def finalise(self):
"""
Write out the last frame
"""
self.onlast = 1
if self.lastres is not None:
ret = connectedpixels.blob_moments(self.lastres)
def mergelast(self):
"""
Merge the last two images searches
"""
if self.lastnp == "FIRST":
# No previous image available, this was the first
# Swap the blob images
self.lastbl, self.blim = self.blim, self.lastbl
self.lastnp = self.npk
self.lastres = self.res
return
if self.npk > 0 and self.lastnp > 0:
# Thanks to Stine West for finding a bug here
#
self.npk = connectedpixels.bloboverlaps(self.lastbl,
self.lastnp,
self.lastres,
self.blim,
self.npk,
self.res,
self.verbose)
if self.lastnp > 0:
# Fill out the moments of the "closed" peaks
# print "calling blobmoments with",self.lastres
ret = connectedpixels.blob_moments(self.lastres[:self.lastnp])
# lastres is now moved forward into res
self.lastnp = self.npk # This is array dim
if self.npk > 0:
self.lastres = self.res[:self.npk] # free old lastres I hope
else:
self.lastres = None
# Also swap the blob images
self.lastbl, self.blim = self.blim, self.lastbl
def output2dpeaks(self):
"""
Write something compatible with the old ImageD11 format
which fabian is reading.
This is called before mergelast, so we write self.npk/self.res
"""
ret = connectedpixels.blob_moments(self.res)
for i in self.res[:self.npk]:
if i[s_1] < 0.1:
raise Exception("Empty peak on current frame")
i[s_cen], i[f_cen] = self.corrector.correct(i[s_raw], i[f_raw])
def find_peaks(group, threshold=None, z_min=None, z_max=None):
field = group.nxsignal
try:
mask = field.nxentry['instrument/detector/pixel_mask'].nxdata
if len(mask.shape) > 2:
mask = mask[0]
except Exception:
mask = None
if threshold is None:
if 'maximum' in field.nxgroup.attrs:
threshold = np.float32(field.nxgroup.maximum) / 20
elif 'maximum' in field.attrs:
threshold = np.float32(field.maximum) / 20
else:
raise NeXusError('Must give threshold if the field maximum is unknown')
if z_min == None:
z_min = 0
if z_max == None:
z_max = field.shape[0]
lio = labelimage(field.shape[-2:], flipper=flip1)
allpeaks = []
if len(field.shape) == 2:
res = None
else:
chunk_size = field.nxfile[field.nxpath].chunks[0]
pixel_tolerance = 50
frame_tolerance = 10
for i in range(0, field.shape[0], chunk_size):
try:
if i + chunk_size > z_min and i < z_max:
print 'Processing', i
v = field[i:i+chunk_size,:,:].nxdata
for j in range(chunk_size):
if i+j >= z_min and i+j <= z_max:
omega = np.float32(i+j)
lio.peaksearch(v[j], threshold, omega)
if lio.res is not None:
blob_moments(lio.res)
for k in range(lio.res.shape[0]):
res = lio.res[k]
peak = NXpeak(res[0], res[22],
res[23], res[24], omega,
res[27], res[26], res[29],
threshold,
pixel_tolerance,
frame_tolerance)
if peak.isvalid(mask):
allpeaks.append(peak)
except IndexError as error:
pass
if not allpeaks:
raise NeXusError('No peaks found')
allpeaks = sorted(allpeaks)
merged_peaks = []
for z in range(z_min, z_max+1):
frame = [peak for peak in allpeaks if peak.z == z]
if not merged_peaks:
merged_peaks.extend(frame)
else:
for peak1 in frame:
combined = False
for peak2 in last_frame:
if peak1 == peak2:
for idx in range(len(merged_peaks)):
if peak1 == merged_peaks[idx]:
break
peak1.combine(merged_peaks[idx])
merged_peaks[idx] = peak1
combined = True
break
if not combined:
reversed_peaks = [p for p in reversed(merged_peaks)
if p.z >= peak1.z - frame_tolerance]
for peak2 in reversed_peaks:
if peak1 == peak2:
for idx in range(len(merged_peaks)):
if peak1 == merged_peaks[idx]:
break
peak1.combine(merged_peaks[idx])
merged_peaks[idx] = peak1
combined = True
break
if not combined:
merged_peaks.append(peak1)
if frame:
last_frame = frame
merged_peaks = sorted(merged_peaks)
for peak in merged_peaks:
peak.merge()
merged_peaks = sorted(merged_peaks)
peaks = merged_peaks
print '%s peaks found' % len(peaks)
if len(peaks) > 0:
write_peaks(field, peaks)
def find_peaks(self):
field = self.entry["data"].nxsignal
try:
self.mask = self.entry["instrument/detector/pixel_mask"]
except NeXusError:
self.mask = None
self.layout.removeWidget(self.find_button)
self.find_button.setVisible(False)
if len(field.shape) == 2:
self.layout.addWidget(self.close_buttons(save=True))
elif len(field.shape) > 2:
self.layout.addLayout(self.progress_layout(save=True))
threshold = self.get_threshold()
self.blim = np.zeros(field.shape[-2:], np.int32)
self.verbose = 0
lio = labelimage(field.shape[-2:], flipper=flip1)
allpeaks = []
if len(field.shape) == 2:
res = None
else:
chunk_size = field.nxfile[field.nxpath].chunks[0]
z_min, z_max = self.get_limits()
pixel_tolerance, frame_tolerance = self.get_tolerance()
self.progress_bar.setRange(z_min, z_max)
for i in range(0, field.shape[0], chunk_size):
try:
if i + chunk_size > z_min and i < z_max:
self.progress_bar.setValue(i)
self.update_progress()
v = field[i : i + chunk_size, :, :].nxdata
for j in range(chunk_size):
if i + j >= z_min and i + j <= z_max:
omega = np.float32(i + j)
lio.peaksearch(v[j], threshold, omega)
if lio.res is not None:
blob_moments(lio.res)
for k in range(lio.res.shape[0]):
res = lio.res[k]
peak = NXpeak(
res[0],
res[22],
res[23],
res[24],
omega,
res[27],
res[26],
res[29],
threshold,
pixel_tolerance,
frame_tolerance,
)
if peak.isvalid(self.mask):
allpeaks.append(peak)
except IndexError as error:
pass
if not allpeaks:
self.reject()
report_error("Finding peaks", "No peaks found")
allpeaks = sorted(allpeaks)
self.progress_bar.reset()
self.progress_bar.setRange(z_min, z_max)
merged_peaks = []
for z in range(z_min, z_max + 1):
self.progress_bar.setValue(z)
self.update_progress()
frame = [peak for peak in allpeaks if peak.z == z]
if not merged_peaks:
merged_peaks.extend(frame)
else:
for peak1 in frame:
combined = False
for peak2 in last_frame:
if peak1 == peak2:
for idx in range(len(merged_peaks)):
if peak1 == merged_peaks[idx]:
break
peak1.combine(merged_peaks[idx])
merged_peaks[idx] = peak1
combined = True
break
if not combined:
reversed_peaks = [p for p in reversed(merged_peaks) if p.z >= peak1.z - frame_tolerance]
for peak2 in reversed_peaks:
if peak1 == peak2:
for idx in range(len(merged_peaks)):
if peak1 == merged_peaks[idx]:
break
peak1.combine(merged_peaks[idx])
merged_peaks[idx] = peak1
combined = True
break
if not combined:
merged_peaks.append(peak1)
if frame:
last_frame = frame
merged_peaks = sorted(merged_peaks)
for peak in merged_peaks:
peak.merge()
merged_peaks = sorted(merged_peaks)
self.peaks = merged_peaks
self.progress_bar.setVisible(False)
self.peak_count.setText("%s peaks found" % len(self.peaks))
self.peak_count.setVisible(True)
