# HG changeset patch # User ufz # Date 1734382576 0 # Node ID 5ad32d18fe820f107c23138697fe8419ef5e2767 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46 diff -r 000000000000 -r 5ad32d18fe82 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,19 @@ +# OMERO import images + +## Set up user credentials on Galaxy to connect to other omero instance + +To enable users to set their credentials for this tool, +make sure the file `config/user_preferences_extra.yml` has the following section: + +``` + omero_account: + description: Your OMERO instance connection credentials + inputs: + - name: username + label: Username + type: text + required: False + - name: password + label: Password + type: password + required: False \ No newline at end of file diff -r 000000000000 -r 5ad32d18fe82 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,56 @@ + + + 5.18.0 + 3.0.1 + 23.0 + + + + ezomero + pandas + + + + + + + omero-py + + openjdk + + + + + + + + ^[a-zA-Z0-9._-]*$ + '..' not in value + + + + + + + --host '$omero_host' + --port $omero_port + + + + + + + + **OMERO-suite Security Diclaimer:** To utilize the OMERO tools, the user must trust Galaxy instances. + The configuration file, which contains your OMERO password and username, is stored in the job working directory. + This directory only exists during the runtime of the job and should only be accessible by the system user that runs the job. + However, please be aware that your username and password may be exposed to users with administrative rights. + We are working on increasing the security of the OMERO suite + + + \ No newline at end of file diff -r 000000000000 -r 5ad32d18fe82 omero_dataset_to_plate.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omero_dataset_to_plate.py Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,127 @@ +import argparse +import csv +import json +import re +import sys +from collections import defaultdict + + +import omero +from omero.gateway import BlitzGateway +from omero.rtypes import rint, rstring + + +def convert_dataset_to_plate(host, user, pws, port, dataset_id, log_file, mapping_file, delete_dataset): + """ + Connect to OMERO server, convert a dataset to a plate using the specified well mapping file + """ + conn = BlitzGateway(user, pws, host=host, port=port, secure=True) + if not conn.connect(): + sys.exit("ERROR: Failed to connect to OMERO server") + + def log_message(message, status="INFO"): + with open(log_file, 'w') as f: + f.write(f"{message}") + + dataset = conn.getObject("Dataset", dataset_id) + if dataset is None: + conn.close() + sys.exit("ERROR: Dataset not found") + + update_service = conn.getUpdateService() + + # Create a Plate + plate = omero.model.PlateI() + plate.name = rstring(dataset.getName()) + plate = update_service.saveAndReturnObject(plate) + + # Parse the mapping file + image_to_well_mapping = {} + if mapping_file: + with open(mapping_file, 'r') as f: + reader = csv.DictReader(f, delimiter='\t') + for row in reader: + filename = row['Filename'] + well = row['Well'] + match = re.match(r"([A-Z])(\d+)", well) + if match: + row_char, col = match.groups() + row = ord(row_char.upper()) - ord('A') + col = int(col) - 1 + image_to_well_mapping[filename] = (row, col) + else: + conn.close() + sys.exit(f"Invalid well format '{well}' for file '{filename}'") + + # List the dataset children + images = list(dataset.listChildren()) + if not images: + conn.close() + sys.exit("ERROR: No images found in dataset") + + # Compare images in the mapping file and in the dataset + grouped_images = defaultdict(list) + for image in images: + image_name = image.getName() + if image_to_well_mapping: + if image_name in image_to_well_mapping: + row, col = image_to_well_mapping[image_name] + grouped_images[(row, col)].append(image) + else: + conn.close() + sys.exit(f"Image '{image_name}' not found in mapping file.") + + # Assign images to the well based on the mapping file + for (row, col), imgs_in_group in grouped_images.items(): + well = omero.model.WellI() + well.plate = omero.model.PlateI(plate.id.val, False) + well.column = rint(col) + well.row = rint(row) + + for image in imgs_in_group: + ws = omero.model.WellSampleI() + ws.image = omero.model.ImageI(image.id, False) + ws.well = well + well.addWellSample(ws) + + try: + update_service.saveObject(well) + except ValueError as e: + conn.close() + sys.exit("ERROR: Failed to update plate for dataset '{}' due to: {}".format(dataset.getName(), str(e))) + + # Close the connection and, in case, delete the dataset + if delete_dataset is True: + conn.deleteObjects("Dataset", [dataset_id], wait=True) + log_message(f"Images from Dataset {dataset_id} successfully added to Plate {plate.id.val}") + conn.close() + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Convert an OMERO dataset to a plate.") + parser.add_argument("--credential-file", dest="credential_file", type=str, required=True, + help="Credential file (JSON file with username and password for OMERO)") + parser.add_argument('--host', required=True, help='OMERO host') + parser.add_argument('--port', required=True, type=int, help='OMERO port') + parser.add_argument('--dataset_id', type=int, required=True, help="Dataset ID to convert plate") + parser.add_argument('--log_file', default='metadata_import_log.txt', + help='Path to the log file') + parser.add_argument('--mapping_file', + help='Tabular file mapping filenames to well positions (2 columns: filename, Well)') + parser.add_argument('--delete_dataset', action='store_true', + help='Flag to delete the original dataset') + args = parser.parse_args() + + with open(args.credential_file, 'r') as f: + crds = json.load(f) + + convert_dataset_to_plate( + user=crds['username'], + pws=crds['password'], + host=args.host, + port=args.port, + dataset_id=args.dataset_id, + log_file=args.log_file, + mapping_file=args.mapping_file, + delete_dataset=args.delete_dataset + ) diff -r 000000000000 -r 5ad32d18fe82 omero_dataset_to_plate.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omero_dataset_to_plate.xml Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,67 @@ + + with omero-py + + macros.xml + 3 + + + omero + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Description +----------- +- Tool to convert an existing dataset to a plate in OMERO +- The tool is taking as input a mapping tabular file with Filename and Well Position: + +------------+---------------+ + | Filename | Well | + +============+===============+ + | image1.tiff| A2 | + +------------+---------------+ + | image2.tiff| B5 | + +------------+---------------+ + | image3.tiff| H12 | + +------------+---------------+ +@SECURITY_DISCLAIMER@ + + + 10.1038/nmeth.1896 + + diff -r 000000000000 -r 5ad32d18fe82 omero_filter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omero_filter.py Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,77 @@ +import argparse +import csv +import json +import sys + +import ezomero as ez + + +def filter_ids_ezo(user, pws, host, port, filter, id, value1, value2=None, tsv_file="filter_list.tsv"): + + # Transform the id input in a list of integer + id = id.split(',') + id = list(map(int, id)) + + # Function to write tabular file from the ezomero output + def write_ids_to_tsv(data): + with open(tsv_file, 'w', newline='') as f: + writer = csv.writer(f, delimiter='\t') + for item in data: + writer.writerow([item]) # Write each ID + + with ez.connect(user, pws, "", host, port, secure=True) as conn: + + if filter == "filename": + fn_ids = ez.filter_by_filename(conn, id, value1) + write_ids_to_tsv(fn_ids) + return fn_ids + + elif filter == "KP": + kp_ims = ez.filter_by_kv(conn, id, value1, value2) + write_ids_to_tsv(kp_ims) + return kp_ims + + elif filter == "tag": + tg_dict = ez.filter_by_tag_value(conn, id, value1) + write_ids_to_tsv(tg_dict) + return tg_dict + + else: + sys.exit(f"Unsupported object type: {filter}") + + +# Argument parsing +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Fetch and save data as TSV based on object type.") + parser.add_argument("--credential-file", dest="credential_file", type=str, required=True, + help="Credential file (JSON file with username and password for OMERO)") + parser.add_argument('--host', required=True, + help="Host server address.") + parser.add_argument('--port', required=True, type=int, + help='OMERO port') + parser.add_argument('--filter', required=True, + help="Filter type - Filename, Key-Value Pairs, Tag") + parser.add_argument('--id', required=True, + help="List of images IDs") + parser.add_argument('--value1', required=True, + help="First