def __init__(self, file_name):
self.base_name, ext = os.path.splitext(file_name)
if len(ext) > 0 and ext in (".gz", ".his", ".tgz"):
self.file_type = 'his'
self.data_file = HisFile(file_name)
elif len(ext) > 0 and ext in ".txt":
self.file_type = 'txt'
self.data_file = numpy.loadtxt(file_name)
else:
raise GeneralError(
'Files other than txt, his, tgz and gz are not supported')
def __init__(self, file_name):
self.base_name, ext = os.path.splitext(file_name)
if len(ext) > 0 and ext in (".gz", ".his", ".tgz"):
self.file_type = 'his'
self.data_file = HisFile(file_name)
elif len(ext) > 0 and ext in ".txt":
self.file_type = 'txt'
self.data_file = numpy.loadtxt(file_name)
else:
raise GeneralError(
'Files other than txt, his, tgz and gz are not supported')
class SpectrumParser:
def __init__(self, file_name):
self.base_name, ext = os.path.splitext(file_name)
if len(ext) > 0 and ext in (".gz", ".his", ".tgz"):
self.file_type = 'his'
self.data_file = HisFile(file_name)
elif len(ext) > 0 and ext in ".txt":
self.file_type = 'txt'
self.data_file = numpy.loadtxt(file_name)
else:
raise GeneralError(
'Files other than txt, his, tgz and gz are not supported')
def parse(self, spectrum, show, pause):
spectra_ids = spectrum.get('id')
id_list = []
if self.file_type == 'his':
for element in spectra_ids.split(','):
element = element.split('-')
if len(element) > 1:
new_elements = []
for i in range(int(element[0]), int(element[1]) + 1):
id_list.append(i)
else:
id_list.append(int(element[0]))
elif self.file_type == 'txt':
if spectra_ids != '':
raise GeneralError('Spectrum id not supported for txt files')
else:
id_list.append('')
peaks = spectrum.findall('peak')
x_min = int(spectrum.get('min'))
x_max = int(spectrum.get('max'))
smin = spectrum.get('smin')
smax = spectrum.get('smax')
for spectrum_id in id_list:
plot_name = '{}_{}'.format(self.base_name, spectrum_id)
PF = PeakFitter(peaks, spectrum.get('baseline'), plot_name)
if self.file_type == 'txt':
data_x = self.data_file[x_min:x_max, 0]
data_y = self.data_file[x_min:x_max, 1]
if self.data_file.shape[1] == 2:
data_dy = []
for y in data_y:
dy = numpy.sqrt(y) if y > 0 else 1.0
data_dy.append(dy)
data_dy = numpy.array(data_dy)
else:
data_dy = self.data_file[x_min:x_max, 2]
for iy, y in enumerate(data_dy):
if y <= 0:
data_dy[iy] = 1.0
elif self.file_type == 'his':
data = self.data_file.load_histogram(spectrum_id)
if data[0] != 1:
raise GeneralError('Only 1D histograms are supported')
data_x = data[1][x_min:x_max]
data_y = data[3][x_min:x_max]
data_dy = []
for y in data_y:
dy = numpy.sqrt(y) if y > 0 else 1.0
data_dy.append(dy)
data_dy = numpy.array(data_dy)
if smin is not None and smax is not None:
width = [float(smin), float(smax)]
else:
width = None
fit_result = PF.fit(data_x, data_y, data_dy, width=width)
if show == 'plot' or show == 'svg':
plt.clf()
plt.xlabel('Channel')
plt.ylabel('Counts')
plt.plot(data_x, data_y, linestyle='steps-mid')
plt.plot(data_x, fit_result['baseline'], linestyle='--')
plt.plot(fit_result['x_axis'], fit_result['fit'], linewidth=1.0)
if show == 'svg':
svg_name = 'fit_{0}_{1}_{2}'.format(plot_name,
int(data_x[0]), int(data_x[-1]))
svg_name = svg_name.replace('.', '').\
replace('/', '') + '.svg'
plt.savefig(svg_name)
else:
plt.show()
plt.draw()
time.sleep(pause)
elif show == 'quiet':
pass
for i, peak in enumerate(peaks):
