imagesWithinWell) { + // get KVP corresponding to the current well + // Initiate a list of keyValues for the wellId + // (or use the existing one) + List<MapPair> keyValues = [] + if(keyValuesPerWell.containsKey(wellId)) + keyValues = keyValuesPerWell.get(wellId) + keyValues.addAll(globalKeyValues) + + // create an Image node in the ome-xml + imgInWellPosToListMap.put(wellId+ "_" +image.getProperty(IMG_POS_IN_WELL),imgCmp) + ome.addImage(makeImage(imgCmp++, image, keyValues, pixelSize)) + } + } + + // create Plate node + ome.addPlate(makePlate(wellToImagesMap, imgInWellPosToListMap, pixelSize, ome)) + + // add annotation nodes + ome.setStructuredAnnotations(annotations) + + return ome +} + +/** + * create an image xml-element, populated with annotations, channel, pixels and path elements + * + * @param index image ID + * @param imageName + * @param keyValues + * @param pixelSize + * @return an image xml-element + */ +def makeImage(int index, ImagePlus imagePlus, List<MapPair> keyValues, double pixelSize) { + // Create <Image/> + Image image = new Image() + image.setID("Image:" + index) + // The image name is the name of the file without extension + image.setName(((String)imagePlus.getProperty(FILE_NAME)).split("\\.")[0]) + // Set the acquisitionDate: + if (imagePlus.getProperty(FIRST_ACQUISITION_DATE) != "NA") { + image.setAcquisitionDate(new Timestamp(imagePlus.getProperty(FIRST_ACQUISITION_DATE) + "T" + imagePlus.getProperty(FIRST_ACQUISITION_TIME))) + // Also add it to the key values: + keyValues.add(new MapPair("acquisition.day", (String)imagePlus.getProperty(FIRST_ACQUISITION_DATE))) + keyValues.add(new MapPair("acquisition.time", (String)imagePlus.getProperty(FIRST_ACQUISITION_TIME))) + keyValues.add(new MapPair("relative.acquisition.hours", (String)imagePlus.getProperty(RELATIVE_ACQUISITION_HOUR))) + } + // Create <MapAnnotations/> + MapAnnotation mapAnnotation = new MapAnnotation() + mapAnnotation.setID("ImageKeyValueAnnotation:" + index) + mapAnnotation.setNamespace(GENERAL_ANNOTATION_NAMESPACE) + mapAnnotation.setValue(keyValues) + annotations.addMapAnnotation(mapAnnotation); // add the KeyValues to the general structured annotation element + image.linkAnnotation(mapAnnotation) + + // Create <Pixels/> + Pixels pixels = new Pixels() + pixels.setID("Pixels:" + index) + pixels.setSizeX(new PositiveInteger(imagePlus.getWidth())) + pixels.setSizeY(new PositiveInteger(imagePlus.getHeight())) + pixels.setSizeZ(new PositiveInteger(imagePlus.getNSlices())) + pixels.setSizeC(new PositiveInteger(imagePlus.getNChannels())) + pixels.setSizeT(new PositiveInteger(imagePlus.getNFrames())) + pixels.setDimensionOrder((DimensionOrder) imagePlus.getProperty(DIMENSION_ORDER)) + pixels.setType(getPixelType(imagePlus)) + pixels.setPhysicalSizeX(new Length(pixelSize, UNITS.MICROMETER)) + pixels.setPhysicalSizeY(new Length(pixelSize, UNITS.MICROMETER)) + + // Create <TiffData/> under <Pixels/> + TiffData tiffData = new TiffData() + tiffData.setFirstC(new NonNegativeInteger(0)) + tiffData.setFirstT(new NonNegativeInteger(0)) + tiffData.setFirstZ(new NonNegativeInteger(0)) + tiffData.setPlaneCount(new NonNegativeInteger(imagePlus.getNSlices()*imagePlus.getNChannels()*imagePlus.getNFrames())) + + // Create <UUID/> under <TiffData/> + UUID uuid = new UUID() + uuid.setFileName((String)imagePlus.getProperty(FILE_NAME)) + uuid.setValue(java.util.UUID.randomUUID().toString()) + tiffData.setUUID(uuid) + + // Put <TiffData/> under <Pixels/> + pixels.addTiffData(tiffData) + + // Create <Channel/> under <Pixels/> + LUT[] luts = imagePlus.getLuts() + for (int i = 0; i < luts.length; i++) { + Channel channel = new Channel() + channel.setID("Channel:" + i) + channel.setColor(new Color(luts[i].getRed(255),luts[i].getGreen(255), luts[i].getBlue(255),255)) + pixels.addChannel(channel) + } + + // Put <Pixels/> under <Image/> + image.setPixels(pixels) + + return image +} + + +/** + * get pixel type based on the imagePlus type + * @param imp + * @return pixel type + */ +def getPixelType(ImagePlus imp){ + switch (imp.getType()) { + case ImagePlus.GRAY8: + return PixelType.UINT8 + case ImagePlus.GRAY16: + return PixelType.UINT16 + case ImagePlus.GRAY32: + return PixelType.FLOAT + default: + return PixelType.FLOAT + } +} + +/** + * create a Plate xml-element, populated with wells and their attributes + * @param imagesName + * @return Plate xml-element + */ +def makePlate(Map<String, List<ImagePlus>> wellToImagesMap, Map<String, Integer> imgPosInListMap, double pixelSize, OME ome) { + // Create <Plate/> + Plate plate = new Plate() + plate.setName(PLATE_NAME) + plate.setID(PLATE_ID) + plate.setRows(WELL_ROWS) + plate.setColumns(WELL_COLS) + plate.setRowNamingConvention(WELL_ROW) + plate.setColumnNamingConvention(WELL_COL) + + // for each image (one image per well) + for (String wellId: wellToImagesMap.keySet()) { + // get well position from image name + List<ImagePlus> imagesWithinWell = wellToImagesMap.get(wellId) + + // get well position from image name + int row = convertLetterToNumber(wellId.substring(0, 1)) + int col = Integer.parseInt(wellId.substring(1)) - 1 + + // row and col should correspond to a real well + if(row >= 0 && col >= 0 && col < 12) { + // Create <Well/> under <Plate/> + Well well = new Well() + well.setID(String.format("Well:%d_%d", row, col)) + well.setRow(new NonNegativeInteger(row)) + well.setColumn(new NonNegativeInteger(col)) + + for (ImagePlus imagePlus : imagesWithinWell) { + int wellSampleIndex = imgPosInListMap.get(wellId + "_" + imagePlus.getProperty(IMG_POS_IN_WELL)) + + // Create <WellSample/> under <Well/> + WellSample sample = new WellSample() + sample.setID(String.format("WellSample:%d", wellSampleIndex)) + sample.setIndex(new NonNegativeInteger(wellSampleIndex)) + if (imagePlus.getCalibration() != null) { + sample.setPositionX(new Length(imagePlus.getCalibration().xOrigin * pixelSize, UNITS.MICROMETER)) + sample.setPositionY(new Length(imagePlus.getCalibration().yOrigin * pixelSize, UNITS.MICROMETER)) + } + sample.linkImage(ome.getImage(wellSampleIndex)) + + // Put <WellSample/> under <Well/> + well.addWellSample(sample) + } + + // Put <Well/> under <Plate/> + plate.addWell(well) + } + } + return plate +} + +/** + * convert the XML metadata document into string + * + * @param document + * @return + * @throws TransformerException + * @throws UnsupportedEncodingException + */ +def asString(Document document) throws TransformerException, UnsupportedEncodingException { + TransformerFactory transformerFactory = TransformerFactory.newInstance() + Transformer transformer = transformerFactory.newTransformer() + + //Setup indenting to "pretty print" + transformer.setOutputProperty(OutputKeys.INDENT, "yes") + transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4") + + Source source = new DOMSource(document) + ByteArrayOutputStream os = new ByteArrayOutputStream() + Result result = new StreamResult(new OutputStreamWriter(os, "utf-8")) + transformer.transform(source, result) + + return os.toString() +} + +/** + * add document header + * + * @param root + * @param document + */ +def postProcess(Element root, Document document) { + root.setAttribute("xmlns", XML_NS) + root.setAttribute("xmlns:xsi", XSI_NS) + root.setAttribute("xsi:schemaLocation", XML_NS + " " + SCHEMA_LOCATION) + root.setAttribute("UUID", java.util.UUID.randomUUID().toString()) + document.appendChild(root) +} + + +/** + * read Incucyte plate-scheme XML file, extract attributes per well and convert attributes to OMERO-compatible + * keys-value pairs XML elements. + * + * @param path Incucyte plate-scheme XML file path + * @return Map of OME-XML compatible key-values per well + */ +def parseIncucyteXML(String path, Boolean ignoreConcentration, Boolean ignorePassage, Boolean ignoreSeeding) { + Map<String, List<MapPair>> keyValuesPerWell = new HashMap<>() + + final String rowAttribute = "row" + final String columnAttribute = "col" + + final String wellNode = "well" + final String itemsNode = "items" + final String wellItemNode = "wellItem" + final String referenceItemNode = "referenceItem" + + // There are 3 types of referenceItem: Compound, CellType, GrowthCondition + // + // For the Compound, each well can have a concentration and a concentrationUnits + // the referenceItem has a displayName + // The key should be: displayName (concentrationUnits) + // The value should be: concentration + // However, if ignoreConcentration is set to true: + // The key should be: displayName (NA) + // The value should be: 1 + // + // For the CellType, each well can have a passage, a seedingDensity and a seedingDensityUnits + // the referenceItem has a displayName + // The passage key should be: displayName_passage + // The value should be: passage + // However, if ignorePassage is set to true no key value should be stored for this + // Then: + // The seeding key should be: displayName_seedingDensity (seedingDensityUnits) + // The value should be: seedingDensity + // However, if ignoreSeeding is set to true: + // The key should be: displayName + // The value should be: "yes" + // + // For the GrowthCondition, the referenceItem has a displayName + // The key should be: displayName + // The value should be: "yes" + + try { + // create an document + DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance() + DocumentBuilder dBuilder = dbFactory.newDocumentBuilder() + + // read the xml file + Document doc = dBuilder.parse(new File(path)) + doc.getDocumentElement().normalize() + + // get all "well" nodes + NodeList wellList = doc.getElementsByTagName(wellNode) + + for(int i = 0; i < wellList.getLength(); i++) { + Node well = wellList.item(i) + + // extract well attributes + String row = well.getAttributes().getNamedItem(rowAttribute).getTextContent() + int r = row as int + String col = well.getAttributes().getNamedItem(columnAttribute).getTextContent() + String wellNumber = LETTERS.substring(r, r + 1) + (Integer.parseInt(col)+ 1) + + // extract items node, under well node + Node items = ((Element)well).getElementsByTagName(itemsNode).item(0) + if (items != null) { + // get all "wellItem" nodes, under items node + NodeList wellItemList = ((Element)items).getElementsByTagName(wellItemNode) + + // read referenceItem node's attributes and convert them into key-values + List<MapPair> keyValues = new ArrayList<>() + for (int j = 0; j < wellItemList.getLength(); j++) { + Node wellItem = wellItemList.item(j) + // extract referenceItem node, under wellItem node + Node referenceItem = ((Element)wellItem).getElementsByTagName(referenceItemNode).item(0) + String wellType = wellItem.getAttributes().getNamedItem("type").getTextContent() + + // select the right key-values + switch (wellType){ + case "Compound": + String compound_name = referenceItem.getAttributes().getNamedItem("displayName").getTextContent() + if (ignoreConcentration) { + keyValues.add(new MapPair(compound_name + " (NA)", "1")) + } else { + String unit = wellItem.getAttributes().getNamedItem("concentrationUnits").getTextContent() + unit = unit.replace("\u00B5", "u") + String value = wellItem.getAttributes().getNamedItem("concentration").getTextContent() + keyValues.add(new MapPair(compound_name + " (" + unit + ")", value)) + } + break + case "CellType": + String cell_name = referenceItem.getAttributes().getNamedItem("displayName").getTextContent() + if (!ignorePassage) { + String passage = wellItem.getAttributes().getNamedItem("passage").getTextContent() + keyValues.add(new MapPair(cell_name + "_passage", passage)) + } + if (ignoreSeeding) { + keyValues.add(new MapPair(cell_name, "yes")) + } else { + String unit = wellItem.getAttributes().getNamedItem("seedingDensityUnits").getTextContent() + unit = unit.replace("\u00B5", "u") + String value = wellItem.getAttributes().getNamedItem("seedingDensity").getTextContent() + keyValues.add(new MapPair(cell_name + "_seedingDensity (" + unit + ")", value)) + } + break + case "GrowthCondition": + String growth_condition = referenceItem.getAttributes().getNamedItem("displayName").getTextContent() + keyValues.add(new MapPair(growth_condition, "yes")) + break + } + } + keyValuesPerWell.put(wellNumber,keyValues) + + } + } + return keyValuesPerWell + } catch (Exception e) { + println "XML platemap could not be parsed" + e.printStackTrace() + return new HashMap<>() + } +} + +/** + * make a list of all key-values that are common to all images + * + * @param objective + * @param commonKeyValues (a String with the following format: key1=value1;key2=value2) + * @return a list of OME-XML key-values + */ +def getGlobalKeyValues(int objective, String commonKeyValues){ + List<MapPair> keyValues = new ArrayList<>() + keyValues.add(new MapPair("groovy_version", VERSION)) + keyValues.add(new MapPair("objective", objectives[objective])) + if (commonKeyValues != "") { + String[] keyValList = commonKeyValues.split(';') + for (int i = 0; i < keyValList.size(); i ++) { + String keyval = keyValList[i] + String[] keyvalsplit = keyval.split('=') + int nPieces = keyvalsplit.size() + String value = keyvalsplit[nPieces - 1] + String key = keyvalsplit[0] + // In case there are '=' in key + for (int j = 1; j < nPieces - 1; j++) { + key += '=' + keyvalsplit[j] + } + keyValues.add(new