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MarcelRosierMarcelRosier
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Notebook reruns
Remove pip install outputs
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‎panoptica/example_config.ipynb‎

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"Requirement already satisfied: panoptica in /opt/anaconda3/envs/seg11panoptdev/lib/python3.11/site-packages (from -r requirements.txt (line 1)) (1.0.0.post2.dev0+2f7d01f)\n",
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"!pip install -r requirements.txt"
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"No module named 'pandas'\n",
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"OPTIONAL PACKAGE MISSING\n"
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"import numpy as np\n",
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"data": {
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"text/html": [
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"<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"><span style=\"color: #00ff00; text-decoration-color: #00ff00\">────────────────────────────────────────── </span>Thank you for using <span style=\"font-weight: bold\">panoptica</span><span style=\"color: #00ff00; text-decoration-color: #00ff00\"> ──────────────────────────────────────────</span>\n",
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"</pre>\n"
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"\u001b[92m────────────────────────────────────────── \u001b[0mThank you for using \u001b[1mpanoptica\u001b[0m\u001b[92m ──────────────────────────────────────────\u001b[0m\n"
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"metadata": {},
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"<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"> Please support our development by citing \n",
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"</pre>\n"
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" Please support our development by citing \n"
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"<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"> <span style=\"color: #0000ff; text-decoration-color: #0000ff; text-decoration: underline\">https://github.com/BrainLesion/panoptica#citation</span> -- Thank you! \n",
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"</pre>\n"
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" \u001b[4;94mhttps://github.com/BrainLesion/panoptica#citation\u001b[0m -- Thank you! \n"
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"Saved config into /DATA/NAS/ongoing_projects/hendrik/panoptica/repo/panoptica/test_config.yaml\n"
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"Saved config into /home/marcelrosier/miniconda3/envs/tutorials/lib/python3.10/site-packages/panoptica/test_config.yaml\n"
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"<panoptica.panoptica_evaluator.Panoptica_Evaluator object at 0x7f05ac7b80d0>\n"
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"<panoptica.panoptica_evaluator.Panoptica_Evaluator object at 0x757bd6c23550>\n"
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"-- Got MatchedInstancePair, will evaluate instances\n",
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"\n",
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"+++ MATCHING +++\n",
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"Number of instances in reference (num_ref_instances): 1\n",
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"Number of instances in prediction (num_pred_instances): 1\n",
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"True Positives (tp): 1\n",
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"Number of instances in reference (num_ref_instances): 22\n",
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"Number of instances in prediction (num_pred_instances): 22\n",
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"True Positives (tp): 22\n",
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"Global Binary Dice (global_bin_dsc): 0.9744370224078394\n",
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"+++ INSTANCE +++\n",
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"Segmentation Quality IoU (sq): 0.9501484001456879 +- 0.0\n",
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"Panoptic Quality IoU (pq): 0.9501484001456879\n",
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"Segmentation Quality Dsc (sq_dsc): 0.9744370224078394 +- 0.0\n",
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"Panoptic Quality Dsc (pq_dsc): 0.9744370224078394\n",
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"Segmentation Quality ASSD (sq_assd): 0.1499152780072207 +- 0.0\n",
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"Segmentation Quality Relative Volume Difference (sq_rvd): -0.0006011763989268869 +- 0.0\n",
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"Segmentation Quality IoU (sq): 0.8328184295330796 +- 0.15186064004517466\n",
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"Panoptic Quality IoU (pq): 0.8328184295330796\n",
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"Segmentation Quality Dsc (sq_dsc): 0.900292616009954 +- 0.10253566174957332\n",
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"Panoptic Quality Dsc (pq_dsc): 0.900292616009954\n",
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"Segmentation Quality ASSD (sq_assd): 0.250331887879225 +- 0.07696680402317076\n",
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"Segmentation Quality Relative Volume Difference (sq_rvd): 0.0028133049062930553 +- 0.034518928495505724\n",
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‎panoptica/example_spine_matched_instance.ipynb‎

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"Requirement already satisfied: panoptica in /opt/anaconda3/envs/seg11panoptdev/lib/python3.11/site-packages (from -r requirements.txt (line 1)) (1.0.0.post2.dev0+2f7d01f)\n",
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"Requirement already satisfied: rich in /opt/anaconda3/envs/seg11panoptdev/lib/python3.11/site-packages (from -r requirements.txt (line 3)) (13.6.0)\n",
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"Requirement already satisfied: connected-components-3d<4.0.0,>=3.12.3 in /opt/anaconda3/envs/seg11panoptdev/lib/python3.11/site-packages (from panoptica->-r requirements.txt (line 1)) (3.12.3)\n",
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"Requirement already satisfied: ruamel.yaml<0.19.0,>=0.18.6 in /opt/anaconda3/envs/seg11panoptdev/lib/python3.11/site-packages (from panoptica->-r requirements.txt (line 1)) (0.18.6)\n",
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"Requirement already satisfied: scikit-image<0.23.0,>=0.22.0 in /opt/anaconda3/envs/seg11panoptdev/lib/python3.11/site-packages (from panoptica->-r requirements.txt (line 1)) (0.22.0)\n",
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"Requirement already satisfied: tifffile>=2023.8.25 in /opt/anaconda3/envs/seg11panoptdev/lib/python3.11/site-packages (from auxiliary->-r requirements.txt (line 2)) (2023.8.30)\n",
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"No module named 'pandas'\n",
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