Pauli

Pauli is a flexible tool for loading and working with ExpWiz-created PNG files. It builds heavily on its predecessor, QMLi, trying to streamline and generalize the process of working with the images taken by CameraControl.

Who should use Pauli and what does it do?

Pauli is written as a general as possible and should thus be useful for anybody who runs their experiment using the ExperimentWizard. At its core, Pauli does everything neccessary for going from a folder full of .png images taken by CameraControl to a useable data structure filled with density matrices. To accomplish that, Pauli can detect the shots and loopvars taken, load the images, extract the XML, and run the images through a user defined function to convert them to density matrices.

How is Pauli structured?

Generally speaking, a user should not need to modify Pauli except for the files specific to their experiment and mode. Each "Experiment" (for example, the Lithium-6 machine in Hamburg) has its own subfolder in Pauli/Experiments/ - and inside that subfolder, configuration files can be found for the "Modes" - which can, for example, be different Cameras. These files, however, do not need to be created by hand - a setup script is provided for that. The structure of the Pauli object is defined by the classes found in the main folder.

Pauli (Main Object)
|
|-	constants (PauliConstants object containing Physical Constants)
|	|-	user (struct for all user defined constants, such as atomic masses of the element used) 
|
|-	data (PauliData object containing data loaded from Images)
|	|-	images (All images the user requested to be saved in matrix form)
|	|-	density (Cell array of density matrices)
|	|- 	xml (Cell array of extracted XML in text form)
|	|- 	user (struct for all user defined data)
|
|-	parameters (PauliParameters object containing parameters defining the operation of Pauli defined by the user)
	|-	verbose (flag defining whether output is written to the console)
	|-	loopvars (loopvars used for this run in ExpControl)
	|-	files (Cell array of all filenames found in the folder)
	|-	images (Cell array of shots taken in the folder)
	|-	imagesToLoad (Cell array of shots to be loaded by Pauli)
	|-	imagesToSave (Cell array of shots the user wants to keep after calculating the density matrices) 
	|-	crop (Array with the amount of pixels to be cropped from the images in from {Left, Right, Top Bottom})
	|-	convertToDensityFunctionName (For internal use)
	|-	user (struct for all user defined parameters, such as current, non-constant info about the setup like the magnification)

How is Pauli Setup

• Clone the repository to your MATLAB-Folder (or elsewhere and add it to your path)
• Type Pauli_Setup into the MATLAB console and follow the instructions on screen.
  • You will first be prompted whether you want to create a new Experiment or a new Mode. An Experiment refers to a specific Quantum Gas Machine. A Mode can be anything else - a new Camera, a different density computation method...
  • You then get to set a name for your new Experiment and Mode.
  • The setup script automatically creates all relevant files for you and opens them.
• At this stage, you should have a file open called make_EXPERIMENTNAME_MODENAME.m as well as one called convertToDensity_EXPERIMENTNAME_MODENAME.m
  • Fill in the parameters and constants you need in the make_EXPERIMENTNAME_MODENAME.m and run it once. This will create a MODENAME.pauli file, which you can later load to obtain a Pauli object with all your configuration presets.
  • Enter your Experiments prefered method to calculate a density matrix from the images loaded in the convertToDensity_EXPERIMENTNAME_MODENAME.m. There is an extensive comment describing how and what the parameters are. Feel free to check out other experiments methods for inspiration!
• Thats it! Pauli is ready to be used. If you want to modify your parameters, just modify the make_EXPERIMENTNAME_MODENAME.m and run it again.

How is Pauli used

• Make sure Pauli is on your Matlab Path
• Type pauli = Pauli('Experiments/EXPERIMENTNAME/MODENAME.pauli', 'PATH TO THE FOLDER WITH YOUR IMAGES');
• You are done! Pauli will automatically load your configuration, scan the files in the folder, and load and convert all images.

Advanced use

If you do not want to automatically load all images, but for example only a specific set:

• Type pauli = Pauli('Experiments/EXPERIMENTNAME/MODENAME.pauli');
• Type pauli.autoDetect('PATH TO THE FOLDER WITH YOUR IMAGES');
• Now, pauli.parameters.loopvars contains the different loopvariables detected and the values found in the folder.
• Modify the values to your wishes
• Finally, type pauli.createDensities; to load the images and convert them to densities and run pauli.save; to save the results to speed up future evaluations