MapPair(key, value)) + } + } + return keyValues +} + +/** + * convert alphanumeric well position to numeric position + * + * @param letter + * @return + */ +def convertLetterToNumber(String letter){ + for (int i = 0; i < LETTERS.size(); i++) { + if (LETTERS.substring(i, i + 1) == letter) { + return i + } + } + return -1 +} + +// Returns a date from a label and a date_pattern +def getDate(String label, Pattern date_pattern){ +// println "Trying to get date from " + label + Matcher date_m = date_pattern.matcher(label) + LocalDateTime dateTime + if (date_m.matches()) { + if (date_m.groupCount() == 5) { + dateTime = LocalDateTime.parse(date_m.group(1) + "-" + date_m.group(2) + "-" + date_m.group(3) + "T" + date_m.group(4) + ":" + date_m.group(5)) + } else { + dateTime = LocalDateTime.parse("1970-01-" + 1 + (date_m.group(1) as int) + "T" + date_m.group(2) + ":" + date_m.group(3)) + } + } +// println "Found " + dateTime + return dateTime +} + +// Returns the number of hours +def getHoursFromImp(ImagePlus imp, ImageStack stack, LocalDateTime dateTime_ref, Pattern date_pattern){ + int currentSlice = imp.getCurrentSlice() + String label = stack.getSliceLabel(currentSlice) + LocalDateTime dateTime = getDate(label, date_pattern) + if (dateTime != null) { + return ChronoUnit.HOURS.between(dateTime_ref, dateTime) as int + } else { + return -1 + } +} + + +/** + * ***************************************************************************************************************** + * ************************************************* Imports **************************************************** + * **************************************************************************************************************** + */ + + +import ij.IJ +import ij.ImagePlus +import ij.ImageStack +import ij.io.FileSaver +import ij.io.Opener +import ij.plugin.Concatenator +import ij.plugin.FolderOpener +import ij.plugin.HyperStackConverter +import ij.process.LUT + +import java.awt.GraphicsEnvironment +import java.io.File +import java.time.format.DateTimeFormatter +import java.time.LocalDateTime +import java.time.temporal.ChronoUnit +import java.util.stream.Collectors +import java.util.stream.IntStream +import java.util.regex.* + +import javax.xml.parsers.DocumentBuilder +import javax.xml.parsers.DocumentBuilderFactory +import javax.xml.transform.OutputKeys +import javax.xml.transform.Result +import javax.xml.transform.Source +import javax.xml.transform.Transformer +import javax.xml.transform.TransformerException +import javax.xml.transform.TransformerFactory +import javax.xml.transform.dom.DOMSource +import javax.xml.transform.stream.StreamResult + +import ome.units.UNITS +import ome.units.quantity.Length + +import ome.xml.model.Channel +import ome.xml.model.Image +import ome.xml.model.MapAnnotation +import ome.xml.model.MapPair +import ome.xml.model.OME +import ome.xml.model.Pixels +import ome.xml.model.Plate +import ome.xml.model.StructuredAnnotations +import ome.xml.model.TiffData +import ome.xml.model.UUID +import ome.xml.model.Well +import ome.xml.model.WellSample +import ome.xml.model.enums.DimensionOrder +import ome.xml.model.enums.NamingConvention +import ome.xml.model.enums.PixelType +import ome.xml.model.primitives.Color +import ome.xml.model.primitives.NonNegativeInteger +import ome.xml.model.primitives.PositiveInteger +import ome.xml.model.primitives.Timestamp + +import org.apache.commons.io.filefilter.WildcardFileFilter +import org.apache.commons.io.FilenameUtils + +import org.w3c.dom.Document +import org.w3c.dom.Element +import org.w3c.dom.Node +import org.w3c.dom.NodeList
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/upload_omero.sh Tue Dec 19 15:02:41 2023 +0000 @@ -0,0 +1,17 @@ +#!/bin/bash +omero_server="$1" +omero_user="$(cat $2 | awk 'NR==2{print $0}')" +omero_password="$(cat $2 | awk 'NR==3{print $0}')" +to_create=$3 +screen_name_or_id=$4 + +if [ "$to_create" = "create" ]; then + # Create a screen: + screen_name_or_id=$(omero obj -s ${omero_server} -u ${omero_user} -w ${omero_password} new Screen name="${screen_name_or_id}" | awk -F ":" 'END{print $NF}') + echo "Just created the new screen ${screen_name_or_id}" +fi + +echo "Start upload" +companion_file=$(ls output/*.companion.ome) +omero import -s ${omero_server} -u ${omero_user} -w ${omero_password} -T Screen:id:"${screen_name_or_id}" "${companion_file}" 2>&1 +echo "Upload finished"