rasmus/nafuma
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Open beamline data straight from raw file

Browse source
This commit is contained in:
rasmusvt 2022-03-15 17:13:17 +01:00
parent 1126809c5a
commit ebb98debff
2 changed files with 29 additions and 26 deletions
Download patch file Download diff file Expand all files Collapse all files

49
beamtime/xrd/io.py
View file

@ -23,15 +23,14 @@ def get_image_headers(path):
return image.header
def integrate_1d(calibrant, bins, path=None, image=None, options=None):
def integrate_1d(data, options={}):
''' Integrates an image file to a 1D diffractogram.
Input:
calibrant: path to .poni-file
bins: Number of bins to divide image into
path (optional): path to image file - either this or image must be specified. If both is passed, image is prioritsed
image (optional): image array (Numpy) as extracted from get_image_array
options (optional): dictionary of options
Required content of data:
calibrant (str): path to .poni-file
nbins (int): Number of bins to divide image into
path (str) (optional): path to image file - either this or image must be specified. If both is passed, image is prioritsed
image (str) (optional): image array (Numpy) as extracted from get_image_array
Output:
df: DataFrame contianing 1D diffractogram if option 'return' is True
@ -56,15 +55,15 @@ def integrate_1d(calibrant, bins, path=None, image=None, options=None):
options[option] = default_options[option]
if not image:
image = get_image_array(path)
if 'image' not in data.keys():
data['image'] = get_image_array(data['path'])
ai = pyFAI.load(calibrant)
ai = pyFAI.load(data['calibrant'])
if not options['filename']:
if path:
filename = os.path.join(options['save_folder'], os.path.split(path)[-1].split('.')[0] + options['extension'])
if data['path']:
filename = os.path.join(options['save_folder'], os.path.split(data['path'])[-1].split('.')[0] + options['extension'])
else:
filename = os.path.join(options['save_folder'], 'integrated.dat')
@ -84,10 +83,9 @@ def integrate_1d(calibrant, bins, path=None, image=None, options=None):
os.makedirs(options['save_folder'])
res = ai.integrate1d(image, bins, unit=options['unit'], filename=filename)
res = ai.integrate1d(data['image'], data['nbins'], unit=options['unit'], filename=filename)
if options['return']:
return read_diffractogram(filename)
return read_diffractogram(filename)
@ -245,16 +243,23 @@ def read_diffractogram(path):
return diffractogram
def read_data(path, kind, options=None):
def read_data(data, options={}):
if kind == 'beamline':
diffractogram = read_diffractogram(path)
if data['plot_kind'] == 'beamline':
elif kind == 'recx':
diffractogram = read_brml(path, options=options)
beamline = ['mar3450', 'edf', 'cbf']
elif kind == 'image':
diffractogram = get_image_array(path)
if data['path'].split('.')[-1] in beamline:
diffractogram = integrate_1d(data=data, options=options)
else:
diffractogram = read_diffractogram(data['path'])
elif data['plot_kind'] == 'recx':
diffractogram = read_brml(data['path'], options=options)
elif data['plot_kind'] == 'image':
diffractogram = get_image_array(data['path'])
return diffractogram