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Fix arcsin issue and allow plotting w/o reflection data

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This commit is contained in:
rasmusvt 2022-05-19 21:32:10 +02:00
parent 55b22d5bf1
commit da8907083b
2 changed files with 52 additions and 15 deletions
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42
nafuma/xrd/io.py
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@ -80,7 +80,8 @@ def integrate_1d(data, options={}, index=0):
res = ai.integrate1d(data['image'], options['nbins'], unit=options['unit'], filename=filename)
data['path'][index] = filename
diffractogram, wavelength = read_xy(data=data, options=options, index=index)
diffractogram, _ = read_xy(data=data, options=options, index=index)
wavelength = find_wavelength_from_poni(path=data['calibrant'])
if not options['save']:
os.remove(filename)
@ -282,8 +283,12 @@ def read_brml(data, options={}, index=0):
#if 'wavelength' not in data.keys():
# Find wavelength
for chain in root.findall('./FixedInformation/Instrument/PrimaryTracks/TrackInfoData/MountedOptics/InfoData/Tube/WaveLengthAlpha1'):
wavelength = float(chain.attrib['Value'])
if not data['wavelength'][index]:
for chain in root.findall('./FixedInformation/Instrument/PrimaryTracks/TrackInfoData/MountedOptics/InfoData/Tube/WaveLengthAlpha1'):
wavelength = float(chain.attrib['Value'])
else:
wavelength = data['wavelength'][index]
diffractogram = pd.DataFrame(diffractogram)
@ -306,7 +311,11 @@ def read_xy(data, options={}, index=0):
#if 'wavelength' not in data.keys():
# Get wavelength from scan
wavelength = find_wavelength_from_xy(path=data['path'][index])
if not data['wavelength'][index]:
wavelength = find_wavelength_from_xy(path=data['path'][index])
else:
wavelength = data['wavelength'][index]
with open(data['path'][index], 'r') as f:
position = 0
@ -378,7 +387,7 @@ def read_data(data, options={}, index=0):
if options['offset'] or options['normalise']:
# Make copy of the original intensities before any changes are made through normalisation or offset, to easily revert back if need to update.
diffractogram['I_org'] = diffractogram['I']
@ -387,6 +396,7 @@ def read_data(data, options={}, index=0):
diffractogram = apply_offset(diffractogram, wavelength, index, options)
diffractogram = translate_wavelengths(data=diffractogram, wavelength=wavelength)
return diffractogram, wavelength
@ -506,7 +516,7 @@ def translate_wavelengths(data: pd.DataFrame, wavelength: float, to_wavelength=N
data['2th_cuka'] = np.NAN
data['2th_cuka'].loc[data['2th'] <= max_2th_cuka] = 2*np.arcsin(cuka/wavelength * np.sin((data['2th']/2) * np.pi/180)) * 180/np.pi
data['2th_cuka'].loc[data['2th'] <= max_2th_cuka] = 2*np.arcsin(cuka/wavelength * np.sin((data['2th'].loc[data['2th'] <= max_2th_cuka]/2) * np.pi/180)) * 180/np.pi
# Translate to MoKalpha
moka = 0.71073 # Å
@ -518,7 +528,7 @@ def translate_wavelengths(data: pd.DataFrame, wavelength: float, to_wavelength=N
data['2th_moka'] = np.NAN
data['2th_moka'].loc[data['2th'] <= max_2th_moka] = 2*np.arcsin(moka/wavelength * np.sin((data['2th']/2) * np.pi/180)) * 180/np.pi
data['2th_moka'].loc[data['2th'] <= max_2th_moka] = 2*np.arcsin(moka/wavelength * np.sin((data['2th'].loc[data['2th'] <= max_2th_moka]/2) * np.pi/180)) * 180/np.pi
# Convert to other parameters
@ -537,7 +547,7 @@ def translate_wavelengths(data: pd.DataFrame, wavelength: float, to_wavelength=N
data['2th'] = np.NAN
data['2th'].loc[data['2th_cuka'] <= max_2th] = 2*np.arcsin(to_wavelength/cuka * np.sin((data['2th_cuka']/2) * np.pi/180)) * 180/np.pi
data['2th'].loc[data['2th_cuka'] <= max_2th] = 2*np.arcsin(to_wavelength/cuka * np.sin((data['2th_cuka'].loc[data['2th_cuka'] <= max_2th]/2) * np.pi/180)) * 180/np.pi
@ -564,6 +574,22 @@ def find_wavelength_from_xy(path):
elif 'Wavelength' in line:
wavelength = float(line.split()[2])*10**10
else:
wavelength = None
return wavelength
def find_wavelength_from_poni(path):
with open(path, 'r') as f:
lines = f.readlines()
for line in lines:
if 'Wavelength' in line:
wavelength = float(line.split()[-1])*10**10
return wavelength