Upload irm_cancer_module.py
Browse files- irm_cancer_module.py +74 -0
irm_cancer_module.py
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import nibabel as nib
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import numpy as np
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import os
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import cv2
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def run(files):
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data = []
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for f in files:
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img = nib.load(f).get_fdata()
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data.append(img)
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seg = np.zeros_like(data[0], dtype=np.uint8)
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# Segmentation fictive (tu remplaceras par ton modèle réel)
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seg[data[0] > np.percentile(data[0], 99)] = 4 # Enhancing Tumor (ET)
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seg[data[1] > np.percentile(data[1], 99)] = 1 # NCR/NET
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seg[data[2] > np.percentile(data[2], 99)] = 2 # Edema
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voxel_volume_ml = np.prod(nib.load(files[0]).header.get_zooms()) / 1000.0
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voxels = int((seg > 0).sum())
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volume_ml = voxels * voxel_volume_ml
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# Décomposition par classes
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ncr_voxels = int((seg == 1).sum())
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ed_voxels = int((seg == 2).sum())
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et_voxels = int((seg == 4).sum())
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ncr_vol = ncr_voxels * voxel_volume_ml
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ed_vol = ed_voxels * voxel_volume_ml
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et_vol = et_voxels * voxel_volume_ml
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# Rapport enrichi
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report_text = f"""
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==== Compte-rendu automatique de segmentation ====
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Modalités utilisées : FLAIR, T1, T1CE, T2
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--- Volumétrie ---
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Volume tumoral total : {volume_ml:.2f} ml ({voxels} voxels)
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- Nécrose / non rehaussé (NCR/NET) : {ncr_vol:.2f} ml ({ncr_voxels} voxels)
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- Œdème péri-tumoral (ED) : {ed_vol:.2f} ml ({ed_voxels} voxels)
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- Masse rehaussée (ET) : {et_vol:.2f} ml ({et_voxels} voxels)
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--- Interprétation clinique ---
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- Masse suspectée détectée.
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{ "- Présence de zones nécrotiques." if ncr_voxels > 0 else "" }
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{ "- Œdème détecté." if ed_voxels > 0 else "" }
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{ "- Rehaussement détecté → suspicion de tumeur de haut grade." if et_voxels > 0 else "- Pas de rehaussement visible." }
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- Volume > 100 ml → effet de masse probable.
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--- Recommandations ---
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1. Discussion multidisciplinaire (neuro-oncologie).
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2. IRM avec injection + séquence de perfusion si dispo.
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3. Biopsie/examen histologique recommandé.
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⚠️ Rapport généré automatiquement, non destiné à remplacer un avis médical.
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"""
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# Sauvegardes dans /tmp
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output_dir = "/tmp/output"
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os.makedirs(output_dir, exist_ok=True)
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nii_path = os.path.join(output_dir, "irm_image.nii.gz")
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report_path = os.path.join(output_dir, "rapport.txt")
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mask_path = os.path.join(output_dir, "mask_preview.png")
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nib.save(nib.Nifti1Image(data[0], np.eye(4)), nii_path)
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with open(report_path, "w") as f: f.write(report_text)
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# Sauvegarde du masque visible (couleur)
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slice_idx = seg.shape[2] // 2
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mask_rgb = cv2.applyColorMap((seg[:,:,slice_idx] * 60).astype(np.uint8), cv2.COLORMAP_JET)
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cv2.imwrite(mask_path, mask_rgb)
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return seg, report_text, (nii_path, report_path, mask_path)
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