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Proposal: library of convolution kernels #268

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phargogh opened this issue Jul 20, 2022 · 1 comment · Fixed by #303
Closed

Proposal: library of convolution kernels #268

phargogh opened this issue Jul 20, 2022 · 1 comment · Fixed by #303
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@phargogh
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enhancement New feature or request in progress Working on it!
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2.4.0

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@phargogh
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pygeoprocessing.convolve_2d has some pretty stringent requirements for how a kernel must be formatted (must be a spatial raster, best if it's tiled, spatial reference needs to be set, but it doesn't matter what it is), and so just formatting your kernel correctly is a pretty high bar before convolve_2d can even be used.

I propose:

  • Creating a library of convolution kernels, pygeoprocessing.kernels containing kernel-related utilities
  • Moving kernel creation functions used in InVEST that follow standard kernel models (e.g. gaussian, linear, etc.) over to pygeoprocessing.kernels
  • Creating some helper functions (as needed) in this subpackage to help standardize the creation of kernels.
@phargogh phargogh added the enhancement New feature or request label Jul 20, 2022
@phargogh phargogh self-assigned this Jul 20, 2022
@phargogh phargogh added the in progress Working on it! label Nov 1, 2022
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Nov 1, 2022
@phargogh
Starting a kernels module.
e99fd4b 
The first function there is to create a distance-based kernel.

Untested, but linting passes.

RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Nov 1, 2022
@phargogh
Adding InVEST convolution kernels.
c92a82f 
These _should_ work, but there's still a need to test them and make sure
that they cover all the edge cases we're using in InVEST.

RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Nov 1, 2022
@phargogh
Adding a function to create a kernel easily from a numpy array.
9e00749 
RE:natcap#268
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phargogh commented Nov 1, 2022

Working on this in my fork at feature/268-library-of-convolution-kernels.

@dcdenu4 dcdenu4 mentioned this issue Nov 2, 2022
Closed
@phargogh phargogh mentioned this issue Nov 5, 2022
Merged
@phargogh phargogh added this to the 2.4.0 milestone Dec 2, 2022
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 5, 2023
@phargogh
Only taking sum of kernel if normalizing.
58e8e8c 
Also adding max_dist to locals exposed during eval. RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 5, 2023
@phargogh
Correcting eval() call syntax. RE:natcap#268
ccef62c
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 5, 2023
@phargogh
Creating TIFF kernels instead of GeoTIFFs.
3aae274 
I remember GDAL issuing a warning a long time ago if no SRS was defined,
but that no longer seems to be the case.  Both GDAL and QGIS seem to
have decided that the SRS doesn't matter any longer.  This commit
removes the spatial metadata information from kernel creation.

RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 5, 2023
@phargogh
Factoring masking out to the kernel creation function.
57e74a2 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 5, 2023
@phargogh
Abbreviating several kernels to expressions.
c6b7423 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 5, 2023
@phargogh
Abbreviating gaussian and renaming to normal.
3af2a67 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 5, 2023
@phargogh
Removing unused imports and functions.
01a4967 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 5, 2023
@phargogh
Correcting subpackage list in setup.py. RE:natcap#268
52ef893
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 5, 2023
@phargogh
Using **kwargs for passing kwargs to underlying kernel func.
0f3f7f0 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 5, 2023
@phargogh
Allowing kernel radius to be defined by the user.
d662e87 
Needed for the InVEST Stormwater model. RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 5, 2023
@phargogh
Exp decay kernel now distinguishes btw expected, max dists.
ac98cdb 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 5, 2023
@phargogh
A couple mild bugfixes.
0c07a27 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 5, 2023
@phargogh
Refactoring kernels to be more explicit about needed args.
ad6ce29 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 8, 2023
@phargogh
Fleshing out docstring for exp decay. RE:natcap#268
4b0d7c1
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 8, 2023
@phargogh
Fleshing out docstring for normal distribution.
77357f9 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 8, 2023
@phargogh
Fleshing out linear decay kernel docstring.
a439764 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 8, 2023
@phargogh
Adding a docstring for parabolic decay.
3522b1b 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 8, 2023
@phargogh
Adding a docstring and dimensionality assertion.
c8a4507 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 8, 2023
@phargogh
Finishing docstring, signature for dichotomous kernel.
ee7ec72 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 8, 2023
@phargogh
Removing 'parabolic dacay' - not general enough for this.
4777f14 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 8, 2023
@phargogh
Starting a test file for kernels.
f6c66ef 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 8, 2023
@phargogh
Testing dochotomous kernel. RE:natcap#268
1de0606
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 8, 2023
@phargogh
Testing exponential decay. RE:natcap#268
155e135
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 8, 2023
@phargogh
Adding a test for linear decay. RE:natcap#268
7c61240
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 8, 2023
@phargogh
Adding a test for normal distribution decay. RE:natcap#268
562cb1b
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 8, 2023
@phargogh
Testing the kernel callable. RE:natcap#268
7965118
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 8, 2023
@phargogh
Minor docs updates, noting changes in HISTORY. RE:natcap#268
93589c8
@phargogh phargogh mentioned this issue Feb 8, 2023
Merged
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 9, 2023
@phargogh
Minor docstring fixes. RE:natcap#268
aa083cf
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 11, 2023
@phargogh
Renaming create_kernel to create_distance_decay_kernel.
b6fa7a6 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 11, 2023
@phargogh
Renaming function kwarg to be more specific.
7bc24b4 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 11, 2023
@phargogh
Improvements to docstrings. RE:natcap#268
b558503
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 11, 2023
@phargogh
Removing pixel_radius parameter from normal distribution.
3efbd92 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 11, 2023
@phargogh
Renaming pixel_radius to apothem. RE:natcap#268
4e99b96
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 11, 2023
@phargogh
Improving module documentation.
ecbad36 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 13, 2023
@phargogh
Improving docstring for numpy_array_to_raster. RE:natcap#268
8fb9829
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 15, 2023
@phargogh
Making apothem the floor of max_distance and asserting comparison.
5a54c3b 
RE:natcap#268
phargogh added a commit to phargogh/pygeoprocessing that referenced this issue Feb 22, 2023
@phargogh
Removing the apothem - no longer needed.
fc3e186 
RE:natcap#268
@emlys emlys closed this as completed in #303 Mar 2, 2023
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