def pyobjs_to_h5(g4tracks, pixnoise, filename, v):
"""
Given the python object lists, write to HDF5 file at filename.
"""
with h5py.File(filename, "w", libver="latest", driver="core") as f:
for ind in range(len(g4tracks)):
pyobj_to_h5 = {}
indstr = "{:05d}".format(ind)
g = f.create_group(indstr)
# write g4track
if g4tracks[ind]:
filejob.vprint(v, 3, "Writing " + str(ind) + " g4track at " + time.ctime())
trackio.write_object_to_hdf5(g4tracks[ind], g, "g4track", pyobj_to_h5=pyobj_to_h5)
# write each pixnoise
for key, val in pixnoise.iteritems():
filejob.vprint(v, 4, "Writing " + str(ind) + " " + key + " at " + time.ctime())
if isinstance(val[ind], trackdata.Track):
trackio.write_object_to_hdf5(val[ind], g, key, pyobj_to_h5=pyobj_to_h5)
else:
# track error code
t = g.create_group(key)
t.attrs["errorcode"] = val[ind]
def pyobjs_to_h5(g4tracks, pixnoise, filename, v):
"""
Given the python object lists, write to HDF5 file at filename.
"""
with h5py.File(filename, 'w', libver='latest', driver='core') as f:
for ind in range(len(g4tracks)):
pyobj_to_h5 = {}
indstr = '{:05d}'.format(ind)
g = f.create_group(indstr)
# write g4track
if g4tracks[ind]:
filejob.vprint(
v, 3,
'Writing ' + str(ind) + ' g4track at ' + time.ctime())
trackio.write_object_to_hdf5(g4tracks[ind],
g,
'g4track',
pyobj_to_h5=pyobj_to_h5)
# write each pixnoise
for key, val in pixnoise.iteritems():
filejob.vprint(
v, 4,
'Writing ' + str(ind) + ' ' + key + ' at ' + time.ctime())
if isinstance(val[ind], trackdata.Track):
trackio.write_object_to_hdf5(val[ind],
g,
key,
pyobj_to_h5=pyobj_to_h5)
else:
# track error code
t = g.create_group(key)
t.attrs['errorcode'] = val[ind]
def pyobj_from_h5(h5filename, v):
"""
Given a file in h5matlab format, return list of objects
(trackdata.G4Track and trackdata.Track)
h5filename: complete filename string
"""
n_to_run = 10000
n_run = 0
with h5py.File(h5filename, 'r', driver='core') as f:
# get max index number
indices = []
for key in f.keys():
indices.append(int(key))
max_index = np.max(np.array(indices))
filejob.vprint(v, 3, '\n Got max_index at ' + time.ctime())
# initialize array of g4tracks, and dict of diffused tracks
g4tracks = [[] for i in range(max_index + 1)]
pixnoise = {}
# construct tracks
for track_key in f.keys():
if n_run > n_to_run:
continue
filejob.vprint(v, 3,
'Starting ' + track_key + ' at ' + time.ctime())
n_run += 1
evt = f[track_key]
ind = int(track_key)
g4tracks[ind] = trackdata.G4Track.from_h5matlab(evt)
for pn_key in evt.keys():
if not pn_key.startswith('pix'):
continue
if pn_key not in pixnoise:
# initialize pixnoise dict entry
pixnoise[pn_key] = [[] for i in range(max_index + 1)]
# add to existing dict
this_track = trackdata.Track.from_h5matlab(
evt[pn_key], g4track=g4tracks[ind])
# debug
if this_track is None:
pdb.set_trace()
pixnoise[pn_key][ind] = this_track
return g4tracks, pixnoise
def pyobj_from_h5(h5filename, v):
"""
Given a file in h5matlab format, return list of objects
(trackdata.G4Track and trackdata.Track)
h5filename: complete filename string
"""
n_to_run = 10000
n_run = 0
with h5py.File(h5filename, "r", driver="core") as f:
# get max index number
indices = []
for key in f.keys():
indices.append(int(key))
max_index = np.max(np.array(indices))
filejob.vprint(v, 3, "\n Got max_index at " + time.ctime())
# initialize array of g4tracks, and dict of diffused tracks
g4tracks = [[] for i in range(max_index + 1)]
pixnoise = {}
# construct tracks
for track_key in f.keys():
if n_run > n_to_run:
continue
filejob.vprint(v, 3, "Starting " + track_key + " at " + time.ctime())
n_run += 1
evt = f[track_key]
ind = int(track_key)
g4tracks[ind] = trackdata.G4Track.from_h5matlab(evt)
for pn_key in evt.keys():
if not pn_key.startswith("pix"):
continue
if pn_key not in pixnoise:
# initialize pixnoise dict entry
pixnoise[pn_key] = [[] for i in range(max_index + 1)]
# add to existing dict
this_track = trackdata.Track.from_h5matlab(evt[pn_key], g4track=g4tracks[ind])
# debug
if this_track is None:
pdb.set_trace()
pixnoise[pn_key][ind] = this_track
return g4tracks, pixnoise
def h5m_to_pyml(loadfile, savefile, v):
"""
Main work
"""
filejob.vprint(v, 2, "~ Loading " + loadfile + " at " + time.ctime() + " ~")
g4tracks, pixnoise = pyobj_from_h5(loadfile, v)
filejob.vprint(v, 1, "> Saving " + savefile + " at " + time.ctime() + " <")
pyobjs_to_h5(g4tracks, pixnoise, savefile, v)
filejob.vprint(v, 2, "= Finished " + savefile + " at " + time.ctime() + " =")
def h5m_to_pyml(loadfile, savefile, v):
"""
Main work
"""
filejob.vprint(v, 2,
'~ Loading ' + loadfile + ' at ' + time.ctime() + ' ~')
g4tracks, pixnoise = pyobj_from_h5(loadfile, v)
filejob.vprint(v, 1, '> Saving ' + savefile + ' at ' + time.ctime() + ' <')
pyobjs_to_h5(g4tracks, pixnoise, savefile, v)
filejob.vprint(v, 2,
'= Finished ' + savefile + ' at ' + time.ctime() + ' =')
def get_results(loadfile, savefile, v):
"""
Get all the important numbers for each event.
(basic info:)
Etot
Edep
Etrack
alpha_true
beta_true
errorcode
file
ind
(ridge following result:)
alpha_rf
(moments result:)
alpha_m
(general rejection parameters:)
min_end_energy
max_end_energy
n_ends
(moments rejection parameters:)
phi
edge_pixels
edge_segments
(Monte Carlo rejection parameters:)
overlap flag
wrong_end flag
early_scatter flag
total_scatter_angle
"""
progressflag = not file_vars()[0]
pn = 'pix10_5noise15'
HTname = 'python HT v1.52'
MTname = 'moments v1.0'
vprint(
v, 1, 'Starting {} at {} with {}% mem usage'.format(
loadfile, time.ctime(),
psutil.virtual_memory().percent))
datalen = 1000
# basic info
energy_tot_kev = np.nan * np.ones(datalen)
energy_dep_kev = np.nan * np.ones(datalen)
energy_track_kev = np.nan * np.ones(datalen)
alpha_true_deg = np.nan * np.ones(datalen)
beta_true_deg = np.nan * np.ones(datalen)
trk_errorcode = np.nan * np.ones(datalen)
cl_errorcode = np.nan * np.ones(datalen)
mom_errorcode = np.nan * np.ones(datalen)
filename = ['' for _ in xrange(datalen)]
fileind = np.nan * np.ones(datalen)
# ridge following
alpha_ridge_deg = np.nan * np.ones(datalen)
# moments
alpha_moments_deg = np.nan * np.ones(datalen)
# rejection
min_end_energy_kev = np.nan * np.ones(datalen)
max_end_energy_kev = np.nan * np.ones(datalen)
n_ends = np.nan * np.ones(datalen)
phi_deg = np.nan * np.ones(datalen)
edge_pixels = np.nan * np.ones(datalen)
edge_segments = np.nan * np.ones(datalen)
# monte carlo
overlap_flag = np.nan * np.ones(datalen)
wrong_end_flag = np.nan * np.ones(datalen)
early_scatter_flag = np.nan * np.ones(datalen)
total_scatter_angle_deg = np.nan * np.ones(datalen)
try:
with h5py.File(loadfile, 'r',
driver='core') as f, h5py.File(savefile,
'a',
driver='core') as h5save:
if progressflag:
pbar = progressbar.ProgressBar(widgets=[
progressbar.Percentage(), ' ',
progressbar.Bar(), ' ',
progressbar.ETA()
],
maxval=datalen)
pbar.start()
for ind in xrange(datalen):
indstr = '{:05d}'.format(ind)
trkstr = indstr
clstr = 'cl_' + indstr
momstr = 'mom_' + indstr
this_trk_errorcode = 0
this_cl_errorcode = 0
this_mom_errorcode = 0
