diff --git a/Analyser/ImagingAnalyser.py b/Analyser/ImagingAnalyser.py index 068918a..488e68c 100644 --- a/Analyser/ImagingAnalyser.py +++ b/Analyser/ImagingAnalyser.py @@ -196,16 +196,16 @@ class ImageAnalyser(): return dataSet.isel(x=slice(x_start, x_end), y=slice(y_start, y_end)) def get_OD(self, imageAtom, imageBackground, imageDrak): - """_summary_ - - :param imageAtom: _description_ - :type imageAtom: _type_ - :param imageBackground: _description_ - :type imageBackground: _type_ - :param imageDrak: _description_ - :type imageDrak: _type_ - :return: _description_ - :rtype: _type_ + """Calculate the OD image for absorption imaging. + + :param imageAtom: The image with atoms + :type imageAtom: numpy array + :param imageBackground: The image without atoms + :type imageBackground: numpy array + :param imageDrak: The image without light + :type imageDrak: numpy array + :return: The OD images + :rtype: numpy array """ numerator = np.atleast_1d(imageBackground - imageDrak) @@ -222,9 +222,29 @@ class ImageAnalyser(): return imageOD def get_Ncount(self, dataSet, dim=['x', 'y'], **kwargs): + """Sum all the value in the image to give the Ncount. + + :param dataSet: The images + :type dataSet: xarray DataArray or DataSet + :param dim: The dimensions to take the sumation, defaults to ['x', 'y'] + :type dim: list, optional + :return: The Ncount + :rtype: xarray DataArray or DataSet + """ return dataSet.sum(dim=['x', 'y'], **kwargs) def get_absorption_images(self, dataSet, dask='allowed', keep_attrs=True, **kwargs): + """Calculate the OD images for absorption imaging. + + :param dataSet: The data from absorption imaging. + :type dataSet: xarray DataSet + :param dask: over write of the same argument in xarray.apply_ufunc, defaults to 'allowed' + :type dask: str, optional + :param keep_attrs: over write of the same argument in xarray.apply_ufunc, defaults to True + :type keep_attrs: bool, optional + :return: The data including the OD images. + :rtype: xarray DataSet + """ kwargs.update( { @@ -244,7 +264,16 @@ class ImageAnalyser(): return dataSet def remove_background(self, dataSet, dask='allowed', keep_attrs=True, **kwargs): - + """Remove the background for the given image data + + :param dataSet: The data from absorption imaging. + :type dataSet: xarray DataSet + :param dask: over write of the same argument in xarray.apply_ufunc, defaults to 'allowed' + :type dask: str, optional + :param keep_attrs: over write of the same argument in xarray.apply_ufunc, defaults to True + :type keep_attrs: bool, optional + """ + kwargs.update( { 'dask': dask,