From 521f75e1129f395df30a52513d535dbd26ae70ca Mon Sep 17 00:00:00 2001
From: Felipe Delestro Matos <fima@pop-os.localdomain>
Date: Tue, 5 Mar 2024 11:34:42 +0100
Subject: [PATCH] Example notebook for annotation tool
---
docs/notebooks/annotation_tool.ipynb | 53 ++++++++++++++++++++++++----
1 file changed, 47 insertions(+), 6 deletions(-)
diff --git a/docs/notebooks/annotation_tool.ipynb b/docs/notebooks/annotation_tool.ipynb
index 9089f962..777be86c 100644
--- 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",
- "interface.launch(ndimage.zoom(img[0], 3, order=0))"
+ "app = annotation_tool.launch(vol[0], server_name=\"10.197.104.229\")"
+ ]
+ },
+ {
+ "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)"
]
}
],
--
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