filename[ind] = os.path.split(loadfile)[-1]
fileind[ind] = ind
# track and algorithm alpha's
try:
this_trk = Track.from_hdf5(f[trkstr][pn])
except KeyError:
# could be an MException from MATLAB
this_trk_errorcode = 10
trk_errorcode[ind] = this_trk_errorcode
continue
except trackio.InterfaceError:
read_errorcode = f[trkstr][pn].attrs['errorcode']
if read_errorcode > 0:
# multiplicity event
this_trk_errorcode = read_errorcode
trk_errorcode[ind] = this_trk_errorcode
continue
else:
raise
energy_tot_kev[ind] = this_trk.g4track.energy_tot_kev
energy_dep_kev[ind] = this_trk.g4track.energy_dep_kev
energy_track_kev[ind] = this_trk.energy_kev
alpha_true_deg[ind] = this_trk.g4track.alpha_deg
beta_true_deg[ind] = this_trk.g4track.beta_deg
alpha_ridge_deg[ind] = this_trk[HTname].alpha_deg
alpha_moments_deg[ind] = this_trk[MTname].alpha_deg
# classifier
this_cl = cl.Classifier.from_hdf5(f[clstr][pn])
min_end_energy_kev[ind] = this_cl.min_end_energy
max_end_energy_kev[ind] = this_cl.max_end_energy
n_ends[ind] = this_cl.n_ends
overlap_flag[ind] = this_cl.overlap
wrong_end_flag[ind] = this_cl.wrong_end
if this_cl.error == 'TrackTooShortError':
this_cl_errorcode = 8
else:
early_scatter_flag[ind] = this_cl.early_scatter
total_scatter_angle_deg[ind] = (
this_cl.total_scatter_angle / np.pi * 180)
# moments info
try:
this_mom = tm.MomentsReconstruction.from_hdf5(
f[momstr][pn])
except trackio.InterfaceError:
if f[momstr][pn].attrs['errorcode'] == 4:
# no ends found
this_mom_errorcode = 4
else:
raise
else:
if this_mom.error == 'CheckSegmentBoxError':
this_mom_errorcode = 9
elif this_mom.error == 'what the heck happened?':
this_mom.errorcode = 11
elif this_mom.error == 'Rotation angle conditions not met':
this_mom.errorcode = 12
else:
phi_deg[ind] = this_mom.phi / np.pi * 180
edge_pixels[ind] = this_mom.edge_pixel_count
edge_segments[ind] = this_mom.edge_pixel_segments
trk_errorcode[ind] = this_trk_errorcode
cl_errorcode[ind] = this_cl_errorcode
mom_errorcode[ind] = this_mom_errorcode
if progressflag:
pbar.update(ind)
# save to file
# basic info
h5save.create_dataset('energy_tot_kev',
shape=(datalen, ),
data=energy_tot_kev)
h5save.create_dataset('energy_dep_kev',
shape=(datalen, ),
data=energy_dep_kev)
h5save.create_dataset('energy_track_kev',
shape=(datalen, ),
data=energy_track_kev)
h5save.create_dataset('alpha_true_deg',
shape=(datalen, ),
data=alpha_true_deg)
h5save.create_dataset('beta_true_deg',
shape=(datalen, ),
data=beta_true_deg)
h5save.create_dataset('trk_errorcode',
shape=(datalen, ),
data=trk_errorcode,
dtype='f2')
h5save.create_dataset('cl_errorcode',
shape=(datalen, ),
data=cl_errorcode,
dtype='f2')
h5save.create_dataset('mom_errorcode',
shape=(datalen, ),
data=mom_errorcode,
dtype='f2')
h5save.create_dataset('filename',
shape=(datalen, ),
data=filename,
dtype=h5py.special_dtype(vlen=str))
h5save.create_dataset('fileind',
shape=(datalen, ),
data=fileind,
dtype='f4')
# ridge following
h5save.create_dataset('alpha_ridge_deg',
shape=(datalen, ),
data=alpha_ridge_deg)
# moments
h5save.create_dataset('alpha_moments_deg',
shape=(datalen, ),
data=alpha_moments_deg)
# rejection parameters
h5save.create_dataset('min_end_energy_kev',
shape=(datalen, ),
data=min_end_energy_kev)
h5save.create_dataset('max_end_energy_kev',
shape=(datalen, ),
data=max_end_energy_kev)
h5save.create_dataset('n_ends',
shape=(datalen, ),
data=n_ends,
dtype='f4')
h5save.create_dataset('phi_deg', shape=(datalen, ), data=phi_deg)
h5save.create_dataset('edge_pixels',
shape=(datalen, ),
data=edge_pixels,
