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MarcelRosierMarcelRosier
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Fix paths in colab env
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4 files changed

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‎panoptica/example_config.ipynb‎

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{
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"text": [
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"No module named 'pandas'\n",
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"OPTIONAL PACKAGE MISSING\n"
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]
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],
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"outputs": [],
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"source": [
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"import numpy as np\n",
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"from auxiliary.nifti.io import read_nifti\n",
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},
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"cell_type": "code",
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{
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" 106, 107, 108, 202, 203, 204, 205, 206, 207, 208], dtype=uint8))"
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"ref_masks = read_nifti(\"./spine_seg/matched_instance/ref.nii.gz\")\n",
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"pred_masks = read_nifti(\"./spine_seg/matched_instance/pred.nii.gz\")\n",
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"ref_masks = read_nifti(f\"{BASE_PATH}/spine_seg/matched_instance/ref.nii.gz\")\n",
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"pred_masks = read_nifti(f\"{BASE_PATH}/spine_seg/matched_instance/pred.nii.gz\")\n",
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"\n",
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"# labels are matching\n",
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"np.unique(ref_masks), np.unique(pred_masks)"
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},
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"cell_type": "code",
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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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"<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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"text": [
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"<panoptica.panoptica_evaluator.Panoptica_Evaluator object at 0x7002f42cf040>\n"
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"<panoptica.panoptica_evaluator.Panoptica_Evaluator object at 0x7002f42ccd60>\n"
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{

‎panoptica/example_spine_matched_instance.ipynb‎

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"name": "stdout",
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"text": [
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"No module named 'pandas'\n",
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"OPTIONAL PACKAGE MISSING\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"import numpy as np\n",
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"from auxiliary.nifti.io import read_nifti\n",
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},
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" 106, 107, 108, 202, 203, 204, 205, 206, 207, 208], dtype=uint8))"
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"output_type": "execute_result"
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}
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],
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"source": [
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"ref_masks = read_nifti(\"./spine_seg/matched_instance/ref.nii.gz\")\n",
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"pred_masks = read_nifti(\"./spine_seg/matched_instance/pred.nii.gz\")\n",
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"ref_masks = read_nifti(f\"{BASE_PATH}/spine_seg/matched_instance/ref.nii.gz\")\n",
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"pred_masks = read_nifti(f\"{BASE_PATH}/spine_seg/matched_instance/pred.nii.gz\")\n",
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"\n",
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"# labels are matching\n",
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"np.unique(ref_masks), np.unique(pred_masks)"
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},
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{
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"cell_type": "code",
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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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"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\"> 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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],
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" \u001b[4;94mhttps://github.com/BrainLesion/panoptica#citation\u001b[0m -- Thank you! \n"
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{

‎panoptica/example_spine_matching_algorithm.ipynb‎

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}
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"source": [
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"ref_masks = read_nifti(\"./spine_seg/unmatched_instance/ref.nii.gz\")\n",
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"pred_masks = read_nifti(\"./spine_seg/unmatched_instance/pred.nii.gz\")\n",
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"ref_masks = read_nifti(f\"{BASE_PATH}/spine_seg/unmatched_instance/ref.nii.gz\")\n",
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"pred_masks = read_nifti(f\"{BASE_PATH}/spine_seg/unmatched_instance/pred.nii.gz\")\n",
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"\n",
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"# labels are unmatched instances\n",
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"pred_masks[pred_masks == 27] = 26 # For later\n",

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