Visualization#

In the Visualization tab, users create publication-quality figures, including 2D contour maps, ΔA spectral and kinetic slices, and specialized plots for local and global fits. Graphical attributes including colors, axis limits and scales, legends, normalizations, figure sizes, and fonts can be adjusted interactively or via Matplotlib’s rcParams. Complete matplotlibrc files may be loaded to match journal styles. Figures export to vector formats (PDF, SVG) or raster images (JPG, PNG, TIFF), and underlying data can be saved as CSV for use in external graphic tools.

Dataset Widget

select the dataset to which the processing should be applied.
Plot Widget

select the plot type.
- 2D Plot
  
  Plot the 2D hypersphere of the dataset
- ΔA Plot
  
  Plot spectral slices at selected delay times
- Kin Trace
  
  Plot kinetic slices at selected wavelengths
- Local Fit
  - Kin Trace
    
    Plot fit results at selected local fit wavelength
  - Posterior Dist
    
    Plot the corner representation of the results of the MCMC parameter posterior analysis
- Global Fit
  - 2D Plot
    
    Plot the 2D hypersphere of the fitted data or the residuals of a selected global fit
  - EAS/DAS/SAS
    
    Plot the Evolution-associated, decay-associated or species-associated spectra of a selected global fit
  - Concentration
    
    Plot the time-dependendt evolution of the concentration of each component of a selected global fit
  - ΔA Plot
    
    Plot spectral slices at selected delay times of a selected global fit
  - Kin Trace
    
    Plot kinetic slices at selected wavelengths of a selected global fit
  - Posterior Dist
    
    Plot the corner representation of the results of the MCMC parameter posterior analysis
Figure Style Widget

Figure styling widget, applied to every plot type and used for exporting
- Add rcParam
  
  add a matplotlib rcParam key and value pair to temporarily overwrite the current rcParams style sheet. In the toolbar, a new or custom rcParams style sheet can be loaded in (see Main Window for mor information). More infomrations on the various rcParams can be found in the matplotlib user guide.
- Figure Size
  
  Set the figure dimensions: first entry width, second entry height. Accepted units are inch (“), mm or cm.
- Show Real Size?
  
  If checked, the figure canvas will be adjusted to match the actual real-world figure dimensions.
- Figure Font
  
  Select one preinstalled font on your local machine
- Font Style
  
  Select one available font style of the selected and installed font family
- Label Size
  
  Set the size of all axes labels, legends, and titles in point.
- Tick Size
  
  Set the size of all tick labels in point.
- Format
  
  Select a vector graphic or rastergraphic format. If a rastergraphic (e.g. png, jpg, tiff) is selected, the DPI value can be set subsequently. If a vector graphics format is selected, the text information can be saved as text or as Path. Rendering as text gives the opportunity to change the text with a suitable vector graphics editing program like Inkscape. However, different image displaying programs might change the font style and family slightly if the font is not available on the target device. Saving as path burrys the text information as object information, so no text editing is possible afterwards. However, the text will always be displayed as expected and no preinstalled font is necessary at the target device.
- Result Dir
  
  Set the path, where the figure will be saved to. If none is set, the project path will be used or a file dialog will open up.
- Save
  
  Save the figure with the current settings to the current directory. Depending on the metadata, filenames and subfolders will be automatically created.
- Save as..
  
  Opens a file dialog where the user can select a directory to which the figure will be saved to.
- export data
  
  In the figure canvas, export data saves the data to produce the current figure to CSV using the results directory set in the Figure Style Widget.
Plot Properties

The Plot Properties change depending on the plot type selected in the Plot Widget
- 2D Plot
  - Wavelength
    
    set the minimum (left) and maximum (right) wavelength value which will be plotted. Leaving this empty will use the minimum / maximum value available in the dataset.
  - Delay
    
    set the minimum (left) and maximum (right) delay value which will be plotted. Leaving this empty will use the minimum / maximum value available in the dataset.
  - ΔA
    
    set the minimum (left) and maximum (right) ΔA value in mOD which will be plotted. Leaving this empty will use the minimum / maximum value available in the dataset. The spinbox sets the center of the colorbar in mOD.
  - Lin/Log Transition
    
    set delay time from where on the delay axis changes from a linear to a logarithmic scale.
  - Ratio (Lin|Log|ss)
    
