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377b913 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# File: annotations_to_csv.py
#
# Convert manually-placed anatomical landmarks (the GOLD STANDARD) into the
# --landmarks-csv format that prepare_data.py consumes:
#
# volume_name,index,x,y,z
#
# Supported inputs:
# * 3D Slicer markups .mrk.json (Slicer 5+) --format slicer-json
# * 3D Slicer fiducials .fcsv --format fcsv
# * ITK-SNAP label / simple "x y z name" text --format xyz
#
# IMPORTANT: Slicer/ITK-SNAP store points in PHYSICAL (LPS/RAS) millimetre
# coordinates. The RL pipeline works in VOXEL indices. Pass the matching
# converted NIfTI with --nii so points are mapped physical -> voxel correctly
# (requires SimpleITK; without it, points are assumed already in voxel indices).
#
# Usage:
# python annotations_to_csv.py --format slicer-json \
# --in caseA.mrk.json --volume-name 3_MRI00019_20241125_15_s2458 \
# --nii data/images/3_MRI00019_20241125_15_s2458.nii.gz --out points.csv
import argparse
import json
import os
try:
import SimpleITK as sitk
_HAVE_SITK = True
except Exception:
_HAVE_SITK = False
def _phys_to_voxel(points_mm, nii):
"""Map physical LPS mm -> voxel index using the NIfTI geometry."""
if not (nii and _HAVE_SITK and os.path.exists(nii)):
return [tuple(round(c) for c in p) for p in points_mm]
img = sitk.ReadImage(nii)
out = []
for p in points_mm:
vox = img.TransformPhysicalPointToIndex([float(p[0]), float(p[1]), float(p[2])])
out.append(tuple(int(v) for v in vox))
return out
def read_slicer_json(path):
data = json.load(open(path))
pts = []
for mk in data.get("markups", []):
for cp in mk.get("controlPoints", []):
pts.append(cp["position"]) # [x,y,z] in the file's coordinate system
return pts
def read_fcsv(path):
pts = []
for line in open(path):
if line.startswith("#") or not line.strip():
continue
f = line.split(",")
if len(f) >= 4:
pts.append([float(f[1]), float(f[2]), float(f[3])])
return pts
def read_xyz(path):
pts = []
for line in open(path):
f = line.replace(",", " ").split()
if len(f) >= 3:
try:
pts.append([float(f[0]), float(f[1]), float(f[2])])
except ValueError:
continue
return pts
def main():
ap = argparse.ArgumentParser()
ap.add_argument("--format", required=True, choices=["slicer-json", "fcsv", "xyz"])
ap.add_argument("--in", dest="inp", required=True)
ap.add_argument("--volume-name", required=True,
help="must match the .nii.gz basename produced by prepare_data.py")
ap.add_argument("--nii", default=None, help="matching converted volume (for mm->voxel)")
ap.add_argument("--out", default="points.csv")
ap.add_argument("--append", action="store_true")
a = ap.parse_args()
reader = {"slicer-json": read_slicer_json, "fcsv": read_fcsv, "xyz": read_xyz}[a.format]
pts_mm = reader(a.inp)
pts = _phys_to_voxel(pts_mm, a.nii)
mode = "a" if a.append else "w"
write_header = not (a.append and os.path.exists(a.out))
with open(a.out, mode) as f:
if write_header:
f.write("volume_name,index,x,y,z\n")
for i, (x, y, z) in enumerate(pts):
f.write(f"{a.volume_name},{i},{int(x)},{int(y)},{int(z)}\n")
print(f"wrote {len(pts)} points for {a.volume_name} -> {a.out}"
+ ("" if (a.nii and _HAVE_SITK) else " [assumed voxel coords; pass --nii + SimpleITK for mm->voxel]"))
if __name__ == "__main__":
main()
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