def split(rawfolder, file_contains='LDE', print_status=False, *arg, **kw):
windows = kw.pop('windows', [1, 2])
ch0maxtime = kw.pop('ch0maxtime', 700)
ch1maxtime = kw.pop('ch1maxtime', 700)
allfiles = [ f for f in os.listdir(rawfolder) if file_contains in f and \
f[:1] != '.' and f[-4:] == '.npz' ]
lastidx = len(allfiles)
# we don't have too much data left over, so can use this approach
finaldata = np.zeros((0, 4), dtype=np.uint)
windowdata = [np.zeros((0, 4), dtype=np.uint) for w in windows]
sync_of = 0
for i, f in enumerate(allfiles):
if print_status:
print 'file %d (%d) ...' % (i + 1, len(allfiles))
fp = os.path.join(rawfolder, f)
data = hht3.data_from_file(fp,
ch0_lastbin=ch0maxtime,
ch1_lastbin=ch1maxtime,
*arg,
**kw)
if len(data) == 0:
continue
data[:, 0] += sync_of + 100
sync_of = data[-1, 0] + 1
data = hht3.filter_counts_on_marker(data, 1, windows)
if len(data) == 0:
continue
_windowdata = []
for w in windows:
_wd = hht3.filter_counts_on_marker(data, 1, [w])
_wd = hht3.delete_markers(_wd, 1)
_windowdata.append(_wd)
data = hht3.delete_markers(data, 1)
finaldata = np.vstack((finaldata, data))
for i, w in enumerate(windows):
windowdata[i] = np.vstack((windowdata[i], _windowdata[i]))
ret = [finaldata]
ret.extend(windowdata)
return tuple(ret)
def split(rawfolder, file_contains='LDE', print_status=False, *arg, **kw):
windows = kw.pop('windows', [1,2])
ch0maxtime = kw.pop('ch0maxtime', 700)
ch1maxtime = kw.pop('ch1maxtime', 700)
allfiles = [ f for f in os.listdir(rawfolder) if file_contains in f and \
f[:1] != '.' and f[-4:] == '.npz' ]
lastidx = len(allfiles)
# we don't have too much data left over, so can use this approach
finaldata = np.zeros((0,4), dtype=np.uint)
windowdata = [ np.zeros((0,4), dtype=np.uint) for w in windows ]
sync_of = 0
for i,f in enumerate(allfiles):
if print_status:
print 'file %d (%d) ...' % (i+1, len(allfiles))
fp = os.path.join(rawfolder, f)
data = hht3.data_from_file(fp, ch0_lastbin=ch0maxtime,
ch1_lastbin=ch1maxtime, *arg, **kw)
if len(data) == 0:
continue
data[:,0] += sync_of + 100
sync_of = data[-1,0] + 1
data = hht3.filter_counts_on_marker(data, 1, windows)
if len(data) == 0:
continue
_windowdata = []
for w in windows:
_wd = hht3.filter_counts_on_marker(data, 1, [w])
_wd = hht3.delete_markers(_wd,1)
_windowdata.append(_wd)
data = hht3.delete_markers(data, 1)
finaldata = np.vstack((finaldata, data))
for i,w in enumerate(windows):
windowdata[i] = np.vstack((windowdata[i], _windowdata[i]))
ret = [finaldata]
ret.extend(windowdata)
return tuple(ret)
def filter_markers(data, sync_range=range(1,301), delete=True):
data = hht3.filter_counts_on_marker(data, 1, sync_range)
if len(data) > 0 and delete:
print 'delete markers'
data = hht3.delete_markers(data, 1)
return data
def filter_markers(data, sync_range=range(1,301), delete=True):
data = hht3.filter_counts_on_marker(data, 1, sync_range)
if len(data) > 0 and delete:
print 'delete markers'
data = hht3.delete_markers(data, 1)
return data
