def test_IO_obj_dict(filename):
"""
test obj_dict hardlink capability
"""
from etrack.reconstruction import evaluation
# first, check a single object which is listed in obj_dict
alg_results = evaluation.generate_random_alg_results(length=10000)
alg_results.parent = [alg_results]
with h5py.File(filename, 'w') as h5file:
write_object_to_hdf5(
alg_results, h5file, 'alg_results')
with h5py.File(filename, 'r') as h5file:
ar2 = read_object_from_hdf5(
h5file['alg_results'])
assert ar2['parent'][0] is ar2
os.remove(filename)
# check alpha_unc and beta_unc
alg_results.add_default_uncertainties()
alg_results.parent = [alg_results]
with h5py.File(filename, 'w') as h5file:
write_object_to_hdf5(
alg_results, h5file, 'alg_results')
with h5py.File(filename, 'r') as h5file:
ar2 = read_object_from_hdf5(
h5file['alg_results'])
assert ar2['parent'][0] is ar2
assert ar2['alpha_unc'] is ar2['uncertainty_list'][0]
assert ar2['beta_unc'] is ar2['uncertainty_list'][1]
os.remove(filename)
# check obj_dict with multiple objects written to the same file
# (has to be written in the same file session)
ar1 = evaluation.generate_random_alg_results(length=10000)
ar1.add_default_uncertainties()
ar2 = evaluation.generate_random_alg_results(length=1000)
ar2.add_default_uncertainties()
pyobj_to_h5 = {}
with h5py.File(filename, 'a') as h5file:
write_object_to_hdf5(ar1, h5file, 'ar1', pyobj_to_h5=pyobj_to_h5)
write_object_to_hdf5(ar2, h5file, 'ar2', pyobj_to_h5=pyobj_to_h5)
# should be hardlinked
write_object_to_hdf5(ar1, h5file, 'ar3', pyobj_to_h5=pyobj_to_h5)
h5_to_pydict = {}
with h5py.File(filename, 'r') as h5file:
ar1r = read_object_from_hdf5(h5file['ar1'], h5_to_pydict=h5_to_pydict)
ar2r = read_object_from_hdf5(h5file['ar2'], h5_to_pydict=h5_to_pydict)
ar3r = read_object_from_hdf5(h5file['ar3'], h5_to_pydict=h5_to_pydict)
check_alg_results_IO(ar1r, ar1, uncertainty_flag=True)
check_alg_results_IO(ar2r, ar2, uncertainty_flag=True)
check_alg_results_IO(ar3r, ar1, uncertainty_flag=True)
# this is the hardlink test:
assert ar1r is ar3r
os.remove(filename)
def test_IO_obj_dict(filename):
"""
test obj_dict hardlink capability
"""
from etrack.reconstruction import evaluation
# first, check a single object which is listed in obj_dict
alg_results = evaluation.generate_random_alg_results(length=10000)
alg_results.parent = [alg_results]
with h5py.File(filename, 'w') as h5file:
write_object_to_hdf5(alg_results, h5file, 'alg_results')
with h5py.File(filename, 'r') as h5file:
ar2 = read_object_from_hdf5(h5file['alg_results'])
assert ar2['parent'][0] is ar2
os.remove(filename)
# check alpha_unc and beta_unc
alg_results.add_default_uncertainties()
alg_results.parent = [alg_results]
with h5py.File(filename, 'w') as h5file:
write_object_to_hdf5(alg_results, h5file, 'alg_results')
with h5py.File(filename, 'r') as h5file:
ar2 = read_object_from_hdf5(h5file['alg_results'])
assert ar2['parent'][0] is ar2
assert ar2['alpha_unc'] is ar2['uncertainty_list'][0]
assert ar2['beta_unc'] is ar2['uncertainty_list'][1]
os.remove(filename)
# check obj_dict with multiple objects written to the same file
# (has to be written in the same file session)
ar1 = evaluation.generate_random_alg_results(length=10000)
ar1.add_default_uncertainties()
ar2 = evaluation.generate_random_alg_results(length=1000)
ar2.add_default_uncertainties()
pyobj_to_h5 = {}
with h5py.File(filename, 'a') as h5file:
write_object_to_hdf5(ar1, h5file, 'ar1', pyobj_to_h5=pyobj_to_h5)
write_object_to_hdf5(ar2, h5file, 'ar2', pyobj_to_h5=pyobj_to_h5)
# should be hardlinked
write_object_to_hdf5(ar1, h5file, 'ar3', pyobj_to_h5=pyobj_to_h5)
h5_to_pydict = {}
with h5py.File(filename, 'r') as h5file:
ar1r = read_object_from_hdf5(h5file['ar1'], h5_to_pydict=h5_to_pydict)
