Imagings code

Architecture

The Imagings folder is defined as a module loaded in CAtImaPy main code.

The code used to acquire, analyze, plot and save series of measurements is included in the class ImagingClass described below. This class defines the Imaging object, attribute of mainWin. The Imaging object contains the information over a measurement and is saved in string and pickle formats in ‘.txt’ and ‘.imo’ files respectively.

Fitting of functions performed in ImagingClass methods uses the sub-module fittool. In this module, the FitUtility performs the fit of a function (instance of FitFunction) on the data. The defined functions available for fitting are listed in fitFunctionsList variable.

ImagingsClass

class Imagings.ImagingClass(dirAndFileName='', mplwidgetImage=None, mplwidgetAnalysisGraph=None)

Bases: object

Class of Imaging object : the center object for aquisition, analysis and saving

__init__(dirAndFileName='', mplwidgetImage=None, mplwidgetAnalysisGraph=None)

Initialize the Imaging object

Keyword Arguments:

• dirAndFileName='' (str) – Absolute path file name with appended number but without extension

• mplwidgetImage=None (None or UImatplotlibWidget) – to plot images or atomic density on UI left graph

• mplwidgetAnalysisGraph=None (None or UImatplotlibWidget) – to plot analysis on UI right graph

Returns:

ImagingClass object

atom_imaging(Camera, averages=1)

Do one point measurements and analysis

Parameters:

Camera (CameraClass) – Camera object

Keyword Arguments:

averages=1 (int) – number of averages

Returns:

If scan performed normally (bool)

fit_Atomic_Cloud_1D(atomicDensityIntZperum2, ROIi, plotFit1D=False)

Make fits for estimation of cloud radii, positions with Gaussian functions.

Fits are done on data integrated along one axis. Fits are done a second time with adjusted position and integration width dependin on other axis results.

Parameters:

• atomicDensityIntZperum2 (2D numpy array float) – measured atomic density data

• ROIi (int) – analysis ROI index (relative to ROI Tabs)

Keyword Arguments:

False (plotFit1D =) – If True, open window to show the 1D fits

Returns:

4-Tuple of 2-list with fit results where the axes are [Y, X]

Return type:

cloudRadiipx, cloudPositionspx, cloudRadiium, cloudPositionsum

fit_LT_measurement(ui)

Fit exponential atom number decay for lifetime measurement

Parameters:

ui (UI.Ui_MainWindow) – GUI object to collect and pass variables and graphs

fit_T_measurement(ui)

Fit results of time of flight scan for temperature measurement

Parameters:

ui (UI.Ui_MainWindow) – GUI object to collect and pass variables and graphs

imaging_scan(Camera, ui)

Do a standard scan of acquistion and analysis (Imaging tab)

Parameters:

• Camera (CameraClass) – Camera object

• ui (UI.Ui_MainWindow) – GUI object to collect and pass variables and graphs

Returns:

If scan performed normally (bool)

imaging_scan_measurement(Camera, ui, averages=1, scans=1)

Do a one-axis scan of measurements and analysis

Parameters:

• Camera (CameraClass) – Camera object

• ui (UI.Ui_MainWindow) – GUI object to collect and pass variables and graphs

Keyword Arguments:

• averages=1 (int) – number of averages (atom_imaging) per scan point

• scans=1 (int) – lenght of scan axis (number of scan points)

Returns:

If scan performed normally (bool)

lifetime_measurement_scan(Camera, ui)

Do a scan of lifetime measurements and analysis (Lifetime tab)

Parameters:

• Camera (CameraClass) – Camera object

• ui (UI.Ui_MainWindow) – GUI object to collect and pass variables and graphs

Returns:

If scan performed normally (bool)

load_imaging_vars_from_dict(dirAndFileName)

Load Imaging object variable from dictionary saved in file

Parameters:

dirAndFileName (str) – Absolute path file name with appended number but without extension

plotAnalysis_update()

Update the analysis (right) graph. Used after changes in Plot tab.

plot_2Ddata_on_mplwidgetImage(data2D, title='Atomic density [atoms/micron^2]')

Show 2Ddata on the left graph in jet colorscale.

