regular backup

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(
             {
@@ -244,6 +264,15 @@ 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(
             {