Change plotting method to allow for multiple diffractograms
This commit is contained in:
rasmusvt
parent
9bb52fe819
commit
da2b2f855b
3 changed files with 124 additions and 51 deletions
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@ -313,6 +313,17 @@ def update_widgets(options):
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if widget['state'] != options['x_vals']:
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for arg in widget[f'{options["x_vals"]}_default']:
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# If new min value is larger than previous max, or new max value is smaller than previous min, set the opposite first
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if arg == 'min':
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if widget[f'{options["x_vals"]}_default']['min'] > getattr(widget['w'], 'max'):
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setattr(widget['w'], 'max', widget[f'{options["x_vals"]}_default']['max'])
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elif arg == 'max':
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if widget[f'{options["x_vals"]}_default']['max'] < getattr(widget['w'], 'min'):
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setattr(widget['w'], 'min', widget[f'{options["x_vals"]}_default']['min'])
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setattr(widget['w'], arg, widget[f'{options["x_vals"]}_default'][arg])
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widget['state'] = options['x_vals']
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@ -27,7 +27,7 @@ def get_image_headers(path):
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return image.header
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def integrate_1d(data, options={}):
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def integrate_1d(data, options={}, index=0):
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''' Integrates an image file to a 1D diffractogram.
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Required content of data:
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@ -52,10 +52,13 @@ def integrate_1d(data, options={}):
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options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
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if not isinstance(data['path'], list):
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data['path'] = [data['path']]
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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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data['image'] = get_image_array(data['path'][index])
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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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@ -70,18 +73,18 @@ def integrate_1d(data, options={}):
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res = ai.integrate1d(data['image'], data['nbins'], unit=options['unit'], filename=filename)
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data['path'] = filename
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diffractogram = read_xy(data=data, options=options)
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data['path'][index] = filename
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diffractogram, wavelength = read_xy(data=data, options=options)
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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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return diffractogram, wavelength
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def make_filename(data, options):
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def make_filename(options, path=None):
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# Define save location for integrated diffractogram data
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if not options['save']:
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@ -93,7 +96,7 @@ def make_filename(data, options):
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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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if 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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@ -176,12 +179,12 @@ def view_integrator(calibrant):
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def read_brml(data, options={}):
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def read_brml(data, options={}, index=0):
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required_options = ['extract_folder', 'save_folder']
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default_options = {
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'extract_folder': 'tmp',
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'extract_folder': 'tmp/',
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'save_folder': None
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}
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@ -194,7 +197,7 @@ def read_brml(data, options={}):
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# Extract the RawData0.xml file from the brml-file
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with zipfile.ZipFile(data['path'], 'r') as brml:
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with zipfile.ZipFile(data['path'][index], 'r') as brml:
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for info in brml.infolist():
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if "RawData" in info.filename:
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brml.extract(info.filename, options['extract_folder'])
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@ -233,9 +236,10 @@ def read_brml(data, options={}):
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diffractogram.append({'2th': twotheta, 'I': intensity})
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if 'wavelength' not in data.keys():
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#if 'wavelength' not in data.keys():
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# Find wavelength
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for chain in root.findall('./FixedInformation/Instrument/PrimaryTracks/TrackInfoData/MountedOptics/InfoData/Tube/WaveLengthAlpha1'):
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data['wavelength'] = float(chain.attrib['Value'])
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wavelength = float(chain.attrib['Value'])
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diffractogram = pd.DataFrame(diffractogram)
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@ -249,15 +253,16 @@ def read_brml(data, options={}):