Parameters:

data2D (2D numpy array) – 2D data to plot

Keyword Arguments:

[atoms/micron^2]' (title = 'Atomic density) – Title for the left graph

plot_Image_on_mplwidgetImage(imageToPlot, title='Camera image')

Show a camera image on the left graph in grey colorscale.

Parameters:

imageToPlot (2D numpy array) – image to plot

Keyword Arguments:

image' (title = 'Camera) – Title for the left graph

plot_LT_measurement()

Plot results of time scan for lifetime measurement

plot_T_measurement()

Plot results of time of flight scan for temperature measurement

plot_scan_results()

Plot results of standard scan (Imaging tab)

print_dict_full(d, indentation=0)

Returns a string representation of the content of a dictionary for saving.

No line limits, arrays limited to 10000 elements

Parameters:

d (dict) – dictionary to print

Keyword Arguments:

indentation (int) – number of initial linespaces, used in recursive call of function when item is dict

Returns:

String representation of the dict (str)

save_images(dirAndFileNameImages, saveImagesFormat=None)

Save images taken during last atom_imaging.

Parameters:

dirAndFileNameImages (str) – Absolute path file name with appended number and scan(s) number(s) but without extension

Keyword Arguments:

saveImagesFormat=None (None or str) – file format : 0:NPZ (numpy) 1: PNG, 2: TIFF, if None or not int or not 0<= <=2 : take saveImagesFormat attribute

save_images_during_atom_imaging(averages=1)

Save images automatically (called in atom imaging).

save_imaging_vars_as_dict(dirAndFileName=None, SaveAtomicDensity=True)

Save Imaging object as a dictionnary

Save two files : one ‘.txt’ without 2D data and one ‘.imo’ (binary pickle format) 2D data is not saved except atomic density if asked

Parameters:

• dirAndFileName (None or str) – Absolute path file name with appended number but without extension

• SaveAtomicDensity (bool) – Decide if 2D data of atomic density should be saved in ‘.imo’ file

set_Imaging_variables_from_cam(Camera)

Initialize some Imaging object variables from the Camera object variables

Parameters:

Camera (CameraClass) – Camera object

set_ROIs_from_ROIarray(ROIarray)

Refresh analysis ROI defintions from ROIarray loaded from UI

Parameters:

ROIarray (numpy array 6*n dtype = str) – analysis ROI defintions

temperature_measurement_scan(Camera, ui)

Do a scan of temperature measurements and analysis (Temperature tab)

Parameters:

• Camera (CameraClass) – Camera object

• ui (UI.Ui_MainWindow) – GUI object to collect and pass variables and graphs

Returns:

If scan performed normally (bool)

Fitting

class Imagings.fittool.FitUtility(x, y, fitFunction, yerr=None, p_in=None, p_fix=None, NumberOfSteps=None, printbool=False)

Bases: object

Class to fit function to data.

__init__(x, y, fitFunction, yerr=None, p_in=None, p_fix=None, NumberOfSteps=None, printbool=False)

Initialize class instance and fit function to data

Parameters:

• x (list or np.array or None) – x vector of data to fit. If None, then x=np.arange(len(y)).

• y (list or np.array) – y vector of data to fit.

• fitFunction (FitFunction) – the function to fit to data.

Keyword Arguments:

• yerr (list or np.array or None) – the error in the y vector.

• p_in (list or None) – initial fit parameters.

• p_fix (list or None) – array of strings or values.

• NumberOfSteps (int or None) – number how many y-fitted points will generated for plotting arrays xfit and yfit. If None, NumberOfSteps = len(y).

• printbool (bool) – if the parameters info of the fit should be printed.

class Imagings.fittool.FitFunction

Bases: object

Class of function for use in FitUtility

__init__()

execute(p, x)

Function execution.

Parameters:

• p (list(float)) – function parameters.

• x (float) – function variable.

Returns:

function value.

Return type:

y (float)

getinits(x, y)

Automatic initialization of function parameters.

Parameters:

• x (list or np.array) – x vector of data to fit.

• y (list or np.array) – y vector of data to fit.

Returns:

function parameters.

Return type:

pinits (list(float))