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Merge pull request #5 from rasmusthog/rasmus_pyfai

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Add option to use mask with pyfai-integrations
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Rasmus Vester Thøgersen 2022-06-13 09:06:15 +00:00 • committed by GitHub
commit a7f6abe0b9
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1 changed files with 14 additions and 4 deletions
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18
nafuma/xrd/io.py
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@ -40,12 +40,13 @@ def integrate_1d(data, options={}, index=0):
df: DataFrame contianing 1D diffractogram if option 'return' is True df: DataFrame contianing 1D diffractogram if option 'return' is True
''' '''
required_options = ['unit', 'nbins', 'save', 'save_filename', 'save_extension', 'save_folder', 'overwrite', 'extract_folder'] required_options = ['unit', 'npt', 'save', 'save_filename', 'save_extension', 'save_folder', 'overwrite', 'extract_folder', 'error_model']
default_options = { default_options = {
'unit': '2th_deg', 'unit': '2th_deg',
'nbins': 3000, 'npt': 3000,
'extract_folder': 'tmp', 'extract_folder': 'tmp',
'error_model': None,
'save': False, 'save': False,
'save_filename': None, 'save_filename': None,
'save_extension': '_integrated.xy', 'save_extension': '_integrated.xy',
@ -61,6 +62,13 @@ def integrate_1d(data, options={}, index=0):
# Get image array from filename if not passed # Get image array from filename if not passed
if 'image' not in data.keys() or not data['image']: if 'image' not in data.keys() or not data['image']:
data['image'] = get_image_array(data['path'][index]) data['image'] = get_image_array(data['path'][index])
# Load mask
if 'mask' in data.keys():
mask = get_image_array(data['mask'])
else:
mask = None
# Instanciate the azimuthal integrator from pyFAI from the calibrant (.poni-file) # Instanciate the azimuthal integrator from pyFAI from the calibrant (.poni-file)
@ -76,8 +84,10 @@ def integrate_1d(data, options={}, index=0):
if not os.path.isdir(options['save_folder']): if not os.path.isdir(options['save_folder']):
os.makedirs(options['save_folder']) os.makedirs(options['save_folder'])
res = ai.integrate1d(data['image'], options['nbins'], unit=options['unit'], filename=filename)
res = ai.integrate1d(data['image'], npt=options['npt'], mask=mask, error_model=options['error_model'], unit=options['unit'], filename=filename)
data['path'][index] = filename data['path'][index] = filename
diffractogram, _ = read_xy(data=data, options=options, index=index) diffractogram, _ = read_xy(data=data, options=options, index=index)
@ -312,7 +322,7 @@ def read_xy(data, options={}, index=0):
#if 'wavelength' not in data.keys(): #if 'wavelength' not in data.keys():
# Get wavelength from scan # Get wavelength from scan
if not data['wavelength'][index]: if not 'wavelength' in data.keys() or data['wavelength'][index]:
wavelength = find_wavelength_from_xy(path=data['path'][index]) wavelength = find_wavelength_from_xy(path=data['path'][index])
else: else:
wavelength = data['wavelength'][index] wavelength = data['wavelength'][index]