Merge pull request #6 from BiAPoL/add-pixel-size-setting-demo

Tutorial on how to set pixel sizes

docs/_toc.yml

@@ -6,6 +6,7 @@ chapters:
   - file: notebooks/metadata/Readme
     sections:
     - file: notebooks/metadata/key_value_pairs
+    - file: notebooks/metadata/setting_pixel_sizes
   - file: instructions/transfer_dataset
   - file: notebooks/synchronize_tags
 

docs/notebooks/metadata/key_value_pairs.ipynb

@@ -26,7 +26,7 @@
    "outputs": [],
    "source": [
     "host = 'omero-int.biotec.tu-dresden.de'\n",
-    "user = 'johamuel'  # replace this with your username\n",
+    "user = ''  # replace this with your username\n",
     "secure = True\n",
     "port = 4064\n",
     "group = 'default'\n",

docs/notebooks/metadata/setting_pixel_sizes.ipynb

@@ -0,0 +1,168 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Setting pixel sizes of an image\n",
+    "\n",
+    "A key part of the metadata are the pixel/voxel sizes of image data. When upload processed image data to OMERO, they are by default not part of the uploaded data but a key part you wish to add to your data. Following up [this dicsussion](https://forum.image.sc/t/specifying-pixel-size-using-python-bridge-for-omero-ezomero/81729/2) on image.sc, here's how you can do it using [omero-py](https://pypi.org/project/omero-py/):"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import omero\n",
+    "import ezomero\n",
+    "\n",
+    "from omero.model.enums import UnitsLength"
+   ]
+  },
+  {
+   "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": [
+    "We first need to retrieve the remote object:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "image_object = conn.getObject(\"Image\", 330)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "If there are already pixel sizes set, you can retrieve them like this:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Pixel size X:  0.2\n",
+      "Pixel size Y:  0.2\n",
+      "Pixel size Z:  2.0\n"
+     ]
+    }
+   ],
+   "source": [
+    "print('Pixel size X: ', image_object.getPixelSizeX())\n",
+    "print('Pixel size Y: ', image_object.getPixelSizeY())\n",
+    "print('Pixel size Z: ', image_object.getPixelSizeZ())"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "If you want to set them yourself, you can do it like this:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "unit_x = omero.model.LengthI(0.5, UnitsLength.MICROMETER)\n",
+    "unit_y = omero.model.LengthI(0.5, UnitsLength.MICROMETER)\n",
+    "unit_z = omero.model.LengthI(3, UnitsLength.MICROMETER)\n",
+    "\n",
+    "primary_pixels_object = image_object.getPrimaryPixels()._obj\n",
+    "primary_pixels_object.setPhysicalSizeX(unit_x)\n",
+    "primary_pixels_object.setPhysicalSizeY(unit_y)\n",
+    "primary_pixels_object.setPhysicalSizeZ(unit_z)\n",
+    "\n",
+    "# update the image object\n",
+    "conn.getUpdateService().saveObject(primary_pixels_object)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We can doublecheck whether this worked:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Pixel size X:  0.5\n",
+      "Pixel size Y:  0.5\n",
+      "Pixel size Z:  3.0\n"
+     ]
+    }
+   ],
+   "source": [
+    "image_object = conn.getObject(\"Image\", 330)\n",
+    "\n",
+    "print('Pixel size X: ', image_object.getPixelSizeX())\n",
+    "print('Pixel size Y: ', image_object.getPixelSizeY())\n",
+    "print('Pixel size Z: ', image_object.getPixelSizeZ())"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "omero",
+   "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
+}