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Jianshun Gao 2023-07-05 16:00:47 +02:00
parent 68bded568b
commit 60c2612d0a
1 changed files with 38 additions and 9 deletions
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47
Analyser/ImagingAnalyser.py
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@ -196,16 +196,16 @@ class ImageAnalyser():
return dataSet.isel(x=slice(x_start, x_end), y=slice(y_start, y_end)) return dataSet.isel(x=slice(x_start, x_end), y=slice(y_start, y_end))
def get_OD(self, imageAtom, imageBackground, imageDrak): def get_OD(self, imageAtom, imageBackground, imageDrak):
"""_summary_ """Calculate the OD image for absorption imaging.
:param imageAtom: _description_ :param imageAtom: The image with atoms
:type imageAtom: _type_ :type imageAtom: numpy array
:param imageBackground: _description_ :param imageBackground: The image without atoms
:type imageBackground: _type_ :type imageBackground: numpy array
:param imageDrak: _description_ :param imageDrak: The image without light
:type imageDrak: _type_ :type imageDrak: numpy array
:return: _description_ :return: The OD images
:rtype: _type_ :rtype: numpy array
""" """
numerator = np.atleast_1d(imageBackground - imageDrak) numerator = np.atleast_1d(imageBackground - imageDrak)
@ -222,9 +222,29 @@ class ImageAnalyser():
return imageOD return imageOD
def get_Ncount(self, dataSet, dim=['x', 'y'], **kwargs): 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) return dataSet.sum(dim=['x', 'y'], **kwargs)
def get_absorption_images(self, dataSet, dask='allowed', keep_attrs=True, **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( kwargs.update(
{ {
@ -244,6 +264,15 @@ class ImageAnalyser():
return dataSet return dataSet
def remove_background(self, dataSet, dask='allowed', keep_attrs=True, **kwargs): 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( kwargs.update(
{ {