searching values - Filename, Key, Tag") + parser.add_argument('--value2', required=False, + help="Second searching values - Value (necessary just for Key-Value Pairs filter") + parser.add_argument('--tsv_file', default='filter_list.tsv', + help="Output TSV file path.") + args = parser.parse_args() + + if args.filter == "KP" and args.value2 is None: + raise ValueError("'--value 2' is necessary to retrieve KP") + + with open(args.credential_file, 'r') as f: + crds = json.load(f) + + # Call the main function to get the object and save it as a TSV + filter_ids_ezo(user=crds['username'], pws=crds['password'], host=args.host, + port=args.port, + filter=args.filter, + value1=args.value1, + value2=args.value2, + id=args.id, + tsv_file=args.tsv_file) diff -r 000000000000 -r 5ad32d18fe82 omero_get_id.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omero_get_id.py Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,116 @@ +import argparse +import csv +import json +import sys + +import ezomero as ez + + +def get_ids_ezo(user, pws, host, port, final_obj_type, parent_obj_type, parent_id=None, tsv_file="id_list.tsv"): + + # Function to write tabular file from the ezomero output + def write_ids_to_tsv(data): + with open(tsv_file, 'w', newline='') as f: + writer = csv.writer(f, delimiter='\t') + for item in data: + writer.writerow([item]) # Write each ID + + with ez.connect(user, pws, "", host, port, secure=True) as conn: + + if final_obj_type == "Project": + proj_ids = ez.get_project_ids(conn) + write_ids_to_tsv(proj_ids) + return proj_ids + + elif final_obj_type == "Dataset": + args = {'project': None} + if parent_obj_type == "Project": + args['project'] = parent_id + ds_ids = ez.get_dataset_ids(conn, **args) + write_ids_to_tsv(ds_ids) + return ds_ids + + elif final_obj_type == "Image": + args = { + 'project': None, + 'dataset': None, + 'plate': None, + 'well': None + } + if parent_obj_type == "Project": + args['project'] = parent_id + elif parent_obj_type == "Dataset": + args['dataset'] = parent_id + elif parent_obj_type == "Plate": + args['plate'] = parent_id + elif parent_obj_type == "Well": + args['well'] = parent_id + elif parent_obj_type != "All": + raise ValueError("Object set as parent_obj_type is not compatible") + + ds_ims = ez.get_image_ids(conn, **args) + write_ids_to_tsv(ds_ims) + return ds_ims + + elif final_obj_type == "Annotation": + map_annot_ids = ez.get_map_annotation_ids(conn, parent_obj_type, parent_id) + write_ids_to_tsv(map_annot_ids) + return map_annot_ids + + elif final_obj_type == "Tag": + tag_ids = ez.get_tag_ids(conn, parent_obj_type, parent_id) + write_ids_to_tsv(tag_ids) + return tag_ids + + elif final_obj_type == "Roi": + roi_ids = ez.get_roi_ids(conn, parent_id) + write_ids_to_tsv(roi_ids) + return roi_ids + + elif final_obj_type == "Table": + file_ann_ids = ez.get_file_annotation_ids(conn, parent_obj_type, parent_id) + write_ids_to_tsv(file_ann_ids) + return file_ann_ids + + else: + sys.exit(f"Unsupported object type: {filter}") + + +# Argument parsing +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Fetch OMERO object IDs as TSV from parent object.") + parser.add_argument("--credential-file", dest="credential_file", type=str, + required=True, help="Credential file (JSON file with username and password for OMERO)") + parser.add_argument('--host', required=True, + help="Host server address.") + parser.add_argument('--port', required=True, type=int, + help='OMERO port') + parser.add_argument('--final_obj_type', required=True, + help="Type of object to fetch ID: Project, Dataset, Image, Annotation, Tag, Roi, or Table.") + parser.add_argument('--parent_obj_type', required=True, + help="Type of object from which you fetch IDs: Project, Dataset, Plate, Well, Image (or 'All' if you want to get all objects).") + parser.add_argument('--parent_id', required=False, type=int, + help="ID of the OMERO object in `--parent_obj_type`, not required if you used `--parent_obj_type All`.") + parser.add_argument('--tsv_file', default='id_list.tsv', + help="Output TSV file path.") + args = parser.parse_args() + + if args.parent_id is None and args.parent_obj_type != "All": + raise ValueError("ID is only optional is you use `--parent_obj_type All`") + + if args.final_obj_type == "Roi" and args.parent_obj_type != "Image": + raise ValueError("Roi IDs can only be retrived from images, use `--parent_obj_type Image`") + + if args.parent_obj_type == "All" and args.final_obj_type not in ["Image", "Dataset", "Project"]: + raise ValueError("Only Images, Datasets and Projects is compatible with `--parent_obj_type All`") + + with open(args.credential_file, 'r') as f: + crds = json.load(f) + + # Call the main function to get the object and save it as a TSV + get_ids_ezo(user=crds['username'], pws=crds['password'], host=args.host, + port=args.port, + final_obj_type=args.final_obj_type, + parent_obj_type=args.parent_obj_type, + parent_id=args.parent_id, + tsv_file=args.tsv_file) diff -r 000000000000 -r 5ad32d18fe82 omero_get_value.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omero_get_value.py Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,98 @@ +import argparse +import csv +import json +import sys + +import ezomero as ez + + +def get_object_ezo(user, pws, host, port, obj_type, ids, tsv_file): + # Function to write tabular file from the ezomero output + def write_values_to_tsv(data, header): + with open(tsv_file, 'w', newline='') as f: + writer = csv.writer(f, delimiter='\t') + writer.writerow([header]) # Write the header + for item in data: + writer.writerow([item]) # Write each value + + # Function to write tabular file from a dictionary ezomero output + def write_dict_to_tsv(data, headers): + with open(tsv_file, 'w', newline='') as f: + writer = csv.writer(f, delimiter='\t') + writer.writerow(headers) # Write the headers + for key, value in data.items(): + writer.writerow([key, value]) # Write each key-value pair + + # Function to write tabular file from list of list ezomero output + def write_table_to_tsv(data): + with open(tsv_file, 'w') as f: + for row in data: + f.write('\t'.join([str(val) for val in row]) + '\n') + + with ez.connect(user, pws, "", host, port, secure=True) as conn: + if obj_type == "Annotation": + ma_dict = {} + for maid in ids: + current_ma_dict = ez.get_map_annotation(conn, maid) + ma_dict = {**ma_dict, **current_ma_dict} + write_dict_to_tsv(ma_dict, ["Annotation ID", "Annotation Value"]) + return ma_dict + elif obj_type == "Tag": + tags = [] + for tag_id in ids: + tags.append(ez.get_tag(conn, tag_id)) + # Sort the tags for consistency: + tags.sort + write_values_to_tsv(tags, "Tags") + return tags + elif obj_type == "Table": + if len(ids) > 1: + raise ValueError("Only one table can be exported at a time") + table = ez.get_table(conn, ids[0]) + write_table_to_tsv(table) + return table + + else: + sys.exit(f"Unsupported object type: {filter}") + + +# Argument parsing +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Fetch and save data as TSV based on object type.") + parser.add_argument("--credential-file", dest="credential_file", type=str, + required=True, help="Credential file (JSON file with username and password for OMERO)") + parser.add_argument('--host', required=True, + help="Host server address.") + parser.add_argument('--port', required=True, type=int, + help='OMERO port') + parser.add_argument('--obj_type', required=True, + help="Type of object to fetch: Annotation, Table or Tag.") + group = parser.add_mutually_exclusive_group() + group.add_argument('--ids', nargs='+', type=int, + help="IDs of the OMERO objects.") + group.add_argument('--ids_path', + help="File with IDs of the OMERO objects (one per line).") + parser.add_argument('--tsv_file', default='id_list.tsv', required=True, + help="Output TSV file path.") + args = parser.parse_args() + + if args.ids_path: + args.ids = [] + with open(args.ids_path, 'r') as f: + for line in f: + try: + args.ids.append(int(line)) + except ValueError: + print(f"{line.strip()} is not a valid ID.") + if len(args.ids) == 0: + raise ValueError("Cound not find a single ID in the file.") + + with open(args.credential_file, 'r') as f: + crds = json.load(f) + + # Call the main function to get the object and save it as a TSV + get_object_ezo(user=crds['username'], pws=crds['password'], host=args.host, + port=args.port, + obj_type=args.obj_type, + ids=args.ids, + tsv_file=args.tsv_file) diff -r 000000000000 -r 5ad32d18fe82 omero_metadata_upload.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omero_metadata_upload.py Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,101 @@ +import argparse +import json +from datetime import datetime + +import ezomero as ez +import pandas as pd + + +def metadata_import_ezo(user, pws, host, port, obj_type, did=None, ann_type="table", ann_file=None, an_name=None, + log_file='metadata_import_log.txt'): + def upload_metadata(conn, obj_type, did, data_dict, df, ann_type, an_name): + try: + if ann_type == "KV": + id_map_ann = ez.post_map_annotation(conn, obj_type, object_id=int(did), kv_dict=data_dict, ns=an_name) + ma_dict = ez.get_map_annotation(conn, id_map_ann) + return ma_dict + elif ann_type == "table": + id_tb_ann = ez.post_table(conn, df, object_type=obj_type, object_id=int(did), title=an_name, + headers=True) + tb_dict = ez.get_table(conn, id_tb_ann) + return tb_dict + except Exception as e: + log_error(f"Error uploading metadata for {obj_type} with ID {did}: {str(e)}") + return None + + def log_error(message): + with open(log_file, 'w') as f: + f.write(f"ERROR: {message}\n") + + def log_success(message): + with open(log_file, 'w') as f: + f.write(f"SUCCESS: {message}\n") + + try: + df = pd.read_csv(ann_file, delimiter='\t') + except FileNotFoundError as e: + log_error(f"Annotation file not found: {str(e)}") + return + + if ann_type == "table": + data_dict = df.to_dict(orient='records') + elif ann_type == "KV": + data_dict = {col: df[col].iloc[0] for col in df.columns} + + try: + with ez.connect(user, pws, "", host, port, secure=True) as conn: + if obj_type == "project": + if did is None: + did = ez.post_project(conn, project_name=str(datetime.now())) + result = upload_metadata(conn, "Project", did, data_dict, df, ann_type, an_name) + elif obj_type == "screen": + if did is None: + did = ez.post_screen(conn, screen_name=str(datetime.now())) + result = upload_metadata(conn, "Screen", did, data_dict, df, ann_type, an_name) + elif obj_type == "dataset": + if did is None: + did = ez.post_dataset(conn, dataset_name=str(datetime.now())) + result = upload_metadata(conn, "Dataset", did, data_dict, df, ann_type, an_name) + elif obj_type == "plate": + result = upload_metadata(conn, "Plate", did, data_dict, df, ann_type, an_name) + elif obj_type == "well": + result = upload_metadata(conn, "Well", did, data_dict, df, ann_type, an_name) + elif obj_type == "image": + result = upload_metadata(conn, "Image", did, data_dict, df, ann_type, an_name) + else: + raise ValueError("Unsupported object type provided: {}".format(obj_type)) + + if result is not None: + log_success(f"Successfully uploaded metadata for {obj_type} with ID {did}. Result: {result}") + else: + log_error(f"Failed to upload metadata for {obj_type} with ID {did}.") + + conn.close() + + except Exception as e: + log_error(f"Connection error: {str(e)}") + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description='Import metadata into OMERO.') + parser.add_argument("--credential-file", dest="credential_file", type=str, required=True, + help="Credential file (JSON file with username and password for OMERO)") + parser.add_argument('--host', required=True, help='OMERO host') + parser.add_argument('--port', required=True, type=int, help='OMERO port') + parser.add_argument('--obj_type', required=True, choices=['project', 'screen', 'dataset', 'plate', + 'well ', 'image'], + help='Type of OMERO object') + parser.add_argument('--did', type=int, help='ID of the object (if it exists)') + parser.add_argument('--ann_type', required=True, choices=['table', 'KV'], help='Annotation type') + parser.add_argument('--ann_file', required=True, help='Path to the annotation file') + parser.add_argument('--an_name', required=True, help='Namespace or title for the annotation') + parser.add_argument('--log_file', default='metadata_import_log.txt', help='Path to the log file') + + args = parser.parse_args() + + with open(args.credential_file, 'r') as f: + crds = json.load(f) + + metadata_import_ezo(user=crds['username'], pws=crds['password'], host=args.host, port=args.port, + obj_type=args.obj_type, did=args.did, ann_type=args.ann_type, + ann_file=args.ann_file, an_name=args.an_name, log_file=args.log_file) diff -r 000000000000 -r 5ad32d18fe82 omero_roi_upload.