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return diffractogram
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return diffractogram, wavelength
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def read_xy(data, options={}):
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def read_xy(data, options={}, index=0):
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if 'wavelength' not in data.keys():
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find_wavelength_from_xy(data=data)
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#if 'wavelength' not in data.keys():
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# Get wavelength from scan
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wavelength = find_wavelength_from_xy(path=data['path'][index])
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with open(data['path'], 'r') as f:
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with open(data['path'][index], 'r') as f:
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position = 0
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current_line = f.readline()
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@ -276,37 +281,37 @@ def read_xy(data, options={}):
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diffractogram.columns = ['2th', 'I', 'sigma']
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return diffractogram
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return diffractogram, wavelength
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def read_data(data, options={}):
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def read_data(data, options={}, index=0):
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beamline_extensions = ['mar3450', 'edf', 'cbf']
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file_extension = data['path'].split('.')[-1]
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file_extension = data['path'][index].split('.')[-1]
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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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diffractogram, wavelength = integrate_1d(data=data, options=options, index=index)
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elif file_extension == 'brml':
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diffractogram = read_brml(data=data, options=options)
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diffractogram, wavelength = read_brml(data=data, options=options, index=index)
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elif file_extension in['xy', 'xye']:
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diffractogram = read_xy(data=data, options=options)
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diffractogram, wavelength = read_xy(data=data, options=options, index=index)
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diffractogram = translate_wavelengths(data=diffractogram, wavelength=data['wavelength'])
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diffractogram = translate_wavelengths(data=diffractogram, wavelength=wavelength)
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return diffractogram
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return diffractogram, wavelength
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def load_reflection_table(data, options={}):
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required_options = ['wavelength', 'to_wavelength']
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required_options = ['ref_wavelength', 'to_wavelength']
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default_options = {
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'wavelength': 1.54059,
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'ref_wavelength': 1.54059,
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'to_wavelength': None
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}
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@ -333,7 +338,7 @@ def load_reflection_table(data, options={}):
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# Set the new modified headers as the headers of
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reflections.columns = headers
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reflections = translate_wavelengths(data=reflections, wavelength=options['wavelength'], to_wavelength=options['to_wavelength'])
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reflections = translate_wavelengths(data=reflections, wavelength=options['ref_wavelength'], to_wavelength=options['to_wavelength'])
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#print(reflections)
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@ -379,6 +384,7 @@ def translate_wavelengths(data, wavelength, to_wavelength=None):
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if to_wavelength:
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if to_wavelength > cuka:
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max_2th = 2*np.arcsin(cuka/to_wavelength) * 180/np.pi
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else:
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@ -395,19 +401,24 @@ def translate_wavelengths(data, wavelength, to_wavelength=None):
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def find_wavelength_from_xy(data):
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def find_wavelength_from_xy(path):
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wavelength_dict = {'Cu': 1.54059, 'Mo': 0.71073}
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with open(data['path'], 'r') as f:
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with open(path, 'r') as f:
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lines = f.readlines()
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for line in lines:
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# For .xy-files output from EVA
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if 'Anode' in line:
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anode = line.split()[8].strip('"')
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data['wavelength'] = wavelength_dict[anode]
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wavelength = wavelength_dict[anode]
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# For .xy-files output from pyFAI integration
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elif 'Wavelength' in line:
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data['wavelength'] = float(line.split()[2])*10**10
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wavelength = float(line.split()[2])*10**10
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return wavelength
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@ -43,12 +43,25 @@ def plot_diffractogram(data, options={}):
