Implementing the RHE Filter #205

GillySpace27 · 2024-06-03T20:31:17Z

PR Description

The Radial package has been updated to include the Radial Histogram Equalizing Filter as well as a double-sided gamma function that we call an Upsilon function that is utility that could be useful elsewhere.

Implementation follows chapter 3 of my thesis: https://www.proquest.com/docview/2759080511, as well as a journal article in prep (Gilly 2024).
This PR addresses the following issue: #204

sunkit_image/tests/test_radial.py

sunkit_image/utils/utils.py

GillySpace27 · 2024-06-21T17:56:43Z

I added an example and it runs! I don't know what to do about the pre-commit tests though.

nabobalis · 2024-06-21T18:03:02Z

I added an example and it runs! I don't know what to do about the pre-commit tests though.

You can run the pre-commit locally using tox, tox -e codestyle and it will autofix what it can.
The ones left over need to fixed manually.

It seems to be complaining about the commented out test code which we can remove or uncomment out if its useful?

GillySpace27 · 2024-07-02T17:03:16Z

Is there anything else that needs to be done for this pull request? The changelog maybe?

nabobalis · 2024-07-02T17:28:35Z

Is there anything else that needs to be done for this pull request? The changelog maybe?

I'll review it again but for now I think a changelog entry is still missing.

GillySpace27 · 2024-07-02T17:38:48Z

Should I address the failing tests, or do you do that?

nabobalis · 2024-07-02T17:44:27Z

The build_docs is failing to download the data from the VSO in a different example. There isn't anything we can do.

GillySpace27 · 2024-07-05T22:05:08Z

I made another version of the example using functions and I wanted to see if it was better or not. I also added logging. Do y'all like either of those choices? It seems something might need to be changed to allow the images to appear in-line like before. I placed the functionalized version in a separate file for now.

nabobalis · 2024-07-05T22:56:06Z

I made another version of the example using functions and I wanted to see if it was better or not. I also added logging. Do y'all like either of those choices? It seems something might need to be changed to allow the images to appear in-line like before. I placed the functionalized version in a separate file for now.

I am personally not a fan. I don't see the objective of using functions like that.

changelog/205.bugfix.rst

changelog/205.feature.rst

changelog/205.doc.rst

examples/radial_gradient_filters.py

sunkit_image/radial.py

sunkit_image/utils/utils.py

nabobalis · 2024-07-19T16:56:01Z

Sorry for the lack of response.

Thanks for the PR @GillySpace27 and thanks for putting up with the long review.

for more information, see https://pre-commit.ci

nabobalis · 2024-07-19T17:10:12Z

Can you check once more that the figure test output looks correct @GillySpace27?

The output image

GillySpace27 · 2024-07-19T18:01:06Z

The images at this link<https://output.circle-artifacts.com/output/job/3b424f3b-a39d-470c-8ea8-680bc2fe46c7/artifacts/0/.tmp/py312-figure/figure_test_images/fig_comparison.html> seem correct. Thanks! From: Nabil Freij ***@***.***> Date: Friday, July 19, 2024 at 11:10 AM To: sunpy/sunkit-image ***@***.***> Cc: Gilbert, Gilly ***@***.***>, Mention ***@***.***> Subject: Re: [sunpy/sunkit-image] Implementing the RHE Filter (PR #205) [EXTERNAL EMAIL] Can you check once more that the figure test output looks correct @GillySpace27<https://urldefense.com/v3/__https:/github.com/GillySpace27__;!!D-JDmu3Lc2wo0Jiybg!eCXaTl94CsQp3OmwsnYAWfB98natmHItXR_hxzdaAdNuohmo6aCYBrKT0bJSAg4fLXbpuOMz8dZ7n76lswBu$>?

GillySpace27 · 2024-07-31T20:46:38Z

When will this show up in new versions of the package? I thought it would be there today but it doesn't seem to be.

