Add translation functions
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rasmusvt
parent
f2902aed3a
commit
0e4f14a6e3
2 changed files with 137 additions and 59 deletions
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@ -8,6 +8,9 @@ import zipfile
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import xml.etree.ElementTree as ET
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import beamtime.auxillary as aux
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def get_image_array(path):
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image = fabio.open(path)
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@ -29,66 +32,95 @@ def integrate_1d(data, options={}):
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Required content of data:
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calibrant (str): path to .poni-file
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nbins (int): Number of bins to divide image into
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path (str) (optional): path to image file - either this or image must be specified. If both is passed, image is prioritsed
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image (str) (optional): image array (Numpy) as extracted from get_image_array
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path (str) (optional, dependent on image): path to image file - either this or image must be specified. If both is passed, image is prioritsed
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image (NumPy 2D Array) (optional, dependent on path): image array as extracted from get_image_array
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Output:
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df: DataFrame contianing 1D diffractogram if option 'return' is True
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'''
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required_options = ['unit', 'extension', 'filename', 'save_folder', 'overwrite', 'return']
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required_options = ['unit', 'save', 'save_filename', 'save_extension', 'save_folder', 'overwrite']
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default_options = {
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'unit': '2th_deg',
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'extension': '_integrated.dat',
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'filename': None,
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'save': False,
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'save_filename': None,
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'save_extension': '_integrated.xy',
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'save_folder': '.',
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'overwrite': False,
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'return': False}
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'overwrite': False}
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if not options:
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options = default_options
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else:
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for option in required_options:
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if option not in options.keys():
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options[option] = default_options[option]
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options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
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# Get image array from filename if not passed
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if 'image' not in data.keys():
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data['image'] = get_image_array(data['path'])
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# Instanciate the azimuthal integrator from pyFAI from the calibrant (.poni-file)
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ai = pyFAI.load(data['calibrant'])
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if not options['filename']:
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if data['path']:
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filename = os.path.join(options['save_folder'], os.path.split(data['path'])[-1].split('.')[0] + options['extension'])
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else:
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filename = os.path.join(options['save_folder'], 'integrated.dat')
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if not options['overwrite']:
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trunk = os.path.join(options['save_folder'], filename.split('\\')[-1].split('.')[0])
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extension = filename.split('.')[-1]
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counter = 0
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while os.path.isfile(filename):
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counter_string = str(counter)
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filename = trunk + '_' + counter_string.zfill(4) + '.' + extension
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counter += 1
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# Determine filename
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filename = make_filename(data=data, options=options)
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# Make save_folder if this does not exist already
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if not os.path.isdir(options['save_folder']):
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os.makedirs(options['save_folder'])
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res = ai.integrate1d(data['image'], data['nbins'], unit=options['unit'], filename=filename)
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return read_diffractogram(filename)
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diffractogram = read_xy(filename)
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if not options['save']:
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os.remove(filename)
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shutil.rmtree('tmp')
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return diffractogram
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def make_filename(data, options):
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# Define save location for integrated diffractogram data
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if not options['save']:
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options['save_folder'] = 'tmp'
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filename = os.path.join(options['save_folder'], 'tmp_diff.dat')
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elif options['save']:
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# Case 1: No filename is given.
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if not options['save_filename']:
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# If a path is given instead of an image array, the path is taken as the trunk of the savename
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if data['path']:
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# Make filename by joining the save_folder, the filename (with extension deleted) and adding the save_extension
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filename = os.path.join(options['save_folder'], os.path.split(data['path'])[-1].split('.')[0] + options['save_extension'])
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else:
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# Make filename just "integrated.dat" in the save_folder
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filename = os.path.join(options['save_folder'], 'integrated.xy')
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else:
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filename = os.path.join(options['save_folder'], options['save_filename'])
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if not options['overwrite']:
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trunk = filename.split('.')[0]
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extension = filename.split('.')[-1]
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counter = 0
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while os.path.isfile(filename):
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# Rename first file to match naming scheme if already exists
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if counter == 0:
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os.rename(filename, trunk + '_' + str(counter).zfill(4) + '.' + extension)
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# Increment counter and make new filename
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counter += 1
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counter_string = str(counter)
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filename = trunk + '_' + counter_string.zfill(4) + '.' + extension
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return filename
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@ -220,16 +252,15 @@ def read_brml(path, options=None):
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return diffractogram
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def read_diffractogram(path):
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def read_xy(data):
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with open(path, 'r') as f:
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with open(data['path'], 'r') as f:
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position = 0
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current_line = f.readline()
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while current_line[0] == '#':
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while current_line[0] == '#' or "\'":
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find_wavelength(line=current_line, data=data)
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position = f.tell()
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current_line = f.readline()
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@ -237,7 +268,10 @@ def read_diffractogram(path):
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diffractogram = pd.read_csv(f, header=None, delim_whitespace=True)
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diffractogram.columns = ['2th', 'I']
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if diffractogram.shape[1] == 2:
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diffractogram.columns = ['2th', 'I']
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elif diffractogram.shape[1] == 3:
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diffractogram.columns = ['2th', 'I', 'sigma']
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return diffractogram
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@ -245,22 +279,17 @@ def read_diffractogram(path):
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def read_data(data, options={}):
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if data['plot_kind'] == 'beamline':
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beamline_extensions = ['mar3450', 'edf', 'cbf']
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file_extension = data['path'].split('.')[-1]
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beamline = ['mar3450', 'edf', 'cbf']
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if data['path'].split('.')[-1] in beamline:
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diffractogram = integrate_1d(data=data, options=options)
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if file_extension in beamline_extensions:
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diffractogram = integrate_1d(data=data, options=options)
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else:
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diffractogram = read_diffractogram(data['path'])
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elif data['plot_kind'] == 'recx':
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diffractogram = read_brml(data['path'], options=options)
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elif data['plot_kind'] == 'image':
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diffractogram = get_image_array(data['path'])
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elif file_extension == 'brml':
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diffractogram = read_brml(path=data['path'], options=options)
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elif file_extension in['xy', 'xye']:
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diffractogram = read_xy(data['path'])
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return diffractogram
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@ -290,4 +319,50 @@ def load_reflection_table(path):
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# Set the new modified headers as the headers of
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reflections.columns = headers
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return reflections
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return reflections
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def translate_wavelengths(diffractogram, wavelength):
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# Translate to CuKalpha
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cuka = 1.54059 # Å
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if cuka > wavelength:
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max_2th_cuka = 2*np.arcsin(wavelength/cuka) * 180/np.pi
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else:
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max_2th_cuka = diffractogram['2th'].max()
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diffractogram['2th_cuka'] = np.NAN
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diffractogram['2th_cuka'].loc[diffractogram['2th'] <= max_2th_cuka] = 2*np.arcsin(cuka/wavelength * np.sin((diffractogram['2th']/2) * np.pi/180)) * 180/np.pi
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# Translate to MoKalpha
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moka = 0.71073 # Å
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if moka > wavelength:
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max_2th_moka = 2*np.arcsin(wavelength/moka) * 180/np.pi
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else:
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max_2th_moka = diffractogram['2th'].max()
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diffractogram['2th_moka'] = np.NAN
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diffractogram['2th_moka'].loc[diffractogram['2th'] <= max_2th_moka] = 2*np.arcsin(moka/wavelength * np.sin((diffractogram['2th']/2) * np.pi/180)) * 180/np.pi
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# Convert to other parameters
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diffractogram['d'] = wavelength / (2*np.sin(2*diffractogram['2th']) * 180/np.pi)
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diffractogram['1/d'] = 1/diffractogram['d']
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diffractogram['q'] = np.abs((4*np.pi/wavelength)*np.sin(diffractogram['2th']/2 * np.pi/180))
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diffractogram['q2'] = diffractogram['q']**2
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diffractogram['q4'] = diffractogram['q']**4
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def find_wavelength(line, data):
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# Find from EVA-exports
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wavelength_dict = {'Cu': 1.54059, 'Mo': 0.71073}
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if 'Anode' in line:
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