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:alt: Image.sc forum
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:target: https://github.com/ome/omero-figure/actions
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:target: https://badge.fury.io/py/omero-figure
OMERO.figure
============
An OMERO.web app for creating figures from images in OMERO.
For full details see `SUPPORT.md <https://github.com/ome/omero-figure/blob/master/SUPPORT.md>`_.
Requirements
------------
* OMERO.web 5.6.0 or newer.
Installing from PyPI
--------------------
This section assumes that an OMERO.web is already installed.
Install the app using `pip <https://pip.pypa.io/en/stable/>`_:
NB: You need to ensure that you are running ``pip`` from the python environment
where ``omero-web`` is installed. Depending on your install, you may need to
call ``pip`` with, for example: ``/path/to_web_venv/venv/bin/pip install ...``
::
$ pip install -U omero-figure
Add figure custom app to your installed web apps:
::
$ omero config append omero.web.apps '"omero_figure"'
Display a link to 'Figure' at the top of the webclient:
::
$ omero config append omero.web.ui.top_links '["Figure", "figure_index",
{"title": "Open Figure in new tab", "target": "_blank"}]'
Add 'Figure' to the 'Open with' options, available from context menu on
the webclient tree:
::
$ omero config append omero.web.open_with '["omero_figure", "new_figure",
{"supported_objects":["images"], "target": "_blank", "label": "OMERO.figure"}]'
Now restart OMERO.web as normal.
Enabling figure export
----------------------
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:
::
$ 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``:
::
$ 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
``/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:
* Install `reportlab <https://bitbucket.org/rptlab/reportlab>`_ PDF python package.
This needs to be installed in the virtual environment where the ``OMERO.server`` is installed. Depending on your install, you may need to
call ``pip`` with, for example: ``/path/to_server_venv/venv/bin/pip install ...``
::
$ pip install reportlab
* Optional: Figure legends can be formatted using Markdown syntax. To see this correctly in the exported PDF info page, we need `Python Markdown <https://python-markdown.github.io/>`_:
::
$ pip install markdown
Upgrading OMERO.figure
----------------------
After upgrading OMERO.figure with:
::
$ pip install -U omero-figure
You need to update the Figure export script using one of the 2 options described
above. If using *Option 1*, you need to *replace* the existing script:
::
# Get the ID of the existing Figure_To_Pdf script:
$ omero script list
# Replace the script
$ cd omero_figure/scripts
$ omero script replace <SCRIPT_ID> omero/figure_scripts/Figure_To_Pdf.py
Development
-----------
We use `vite.js <https://vitejs.dev/>`_ to build and serve the app during development.
Install Node from https://nodejs.org, then:
::
$ cd omero-figure
$ npm install
To serve the app at http://localhost:8080/ using the vite dev server
(this will automatically refresh the page when changes are saved):
::
$ npm run start
If you are editing the Shape-Editor code, you can view the test page at
http://localhost:8080/shapeEditorTest.html
CORS
****
During development, we load and save figure files to an omero-web server.
You will need to have CORS enabled on your local omero-web server at
http://localhost:4080/ and be logged in already.
This URL can be edited in `src/index.html`.
You MUST access the figure app at http://localhost:8080/ (NOT http://127.0.0.1:8080/)
for CORS to work.
NB: in general, POST actions such as saving of figure files or exporting figures doesn't
yet work with the dev server. To test these actions, build the app as described below:
Build
-----
To build the app:
::
$ npm run build
This compiles index.html and other static assets into correct locations to be
served by the Django `omero-web` server.
To serve this on a local omero-web, set config as above and install with:
::
$ pip install -e .
In order to build whenever changes are saved within the `src/` directory:
::
$ npm run watch
Release process
---------------
This repository uses `bump2version <https://pypi.org/project/bump2version/>`_ to manage version numbers.
To tag a release run::
$ bumpversion release
This will remove the ``.dev0`` suffix from the current version, commit, and tag the release.
To switch back to a development version run::
$ bumpversion --no-tag [major|minor|patch]
specifying ``major``, ``minor`` or ``patch`` depending on whether the development branch will be a `major, minor or patch release <https://semver.org/>`_. This will also add the ``.dev0`` suffix.
Remember to ``git push`` all commits and tags.
License
-------
OMERO.figure is released under the AGPL.
Copyright
---------
2016-2024, The Open Microscopy Environment
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Depending on your install, you may need to\ncall ``pip`` with, for example: ``/path/to_web_venv/venv/bin/pip install ...``\n\n::\n\n $ pip install -U omero-figure\n\nAdd figure custom app to your installed web apps:\n\n::\n\n $ omero config append omero.web.apps '\"omero_figure\"'\n\nDisplay a link to 'Figure' at the top of the webclient:\n\n::\n\n $ omero config append omero.web.ui.top_links '[\"Figure\", \"figure_index\",\n {\"title\": \"Open Figure in new tab\", \"target\": \"_blank\"}]' \n\n\nAdd 'Figure' to the 'Open with' options, available from context menu on\nthe webclient tree:\n\n::\n\n $ omero config append omero.web.open_with '[\"omero_figure\", \"new_figure\",\n {\"supported_objects\":[\"images\"], \"target\": \"_blank\", \"label\": \"OMERO.figure\"}]'\n\nNow restart OMERO.web as normal.\n\n\nEnabling figure export\n----------------------\n\nThis section assumes that an OMERO.server is already installed.\n\nFigures 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\ninstalled in the OMERO.server virtual environment.\n\nThe script can be uploaded using two alternative workflows, both of which require you to have the correct admin privileges.\nTo find where OMERO.figure has been installed using pip, run:\n\n::\n\n $ pip show omero-figure\n\nThe 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.\n\n*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``:\n\n::\n\n $ cd omero_figure/scripts\n $ omero script upload omero/figure_scripts/Figure_To_Pdf.py --official\n\n*Option 2*: Alternatively, before starting the OMERO.server, copy the script from the figure install\n``/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.\n\n*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.\nSelect the ``Figure_To_Pdf.py`` script from the directory where you copied it to locally and upload it into the directory ``omero/figure_scripts``.\n\nNow install the script's dependencies:\n\n\n* Install `reportlab <https://bitbucket.org/rptlab/reportlab>`_ PDF python package.\n This needs to be installed in the virtual environment where the ``OMERO.server`` is installed. Depending on your install, you may need to\n call ``pip`` with, for example: ``/path/to_server_venv/venv/bin/pip install ...``\n\n::\n\n $ pip install reportlab\n\n* Optional: Figure legends can be formatted using Markdown syntax. To see this correctly in the exported PDF info page, we need `Python Markdown <https://python-markdown.github.io/>`_:\n\n::\n\n $ pip install markdown\n\nUpgrading OMERO.figure\n----------------------\n\nAfter upgrading OMERO.figure with:\n\n::\n\n $ pip install -U omero-figure\n\nYou need to update the Figure export script using one of the 2 options described\nabove. 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