updated documentation

docs/examples.rst

@@ -11,7 +11,7 @@ An end-to-end example of a `SPHERE/ZIMPOL <https://www.eso.org/sci/facilities/pa
 VLT/NACO Mp dithering data
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Here we show a processing example of a pupil-stabilized data set of beta Pic as in `Stolker et al. (2019) <https://ui.adsabs.harvard.edu/abs/2019A%26A...622A.156C>`_ (see also :ref:`running`). This archival data set was obtained with `VLT/NACO <https://www.eso.org/sci/facilities/paranal/instruments/naco.html>`_ in the Mp band, which can be downloaded from the ESO archive under program ID |data|. A dithering pattern was applied to sample the sky background. Before starting the data reduction, it is useful to sort the various required science and calibration files into separate folders. Also, it is important to provide the correct NACO keywords in the configuration file (see :ref:`configuration` section).
+Here we show a processing example of a pupil-stabilized data set of beta Pic as in `Stolker et al. (2019) <http://ui.adsabs.harvard.edu/abs/2019A%26A...621A..59S>`_ (see also :ref:`running`). This archival data set was obtained with `VLT/NACO <https://www.eso.org/sci/facilities/paranal/instruments/naco.html>`_ in the Mp band, which can be downloaded from the ESO archive under program ID |data|. A dithering pattern was applied to sample the sky background. Before starting the data reduction, it is useful to sort the various required science and calibration files into separate folders. Also, it is important to provide the correct NACO keywords in the configuration file (see :ref:`configuration` section).
 
 Now we can start the data reduction by first importing the Pypeline and the required pipeline modules, for example:
 

pynpoint/processing/fluxposition.py

@@ -238,11 +238,12 @@ def __init__(self,
             single value or a range/list of values. In the latter case, the `res_out_tag` and
             `flux_position_tag` contain a 3 digit number with the number of PCs.
         cent_size : float
-            Radius of the central mask (arcsec). No mask is used when set to None.
+            Radius of the central mask (arcsec). No mask is used when set to None. Masking is done
+            after the artificial planet is injected.
         edge_size : float
             Outer radius (arcsec) beyond which pixels are masked. No outer mask is used when set to
             None. The radius will be set to half the image size if the argument is larger than half
-            the image size.
+            the image size. Masking is done after the artificial planet is injected.
         extra_rot : float
             Additional rotation angle of the images in clockwise direction (deg).
         residuals : str
@@ -678,7 +679,7 @@ def __init__(self,
             either a single image (2D) or a cube (3D) with the dimensions equal to *image_in_tag*.
         chain_out_tag : str
             Tag of the database entry with the Markov chain that is written as output. The shape
-            of the array is (nwalkers*nsteps, 3).
+            of the array is (nwalkers, nsteps, 3).
         param : tuple(float, float, float)
             The approximate separation (arcsec), angle (deg), and contrast (mag), for example
             obtained with the :class:`~pynpoint.processing.fluxposition.SimplexMinimizationModule`.
@@ -703,7 +704,8 @@ def __init__(self,
         mask : tuple(float, float), None
             Inner and outer mask radius (arcsec) for the PSF subtraction. Both elements of the
             tuple can be set to None. Masked pixels are excluded from the PCA computation,
-            resulting in a smaller runtime.
+            resulting in a smaller runtime. Masking is done after the artificial planet is
+            injected.
         extra_rot : float
             Additional rotation angle of the images (deg).
         merit : str