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Add change modes in interactive mode

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This commit is contained in:
rasmusvt 2022-03-16 16:16:05 +01:00
parent 6f2d96005d
commit a96210cf07
2 changed files with 43 additions and 48 deletions
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82
beamtime/xrd/io.py
View file

@ -69,8 +69,8 @@ def integrate_1d(data, options={}):
res = ai.integrate1d(data['image'], data['nbins'], unit=options['unit'], filename=filename)
diff_data = {'path': filename}
diffractogram = read_xy(data=diff_data, options=options)
data['path'] = filename
diffractogram = read_xy(data=data, options=options)
if not options['save']:
os.remove(filename)
@ -175,24 +175,17 @@ def view_integrator(calibrant):
def read_brml(path, options=None):
def read_brml(data, options={}):
required_options = ['extract_folder', 'save_folder']
default_options = {
'extract_folder': 'temp',
'extract_folder': 'tmp',
'save_folder': None
}
if not options:
options = default_options
else:
for option in required_options:
if option not in options.keys():
options[option] = default_options[option]
options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
if not os.path.isdir(options['extract_folder']):
@ -200,7 +193,7 @@ def read_brml(path, options=None):
# Extract the RawData0.xml file from the brml-file
with zipfile.ZipFile(path, 'r') as brml:
with zipfile.ZipFile(data['path'], 'r') as brml:
for info in brml.infolist():
if "RawData" in info.filename:
brml.extract(info.filename, options['extract_folder'])
@ -223,21 +216,26 @@ def read_brml(path, options=None):
if scantype.text == 'StillScan':
if chain.get('Description') == 'Originally measured data.':
for data in chain.findall('Datum'):
data = data.text.split(',')
data = [float(i) for i in data]
twotheta, intensity = float(data[2]), float(data[3])
for scandata in chain.findall('Datum'):
scandata = scandata.text.split(',')
scandata = [float(i) for i in scandata]
twotheta, intensity = float(scandata[2]), float(scandata[3])
else:
if chain.get('Description') == 'Originally measured data.':
for data in chain.findall('Datum'):
data = data.text.split(',')
twotheta, intensity = float(data[2]), float(data[3])
for scandata in chain.findall('Datum'):
scandata = scandata.text.split(',')
twotheta, intensity = float(scandata[2]), float(scandata[3])
if twotheta > 0:
diffractogram.append({'2th': twotheta, 'I': intensity})
if 'wavelength' not in data.keys():
for chain in root.findall('./FixedInformation/Instrument/PrimaryTracks/TrackInfoData/MountedOptics/InfoData/Tube/WaveLengthAlpha1'):
data['wavelength'] = float(chain.attrib['Value'])
diffractogram = pd.DataFrame(diffractogram)
@ -253,10 +251,10 @@ def read_brml(path, options=None):
return diffractogram
def read_xy(data, options):
def read_xy(data, options={}):
if 'wavelength' not in data.keys():
find_wavelength(data=data, file_ext='xy')
find_wavelength_from_xy(data=data)
with open(data['path'], 'r') as f:
position = 0
@ -294,6 +292,9 @@ def read_data(data, options={}):
elif file_extension in['xy', 'xye']:
diffractogram = read_xy(data=data, options=options)
diffractogram = translate_wavelengths(diffractogram=diffractogram, wavelength=data['wavelength'])
return diffractogram
@ -361,30 +362,23 @@ def translate_wavelengths(diffractogram, wavelength):
diffractogram['q4'] = diffractogram['q']**4
def find_wavelength(data, file_ext):
# Find from EVA-exports (.xy)
if file_ext == 'xy':
wavelength_dict = {'Cu': 1.54059, 'Mo': 0.71073}
with open(data['path'], 'r') as f:
lines = f.readlines()
for line in lines:
if 'Anode' in line:
anode = line.split()[8].strip('"')
data['wavelength'] = wavelength_dict[anode]
return diffractogram
# Find from .poni-file
if file_ext in ['mar3450', 'edf', 'cbf']:
if 'calibrant' in data.keys():
with open(data['calibrant'], 'r') as f:
lines = f.readlines()
for line in lines:
if 'Wavelength' in line:
data['wavelength'] = float(line.split[-1])
def find_wavelength_from_xy(data):
wavelength_dict = {'Cu': 1.54059, 'Mo': 0.71073}
with open(data['path'], 'r') as f:
lines = f.readlines()
for line in lines:
if 'Anode' in line:
anode = line.split()[8].strip('"')
data['wavelength'] = wavelength_dict[anode]
elif 'Wavelength' in line:
data['wavelength'] = float(line.split()[2])*10**10

3
beamtime/xrd/plot.py
View file

@ -151,7 +151,8 @@ def plot_diffractogram_interactive(data, options):
line=widgets.ToggleButton(value=True),
reflections_plot=widgets.ToggleButton(value=True),
reflections_indices=widgets.ToggleButton(value=False),
xlim=widgets.IntRangeSlider(value=options['xlim'], min=options['xlim'][0], max=options['xlim'][1], step=1, description='xlim', layout=widgets.Layout(width='1000px')))
x_vals=widgets.Dropdown(options=['2th', 'd', '1/d', 'q', 'q4', 'q4', '2th_cuka', '2th_moka'], value='2th', description='X-values'),
xlim=widgets.FloatRangeSlider(value=options['xlim'], min=options['xlim'][0], max=options['xlim'][1], step=1, description='xlim', layout=widgets.Layout(width='1000px')))
else:
w = widgets.interactive(btp.ipywidgets_update, func=widgets.fixed(plot_diffractogram), data=widgets.fixed(data), options=widgets.fixed(options),