example tiled code

.github/workflows/staging-deploy.yml

@@ -17,6 +17,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+          if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names

.gitignore

@@ -18,4 +18,7 @@ env
 
 .theia/
 *.tiff
-*.tif
+*.tif
+
+.env
+config.py

examples/requirements.txt

@@ -0,0 +1,3 @@
+jupyterlab
+ipykernel
+matplotlib

examples/tiled.ipynb

@@ -0,0 +1,165 @@
+{
+ "cells": [
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Demonstration of Tiled Functionality\n",
+    "This notebook demonstrates how to connect to tiled using the python client. \n",
+    "\n",
+    "Not that config.py is in gitignore because it contains the api_key. It should look like:\n",
+    "\n",
+    "```\n",
+    "api_key=\"<key>\"\n",
+    "```\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# import tempfile  used for on_disk cache\n",
+    "import ipywidgets as widgets\n",
+    "import matplotlib.pyplot as plt\n",
+    "import matplotlib.animation as animation \n",
+    "from tiled.client import from_uri\n",
+    "from tiled.client.cache import Cache\n",
+    "# from tiled.client import show_logs\n",
+    "import config\n",
+    "\n",
+    "%matplotlib widget\n",
+    "\n",
+    "# displays details of tiled client http traffic\n",
+    "# it's a little wordy but often extremely useful\n",
+    "# show_logs()\n",
+    "\n",
+    "####\n",
+    "# Setup client-side caching. Commented out because this exposed a bug in \n",
+    "# client caching https://github.com/bluesky/tiled/issues/471\n",
+    "# cache = Cache.on_disk(\n",
+    "#     tempfile.gettempdir(),\n",
+    "#     capacity=2e9 #2GB\n",
+    "# )\n",
+    "# cache = Cache.in_memory(capacity=2e9) # 2GB\n",
+    "\n",
+    "# create a Tiled client\n",
+    "client = from_uri(\n",
+    "    \"https://mlex-segmentation.als.lbl.gov\", \n",
+    "    api_key=config.api_key)\n",
+    "    # cache=cache)\n",
+    "\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data = client['data']\n",
+    "reconstruction = data['rec20221222_085501_looking_from_above_spiralUP_CounterClockwise_endPointAtDoor']\n",
+    " "
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Grab a frame!"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "frame_num_text = widgets.Text(value='Hello World', disabled=True)\n",
+    "fig = plt.figure()\n",
+    "im = plt.imshow(reconstruction[0], animated=True)\n",
+    "\n"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Grab a reduced frame\n",
+    "This shows a very simple downcasting method. The downcasting happens in the server, saving traffic across the wire."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "frame_num_text = widgets.Text(value='Hello World', disabled=True)\n",
+    "fig = plt.figure()\n",
+    "im = plt.imshow(reconstruction[0, ::10, ::10], animated=True)"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Animate across the images\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "frame_num_text = widgets.Text(value='Hello World', disabled=True)\n",
+    "fig = plt.figure()\n",
+    "im = plt.imshow(reconstruction[0, ::10, ::10], animated=True)\n",
+    "\n",
+    "# animation function \n",
+    "def updatefig(i):\n",
+    "    im.set_array(reconstruction[i, ::10, ::10])\n",
+    "    return im, \n",
+    "\n",
+    "ani = animation.FuncAnimation(fig, updatefig, frames=range(len(reconstruction)) , interval=50, blit=True)\n",
+    "plt.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "tiled_client",
+   "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": "3.11.3"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

requirements-dev.txt

@@ -0,0 +1,2 @@
+black==22.10.0
+flake8==6.0.0

requirements.txt

@@ -22,5 +22,4 @@ tifffile==2023.4.12
 tzdata==2023.3
 Werkzeug==2.2.3
 zipp==3.15.0
-black==22.10.0
-flake8==6.0.0
+tiled[client]==0.1.0a96