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options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
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# Convert data['path'] to list to allow iteration over this to accommodate both single and multiple diffractograms
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if not isinstance(data['path'], list):
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data['path'] = [data['path']]
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if not 'diffractogram' in data.keys():
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diffractogram = xrd.io.read_data(data=data, options=options)
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data['diffractogram'] = diffractogram
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# Initialise empty list for diffractograms and wavelengths
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data['diffractogram'] = [None for _ in range(len(data['path']))]
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data['wavelength'] = [None for _ in range(len(data['path']))]
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for index in range(len(data['path'])):
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diffractogram, wavelength = xrd.io.read_data(data=data, options=options, index=index)
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data['diffractogram'][index] = diffractogram
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data['wavelength'][index] = wavelength
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else:
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diffractogram = data['diffractogram']
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if not isinstance(data['diffractogram'], list):
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data['diffractogram'] = [data['diffractogram']]
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data['wavelength'] = [data['wavelength']]
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# Sets the xlim if this has not bee specified
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if not options['xlim']:
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@ -95,6 +108,7 @@ def plot_diffractogram(data, options={}):
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colours = btp.generate_colours(options['palettes'])
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for diffractogram in data['diffractogram']:
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if options['line']:
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diffractogram.plot(x=options['x_vals'], y=options['y_vals'], ax=ax, c=next(colours), zorder=1)
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@ -110,7 +124,7 @@ def plot_diffractogram(data, options={}):
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# Make the reflection plots
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if options['reflections_plot'] and options['reflections_data']:
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options['xlim'] = ax.get_xlim()
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options['to_wavelength'] = data['wavelength']
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options['to_wavelength'] = data['wavelength'][0]
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for reference, axis in zip(options['reflections_data'], ref_axes):
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plot_reflection_table(data=reference, ax=axis, options=options)
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@ -118,7 +132,7 @@ def plot_diffractogram(data, options={}):
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# Print the reflection indices
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if options['reflections_indices'] and options['reflections_data']:
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options['xlim'] = ax.get_xlim()
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options['to_wavelength'] = data['wavelength']
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options['to_wavelength'] = data['wavelength'][0]
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for reference in options['reflections_data']:
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plot_reflection_indices(data=reference, ax=indices_ax, options=options)
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@ -149,17 +163,54 @@ def determine_grid_layout(options):
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def plot_diffractogram_interactive(data, options):
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minmax = {'2th': [None, None], '2th_cuka': [None, None], '2th_moka': [None, None], 'd': [None, None], '1/d': [None, None], 'q': [None, None], 'q2': [None, None], 'q4': [None, None]}
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for index, diffractogram in enumerate(data['diffractogram']):
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if not minmax['2th'][0] or diffractogram['2th'].min() < minmax['2th'][0]:
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minmax['2th'][0] = diffractogram['2th'].min()
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min_index = index
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if not minmax['2th'][1] or diffractogram['2th'].max() > minmax['2th'][1]:
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minmax['2th'][1] = diffractogram['2th'].max()
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max_index = index
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minmax['2th_cuka'][0], minmax['2th_cuka'][1] = data['diffractogram'][min_index]['2th_cuka'].min(), data['diffractogram'][max_index]['2th_cuka'].max()
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minmax['2th_moka'][0], minmax['2th_moka'][1] = data['diffractogram'][min_index]['2th_moka'].min(), data['diffractogram'][max_index]['2th_moka'].max()
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minmax['d'][0], minmax['d'][1] = data['diffractogram'][max_index]['d'].min(), data['diffractogram'][min_index]['d'].max()
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minmax['1/d'][0], minmax['1/d'][1] = data['diffractogram'][min_index]['1/d'].min(), data['diffractogram'][max_index]['1/d'].max()
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minmax['q'][0], minmax['q'][1] = data['diffractogram'][min_index]['q'].min(), data['diffractogram'][max_index]['q'].max()
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minmax['q2'][0], minmax['q2'][1] = data['diffractogram'][min_index]['q2'].min(), data['diffractogram'][max_index]['q2'].max()
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minmax['q4'][0], minmax['q4'][1] = data['diffractogram'][min_index]['q4'].min(), data['diffractogram'][max_index]['q4'].max()
