adding some extra citations to functions
@@ -297,6 +297,12 @@ def trim_saddle_points(peaks, dt, max_iters=10):
-------
image : ND-array
An image with fewer peaks than the input image
+
+ References
+ ----------
+ [1] Gostick, J. "A versatile and efficient network extraction algorithm
+ using marker-based watershed segmenation". Physical Review E. (2017)
+
"""
peaks = sp.copy(peaks)
if dt.ndim == 2:
@@ -356,6 +362,11 @@ def trim_nearby_peaks(peaks, dt):
Each pair of peaks is considered simultaneously, so for a triplet of peaks
each pair is considered. This ensures that only the single peak that is
furthest from the solid is kept. No iteration is required.
+
+ References
+ ----------
+ [1] Gostick, J. "A versatile and efficient network extraction algorithm
+ using marker-based watershed segmenation". Physical Review E. (2017)
"""
peaks = sp.copy(peaks)
if dt.ndim == 2:
@@ -870,13 +881,24 @@ def local_thickness(im, sizes=25, mode='hybrid'):
image : ND-array
A copy of ``im`` with the pore size values in each voxel
+ See Also
+ --------
+ porosimetry
+
Notes
-----
The term *foreground* is used since this function can be applied to both
- pore space or the solid, whichever is set to True.
+ pore space or the solid, whichever is set to ``True``.
- This function is identical to porosimetry with ``access_limited`` set to
- ``False``.
+ This function is identical to ``porosimetry`` with ``access_limited`` set
+ to ``False``.
+
+ The way local thickness is found in PoreSpy differs from the traditional
+ method (i.e. `used in ImageJ <https://imagej.net/Local_Thickness>`_).
+ Our approach is probably slower, but it allows for the same code to be
+ used for ``local_thickness`` and ``porosimetry``, since we can 'trim'
+ invaded regions that are not connected to the inlets in the ``porosimetry``
+ function. This is not needed in ``local_thickness`` however.
"""
im_new = porosimetry(im=im, sizes=sizes, access_limited=False, mode=mode)
@@ -945,9 +967,17 @@ def porosimetry(im, sizes=25, inlets=None, access_limited=True,
invading sphere. Of course, ``r`` can be converted to capillary
pressure using your favorite model.
+ Notes
+ -----
+ There are many ways to perform this filter, and PoreSpy offer 3, which
+ users can choose between via the ``mode`` argument. These methods all
+ work in a similar way by finding which foreground voxels can accomodate
+ a sphere of a given radius, then repeating for smaller radii.
+
See Also
--------
fftmorphology
+ local_thickness
"""
def trim_blobs(im, inlets):
