def run_HT_file(h5f, v, dry_run):
"""
Handle one file: h5f['00000']['pix10_5noise0'] and so
"""
for track_key in h5f.keys():
# h5save.create_group(track_key)
if v > 1:
print(' Starting', track_key, 'at', time.ctime())
this_h5track = h5f[track_key]
h5_to_pydict = {}
pydict_to_pyobj = {}
pyobj_to_h5 = {}
pix_list = ['pix2_5noise0', 'pix10_5noise0']
if (pix_list[0] not in this_h5track.keys()
or pix_list[1] not in this_h5track.keys()):
continue
for _, pix_key in enumerate(pix_list):
# if not pix_key.startswith('pix'):
# continue
alg_name = 'python HT v1.5'
alg_name2 = 'python HT v1.5a'
if v > 2:
print(' Starting', pix_key, 'at', time.ctime())
this_h5pix = this_h5track[pix_key]
if 'algorithms' not in this_h5pix.keys():
continue
if alg_name in this_h5pix['algorithms'].keys():
continue
if v > 3:
print(' Building Track object...', time.ctime())
this_track = trackdata.Track.from_hdf5(
this_h5pix,
h5_to_pydict=h5_to_pydict,
pydict_to_pyobj=pydict_to_pyobj)
if v > 3:
print(' Running HybridTrack...', time.ctime())
try:
HTout, HTinfo = hybridtrack.reconstruct(
this_track.image, pixel_size_um=this_track.pixel_size_um)
HTout2, HTinfo2 = hybridtrack2.reconstruct(
this_track.image, pixel_size_um=this_track.pixel_size_um)
except Exception: # hybridtrack.HybridTrackError, hybridtrack2.HybridTrackError:
if v > 1:
print(' HybridTrackError on', track_key, 'at',
time.ctime())
continue
this_track.add_algorithm(alg_name,
alpha_deg=HTinfo.alpha_deg,
beta_deg=HTinfo.beta_deg,
info=HTinfo)
this_track.add_algorithm(alg_name2,
alpha_deg=HTinfo2.alpha_deg,
beta_deg=HTinfo2.beta_deg,
info=HTinfo2)
if v > 2:
print(' Appending to file', pix_key, 'at', time.ctime())
# append to same file
if dry_run:
continue
trackio.write_object_to_hdf5(this_track.algorithms[alg_name],
this_h5pix['algorithms'],
alg_name,
pyobj_to_h5=pyobj_to_h5)
trackio.write_object_to_hdf5(this_track.algorithms[alg_name2],
this_h5pix['algorithms'],
alg_name2,
pyobj_to_h5=pyobj_to_h5)
def run_HT_file(h5f, v, dry_run):
"""
Handle one file: h5f['00000']['pix10_5noise0'] and so
"""
for track_key in h5f.keys():
# h5save.create_group(track_key)
if v > 1:
print(' Starting', track_key, 'at', time.ctime())
this_h5track = h5f[track_key]
h5_to_pydict = {}
pydict_to_pyobj = {}
pyobj_to_h5 = {}
pix_list = ['pix2_5noise0', 'pix10_5noise0']
if (pix_list[0] not in this_h5track.keys() or
pix_list[1] not in this_h5track.keys()):
continue
for _, pix_key in enumerate(pix_list):
# if not pix_key.startswith('pix'):
# continue
alg_name = 'python HT v1.5'
alg_name2 = 'python HT v1.5a'
if v > 2:
print(' Starting', pix_key, 'at', time.ctime())
this_h5pix = this_h5track[pix_key]
if 'algorithms' not in this_h5pix.keys():
continue
if alg_name in this_h5pix['algorithms'].keys():
continue
if v > 3:
print(' Building Track object...', time.ctime())
this_track = trackdata.Track.from_hdf5(
this_h5pix,
h5_to_pydict=h5_to_pydict, pydict_to_pyobj=pydict_to_pyobj)
if v > 3:
print(' Running HybridTrack...', time.ctime())
try:
HTout, HTinfo = hybridtrack.reconstruct(
this_track.image, pixel_size_um=this_track.pixel_size_um)
HTout2, HTinfo2 = hybridtrack2.reconstruct(
this_track.image, pixel_size_um=this_track.pixel_size_um)
except Exception: # hybridtrack.HybridTrackError, hybridtrack2.HybridTrackError:
if v > 1:
print(' HybridTrackError on', track_key,
'at', time.ctime())
continue
this_track.add_algorithm(
alg_name,
alpha_deg=HTinfo.alpha_deg, beta_deg=HTinfo.beta_deg,
info=HTinfo)
this_track.add_algorithm(
alg_name2,
alpha_deg=HTinfo2.alpha_deg, beta_deg=HTinfo2.beta_deg,
info=HTinfo2)
if v > 2:
print(' Appending to file', pix_key, 'at', time.ctime())
# append to same file
if dry_run:
continue
trackio.write_object_to_hdf5(
this_track.algorithms[alg_name],
this_h5pix['algorithms'], alg_name,
pyobj_to_h5=pyobj_to_h5)
trackio.write_object_to_hdf5(
this_track.algorithms[alg_name2],
this_h5pix['algorithms'], alg_name2,
pyobj_to_h5=pyobj_to_h5)
eventname = 'event{:05d}'.format(i)
if eventname in h5file:
event = h5file[eventname]
trackname = 'trackimage2.5'
# print(trackname)
# print(event)
if trackname in event:
this_image_object = event[trackname]
this_image = np.zeros(this_image_object.shape)
this_image_object.read_direct(this_image)
aname = 'matlab_alpha'
if aname in event[trackname].attrs:
mat_alpha[i] = event[trackname].attrs[aname]
try:
# reverse the transpose MATLAB did during h5create
__, info[i] = hybridtrack.reconstruct(this_image.T,
pixel_size_um=2.5)
py_alpha[i] = info[i].alpha_deg
except hybridtrack.InfiniteLoop:
print('Infinite loop on event #{}'.format(i))
except hybridtrack.NoEndsFound:
print('No ends found on event #{}'.format(i))
except Exception:
print('Other error:')
print(Exception)
pbar.update(i)
pbar.finish()
np.savez('alpha2.5.npz', py_alpha=py_alpha, mat_alpha=mat_alpha)
for i in range(len(h5file)):
eventname = "event{:05d}".format(i)
if eventname in h5file:
event = h5file[eventname]
trackname = "trackimage2.5"
# print(trackname)
# print(event)
if trackname in event:
this_image_object = event[trackname]
this_image = np.zeros(this_image_object.shape)
this_image_object.read_direct(this_image)
aname = "matlab_alpha"
if aname in event[trackname].attrs:
mat_alpha[i] = event[trackname].attrs[aname]
try:
# reverse the transpose MATLAB did during h5create
__, info[i] = hybridtrack.reconstruct(this_image.T, pixel_size_um=2.5)
py_alpha[i] = info[i].alpha_deg
except hybridtrack.InfiniteLoop:
print("Infinite loop on event #{}".format(i))
except hybridtrack.NoEndsFound:
print("No ends found on event #{}".format(i))
except Exception:
print("Other error:")
print(Exception)
pbar.update(i)
pbar.finish()
np.savez("alpha2.5.npz", py_alpha=py_alpha, mat_alpha=mat_alpha)