dtype='f4')
h5save.create_dataset('edge_segments',
shape=(datalen, ),
data=edge_segments,
dtype='f2')
# Monte Carlo
h5save.create_dataset('overlap_flag',
shape=(datalen, ),
data=overlap_flag,
dtype='f2')
h5save.create_dataset('wrong_end_flag',
shape=(datalen, ),
data=wrong_end_flag,
dtype='f2')
h5save.create_dataset('early_scatter_flag',
shape=(datalen, ),
data=early_scatter_flag,
dtype='f2')
h5save.create_dataset('total_scatter_angle_deg',
shape=(datalen, ),
data=total_scatter_angle_deg)
if progressflag:
pbar.finish()
except NotImplementedError:
pass
def classify_etc(loadfile, savefile, v):
"""
1. Moments algorithm
2. HybridTrack algorithm
3. Classify
"""
progressflag = not file_vars()[0]
pn = 'pix10_5noise15'
HTname = 'python HT v1.52'
MTname = 'moments v1.0'
vprint(v, 1, 'Starting {} at {} with {}% mem usage'.format(
loadfile, time.ctime(), psutil.virtual_memory().percent))
pyobj_to_h5 = {}
try:
with h5py.File(loadfile, 'a', driver='core') as f, h5py.File(
savefile, 'a', driver='core') as h5save:
#
n = 0
if progressflag:
pbar = progressbar.ProgressBar(
widgets=[progressbar.Percentage(), ' ',
progressbar.Bar(), ' ',
progressbar.ETA()], maxval=len(f))
pbar.start()
keylist = f.keys()
keylist.sort()
for ind in keylist:
vprint(v, 3, 'Beginning track {} in {}'.format(ind, loadfile))
if int(ind) % 50 == 0:
vprint(v, 2,
'Beginning track {} in {}'.format(ind, loadfile))
# evt is for the G4Track object
evt = f[ind]
# shouldn't get a KeyError because we are looping over ind
# trk is for the Track object
try:
trk = evt[pn]
except KeyError:
vprint(v, 1,
'**Missing key {} in {}{}, skipping'.format(
pn, loadfile, evt.name))
continue
trkpath = ind + '/' + pn
errorcode = 0
n += 1
if n > 50:
# testing
# vprint(v, 1, 'Finished 50 files, exiting')
# break
pass
# load G4Track
vprint(v, 3, 'Loading G4Track {} in {}'.format(ind, loadfile))
try:
this_g4track = G4Track.from_dth5(evt)
except trackio.InterfaceError:
vprint(v, 2, 'InterfaceError in G4Track at {}, {}'.format(
loadfile, ind))
continue
# load Track
vprint(v, 3, 'Loading Track {} in {}'.format(ind, loadfile))
try:
this_track = Track.from_dth5(trk, g4track=this_g4track)
except trackio.InterfaceError:
vprint(v, 2, 'InterfaceError in Track at {}, {}'.format(
loadfile, ind))
continue
# check for error codes - Track.from_dth5 may return an int
if isinstance(this_track, int):
this_save = h5save.create_group(trkpath)
this_save.attrs.create(
'errorcode', this_track, shape=np.shape(this_track))
continue
# run moments algorithm
vprint(v, 3, 'Running moments on track {} in {}'.format(
ind, loadfile))
try:
mom = tm.MomentsReconstruction(this_track.image)
mom.reconstruct()
except ht.NoEndsFound:
mom.alpha = None
errorcode = 4
this_save = h5save.create_group('mom_' + trkpath)
this_save.attrs.create(
'errorcode', errorcode, shape=np.shape(errorcode))
else:
# write into savefile
trackio.write_object_to_hdf5(
mom, h5save, 'mom_' + trkpath, pyobj_to_h5=pyobj_to_h5)
# write into track object
if mom.alpha:
this_track.add_algorithm(
MTname,
alpha_deg=mom.alpha * 180 / np.pi,
beta_deg=np.nan, info=None)
else:
this_track.add_algorithm(
MTname,
alpha_deg=np.nan,
beta_deg=np.nan, info=None)
# run HT algorithm (v1.52)
vprint(v, 3, 'Running HT on track {} in {}'.format(
ind, loadfile))
try:
_, HTinfo = ht.reconstruct(this_track)
except (ht.InfiniteLoop, ht.NoEndsFound):
# write empty into track object
this_track.add_algorithm(
HTname,
alpha_deg=np.nan,
beta_deg=np.nan,
info=None)
else:
# trim memory usage
if hasattr(HTinfo, 'ridge'):
