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create_project.py
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create_project.py
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# new spec
# from mobie import add_image, add_segmentation
# old spec
from mobie import initialize_dataset
def add_cell(path, ds_name, resolution, key='*.tif'):
scale_factors = 5 * [[2, 2, 2]]
chunks = [64, 64, 64]
root = '/g/emcf/pape/sponge-fibsem-project/data'
# new spec
# add_image(path, key, root=root, dataset_name=ds_name,
# image_name='raw', resolution=resolution, scale_factors=scale_factors,
# menu_name='fibsem', target='local', chunks=chunks, max_jobs=16)
# old spec
initialize_dataset(path, key, root=root, dataset_name=ds_name,
raw_name='fibsem-raw', resolution=resolution,
scale_factors=scale_factors,
target='local', chunks=chunks, max_jobs=24)
def add_cell1():
path = '/g/emcf/schwab/For Constantin/aligned_cropped_cell1'
res = [0.008] * 3
add_cell(path, 'cell1', resolution=res)
def add_cell3():
path = '/g/emcf/schwab/For Constantin/aligned_cropped_cell3'
res = [0.008, 0.005, 0.005]
add_cell(path, 'cell3', resolution=res)
# Is this one of the cells above? Or is it a different one.
def add_chamber_raw():
path = '/g/emcf/schwab/For Constantin/choano_chambr/corrected-full'
resolution = [0.015, 0.015, 0.015]
ds_name = 'choanocyte-chamber'
add_cell(path, ds_name, resolution)
if __name__ == '__main__':
# add_cell1()
# add_cell3()
add_chamber_raw()