pyviblib.gui.figures

Classes for plotting based on Matplotlib

Classes

BaseFigure

base class for all figures

BaseSpectrumFigure

template spectrum

SingleMoleculeSpectraFigure

spectra of a single molecule

RamanROADegcircCalcFigure

Raman/ROA spectra of a single molecule

RamanROADegcircCalcMixtureFigure

Raman/ROA spectra of a mixture

IRVCDCalcFigure

IR/VCD/g spectra for a single molecule

IRVCDCalcMixtureFigure

IR/VCD spectra of a mixture

MultipleSpectraFigure

spectra for several molecules

RamanROADegcircExpFigure

experimental Raman/ROA spectra

IRExpFigure

experimental IR spectra

PercentageFigure

showing composition as a bar chart

DCMSumsFigure

sums of internuclear distances

VOASimilarityCurvesFigure

Raman/ROA similarity curves

VibLocalizationsFigure

localizations of vibrations on a fragment

CumulatedNormalizedVibSumsFigure

calculated cumulated normalized vibrational sums of VROA

ExpROACumulatedNormalizedSumsFigure

experimental cumulated normalized sums of ROA intensities

Author:Maxim Fedorovsky

class pyviblib.gui.figures.BaseFigure(master, **kw)

Base class for all figures.

This class defines a set of protected methods which are called in the constructor in the following sequence:

_init_vars()

initialize some variables

_declare_properties()

declare properties of the widget

_bind_events()

bind events

These methods are intended to be overridden in subclasses. The base class implementations do nothing.

The following protected instance variables are created:

_smartdict

to store options

_varsdict

to store GUI variables

The following read-only properties are exposed:

tk_canvas

Tkinter.Canvas to be used in GUI

settings

reference to self._smartdict

export_XY

data to be exported

The following public method is exported:

save()

save the figure

Initializer of the class.

Parameter:master – parent widget

Accepts all keywords arguments of the matplotlib.figure.Figure initializer.

save(filename, **kw)

Save the figure.

Parameters:

• filename – file name to save to
• dpi – resolution in dots per inch (default 150).
• CompatibilityLevel – PDF compatibility level (default ‘1.4’)
• orientation – ‘landscape’ or ‘portrait’ (default ‘portrait’)
• size – size in inches to set (default None), if None, use the current size
• restoresize – restore the current size (default True)
• use_ps2pdf – whether to use the ps2pdf command for PDF (default False)

class pyviblib.gui.figures.BaseSpectrumFigure(master, **kw)

Template spectrum.

The plotting region is be defined in the class.

The following readable and writable properties are exposed:

canvas_changed

canvas state

xlim

region of wavenumbers

The following public methods are exposed:

get_spectra_axes()

get a reference to spectra axes

restore_last_zoom()

restore the last plotting region

save()

save the figure

Initializer of the class.

Parameter:master – parent widget

static get_representation_as_index(repr_string)

Get the representation type (0 - curves, 1 - stick).

get_spectra_axes(name)

Get a reference of an axes.

Parameter:name – ‘axes_%s’ % name key should be in the internal dictionary

restore_last_zoom()

Restore the last viewing region.

save(filename, **kw)

Save the figure.

Parameters:

• filename – file name to save to
• size – size in inches (default None) if None, keep the current size
• limits –

  One of the following:

  • ‘default’ - 1900-100
  • ‘current’ - do not change

class pyviblib.gui.figures.SingleMoleculeSpectraFigure(master, mol, **kw)

Spectra of a single molecule. The spectra consist of three parts.

The following read-only property is exposed:

molecule

molecule whose spectra are to be plotted

Initializer of the class.

Parameters:

• master – parent widget
• mol – molecule with the normal modes

Accepts all the keyword arguments of the base class.

class pyviblib.gui.figures.RamanROADegcircCalcFigure(master, mol, **kw)

Calculated Raman/ROA/Degree of circularity spectra.

