Mercurial > repos > ufz > omero_roi_import
changeset 2:4f4dc352d660 draft
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 266752b0162fbdb32f132a6702cb661ae36f48f0
| author | ufz |
|---|---|
| date | Thu, 12 Sep 2024 16:30:36 +0000 |
| parents | e957793051a8 |
| children | dfe0aae1495c |
| files | omero_metadata_upload.py omero_roi_import.xml omero_roi_upload.py test-data/input_roi_minimal.tsv test-data/output_table_roi.txt test-data/output_table_roi_minimal.txt |
| diffstat | 6 files changed, 70 insertions(+), 28 deletions(-) [+] |
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--- a/omero_metadata_upload.py Fri Sep 06 08:26:12 2024 +0000 +++ b/omero_metadata_upload.py Thu Sep 12 16:30:36 2024 +0000 @@ -1,4 +1,5 @@ import argparse +import json from datetime import datetime import ezomero as ez @@ -73,8 +74,7 @@ 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("--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', 'image'], @@ -87,6 +87,9 @@ args = parser.parse_args() - metadata_import_ezo(user=args.user, pws=args.pws, host=args.host, port=args.port, + 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)
--- a/omero_roi_import.xml Fri Sep 06 08:26:12 2024 +0000 +++ b/omero_roi_import.xml Thu Sep 12 16:30:36 2024 +0000 @@ -3,7 +3,7 @@ <description> with ezomero </description> <macros> <token name="@TOOL_VERSION@">5.18.0</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> </macros> <xrefs> <xref type="bio.tools">omero</xref> @@ -15,15 +15,22 @@ <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' + python '$__tool_directory__/omero_roi_upload.py' + --input_file '$input' + --image_id $id + --credential-file '$credentials' + --host '$omero_host' + --port $omero_port + --log_file '$log' ]]></command> + <configfiles> + <configfile name="credentials"><![CDATA[ +{ + "username": "$__user__.extra_preferences.get('omero_account|username', $test_username)", + "password": "$__user__.extra_preferences.get('omero_account|password', $test_password)" +} + ]]></configfile> + </configfiles> <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" value="" optional="false" label="Image ID where annotate the ROIs"/> @@ -52,6 +59,19 @@ </assert_contents> </output> </test> + <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_minimal.tsv"/> + <param name="test_username" value="root"/> + <param name="test_password" value="omero"/> + <output name="log" value="output_table_roi_minimal.txt" ftype="txt"> + <assert_contents> + <has_text text="ROI ID: 8 for row 1"/> + </assert_contents> + </output> + </test> </tests> <help> @@ -62,7 +82,7 @@ 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**: +**Column Headers** (not all columns are required for all shapes): - 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 @@ -74,6 +94,10 @@ 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. +- *Label*: + + Any ROI can be labelled using the column **label**, this label will appear on the OMERO web interface. + - *Text Labels*: The **label** and **fontSize** columns are used for the Label shape, specifying the text content and font size. @@ -84,11 +108,11 @@ - *Point Coordinates*: - The **points** column is used for defining multiple points in shapes like Polygon and Polyline. The points are listed as coordinate pairs. + The **points** column is used for defining multiple points in shapes like Polygon and Polyline. The points are listed as coordinate pairs, like '(300,300),(350,350),(300,400)' - *Colors*: - The **fill_color** and **stroke_color** columns define the fill and stroke colors of the shapes in RGBA format. + The **fill_color** and **stroke_color** columns define the fill and stroke colors of the shapes in RGBA format, like '(0,255,255,128)'. - *Stroke Width*: @@ -100,7 +124,7 @@ - *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. + The **roi_name** and **roi_description** columns provide a name and description for each ROI, allowing for easy identification and documentation within OMERO however they do not appear on the OMERO web interface. </help> <citations>
--- a/omero_roi_upload.py Fri Sep 06 08:26:12 2024 +0000 +++ b/omero_roi_upload.py Thu Sep 12 16:30:36 2024 +0000 @@ -1,6 +1,8 @@ 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 @@ -35,6 +37,7 @@ 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') @@ -60,7 +63,7 @@ y2=row['y2'], markerStart=row.get('markerStart', None), markerEnd=row.get('markerEnd', None), - label=row.get('label', None), + label=row.get('label'), z=row.get('z'), c=row.get('c'), t=row.get('t'), @@ -75,6 +78,7 @@ 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') @@ -85,6 +89,7 @@ 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') @@ -95,6 +100,7 @@ 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') @@ -108,6 +114,7 @@ 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') @@ -119,6 +126,8 @@ # 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) @@ -143,17 +152,19 @@ 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("--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=args.user, - password=args.psw, + user=crds['username'], + password=crds['password'], port=args.port, group="", secure=True
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_roi_minimal.tsv Thu Sep 12 16:30:36 2024 +0000 @@ -0,0 +1,2 @@ +shape points label +Polygon (300,300),(350,350),(300,400) Example ROI
--- a/test-data/output_table_roi.txt Fri Sep 06 08:26:12 2024 +0000 +++ b/test-data/output_table_roi.txt Thu Sep 12 16:30:36 2024 +0000 @@ -1,14 +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'} +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': 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'} +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': 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'} +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': 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'} +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': 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'} +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': 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'} +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': 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'} +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