def get_hhpludata(hhdata):
hhpludata = hht3.filter_counts_on_marker(hhdata, 2, [-1,0])
hhpludata1 = hht3.filter_counts_on_marker(hhdata, 2, [-1])
hhpludata2 = hht3.filter_counts_on_marker(hhdata, 2, [0])
# some sanity checks
if (len(hhpludata)==0):
print 'no valid hhpludata'
else:
print ''
print 'HH SSROs: %d' % len(hhpludata[
np.logical_and(hhpludata[:,3]==1, hhpludata[:,2]==2)])
print ''
print 'counts + PLU: %d' % len(hhpludata[hhpludata[:,3]==0])
print 'counts in window 1 + PLU: %d' % len(hhpludata1[hhpludata1[:,3]==0])
print 'counts in window 2 + PLU: %d' % len(hhpludata2[hhpludata2[:,3]==0])
return hhpludata, hhpludata1, hhpludata2
def get_hhpludata(hhdata):
hhpludata = hht3.filter_counts_on_marker(hhdata, 2, [-1,0])
hhpludata1 = hht3.filter_counts_on_marker(hhdata, 2, [-1])
hhpludata2 = hht3.filter_counts_on_marker(hhdata, 2, [0])
# some sanity checks
if (len(hhpludata)==0):
print 'no valid hhpludata'
else:
print ''
print 'HH SSROs: %d' % len(hhpludata[
np.logical_and(hhpludata[:,3]==1, hhpludata[:,2]==2)])
print ''
print 'counts + PLU: %d' % len(hhpludata[hhpludata[:,3]==0])
print 'counts in window 1 + PLU: %d' % len(hhpludata1[hhpludata1[:,3]==0])
print 'counts in window 2 + PLU: %d' % len(hhpludata2[hhpludata2[:,3]==0])
return hhpludata, hhpludata1, hhpludata2
def prepare_correlations(datfolder, datfile='hh_prefiltered_events.npz'):
# HH data
d = np.load(os.path.join(datfolder, datfile))
hhdata = d['data']
d.close()
hhpludat = hht3.filter_counts_on_marker(hhdata, 2, [-1,0])
hhpludat1 = hht3.filter_counts_on_marker(hhdata, 2, [-1])
hhpludat2 = hht3.filter_counts_on_marker(hhdata, 2, [0])
### some sanity checks
print ''
print 'HH SSROs: %d' % len(hhpludat[
np.logical_and(hhpludat[:,3]==1, hhpludat[:,2]==2)])
print ''
print 'counts + PLU: %d' % len(hhpludat[hhpludat[:,3]==0])
print 'counts in window 1 + PLU: %d' % len(hhpludat1[hhpludat1[:,3]==0])
print 'counts in window 2 + PLU: %d' % len(hhpludat2[hhpludat2[:,3]==0])
return hhpludat
def prepare_correlations(datfolder, datfile='hh_prefiltered_events.npz'):
# HH data
d = np.load(os.path.join(datfolder, datfile))
hhdata = d['data']
d.close()
hhpludat = hht3.filter_counts_on_marker(hhdata, 2, [-1, 0])
hhpludat1 = hht3.filter_counts_on_marker(hhdata, 2, [-1])
hhpludat2 = hht3.filter_counts_on_marker(hhdata, 2, [0])
### some sanity checks
print ''
print 'HH SSROs: %d' % len(hhpludat[np.logical_and(hhpludat[:, 3] == 1,
hhpludat[:, 2] == 2)])
print ''
print 'counts + PLU: %d' % len(hhpludat[hhpludat[:, 3] == 0])
print 'counts in window 1 + PLU: %d' % len(hhpludat1[hhpludat1[:, 3] == 0])
print 'counts in window 2 + PLU: %d' % len(hhpludat2[hhpludat2[:, 3] == 0])
return hhpludat
def plot_counts_vs_time(windowdata,
savepath,
window=1,
bins=700,
save_prefix='',
save_postfix=''):
gated = hht3.filter_counts_on_marker(windowdata, 2, [window - 2])
print 'length of window data = ', len(windowdata)
fig = plt.figure()
t0, t1 = hht3.get_click_times(windowdata)
h0y, h0x = np.histogram(t0, bins=bins, range=(0, bins - 1))
h1y, h1x = np.histogram(t1, bins=bins, range=(0, bins - 1))
g_t0, g_t1 = hht3.get_click_times(gated)
g_h0y, g_h0x = np.histogram(g_t0, bins=bins, range=(0, bins - 1))
g_h1y, g_h1x = np.histogram(g_t1, bins=bins, range=(0, bins - 1))
ax = plt.subplot(121)
ax.semilogy(g_h0x[:-1], g_h0y, color='g', label='ch0 gated')
ax.semilogy(h0x[:-1], h0y, label='ch0', color='b')
ax.set_xlabel('Bins')
ax.legend()
ax = plt.subplot(122)
ax.semilogy(h1x[:-1], h1y, label='ch1')
ax.semilogy(g_h1x[:-1], g_h1y, label='ch1 gated')
ax.set_xlabel('Bins')
ax.legend()
plt.suptitle('Clicks after optical pulse, window %d' % window)
fig.savefig(os.path.join(savepath,'%shistogram_window%s%s.pdf' % \
(save_prefix,window,save_postfix)))
np.savez(os.path.join(savepath, 'histogram_window%s.npz' % window),
window_number=window,
window_data=windowdata,
ch0=h0y,
ch0_xaxis=h0x[:-1],
ch0_gated=g_h0y,
ch0_gated_xaxis=g_h0x[:-1],
ch1=h1y,
ch1_xaxis=h1x[:-1],
ch1_gated=g_h1y,
ch1_gated_xaxis=g_h1x[:-1])
return True
def plot_counts_vs_time(windowdata, savepath, window=1, bins=700,
save_prefix='', save_postfix=''):
gated = hht3.filter_counts_on_marker(windowdata, 2, [window-2])
print 'length of window data = ',len(windowdata)
fig = plt.figure()
t0, t1 = hht3.get_click_times(windowdata)
h0y, h0x = np.histogram(t0, bins=bins, range=(0,bins-1))
h1y, h1x = np.histogram(t1, bins=bins, range=(0,bins-1))
g_t0, g_t1 = hht3.get_click_times(gated)
g_h0y, g_h0x = np.histogram(g_t0, bins=bins, range=(0,bins-1))
g_h1y, g_h1x = np.histogram(g_t1, bins=bins, range=(0,bins-1))
ax = plt.subplot(121)
ax.semilogy(g_h0x[:-1], g_h0y, color = 'g', label='ch0 gated')
ax.semilogy(h0x[:-1], h0y, label='ch0', color = 'b')
ax.set_xlabel('Bins')
ax.legend()
ax = plt.subplot(122)
ax.semilogy(h1x[:-1], h1y, label='ch1')
ax.semilogy(g_h1x[:-1], g_h1y, label='ch1 gated')
ax.set_xlabel('Bins')
ax.legend()
plt.suptitle('Clicks after optical pulse, window %d' % window)
fig.savefig(os.path.join(savepath,'%shistogram_window%s%s.pdf' % \
(save_prefix,window,save_postfix)))
np.savez(os.path.join(savepath, 'histogram_window%s.npz'%window),
window_number = window,
window_data = windowdata,
ch0 = h0y,
ch0_xaxis = h0x[:-1],
ch0_gated = g_h0y,
ch0_gated_xaxis = g_h0x[:-1],
ch1 = h1y,
ch1_xaxis = h1x[:-1],
ch1_gated = g_h1y,
ch1_gated_xaxis = g_h1x[:-1])
return True
def prepare(datfolder, rawfolder, *arg, **kw):
global setup
#############################
#### LOAD ADWIN LT1 DATA ####
#############################
# load adwin autodata
fn = os.path.join(datfolder,
ADWINLT1FOLDER+('-%.'+str(DATIDXDIGITS)+'d') % DATIDX,
ADWINDATAFN)
d = np.load(fn)
noof_SSROs_adwin_LT1 = d['get_noof_SSROs']
noof_SSRO_triggers_LT1 = d['get_noof_SSRO_triggers']
d.close()
#############################
#### LOAD ADWIN LT2 DATA ####
#############################
sn = os.path.join(datfolder,
ADWINLT2FOLDER+('-%.'+str(DATIDXDIGITS)+'d') % DATIDX,
ADWINDATAFN)
s = np.load(sn)
noof_PLU_markers = s['get_noof_PLU_markers']
noof_SSROs_adwin_LT2 = s['get_noof_SSROs']
s.close()
############################################
### LOADING SSRO DATA###
############################################
fn = os.path.join(datfolder,
DATFILEBASE+('-%.'+str(DATIDXDIGITS)+'d.npz') % DATIDX)
d = np.load(fn)
SSROs_adwin_LT1 = d['adwin_lt1_SSRO']
SSROs_adwin_LT2 = d['adwin_lt2_SSRO']
############################################
### COMPENSATING A MISMATCH IN SSRO DATA ###
############################################
#filling up SSROs_adwin_lt1 with -1 where LT2 missed a PLU
SSROs_adwin_LT1, added_idxs = correct_ssro_mismatch(SSROs_adwin_LT1,
SSROs_adwin_LT2, noof_PLU_markers,noof_SSROs_adwin_LT1,
noof_SSROs_adwin_LT2)
######################################
######################################
######################################
if setup == 'lt2':
CRs_adwin = d['adwin_lt2_CR']
else:
CRs_adwin = d['adwin_lt1_CR']
d.close()
# load HH data
hh_prefiltered, window1, window2 = split(rawfolder, *arg, **kw)
hhpludat = hht3.filter_counts_on_marker(
hh_prefiltered, 2, [-1,0])
np.savez(os.path.join(datfolder, 'hh_prefiltered_events'),
data=hh_prefiltered)
np.savez(os.path.join(datfolder, 'window1_events'),
data=window1)
np.savez(os.path.join(datfolder, 'window2_events'),
data=window2)
# more preparations
SSROs_adwin_LT1 = SSROs_adwin_LT1[:noof_SSRO_triggers_LT1+added_idxs]
SSROs_adwin_LT2 = SSROs_adwin_LT2[:noof_PLU_markers]
if setup == 'lt1':
CRs_adwin = CRs_adwin[:noof_SSRO_triggers_LT1]
######################################
######################################
######################################
print 'PLU markers on adwin lt2:', noof_PLU_markers
print '\nLength of ADwin LT1 SSRO array after addition: '\
, len(SSROs_adwin_LT1)
print 'Length of ADwin LT2 SSRO array: ', len(SSROs_adwin_LT2)
######################################
######################################
######################################
### first some sanity checks
invalid_SSROs_adwin = np.where(SSROs_adwin_LT1==-1)[0] \
if setup =='lt1' else np.where(SSROs_adwin_LT2==-1)[0]
print ''
print 'adwin detected SSROs: %d' % \
(noof_SSRO_triggers_LT1 if setup=='lt1' else noof_PLU_markers)
print ' thereof invalid: %d' % len(invalid_SSROs_adwin)
print 'HH SSROs: %d' % len(hhpludat[
np.logical_and(hhpludat[:,3]==1, hhpludat[:,2]==2)])
print ''
### plot counts
if(kw.get('do_plot',False)):
plot_counts_vs_time(window1, datfolder, window=1)
plot_counts_vs_time(window2, datfolder, window=2)
ret = SSROs_adwin_LT1 if setup=='lt1' else SSROs_adwin_LT2
return ret
def filter_PLU(data, mchan=2):
filtered = hht3.filter_counts_on_marker(data, mchan, delta_syncs=[0])
return filtered
def prepare(datfolder, rawfolder, *arg, **kw):
global setup
#############################
#### LOAD ADWIN LT1 DATA ####
#############################
# load adwin autodata
fn = os.path.join(
datfolder, ADWINLT1FOLDER + ('-%.' + str(DATIDXDIGITS) + 'd') % DATIDX,
ADWINDATAFN)
d = np.load(fn)
noof_SSROs_adwin_LT1 = d['get_noof_SSROs']