ar2r = read_object_from_hdf5(h5file['ar2'], h5_to_pydict=h5_to_pydict)
ar3r = read_object_from_hdf5(h5file['ar3'], h5_to_pydict=h5_to_pydict)
check_alg_results_IO(ar1r, ar1, uncertainty_flag=True)
check_alg_results_IO(ar2r, ar2, uncertainty_flag=True)
check_alg_results_IO(ar3r, ar1, uncertainty_flag=True)
# this is the hardlink test:
assert ar1r is ar3r
os.remove(filename)
def test_IO_user_objects(filename):
"""
single user object
multi-level user objects
"""
# don't import at top of file! circular import with evaluation.py
from etrack.reconstruction import evaluation
# Real Classes:
# single user-defined object
alg_results = evaluation.generate_random_alg_results(length=10000)
with h5py.File(filename, 'w') as h5file:
write_object_to_hdf5(
alg_results, h5file, 'alg_results')
with h5py.File(filename, 'r') as h5file:
ar2 = read_object_from_hdf5(h5file['alg_results'])
check_alg_results_IO(ar2, alg_results, uncertainty_flag=False)
os.remove(filename)
# multi-level object
alg_results.add_default_uncertainties()
with h5py.File(filename, 'w') as h5file:
write_object_to_hdf5(
alg_results, h5file, 'alg_results')
with h5py.File(filename, 'r') as h5file:
ar2 = read_object_from_hdf5(h5file['alg_results'])
check_alg_results_IO(ar2, alg_results, uncertainty_flag=True)
os.remove(filename)
def test_IO_user_objects(filename):
"""
single user object
multi-level user objects
"""
# don't import at top of file! circular import with evaluation.py
from etrack.reconstruction import evaluation
# Real Classes:
# single user-defined object
alg_results = evaluation.generate_random_alg_results(length=10000)
with h5py.File(filename, 'w') as h5file:
write_object_to_hdf5(alg_results, h5file, 'alg_results')
with h5py.File(filename, 'r') as h5file:
ar2 = read_object_from_hdf5(h5file['alg_results'])
check_alg_results_IO(ar2, alg_results, uncertainty_flag=False)
os.remove(filename)
# multi-level object
alg_results.add_default_uncertainties()
with h5py.File(filename, 'w') as h5file:
write_object_to_hdf5(alg_results, h5file, 'alg_results')
with h5py.File(filename, 'r') as h5file:
ar2 = read_object_from_hdf5(h5file['alg_results'])
check_alg_results_IO(ar2, alg_results, uncertainty_flag=True)
os.remove(filename)
def test_IO_overwrite(filename):
"""
test the ability to overwrite objects in an existing HDF5 file
"""
from etrack.reconstruction import evaluation
# simple overwrite
alg_results = evaluation.generate_random_alg_results(length=10000)
alg_results.add_default_uncertainties()
with h5py.File(filename, 'a') as h5file:
write_object_to_hdf5(
alg_results, h5file, 'alg_results')
with h5py.File(filename, 'a') as h5file:
write_object_to_hdf5(
alg_results, h5file, 'alg_results')
with h5py.File(filename, 'r') as h5file:
ar2 = read_object_from_hdf5(h5file['alg_results'])
check_alg_results_IO(ar2, alg_results, uncertainty_flag=True)
os.remove(filename)
# writing two objects to the same file
ar1 = evaluation.generate_random_alg_results(length=10000)
ar1.add_default_uncertainties()
ar2 = evaluation.generate_random_alg_results(length=1000)
ar2.add_default_uncertainties()
with h5py.File(filename, 'a') as h5file:
write_object_to_hdf5(ar1, h5file, 'ar1')
write_object_to_hdf5(ar2, h5file, 'ar2')
with h5py.File(filename, 'r') as h5file:
ar1r = read_object_from_hdf5(h5file['ar1'])
ar2r = read_object_from_hdf5(h5file['ar2'])
check_alg_results_IO(ar1r, ar1, uncertainty_flag=True)
check_alg_results_IO(ar2r, ar2, uncertainty_flag=True)
# overwriting just one of the two objects
ar3 = evaluation.generate_random_alg_results(length=1000)
ar3.add_default_uncertainties()
with h5py.File(filename, 'a') as h5file:
write_object_to_hdf5(ar3, h5file, 'ar1')
with h5py.File(filename, 'r') as h5file:
ar1r = read_object_from_hdf5(h5file['ar1'])
ar2r = read_object_from_hdf5(h5file['ar2'])
check_alg_results_IO(ar1r, ar3, uncertainty_flag=True)
check_alg_results_IO(ar2r, ar2, uncertainty_flag=True)
os.remove(filename)
def test_IO_overwrite(filename):
"""
test the ability to overwrite objects in an existing HDF5 file
"""
from etrack.reconstruction import evaluation
# simple overwrite
alg_results = evaluation.generate_random_alg_results(length=10000)
alg_results.add_default_uncertainties()
with h5py.File(filename, 'a') as h5file:
write_object_to_hdf5(alg_results, h5file, 'alg_results')
with h5py.File(filename, 'a') as h5file:
write_object_to_hdf5(alg_results, h5file, 'alg_results')
with h5py.File(filename, 'r') as h5file:
ar2 = read_object_from_hdf5(h5file['alg_results'])
check_alg_results_IO(ar2, alg_results, uncertainty_flag=True)
os.remove(filename)
# writing two objects to the same file
ar1 = evaluation.generate_random_alg_results(length=10000)
ar1.add_default_uncertainties()
ar2 = evaluation.generate_random_alg_results(length=1000)
ar2.add_default_uncertainties()
with h5py.File(filename, 'a') as h5file:
write_object_to_hdf5(ar1, h5file, 'ar1')
write_object_to_hdf5(ar2, h5file, 'ar2')
with h5py.File(filename, 'r') as h5file:
ar1r = read_object_from_hdf5(h5file['ar1'])
ar2r = read_object_from_hdf5(h5file['ar2'])
check_alg_results_IO(ar1r, ar1, uncertainty_flag=True)
check_alg_results_IO(ar2r, ar2, uncertainty_flag=True)
# overwriting just one of the two objects
ar3 = evaluation.generate_random_alg_results(length=1000)
ar3.add_default_uncertainties()
with h5py.File(filename, 'a') as h5file:
write_object_to_hdf5(ar3, h5file, 'ar1')
with h5py.File(filename, 'r') as h5file:
ar1r = read_object_from_hdf5(h5file['ar1'])
ar2r = read_object_from_hdf5(h5file['ar2'])
check_alg_results_IO(ar1r, ar3, uncertainty_flag=True)
check_alg_results_IO(ar2r, ar2, uncertainty_flag=True)
os.remove(filename)
def test_write_objects_to_hdf5():
"""
test the multiple-object form of writing
"""
from etrack.reconstruction import evaluation
filename = generate_random_filename(ext='')
filename_h5 = filename + '.h5'
filename_hdf5 = filename + '.hdf5'
# h5file provided
# single object
ar = evaluation.generate_random_alg_results(length=1000)
ar.add_default_uncertainties()
with h5py.File(filename_h5, 'a') as h5file:
write_objects_to_hdf5(h5file, ar=ar)
with h5py.File(filename_h5, 'r') as h5file:
ar_read = read_object_from_hdf5(h5file['ar'])
check_alg_results_IO(ar_read, ar, uncertainty_flag=True)
os.remove(filename_h5)
# h5file provided
# multiple objects
ar1 = evaluation.generate_random_alg_results(length=1000)
ar1.add_default_uncertainties()
ar2 = evaluation.generate_random_alg_results(length=2000)
ar2.add_default_uncertainties()
ar3 = evaluation.generate_random_alg_results(length=3000)
ar3.add_default_uncertainties()
with h5py.File(filename_h5, 'a') as h5file:
filename_written = write_objects_to_hdf5(
h5file,
ar1=ar1, ar2=ar2, ar3=ar3, aunc=ar1.alpha_unc)
assert filename_written == filename_h5
h5_to_pydict = {}
with h5py.File(filename_h5, 'r') as h5file:
ar1_read = read_object_from_hdf5(
h5file['ar1'], h5_to_pydict=h5_to_pydict)
ar2_read = read_object_from_hdf5(
h5file['ar2'], h5_to_pydict=h5_to_pydict)
ar3_read = read_object_from_hdf5(
h5file['ar3'], h5_to_pydict=h5_to_pydict)
aunc = read_object_from_hdf5(h5file['aunc'], h5_to_pydict=h5_to_pydict)
check_alg_results_IO(ar1_read, ar1, uncertainty_flag=True)
check_alg_results_IO(ar2_read, ar2, uncertainty_flag=True)
check_alg_results_IO(ar3_read, ar3, uncertainty_flag=True)
# check hard link across multiple write calls (within a file session)
assert aunc is ar1_read['alpha_unc']
os.remove(filename_h5)
# filename provided, including extension (single object)
filename_written = write_objects_to_hdf5(filename_h5, ar=ar)
assert filename_written == filename_h5
with h5py.File(filename_h5, 'r') as h5file:
ar_read = read_object_from_hdf5(h5file['ar'])
check_alg_results_IO(ar_read, ar, uncertainty_flag=True)
os.remove(filename_h5)
# filename provided as *.hdf5
filename_written = write_objects_to_hdf5(filename_hdf5, ar=ar)
assert filename_written == filename_hdf5
with h5py.File(filename_hdf5, 'r') as h5file:
ar_read = read_object_from_hdf5(h5file['ar'])
check_alg_results_IO(ar_read, ar, uncertainty_flag=True)
os.remove(filename_hdf5)
# filename provided without extension. check that extension is added
filename_written = write_objects_to_hdf5(filename, ar=ar)
assert filename_written == filename_h5
with h5py.File(filename_h5, 'r') as h5file:
ar_read = read_object_from_hdf5(h5file['ar'])
check_alg_results_IO(ar_read, ar, uncertainty_flag=True)
os.remove(filename_h5)
def test_write_objects_to_hdf5():
"""
test the multiple-object form of writing
"""
from etrack.reconstruction import evaluation
filename = generate_random_filename(ext='')
filename_h5 = filename + '.h5'
filename_hdf5 = filename + '.hdf5'
# h5file provided
# single object
ar = evaluation.generate_random_alg_results(length=1000)
ar.add_default_uncertainties()
with h5py.File(filename_h5, 'a') as h5file:
write_objects_to_hdf5(h5file, ar=ar)
with h5py.File(filename_h5, 'r') as h5file:
ar_read = read_object_from_hdf5(h5file['ar'])
check_alg_results_IO(ar_read, ar, uncertainty_flag=True)
os.remove(filename_h5)
# h5file provided
# multiple objects
ar1 = evaluation.generate_random_alg_results(length=1000)
ar1.add_default_uncertainties()
ar2 = evaluation.generate_random_alg_results(length=2000)
ar2.add_default_uncertainties()
ar3 = evaluation.generate_random_alg_results(length=3000)
ar3.add_default_uncertainties()
with h5py.File(filename_h5, 'a') as h5file:
filename_written = write_objects_to_hdf5(h5file,
ar1=ar1,
ar2=ar2,
ar3=ar3,
aunc=ar1.alpha_unc)
assert filename_written == filename_h5
h5_to_pydict = {}
with h5py.File(filename_h5, 'r') as h5file:
ar1_read = read_object_from_hdf5(h5file['ar1'],
h5_to_pydict=h5_to_pydict)
ar2_read = read_object_from_hdf5(h5file['ar2'],
h5_to_pydict=h5_to_pydict)
ar3_read = read_object_from_hdf5(h5file['ar3'],
h5_to_pydict=h5_to_pydict)
aunc = read_object_from_hdf5(h5file['aunc'], h5_to_pydict=h5_to_pydict)
check_alg_results_IO(ar1_read, ar1, uncertainty_flag=True)
check_alg_results_IO(ar2_read, ar2, uncertainty_flag=True)
check_alg_results_IO(ar3_read, ar3, uncertainty_flag=True)
# check hard link across multiple write calls (within a file session)
assert aunc is ar1_read['alpha_unc']
os.remove(filename_h5)
# filename provided, including extension (single object)
filename_written = write_objects_to_hdf5(filename_h5, ar=ar)
assert filename_written == filename_h5
with h5py.File(filename_h5, 'r') as h5file:
ar_read = read_object_from_hdf5(h5file['ar'])
check_alg_results_IO(ar_read, ar, uncertainty_flag=True)
os.remove(filename_h5)
# filename provided as *.hdf5
filename_written = write_objects_to_hdf5(filename_hdf5, ar=ar)
assert filename_written == filename_hdf5
with h5py.File(filename_hdf5, 'r') as h5file:
ar_read = read_object_from_hdf5(h5file['ar'])
check_alg_results_IO(ar_read, ar, uncertainty_flag=True)
os.remove(filename_hdf5)
# filename provided without extension. check that extension is added
filename_written = write_objects_to_hdf5(filename, ar=ar)
assert filename_written == filename_h5
with h5py.File(filename_h5, 'r') as h5file:
ar_read = read_object_from_hdf5(h5file['ar'])
check_alg_results_IO(ar_read, ar, uncertainty_flag=True)
os.remove(filename_h5)