If you want to use Arial fonts, install it: apt-get install msttcorefonts

The following public method is exported:

plot_spectra()

plot the spectra

The following static methods are exported:

get_scattering_as_index()

get the scattering type

get_tex_spectrum_label()

get the TeX source for labels

get_tex_spectrum_units()

get the TeX source for units

Initializer of the class.

Parameters:

• master – parent widget
• mol – molecule
• sync_zoom_figures – list of figures to synchronize with

static get_scattering_as_index(scat_string)

Get the scattering type as integer.

Parameter:scat_string – one of resources.STRINGS_SCATTERING_TYPES

static get_tex_spectrum_label(type_, scattering, representation, contr_raman=0, contr_roa=0, contr_weight=True)

Return the TeX source for the spectra label.

Parameters:

• type –

  type of the spectrum:

  • 0(raman)
  • 1(roa)
  • 2(degcirc)
• scattering – scattering as integer
• representation – representation as integer
• contr_raman –

  defines how the Raman intensity is to be calculated:

  • 0 – the full intensity
  • 1 – only the contribution of a2
  • 2 – only the contribution of b2

• contr_roa –

  defines how the ROA intensity is to be calculated:

  • 0 – the full intensity
  • 1 – only the contribution of aG’
  • 2 – only the contribution of b2G
  • 3 – only the contribution of b2A
• contr_weight – whether to weight the Raman and ROA intensities. Only relevant if 0 < contr_raman or 0 < contr_roa

static get_tex_spectrum_units(representation, multfactor)

Return the TeX source for the units.

Parameters:

• representation – representation as integer
• multfactor – order of magnitude

plot_spectra(**kw)

Plot the spectra.

Parameters:

• scattering – resources.STRINGS_SCATTERING_TYPES (default ‘Backward’)
• representation – ‘Curves’ or ‘Stick’ (default ‘Curves’)
• lim_wavenumbers – left_nu, right_nu) ; left_nu > right_nu (default (1900., 100.))
• tick_wavenumbers – major tick (default 200.)
• labels_fontsize – font size of the axes and spectra labels (default 17)
• N_G – number of Gauss functions for fitting
• FWHM_is – full width at half maximum for the isotropic bandwidth (a2, aG) (default 3.5)
• FWHM_anis – full width at half maximum for the anisotropic bandwidth (b2, b2G, b2A) (default 10.)
• FWHM_inst – full width at half maximum for the Gaussian instrument profile (default 7.)
• title1 – Title at the top of the figure (default ‘’)
• title2 – Smaller title beneath the title1 (default ‘’)
• groups_AB – unless None, plot additionally a second spectrum with either AA, AB or BB contribution. Format: [group_A, group_B, t] (default None)
• parallel – whether to use parallel calculation
• contr_raman –

  defines how the Raman intensity is to be calculated:

  • 0 – the full intensity
  • 1 – only the contribution of a2
  • 2 – only the contribution of b2

• contr_roa –

  defines how the ROA intensity is to be calculated:

  • 0 – the full intensity
  • 1 – only the contribution of aG’
  • 2 – only the contribution of b2G
  • 3 – only the contribution of b2A
• contr_weight – whether to weight the Raman and ROA intensities. Only relevant if 0 < contr_raman or 0 < contr_roa

class pyviblib.gui.figures.RamanROADegcircCalcMixtureFigure(master, mols, composition, **kw)

Calculated Raman/ROA/Degree of circularity spectra of a mixture of molecules.

The following read-only properties are exposed:

XY_data

X and Y for the single molecules

The following public method is exposed:

plot_spectra()

plot the spectra

Initializer of the class.

Parameters:

• master – parent widget
• mols – list of molecules
• composition – composition of the mixture (null-based ndarray)
• sync_zoom_figures – list of figures to synchronize with (default None)

plot_spectra(**kw)

Plot the spectra of a mixture of the molecules.

Parameters:

• scattering – resources.STRINGS_SCATTERING_TYPES (default ‘Backward’)
• representation – ‘Curves’ or ‘Stick’ (default ‘Curves’)
• lim_wavenumbers – left_nu, right_nu) ; left_nu > right_nu (default (1900., 100.))
• tick_wavenumbers – major tick (default 200.)
• labels_fontsize – font size of the axes and spectra labels (default 17)
• N_G – number of Gauss functions for fitting
• FWHM_is – full width at half maximum for the isotropic bandwidth (a2, aG) (default 3.5)
• FWHM_anis – full width at half maximum for the anisotropic bandwidth (b2, b2G, b2A) (default 10.)
• FWHM_inst – full width at half maximum for the Gaussian instrument profile (default 7.)
• title1 – Title at the top of the figure (default ‘’)
• title2 – Smaller title beneath the title1 (default ‘’)
• weight_spectra – weight spectra with the percentages (default True)
• curves_weighted_sum – plot the weighted sum spectrum (default True)
• spectra_colors – colors for the individual spectra (default None) used if curves_weighted_sum is False
• spectra_linewidths – linewidths for the individual spectra (default None), used if curves_weighted_sum is False
• plot_fragments – whether to plot fragments’ spectra
• groups_to_include – used if plot_fragments
• contr_raman –

  defines how the Raman intensity is to be calculated:

  • 0 – the full intensity
  • 1 – only the contribution of a2
  • 2 – only the contribution of b2

• contr_roa –

  defines how the ROA intensity is to be calculated:

  • 0 – the full intensity
  • 1 – only the contribution of aG’
  • 2 – only the contribution of b2G
  • 3 – only the contribution of b2A
• contr_weight – whether to weight the Raman and ROA intensities. Only relevant if 0 < contr_raman or 0 < contr_roa
• distance_terms –

  distance terms

  • 0 – usual (local term + non-local term)
  • 1 – local term
  • 2 – non-local term (zero for a2, b2 and aG’)

class pyviblib.gui.figures.IRVCDCalcFigure(master, mol, **kw)

Calculated IR/VCD/g spectra.

Initializer of the class.

Parameters:

• master – parent widget
• mol – molecule
• sync_zoom_figures – list of figures to synchronize with (default None)

static get_tex_spectrum_label(type_, representation, multfactor)

Return the TeX source for the spectra label.

Parameters:

• type –

  type of the spectrum:

  • 0 – ir
  • 1 – vcd
  • 2 – g
• representation – representation as integer
• multfactor – multiply factor (for g)

static get_tex_spectrum_units(type_, representation, multfactor)

Return the TeX source for the spectra units.

Parameters:

• type –

  type of the spectrum:

  • 0 – ir
  • 1 – vcd
  • 2 – g
• representation – representation as integer
• multfactor – multiply factor (for g)

plot_spectra(**kw)

Plot the spectra.

Parameters:

• representation – ‘Curves’ or ‘Stick’ (default ‘Curves’)
• lim_wavenumbers – (left_nu, right_nu) ; left_nu > right_nu (default (1900., 100.))
• tick_wavenumbers – major tick (default 200.)
• labels_fontsize – font size of the axes and spectra labels (default 17)
• N_G – number of Gauss functions for fitting
• FWHM_fit – full width at half maximum for the curves (default 10.)
• FWHM_inst – full width at half maximum for the Gaussian instrument profile (default 10.)
• title1 – Title at the top of the figure (default ‘’)
• title2 – Smaller title beneath the title1 (default ‘’)

class pyviblib.gui.figures.IRVCDCalcMixtureFigure(master, mols, composition, **kw)

Calculated IR/VCD/g spectra of a mixture of molecules.

The following read-only properties are exposed:

XY_data

X and Y for the single molecules

The following public method is exposed:

plot_spectra

plot the spectra

Initializer of the class.

Parameters:

• master – parent widget
• mols – list of molecules
• composition – composition of the mixture (null-based ndarray)
• sync_zoom_figures – list of figures to synchronize with

plot_spectra(**kw)

Plot the spectra of a mixture of the molecules.