    set the relative height of the linear, logarithmic and steady-state (optional) areas of the plot
  - Hide Area
    
    set the minimum (left) and maximum (right) x-axes value which will be left empty in the figure. Usefull for hiding scattered light area or areas of low detector sensitivity.
  - Colormap
    
    ticking the checkbox will display the colorbar. Different colorschemes can be selected in the dropdown menu, right or bottom will locate the colorbar accordingly.
  - Display ΔA Cuts
    
    if checked, the selected ΔA cuts in the ΔA Plot window are displayed with the related colors.
  - Display Kinetic Cuts
    
    if checked, the selected kinetic cuts in the Kin Trace window are displayed with the related colors.
  - Display 2nd Axis
    
    plots a second energy axis on top in eV.
  - Display Metadata
    
    displays the metadata set in the Import Tab as the title.
  - Display Pump
    
    displays the pump wavelength as a vertical line. the pump wavelength needs to be set first in the Import Tab.
- DeltaA Plot
  - Wavelength
    
    set the minimum (left) and maximum (right) wavelength value which will be plotted. Leaving this empty will use the minimum / maximum value available in the dataset.
  - ΔA
    
    set the minimum (left) and maximum (right) ΔA value in mOD which will be plotted. The scale (linear, logarithmic or semi-logarithmic) can be set in the drop-down menu. If linlog is selected, a value where the scale switches from linear to logarithmic can be set.
  - Show Legend
    
    if ticked, displays the legend at the current positional argument. Outside positions the legend on the right next to the figure, best lets matplotlib decide where to plot the legend and the other arguments display the legend accordingly.
  - Delay Times
    
    set the delay times which will be displayed in the figure, separated by commas.
  - Colors
    
    the field on the right side accepts named matplotlib colors (e.g. blue, r, coral, etc) or hex values (e.g. #123456). Each color value correspond to one slice and must be separated by a comma. Further, a gradient colorscheme or the default color cylcer of the current global style (-) can be used. If the number of custom colors set is lower than the slices, the current gradient colorschme is used.
  - Hide Area
    
    set the minimum (left) and maximum (right) x-axes value which will be left empty in the figure. Usefull for hiding scattered light area or areas of low detector sensitivity.
  - Display 2nd Axis
    
    if checked, plots a second energy axis on top in eV.
  - Display Metadata
    
    if checked, displays the metadata set in the Import Tab as the title.
  - Display Pump
    
    if checked, displays the pump wavelength as a vertical line. the pump wavelength needs to be set first in the Import Tab.
- Kin Trace
  - Delay
    
    set the minimum (left) and maximum (right) delay value which will be plotted. The scale (linear, logarithmic or semi-logarithmic) can be set in the drop-down menu. If linlog is selected, a value where the scale switches from linear to logarithmic can be set.
  - ΔA
    
    set the minimum (left) and maximum (right) ΔA value in mOD which will be plotted. The scale (linear, logarithmic or semi-logarithmic) can be set in the drop-down menu. If linlog is selected, a value where the scale switches from linear to logarithmic can be set.
  - Show Legend
    
    if ticked, displays the legend at the current positional argument. Outside positions the legend on the right next to the figure, best lets matplotlib decide where to plot the legend and the other arguments display the legend accordingly.
  - Wavelengths
    
    set the wavelengths which will be displayed in the figure, separated by commas.
  - Colors
    
    the field on the right side accepts named matplotlib colors (e.g. blue, r, coral, etc) or hex values (e.g. #123456). Each color value correspond to one slice and must be separated by a comma. Further, a gradient colorscheme or the default color cylcer of the current global style (-) can be used. If the number of custom colors set is lower than the slices, the current gradient colorschme is used.
  - Normalize
    
    if checked, the ΔA values are normalized so that the maximum absolute value is 1 within the given interval.
  - Absolute Values
    
    if checked, the absolute (only positive) values are displayed. Might be valuable when comparing a bleaching and an induced absorption signal.
  - Display Metadata
    
    if checked, displays the metadata set in the Import Tab as the title.
- Kin Trace (Local Fit)
  - Select Kinetic Fits
    
    select one or multiple local fits to be displayed. Local fits must be performed and saved first in the Local Fitting tab.
  - Colors
    
    the field on the right side accepts named matplotlib colors (e.g. blue, r, coral, etc) or hex values (e.g. #123456). Each color value correspond to one local fit and must be separated by a comma. Further, a gradient colorscheme or the default color cylcer of the current global style (-) can be used. If the number of custom colors set is lower than the components, the current gradient colorschme is used.
  - Delay
    
    set the minimum (left) and maximum (right) delay value which will be plotted. The scale (linear, logarithmic or semi-logarithmic) can be set in the drop-down menu. If linlog is selected, a value where the scale switches from linear to logarithmic can be set.
  - ΔA
    
    set the minimum (left) and maximum (right) ΔA value in mOD which will be plotted. The scale (linear, logarithmic or semi-logarithmic) can be set in the drop-down menu. If linlog is selected, a value where the scale switches from linear to logarithmic can be set.
  - Show Legend
    
    if ticked, displays the legend at the current positional argument. Outside positions the legend on the right next to the figure, best lets matplotlib decide where to plot the legend and the other arguments display the legend accordingly.
  - Normalize
    
    if checked, the ΔA values are normalized so that the maximum absolute value is 1 within the given interval.
  - Absolute Values
    
    if checked, the absolute (only positive) values are displayed. Might be valuable when comparing a bleaching and an induced absorption signal.
  - Show Experimental Data
    
    if checked, experimental data will be displayed as crosses together with the fitted lines
  - Show Components
    
    if checked, the underlying components, or Coherent Artifacts are displayed with dashed lines (only when more than one component is used to fit the data).
  - Show Lifetimes
    
    if checked, the lifetime values are displayed in the legend
  - Show Residuals
    
    if checked, the residuals are plotted below the figure.
  - Display Metadata
    
    if checked, displays the metadata set in the Import Tab as the title.
- Posterior Dist (Local Fit)
  
  most settings are based on the API of the underlying corner package in python which can be found here.
  - Select Fit
    
    select one local fit to be displayed. Local fits and a parameter space analysis must be performed and saved first in the Local Fitting tab.
  - Bins
    
    set the number of bins used for the histogram.
  - Label Pad
    
    set spacing between the label and the figures and tick labels. This parameter generally needs to be tweaked to avoid clipping.
  - Subplot Pad
    
    set the spacing between each subplot.
  - Max # of Ticks
    
    set the maximum number of ticks for each subplot.
  - Show Values
    
    if checked, the “true” values of the MCMC posterior analysis of each parameter are displayed as straight lines.
  - Show Errors
    
    if checked, the values plus minus the 16th and 84th percentile (corresponding to the 1-sigma level) are displayed above each column.
  - Show Median
    
    if checked, the values plus minus the 16th and 84th percentile are displayed in the histogram as dashed lines corresponding to the 1-sigma level as well as the median.
  - Show Datapoints
    
    if checked, every individual datapoint is plotted.
  - Show Contours
    
    if checked, contour lines are plotted.
  - Plot Density
    
    if checked, a grayscale density map is plotted.
- 2D Plot (Global Fit)
  - Select Global Fit
    
    select one gloabl fit to be displayed. Global fits must be performed and saved first in the Global Fitting tab.
  - Type
    
    simulated plots the simulated dataset, residuals plots the 2D residual map and merge plots the residuals higher than a threshold value overlayed with the simulated data (positive deviations in white, negative deviations in black).
  - Wavelength
    
    set the minimum (left) and maximum (right) wavelength value which will be plotted. Leaving this empty will use the minimum / maximum value available in the dataset.
  - Delay
    
    set the minimum (left) and maximum (right) delay value which will be plotted. Leaving this empty will use the minimum / maximum value available in the dataset.
  - ΔA
    
    set the minimum (left) and maximum (right) ΔA value in mOD which will be plotted. Leaving this empty will use the minimum / maximum value available in the dataset. The spinbox sets the center of the colorbar in mOD.
  - Lin/Log Transition
    
    set delay time from where on the delay axis changes from a linear to a logarithmic scale.
  - Ratio (Lin|Log)
    
    set the relative height of the linear and logarithmic areas of the plot.
  - Colormap
    
    ticking the checkbox will display the colorbar. Different colorschemes can be selected in the dropdown menu, right or bottom will locate the colorbar accordingly.
  - Hide Area
    
    set the minimum (left) and maximum (right) x-axes value which will be left empty in the figure. Usefull for hiding scattered light area or areas of low detector sensitivity.
  - Display 2nd Axis
    
    plots a second energy axis on top in eV.
  - Display Metadata
    
    displays the metadata set in the Import Tab as the title.
  - Display Pump
    
    displays the pump wavelength as a vertical line. the pump wavelength needs to be set first in the Import Tab.
- EAS/DAS/SAS (Global Fit)
  - Select Global Fit
    
    select one gloabl fit to be displayed. Global fits must be performed and saved first in the Global Fitting tab.
  - Wavelength
    
    set the minimum (left) and maximum (right) wavelength value which will be plotted. Leaving this empty will use the minimum / maximum value available in the dataset.
  - ΔA
    
    set the minimum (left) and maximum (right) ΔA value in mOD which will be plotted. The scale (linear, logarithmic or semi-logarithmic) can be set in the drop-down menu. If linlog is selected, a value where the scale switches from linear to logarithmic can be set.
  - Show Legend
    
    if ticked, displays the legend at the current positional argument. Outside positions the legend on the right next to the figure, best lets matplotlib decide where to plot the legend and the other arguments display the legend accordingly.
  - Normalize
    
    if checked, the ΔA values are normalized so that the maximum absolute value is 1 within the given interval.
  - Colors
    
    the field on the right side accepts named matplotlib colors (e.g. blue, r, coral, etc) or hex values (e.g. #123456). Each color value correspond to one slice and must be separated by a comma. Further, a gradient colorscheme or the default color cylcer of the current global style (-) can be used. If the number of custom colors set is lower than the slices, the current gradient colorschme is used.
  - Hide Area
    
    set the minimum (left) and maximum (right) x-axes value which will be left empty in the figure. Usefull for hiding scattered light area or areas of low detector sensitivity.
  - Display 2nd Axis
    
    if checked, plots a second energy axis on top in eV.
  - Display Metadata
    
    if checked, displays the metadata set in the Import Tab as the title.
  - Display Pump
    
    if checked, displays the pump wavelength as a vertical line. the pump wavelength needs to be set first in the Import Tab.
- Concentration (Global Fit)
  - Select Global Fit
    
    select one gloabl fit to be displayed. Global fits must be performed and saved first in the Global Fitting tab.
  - Delay
    
    set the minimum (left) and maximum (right) delay value which will be plotted. The scale (linear, logarithmic or semi-logarithmic) can be set in the drop-down menu. If linlog is selected, a value where the scale switches from linear to logarithmic can be set.
  - Conc
    
    set the minimum (left) and maximum (right) relative concentration value will be plotted. The scale (linear, logarithmic or semi-logarithmic) can be set in the drop-down menu. If linlog is selected, a value where the scale switches from linear to logarithmic can be set.
  - Show Legend
    
    if ticked, displays the legend at the current positional argument. Outside positions the legend on the right next to the figure, best lets matplotlib decide where to plot the legend and the other arguments display the legend accordingly.
  - Colors
    
    the field on the right side accepts named matplotlib colors (e.g. blue, r, coral, etc) or hex values (e.g. #123456). Each color value correspond to one slice and must be separated by a comma. Further, a gradient colorscheme or the default color cylcer of the current global style (-) can be used. If the number of custom colors set is lower than the slices, the current gradient colorschme is used.
  - Display Metadata
    
    if checked, displays the metadata set in the Import Tab as the title.
- DeltaA Plot (Global Fit)
  - Select Global Fit
    
    select one gloabl fit to be displayed. Global fits must be performed and saved first in the Global Fitting tab.
  - Wavelength
    
    set the minimum (left) and maximum (right) wavelength value which will be plotted. Leaving this empty will use the minimum / maximum value available in the dataset.
  - ΔA
    
    set the minimum (left) and maximum (right) ΔA value in mOD which will be plotted. The scale (linear, logarithmic or semi-logarithmic) can be set in the drop-down menu. If linlog is selected, a value where the scale switches from linear to logarithmic can be set.
  - Show Legend
    
    if ticked, displays the legend at the current positional argument. Outside positions the legend on the right next to the figure, best lets matplotlib decide where to plot the legend and the other arguments display the legend accordingly.
  - Delay Times
    
    set the delay times which will be displayed in the figure, separated by commas.
  - Colors
    
    the field on the right side accepts named matplotlib colors (e.g. blue, r, coral, etc) or hex values (e.g. #123456). Each color value correspond to one slice and must be separated by a comma. Further, a gradient colorscheme or the default color cylcer of the current global style (-) can be used. If the number of custom colors set is lower than the slices, the current gradient colorschme is used.
  - Hide Area
    
    set the minimum (left) and maximum (right) x-axes value which will be left empty in the figure. Usefull for hiding scattered light area or areas of low detector sensitivity.
  - Show Experimental Data
    
    if checked, experimental data will be displayed as crosses together with the fitted lines.
  - Show Residuals
    
    if checked, the residuals are plotted below the figure.
  - Display 2nd Axis
    
    if checked, plots a second energy axis on top in eV.
  - Display Metadata
    
    if checked, displays the metadata set in the Import Tab as the title.
  - Display Pump
    
    if checked, displays the pump wavelength as a vertical line. the pump wavelength needs to be set first in the Import Tab.
- Kin Trace (Global Fit)
  - Select Global Fit
    
    select one gloabl fit to be displayed. Global fits must be performed and saved first in the Global Fitting tab.
  - Delay
    
    set the minimum (left) and maximum (right) delay value which will be plotted. The scale (linear, logarithmic or semi-logarithmic) can be set in the drop-down menu. If linlog is selected, a value where the scale switches from linear to logarithmic can be set.
  - ΔA
    
    set the minimum (left) and maximum (right) ΔA value in mOD which will be plotted. The scale (linear, logarithmic or semi-logarithmic) can be set in the drop-down menu. If linlog is selected, a value where the scale switches from linear to logarithmic can be set.
  - Show Legend
    
    if ticked, displays the legend at the current positional argument. Outside positions the legend on the right next to the figure, best lets matplotlib decide where to plot the legend and the other arguments display the legend accordingly.
  - Wavelengths
    
    set the wavelengths which will be displayed in the figure, separated by commas.
  - Colors
    
    the field on the right side accepts named matplotlib colors (e.g. blue, r, coral, etc) or hex values (e.g. #123456). Each color value correspond to one slice and must be separated by a comma. Further, a gradient colorscheme or the default color cylcer of the current global style (-) can be used. If the number of custom colors set is lower than the slices, the current gradient colorschme is used.
  - Normalize
    
    if checked, the ΔA values are normalized so that the maximum absolute value is 1 within the given interval.
  - Absolute Values
    
    if checked, the absolute (only positive) values are displayed. Might be valuable when comparing a bleaching and an induced absorption signal.
  - Show Experimental Data
    
    if checked, experimental data will be displayed as crosses together with the fitted lines.
  - Show Residuals
    
    if checked, the residuals are plotted below the figure.
  - Display Metadata
    
    if checked, displays the metadata set in the Import Tab as the title.
- Posterior Dist (Global Fit)
  
  most settings are based on the API of the underlying corner package in python which can be found here.
  - Select Fit
    
    select one gloabl fit to be displayed. Global fits and a parameter space analysis must be performed and saved first in the Global Fitting tab.
  - Bins
    
    set the number of bins used for the histogram.
  - Label Pad
    
    set spacing between the label and the figures and tick labels. This parameter generally needs to be tweaked to avoid clipping.
  - Subplot Pad
    
    set the spacing between each subplot.
  - Max # of Ticks
    
    set the maximum number of ticks for each subplot.
  - Show Values
    
    if checked, the “true” values of the MCMC posterior analysis of each parameter are displayed as straight lines.
  - Show Errors
    
    if checked, the values plus minus the 16th and 84th percentile (corresponding to the 1-sigma level) are displayed above each column.
  - Show Median
    
    if checked, the values plus minus the 16th and 84th percentile are displayed in the histogram as dashed lines corresponding to the 1-sigma level as well as the median.
  - Show Datapoints
    
    if checked, every individual datapoint is plotted.
  - Show Contours
    
    if checked, contour lines are plotted.
  - Plot Density
    
    if checked, a grayscale density map is plotted.