def get_mca(self, mca=1, with_rois=True):
if self._xsp3 is None:
self.connect()
time.sleep(0.5)
emca = self._xsp3.mcas[mca - 1]
if with_rois:
emca.get_rois()
counts = self.get_array(mca=mca)
if max(counts) < 1.0:
counts = 0.5 * np.ones(len(counts))
counts[0] = 2.0
thismca = MCA(counts=counts, offset=0.0, slope=0.01)
thismca.energy = self.get_energy()
thismca.counts = counts
thismca.quad = 0.0
thismca.rois = []
if with_rois:
for eroi in emca.rois:
thismca.rois.append(
ROI(name=eroi.name,
address=eroi._prefix,
left=eroi.left,
right=eroi.right))
return thismca
def get_mca(self, mca=1, with_rois=True):
if self._xsp3 is None:
self.connect()
time.sleep(0.5)
emca = self._xsp3.mcas[mca-1]
if with_rois:
emca.get_rois()
counts = self.get_array(mca=mca)
if max(counts) < 1.0:
counts = 0.5*np.ones(len(counts))
counts[0] = 2.0
thismca = MCA(counts=counts, offset=0.0, slope=0.01)
thismca.energy = self.get_energy()
thismca.counts = counts
thismca.quad = 0.0
thismca.rois = []
if with_rois:
for eroi in emca.rois:
thismca.rois.append(ROI(name=eroi.name, address=eroi._prefix,
left=eroi.left, right=eroi.right))
return thismca
def get_mca(self, mca=1, with_rois=True):
"""return an MCA object """
emca = self._xmap.mcas[mca - 1]
if with_rois:
emca.get_rois()
counts = self.get_array(mca=mca)
if max(counts) < 1.0:
counts = 0.5 * np.ones(len(counts))
counts[0] = 2.0
thismca = MCA(counts=counts, offset=emca.CALO, slope=emca.CALS)
thismca.energy = emca.get_energy()
thismca.counts = counts
thismca.real_time = emca.ERTM
thismca.live_time = emca.ELTM
thismca.rois = []
if with_rois:
for eroi in emca.rois:
thismca.rois.append(
ROI(name=eroi.NM,
address=eroi.address,
left=eroi.LO,
right=eroi.HI))
return thismca
def get_mca(self, mca=1, with_rois=True):
"""return an MCA object """
emca = self._xmap.mcas[mca-1]
if with_rois:
emca.get_rois()
counts = self.get_array(mca=mca)
if max(counts) < 1.0:
counts = 0.5*np.ones(len(counts))
counts[0] = 2.0
thismca = MCA(counts=counts, offset=emca.CALO, slope=emca.CALS)
thismca.energy = emca.get_energy()
thismca.counts = counts
thismca.real_time = emca.ERTM
thismca.live_time = emca.ELTM
thismca.rois = []
if with_rois:
for eroi in emca.rois:
thismca.rois.append(ROI(name=eroi.NM, address=eroi.address,
left=eroi.LO, right=eroi.HI))
return thismca
def read(self, filename=None, bad=None):
"""read GSE MCA file"""
self.filename = filename
if bad is None:
bad = self.bad
fh = open(filename)
lines = fh.readlines()
fh.close()
nrow = 0
data_mode = 'HEADER'
counts = []
rois = []
environ = []
head = self.header = GSEMCA_Header()
for l in lines:
l = l.strip()
if len(l) < 1: continue
if data_mode == 'DATA':
counts.append(str2ints(l))
else:
pos = l.find(' ')
if (pos == -1): pos = len(l)
tag = l[0:pos].strip().lower()
if tag.endswith(':'):
tag = tag[:-1]
val = l[pos:len(l)].strip()
if tag in ('version', 'date'):
setattr(head, tag, val)
elif tag in ('elements', 'channels'):
setattr(head, tag, int(val))
elif tag in ('real_time', 'live_time', 'cal_offset',
'cal_slope', 'cal_quad'):
setattr(head, tag, str2floats(val))
elif tag == 'rois':
head.rois = str2ints(val)
self.nrois = max(head.rois)
elif tag == 'data':
data_mode = 'DATA'
elif tag == 'environment':
addr, val = val.split('="')
val, desc = val.split('"')
val = val.strip()
desc = desc.strip()
if desc.startswith('(') and desc.endswith(')'):
desc = desc[1:-1]
environ.append((desc, val, addr))
elif tag[0:4] == 'roi_':
iroi, item = tag[4:].split('_')
iroi = int(iroi)
if iroi >= len(rois):
for ir in range(1 + iroi - len(rois)):
rois.append({'label': [], 'right': [], 'left': []})
if item == "label":
rois[iroi]['label'] = str2str(val, delim='&')
elif item == "left":
rois[iroi]['left'] = str2ints(val)
elif item == "right":
rois[iroi]['right'] = str2ints(val)
else:
pass # print(" Warning: " , tag, " is not supported here!")
