Merge pull request #4 from rasmusthog/rasmus_small_improvements
Rasmus small improvements
This commit is contained in:
Rasmus Vester Thøgersen
GitHub
commit
9490c338c1
4 changed files with 140 additions and 51 deletions
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@ -178,19 +178,17 @@ def process_batsmall_data(df, options=None):
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def splice_cycles(df, options: dict) -> pd.DataFrame:
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''' Splices two cycles together - if e.g. one charge cycle are split into several cycles due to change in parameters.
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Incomplete, only accomodates BatSmall so far.'''
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Incomplete, only accomodates BatSmall so far, and only for charge.'''
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if options['kind'] == 'batsmall':
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# Creates masks for charge and discharge curves
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chg_mask = df['current'] >= 0
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dchg_mask = df['current'] < 0
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# Loop through all the cycling steps, change the current and capacities in the
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for i in range(df["count"].max()):
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sub_df = df.loc[df['count'] == i+1]
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sub_df_chg = sub_df.loc[chg_mask]
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#sub_df_dchg = sub_df.loc[dchg_mask]
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# get indices where the program changed
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chg_indices = sub_df_chg[sub_df_chg["comment"].str.contains("program")==True].index.to_list()
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@ -203,33 +201,16 @@ def splice_cycles(df, options: dict) -> pd.DataFrame:
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if chg_indices:
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last_chg = chg_indices.pop()
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#dchg_indices = sub_df_dchg[sub_df_dchg["comment"].str.contains("program")==True].index.to_list()
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#if dchg_indices:
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# del dchg_indices[0]
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if chg_indices:
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for i in chg_indices:
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add = df['specific_capacity'].iloc[i-1]
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df['specific_capacity'].iloc[i:last_chg] = df['specific_capacity'].iloc[i:last_chg] + add
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#if dchg_indices:
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# for i in dchg_indices:
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# add = df['specific_capacity'].iloc[i-1]
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# df['specific_capacity'].iloc[i:last_dchg] = df['specific_capacity'].iloc[i:last_dchg] + add
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return df
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def process_neware_data(df, options={}):
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""" Takes data from NEWARE in a DataFrame as read by read_neware() and converts units, adds columns and splits into cycles.
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@ -5,17 +5,21 @@ import pandas as pd
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import numpy as np
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import math
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import ipywidgets as widgets
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from IPython.display import display
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import nafuma.electrochemistry as ec
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import nafuma.plotting as btp
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import nafuma.auxillary as aux
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def plot_gc(data, options=None):
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# Update options
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required_options = ['x_vals', 'y_vals', 'which_cycles', 'charge', 'discharge', 'colours', 'differentiate_charge_discharge', 'gradient', 'rc_params', 'format_params']
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required_options = ['x_vals', 'y_vals', 'which_cycles', 'charge', 'discharge', 'colours', 'differentiate_charge_discharge', 'gradient', 'interactive', 'interactive_session_active', 'rc_params', 'format_params']
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default_options = {
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'x_vals': 'capacity', 'y_vals': 'voltage',
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'which_cycles': 'all',
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@ -23,15 +27,17 @@ def plot_gc(data, options=None):
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'colours': None,
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'differentiate_charge_discharge': True,
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'gradient': False,
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'interactive': False,
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'interactive_session_active': False,
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'rc_params': {},
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'format_params': {}}
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options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
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# Prepare plot, and read and process data
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fig, ax = btp.prepare_plot(options=options)
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if not 'cycles' in data.keys():
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data['cycles'] = ec.io.read_data(data=data, options=options)
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# Update list of cycles to correct indices
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@ -39,6 +45,15 @@ def plot_gc(data, options=None):
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colours = generate_colours(cycles=data['cycles'], options=options)
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if options['interactive']:
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options['interactive'], options['interactive_session_active'] = False, True
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plot_gc_interactive(data=data, options=options)
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return
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# Prepare plot, and read and process data
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fig, ax = btp.prepare_plot(options=options)
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for i, cycle in enumerate(data['cycles']):
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if i in options['which_cycles']:
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@ -49,25 +64,42 @@ def plot_gc(data, options=None):
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cycle[1].plot(x=options['x_vals'], y=options['y_vals'], ax=ax, c=colours[i][1])
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if options['interactive_session_active']:
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update_labels(options, force=True)
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else:
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update_labels(options)
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print(options['xunit'])
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fig, ax = btp.adjust_plot(fig=fig, ax=ax, options=options)
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#if options['interactive_session_active']:
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return data['cycles'], fig, ax
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def plot_gc_interactive(data, options):
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def update_labels(options):
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w = widgets.interactive(btp.ipywidgets_update, func=widgets.fixed(plot_gc), data=widgets.fixed(data), options=widgets.fixed(options),
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charge=widgets.ToggleButton(value=True),
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discharge=widgets.ToggleButton(value=True),
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x_vals=widgets.Dropdown(options=['specific_capacity', 'capacity', 'ions', 'voltage', 'time', 'energy'], value='specific_capacity', description='X-values')
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)
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if 'xlabel' not in options.keys():
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options['widget'] = w
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display(w)
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def update_labels(options, force=False):
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if 'xlabel' not in options.keys() or force:
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options['xlabel'] = options['x_vals'].capitalize().replace('_', ' ')
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if 'ylabel' not in options.keys():
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if 'ylabel' not in options.keys() or force:
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options['ylabel'] = options['y_vals'].capitalize().replace('_', ' ')
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if 'xunit' not in options.keys():
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if 'xunit' not in options.keys() or force:
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if options['x_vals'] == 'capacity':
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options['xunit'] = options['units']['capacity']
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elif options['x_vals'] == 'specific_capacity':
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@ -78,7 +110,7 @@ def update_labels(options):
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options['xunit'] = None
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if 'yunit' not in options.keys():
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if 'yunit' not in options.keys() or force:
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if options['y_vals'] == 'voltage':
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options['yunit'] = options['units']['voltage']
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@ -59,9 +59,10 @@ def integrate_1d(data, options={}, index=0):
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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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if 'image' not in data.keys() or not data['image']:
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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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@ -72,11 +73,15 @@ def integrate_1d(data, options={}, index=0):
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if not os.path.isdir(options['extract_folder']):
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os.makedirs(options['extract_folder'])
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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'], options['nbins'], unit=options['unit'], filename=filename)
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data['path'][index] = filename
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diffractogram, wavelength = read_xy(data=data, options=options, index=index)
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diffractogram, _ = read_xy(data=data, options=options, index=index)
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wavelength = find_wavelength_from_poni(path=data['calibrant'])
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if not options['save']:
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os.remove(filename)
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@ -278,8 +283,12 @@ def read_brml(data, options={}, index=0):
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#if 'wavelength' not in data.keys():
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# Find wavelength
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if not data['wavelength'][index]:
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for chain in root.findall('./FixedInformation/Instrument/PrimaryTracks/TrackInfoData/MountedOptics/InfoData/Tube/WaveLengthAlpha1'):
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wavelength = float(chain.attrib['Value'])
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else:
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wavelength = data['wavelength'][index]
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diffractogram = pd.DataFrame(diffractogram)
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@ -302,7 +311,11 @@ def read_xy(data, options={}, index=0):
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#if 'wavelength' not in data.keys():
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# Get wavelength from scan
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if not data['wavelength'][index]:
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wavelength = find_wavelength_from_xy(path=data['path'][index])
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else:
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wavelength = data['wavelength'][index]
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with open(data['path'][index], 'r') as f:
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position = 0
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@ -326,6 +339,38 @@ def read_xy(data, options={}, index=0):
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return diffractogram, wavelength
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def strip_headers_from_xy(path: str, filename=None) -> None:
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''' Strips headers from a .xy-file'''
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xy = []
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with open(path, 'r') as f:
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lines = f.readlines()
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headerlines = 0
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for line in lines:
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if line[0] == '#':
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headerlines += 1
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else:
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xy.append(line)
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if not filename:
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ext = path.split('.')[-1]
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filename = path.split(f'.{ext}')[0] + f'_noheaders.{ext}'
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with open(filename, 'w') as f:
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for line in xy:
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f.write(line)
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def read_data(data, options={}, index=0):
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beamline_extensions = ['mar3450', 'edf', 'cbf']
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@ -351,6 +396,7 @@ def read_data(data, options={}, index=0):
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diffractogram = apply_offset(diffractogram, wavelength, index, options)
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diffractogram = translate_wavelengths(data=diffractogram, wavelength=wavelength)
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return diffractogram, wavelength
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@ -470,7 +516,7 @@ def translate_wavelengths(data: pd.DataFrame, wavelength: float, to_wavelength=N
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data['2th_cuka'] = np.NAN
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data['2th_cuka'].loc[data['2th'] <= max_2th_cuka] = 2*np.arcsin(cuka/wavelength * np.sin((data['2th']/2) * np.pi/180)) * 180/np.pi
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data['2th_cuka'].loc[data['2th'] <= max_2th_cuka] = 2*np.arcsin(cuka/wavelength * np.sin((data['2th'].loc[data['2th'] <= max_2th_cuka]/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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@ -482,7 +528,7 @@ def translate_wavelengths(data: pd.DataFrame, wavelength: float, to_wavelength=N
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data['2th_moka'] = np.NAN
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data['2th_moka'].loc[data['2th'] <= max_2th_moka] = 2*np.arcsin(moka/wavelength * np.sin((data['2th']/2) * np.pi/180)) * 180/np.pi
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data['2th_moka'].loc[data['2th'] <= max_2th_moka] = 2*np.arcsin(moka/wavelength * np.sin((data['2th'].loc[data['2th'] <= max_2th_moka]/2) * np.pi/180)) * 180/np.pi
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# Convert to other parameters
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@ -501,7 +547,7 @@ def translate_wavelengths(data: pd.DataFrame, wavelength: float, to_wavelength=N
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data['2th'] = np.NAN
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data['2th'].loc[data['2th_cuka'] <= max_2th] = 2*np.arcsin(to_wavelength/cuka * np.sin((data['2th_cuka']/2) * np.pi/180)) * 180/np.pi
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data['2th'].loc[data['2th_cuka'] <= max_2th] = 2*np.arcsin(to_wavelength/cuka * np.sin((data['2th_cuka'].loc[data['2th_cuka'] <= max_2th]/2) * np.pi/180)) * 180/np.pi
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@ -528,6 +574,22 @@ def find_wavelength_from_xy(path):
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elif 'Wavelength' in line:
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wavelength = float(line.split()[2])*10**10
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else:
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wavelength = None
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return wavelength
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def find_wavelength_from_poni(path):
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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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if 'Wavelength' in line:
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wavelength = float(line.split()[-1])*10**10
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return wavelength
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@ -13,7 +13,6 @@ import nafuma.xrd as xrd
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import nafuma.auxillary as aux
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import nafuma.plotting as btp
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def plot_diffractogram(data, options={}):
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''' Plots a diffractogram.