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omero_roi_upload.py Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,176 @@ +import argparse +import json +import re + +import numpy as np +import pandas as pd +from ezomero import connect, post_roi +from ezomero.rois import Ellipse, Label, Line, Point, Polygon, Polyline, Rectangle + + +def parse_color(color_str): + if not color_str: + return None + return tuple(map(int, re.findall(r'\d+', color_str))) + + +def parse_points(points_str): + if not points_str: + return None + # Remove leading and trailing brackets and split into individual points + points_str = points_str.strip("[]") + points = points_str.split("),(") + points = [point.strip("()") for point in points] # Remove any remaining parentheses + return [tuple(map(float, point.split(','))) for point in points] + + +def create_shape(row): + shape_type = row['shape'] + shape = None + + if shape_type == 'Ellipse': + shape = Ellipse( + x=row['x'], + y=row['y'], + x_rad=row['x_rad'], + y_rad=row['y_rad'], + z=row.get('z'), + c=row.get('c'), + t=row.get('t'), + label=row.get('label'), + fill_color=parse_color(row.get('fill_color')), + stroke_color=parse_color(row.get('stroke_color')), + stroke_width=row.get('stroke_width') + ) + elif shape_type == 'Label': + shape = Label( + x=row['x'], + y=row['y'], + label=row['label'], + fontSize=row['fontSize'], + z=row.get('z'), + c=row.get('c'), + t=row.get('t'), + fill_color=parse_color(row.get('fill_color')), + stroke_color=parse_color(row.get('stroke_color')), + stroke_width=row.get('stroke_width') + ) + elif shape_type == 'Line': + shape = Line( + x1=row['x1'], + y1=row['y1'], + x2=row['x2'], + y2=row['y2'], + markerStart=row.get('markerStart', None), + markerEnd=row.get('markerEnd', None), + label=row.get('label'), + z=row.get('z'), + c=row.get('c'), + t=row.get('t'), + fill_color=parse_color(row.get('fill_color')), + stroke_color=parse_color(row.get('stroke_color')), + stroke_width=row.get('stroke_width') + ) + elif shape_type == 'Point': + shape = Point( + x=row['x'], + y=row['y'], + z=row.get('z'), + c=row.get('c'), + t=row.get('t'), + label=row.get('label'), + fill_color=parse_color(row.get('fill_color')), + stroke_color=parse_color(row.get('stroke_color')), + stroke_width=row.get('stroke_width') + ) + elif shape_type == 'Polygon': + shape = Polygon( + points=parse_points(row['points']), + z=row.get('z'), + c=row.get('c'), + t=row.get('t'), + label=row.get('label'), + fill_color=parse_color(row.get('fill_color')), + stroke_color=parse_color(row.get('stroke_color')), + stroke_width=row.get('stroke_width') + ) + elif shape_type == 'Polyline': + shape = Polyline( + points=parse_points(row['points']), + z=row.get('z'), + c=row.get('c'), + t=row.get('t'), + label=row.get('label'), + fill_color=parse_color(row.get('fill_color')), + stroke_color=parse_color(row.get('stroke_color')), + stroke_width=row.get('stroke_width') + ) + elif shape_type == 'Rectangle': + shape = Rectangle( + x=row['x'], + y=row['y'], + width=row['width'], + height=row['height'], + z=row.get('z'), + c=row.get('c'), + t=row.get('t'), + label=row.get('label'), + fill_color=parse_color(row.get('fill_color')), + stroke_color=parse_color(row.get('stroke_color')), + stroke_width=row.get('stroke_width') + ) + return shape + + +def main(input_file, conn, image_id, log_file): + # Open log file + with open(log_file, 'w') as log: + df = pd.read_csv(input_file, sep='\t') + # Replace nan to none + df = df.replace({np.nan: None}) + for index, row in df.iterrows(): + msg = f"Processing row {index + 1}/{len(df)}: {row.to_dict()}" + print(msg) + log.write(msg + "\n") + shape = create_shape(row) + if shape: + roi_name = row['roi_name'] if 'roi_name' in row else None + roi_description = row['roi_description'] if 'roi_description' in row else None + roi_id = post_roi(conn, image_id, [shape], name=roi_name, description=roi_description) + msg = f"ROI ID: {roi_id} for row {index + 1}" + print(msg) + log.write(msg + "\n") + else: + msg = f"Skipping row {index + 1}: Unable to create shape" + print(msg) + log.write(msg + "\n") + + +if __name__ == "__main__": + parser = argparse.ArgumentParser( + description="Create shapes from a tabular file and optionally post them as an ROI to OMERO.") + parser.add_argument("--input_file", help="Path to the input tabular file.") + parser.add_argument("--image_id", type=int, required=True, help="ID of the image to which the ROI will be linked") + parser.add_argument("--host", type=str, required=True, help="OMERO server host") + parser.add_argument("--credential-file", dest="credential_file", type=str, required=True, help="Credential file (JSON file with username and password for OMERO)") + parser.add_argument("--port", type=int, default=4064, help="OMERO server port") + parser.add_argument("--log_file", type=str, default="process.txt", help="Log file path") + + args = parser.parse_args() + + with open(args.credential_file, 'r') as f: + crds = json.load(f) + + conn = connect( + host=args.host, + user=crds['username'], + password=crds['password'], + port=args.port, + group="", + secure=True + ) + + try: + main(args.input_file, conn, args.image_id, args.log_file) + finally: + conn.close() diff -r 000000000000 -r 5ad32d18fe82 test-data/dataset_conversion_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_conversion_log.txt Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,1 @@ +Images from Dataset 2 successfully added to Plate 1 \ No newline at end of file diff -r 000000000000 -r 5ad32d18fe82 test-data/input1.tif Binary file test-data/input1.tif has changed diff -r 000000000000 -r 5ad32d18fe82 test-data/input2.tif Binary file test-data/input2.tif has changed diff -r 000000000000 -r 5ad32d18fe82 test-data/input_roi.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_roi.tsv Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,8 @@ +shape x y x_rad y_rad label fontSize x1 y1 x2 y2 points width height fill_color stroke_color stroke_width z c t roi_name roi_description +Ellipse 50.0 50.0 20.0 10.0 (255,0,0,128) (0,0,0,255) 2 0 0 0 Example ROI This is an example ROI +Label 100.0 100.0 Test Label 12.0 (255,255,255,0) (0,0,255,255) 1 0 0 0 Example ROI This is an example ROI +Line 200.0 200.0 250.0 250.0 (0,255,0,128) (0,0,0,255) 2 0 1 0 Example ROI This is an example ROI +Point 150.0 150.0 (0,0,255,128) (255,0,0,255) 3 0 2 0 Example ROI This is an example ROI +Polygon (300,300),(350,350),(300,400) (255,255,0,128) (0,0,0,255) 2 1 0 0 Example ROI This is an example ROI +Polyline (400,400),(450,450),(400,500) (0,255,255,128) (0,0,0,255) 3 0 0 0 Example ROI This is an example ROI +Rectangle 500.0 500.0 100.0 50.0 (255,0,255,128) (0,0,0,255) 2 0 0 0 Example ROI This is an example ROI diff -r 000000000000 -r 5ad32d18fe82 test-data/input_roi_minimal.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_roi_minimal.tsv Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,2 @@ +shape points label +Polygon (300,300),(350,350),(300,400) Example ROI diff -r 000000000000 -r 5ad32d18fe82 test-data/mapping.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapping.tsv Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,3 @@ +Filename Well +sample_A03_image.jpg A2 +sample_H11_image.jpg H5 diff -r 000000000000 -r 5ad32d18fe82 test-data/metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metadata.tsv Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,2 @@ +Key1 Key2 +Value1 Value2 \ No newline at end of file diff -r 000000000000 -r 5ad32d18fe82 test-data/omero_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/omero_output.txt Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,2 @@ +Image:5 +Image:6 diff -r 000000000000 -r 5ad32d18fe82 test-data/output_KV_import.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_KV_import.txt Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,1 @@ +SUCCESS: Successfully uploaded metadata for dataset with ID 4. Result: {'Key1': 'Value1', 'Key2': 'Value2'} diff -r 000000000000 -r 5ad32d18fe82 test-data/output_filter_filename.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_filter_filename.tsv Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,1 @@ +1 diff -r 000000000000 -r 5ad32d18fe82 test-data/output_filter_tag.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_filter_tag.tsv Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,1 @@ +1 diff -r 000000000000 -r 5ad32d18fe82 test-data/output_ids_dataset.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_ids_dataset.tsv Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,1 @@ +1 diff -r 000000000000 -r 5ad32d18fe82 test-data/output_ids_image.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_ids_image.tsv Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,2 @@ +1 +2 diff -r 000000000000 -r 5ad32d18fe82 test-data/output_ids_project.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_ids_project.tsv Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,1 @@ +1 diff -r 000000000000 -r 5ad32d18fe82 test-data/output_table_import.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_table_import.txt Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,2 @@ +SUCCESS: Successfully uploaded metadata for project with ID 2. Result: Key1 Key2 +0 Value1 Value2 diff -r 000000000000 -r 5ad32d18fe82 test-data/output_table_roi.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_table_roi.txt Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,14 @@ +Processing row 1/7: {'shape': 'Ellipse', 'x': 50.0, 'y': 50.0, 'x_rad': 20.0, 'y_rad': 10.0, 'label': None, 'fontSize': None, 'x1': None, 'y1': None, 'x2': None, 'y2': None, 'points': None, 'width': None, 'height': None, 'fill_color': '(255,0,0,128)', 'stroke_color': '(0,0,0,255)', 'stroke_width': 2, 'z': 0, 'c': 0, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'} +ROI ID: 1 for row 1 +Processing row 2/7: {'shape': 'Label', 'x': 100.0, 'y': 100.0, 'x_rad': None, 'y_rad': None, 'label': 'Test Label', 'fontSize': 12.0, 'x1': None, 'y1': None, 'x2': None, 'y2': None, 'points': None, 'width': None, 'height': None, 'fill_color': '(255,255,255,0)', 'stroke_color': '(0,0,255,255)', 'stroke_width': 1, 'z': 0, 'c': 0, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'} +ROI ID: 2 for row 2 +Processing row 3/7: {'shape': 'Line', 'x': None, 'y': None, 'x_rad': None, 'y_rad': None, 'label': None, 'fontSize': None, 'x1': 200.0, 'y1': 200.0, 'x2': 250.0, 'y2': 250.0, 'points': None, 'width': None, 'height': None, 'fill_color': '(0,255,0,128)', 'stroke_color': '(0,0,0,255)', 'stroke_width': 2, 'z': 0, 'c': 1, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'} +ROI ID: 3 for row 3 +Processing row 4/7: {'shape': 'Point', 'x': 150.0, 'y': 150.0, 'x_rad': None, 'y_rad': None, 'label': None, 'fontSize': None, 'x1': None, 'y1': None, 'x2': None, 'y2': None, 'points': None, 'width': None, 'height': None, 'fill_color': '(0,0,255,128)', 'stroke_color': '(255,0,0,255)', 'stroke_width': 3, 'z': 0, 'c': 2, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'} +ROI ID: 4 for row 4 +Processing row 5/7: {'shape': 'Polygon', 'x': None, 'y': None, 'x_rad': None, 'y_rad': None, 'label': None, 'fontSize': None, 'x1': None, 'y1': None, 'x2': None, 'y2': None, 'points': '(300,300),(350,350),(300,400)', 'width': None, 'height': None, 'fill_color': '(255,255,0,128)', 'stroke_color': '(0,0,0,255)', 'stroke_width': 2, 'z': 1, 'c': 0, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'} +ROI ID: 5 for row 5 +Processing row 6/7: {'shape': 'Polyline', 'x': None, 'y': None, 'x_rad': None, 'y_rad': None, 'label': None, 'fontSize': None, 'x1': None, 'y1': None, 'x2': None, 'y2': None, 'points': '(400,400),(450,450),(400,500)', 'width': None, 'height': None, 'fill_color': '(0,255,255,128)', 'stroke_color': '(0,0,0,255)', 'stroke_width': 3, 'z': 0, 'c': 0, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'} +ROI ID: 6 for row 6 +Processing row 7/7: {'shape': 'Rectangle', 'x': 500.0, 'y': 500.0, 'x_rad': None, 'y_rad': None, 'label': None, 'fontSize': None, 'x1': None, 'y1': None, 'x2': None, 'y2': None, 'points': None, 'width': 100.0, 'height': 50.0, 'fill_color': '(255,0,255,128)', 'stroke_color': '(0,0,0,255)', 'stroke_width': 2, 'z': 0, 'c': 0, 't': 0, 'roi_name': 'Example ROI', 'roi_description': 'This is an example ROI'} +ROI ID: 7 for row 7 diff -r 000000000000 -r 5ad32d18fe82 test-data/output_table_roi_minimal.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_table_roi_minimal.txt Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,2 @@ +Processing row 1/1: {'shape': 'Polygon', 'points': '(300,300),(350,350),(300,400)', 'label': 'Example ROI'} +ROI ID: 8 for row 1 diff -r 000000000000 -r 5ad32d18fe82 test-data/output_target_import.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_target_import.txt Mon Dec 16 20:56:16 2024 +0000 @@ -0,0 +1,1 @@ +SUCCESS: Successfully uploaded metadata for dataset with ID 1. Result: {'Key1': 'Value1', 'Key2': 'Value2'}