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# options['widgets'] = {
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# 'xlim': {
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# 'w': widgets.FloatRangeSlider(value=[data['diffractogram']['2th'].min(), data['diffractogram']['2th'].max()], min=data['diffractogram']['2th'].min(), max=data['diffractogram']['2th'].max(), step=0.5, layout=widgets.Layout(width='95%')),
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# '2th_default': {'min': data['diffractogram']['2th'].min(), 'max': data['diffractogram']['2th'].max(), 'value': [data['diffractogram']['2th'].min(), data['diffractogram']['2th'].max()], 'step': 0.5},
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# '2th_cuka_default': {'min': data['diffractogram']['2th_cuka'].min(), 'max': data['diffractogram']['2th_cuka'].max(), 'value': [data['diffractogram']['2th_cuka'].min(), data['diffractogram']['2th_cuka'].max()], 'step': 0.5},
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# '2th_moka_default': {'min': data['diffractogram']['2th_moka'].min(), 'max': data['diffractogram']['2th_moka'].max(), 'value': [data['diffractogram']['2th_moka'].min(), data['diffractogram']['2th_moka'].max()], 'step': 0.5},
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# 'd_default': {'min': data['diffractogram']['d'].min(), 'max': data['diffractogram']['d'].max(), 'value': [data['diffractogram']['d'].min(), data['diffractogram']['d'].max()], 'step': 0.5},
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# '1/d_default': {'min': data['diffractogram']['1/d'].min(), 'max': data['diffractogram']['1/d'].max(), 'value': [data['diffractogram']['1/d'].min(), data['diffractogram']['1/d'].max()], 'step': 0.5},
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# 'q_default': {'min': data['diffractogram']['q'].min(), 'max': data['diffractogram']['q'].max(), 'value': [data['diffractogram']['q'].min(), data['diffractogram']['q'].max()], 'step': 0.5},
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# 'q2_default': {'min': data['diffractogram']['q2'].min(), 'max': data['diffractogram']['q2'].max(), 'value': [data['diffractogram']['q2'].min(), data['diffractogram']['q2'].max()], 'step': 0.5},
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# 'q4_default': {'min': data['diffractogram']['q4'].min(), 'max': data['diffractogram']['q4'].max(), 'value': [data['diffractogram']['q4'].min(), data['diffractogram']['q4'].max()], 'step': 0.5},
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# 'state': '2th'
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# }
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# }
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options['widgets'] = {
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'xlim': {
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'w': widgets.FloatRangeSlider(value=[data['diffractogram']['2th'].min(), data['diffractogram']['2th'].max()], min=data['diffractogram']['2th'].min(), max=data['diffractogram']['2th'].max(), step=0.5, layout=widgets.Layout(width='95%')),
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'2th_default': {'min': data['diffractogram']['2th'].min(), 'max': data['diffractogram']['2th'].max(), 'value': [data['diffractogram']['2th'].min(), data['diffractogram']['2th'].max()], 'step': 0.5},
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'2th_cuka_default': {'min': data['diffractogram']['2th_cuka'].min(), 'max': data['diffractogram']['2th_cuka'].max(), 'value': [data['diffractogram']['2th_cuka'].min(), data['diffractogram']['2th_cuka'].max()], 'step': 0.5},
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'2th_moka_default': {'min': data['diffractogram']['2th_moka'].min(), 'max': data['diffractogram']['2th_moka'].max(), 'value': [data['diffractogram']['2th_moka'].min(), data['diffractogram']['2th_moka'].max()], 'step': 0.5},
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'd_default': {'min': data['diffractogram']['d'].min(), 'max': data['diffractogram']['d'].max(), 'value': [data['diffractogram']['d'].min(), data['diffractogram']['d'].max()], 'step': 0.5},
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'1/d_default': {'min': data['diffractogram']['1/d'].min(), 'max': data['diffractogram']['1/d'].max(), 'value': [data['diffractogram']['1/d'].min(), data['diffractogram']['1/d'].max()], 'step': 0.5},
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'q_default': {'min': data['diffractogram']['q'].min(), 'max': data['diffractogram']['q'].max(), 'value': [data['diffractogram']['q'].min(), data['diffractogram']['q'].max()], 'step': 0.5},
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'q2_default': {'min': data['diffractogram']['q2'].min(), 'max': data['diffractogram']['q2'].max(), 'value': [data['diffractogram']['q2'].min(), data['diffractogram']['q2'].max()], 'step': 0.5},
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'q4_default': {'min': data['diffractogram']['q4'].min(), 'max': data['diffractogram']['q4'].max(), 'value': [data['diffractogram']['q4'].min(), data['diffractogram']['q4'].max()], 'step': 0.5},
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'w': widgets.FloatRangeSlider(value=[minmax['2th'][0], minmax['2th'][1]], min=minmax['2th'][0], max=minmax['2th'][1], step=0.5, layout=widgets.Layout(width='95%')),
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'2th_default': {'min': minmax['2th'][0], 'max': minmax['2th'][1], 'value': [minmax['2th'][0], minmax['2th'][1]], 'step': 0.5},
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'2th_cuka_default': {'min': minmax['2th_cuka'][0], 'max': minmax['2th_cuka'][1], 'value': [minmax['2th_cuka'][0], minmax['2th_cuka'][1]], 'step': 0.5},
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'2th_moka_default': {'min': minmax['2th_moka'][0], 'max': minmax['2th_moka'][1], 'value': [minmax['2th_moka'][0], minmax['2th_moka'][1]], 'step': 0.5},
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'd_default': {'min': minmax['d'][0], 'max': minmax['d'][1], 'value': [minmax['d'][0], minmax['d'][1]], 'step': 0.5},
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'1/d_default': {'min': minmax['1/d'][0], 'max': minmax['1/d'][1], 'value': [minmax['1/d'][0], minmax['1/d'][1]], 'step': 0.5},
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'q_default': {'min': minmax['q'][0], 'max': minmax['q'][1], 'value': [minmax['q'][0], minmax['q'][1]], 'step': 0.5},
|
||||
'q2_default': {'min': minmax['q2'][0], 'max': minmax['q2'][1], 'value': [minmax['q2'][0], minmax['q2'][1]], 'step': 0.5},
|
||||
'q4_default': {'min': minmax['q4'][0], 'max': minmax['q4'][1], 'value': [minmax['q4'][0], minmax['q4'][1]], 'step': 0.5},
|
||||
'state': '2th'
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue