Example notebook for annotation tool

521f75e1 · Felipe Delestro Matos · a1f9598c · 521f75e1
Commit 521f75e1 authored 1 year ago by Felipe Delestro Matos
--- a/docs/notebooks/annotation_tool.ipynb
+++ b/docs/notebooks/annotation_tool.ipynb
@@ -7,19 +7,60 @@
   "outputs": [],
   "source": [
    "import qim3d\n",
-    "from scipy import ndimage\n",
    "import matplotlib.pyplot as plt\n",
-    "qim3d.io.logger.level(\"info\")\n",
    "\n",
    "# Load example image\n",
-    "img = qim3d.examples.bone_128x128x128\n",
+    "vol = qim3d.examples.bone_128x128x128\n",
    "\n",
    "# Start annotation tool\n",
-    "interface = qim3d.gui.annotation_tool.Interface()\n",
+    "annotation_tool = qim3d.gui.annotation_tool.Interface()\n",
    "\n",
    "# We can directly pass the image we loaded to the interface\n",
-    "#interface.launch()\n",
+    "app = annotation_tool.launch(vol[0], server_name=\"10.197.104.229\")"
-    "interface.launch(ndimage.zoom(img[0], 3, order=0))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "annotation_tool.get_result()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib inline\n",
+    "import matplotlib.pyplot as plt\n",
+    "from IPython.display import clear_output\n",
+    "import numpy as np\n",
+    "import time\n",
+    "\n",
+    "while True:\n",
+    "    clear_output(wait=True)    \n",
+    "    masks_dict = annotation_tool.get_result()\n",
+    "    if len(masks_dict) == 0:\n",
+    "        masks_dict[\"No mask\"] = np.zeros((32,32))\n",
+    "    \n",
+    "    fig, axs = plt.subplots(1, len(masks_dict), figsize=(8,3))\n",
+    "\n",
+    "    if len(masks_dict) == 1:\n",
+    "        axs = [axs]\n",
+    "    for idx, (name, mask) in enumerate(masks_dict.items()):\n",
+    "\n",
+    "        axs[idx].imshow(mask, cmap='gray', interpolation='none')\n",
+    "        axs[idx].set_title(name)\n",
+    "        axs[idx].axis('off')\n",
+    "    \n",
+    "    plt.tight_layout()\n",
+    "\n",
+    "    \n",
+    "    plt.show()\n",
+    "    time.sleep(2)"
   ]
  }
 ],

 %% Cell type:code id: tags:
 ``` python
 import qim3d
-from scipy import ndimage
 import matplotlib.pyplot as plt
-qim3d.io.logger.level("info")
 # Load example image
-img = qim3d.examples.bone_128x128x128
+vol = qim3d.examples.bone_128x128x128
 # Start annotation tool
-interface = qim3d.gui.annotation_tool.Interface()
+annotation_tool = qim3d.gui.annotation_tool.Interface()
 # We can directly pass the image we loaded to the interface
-#interface.launch()
+app = annotation_tool.launch(vol[0], server_name="10.197.104.229")
-interface.launch(ndimage.zoom(img[0], 3, order=0))
+```
+%% Cell type:code id: tags:
+``` python
+annotation_tool.get_result()
+```
+%% Cell type:code id: tags:
+``` python
+%matplotlib inline
+import matplotlib.pyplot as plt
+from IPython.display import clear_output
+import numpy as np
+import time
+while True:
+    clear_output(wait=True)
+    masks_dict = annotation_tool.get_result()
+    if len(masks_dict) == 0:
+        masks_dict["No mask"] = np.zeros((32,32))
+    fig, axs = plt.subplots(1, len(masks_dict), figsize=(8,3))
+    if len(masks_dict) == 1:
+        axs = [axs]
+    for idx, (name, mask) in enumerate(masks_dict.items()):
+        axs[idx].imshow(mask, cmap='gray', interpolation='none')
+        axs[idx].set_title(name)
+        axs[idx].axis('off')
+    plt.tight_layout()
+    plt.show()
+    time.sleep(2)
 ```