Parameters:

• representation – ‘Curves’ or ‘Stick’ (default ‘Curves’)
• lim_wavenumbers – left_nu, right_nu) ; left_nu > right_nu (default (1900., 100.))
• tick_wavenumbers – major tick (default 200.)
• labels_fontsize – font size of the axes and spectra labels (default 17)
• N_G – number of Gauss functions for fitting
• FWHM_fit – full width at half maximum for the curves (default 10.)
• FWHM_inst – full width at half maximum for the Gaussian instrument profile (default 10.)
• title1 – Title at the top of the figure (default ‘’)
• title2 – Smaller title beneath the title1 (default ‘’)
• weight_spectra – weight spectra with the percentages (default True)
• curves_weighted_sum – plot the weighted sum spectrum (default True)
• spectra_colors – colors for the individual spectra (default None) used if curves_weighted_sum is False
• spectra_linewidths – linewidths for the individual spectra (default None), used if curves_weighted_sum is False

class pyviblib.gui.figures.MultipleSpectraFigure(master, **kw)

Plotting spectra of several molecules.

The following read-only properties are exposed:

ylim

y limits

multfactor

order of magnitude of the y values

The following public method is exported:

plot_spectra()

plot the spectra

Initializer of the class.

Parameters:

• master – parent widget
• mols – list of molecules (default None)
• nspectra – number of spectra (default None), must be supplied unless the mols argument is given

static get_rect_spectrum(no, spectrum_width, spectrum_height)

Return the bounding rectangle for a spectrum

plot_spectra(XY, **kw)

Plot the spectra.

Parameters:

• XY – [ [X1, Y1, Y_g], ... ] Y_g is optional
• autoresize – if True, the size of a single spectrum is calculated automatically
• spectrum_size – (w, h) in cm, used if autoresize is set to False
• label_type –

  type of the spectra label:

  • None - no label
  • 0 - raman
  • 1 - roa
  • 2 - degcirc
  • 3 - ir
  • 4 - vcd
  • 5 - g
• data_calc – True for calculated data, False for experimental (default True)
• molecule_labels – list of the labels of the subplots
• make_degcirc – apply the axis setting of a degree of circularity spectrum
• mark_vibs – list of vibrations to be marked (fit: +-5 for each peak, stick: the vibrations)
• normalize_energy – whether to normalize exp. Raman/ROA to the laser energy (default True)
• datatype – type of the data for experimental infrared absorption spectra (default None)
• contr_raman –

  defines how the Raman intensity is to be calculated:

  • 0 – the full intensity
  • 1 – only the contribution of a2
  • 2 – only the contribution of b2

• contr_roa –

  defines how the ROA intensity is to be calculated:

  • 0 – the full intensity
  • 1 – only the contribution of aG’
  • 2 – only the contribution of b2G
  • 3 – only the contribution of b2A
• contr_weight – whether to weight the Raman and ROA intensities. Only relevant if 0 < contr_raman or 0 < contr_roa

The method accepts all the keyword arguments of RamanROADegcircCalcFigure.plot_spectra().

class pyviblib.gui.figures.RamanROADegcircExpFigure(master, exp_data, **kw)

Experimental Raman / ROA / Degree of circularity spectra.

The following read-only property are exposed:

exp_data

list with the experimental data

raw_data

laser_energy, X, raman, roa, degcirc

The following public method is exposed:

plot_spectra()

plot the spectra

The following static method is exported:

process_raw_data()

process raw experimental data

Initializer of the class.

Parameters:

• master – parent widget
• exp_data – list with the experimental data
• parser – unless None, it is RamanROAExpSpectraFileParser and suppose to be used instead of exp_data (default None)

Accepts all the keyword arguments of the base class.

static get_tex_spectrum_label(type_, scattering)

Return the TeX source for the spectra label.

Parameters:

• type – type of the spectrum: 0(raman), 1(roa), 2(degcirc)
• scattering – scattering as integer

static get_tex_spectrum_units(multfactor, normalize_energy)

Return the TeX source for the units.

