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CBP branch #99

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3799801
add amplitude errors in output
jeremyneveu Jul 3, 2022
e630075
update HGAR lines dublets
jeremyneveu Mar 30, 2023
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4 changes: 0 additions & 4 deletions spectractor/extractor/dispersers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -366,16 +366,12 @@ def load_files(self, verbose=False):
a = np.loadtxt(filename)
self.N_input = a[0]
self.N_err = a[1]
else:
raise FileNotFoundError(f"Failed to load {filename} for {self.label}")

filename = os.path.join(self.data_dir, self.label, "full_name.txt")
if os.path.isfile(filename):
with open(filename, 'r') as f:
for line in f: # MFL: you really just want the last line of the file?
self.full_name = line.rstrip('\n')
else:
raise FileNotFoundError(f"Failed to load {filename} for {self.label}")

filename = os.path.join(self.data_dir, self.label, "transmission.txt")
if os.path.isfile(filename):
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19 changes: 12 additions & 7 deletions spectractor/extractor/spectroscopy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -472,22 +472,24 @@ def print_detected_lines(self, output_file_name="", overwrite=False, print_table
popt = line.fit_popt
peak_pos = popt[bgd_npar + 3 * j + 1]
FWHM = np.abs(popt[bgd_npar + 3 * j + 2]) * 2.355
signal_level = popt[bgd_npar + 3 * j]
err = np.sqrt(line.fit_pcov[bgd_npar + 3 * j + 1, bgd_npar + 3 * j + 1])
amplitude = popt[bgd_npar + 3 * j]
detected_err = np.sqrt(line.fit_pcov[bgd_npar + 3 * j + 1, bgd_npar + 3 * j + 1])
amplitude_err = np.sqrt(line.fit_pcov[bgd_npar + 3 * j, bgd_npar + 3 * j])
if line.high_snr:
rows.append((line.label, line.wavelength, peak_pos, peak_pos - line.wavelength, err,
FWHM, signal_level, line.fit_snr, line.fit_chisq, line.fit_eqwidth_mod,
rows.append((line.label, line.wavelength, peak_pos, peak_pos - line.wavelength, detected_err,
FWHM, amplitude, amplitude_err, line.fit_snr, line.fit_chisq, line.fit_eqwidth_mod,
line.fit_eqwidth_data))
j += 1
t = None
if len(rows) > 0:
t = Table(rows=rows, names=(
'Line', 'Tabulated', 'Detected', 'Shift', 'Err', 'FWHM', 'Amplitude', 'SNR', 'Chisq', 'Eqwidth_mod',
'Line', 'Tabulated', 'Detected', 'Shift', 'Detected_err', 'FWHM', 'Amplitude', 'Amplitude_err', 'SNR', 'Chisq', 'Eqwidth_mod',
'Eqwidth_data'),
dtype=('a12', 'f4', 'f4', 'f4', 'f4', 'f4', 'f4', 'f4', 'f4', 'f4', 'f4'))
dtype=('a12', 'f4', 'f4', 'f4', 'f4', 'f4', 'f4', 'f4', 'f4', 'f4', 'f4', 'f4'))
for col in t.colnames[1:6]:
t[col].unit = 'nm'
t[t.colnames[5]].unit = amplitude_units
t[t.colnames[6]].unit = amplitude_units
for col in t.colnames[-2:]:
t[col].unit = 'nm'
t[t.colnames[-3]].unit = 'reduced'
Expand Down Expand Up @@ -598,13 +600,16 @@ def print_detected_lines(self, output_file_name="", overwrite=False, print_table
AR4 = Line(727.294, atmospheric=False, label=r'$Ar$', label_pos=[0.007, 0.02])
AR5 = Line(738.393, atmospheric=False, label=r'$Ar$', label_pos=[0.007, 0.02])
AR6 = Line(750.387, atmospheric=False, label=r'$Ar$', label_pos=[0.007, 0.02])
AR6_2 = Line(751.465, atmospheric=False, label=r'$Ar$', label_pos=[0.007, 0.02])
AR7 = Line(763.511, atmospheric=False, label=r'$Ar$', label_pos=[0.007, 0.02])
AR8 = Line(772.376, atmospheric=False, label=r'$Ar$', label_pos=[0.007, 0.02])
AR9 = Line(794.818, atmospheric=False, label=r'$Ar$', label_pos=[0.007, 0.02])
AR10 = Line(800.616, atmospheric=False, label=r'$Ar$', label_pos=[0.007, 0.02])
AR10_2 = Line(801.479, atmospheric=False, label=r'$Ar$', label_pos=[0.007, 0.02])
AR11 = Line(811.531, atmospheric=False, label=r'$Ar$', label_pos=[0.007, 0.02])
AR12 = Line(826.452, atmospheric=False, label=r'$Ar$', label_pos=[0.007, 0.02])
AR13 = Line(842.465, atmospheric=False, label=r'$Ar$', label_pos=[0.007, 0.02])
AR13_2 = Line(840.621, atmospheric=False, label=r'$Ar$', label_pos=[0.007, 0.02])
AR14 = Line(852.144, atmospheric=False, label=r'$Ar$', label_pos=[0.007, 0.02])
AR15 = Line(866.794, atmospheric=False, label=r'$Ar$', label_pos=[0.007, 0.02])
AR16 = Line(912.297, atmospheric=False, label=r'$Ar$', label_pos=[0.007, 0.02])
Expand All @@ -614,7 +619,7 @@ def print_detected_lines(self, output_file_name="", overwrite=False, print_table
HG13 = Line(1013.976, atmospheric=False, label=r'$Hg$', label_pos=[0.007, 0.02])

HGAR_LINES = [HG1, HG2, HG3, HG4, HG5, HG6, HG7, HG8, HG9, HG10, HG11, HG12,
AR1, AR2, AR3, AR4, AR5, AR6, AR7, AR8, AR9, AR10, AR11, AR12, AR13, AR14, AR15, AR16, AR17, AR18, AR19, HG13]
AR1, AR2, AR3, AR4, AR5, AR6, AR6_2, AR7, AR8, AR9, AR10, AR10_2, AR11, AR12, AR13_2, AR13, AR14, AR15, AR16, AR17, AR18, AR19, HG13]

if __name__ == "__main__":
import doctest
Expand Down