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Open beamline data straight from raw file

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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
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49
beamtime/xrd/io.py
View file

@ -23,15 +23,14 @@ def get_image_headers(path):
return image.header 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. ''' Integrates an image file to a 1D diffractogram.
Input: Required content of data:
calibrant: path to .poni-file calibrant (str): path to .poni-file
bins: Number of bins to divide image into nbins (int): 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 path (str) (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 image (str) (optional): image array (Numpy) as extracted from get_image_array
options (optional): dictionary of options
Output: Output:
df: DataFrame contianing 1D diffractogram if option 'return' is True 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] options[option] = default_options[option]
if not image: if 'image' not in data.keys():
image = get_image_array(path) data['image'] = get_image_array(data['path'])
ai = pyFAI.load(calibrant) ai = pyFAI.load(data['calibrant'])
if not options['filename']: if not options['filename']:
if path: if data['path']:
filename = os.path.join(options['save_folder'], os.path.split(path)[-1].split('.')[0] + options['extension']) filename = os.path.join(options['save_folder'], os.path.split(data['path'])[-1].split('.')[0] + options['extension'])
else: else:
filename = os.path.join(options['save_folder'], 'integrated.dat') 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']) 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 return diffractogram
def read_data(path, kind, options=None): def read_data(data, options={}):
if kind == 'beamline': if data['plot_kind'] == 'beamline':
diffractogram = read_diffractogram(path)
elif kind == 'recx': beamline = ['mar3450', 'edf', 'cbf']
diffractogram = read_brml(path, options=options)
elif kind == 'image': if data['path'].split('.')[-1] in beamline:
diffractogram = get_image_array(path) 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 return diffractogram

6
beamtime/xrd/plot.py
View file

@ -19,7 +19,7 @@ def plot_diffractogram(plot_data, options={}):
plot_data (dict): Must include path = string to diffractogram data, and plot_kind = (recx, beamline, image)''' plot_data (dict): Must include path = string to diffractogram data, and plot_kind = (recx, beamline, image)'''
# Update options # Update options
required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'line', 'scatter', required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'line', 'scatter', 'xlim', 'ylim',
'reflections_plot', 'reflections_indices', 'reflections_data', 'plot_kind', 'palettes', 'interactive', 'rc_params', 'format_params'] 'reflections_plot', 'reflections_indices', 'reflections_data', 'plot_kind', 'palettes', 'interactive', 'rc_params', 'format_params']
default_options = { default_options = {
@ -59,8 +59,6 @@ def plot_diffractogram(plot_data, options={}):
if len(options['reflections_data']) >= 1: if len(options['reflections_data']) >= 1:
options = determine_grid_layout(options=options) options = determine_grid_layout(options=options)
print(options['format_params']['nrows'])
# Prepare plot, and read and process data # Prepare plot, and read and process data
@ -84,7 +82,7 @@ def plot_diffractogram(plot_data, options={}):
colours = btp.generate_colours(options['palettes']) colours = btp.generate_colours(options['palettes'])
diffractogram = xrd.io.read_data(path=plot_data['path'], kind=plot_data['plot_kind'], options=options) diffractogram = xrd.io.read_data(data=plot_data)
if options['line']: if options['line']: