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Added logger decorator to all functions #841

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Added logger decorator to all functions #841

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b8ee763
Added function log
Daniel-olaO May 24, 2023
94ed69c
Merge branch 'dev' into func-log
Daniel-olaO Jun 6, 2023
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1 change: 1 addition & 0 deletions porespy/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@
from . import simulations
from . import visualization
from . import io
from porespy.tools import log_entry_exit
# The dns module will be deprecated in V3, in favor of simulations
from . import dns

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36 changes: 32 additions & 4 deletions porespy/filters/_funcs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
from porespy.tools import get_border, subdivide, recombine, make_contiguous
from porespy.tools import unpad, extract_subsection
from porespy.tools import ps_disk, ps_ball, ps_round
from porespy.tools import log_entry_exit
from porespy import settings
from porespy.tools import get_tqdm

Expand Down Expand Up @@ -51,6 +52,8 @@

@deprecated("The ibip function will be moved to the"
+ " ``simulations`` module in a future version")

@log_entry_exit
def ibip(**kwargs):
r"""
This function has been moved to the ``simulations`` module, please use that.
Expand All @@ -61,6 +64,8 @@ def ibip(**kwargs):

@deprecated("The ibip_gpu function will be moved to the"
+ " ``simulations`` module in a future version")

@log_entry_exit
def ibip_gpu(**kwargs):
r"""
This function has been moved to the ``simulations`` module, please use that.
Expand All @@ -69,6 +74,7 @@ def ibip_gpu(**kwargs):
return ibip_gpu(**kwargs)


@log_entry_exit
def find_trapped_regions(seq, outlets=None, bins=25, return_mask=True):
r"""
Find the trapped regions given an invasion sequence image
Expand Down Expand Up @@ -146,6 +152,7 @@ def find_trapped_regions(seq, outlets=None, bins=25, return_mask=True):
return seq


@log_entry_exit
def apply_padded(im, pad_width, func, pad_val=1, **kwargs):
r"""
Applies padding to an image before sending to ``func``, then extracts
Expand Down Expand Up @@ -185,6 +192,7 @@ def apply_padded(im, pad_width, func, pad_val=1, **kwargs):
return result


@log_entry_exit
def trim_small_clusters(im, size=1):
r"""
Remove isolated voxels or clusters of a given size or smaller
Expand Down Expand Up @@ -220,6 +228,7 @@ def trim_small_clusters(im, size=1):
return filtered_array


@log_entry_exit
def hold_peaks(im, axis=-1, ascending=True):
r"""
Replaces each voxel with the highest value along the given axis.
Expand Down Expand Up @@ -273,6 +282,7 @@ def hold_peaks(im, axis=-1, ascending=True):
return result


@log_entry_exit
def distance_transform_lin(im, axis=0, mode="both"):
r"""
Replaces each void voxel with the linear distance to the nearest solid
Expand Down Expand Up @@ -343,6 +353,7 @@ def distance_transform_lin(im, axis=0, mode="both"):
return f


@log_entry_exit
def find_disconnected_voxels(im, conn=None, surface=False):
r"""
Identifies all voxels that are not connected to the edge of the image.
Expand Down Expand Up @@ -409,6 +420,8 @@ def find_disconnected_voxels(im, conn=None, surface=False):
return holes



@log_entry_exit
def fill_blind_pores(im, conn=None, surface=False):
r"""
Fills all blind pores that are isolated from the main void space.
Expand Down Expand Up @@ -452,6 +465,8 @@ def fill_blind_pores(im, conn=None, surface=False):
return im



@log_entry_exit
def trim_floating_solid(im, conn=None, surface=False):
r"""
Removes all solid that that is not attached to main solid structure.
Expand Down Expand Up @@ -495,6 +510,7 @@ def trim_floating_solid(im, conn=None, surface=False):
return im


@log_entry_exit
def trim_nonpercolating_paths(im, inlets, outlets, strel=None):
r"""
Remove all nonpercolating paths between specified locations
Expand Down Expand Up @@ -546,6 +562,7 @@ def trim_nonpercolating_paths(im, inlets, outlets, strel=None):
return new_im


@log_entry_exit
def trim_extrema(im, h, mode="maxima"):
r"""
Trims local extrema in greyscale values by a specified amount.
Expand Down Expand Up @@ -593,6 +610,7 @@ def trim_extrema(im, h, mode="maxima"):
return result


@log_entry_exit
def flood(im, labels, mode="max"):
r"""
Floods/fills each region in an image with a single value based on the
Expand Down Expand Up @@ -663,6 +681,7 @@ def flood(im, labels, mode="max"):
return flooded


@log_entry_exit
def flood_func(im, func, labels=None):
r"""
Flood each isolated region in an image with a constant value calculated by
Expand Down Expand Up @@ -720,6 +739,7 @@ def flood_func(im, func, labels=None):
return flooded


@log_entry_exit
def find_dt_artifacts(dt):
r"""
Label points in a distance transform that are closer to image boundary
Expand Down Expand Up @@ -761,6 +781,7 @@ def find_dt_artifacts(dt):
return result


@log_entry_exit
def region_size(im):
r"""
Replace each voxel with the size of the region to which it belongs
Expand Down Expand Up @@ -803,6 +824,7 @@ def region_size(im):
return counts[im]


@log_entry_exit
def apply_chords(im, spacing=1, axis=0, trim_edges=True, label=False):
r"""
Adds chords to the void space in the specified direction.
Expand Down Expand Up @@ -865,7 +887,7 @@ def apply_chords(im, spacing=1, axis=0, trim_edges=True, label=False):
result = result > 0
return result


@log_entry_exit
def apply_chords_3D(im, spacing=0, trim_edges=True):
r"""
Adds chords to the void space in all three principle directions.
Expand Down Expand Up @@ -924,6 +946,7 @@ def apply_chords_3D(im, spacing=0, trim_edges=True):
return chords


@log_entry_exit
def local_thickness(im, sizes=25, mode="hybrid", divs=1):
r"""
For each voxel, this function calculates the radius of the largest
Expand Down Expand Up @@ -1003,7 +1026,7 @@ def local_thickness(im, sizes=25, mode="hybrid", divs=1):
divs=divs)
return im_new


@log_entry_exit
def porosimetry(im, sizes=25, inlets=None, access_limited=True, mode='hybrid',
divs=1):
r"""
Expand Down Expand Up @@ -1180,7 +1203,7 @@ def porosimetry(im, sizes=25, inlets=None, access_limited=True, mode='hybrid',
raise Exception("Unrecognized mode " + mode)
return imresults


@log_entry_exit
def trim_disconnected_blobs(im, inlets, strel=None):
r"""
Removes foreground voxels not connected to specified inlets.
Expand Down Expand Up @@ -1238,7 +1261,7 @@ def trim_disconnected_blobs(im, inlets, strel=None):
im2 = im2 * im
return im2


@log_entry_exit
def _get_axial_shifts(ndim=2, include_diagonals=False):
r"""
Helper function to generate the axial shifts that will be performed on
Expand Down Expand Up @@ -1267,6 +1290,7 @@ def _get_axial_shifts(ndim=2, include_diagonals=False):
return np.vstack((x, y, z)).T


@log_entry_exit
def _make_stack(im, include_diagonals=False):
r"""
Creates a stack of images with one extra dimension to the input image
Expand Down Expand Up @@ -1299,6 +1323,7 @@ def _make_stack(im, include_diagonals=False):
return stack


@log_entry_exit
def nphase_border(im, include_diagonals=False):
r"""
Identifies the voxels in regions that border *N* other regions.
Expand Down Expand Up @@ -1355,6 +1380,7 @@ def nphase_border(im, include_diagonals=False):
return out[1:-1, 1:-1, 1:-1].copy()


@log_entry_exit
def prune_branches(skel, branch_points=None, iterations=1):
r"""
Remove all dangling ends or tails of a skeleton
Expand Down Expand Up @@ -1427,6 +1453,7 @@ def prune_branches(skel, branch_points=None, iterations=1):
return im_result


@log_entry_exit
def chunked_func(func,
overlap=None,
divs=2,
Expand Down Expand Up @@ -1511,6 +1538,7 @@ def chunked_func(func,
"""

@dask.delayed
@log_entry_exit
def apply_func(func, **kwargs):
# Apply function on sub-slice of overall image
return func(**kwargs)
Expand Down
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