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import os, glob |
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import numpy as np |
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from PIL import Image |
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import pydicom |
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import nibabel as nib |
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def load_slices_from_folder(folder, glob_pattern="*.png", sort_numerically=True): |
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paths = sorted(glob.glob(os.path.join(folder, glob_pattern))) |
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if sort_numerically: |
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try: |
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paths = sorted(paths, key=lambda p: int(''.join(filter(str.isdigit, os.path.basename(p))) or 0)) |
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except Exception: |
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pass |
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slices = [np.array(Image.open(p).convert("L")) for p in paths] |
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vol = np.stack(slices, axis=0) |
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return vol.astype(np.float32) |
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def load_dicom_folder(folder): |
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files = [p for p in glob.glob(os.path.join(folder, "**"), recursive=False) if os.path.isfile(p)] |
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ds = [] |
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for f in files: |
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try: |
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d = pydicom.dcmread(f) |
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ds.append((getattr(d, "InstanceNumber", 0), d)) |
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except Exception: |
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continue |
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ds = sorted(ds, key=lambda x: x[0]) |
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imgs = [d.pixel_array for _, d in ds] |
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vol = np.stack(imgs, axis=0).astype(np.float32) |
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return vol |
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def load_nifti(path): |
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nii = nib.load(path) |
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arr = nii.get_fdata().astype(np.float32) |
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if arr.ndim == 3: |
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return np.transpose(arr, (2,1,0)) |
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return arr |
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def save_mesh_ply(verts, faces, out_path, normals=None, colors=None): |
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import numpy as np |
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with open(out_path, 'w') as f: |
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f.write("ply\nformat ascii 1.0\n") |
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f.write(f"element vertex {len(verts)}\n") |
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f.write("property float x\nproperty float y\nproperty float z\n") |
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if colors is not None: |
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f.write("property uchar red\nproperty uchar green\nproperty uchar blue\n") |
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if normals is not None: |
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f.write("property float nx\nproperty float ny\nproperty nz\n") |
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f.write(f"element face {len(faces)}\n") |
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f.write("property list uchar int vertex_indices\n") |
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f.write("end_header\n") |
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for i, v in enumerate(verts): |
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line = f"{v[0]} {v[1]} {v[2]}" |
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if colors is not None: |
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c = (np.clip(colors[i], 0, 1) * 255).astype(int) |
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line += f" {c[0]} {c[1]} {c[2]}" |
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if normals is not None: |
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n = normals[i] |
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line += f" {n[0]} {n[1]} {n[2]}" |
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f.write(line + "\n") |
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for face in faces: |
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f.write(f"3 {face[0]} {face[1]} {face[2]}\n") |
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