`(base) cgilbert@GillyMacbook ~ % conda_create_ARM sunkit python=3.9
Collecting package metadata (current_repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
current version: 22.9.0
latest version: 24.7.1

Please update conda by running

$ conda update -n base -c defaults conda

Package Plan

environment location: /opt/homebrew/anaconda3/envs/sunkit

added / updated specs:
- python=3.9

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
python-3.9.19              |       hb885b13_1        11.7 MB
setuptools-69.5.1          |   py39hca03da5_0        1004 KB
wheel-0.43.0               |   py39hca03da5_0         107 KB
------------------------------------------------------------
                                       Total:        12.8 MB

The following NEW packages will be INSTALLED:

ca-certificates pkgs/main/osx-arm64::ca-certificates-2024.7.2-hca03da5_0 None
libcxx pkgs/main/osx-arm64::libcxx-14.0.6-h848a8c0_0 None
libffi pkgs/main/osx-arm64::libffi-3.4.4-hca03da5_1 None
ncurses pkgs/main/osx-arm64::ncurses-6.4-h313beb8_0 None
openssl pkgs/main/osx-arm64::openssl-3.0.14-h80987f9_0 None
pip pkgs/main/osx-arm64::pip-24.0-py39hca03da5_0 None
python pkgs/main/osx-arm64::python-3.9.19-hb885b13_1 None
readline pkgs/main/osx-arm64::readline-8.2-h1a28f6b_0 None
setuptools pkgs/main/osx-arm64::setuptools-69.5.1-py39hca03da5_0 None
sqlite pkgs/main/osx-arm64::sqlite-3.45.3-h80987f9_0 None
tk pkgs/main/osx-arm64::tk-8.6.14-h6ba3021_0 None
tzdata pkgs/main/noarch::tzdata-2024a-h04d1e81_0 None
wheel pkgs/main/osx-arm64::wheel-0.43.0-py39hca03da5_0 None
xz pkgs/main/osx-arm64::xz-5.4.6-h80987f9_1 None
zlib pkgs/main/osx-arm64::zlib-1.2.13-h18a0788_1 None

Proceed ([y]/n)?

Downloading and Extracting Packages
setuptools-69.5.1 | 1004 KB | ########################################################################################################################################################################### | 100%
wheel-0.43.0 | 107 KB | ########################################################################################################################################################################### | 100%
python-3.9.19 | 11.7 MB | ########################################################################################################################################################################### | 100%
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$ conda activate sunkit

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$ conda deactivate

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Installing collected packages: zipp, tqdm, six, PyYAML, pyparsing, pillow, packaging, numpy, networkx, multidict, kiwisolver, idna, frozenlist, fonttools, cycler, attrs, async-timeout, astropy-iers-data, aiohappyeyeballs, aioftp, yarl, tifffile, scipy, python-dateutil, pyerfa, lazy-loader, importlib-resources, imageio, contourpy, aiosignal, scikit-image, matplotlib, astropy, aiohttp, parfive, sunpy, sunkit-image
Successfully installed PyYAML-6.0.1 aioftp-0.22.3 aiohappyeyeballs-2.3.4 aiohttp-3.10.0 aiosignal-1.3.1 astropy-6.0.1 astropy-iers-data-0.2024.7.29.0.32.7 async-timeout-4.0.3 attrs-23.2.0 contourpy-1.2.1 cycler-0.12.1 fonttools-4.53.1 frozenlist-1.4.1 idna-3.7 imageio-2.34.2 importlib-resources-6.4.0 kiwisolver-1.4.5 lazy-loader-0.4 matplotlib-3.9.1 multidict-6.0.5 networkx-3.2.1 numpy-1.26.4 packaging-24.1 parfive-2.1.0 pillow-10.4.0 pyerfa-2.0.1.4 pyparsing-3.1.2 python-dateutil-2.9.0.post0 scikit-image-0.24.0 scipy-1.13.1 six-1.16.0 sunkit-image-0.5.1 sunpy-5.1.5 tifffile-2024.7.24 tqdm-4.66.4 yarl-1.9.4 zipp-3.19.2
(sunkit) cgilbert@GillyMacbook ~ % which python
/opt/homebrew/anaconda3/envs/sunkit/bin/python
(sunkit) cgilbert@GillyMacbook ~ % python
Python 3.9.19 (main, May 6 2024, 14:39:30)
[Clang 14.0.6 ] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.

