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import os
# from pathlib import Path
from shutil import copyfile
# TODO need to replace the name in xml to make this work out of the box
def export_segmentation(folder, name, dest_folder, out_name):
seg_file = os.path.join(folder, 'segmentations', '%s.h5' % name)
xml_file = os.path.join(folder, 'segmentations', '%s.xml' % name)
table_file = os.path.join(folder, 'tables', name, 'default.csv')
assert os.path.exists(seg_file)
assert os.path.exists(xml_file)
assert os.path.exists(table_file), table_file
seg_out = os.path.join(dest_folder, '%s.h5' % out_name)
print("Copying segmentation from", seg_file, "to", seg_out)
copyfile(seg_file, seg_out)
xml_out = os.path.join(dest_folder, '%s.xml' % out_name)
print("Copying xml from", xml_file, "to", xml_out)
copyfile(xml_file, xml_out)
table_out = os.path.join(dest_folder, 'tables', '%s.csv' % out_name)
print("Copying table from", table_file, "to", table_out)
copyfile(table_file, table_out)
def export_tag(tag, export_cells=False, export_cilia=False):
tag_folder = './data/%s' % tag
assert os.path.exists(tag_folder)
dest_folder = '/g/arendt/EM_6dpf_segmentation/EM-Prospr'
if export_cells:
name = 'sbem-6dpf-1-whole-segmented-cells-labels'
out_name = 'em-segmented-cells-new-labels'
export_segmentation(tag_folder, name, dest_folder, out_name)
if export_cilia:
name = 'sbem-6dpf-1-whole-segmented-cilia-labels'
out_name = 'em-segmented-cilia-labels'
export_segmentation(tag_folder, name, dest_folder, out_name)
if __name__ == '__main__':
# export_tag('0.1.1', export_cells=True)
export_tag('0.1.0', export_cilia=True)