if HTinfo.ridge:
for ridgept in HTinfo.ridge:
ridgept.cuts = None
ridgept.best_cut = None
# write into track object
this_track.add_algorithm(
HTname,
alpha_deg=HTinfo.alpha_deg,
beta_deg=HTinfo.beta_deg,
info=HTinfo)
# write py HDF5 format into savefile (including alg outputs)
try:
trackio.write_object_to_hdf5(
this_track, h5save, trkpath,
pyobj_to_h5=pyobj_to_h5)
except trackio.InterfaceError:
vprint(v, 1, 'InterfaceError writing to file at ' +
'{}, {}'.format(savefile, ind))
continue
# run classifier
vprint(v, 3, 'Running MC classifier on track {} in {}'.format(
ind, loadfile))
classifier = cl.Classifier(this_track.g4track)
try:
classifier.mc_classify()
except cl.TrackTooShortError:
classifier.error = 'TrackTooShortError'
else:
vprint(v, 3,
'Running ends classifier on track {} in {}'.format(
ind, loadfile))
try:
classifier.end_classify(this_track, mom=mom)
except tp.G4TrackTooBigError:
classifier.error = 'G4TrackTooBigError'
except cl.NoEnds:
classifier.error = 'NoEnds'
# write into savefile
vprint(v, 3, 'Writing classifier into {} for track {}'.format(
savefile, ind))
trackio.write_object_to_hdf5(
classifier, h5save, 'cl_' + trkpath,
pyobj_to_h5=pyobj_to_h5)
if progressflag:
pbar.update(n)
if progressflag:
pbar.finish()
# f gets closed here
except NotImplementedError:
pass
def pyml_run_algs(loadfile, savefile, v):
progressflag = False # turn off for parallel
pnlist = [
'pix2_5noise0',
'pix5noise0',
'pix5noise15',
'pix10_5noise0',
'pix10_5noise15',
'pix10_5noise20',
'pix10_5noise50',
'pix10_5noise100',
'pix10_5noise200',
'pix10_5noise500',
'pix10_5noise1000',
'pix10_5noise2000',
'pix20noise0',
'pix40noise0',
]
alglist = {
'python HT v1.52': ht,
# 'python HT v1.52a': ht_a,
# 1.52a causes RuntimeWarning and possibly breaks something more...
'python HT v1.52b': ht_b,
'python HT v1.52c': ht_c,
'python HT v1.52d': ht_d,
}
tracklist = {}
AR = {}
for pnname in pnlist:
tracklist[pnname] = []
AR[pnname] = {}
for algname in alglist.keys():
AR[pnname][algname] = []
vprint(v, 1, 'Starting {} at {} with {}% mem usage'.format(
loadfile, time.ctime(), psutil.virtual_memory().percent))
try:
with h5py.File(loadfile, 'a', driver='core') as h5load:
filename = h5load.filename
n = 0
if progressflag:
pbar = progressbar.ProgressBar(
widgets=[progressbar.Percentage(), ' ',
progressbar.Bar(), ' ',
progressbar.ETA()], maxval=len(h5load))
pbar.start()
keylist = h5load.keys()
keylist.sort()
for ind in keylist:
if int(ind) % 10 == 0:
vprint(v, 2, ' Running {} #{} at {}'.format(
loadfile, ind, time.ctime()))
trk = h5load[ind]
h5_to_pydict = {}
pydict_to_pyobj = {}
pyobj_to_h5 = {}
n += 1
if n > 50:
# pdb.set_trace()
# continue # TODO temp!
pass
for pnname in pnlist:
try:
pn = trk[pnname]
except KeyError:
vprint(v, 1,
'**Missing key {} in {}{}, skipping'.format(
pnname, loadfile, trk.name))
continue
vprint(v, 3, 'Running {}{} at {}'.format(
loadfile, pn.name, time.ctime()))
# load track
try:
this_track = trackdata.Track.from_hdf5(
pn,
h5_to_pydict=h5_to_pydict,
pydict_to_pyobj=pydict_to_pyobj)
except trackio.InterfaceError:
vprint(v, 2, 'InterfaceError at {}{}'.format(
loadfile, pn.name))
continue
tracklist[pnname].append(this_track)
# each algorithm version
for algname, algfunc in alglist.items():
vprint(v, 4, 'Running alg {} at {}'.format(
algname, time.ctime()))
# check for result
if algname not in this_track.algorithms:
# run algorithm
try:
_, HTinfo = algfunc.reconstruct(this_track)
except algfunc.InfiniteLoop:
continue
except algfunc.NoEndsFound:
