/* * ----------------------------------------------------------------------------- * Copyright (C) 2018-2020 University of Dundee. All rights reserved. * * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 2 of the License, or * (at your option) any later version. * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along * with this program; if not, write to the Free Software Foundation, Inc., * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. * * ------------------------------------------------------------------------------ */ /* * This Groovy script uses ImageJ to analyse particles. * The generated ROIs are then saved back to OMERO. * We create a summary CSV and a summary table of the measurement and attach * them to the dataset. * Use this script in the Scripting Dialog of Fiji (File > New > Script). * Select Groovy as language in the Scripting Dialog. * Error handling is omitted to ease the reading of the script but * this should be added * if used in production to make sure the services are closed * Information can be found at * https://docs.openmicroscopy.org/latest/omero5/developers/Java.html */ #@ String(label="Username") USERNAME #@ String(label="Password", style='password') PASSWORD #@ String(label="Host", value='wss://workshop.openmicroscopy.org/omero-ws') HOST #@ Integer(label="Project ID", value=2331) project_id import java.util.ArrayList import java.lang.Math import java.lang.StringBuffer import java.nio.ByteBuffer import java.io.File import java.io.PrintWriter import java.nio.file.Files // OMERO Dependencies import omero.gateway.Gateway import omero.gateway.LoginCredentials import omero.gateway.SecurityContext import omero.gateway.facility.BrowseFacility import omero.gateway.facility.DataManagerFacility import omero.gateway.facility.MetadataFacility import omero.gateway.facility.ROIFacility import omero.gateway.facility.TablesFacility import omero.gateway.model.FileAnnotationData import omero.gateway.model.MapAnnotationData import omero.gateway.model.DatasetData import omero.gateway.model.ImageData import omero.gateway.model.ProjectData import omero.gateway.model.TableData import omero.gateway.model.TableDataColumn import omero.model.DatasetI import omero.model.ImageI import omero.model.ProjectI import omero.log.SimpleLogger import omero.model.ChecksumAlgorithmI import omero.model.FileAnnotationI import omero.model.OriginalFileI import omero.model.enums.ChecksumAlgorithmSHA1160 import static omero.rtypes.rlong import static omero.rtypes.rstring import org.openmicroscopy.shoola.util.roi.io.ROIReader import ij.IJ import ij.plugin.frame.RoiManager import ij.measure.ResultsTable MAP_KEY = "Channels" save_data = true if (HOST.startsWith("idr")) { save_data = false } def connect_to_omero() { "Connect to OMERO" credentials = new LoginCredentials() credentials.getServer().setHostname(HOST) credentials.getUser().setUsername(USERNAME.trim()) credentials.getUser().setPassword(PASSWORD.trim()) simpleLogger = new SimpleLogger() gateway = new Gateway(simpleLogger) gateway.connect(credentials) return gateway } def get_datasets(gateway, ctx, project_id) { "List all datasets contained in a Project" browse = gateway.getFacility(BrowseFacility) ids = new ArrayList(1) ids.add(new Long(project_id)) projects = browse.getProjects(ctx, ids) return projects[0].getDatasets() } def get_images(gateway, ctx, dataset_id) { "List all images contained in a Dataset" browse = gateway.getFacility(BrowseFacility) ids = new ArrayList(1) ids.add(new Long(dataset_id)) return browse.getImagesForDatasets(ctx, ids) } def get_channels_data(gateway, ctx, image_id) { "List the channels data associated to the specified image" svc = gateway.getFacility(MetadataFacility) return svc.getChannelData(ctx, image_id) } def get_channel_wavelength(gateway, ctx, image_id, dataset_name) { "Load the map annotations and find the channel's wavelength matching the dataset name" svc = gateway.getFacility(MetadataFacility) types = new ArrayList(1) types.add(MapAnnotationData.class) data = new ImageData(new ImageI(image_id, false)) annotations = svc.getAnnotations(ctx, data, types, null) if (annotations.size() == 0) { return "not found" } // Iterate through annotation j = annotations.iterator() wavelength = 0 while (j.hasNext()) { annotation = j.next() if (annotation.getNameSpace().equals(FileAnnotationData.BULK_ANNOTATIONS_NS)) { named_values = annotation.getContent() i = named_values.iterator() while (i.hasNext()) { nv = i.next() if (nv.name.equals(MAP_KEY)) { channels = nv.value.split("; ") channels.each() { ch_name -> values = ch_name.split(":") name = values[1] if (dataset_name.contains(name)) { wavelength = values[0] return } } } } } } return wavelength } def get_port(HOST) { port = 4064 // check if websockets is used if (HOST.startsWith("ws")) { port = 443 } return port } def open_image_plus(HOST, USERNAME, PASSWORD, group_id, image_id) { "Open the image using the Bio-Formats Importer" StringBuilder options = new StringBuilder() options.append("location=[OMERO] open=[omero:server=") options.append(HOST) options.append("\nuser=") options.append(USERNAME.trim()) options.append("\nport=") options.append(get_port(HOST)) options.append("\npass=") options.append(PASSWORD.trim()) options.append("\ngroupID=") options.append(group_id) options.append("\niid=") options.append(image_id) options.append("] ") options.append("windowless=true view=Hyperstack ") IJ.runPlugIn("loci.plugins.LociImporter", options.toString()) } def save_row(rt, table_rows, channel_index, dataset_name, image) { "Create a summary table from the original table" // Remove the rows not corresponding to the specified channel to_delete = new ArrayList() ref = "c:" + channel_index max_bounding_box = 0.0f for (i = 0; i < rt.size(); i++) { label = rt.getStringValue("Label", i) if (label.contains(ref)) { w = rt.getStringValue("Width", i) h = rt.getStringValue("Height", i) area = Float.parseFloat(w) * Float.parseFloat(h) max_bounding_box = Math.max(area, max_bounding_box) } } // Rename the table so we can read the summary table IJ.renameResults("Results") rt = ResultsTable.getResultsTable() for (i = 0; i < rt.size(); i++) { value = rt.getStringValue("Slice", i) if (!value.startsWith(ref)) { to_delete.add(i) } } // Delete the rows we do not need for (i = 0; i < rt.size(); i++) { value = to_delete.get(i) v = value-i rt.deleteRow(v) } rt.updateResults() // Insert values in summary table for (i = 0; i < rt.size(); i++) { rt.setValue("Dataset", i, dataset_name) rt.setValue("Bounding_Box", i, max_bounding_box) rt.setValue("Channel Index", i, channel_index) } headings = rt.getHeadings() for (j = 0; j < rt.size(); j++) { row = new ArrayList() for (i = 0; i < headings.length; i++) { heading = rt.getColumnHeading(i) if (heading.equals("Slice") || heading.equals("Dataset") || heading.equals("Label")) { row.add(rt.getStringValue(i, j)) } else { row.add(new Double(rt.getValue(i, j))) } } row.add(image) table_rows.add(row) } return headings } def create_table_columns(headings) { "Create the table headings from the ImageJ results table" size = headings.size() table_columns = new TableDataColumn[size+1] //populate the headings for (h = 0; h < size; h++) { heading = headings[h] // OMERO.tables queries don't handle whitespace well heading = heading.replace(" ", "_") if (heading.equals("Slice") || heading.equals("Dataset") || heading.equals("Label")) { table_columns[h] = new TableDataColumn(heading, h, String) } else { table_columns[h] = new TableDataColumn(heading, h, Double) } } table_columns[size] = new TableDataColumn("Image", size, ImageData) return table_columns } def save_rois_to_omero(ctx, image_id, imp) { // Save ROI's back to OMERO reader = new ROIReader() roi_list = reader.readImageJROIFromSources(image_id, imp) roi_facility = gateway.getFacility(ROIFacility) result = roi_facility.saveROIs(ctx, image_id, exp_id, roi_list) roivec = new ArrayList() j = result.iterator() while (j.hasNext()) { roidata = j.next() roi_id = roidata.getId() i = roidata.getIterator() while (i.hasNext()) { roi = i.next() shape = roi[0] t = shape.getZ() z = shape.getT() c = shape.getC() shape_id = shape.getId() roivec.add([roi_id, shape_id, z, c, t]) } } return roivec } def upload_csv_to_omero(ctx, file, project_id) { "Upload the CSV file and attach it to the specified project" svc = gateway.getFacility(DataManagerFacility) file_size = file.length() original_file = new OriginalFileI() original_file.setName(rstring(file.getName())) original_file.setPath(rstring(file.getAbsolutePath())) original_file.setSize(rlong(file_size)) checksum_algorithm = new ChecksumAlgorithmI() checksum_algorithm.setValue(rstring(ChecksumAlgorithmSHA1160.value)) original_file.setHasher(checksum_algorithm) original_file.setMimetype(rstring("text/csv")) original_file = svc.saveAndReturnObject(ctx, original_file) store = gateway.getRawFileService(ctx) // Open file and read stream INC = 262144 pos = 0 buf = new byte[INC] ByteBuffer bbuf = null stream = null try { store.setFileId(original_file.getId().getValue()) stream = new FileInputStream(file) while ((rlen = stream.read(buf)) > 0) { store.write(buf, pos, rlen) pos += rlen bbuf = ByteBuffer.wrap(buf) bbuf.limit(rlen) } original_file = store.save() } finally { if (stream != null) { stream.close() } store.close() } // create the file annotation namespace = "training.demo" fa = new FileAnnotationI() fa.setFile(original_file) fa.setNs(rstring(namespace)) data_object = new ProjectData(new