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@ -67,7 +66,14 @@ def plot_diffractogram(data, options={}):
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if not 'diffractogram' in data.keys():
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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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# If wavelength is not manually passed it should be automatically gathered from the .xy-file
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if 'wavelength' not in data.keys():
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data['wavelength'] = [None for _ in range(len(data['path']))]
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else:
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# If only a single value is passed it should be set to be the same for all diffractograms passed
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if not isinstance(data['wavelength'], list):
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data['wavelength'] = [data['wavelength'] 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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@ -75,6 +81,9 @@ def plot_diffractogram(data, options={}):
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data['diffractogram'][index] = diffractogram
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data['wavelength'][index] = wavelength
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# FIXME This is a quick fix as the image is not reloaded when passing multiple beamline datasets
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data['image'] = None
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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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options['xlim'] = [data['diffractogram'][0][options['x_vals']].min(), data['diffractogram'][0][options['x_vals']].max()]
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@ -114,7 +123,7 @@ def plot_diffractogram(data, options={}):
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options['reflections_data'] = [options['reflections_data']]
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# Determine number of subplots and height ratios between them
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if len(options['reflections_data']) >= 1:
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if options['reflections_data'] and len(options['reflections_data']) >= 1:
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options = determine_grid_layout(options=options)
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@ -331,10 +340,10 @@ def plot_diffractogram_interactive(data, options):
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'heatmap_default': {'min': xminmax['heatmap'][0], 'max': xminmax['heatmap'][1], 'value': [xminmax['heatmap'][0], xminmax['heatmap'][1]], 'step': 10}
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},
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'ylim': {
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'w': widgets.FloatRangeSlider(value=[yminmax['start'][2], yminmax['start'][3]], min=yminmax['start'][0], max=yminmax['start'][1], step=0.5, layout=widgets.Layout(width='95%')),
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'w': widgets.FloatRangeSlider(value=[yminmax['start'][2], yminmax['start'][3]], min=yminmax['start'][0], max=yminmax['start'][1], step=0.01, layout=widgets.Layout(width='95%')),
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'state': 'heatmap' if options['heatmap'] else 'diff',
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'diff_default': {'min': yminmax['diff'][0], 'max': yminmax['diff'][1], 'value': [yminmax['diff'][2], yminmax['diff'][3]], 'step': 0.1},
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'heatmap_default': {'min': yminmax['heatmap'][0], 'max': yminmax['heatmap'][1], 'value': [yminmax['heatmap'][0], yminmax['heatmap'][1]], 'step': 0.1}
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'diff_default': {'min': yminmax['diff'][0], 'max': yminmax['diff'][1], 'value': [yminmax['diff'][2], yminmax['diff'][3]], 'step': 0.01},
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'heatmap_default': {'min': yminmax['heatmap'][0], 'max': yminmax['heatmap'][1], 'value': [yminmax['heatmap'][0], yminmax['heatmap'][1]], 'step': 0.01}
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}
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}
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@ -356,7 +365,12 @@ def plot_diffractogram_interactive(data, options):
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w = widgets.interactive(btp.ipywidgets_update, func=widgets.fixed(plot_diffractogram), data=widgets.fixed(data), options=widgets.fixed(options),
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scatter=widgets.ToggleButton(value=False),
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line=widgets.ToggleButton(value=True),
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xlim=options['widgets']['xlim']['w'])
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heatmap=widgets.ToggleButton(value=options['heatmap']),
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x_vals=widgets.Dropdown(options=['2th', 'd', '1/d', 'q', 'q2', 'q4', '2th_cuka', '2th_moka'], value='2th', description='X-values'),
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xlim=options['widgets']['xlim']['w'],
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ylim=options['widgets']['ylim']['w'],
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offset_y=widgets.BoundedFloatText(value=options['offset_y'], min=-5, max=5, step=0.01, description='offset_y'),
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offset_x=widgets.BoundedFloatText(value=options['offset_x'], min=-1, max=1, step=0.01, description='offset_x'))
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options['widget'] = w
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