def get_slice_images(self, xyz_channels):
# First see if the histology file exists before attempting to connect with FlatIron and
# download
hist_dir = Path(self.sess_path.parent.parent, 'histology')
hist_path_rd = None
hist_path_gr = None
if hist_dir.exists():
path_to_rd_image = glob.glob(str(hist_dir) + '/*RD.tif')
if path_to_rd_image:
hist_path_rd = tif2nrrd(Path(path_to_rd_image[0]))
else:
files = download_histology_data(self.subj, self.lab)
if files is not None:
hist_path_rd = files[1]
path_to_gr_image = glob.glob(str(hist_dir) + '/*GR.tif')
if path_to_gr_image:
hist_path_gr = tif2nrrd(Path(path_to_gr_image[0]))
else:
files = download_histology_data(self.subj, self.lab)
if files is not None:
hist_path_gr = files[0]
else:
files = download_histology_data(self.subj, self.lab)
if files is not None:
hist_path_gr = files[0]
hist_path_rd = files[1]
index = self.brain_atlas.bc.xyz2i(
xyz_channels)[:, self.brain_atlas.xyz2dims]
ccf_slice = self.brain_atlas.image[index[:, 0], :, index[:, 2]]
ccf_slice = np.swapaxes(ccf_slice, 0, 1)
label_slice = self.brain_atlas._label2rgb(
self.brain_atlas.label[index[:, 0], :, index[:, 2]])
label_slice = np.swapaxes(label_slice, 0, 1)
width = [self.brain_atlas.bc.i2x(0), self.brain_atlas.bc.i2x(456)]
height = [
self.brain_atlas.bc.i2z(index[0, 2]),
self.brain_atlas.bc.i2z(index[-1, 2])
]
if hist_path_rd:
hist_atlas_rd = atlas.AllenAtlas(hist_path=hist_path_rd)
hist_slice_rd = hist_atlas_rd.image[index[:, 0], :, index[:, 2]]
hist_slice_rd = np.swapaxes(hist_slice_rd, 0, 1)
else:
print('Could not find red histology image for this subject')
hist_slice_rd = np.copy(ccf_slice)
if hist_path_gr:
hist_atlas_gr = atlas.AllenAtlas(hist_path=hist_path_gr)
hist_slice_gr = hist_atlas_gr.image[index[:, 0], :, index[:, 2]]
hist_slice_gr = np.swapaxes(hist_slice_gr, 0, 1)
else:
print('Could not find green histology image for this subject')
hist_slice_gr = np.copy(ccf_slice)
slice_data = {
'hist_rd':
hist_slice_rd,
'hist_gr':
hist_slice_gr,
'ccf':
ccf_slice,
'label':
label_slice,
'scale':
np.array([(width[-1] - width[0]) / ccf_slice.shape[0],
(height[-1] - height[0]) / ccf_slice.shape[1]]),
'offset':
np.array([width[0], height[0]])
}
return slice_data
from atlaselectrophysiology.load_histology import tif2nrrd
from pathlib import Path
import sys
"""
Creates nrrd from image path string
"""
if __name__ == '__main__':
tif2nrrd(Path(*sys.argv[1:]))