ProjectI(project_id, false)) svc.attachAnnotation(ctx, new FileAnnotationData(fa), data_object) } def save_summary_as_omero_table(ctx, rows, columns, project_id) { "Create an OMERO table with the summary result and attach it to the specified project" data = new Object[columns.length][rows.size()] for (r = 0; r < rows.size(); r++) { row = rows.get(r) for (i = 0; i < columns.length; i++) { //Due to a limitation of OMERO.parade multiply value by 100 v = row.get(i) if (v instanceof Double) { v = v * 100 } data[i][r] = v } } // Create the table table_data = new TableData(columns, data) table_facility = gateway.getFacility(TablesFacility) data_object = new ProjectData(new ProjectI(project_id, false)) result = table_facility.addTable(ctx, data_object, "Summary_from_Fiji", table_data) oid = result.getOriginalFileId() // Retrieve the annotation and set the namespace (due to a limitation of JavaGateway) annotations = table_facility.getAvailableTables(ctx, data_object) it = annotations.iterator() while (it.hasNext()) { ann = it.next() if (ann.getFileID() == oid) { ann.setNameSpace(FileAnnotationData.BULK_ANNOTATIONS_NS) gateway.getUpdateService(ctx).saveAndReturnObject(ann.asIObject()) break } } } def save_summary_as_csv(file, rows, columns) { "Save the summary locally as a CSV" stream = null sb = new StringBuilder() try { stream = new PrintWriter(file) l = columns.length for (i = 0; i < l; i++) { sb.append(columns[i].getName()) if (i != (l-1)) { sb.append(", ") } } sb.append("\n") rows.each() { row -> size = row.size() for (i = 0; i < size; i++) { value = row.get(i) if (value instanceof ImageData) { sb.append(value.getId()) } else { sb.append(value) } if (i != (size-1)) { sb.append(", ") } } sb.append("\n") } stream.write(sb.toString()) } finally { stream.close() } } // Connect gateway = connect_to_omero() user = gateway.getLoggedInUser() group_id = user.getGroupId() ctx = new SecurityContext(group_id) exp = gateway.getLoggedInUser() exp_id = exp.getId() table_rows = new ArrayList() table_columns = null // get all the dataset_ids in an project datasets = get_datasets(gateway, ctx, project_id) //Close windows before starting IJ.run("Close All") datasets.each() { d -> dataset_name = d.getName() // for each dataset load the images // get all images_ids in the dataset images = get_images(gateway, ctx, d.getId()) images.each() { image -> if (image.getName().endsWith(".tif")) { return } IJ.run("Close All") id = image.getId() channel_index = 1 // Find the index of the channel matching the dataset name as a string // This section is very specific to the data we are looking at. Each channel has // wavelength information but not name directly associated to it. channel_wavelength = get_channel_wavelength(gateway, ctx, id, dataset_name) channels = get_channels_data(gateway, ctx, id) channels.each() { channel -> em = channel.getEmissionWavelength(null) if (em != null) { v = em.getValue().intValue().toString() if (v.equals(channel_wavelength)) { channel_index = channel.getIndex()+1 println "Found index: "+ channel_index } } } open_image_plus(HOST, USERNAME, PASSWORD, group_id, id) imp = IJ.getImage() // Some analysis which creates ROI's and Results Table IJ.run("8-bit") // white might be required depending on the version of Fiji IJ.run(imp, "Auto Threshold", "method=MaxEntropy stack") IJ.run(imp, "Analyze Particles...", "size=10-Infinity pixel display clear add stack summarize") IJ.run("Set Measurements...", "area mean standard modal min centroid center perimeter bounding feret's summarize stack display redirect=None decimal=3") rt = ResultsTable.getResultsTable() // Save the ROIs if (save_data) { roivec = save_rois_to_omero(ctx, id, imp) } println "creating summary results for image ID " + id headings = save_row(rt, table_rows, channel_index, dataset_name, image) if (table_columns == null) { table_columns = create_table_columns(headings) } // Close the various components IJ.selectWindow("Results") IJ.run("Close") IJ.selectWindow("ROI Manager") IJ.run("Close") imp.changes = false // Prevent "Save Changes?" dialog imp.close() } } //Create the result file tmp_dir = Files.createTempDirectory("Fiji_csv") path = tmp_dir.resolve("idr0021_merged_results.csv") file_path = Files.createFile(path) file = new File(file_path.toString()) // create CSV file save_summary_as_csv(file, table_rows, table_columns) if (save_data) { upload_csv_to_omero(ctx, file, project_id) save_summary_as_omero_table(ctx, table_rows, table_columns, project_id) // delete the local copy of the temporary file and directory dir = new File(tmp_dir.toString()) entries = dir.listFiles() for (i = 0; i < entries.length; i++) { entries[i].delete() } dir.delete() } // Close the connection gateway.disconnect() println "processing done"