#!/usr/bin/env python # -*- coding: utf-8 -*- # ------------------------------------------------------------------------------ # Copyright (C) 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. # ------------------------------------------------------------------------------ """ Creates an OMERO.figure file of a Split-View figure. This an OMERO script that runs server-side. """ import json from io import BytesIO import omero.scripts as scripts from omero.rtypes import rlong, rstring from omero.gateway import BlitzGateway from omero.model import FileAnnotationI, OriginalFileI, TagAnnotationI from omero.sys import ParametersI JSON_FILEANN_NS = "omero.web.figure.json" def channelMarshal(channel): """ Return a dict with all there is to know about a channel. NB: This is copied from omeroweb.webgateway.marshal.py since we don't know that OMERO.web is installed on same environment as scripts @param channel: L{omero.gateway.ChannelWrapper} @return: Dict """ chan = { 'label': channel.getLabel(), 'color': channel.getColor().getHtml(), 'inverted': channel.isInverted(), 'window': {'min': channel.getWindowMin(), 'max': channel.getWindowMax(), 'start': channel.getWindowStart(), 'end': channel.getWindowEnd()}, 'active': False, # channel.isActive() } lut = channel.getLut() if lut and len(lut) > 0: chan['lut'] = lut return chan def get_timestamps(conn, image): """Return a list of times (secs) 1 for each T-index in image.""" params = ParametersI() params.addLong('pid', image.getPixelsId()) query = "from PlaneInfo as Info where"\ " Info.theZ=0 and Info.theC=0 and pixels.id=:pid" info_list = conn.getQueryService().findAllByQuery( query, params, conn.SERVICE_OPTS) timemap = {} for info in info_list: t_index = info.theT.getValue() if info.deltaT is not None: delta_t = info.deltaT.getValue() timemap[t_index] = round(delta_t, 2) time_list = [] for t in range(image.getSizeT()): if t in timemap: time_list.append(timemap[t]) return time_list def create_figure_file(conn, figure_json, figure_name): """Create Figure FileAnnotation from json data.""" if len(figure_json['panels']) == 0: raise Exception('No Panels') first_img_id = figure_json['panels'][0]['imageId'] # we store json in description field... description = {} description['name'] = figure_name description['imageId'] = first_img_id # Try to set Group context to the same as first image conn.SERVICE_OPTS.setOmeroGroup('-1') i = conn.getObject("Image", first_img_id) gid = i.getDetails().getGroup().getId() conn.SERVICE_OPTS.setOmeroGroup(gid) json_bytes = json.dumps(figure_json).encode('utf-8') file_size = len(json_bytes) f = BytesIO() try: f.write(json_bytes) update = conn.getUpdateService() orig_file = conn.createOriginalFileFromFileObj( f, '', figure_name, file_size, mimetype="application/json") finally: f.close() fa = FileAnnotationI() fa.setFile(OriginalFileI(orig_file.getId(), False)) fa.setNs(rstring(JSON_FILEANN_NS)) desc = json.dumps(description) fa.setDescription(rstring(desc)) fa = update.saveAndReturnObject(fa, conn.SERVICE_OPTS) return fa.getId().getValue() def get_ch_label(image, ch_index): channel = image.getChannels()[ch_index] # positions are: top, left, right, leftvert, bottom, topleft, # topright, bottomleft, bottomright return { "text": channel.getLabel(), "size": 12, "position": "top", "color": channel.getColor().getHtml() } def get_image_labels(image, params): """Create image labels from Name or Tags.""" labels = [] if params['Row_Labels'] == 'Name': labels.append({"text": image.getName(), "size": 12, "position": "leftvert", "color": "000000"}) elif params['Row_Labels'] == 'Tags': # Get Tags on the Image for ann in image.listAnnotations(): if ann.OMERO_TYPE == TagAnnotationI: labels.append({ "text": ann.getTextValue(), "size": 12, "position": "leftvert", "color": "000000", }) return labels def get_scalebar_json(): """Return JSON to add a 10 micron scalebar to bottom-right.""" return {"show": True, "length": 10, "units": "MICROMETER", "position": "bottomright", "color": "FFFFFF", "show_label": True, "font_size": 10} def get_panel_json(image, x, y, width, height, c_index=None): """Get json for a figure panel.""" px = image.getPrimaryPixels().getPhysicalSizeX() py = image.getPrimaryPixels().getPhysicalSizeY() # channelMarshal gives us 'active':False for each channel channels = [channelMarshal(x) for x in image.getChannels()] # Just turn on 1 channel if c_index is not None: channels[c_index]['active'] = True else: # Or ALL channels (merged image) for c in channels: c['active'] = True img_json = { "imageId": image.id, "y": y, "x": x, "width": width, "height": height, "orig_width": image.getSizeX(), "orig_height": image.getSizeY(), "sizeT": image.getSizeT(), "sizeZ": image.getSizeZ(), "channels": channels, "name": image.getName(), "theT": image.getDefaultT(), "theZ": image.getDefaultZ(), "labels": [], } if px is not None: img_json["pixel_size_x"] = px.getValue() img_json["pixel_size_x_unit"] = str(px.getUnit()) img_json["pixel_size_x_symbol"] = px.getSymbol() if py is not None: img_json["pixel_size_y"] = py.getValue() if image.getSizeT() > 1: img_json['deltaT'] = get_timestamps(conn, image) return img_json def create_omero_figure(conn, images, params): """Create OMERO.figure from given images.""" figure_json = {"version": 5} panel_width = 80 panel_height = panel_width spacing = panel_width/20 margin = 40 panels_json = [] for row, image in enumerate(images): print('image', image.id, image.name) panel_x = margin panel_y = (row * (panel_height + spacing)) + margin for col in range(image.getSizeC()): j = get_panel_json(image, panel_x, panel_y, panel_width, panel_height, col) if row == 0: j['labels'].append(get_ch_label(image, col)) if col == 0: j['labels'].extend(get_image_labels(image, params)) panels_json.append(j) panel_x += panel_width + spacing # Add merged panel j = get_panel_json(image, panel_x, panel_y, panel_width, panel_height) panels_json.append(j) # Add scalebar to last panel panels_json[-1]['scalebar'] = get_scalebar_json() figure_json['panels'] = panels_json figure_name = params['Figure_Name'] return create_figure_file(conn, figure_json, figure_name) if __name__ == "__main__": dataTypes = [rstring('Image')] labelTypes = [rstring('Name'), rstring('Tags')] client = scripts.client( 'Split_View_Figure.py', """ This script creates an OMERO.figure 'spilt-view' figure. """, scripts.String( "Data_Type", optional=False, grouping="1", description="Choose source of images", values=dataTypes, default="Image"), scripts.List( "IDs", optional=False, grouping="2", description="Dataset or Image IDs.").ofType(rlong(0)), scripts.String( "Row_Labels", optional=False, grouping="3", description="How to label each image", values=labelTypes, default="Name"), scripts.String( "Figure_Name", optional=False, grouping="4", description="Name of the new OMERO.figure", default="Split View Figure"), authors=["Will Moore", "OME Team"], institutions=["University of Dundee"], contact="ome-users@lists.openmicroscopy.org.uk", ) try: # process the list of args above. params = client.getInputs(unwrap=True) print(params) # wrap client to use the Blitz Gateway conn = BlitzGateway(client_obj=client) # Call the main script - returns the new OMERO.figure ann ID images = list(conn.getObjects('Image', params["IDs"])) print(f'Found {len(images)} images') print(images) if len(images) == 0: message = "No images found" else: figure_id = create_omero_figure(conn, images, params) message = "Created figure: %s" % figure_id client.setOutput("Message", rstring(message)) except Exception: raise finally: client.closeSession()