Comparative plotting
The comparative plotting is an important tool to compare different measurements (e.g. different conditions), different fits or steady state spectra. In general you can compare different kinetics (at one or multiple fixed wavelength) with Compare_at_wave , compare different spectra at one or multiple given timepoints with Compare_at_time and compare the extracted spectra (decay associated or species associated) with Compare_DAC. The essential idea is that the parameters in the project that contains the comparative plotting are used for all the plots. So the ta.bordercut or ta.intensity is used for all the plot, independent of e.g. the intensity in the other projects.
New is that the compare functions take “other” as a parameter, which can be either a single or multiple projects (TA - objects). These projects need to be loaded into the program. Loading a project can be done by having them open from prior import or analysis (e.g. when comparing different fits) and then using
More usual other (saved) projects will be opened with the function
. See Opening multiple files for more information on that.
As this comparision very often contains a lot of files the images are automatically saved using the filenames and the wavelength/time points. The images are however open and if the standard approach using QT was used can be manipulated using the GUI tools. So is e.g. the conversion into a linear time-axis currently not implemented, but can easily be achieved by changing the axis in the QT GUI.
A very important function provided by this set of tools is the comparision against other spectra. So can for examples be reference spectra (e.g. UV-vis) be added to the plots.
Normalization and Scaling
An important option is the normalization in a certain window that applies for both Compare_at_time and Compare_at_wave. Very often data needs to be normalized before it can be compared to anything e.g. to the size of the ground state bleach or an excited state absorption. Here I offer the normalization in a certain window in time and space. In this window a value in the “ta” and then each of the “other” projects is calculated. The intensity of each in the other projects (but not of the “ta” project) is then mutliplied by the quotient of this value in this specific window. This means e.g. that even if the kinetics is plotted for 600nm the normalization can be performed at 1-2ps at 450-500nm. This is very useful to plot e.g. the efficiency of product formation in the study of catalytic processes. For this normalization a “window” needs to be defined in the order:
[Start time, End time, Start wavelength, End Wavelength]
Care should be take to where this normalization is performed. The region just around t=0 is dangerous due to the artifacts, that do not represent real values. If external values are suppose to be used for scaling, the individual intensities can be manipulated. For each of the loaded projects ta.ds is the matrix that contains the data. With:
"ta.ds*=1.1"
could for example the individual intensity be raised by 10%. But be aware that with this action you are changing the data in the object. The original data ta.ds_ori remains unchanged. If you save and reload the data, the intensity will revert to the originally measured value.
Compare_at_time
This function plots multiple spectra into the same figure at one or multiple given timepoints (rel_time) and allows for Normalization and Scaling
Very useful to compare the spectra for different solvents or quenchers, or e.g. different fits. The ta.time_width_percent parameter defines if this is a single time (if time_width_percent = 0) or an integrated window.
A normalization window can be given at which all the plotted curves are normalized to. This window does not have to be in the plotted region. See Normalization and Scaling
Very often one would like to compare the measured spectra at a certain time to an external spectrum (e.g. spectro-electro-chemistry or steady state absorption). This can be done by loading a specific spectrum into a DataFrame and handing this data Frame to the comparision function. The function can also be used to plot e.g. the measured spectra vs. an external spectrum without giving any “other” Projects.
For more information, details on the parameter and examples see:
Compare_at_wave
This function plots multiple kinetics into the same figure at one or multiple given wavelength (rel_wave) and allows for Normalization and Scaling Very useful to compare the kinetics for different quencher concentrations or pump powers, or e.g. different fits. The parameter width or the general ta.wavelength_bin defines the width of the spectral window that is integrated and shown.
A normalization window can be given at which all the plotted curves are normalized to. This window does not have to be in the plotted region. See Normalization and Scaling
Often multiple wavelength are to be plotted, and if at the same time many projects go into the same plot, things tend to get messy. As the files are saved separately this approach proofed to be useful.
For more information, details on the parameter and examples see:
Compare_DAC
This is a convenience function to plot multiple extracted spectra (DAS or species associated) into the same figure or into a separate figure each. Other should be ta.plot_func objects (loaded or copied). By standard it plots all into the same window. If all project have the same number of components one can activate “separate_plots” and have each separated (in the order created in the projects).
The “Spectra” parameter allows as before the inclusion of an external spectrum. Others is optional and I use this function often to compare species associated spectra with one or multiple steady state spectra.
For more information, details on the parameter and examples see: