Mercurial > repos > ufz > omero_roi_import
changeset 0:9051b91545f6 draft
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 5b1b30d409355cee98485815c1dd4ac48649bcc1
| author | ufz |
|---|---|
| date | Thu, 05 Sep 2024 11:55:44 +0000 |
| parents | |
| children | e957793051a8 |
| files | README.md omero_metadata_upload.py omero_roi_import.xml omero_roi_upload.py test-data/input1.tif test-data/input2.tif test-data/input_roi.tsv test-data/metadata.tsv test-data/omero_output.txt test-data/output_KV_import.txt test-data/output_table_import.txt test-data/output_table_roi.txt test-data/output_target_import.txt |
| diffstat | 13 files changed, 415 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Thu Sep 05 11:55:44 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omero_metadata_upload.py Thu Sep 05 11:55:44 2024 +0000 @@ -0,0 +1,92 @@ +import argparse +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 == "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('--user', required=True, help='OMERO username') + parser.add_argument('--pws', required=True, help='OMERO password') + 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', '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() + + metadata_import_ezo(user=args.user, pws=args.pws, 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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omero_roi_import.xml Thu Sep 05 11:55:44 2024 +0000 @@ -0,0 +1,109 @@ +<tool id="omero_roi_import" name="OMERO ROI Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" + profile="20.01" license="MIT"> + <description> with ezomero </description> + <macros> + <token name="@TOOL_VERSION@">5.18.0</token> + <token name="@VERSION_SUFFIX@">1</token> + </macros> + <xrefs> + <xref type="bio.tools">omero</xref> + </xrefs> + <requirements> + <requirement type="package" version="3.0.1">ezomero</requirement> + <requirement type="package" version="2.2.2">pandas</requirement> + <!-- openjdk is needed: https://github.com/conda-forge/omero-py-feedstock/pull/16 --> + <requirement type="package" version="21.0.2">openjdk</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python '$__tool_directory__/omero_roi_upload.py' + --input_file '$input' + --image_id $id + --user '$__user__.extra_preferences.get("omero_account|username", $test_username)' + --psw '$__user__.extra_preferences.get("omero_account|password", $test_password)' + --host '$omero_host' + --port $omero_port + --log_file '$log' + ]]></command> + <inputs> + <param argument="input" type="data" format="tabular" optional="false" label="Tab File with ROIs" help="Select ROIs Tabular file"/> + <param argument="id" type="integer" optional="false" label="Image ID where annotate the ROIs"/> + <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 argument="omero_port" type="integer" optional="false" value="4064" label="OMERO port"/> + <param name="test_username" type="hidden" value=""/> + <param name="test_password" type="hidden" value=""/> + </inputs> + <outputs> + <data name="log" format="txt"/> + </outputs> + <tests> + <test> + <param name="omero_host" value="host.docker.internal"/> + <param name="omero_port" value="6064"/> + <param name="id" value="1"/> + <param name="input" value="input_roi.tsv"/> + <param name="test_username" value="root"/> + <param name="test_password" value="omero"/> + <output name="log" value="output_table_roi.txt" ftype="txt"> + <assert_contents> + <has_text text="ROI ID: 7 for row 7"/> + </assert_contents> + </output> + </test> + </tests> + <help> + +Description +----------- + +Tool to upload Regions of Interest (ROIs) to an OMERO server based on shape data provided +in a tabular format (TSV file). The tool reads the shape information from the TSV file, creates the +corresponding ROIs in OMERO, and links them to a specified image. + +**Column Headers**: + + - shape, x, y, x_rad, y_rad, width, height, label, fontSize, x1, y1, x2, y2, points, fill_color, stroke_color, stroke_width, z, c, t, roi_name, roi_description + +- *Shape Type*: + + The **shape** column indicates the type of shape being defined, such as Ellipse, Label, Line, Point, Polygon, Polyline, or Rectangle. + +- *Position and Dimensions*: + + The columns **x**, **y**, **x_rad**, **y_rad**, **width**, and **height** specify the position and dimensions of the shapes, where applicable. For example, Ellipse uses x, y, x_rad, and y_rad, while Rectangle uses x, y, width, and height. + +- *Text Labels*: + + The **label** and **fontSize** columns