experiments.show_viper module

Providing the “Show VIPER” experiment. This experiment is used to adjust the setup for a VIPER measurement. It displays the VIPER signal as well as the four additional types of signals that can be calculated from this type of experiment. For this experiment, the UV/VIS and IR chopper must be running at different frequencies.

VIPER stands for Vibrationally Promoted Electronic Resonance. Frequency domain VIPER experiments use 2 choppers. One chopper chops the IR Pump, the second one chops the UV/VIS Pump. The IR pump excites the molecules to a higher vibrational state. The UV/VIS pump pulse then excites the molecules from that higher vibrational state to an excited electronic state that is also vibrationally excited. An IR probe pulse is used to measure the changes induced in the molecule.

VIPER measurements typically contain 4 different types of signals. These are listed according to their chopper states:

  • (IR off, UV off): Background

  • (IR off, UV on): TRIR + Background

  • (IR on, UV off): IR pump/IR probe + Background

  • (IR on, UV on): VIPER + TRIR + IR pump/IR probe + Background

TRIR stands for transient IR signal.

Note

Chopper:

It is necessary to adjust the chopper phases. The light pulse travels through a different point of the chopper blade than the reference of the chopper itself. This results in a phase shift between the laser and the position on the chopper where the light passes through. To adjust for that it is necessary to carefully set the phase in such a way that the pulse or part of it is not cut of by the chopper blade. (Also make sure that the diameter of the pulse physically fits through the holes in the chopper blade.) It is also necessary to make sure that a HIGH signal is sent to the ADC when the laser pulse was able to pass through the chopper and a LOW signal is sent to the ADC when when the chopper blade was blocking the light. This adjustment is done via external electronics. For this a circuit that delays the TTL output of the chopper is used. For some kind of choppers additional electronics are required to make the chopper run at the desired frequency (frequency divider). For this experiment the IR Chopper typically runs at 1/4 and the UV/VIS Chopper on 1/2 of the laser frequency.

Choppers at low frequencies:

Sometimes when turning the chopper on and off, the choppers’ phase moves relative to the laser. In the case where the frequency is 1/2 of the laser frequency, this might cause the sign of the observed signal to be flipped. When reducing the frequency further, which is necessary for VIPER measurements, the phase can be out of sync in more than just steps of 180°. Additionally, the duty cycle of the TTL that the delay electronics outputs need to be adapted to the correct length (50%). The two facts can be illustrated with the following examples:

Incorrect duty cycle:

Pump light:     1 1 1 1 0 0 0 0 1 1 1 1 0 0 0 0
Chopper output: H H H L L L L L H H H L L L L L

Incorrect phase:

Pump light:     1 1 1 1 0 0 0 0 1 1 1 1 0 0 0 0
Chopper output: L H H H H L L L L H H H H L L L

If chopper output is not set correctly the signal amplitude that is displayed on the GUI is going to be lower than it actually is. Always correct the duty cycle first and then adjust the phase. The duty cycle is adjusted the most easily by connecting the delayed TTL to an oscilloscope and measuring the duty cycle. The phase is set correctly when the signal has the correct sign and the maximum amplitude. We recommend doing this with the respective show signal for each of the choppers, as it displays only what is currently being adjusted instead of this experiment.

The same problem but with an extra layer of complexity arises when using the wobbler.

Note that alternatively this could be remedied by a different method for referencing the chopper. E.g.: Using a photodiode plus additional electronics to reference the laser light directly or using a light barrier to reference the position on the chopper where the laser passes through.

Step by Step Algorithm:

Acquisition:

  1. Preallocate dictionary (data container) which will contain data and information about scan index, delay index etc.

  2. Read the data from the ADC

  3. Place data into dictionary and hand it over to primary processing

Primary Processing:

  1. Preallocate arrays for data, counts, weights, chopper. Here there are 2 states for each chopper

  2. Subtract background from raw data (dark noise)

  3. Linearize response of pixels

  4. Calculate transmission, or more precisely, relative intensity (probe intensity / reference intensity) for each laser shot for each pixel pair

  5. Identify the chopper states for all laser shots using the corresponding channel(s) in the ADCs’ data for both choppers

  6. Sort the data (transmissions) for each state and calculate statistics

  7. Put this information into data container and hand it over to secondary processing

  8. Average the data by weighting equally

  9. Save data (and raw data) including counts and weights if respective checkboxes on GUI were checked

Secondary Processing:

  1. Calculate the absorption (-log10) of the sorted data

  2. Calculate all difference signals:

    • (IR off, UV off): Background

    • (IR off, UV on): TRIR + Background

    • (IR on, UV off): IR pump/IR probe + Background

    • (IR on, UV on): VIPER + TRIR + IR pump/IR probe + Background

    subtract them in the proper way to obtain:

    • TRIR: (IR off, UV on) - (IR off, UV off)

    • Pseudo TRIR: (IR on, UV on) - (IR on, UV off)

    • IR Pump: (IR on, UV off) - (IR off, UV off)

    • Pseudo IR Pump:(IR on, UV on) - (IR off, UV on)

    • VIPER signal: (IR on, UV on) - (IR on, UV off) - (IR off, UV on) + (IR off, UV off)

  3. Calculate the average intensities and standard deviation of the intensities for each pixel

  4. Put this information into data container and hand it over to Pyqtplotting thread

  5. Calculate the numbers which are displayed in the “statistics box” on the GUI

Pyqt Plotting:

  1. Remove old plots

  2. Setup the plot that displays:

    • All four additional signals

    • VIPER signal

    • Standard deviation of shot to shot signal

    • Intensities and their standard deviation (multiplied by 5)

  3. Plot the plots for the first time

  4. Update plots.

Saving:

programming data dimension:
[(2 ([0] is current average scan, [1] is last single scan), n_probe_pixels, n_ir_chopper_states, n_vis_chopper_states)]

saving dimension:
[(n_probe_pixels, n_ir_chopper_states, n_vis_chopper_states)]

raw data dimension:
[(n_channels, samples_to_acquire)]

Folder Structure

In scans/ the first file of 3 contains the data in the saving dimensions. The counts file contains the number of times a given state was observed. This should be used as weights when averaging equally weighted. The weights file contains the inverse variances of a given state for all pixels, etc. The dimensions of these files are as the saving dimension suggests. These files can be used to average in different ways in order to obtain the complete resulting spectrum. Check the actual code of the corresponding experiment to understand how to calculate the desired end result (VIPER spectrum).

The data in /averaged_data is averaged equally weighted (using counts). Likewise to the scan data the difference spectrum still needs to be calculated from the transmissions for every state. Because the array contains the transmissions averaged with counts it is only intended to be used as a first indicator for the measurement.

The /figure folder is currently empty. It is possible to implement plotting of figures which are saved here while the experiment is running. This is however not implemented yet.

The /hardware config folder holds every file which contains hardware configuration parameters. This folder is a compressed copy of the hardware configuration folder in the software’s directory. Here it is possible to look up the ADC configuration to obtain what channel was connected to which hardware element (e.g. chopper - ai78). It is also possible to obtain the R-2R values, the FPAS configuration, the linearization parameters, etc.

The /raw data folder is in the experiments directory only if the “save raw data” checkbox on the GUI was checked. It contains the raw (unedited… as raw as it can get) data. Basically, the voltages which the ADC measured for each channel. The dimensions are as “raw data dimensions” suggests.

The background.npy file is a copy of the most recently collected dark noise background of the MCT detector array. It corrects for dark noise. If no new background was collected before the experiment was started the code will use the latest available background and display a warning in the log.

setupinfo.txt is a ReadMe file that contains the most relevant experimental parameters at first glance. Additionally, the user can decide to write a comment in the readme editor of the GUI. The content of this is written to the notes.txt file.

username/
├── date1_experimentname1_000/
│   ├── averaged_data
│   │   └──  date1_experimentname1_000.npy
│   ├── figures
│   ├── hardware config
│   ├── raw data
│   │   ├──  s000000_date1_experimentname1_000_raw.npy
│   │   ├──  ...
│   │   └──  s000099_date1_experimentname1_000_raw.npy
│   ├── scans
│   │   ├──  s000000_date1_experimentname1_000.npy
│   │   ├──  s000000_counts_date1_experimentname1_000.npy
│   │   ├──  s000000_weights_date1_experimentname1_000.npy
│   │   ├──  ...
│   │   └──  s000099_date1_experimentname1_000.npy
│   ├── setupinfo_date1_experimentname1_000.txt
│   ├── notes_date1_experimentname1_000.txt
│   └── background_date1_experimentname1_000.npy
├── date1_experimentname1_001/
├── date2_experimentname1_000/
└── date2_experimentname2_000/
class Acquisition(adc: analog_digital_converter.AnalogDigitalConverter, spectrometer: triax.Triax, acq_queue: multiprocessing.context.BaseContext.Queue)[source]

Bases: threading.Thread

Acquisition class (python multithreaded). This is where the actual experiment is conducted.

This class is used to control the hardware devices required for the experiment. The sole purpose of it is to collect the data according to the parameters specified for the experiment by moving the delay stages, opening and closing shutters etc.

A dictionary which will contain data and other information (scan index etc.) is instantiated here. The acquisition class passes the collected information (raw data, scan index etc.) to the primary processing class.

Note

No data processing beyond what is required to conduct the experiment should be implemented in this class. The rationale behind this is to minimize down time/ maximize laser time. Data processing costs computation time and will, generally speaking, slow down the measurement process because the computer is busy while the rest of the hardware is idle. If implemented correctly the data processing could be carried out while the data acquisition is waiting for all data to become available. But even in this scenario the problem that the data processing takes longer than the acquisition time can occur and is thus best avoided through parallelisation.

The reason why this class is a child of the threading module instead of the multiprocessing module is that to use multiprocessing all objects passed to the function must be picklable. This is not the case for some of the objects interfacing with the hardware (e.g. ADC). In an ideal scenario the acquisition too, would run in its own process seperated from the GUI thread but this would only be possible with major restructuring of the software.

Parameters

  • adc (ADC) – Analog to digital converter hardware object which is used to communicate with and read data from the ADC.

  • delay_stage (PiStage) – PiStage hardware control object which provides the interface to the delay stage needed for this experiment.

  • spectrometer (Spectrometer) – Spectrometer/Triax hardware class which grants functionality to control the triax spectrometer. Needed to obtain e.g. wavenumber axis etc.

  • acq_queue (Queue) – Multiprocessing queue object that the acquisition thread uses to pass data to the primary processing process.

run()[source]

Method representing the thread’s activity.

You may override this method in a subclass. The standard run() method invokes the callable object passed to the object’s constructor as the target argument, if any, with sequential and keyword arguments taken from the args and kwargs arguments, respectively.

shutdown()[source]
class PrimaryProcessing(acq_queue: multiprocessing.context.BaseContext.Queue, processing_queue: multiprocessing.context.BaseContext.Queue, pixel_idx: numpy.ndarray, probe_pixel_idx: numpy.ndarray, reference_pixel_idx: numpy.ndarray, index_dict: dict, prl: data_processing.PixelResponseLinearization, ir_chopper_info: dict, vis_chopper_info: dict, background_handler: save_data.Background, saver: Optional[save_data.SaveData] = None)[source]

Bases: multiprocessing.context.Process

Primary processing class (python multiprocess). This class’ purpose is to process the raw data to a state where it can be saved onto the hard drive as npy (binary) files.

This step generally includes linearization, normalisation, sorting and averaging. Besides the actual data additional information that is required for post processing purposes is calculated and saved. I.e. counts and weights. The last step of primary processing should always be to pass the data to secondary processing and save it to the hard disk.

Note

The actual signal(s) are generally not intended to be calculated here. Signals and other information that is supposed to be displayed on the GUI should be calculated in secondary processing. The main reason for this is minimizing the risk of an error leading to a crash of the software which then in turn ruins the measurement. The more code that has to run the more likely a crash becomes. Others reasons mostly imply open questions regarding averaging. Generally, shot to shot normalized intensities that are sorted and averaged by their state are saved (m2 method). From this - for a simple experiment at least - the signal can be easily calculated while offering different choices of averaging in post processing. For more complex experiments e.g. VIPER or time domain experiments the argument of saving sorted transmissions instead of signals is even more compelling. In VIPER experiments more than one signal of interest is present in the different states. Saving each signal separately would actually increase the amount of data that has to be saved. For time domain experiments we want to save the data in the time domain for post processing reasons like zeropadding and apodization.

The goal of primary processing is to make the data as compact as possible while keeping as much information and flexibility as possible. Even if the processes later on crash, the data is secured and can be analysed in post processing.

Parameters

  • acq_queue (Queue) – Multiprocessing queue object that the acquisition thread uses to pass data to the primary processing process.

  • processing_queue (Queue) – Multiprocessing queue object that the primary processing process uses to pass data to the secondary processing process.

  • pixel_idx (ndarray) –

    Array that contains the indices of the rows in the ADCs’ data that correspond to pixel input channels. These are specified in the “analog input configuration.json” for each laboratory and can be easily accessed with the attribute “pixel_idx” of the ADC.

    • shape: 1D

    • E.g.: (64) or (128)

  • probe_pixel_idx (ndarray) –

    Array that contains the indices of the rows in the ADCs’ data that correspond to probe pixel input channels. These are specified in the “analog input configuration.json” for each laboratory and can be easily accessed with the attribute “probe_pixel_idx” of the ADC. It is highly relevant that the order the pixels are listed in this array match the order of the array in the reference_pixel_idx argument. This means that if reference pixel 3 is listed first in the other array here probe pixel 3 needs to be listed first as well and so on. Otherwise the intensities on the probe array are not going to be normalized correctly. For the plotting to work correctly the pixels also need to be listed in the order of the wavenumber axis array of the spectrometer.

    • shape: 1D

    • E.g.: (32) or (64)

  • reference_pixel_idx (ndarray) –

    Array that contains the indices of the rows in the ADCs’ data that correspond to reference pixel input channels. These are specified in the “analog input configuration.json” for each laboratory and can be easily accessed with the attribute “reference_pixel_idx” of the ADC. It is highly relevant that the order the pixels are listed in this array match the order of the array in the probe_pixel_idx argument. This means that if probe pixel 10 is listed first in the other array here reference pixel 10 needs to be listed first as well and so on. Otherwise the intensities on the probe array are not going to be normalized correctly. For the plotting to work correctly the pixels also need to be listed in the order of the wavenumber axis array of the spectrometer.

    • shape: 1D

    • E.g.: (32) or (64)

  • index_dict (dict) – Dictionary that maps the names of the input channels to their corresponding row in the ADCs’ data as they are specified in the “analog input configuration.json” for each laboratory. I.e.: It contains the information which entries of the ADCs’ data array belong choppers, wobblers etc. This dictionary can be easily accessed with the attribute “index_dict” of the ADC.

  • prl (PRL) – Pixel response linearization object which grants the functionality to linearize raw data according to the linearization parameters specified in the corresponding pixel_linearization_fit_parameters.json file (for each lab).

  • ir_chopper_info (dict) – Contains the information that is necessary to identify the different chopper states of the chopper that chops the IR pump pulse. It contains the keys “high voltage level” and “name”. “high voltage level” is the voltage read by the ADC when the chopper reference output is high. It is needed as a reference for the digitization function that is used. The “name” key is required to determine to which channel of the adc the chopper is connected and its value needs to match the corresponding key in index_dict.

  • vis_chopper_info (dict) – Contains the information that is necessary to identify the different chopper states of the chopper that chops the UV/VIS pump pulse. It contains the keys “high voltage level” and “name”. “high voltage level” is the voltage read by the ADC when the chopper reference output is high. It is needed as a reference for the digitization function that is used. The “name” key is required to determine to which channel of the adc the chopper is connected and its value needs to match the corresponding key in index_dict.

  • background_handler (Background) – Instance of Background class which can access the most recently collected background. This background is later subtracted from the raw data as dark noise correction.

  • saver (SaveData) – Object that manages saving of data (including counts, weights, probe wavenumber axis etc.) into their respective directories. If None is passed, no data is going to be saved. If the raw data checkbox was checked on the GUI the savers raw data attribute is set to True and the raw data is saved automatically. Defaults to None.

run()[source]

Method to be run in sub-process; can be overridden in sub-class

class PyqtPlotting(widget_pyqtgraph, adc: analog_digital_converter.AnalogDigitalConverter, plot_queue)[source]

Bases: object

Pyqt Plotting class (Qt multithreaded). This class is necessary for displaying plots on the GUI. PyQtGraph is used as the plotting engine. Generally the plots are set up first (type of plot, layout, title etc.). On the first run, the plots are drawn for the first time. Then the plots are updated every iteration. We update the same plot references every time to make it more efficient.

Parameters

  • widget_pyqtgraph (QWidget) – WidgetPyqtgraph object on which the plots are going to be displayed. Has methods for plot manipulation (i.e. removal of plots, autoscale).

  • adc (ADC) – Analog to digital converter hardware object which is used to communicate with and read data from the ADC.

  • plot_queue (Queue) – Multiprocessing queue object that the secondary processing process uses to pass data to the plot thread.

class Signals[source]

Bases: PyQt5.QtCore.QObject

new_data
run()[source]
update_plot(data_container)[source]
class SecondaryProcessing(processing_queue: multiprocessing.context.BaseContext.Queue, plot_queue: multiprocessing.context.BaseContext.Queue, info_queue: multiprocessing.context.BaseContext.Queue)[source]

Bases: multiprocessing.context.Process

Secondary processing class (python multiprocess). This class is used to process the data from the primary processing class such that it can be displayed on the GUI within plots and lineEdits. This generally implies (if applicable):

  • calculation of signals

  • calculation of statistics like standard deviation of intensities and shot to shot standard deviation of signal

  • interpolation for 2D / heatmap plots (see comments in code why this is necessary)

  • Fourier transform and phasing for time domain data

This data is handed over to the plotting thread.

Note

The feature of saving figures/plots to the hard drive should be implemented here if it is needed.

Parameters

  • processing_queue (Queue) – Multiprocessing queue object that the primary processing process uses to pass data to the secondary processing process.

  • plot_queue (Queue) – Multiprocessing queue object that the secondary processing process uses to pass data to the plot thread.

  • info_queue (Queue) – Multiprocessing queue object which is used to transfer/hand over information to lineEdits on GUI. Contains (if applicable) scan index, delay index, interleave index, values for statistics groupBox etc.

run()[source]

Method to be run in sub-process; can be overridden in sub-class

class ShowViper(widget_pyqtgraph, adc: analog_digital_converter.AnalogDigitalConverter, prl: data_processing.PixelResponseLinearization, ir_chopper_info: dict, vis_chopper_info: dict, background_handler: save_data.Background, spectrometer: triax.Triax, info_queue: multiprocessing.context.BaseContext.Queue, saver: Optional[save_data.SaveData] = None)[source]

Bases: object

Parameters

  • widget_pyqtgraph (QWidget) – WidgetPyqtgraph object on which the plots are going to be displayed. Has methods for plot manipulation (i.e. removal of plots, autoscale).

  • adc (ADC) – Analog to digital converter hardware object which is used to communicate with and read data from the ADC.

  • prl (PRL) – Pixel response linearization object which grants the functionality to linearize raw data according to the linearization parameters specified in the corresponding pixel_linearization_fit_parameters.json file (for each lab).

  • ir_chopper_info (dict) – Contains the information that is necessary to identify the different chopper states of the chopper that chops the IR pump pulse. It contains the keys “high voltage level” and “name”. “high voltage level” is the voltage read by the ADC when the chopper reference output is high. It is needed as a reference for the digitization function that is used. The “name” key is required to determine to which channel of the adc the chopper is connected and its value needs to match the corresponding key in index_dict.

  • vis_chopper_info (dict) – Contains the information that is necessary to identify the different chopper states of the chopper that chops the UV/VIS pump pulse. It contains the keys “high voltage level” and “name”. “high voltage level” is the voltage read by the ADC when the chopper reference output is high. It is needed as a reference for the digitization function that is used. The “name” key is required to determine to which channel of the adc the chopper is connected and its value needs to match the corresponding key in index_dict.

  • background_handler (Background) – Instance of Background class which can access the most recently collected background. This background is later subtracted from the raw data as dark noise correction.

  • spectrometer (Spectrometer) – Spectrometer/Triax hardware class which grants functionality to control the triax spectrometer. Needed to obtain e.g. wavenumber axis etc.

  • info_queue (Queue) – Multiprocessing queue object which is used to transfer/hand over information to lineEdits on GUI. Contains (if applicable) scan index, delay index, interleave index, values for statistics groupBox etc.

  • saver (SaveData) – Object that manages saving of data (including counts, weights, probe wavenumber axis etc.) into their respective directories. If None is passed, no data is going to be saved. If the raw data checkbox was checked on the GUI the savers raw data attribute is set to True and the raw data is saved automatically. Defaults to None.

start()[source]