if peak.get('ignore') == 'True':
continue
x0 = PF.params['x{}'.format(i)].value
dx = PF.params['x{}'.format(i)].stderr
A = PF.params['A{}'.format(i)].value
dA = PF.params['A{}'.format(i)].stderr
s = PF.params['s{}'.format(i)].value
E = peaks[i].get('E')
name = peaks[i].get('name')
if name is None:
name = ""
Area = PF.find_area(data_x, i)
print('{:>8} {:>8} {:>8.2f} {:>8.2f}'.\
format(name, E, x0, dx),
'{:>8.1f} {:>8.1f} {:>8.3f} {:>8.1f}'.\
format(A, dA, s, Area))
class SpectrumParser:
def __init__(self, file_name):
self.base_name, ext = os.path.splitext(file_name)
if len(ext) > 0 and ext in (".gz", ".his", ".tgz"):
self.file_type = 'his'
self.data_file = HisFile(file_name)
elif len(ext) > 0 and ext in ".txt":
self.file_type = 'txt'
self.data_file = numpy.loadtxt(file_name)
else:
raise GeneralError(
'Files other than txt, his, tgz and gz are not supported')
def parse(self, spectrum, show, pause):
spectra_ids = spectrum.get('id')
id_list = []
if self.file_type == 'his':
for element in spectra_ids.split(','):
element = element.split('-')
if len(element) > 1:
new_elements = []
for i in range(int(element[0]), int(element[1]) + 1):
id_list.append(i)
else:
id_list.append(int(element[0]))
elif self.file_type == 'txt':
if spectra_ids != '':
raise GeneralError('Spectrum id not supported for txt files')
else:
id_list.append('')
peaks = spectrum.findall('peak')
x_min = int(spectrum.get('min'))
x_max = int(spectrum.get('max'))
smin = spectrum.get('smin')
smax = spectrum.get('smax')
for spectrum_id in id_list:
plot_name = '{}_{}'.format(self.base_name, spectrum_id)
PF = PeakFitter(peaks, spectrum.get('baseline'), plot_name)
if self.file_type == 'txt':
data_x = self.data_file[x_min:x_max, 0]
data_y = self.data_file[x_min:x_max, 1]
data_dy = self.data_file[x_min:x_max, 2]
for iy, y in enumerate(data_dy):
if y <= 0:
data_dy[iy] = 1.0
elif self.file_type == 'his':
data = self.data_file.load_histogram(spectrum_id)
if data[0] != 1:
raise GeneralError('Only 1D histograms are supported')
data_x = data[1][x_min:x_max]
data_y = data[3][x_min:x_max]
data_dy = []
for y in data_y:
dy = numpy.sqrt(y) if y > 0 else 1.0
data_dy.append(dy)
data_dy = numpy.array(data_dy)
if smin is not None and smax is not None:
PF.restrict_width(float(smin), float(smax))
fit_result = PF.fit(data_x, data_y, data_dy, show, pause)
if show == 'plot' or show == 'svg':
plt.clf()
plt.xlabel('Channel')
plt.ylabel('Counts')
plt.plot(data_x, data_y, linestyle='steps-mid')
plt.plot(data_x, fit_result['baseline'], linestyle='--')
plt.plot(fit_result['x_axis'],
fit_result['fit'],
linewidth=1.0)
if show == 'svg':
svg_name = 'fit_{0}_{1}-{2}'.format(
self.plot_name, int(data_x[0]), int(data_x[-1]))
svg_name = svg_name.replace('.', '').\
replace('/', '') + '.svg'
plt.savefig(svg_name)
else:
plt.draw()
time.sleep(pause)
elif show == 'quiet':
pass
for i, peak in enumerate(peaks):
if peak.get('ignore') == 'True':
continue
x0 = PF.params['x{}'.format(i)].value
dx = PF.params['x{}'.format(i)].stderr
A = PF.params['A{}'.format(i)].value
dA = PF.params['A{}'.format(i)].stderr
s = PF.params['s{}'.format(i)].value
E = peaks[i].get('E')
name = peaks[i].get('name')
Area = PF.find_area(data_x, i)
print('{:>8} {:>8} {:>8.2f} {:>8.2f}'.\
format(name, E, x0, dx),
'{:>8.1f} {:>8.1f} {:>8.3f} {:>8.1f}'.\
format(A, dA, s, Area))