noof_SSRO_triggers_LT1 = d['get_noof_SSRO_triggers']
d.close()
#############################
#### LOAD ADWIN LT2 DATA ####
#############################
sn = os.path.join(
datfolder, ADWINLT2FOLDER + ('-%.' + str(DATIDXDIGITS) + 'd') % DATIDX,
ADWINDATAFN)
s = np.load(sn)
noof_PLU_markers = s['get_noof_PLU_markers']
noof_SSROs_adwin_LT2 = s['get_noof_SSROs']
s.close()
############################################
### LOADING SSRO DATA###
############################################
fn = os.path.join(
datfolder,
DATFILEBASE + ('-%.' + str(DATIDXDIGITS) + 'd.npz') % DATIDX)
d = np.load(fn)
SSROs_adwin_LT1 = d['adwin_lt1_SSRO']
SSROs_adwin_LT2 = d['adwin_lt2_SSRO']
############################################
### COMPENSATING A MISMATCH IN SSRO DATA ###
############################################
#filling up SSROs_adwin_lt1 with -1 where LT2 missed a PLU
SSROs_adwin_LT1, added_idxs = correct_ssro_mismatch(
SSROs_adwin_LT1, SSROs_adwin_LT2, noof_PLU_markers,
noof_SSROs_adwin_LT1, noof_SSROs_adwin_LT2)
######################################
######################################
######################################
if setup == 'lt2':
CRs_adwin = d['adwin_lt2_CR']
else:
CRs_adwin = d['adwin_lt1_CR']
d.close()
# load HH data
hh_prefiltered, window1, window2 = split(rawfolder, *arg, **kw)
hhpludat = hht3.filter_counts_on_marker(hh_prefiltered, 2, [-1, 0])
np.savez(os.path.join(datfolder, 'hh_prefiltered_events'),
data=hh_prefiltered)
np.savez(os.path.join(datfolder, 'window1_events'), data=window1)
np.savez(os.path.join(datfolder, 'window2_events'), data=window2)
# more preparations
SSROs_adwin_LT1 = SSROs_adwin_LT1[:noof_SSRO_triggers_LT1 + added_idxs]
SSROs_adwin_LT2 = SSROs_adwin_LT2[:noof_PLU_markers]
if setup == 'lt1':
CRs_adwin = CRs_adwin[:noof_SSRO_triggers_LT1]
######################################
######################################
######################################
print 'PLU markers on adwin lt2:', noof_PLU_markers
print '\nLength of ADwin LT1 SSRO array after addition: '\
, len(SSROs_adwin_LT1)
print 'Length of ADwin LT2 SSRO array: ', len(SSROs_adwin_LT2)
######################################
######################################
######################################
### first some sanity checks
invalid_SSROs_adwin = np.where(SSROs_adwin_LT1==-1)[0] \
if setup =='lt1' else np.where(SSROs_adwin_LT2==-1)[0]
print ''
print 'adwin detected SSROs: %d' % \
(noof_SSRO_triggers_LT1 if setup=='lt1' else noof_PLU_markers)
print ' thereof invalid: %d' % len(invalid_SSROs_adwin)
print 'HH SSROs: %d' % len(hhpludat[np.logical_and(hhpludat[:, 3] == 1,
hhpludat[:, 2] == 2)])
print ''
### plot counts
if (kw.get('do_plot', False)):
plot_counts_vs_time(window1, datfolder, window=1)
plot_counts_vs_time(window2, datfolder, window=2)
ret = SSROs_adwin_LT1 if setup == 'lt1' else SSROs_adwin_LT2
return ret
def filter_PLU(data, mchan=2):
filtered = hht3.filter_counts_on_marker(data, mchan, delta_syncs=[0])
return filtered