continue
# trim memory usage!
if hasattr(HTinfo, 'ridge'):
if HTinfo.ridge:
for ridgept in HTinfo.ridge:
ridgept.cuts = None
ridgept.best_cut = None
# write into track object
try:
this_track.add_algorithm(
algname,
alpha_deg=HTinfo.alpha_deg,
beta_deg=HTinfo.beta_deg,
info=HTinfo)
# write into HDF5
trackio.write_object_to_hdf5(
this_track.algorithms[algname],
pn['algorithms'], algname,
pyobj_to_h5=pyobj_to_h5)
except trackdata.InputError:
# already has this algorithm
pass
if progressflag:
pbar.update(n)
if progressflag:
pbar.finish()
# h5load gets closed
vprint(
v, 1.5,
'\n Finished loading {} at {} with {}% mem usage'.format(
loadfile, time.ctime(), psutil.virtual_memory().percent))
except IOError:
vprint(v, 1, 'IOError: Unable to open file (I think) for {}'.format(
loadfile))
return None
# AlgorithmResults objects
alglist2 = alglist.keys() # + ['matlab HT v1.5']
for pnname in pnlist:
for algname in alglist2:
this_AR = evaluation.AlgorithmResults.from_track_list(
tracklist[pnname], alg_name=algname, filename=filename)
AR[pnname][algname] = this_AR
vprint(v, 2, '\n Created AR objects for {} at {}'.format(
loadfile, time.ctime()))
# write to savefile
try:
with h5py.File(savefile, 'w', driver='core') as h5save:
for pnname, AR_pn in AR.items():
pngroup = h5save.create_group(pnname)
for algname, this_AR in AR_pn.items():
trackio.write_object_to_hdf5(this_AR, pngroup, algname)
vprint(v, 1.5,
'Finished saving {} at {}'.format(savefile, time.ctime()))
except IOError:
vprint(v, 1, 'IOError: Unable to create file (I think) for {}'.format(
savefile))
return None
def pyml_run_algs(loadfile, savefile, v):
progressflag = False # turn off for parallel
pnlist = [
'pix2_5noise0',
'pix5noise0',
'pix5noise15',
'pix10_5noise0',
'pix10_5noise15',
'pix10_5noise20',
'pix10_5noise50',
'pix10_5noise100',
'pix10_5noise200',
'pix10_5noise500',
'pix10_5noise1000',
'pix10_5noise2000',
'pix20noise0',
'pix40noise0',
]
alglist = {
'python HT v1.52': ht,
# 'python HT v1.52a': ht_a,
# 1.52a causes RuntimeWarning and possibly breaks something more...
'python HT v1.52b': ht_b,
'python HT v1.52c': ht_c,
'python HT v1.52d': ht_d,
}
tracklist = {}
AR = {}
for pnname in pnlist:
tracklist[pnname] = []
AR[pnname] = {}
for algname in alglist.keys():
AR[pnname][algname] = []
vprint(
v, 1, 'Starting {} at {} with {}% mem usage'.format(
loadfile, time.ctime(),
psutil.virtual_memory().percent))
try:
with h5py.File(loadfile, 'a', driver='core') as h5load:
filename = h5load.filename
n = 0
if progressflag:
pbar = progressbar.ProgressBar(widgets=[
progressbar.Percentage(), ' ',
progressbar.Bar(), ' ',
progressbar.ETA()
],
maxval=len(h5load))
pbar.start()
keylist = h5load.keys()
keylist.sort()
for ind in keylist:
if int(ind) % 10 == 0:
vprint(
v, 2, ' Running {} #{} at {}'.format(
loadfile, ind, time.ctime()))
trk = h5load[ind]
h5_to_pydict = {}
pydict_to_pyobj = {}
pyobj_to_h5 = {}
n += 1
if n > 50:
# pdb.set_trace()
# continue # TODO temp!
pass
for pnname in pnlist:
try:
pn = trk[pnname]
except KeyError:
vprint(
v, 1, '**Missing key {} in {}{}, skipping'.format(
pnname, loadfile, trk.name))
continue
vprint(
v, 3,
'Running {}{} at {}'.format(loadfile, pn.name,
time.ctime()))
# load track
try:
this_track = trackdata.Track.from_hdf5(
pn,
h5_to_pydict=h5_to_pydict,
pydict_to_pyobj=pydict_to_pyobj)
except trackio.InterfaceError:
vprint(
v, 2,
'InterfaceError at {}{}'.format(loadfile, pn.name))
continue
tracklist[pnname].append(this_track)
# each algorithm version
for algname, algfunc in alglist.items():
vprint(
v, 4, 'Running alg {} at {}'.format(
algname, time.ctime()))
# check for result
if algname not in this_track.algorithms:
# run algorithm
try:
_, HTinfo = algfunc.reconstruct(this_track)
except algfunc.InfiniteLoop:
continue
except algfunc.NoEndsFound:
continue
# trim memory usage!
if hasattr(HTinfo, 'ridge'):
if HTinfo.ridge:
for ridgept in HTinfo.ridge:
ridgept.cuts = None
ridgept.best_cut = None
# write into track object
try:
this_track.add_algorithm(
algname,
alpha_deg=HTinfo.alpha_deg,
beta_deg=HTinfo.beta_deg,
info=HTinfo)
# write into HDF5
trackio.write_object_to_hdf5(
this_track.algorithms[algname],
pn['algorithms'],
algname,
pyobj_to_h5=pyobj_to_h5)
except trackdata.InputError:
# already has this algorithm
pass
if progressflag:
pbar.update(n)
if progressflag:
pbar.finish()
# h5load gets closed
vprint(
v, 1.5,
'\n Finished loading {} at {} with {}% mem usage'.format(
loadfile, time.ctime(),
psutil.virtual_memory().percent))
except IOError:
vprint(
v, 1,
'IOError: Unable to open file (I think) for {}'.format(loadfile))
return None
# AlgorithmResults objects
alglist2 = alglist.keys() # + ['matlab HT v1.5']
for pnname in pnlist:
for algname in alglist2:
this_AR = evaluation.AlgorithmResults.from_track_list(
tracklist[pnname], alg_name=algname, filename=filename)
AR[pnname][algname] = this_AR
vprint(
v, 2,
'\n Created AR objects for {} at {}'.format(loadfile, time.ctime()))
# write to savefile
try:
with h5py.File(savefile, 'w', driver='core') as h5save:
for pnname, AR_pn in AR.items():
pngroup = h5save.create_group(pnname)
for algname, this_AR in AR_pn.items():
trackio.write_object_to_hdf5(this_AR, pngroup, algname)
vprint(v, 1.5,
'Finished saving {} at {}'.format(savefile, time.ctime()))
except IOError:
vprint(
v, 1,
'IOError: Unable to create file (I think) for {}'.format(savefile))
return None
def get_results(loadfile, savefile, v):
"""
Get all the important numbers for each event.
(basic info:)
Etot
Edep
Etrack
alpha_true
beta_true
errorcode
file
ind
(ridge following result:)
alpha_rf
(moments result:)
alpha_m
(general rejection parameters:)
min_end_energy
max_end_energy
n_ends
(moments rejection parameters:)
phi
edge_pixels
edge_segments
(Monte Carlo rejection parameters:)
overlap flag
wrong_end flag
early_scatter flag
total_scatter_angle
"""
progressflag = not file_vars()[0]
pn = 'pix10_5noise15'
HTname = 'python HT v1.52'
MTname = 'moments v1.0'
vprint(v, 1, 'Starting {} at {} with {}% mem usage'.format(
loadfile, time.ctime(), psutil.virtual_memory().percent))
datalen = 1000
# basic info
energy_tot_kev = np.nan * np.ones(datalen)
energy_dep_kev = np.nan * np.ones(datalen)
energy_track_kev = np.nan * np.ones(datalen)
alpha_true_deg = np.nan * np.ones(datalen)
beta_true_deg = np.nan * np.ones(datalen)
trk_errorcode = np.nan * np.ones(datalen)
cl_errorcode = np.nan * np.ones(datalen)
mom_errorcode = np.nan * np.ones(datalen)
filename = ['' for _ in xrange(datalen)]
fileind = np.nan * np.ones(datalen)
# ridge following
alpha_ridge_deg = np.nan * np.ones(datalen)
# moments
alpha_moments_deg = np.nan * np.ones(datalen)
# rejection
min_end_energy_kev = np.nan * np.ones(datalen)
max_end_energy_kev = np.nan * np.ones(datalen)
n_ends = np.nan * np.ones(datalen)
phi_deg = np.nan * np.ones(datalen)
edge_pixels = np.nan * np.ones(datalen)
edge_segments = np.nan * np.ones(datalen)
# monte carlo
overlap_flag = np.nan * np.ones(datalen)
wrong_end_flag = np.nan * np.ones(datalen)
early_scatter_flag = np.nan * np.ones(datalen)
total_scatter_angle_deg = np.nan * np.ones(datalen)
try:
with h5py.File(loadfile, 'r', driver='core') as f, h5py.File(
savefile, 'a', driver='core') as h5save:
if progressflag:
pbar = progressbar.ProgressBar(
widgets=[progressbar.Percentage(), ' ',
progressbar.Bar(), ' ',
progressbar.ETA()], maxval=datalen)
pbar.start()
for ind in xrange(datalen):
indstr = '{:05d}'.format(ind)
trkstr = indstr
clstr = 'cl_' + indstr
momstr = 'mom_' + indstr
this_trk_errorcode = 0
this_cl_errorcode = 0
this_mom_errorcode = 0
filename[ind] = os.path.split(loadfile)[-1]
fileind[ind] = ind
# track and algorithm alpha's
try:
this_trk = Track.from_hdf5(f[trkstr][pn])
except KeyError:
# could be an MException from MATLAB
this_trk_errorcode = 10
trk_errorcode[ind] = this_trk_errorcode
continue
except trackio.InterfaceError:
read_errorcode = f[trkstr][pn].attrs['errorcode']
if read_errorcode > 0:
# multiplicity event
this_trk_errorcode = read_errorcode
trk_errorcode[ind] = this_trk_errorcode
continue
else:
raise
energy_tot_kev[ind] = this_trk.g4track.energy_tot_kev
energy_dep_kev[ind] = this_trk.g4track.energy_dep_kev
energy_track_kev[ind] = this_trk.energy_kev
alpha_true_deg[ind] = this_trk.g4track.alpha_deg
beta_true_deg[ind] = this_trk.g4track.beta_deg
alpha_ridge_deg[ind] = this_trk[HTname].alpha_deg
alpha_moments_deg[ind] = this_trk[MTname].alpha_deg
# classifier
this_cl = cl.Classifier.from_hdf5(f[clstr][pn])
min_end_energy_kev[ind] = this_cl.min_end_energy
max_end_energy_kev[ind] = this_cl.max_end_energy
n_ends[ind] = this_cl.n_ends
overlap_flag[ind] = this_cl.overlap
wrong_end_flag[ind] = this_cl.wrong_end
if this_cl.error == 'TrackTooShortError':
this_cl_errorcode = 8
else:
early_scatter_flag[ind] = this_cl.early_scatter
total_scatter_angle_deg[ind] = (
this_cl.total_scatter_angle / np.pi * 180)
# moments info
try:
this_mom = tm.MomentsReconstruction.from_hdf5(
f[momstr][pn])
except trackio.InterfaceError:
if f[momstr][pn].attrs['errorcode'] == 4:
# no ends found
this_mom_errorcode = 4
else:
raise
else:
if this_mom.error == 'CheckSegmentBoxError':
this_mom_errorcode = 9
elif this_mom.error == 'what the heck happened?':
this_mom.errorcode = 11
elif this_mom.error == 'Rotation angle conditions not met':
this_mom.errorcode = 12
else:
phi_deg[ind] = this_mom.phi / np.pi * 180
edge_pixels[ind] = this_mom.edge_pixel_count
edge_segments[ind] = this_mom.edge_pixel_segments
trk_errorcode[ind] = this_trk_errorcode
cl_errorcode[ind] = this_cl_errorcode
mom_errorcode[ind] = this_mom_errorcode
if progressflag:
pbar.update(ind)
# save to file
# basic info
h5save.create_dataset(
'energy_tot_kev', shape=(datalen,), data=energy_tot_kev)
h5save.create_dataset(
'energy_dep_kev', shape=(datalen,), data=energy_dep_kev)
h5save.create_dataset(
'energy_track_kev', shape=(datalen,), data=energy_track_kev)
h5save.create_dataset(
'alpha_true_deg', shape=(datalen,), data=alpha_true_deg)
h5save.create_dataset(
'beta_true_deg', shape=(datalen,), data=beta_true_deg)
h5save.create_dataset(
'trk_errorcode', shape=(datalen,), data=trk_errorcode,
dtype='f2')
h5save.create_dataset(
'cl_errorcode', shape=(datalen,), data=cl_errorcode,
dtype='f2')
h5save.create_dataset(
'mom_errorcode', shape=(datalen,), data=mom_errorcode,
dtype='f2')
h5save.create_dataset(
'filename', shape=(datalen,), data=filename,
dtype=h5py.special_dtype(vlen=str))
h5save.create_dataset(
'fileind', shape=(datalen,), data=fileind,
dtype='f4')
# ridge following
h5save.create_dataset(
'alpha_ridge_deg', shape=(datalen,), data=alpha_ridge_deg)
# moments
h5save.create_dataset(
'alpha_moments_deg', shape=(datalen,), data=alpha_moments_deg)
# rejection parameters
h5save.create_dataset(
'min_end_energy_kev', shape=(datalen,),
data=min_end_energy_kev)
h5save.create_dataset(
'max_end_energy_kev', shape=(datalen,),
data=max_end_energy_kev)
h5save.create_dataset(
'n_ends', shape=(datalen,), data=n_ends,
dtype='f4')
h5save.create_dataset(
'phi_deg', shape=(datalen,), data=phi_deg)
h5save.create_dataset(
'edge_pixels', shape=(datalen,), data=edge_pixels,
dtype='f4')
h5save.create_dataset(
'edge_segments', shape=(datalen,), data=edge_segments,
dtype='f2')
# Monte Carlo
h5save.create_dataset(
'overlap_flag', shape=(datalen,), data=overlap_flag,
dtype='f2')
h5save.create_dataset(
'wrong_end_flag', shape=(datalen,), data=wrong_end_flag,
dtype='f2')
h5save.create_dataset(
'early_scatter_flag', shape=(datalen,),
data=early_scatter_flag, dtype='f2')
h5save.create_dataset(
'total_scatter_angle_deg', shape=(datalen,),
data=total_scatter_angle_deg)
if progressflag:
pbar.finish()
except NotImplementedError:
pass