#
counts = np.array(counts)
## Data has been read, now store in MCA objects
sum_mca = None
for tag in ('real_time', 'live_time', 'cal_offset', 'cal_slope',
'cal_quad'):
val = getattr(head, tag)
# print( ' Attr ', tag, val)
if len(val) == 1 and head.elements > 1:
val = [val[0]] * head.elements
setattr(head, tag, val)
for imca in range(head.elements):
thismca = MCA(name='mca%i' % (imca + 1),
nchans=head.channels,
counts=counts[:, imca],
start_time=head.date,
offset=head.cal_offset[imca],
slope=head.cal_slope[imca],
quad=head.cal_quad[imca],
real_time=head.real_time[imca],
live_time=head.live_time[imca])
for desc, val, addr in environ:
thismca.add_environ(desc=desc, val=val, addr=addr)
for roi in rois:
left = roi['left'][imca]
right = roi['right'][imca]
label = roi['label'][imca]
if right > 1 and len(label) > 1:
thismca.add_roi(name=label,
left=left,
right=right,
sort=False,
counts=counts[:, imca])
thismca.rois.sort()
self.mcas.append(thismca)
mca0 = self.__get_mca0()
self.counts = self.get_counts()
self.raw = self.get_counts(dt_correct=False)
self.name = 'mcasum'
self.energy = mca0.energy[:]
self.environ = mca0.environ
self.real_time = mca0.real_time
self.live_time = mca0.live_time
self.offset = mca0.offset
self.slope = mca0.slope
self.quad = mca0.quad
self.rois = []
for roi in mca0.rois:
self.add_roi(name=roi.name,
left=roi.left,
right=roi.right,
sort=False,
counts=counts,
to_mcas=False)
self.rois.sort()
return
def read(self, filename=None, bad=None):
"""read GSE MCA file"""
self.filename = filename
if bad is None:
bad = self.bad
fh = open(filename)
lines = fh.readlines()
fh.close()
nrow = 0
data_mode = 'HEADER'
counts = []
rois = []
environ = []
head = self.header = GSEMCA_Header()
for l in lines:
l = l.strip()
if len(l) < 1: continue
if data_mode == 'DATA':
counts.append(str2ints(l))
else:
pos = l.find(' ')
if (pos == -1): pos = len(l)
tag = l[0:pos].strip().lower()
if tag.endswith(':'):
tag = tag[:-1]
val = l[pos:len(l)].strip()
if tag in ('version', 'date'):
setattr(head, tag, val)
elif tag in ('elements', 'channels'):
setattr(head, tag, int(val))
elif tag in ('real_time', 'live_time', 'cal_offset',
'cal_slope', 'cal_quad'):
setattr(head, tag, str2floats(val))
elif tag == 'rois':
head.rois = str2ints(val)
self.nrois = max(head.rois)
elif tag == 'data':
data_mode = 'DATA'
elif tag == 'environment':
addr, val = val.split('="')
val, desc = val.split('"')
val = val.strip()
desc = desc.strip()
if desc.startswith('(') and desc.endswith(')'):
desc = desc[1:-1]
environ.append((desc, val, addr))
elif tag[0:4] == 'roi_':
iroi, item = tag[4:].split('_')
iroi = int(iroi)
if iroi >= len(rois):
for ir in range(1 + iroi - len(rois)):
rois.append({'label':[], 'right':[], 'left':[]})
if item == "label":
rois[iroi]['label'] = str2str(val, delim='&')
elif item == "left":
rois[iroi]['left'] = str2ints(val)
elif item == "right":
rois[iroi]['right'] = str2ints(val)
else:
pass # print(" Warning: " , tag, " is not supported here!")
#
counts = np.array(counts)
## Data has been read, now store in MCA objects
sum_mca = None
for tag in ('real_time', 'live_time', 'cal_offset',
'cal_slope', 'cal_quad'):
val = getattr(head, tag)
# print( ' Attr ', tag, val)
if len(val) == 1 and head.elements > 1:
val = [val[0]]*head.elements
setattr(head, tag, val)
for imca in range(head.elements):
thismca = MCA(name='mca%i' % (imca+1),
nchans=head.channels,
counts=counts[:,imca],
start_time=head.date,
offset=head.cal_offset[imca],
slope=head.cal_slope[imca],
quad=head.cal_quad[imca],
real_time=head.real_time[imca],
live_time=head.live_time[imca])
for desc, val, addr in environ:
thismca.add_environ(desc=desc, val=val, addr=addr)
for roi in rois:
left = roi['left'][imca]
right = roi['right'][imca]
label = roi['label'][imca]
if right > 1 and len(label) > 1:
thismca.add_roi(name=label, left=left, right=right,
sort=False, counts=counts[:,imca])
thismca.rois.sort()
self.mcas.append(thismca)
mca0 = self.__get_mca0()
self.counts = self.get_counts()
self.raw = self.get_counts(dt_correct=False)
self.name = 'mcasum'
self.energy = mca0.energy[:]
self.environ = mca0.environ
self.real_time = mca0.real_time
self.live_time = mca0.live_time
self.offset = mca0.offset
self.slope = mca0.slope
self.quad = mca0.quad
self.rois = []
for roi in mca0.rois:
self.add_roi(name=roi.name, left=roi.left,
right=roi.right, sort=False,
counts=counts, to_mcas=False)
self.rois.sort()
return
