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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,184 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# How to tag and retrieve tags from data\n", | ||
| "\n", | ||
| "Another key concept of organizing data on OMERO (besides [key-value pairs](omero-tools:key-value-pairs)) is given by *tags*. Can be used to group data in a more flexible way than the hierarchy of projects, datasets and images. For a more in-depth explanation of some of the underlying concepts, see [these excellent training materials](https://zenodo.org/records/8323588) regarding OMERO in general." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 1, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "import ezomero" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 2, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "host = 'omero-int.biotec.tu-dresden.de'\n", | ||
| "user = '' # replace this with your username\n", | ||
| "secure = True\n", | ||
| "port = 4064\n", | ||
| "group = 'default'\n", | ||
| "\n", | ||
| "conn = ezomero.connect(host=host, user=user, secure=secure, port=port, group=group)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Tagging data\n", | ||
| "\n", | ||
| "The easiest and most straightforward way to tag your data is arguably to simply do this through the web interface of your OMERO servers. Omero extensions such as the excellent [autotag](https://pypi.org/project/omero-autotag/) extension make setting meaningful tags on your data a breeze. The question then becomes - how do you retrieve tags that have already been added to your data?\n", | ||
| "\n", | ||
| "## Reading tags from OMERO\n", | ||
| "\n", | ||
| "Let's use [ezomero](https://thejacksonlaboratory.github.io/ezomero/) again to retrieve tags that have been added to an image. This will return a list of tags (indicated by their respective ids) that have been added to the image. This is an important concept to grasp: Just like an image, a tag is an object in the OMERO database, and it has a unique identifier (id). This id is what is returned when you retrieve tags from an image." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 6, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "[1088]\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "tag_ids = ezomero.get_tag_ids(conn, object_type='Image', object_id=330, ns=None)\n", | ||
| "print(tag_ids)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "If we want to see the \"value\" of the tag, we can use the `get_tag` function to introspect the ids we just retrieved:" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 7, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "'Fluorescence'" | ||
| ] | ||
| }, | ||
| "execution_count": 7, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "ezomero.get_tag(conn, tag_id=tag_ids[0])" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Adding a tag to data\n", | ||
| "\n", | ||
| "Adding a tag to an image is a little less straightforward. For once, it makes more sense to create and organize the tags through the web interface. The [following tutorial](omero-tools:synchronize-tags) introduces a way to set tags and tag groups from a yaml file, but this is a bit more complicated. For simplicity, let's assume we already created some tags and we know their ids from the web interface:\n", | ||
| "\n", | ||
| "\n", | ||
| "\n", | ||
| "\n", | ||
| "To add this newly created tag to our image, we need to first retrieve both the tag and the image objects from the remote server:" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 14, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "tag_object = conn.getObject('Annotation', 8354)\n", | ||
| "image_object = conn.getObject('Image', 330)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "In the next step, we link the tag to the image:" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "image_object.linkAnnotation(tag_object)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Let's check whether this worked:" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 18, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "Fluorescence (Tag id: 1088)\n", | ||
| "Raw data (Tag id: 8354)\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "tag_ids = ezomero.get_tag_ids(conn, object_type='Image', object_id=330, ns=None)\n", | ||
| "\n", | ||
| "for tag_id in tag_ids:\n", | ||
| " print(ezomero.get_tag(conn, tag_id=tag_id), ' ', f'(Tag id: {tag_id})')" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "stress", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.9.19" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 2 | ||
| } |
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