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add io functions for head models, Adot, einstein optodes
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from .snirf import read_snirf | ||
from .probe_geometry import read_mrk_json, read_digpts, read_einstar_obj | ||
from .anatomy import read_segmentation_masks | ||
from .photogrammetry import read_photogrammetry_einstar, read_einstar, opt_fid_to_xr | ||
from .forward_model import save_Adot, load_Adot |
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import xarray as xr | ||
import cedalion | ||
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def save_Adot(fn: str, Adot: xr.DataArray): | ||
Adot.to_netcdf(fn) | ||
return | ||
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def load_Adot(fn: str): | ||
Adot = xr.open_dataset(fn) | ||
Adot = xr.DataArray( | ||
Adot.to_array()[0], | ||
dims=["channel", "vertex", "wavelength"], | ||
coords={"channel": ("channel", Adot.channel.values), | ||
"wavelength": ("wavelength", Adot.wavelength.values), | ||
"is_brain": ("vertex", Adot.is_brain.values) | ||
} | ||
) | ||
return Adot |
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import cedalion | ||
import cedalion.dataclasses as cdc | ||
import numpy as np | ||
from collections import OrderedDict | ||
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def read_photogrammetry_einstar(fn): | ||
fiducials, optodes = read_einstar(fn) | ||
fiducials, optodes = opt_fid_to_xr(fiducials, optodes) | ||
return fiducials, optodes | ||
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def read_einstar(fn): | ||
with open(fn, 'r') as f: | ||
lines = [[l.strip() for l in line.split(',')] for line in f.readlines()] | ||
lines = [[line[0], [float(l) for l in line[1:]]] for line in lines] | ||
assert lines[0][0] == 'Nz' | ||
assert lines[1][0] == 'Iz' | ||
assert lines[2][0] == 'Rpa' | ||
assert lines[3][0] == 'Lpa' | ||
assert lines[4][0] == 'Cz' | ||
fiducials = OrderedDict(lines[:5]) | ||
optodes = OrderedDict(lines[5:]) | ||
return fiducials, optodes | ||
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def opt_fid_to_xr(fiducials, optodes): | ||
# FIXME: this should get a different CRS | ||
CRS = "ijk" | ||
fiducials = cdc.build_labeled_points(np.array(list(fiducials.values())), | ||
labels=list(fiducials.keys()), | ||
crs=CRS)#, units="mm") | ||
opt = np.array(list(optodes.values())) | ||
types = [] | ||
for lab in list(optodes.keys()): | ||
if lab.startswith('S'): | ||
types.append(cdc.PointType(1)) | ||
elif lab.startswith('D'): | ||
types.append(cdc.PointType(2)) | ||
else: | ||
types.append(cdc.PointType(0)) | ||
optodes = cdc.build_labeled_points(opt, | ||
labels=list(optodes.keys()), | ||
crs=CRS, types=types) | ||
return fiducials, optodes |