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import os
import glob
from .scripts.files import get_h5_path_from_xml, copy_xml_with_newpath
def copy_xmls_and_symlink_h5(name_dict, src_folder, trgt_folder):
for n1, n2 in name_dict.items():
src_xml = os.path.join(src_folder, n1)
trgt_xml = os.path.join(trgt_folder, n2)
# we make a softlink from src to target h5
# NOTE eventually, we want to copy all the data, but
# for now, we use softlinks in order to keep the current
# version of the platy browser working
src_h5 = get_h5_path_from_xml(src_xml, return_absolute_path=True)
trgt_h5 = os.path.splitext(n2)[0] + '.h5'
os.symlink(src_h5, trgt_h5)
copy_xml_with_newpath(src_xml, trgt_xml, trgt_h5)
def make_initial_data_sources():
old_folder = '/g/arendt/EM_6dpf_segmentation/EM-Prospr'
raw_folder = './data/rawdata'
# copy the sbem data
sbem_prefix = 'sbem-6dpf-1-whole'
name_dict = {'em-raw-', 'em-raw',
'em-segmented-', ''}
name_dict = {k: '%s-%s' % (sbem_prefix, v)
for k, v in name_dict.items()}
copy_xmls_and_symlink_h5(name_dict, old_folder, raw_folder)
# copy the prospr meds
prospr_prefix = 'prospr-6dpf-1-whole'
prospr_names = glob.glob(os.path.join(old_folder, "*-MED*"))
prospr_names = [os.path.split(f) for f in prospr_names]
name_dict = {n: '%s-%s' % (prospr_prefix, n) for n in prospr_names}
copy_xmls_and_symlink_h5(name_dict, old_folder, raw_folder)
# copy the fibsem data
fib_prefix = 'fibsem-6dpf-1-parapod'
name_dict = {'em-raw-', 'em-raw',
'em-segmented-', ''}
name_dict = {k: '%s-%s' % (fib_prefix, v)
for k, v in name_dict.items()}
copy_xmls_and_symlink_h5(name_dict, old_folder, raw_folder)
if __name__ == '__main__':
make_initial_data_sources()