are used for the Label shape, specifying the text content and font size. + +- *Line Coordinates*: + + The columns **x1**, **y1**, **x2**, and **y2** are used for defining the start and end points of a Line. + +- *Point Coordinates*: + + The **points** column is used for defining multiple points in shapes like Polygon and Polyline. The points are listed as coordinate pairs. + +- *Colors*: + + The **fill_color** and **stroke_color** columns define the fill and stroke colors of the shapes in RGBA format. + +- *Stroke Width*: + + The **stroke_width** column specifies the width of the stroke or border around the shapes. + +- *Z, C, T Coordinates*: + + The **z**, **c**, and **t** columns indicate the Z-plane, channel, and time point to which the shape is associated in the image stack. + +- *ROI Identification*: + + The **roi_name** and **roi_description** columns provide a name and description for each ROI, allowing for easy identification and documentation within OMERO. + + </help> + <citations> + <citation type="doi">10.1038/nmeth.1896</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omero_roi_upload.py Thu Sep 05 11:55:44 2024 +0000 @@ -0,0 +1,165 @@ +import argparse +import re + +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'), + 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', None), + 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'), + 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'), + 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'), + 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'), + 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') + 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("--user", type=str, required=True, help="OMERO username") + parser.add_argument("--psw", type=str, required=True, help="OMERO password") + 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() + + conn = connect( + host=args.host, + user=args.user, + password=args.psw, + port=args.port, + group="", + secure=True + ) + + try: + main(args.input_file, conn, args.image_id, args.log_file) + finally: + conn.close()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_roi.tsv Thu Sep 05 11:55:44 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metadata.tsv Thu Sep 05 11:55:44 2024 +0000 @@ -0,0 +1,2 @@ +Key1 Key2 +Value1 Value2 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/omero_output.txt Thu Sep 05 11:55:44 2024 +0000 @@ -0,0 +1,2 @@ +Image:3 +Image:4
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_KV_import.txt Thu Sep 05 11:55:44 2024 +0000 @@ -0,0 +1,1 @@ +SUCCESS: Successfully uploaded metadata for dataset with ID 2. Result: {'Key1': 'Value1', 'Key2': 'Value2'}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_table_import.txt Thu Sep 05 11:55:44 2024 +0000 @@ -0,0 +1,2 @@ +SUCCESS: Successfully uploaded metadata for project with ID 2. Result: Key1 Key2 +0 Value1 Value2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_table_roi.txt Thu Sep 05 11:55:44 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': nan, 'fontSize': nan, 'x1': nan, 'y1': nan, 'x2': nan, 'y2': nan, 'points': nan, 'width': nan, 'height': nan, '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': nan, 'y_rad': nan, 'label': 'Test Label', 'fontSize': 12.0, 'x1': nan, 'y1': nan, 'x2': nan, 'y2': nan, 'points': nan, 'width': nan, 'height': nan, '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': nan, 'y': nan, 'x_rad': nan, 'y_rad': nan, 'label': nan, 'fontSize': nan, 'x1': 200.0, 'y1': 200.0, 'x2': 250.0, 'y2': 250.0, 'points': nan, 'width': nan, 'height': nan, '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': nan, 'y_rad': nan, 'label': nan, 'fontSize': nan, 'x1': nan, 'y1': nan, 'x2': nan, 'y2': nan, 'points': nan, 'width': nan, 'height': nan, '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': nan, 'y': nan, 'x_rad': nan, 'y_rad': nan, 'label': nan, 'fontSize': nan, 'x1': nan, 'y1': nan, 'x2': nan, 'y2': nan, 'points': '(300,300),(350,350),(300,400)', 'width': nan, 'height': nan, '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': nan, 'y': nan, 'x_rad': nan, 'y_rad': nan, 'label': nan, 'fontSize': nan, 'x1': nan, 'y1': nan, 'x2': nan, 'y2': nan, 'points': '(400,400),(450,450),(400,500)', 'width': nan, 'height': nan, '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': nan, 'y_rad': nan, 'label': nan, 'fontSize': nan, 'x1': nan, 'y1': nan, 'x2': nan, 'y2': nan, 'points': nan, '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