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Change plotting method to allow for multiple diffractograms

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This commit is contained in:
rasmusvt 2022-03-22 19:57:21 +01:00
parent 9bb52fe819
commit da2b2f855b
3 changed files with 124 additions and 51 deletions
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77
beamtime/xrd/io.py
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@ -27,7 +27,7 @@ def get_image_headers(path):
return image.header
def integrate_1d(data, options={}):
def integrate_1d(data, options={}, index=0):
''' Integrates an image file to a 1D diffractogram.
Required content of data:
@ -51,11 +51,14 @@ def integrate_1d(data, options={}):
'overwrite': False}
options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
if not isinstance(data['path'], list):
data['path'] = [data['path']]
# Get image array from filename if not passed
if 'image' not in data.keys():
data['image'] = get_image_array(data['path'])
data['image'] = get_image_array(data['path'][index])
# Instanciate the azimuthal integrator from pyFAI from the calibrant (.poni-file)
ai = pyFAI.load(data['calibrant'])
@ -70,18 +73,18 @@ def integrate_1d(data, options={}):
res = ai.integrate1d(data['image'], data['nbins'], unit=options['unit'], filename=filename)
data['path'] = filename
diffractogram = read_xy(data=data, options=options)
data['path'][index] = filename
diffractogram, wavelength = read_xy(data=data, options=options)
if not options['save']:
os.remove(filename)
shutil.rmtree('tmp')
return diffractogram
return diffractogram, wavelength
def make_filename(data, options):
def make_filename(options, path=None):
# Define save location for integrated diffractogram data
if not options['save']:
@ -93,7 +96,7 @@ def make_filename(data, options):
# Case 1: No filename is given.
if not options['save_filename']:
# If a path is given instead of an image array, the path is taken as the trunk of the savename
if data['path']:
if path:
# Make filename by joining the save_folder, the filename (with extension deleted) and adding the save_extension
filename = os.path.join(options['save_folder'], os.path.split(data['path'])[-1].split('.')[0] + options['save_extension'])
else:
@ -176,12 +179,12 @@ def view_integrator(calibrant):
def read_brml(data, options={}):
def read_brml(data, options={}, index=0):
required_options = ['extract_folder', 'save_folder']
default_options = {
'extract_folder': 'tmp',
'extract_folder': 'tmp/',
'save_folder': None
}
@ -194,7 +197,7 @@ def read_brml(data, options={}):
# Extract the RawData0.xml file from the brml-file
with zipfile.ZipFile(data['path'], 'r') as brml:
with zipfile.ZipFile(data['path'][index], 'r') as brml:
for info in brml.infolist():
if "RawData" in info.filename:
brml.extract(info.filename, options['extract_folder'])
@ -233,9 +236,10 @@ def read_brml(data, options={}):
diffractogram.append({'2th': twotheta, 'I': intensity})
if 'wavelength' not in data.keys():
for chain in root.findall('./FixedInformation/Instrument/PrimaryTracks/TrackInfoData/MountedOptics/InfoData/Tube/WaveLengthAlpha1'):
data['wavelength'] = float(chain.attrib['Value'])
#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'])
diffractogram = pd.DataFrame(diffractogram)
@ -249,15 +253,16 @@ def read_brml(data, options={}):
return diffractogram
return diffractogram, wavelength
def read_xy(data, options={}):
def read_xy(data, options={}, index=0):
if 'wavelength' not in data.keys():
find_wavelength_from_xy(data=data)
#if 'wavelength' not in data.keys():
# Get wavelength from scan
wavelength = find_wavelength_from_xy(path=data['path'][index])
with open(data['path'], 'r') as f:
with open(data['path'][index], 'r') as f:
position = 0
current_line = f.readline()
@ -276,37 +281,37 @@ def read_xy(data, options={}):
diffractogram.columns = ['2th', 'I', 'sigma']
return diffractogram
return diffractogram, wavelength
def read_data(data, options={}):
def read_data(data, options={}, index=0):
beamline_extensions = ['mar3450', 'edf', 'cbf']
file_extension = data['path'].split('.')[-1]
file_extension = data['path'][index].split('.')[-1]
if file_extension in beamline_extensions:
diffractogram = integrate_1d(data=data, options=options)
diffractogram, wavelength = integrate_1d(data=data, options=options, index=index)
elif file_extension == 'brml':
diffractogram = read_brml(data=data, options=options)
diffractogram, wavelength = read_brml(data=data, options=options, index=index)
elif file_extension in['xy', 'xye']:
diffractogram = read_xy(data=data, options=options)
diffractogram, wavelength = read_xy(data=data, options=options, index=index)
diffractogram = translate_wavelengths(data=diffractogram, wavelength=data['wavelength'])
diffractogram = translate_wavelengths(data=diffractogram, wavelength=wavelength)
return diffractogram
return diffractogram, wavelength
def load_reflection_table(data, options={}):
required_options = ['wavelength', 'to_wavelength']
required_options = ['ref_wavelength', 'to_wavelength']
default_options = {
'wavelength': 1.54059,
'ref_wavelength': 1.54059,
'to_wavelength': None
}
@ -333,7 +338,7 @@ def load_reflection_table(data, options={}):
# Set the new modified headers as the headers of
reflections.columns = headers
reflections = translate_wavelengths(data=reflections, wavelength=options['wavelength'], to_wavelength=options['to_wavelength'])
reflections = translate_wavelengths(data=reflections, wavelength=options['ref_wavelength'], to_wavelength=options['to_wavelength'])
#print(reflections)
@ -378,6 +383,7 @@ def translate_wavelengths(data, wavelength, to_wavelength=None):
if to_wavelength:
if to_wavelength > cuka:
max_2th = 2*np.arcsin(cuka/to_wavelength) * 180/np.pi
@ -395,19 +401,24 @@ def translate_wavelengths(data, wavelength, to_wavelength=None):
def find_wavelength_from_xy(data):
def find_wavelength_from_xy(path):
wavelength_dict = {'Cu': 1.54059, 'Mo': 0.71073}
with open(data['path'], 'r') as f:
with open(path, 'r') as f:
lines = f.readlines()
for line in lines:
# For .xy-files output from EVA
if 'Anode' in line:
anode = line.split()[8].strip('"')
data['wavelength'] = wavelength_dict[anode]
wavelength = wavelength_dict[anode]
# For .xy-files output from pyFAI integration
elif 'Wavelength' in line:
data['wavelength'] = float(line.split()[2])*10**10
wavelength = float(line.split()[2])*10**10
return wavelength