import sunkit_image.radial as rad
dir(rad)
['all', 'builtins', 'cached', 'doc', 'file', 'loader', 'name', 'package', 'spec', '_calculate_fit_radial_intensity', '_fit_polynomial_to_log_radial_intensity', '_normalize_fit_radial_intensity', 'bin_edge_summary', 'equally_spaced_bins', 'find_pixel_radii', 'fnrgf', 'frames', 'get_radial_intensity_summary', 'intensity_enhance', 'np', 'nrgf', 'set_attenuation_coefficients', 'sunpy', 'u']
rad.all
['fnrgf', 'intensity_enhance', 'set_attenuation_coefficients', 'nrgf']
`

nabobalis · 2024-07-31T20:49:25Z

My current plan is to wait for more pull requests to be reviewed and merged and then release v0.6 in a month or so.

GillySpace27 · 2024-07-31T20:55:33Z

Ok, cool! Thanks!

nabobalis · 2024-07-31T21:16:13Z

Sorry for the delay but they're a bunch of open PRs that I would like to get in before a new release as well as I hope the new coalignment API.

GillySpace27 added 5 commits June 2, 2024 17:27

instantiate the RHEF

b77193f

move helper functions to util file

e418a10

make the most basic test

928b064

combine the two layers of abstraction

f86a5a4

update the test run

97c8140

nabobalis reviewed Jun 3, 2024

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nabobalis reviewed Jun 3, 2024

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nabobalis reviewed Jun 3, 2024

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GillySpace27 added 19 commits June 3, 2024 17:01

update first test to sunpy standards

6bff919

remove private functions in __all__

2caaf96

make private functions public for now

16a8f02

fix TypeError

fe9f824

add progress bar

39d9ba5

update rhef tests

c75d218

Merge branch 'sunpy:main' into main

1d565d5

update hash file for rhef

3fad503

remove test_rhef and fix test_multifig_rhef

1e54e74

fix the multifig test

7985a45

update the figure hash

2f8cad5

tweak figure parameters

962016b

fix broken test

63aece5

fix test again

c1420af

update figure hash

3bbcc8e

instantiate the RHEF example

41071a6

improve example formatting

51c7d0a

improve the rhef example

a88c73a

update rhef example

3072aca

tox codestyle

be131e5

nabobalis approved these changes Jul 2, 2024

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GillySpace27 added 7 commits July 5, 2024 14:24

update changelog

755b613

pull helper functions into private methods

fef0f31

crop images

eb03ef5

write and test new functionalized version

74326df

Merge branch 'main' of https://github.com/GillySpace27/sunkit-image

d0a1077

changelog and cosmetic changes

1c51861

fix logging error

a50ce4a

nabobalis requested changes Jul 5, 2024

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respond to code review comments

7ae6c61

nabobalis approved these changes Jul 19, 2024

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Merge branch 'main' into main

07dafbf

pre-commit-ci bot and others added 2 commits July 19, 2024 16:56

[pre-commit.ci] auto fixes from pre-commit.com hooks

5ea54e7

for more information, see https://pre-commit.ci

Update figure_hashes_mpl_390_ft_261_sunpy_513_astropy_610.json

ddb6fe6

nabobalis added 2 commits July 19, 2024 12:16

refs

edc43f4

fix note

7fdb6c3

nabobalis merged commit 83057d1 into sunpy:main Jul 19, 2024
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Implementing the RHE Filter #205

Implementing the RHE Filter #205

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Implementing the RHE Filter #205

Implementing the RHE Filter #205

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GillySpace27 commented Jul 31, 2024

Package Plan

To activate this environment, use

$ conda activate sunkit

To deactivate an active environment, use

$ conda deactivate

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