Parameters:

• representation – representation as integer
• multfactor – order of magnitude
• normalize_energy – whether to normalize to the laser energy

plot_spectra(**kw)

Plot the spectra.

Parameters:

• lim_wavenumbers – (left_nu, right_nu) ; left_nu > right_nu (default (1900., 100.))
• tick_wavenumbers – major tick (default 200.)
• labels_fontsize – font size of the axes and spectra labels (default 17)
• title1 – Title at the top of the figure (default ‘’)
• title2 – Smaller title beneath the title1 (default ‘’)
• smooth – whether to smooth the curves with Savitzky-Golay (default True)
• order – polynomial order for Savitzy-Golay (default 2)
• sg_npoints – total number of points for Savitzky-Golay (default 5)
• normalize_energy – whether to normalize Raman/ROA to the laser energy (default True)
• despike – despike by adding additional points (default True)

static process_raw_data(raw_data, smooth=True, order=2, sg_npoints=5, normalize_energy=True, despike=False)

Process raw experimental data.

If requested the data are normalized to the laser energy, smoothed and despiked.

Parameters:

• raw_data – laser_energy, X, raman, roa, degcirc
• smooth – whether to smooth the curves with Savitzky-Golay
• order – polynomial order for Savitzy-Golay
• sg_npoints – total number of points for Savitzky-Golay
• normalize_energy – whether to normalize Raman/ROA to the laser energy
• despike – despike by adding additional points

Returns:

X, raman_Y, roa_Y, degcirc_Y

class pyviblib.gui.figures.IRExpFigure(master, X, Y, datatype, **kw)

Infrared absorption figure.

The following public method is exposed:

plot_spectra()

plot the spectra

The following static method is exported:

process_raw_data()

process raw experimental data

Initializer of the class.

Parameters:

• master – parent widget
• X – array with wavenumbers in cm**(-1)
• Y – spectrum, see the datatype keyword
• datatype – see resources.STRINGS_EXP_IR_SPECTRA_TYPES

Accepts all the keyword arguments of the base class.

static get_tex_spectrum_label(datatype, multfactor)

Return the TeX source for the spectrum label.

Parameters:

• datatype – 0 (transmittance), 1(absorbance)
• multfactor – order of magnitude

plot_spectra(**kw)

Plot the spectra.

Parameters:

• datatype – see resouces.STRINGS_EXP_IR_SPECTRA_TYPES
• smooth – whether to smooth the curves with Savitzky-Golay
• order – polynomial order for Savitzy-Golay (default 2)
• sg_npoints – total number of points for Savitzky-Golay (default 5)
• despike – despike by adding additional points (default True)

static process_raw_data(raw_data, orig_datatype, new_datatype, smooth=True, order=2, sg_npoints=5, despike=False)

Process raw experimental data.

If requested the data are smoothed and despiked.

Parameters:

• raw_data – X, Y
• orig_datatype – original data type of raw_data
• new_datatype – data type in which the data are to be recalculated
• smooth – whether to smooth the curves with Savitzky-Golay
• order – polynomial order for Savitzy-Golay
• sg_npoints – total number of points for Savitzky-Golay
• despike – despike by adding additional points

Returns:

X, ir_Y

class pyviblib.gui.figures.PercentageFigure(master, Y, **kw)

Bar chart figure for representing e.g. composition of a mixture.

Initializer of the class.

Parameters:

• master – parent widget
• Y – null-based ndarray

class pyviblib.gui.figures.DCMSumsFigure(master, mol, showvib_callback=None, msgBar=None)

Representing the sums of internuclear distances.

The following public method is exposed:

plot_sums()

plot the sums

Initializer of the class.

Parameters:

• master – parent widget
• mol – molecule with the normal modes
• showvib_callback – callback for showing vibrations
• msgBar – message bar

plot_sums(**kw)

Plot the sums of internuclear distances.

Parameters:

• lim_wavenumbers – left_nu, right_nu) ; left_nu > right_nu (default (3400., 0.))
• tick_wavenumbers – major tick (default 400.)
• labels_fontsize – font size of the axes and spectra labels (default 17)
• title1 – Title at the top of the figure (default ‘’)
• title2 – Smaller title beneath the title1 (default ‘’)

class pyviblib.gui.figures.VOASimilarityCurvesFigure(master, mols, X, sim_y1, sim_y2, **kw)

Raman/ROA similarity curves for single intervals.lues

The following public method is exported:

plot_spectra()

plot the spectra

Initializer of the class.

Parameters:

• mols – list of molecules
• X – X
• sim_y1 – Raman similarity curve
• sim_y2 – ROA similarity curve
• show_hint – whether to show hint text (default False)
• ab – experimental correction (default None)
• interp – increase the number of points (default True)
• ramanroa – True for Raman/ROA, otherwise IR/VCD (default True)

plot_spectra(**kw)

Plot the spectra.

class pyviblib.gui.figures.VibLocalizationsFigure(master, mol, fragment, showvib_callback=None, msgBar=None)

Representing the localizations of vibrations on a fragment.

The following public method is exposed:

plot_localizations()

plot the localizations on the fragment

Initializer of the class.

Parameters:

• master – parent widget
• mol – molecule with the normal modes
• fragment – list of atoms in the fragment, the indices are one-based for instance [5, 7, 8])
• showvib_callback – callback for showing vibrations
• msgBar – message bar

plot_localizations(**kw)

Plot the localization of vibrations on the fragment.

Parameters:

• lim_wavenumbers – (left_nu, right_nu) ; left_nu > right_nu (default (3400., 0.))
• tick_wavenumbers – major tick (default 400.)
• labels_fontsize – font size of the axes and spectra labels (default 17)
• title1 – title at the top of the figure (default ‘’)
• title2 – smaller title beneath the title1 (default ‘’)

class pyviblib.gui.figures.CumulatedNormalizedVibSumsFigure(master, mol, showvib_callback=None, msgBar=None)

Calculated cumulated normalized vibrational sums of VROA.

The following public method is exposed:

plot_sums()

plot the cumulated normalized vibrational sums

Initializer of the class.

Parameters:

• master – parent widget
• mol – molecule with the normal modes
• showvib_callback – callback for showing vibrations
• msgBar – message bar

plot_sums(**kw)

plot the cumulated normalized vibrational sums.

Parameters:

• lim_wavenumbers – left_nu, right_nu) ; left_nu > right_nu (default (1900., 0.))
• tick_wavenumbers – major tick (default 200.)
• labels_fontsize – font size of the axes and spectra labels (default 17)
• title1 – Title at the top of the figure (default ‘’)
• title2 – Smaller title beneath the title1 (default ‘’)
• from_ – from (wavenumber)
• to_ – to (wavenumber)
• voa – 0 for ROA, 1 for VCD
• scattering – scattering (string)

class pyviblib.gui.figures.ExpROACumulatedNormalizedSumsFigure(master, raw_data, **kw)

Experimental cumulated normalized sums of ROA intensities.

Initializer of the class.

Parameters:

• master – parent widget
• raw_data – laser_energy, X, raman, roa, degcirc

plot_sums(**kw)

Plot the experimental cumulated normalized sums of ROA.

Parameters:

• lim_wavenumbers – left_nu, right_nu) ; left_nu > right_nu (default (1900., 0.))
• tick_wavenumbers – major tick (default 200.)
• labels_fontsize – font size of the axes and spectra labels (default 17)
• title1 – Title at the top of the figure (default ‘’)
• title2 – Smaller title beneath the title1 (default ‘’)
• from – from (wavenumber)
• to – to (wavenumber)
• smooth – whether to smooth the curves with Savitzky-Golay
• order – polynomial order for Savitzy-Golay
• sg_npoints – total number of points for Savitzky-Golay