Add hyperdaq hook to scanner #99
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A number of changes have been made in this commit to support the addition of a hyper-data acquisition callback function. This function allows an external user to define a function to be called at each position of the scan. This function may also be executed in a separate thread if the 'in_parallel' attribute of the funciton is set. In support of this function, a number of other smaller changes were made. A run_scan function was added in order to facilitate use of CounterAndScanner objects. A callback function for that is also provided so the GUI application pizeoscan.py may update it's display upon completion of a raster line. Unnecessary checks for stage_controller != None were removed since this object does not support instantiation without a stage_controller. (Although, future updates should provide proper type hinting.) The position of the scan is no longer tracked by the CounterAndScan object, but instead relies upon the last_write_values attribute of the stage_controller object.
A misconception about the hardware led to incorrect variable names and documentation. Initially, the piezo actuator that controls the position of the laser light impinging upon a sample was called a "stage" controller due to a misunderstanding of the hardware setup. This labeling perpetuated until this change. All usage of "stage" control has been replaced either with "position" control or actuator, where appropriate. Variable naming may still feel a bit off in places. Please fix if you have better ways of describing functionality.
In particular, shows how to run a test scan based on a 'dummy' position controller and random data generator. This is useful for testing purposes. Also demonstrates how to use hyper data acquisition callback function.
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This PR adds a hook to the ControlAndScanner object -- also known as the NiDaqPiezoScanner -- which can be used to acquire secondary data at each position of the generated 2D image.
An important use case of this hook will be to acquire photon energy spectra at each position of the image, thereby generating a hyper spectral image.
Since not only could photon energy spectra be taken at each position, we call this function the "hyper data acquisition" function. For example, one could be interested in measuring Rabi oscillations or performing Ramsey measurements at each location of a sample if there was desire to image external magnetic fields.
An example Jupyter notebook has been added to demonstrate usage.
Also, some internal changes were made to correct a misconception about the QT3 hardware that was manifested as poor variable names and logging statements. In particular, during the initial development of the confocal scan code, it was thought that the piezo actuator
controlled the position of the stage. This concept resulted in variable names such as
stage_controllerand logging statements that reported the "stage" position. This PR fixes those variable names. Though one can argue this particular change should be done in a separate PR, we do it here for the sake of expediency.