Merge pull request #669 from will-moore/standalone_python_script

Standalone python script

Author: will-moore

README.rst

@@ -70,36 +70,37 @@ Optional: To change the maximum active channel count from the default of 10:
 Now restart OMERO.web as normal.
 
 
-Enabling figure export
-----------------------
+Enabling figure export from OMERO
+---------------------------------
 
 This section assumes that an OMERO.server is already installed.
 
 Figures can be exported as PDF or TIFF files using a script that runs on the OMERO.server. This script needs to be uploaded to the OMERO.server and its dependencies
 installed in the OMERO.server virtual environment.
 
-The script can be uploaded using two alternative workflows, both of which require you to have the correct admin privileges.
-To find where OMERO.figure has been installed using pip, run:
+The script can be uploaded using various workflows, all of which require you to have the correct admin privileges.
+
+*Option 1*: Log in to the webclient as an Admin and open the OMERO.figure app. If the OMERO script is not found or is not up to date, you will
+see a warning message with a button to upload the script. Click the button to upload the script from the OMERO.figure app.
+
+*Option 2*: Upload the script from the installation directory. To find where OMERO.figure has been installed using pip, run:
 
 ::
 
     $ pip show omero-figure
 
 The command will display the absolute path to the directory where the application is installed e.g. ``~/<virtualenv_name>/lib/python3.6/site-packages``. Go to that directory.
 
-*Option 1*: Connect to the OMERO server and upload the script via the CLI. It is important to be in the correct directory when uploading so that the script is uploaded with the full path: ``omero/figure_scripts/Figure_To_Pdf.py``:
+Connect to the OMERO server and upload the script via the CLI. It is important to be in the correct directory when uploading so that the script is uploaded with the full path: ``omero/figure_scripts/Figure_To_Pdf.py``:
 
 ::
 
     $ cd omero_figure/scripts
     $ omero script upload omero/figure_scripts/Figure_To_Pdf.py --official
 
-*Option 2*: Alternatively, before starting the OMERO.server, copy the script from the figure install
+*Option 3*: Alternatively, before starting the OMERO.server, copy the script from the figure install
 ``/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py`` to the OMERO.server ``path/to/OMERO.server/lib/scripts/omero/figure_scripts``. Then restart the OMERO.server.
 
-*Option 3*: Upload the script through the OMERO web interface: For this, log into your OMERO web interface as admin, select the scripts icon and click on the "Upload Script" button.
-Select the ``Figure_To_Pdf.py`` script from the directory where you copied it to locally and upload it into the directory ``omero/figure_scripts``.
-
 Now install the script's dependencies:
 
 
@@ -117,6 +118,34 @@ Now install the script's dependencies:
 
     $ pip install markdown
 
+
+Run Figure export locally
+-------------------------
+
+If your figure contains only OME-Zarr images (no images from OMERO), then
+the export script can be run locally to convert a figure JSON file to PDF or TIFF.
+NB: the OME-Zarr URLs must be accessible from the machine where the export script is run.
+NB: channel LUTs are not currently supported when rendering OME-Zarr images for PDF or TIFFs.
+Any LUTs will be rendered with white color.
+
+Download the figure JSON (File > Save, in the standalone app) then install the export script.
+Here, we create a new conda environment and install the export script:
+
+::
+
+    $ conda create --name figure_export python=3.12
+    $ conda activate figure_export
+    $ pip install "omero-figure[export]"
+
+To export the figure as PDF or TIFF, run the script with the path to the figure JSON and the output file path as arguments:
+Use the ``.pdf`` extension for PDF export and ``.tiff`` for TIFF export. This example exports the
+downloaded `figure_json/my_figure.json` to `my_figure.pdf` in the current directory:
+
+::
+
+    $ figure_export figure_json/my_figure.json my_figure.pdf
+
+
 Upgrading OMERO.figure
 ----------------------
 

omero_figure/cli.py

@@ -0,0 +1,63 @@
+#
+# Copyright (c) 2014-2026 University of Dundee.
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+import argparse
+import os
+
+from omero_figure.scripts.omero.figure_scripts.Figure_To_Pdf \
+    import export_figure
+
+
+def figure_export() -> None:
+    parser = argparse.ArgumentParser(
+        prog="figure_export",
+        description="Export an OMERO Figure file.",
+    )
+    parser.add_argument("input", type=str, help="Path to the input file")
+    parser.add_argument("output", type=str, help="Path to the output file")
+
+    args = parser.parse_args()
+    output_path = args.output
+    print(f"input:  {args.input}")
+    print(f"output: {args.output}")
+
+    if os.path.exists(output_path):
+        print(f"Output file {output_path} already exists; Exiting.")
+        return
+
+    # open and read the input file
+    with open(args.input, 'r') as f:
+        figure_json = f.read()
+
+    fext = output_path.split('.')[-1].lower()
+    file_type = "TIFF" if fext in ['tif', 'tiff'] else "PDF"
+
+    script_args = {
+                    "Figure_JSON": figure_json,
+                    "outputPathName": output_path,
+                    "Export_Option": file_type,
+                    # TODO: Fix URL
+                    "Webclient_URI": "http://localhost:8080/"
+                }
+
+    export_figure(None, script_args)
+
+    print("Figure export completed.")
+
+
+if __name__ == "__main__":
+    figure_export()