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[fix] Fixed Reinhard numpy bug; fixed deprecation issues; updated actions in workflows #60

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merged 13 commits into from
Jan 8, 2025
Merged

[fix] Fixed Reinhard numpy bug; fixed deprecation issues; updated actions in workflows #60

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902ff1f
Fix interpolation arg deprecation with np.percentile
andreped Jan 8, 2025
e9869d4
Fix bug in Reinhard numpy implementation
andreped Jan 8, 2025
9c04baa
Upgrade actions/upload-artifact to v4 for all CIs
andreped Jan 8, 2025
105fe34
Bump actions/download-artifact@v4
andreped Jan 8, 2025
12757da
Renamed CIs
andreped Jan 8, 2025
6f26801
Allow workflow dispatch on test CIs
andreped Jan 8, 2025
0755907
Bump macos-13 in full tests CI
andreped Jan 8, 2025
80af28d
Bump actions/setup-python@v4
andreped Jan 8, 2025
7e6f9a0
Bump actions/checkout@v4
andreped Jan 8, 2025
864f20d
Added mising version bump to build CI
andreped Jan 8, 2025
9d08768
Fix numpy install bug in full tests CI
andreped Jan 8, 2025
08881ed
Revert to interpolation arg
andreped Jan 8, 2025
cb642a5
Deprecated python 3.6 from tests due to opencv deprecation on macos
andreped Jan 8, 2025
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8 changes: 4 additions & 4 deletions .github/workflows/build.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@ jobs:
runs-on: ubuntu-20.04

steps:
- uses: actions/checkout@v3
- uses: actions/setup-python@v3
- uses: actions/checkout@v4
- uses: actions/setup-python@v4
with:
python-version: '3.x'

Expand All @@ -20,7 +20,7 @@ jobs:
- name: Build wheels
run: python setup.py sdist bdist_wheel

- uses: actions/upload-artifact@v3
- uses: actions/upload-artifact@v4
with:
path: ./dist/*

Expand All @@ -31,7 +31,7 @@ jobs:
if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')

steps:
- uses: actions/download-artifact@v3
- uses: actions/download-artifact@v4
with:
name: artifact
path: dist
Expand Down
38 changes: 16 additions & 22 deletions .github/workflows/tests_full.yml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
name: tests
name: Full Tests

on:
push:
Expand All @@ -7,6 +7,7 @@ on:
pull_request:
branches:
- main
workflow_dispatch:

jobs:
build:
Expand All @@ -15,9 +16,9 @@ jobs:
if: startsWith(github.ref, 'refs/tags/v') != true

steps:
- uses: actions/checkout@v1
- uses: actions/checkout@v4
- name: Set up Python 3.6
uses: actions/setup-python@v2
uses: actions/setup-python@v4
with:
python-version: 3.6

Expand All @@ -28,7 +29,7 @@ jobs:
run: python setup.py bdist_wheel

- name: Upload Python wheel
uses: actions/upload-artifact@v2
uses: actions/upload-artifact@v4
with:
name: Python wheel
path: ${{github.workspace}}/dist/torchstain-*.whl
Expand All @@ -39,24 +40,24 @@ jobs:
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ windows-2019, ubuntu-20.04, macos-12 ]
os: [ windows-2019, ubuntu-20.04, macos-13 ]
python-version: [ 3.7, 3.8, 3.9 ]
tf-version: [2.7.0, 2.8.0, 2.9.0]

steps:
- uses: actions/checkout@v1
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}

- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: "Python wheel"

- name: Install dependencies
run: pip install tensorflow==${{ matrix.tf-version }} protobuf==3.20.* opencv-python-headless scikit-image pytest
run: pip install tensorflow==${{ matrix.tf-version }} protobuf==3.20.* opencv-python-headless scikit-image pytest "numpy<2"

- name: Install wheel
run: pip install --find-links=${{github.workspace}} torchstain-*
Expand All @@ -70,31 +71,24 @@ jobs:
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ windows-2019, ubuntu-20.04, macos-12 ]
python-version: [ 3.6, 3.7, 3.8, 3.9 ]
os: [ windows-2019, ubuntu-20.04, macos-13 ]
python-version: [ 3.7, 3.8, 3.9 ]
pytorch-version: [1.8.0, 1.9.0, 1.10.0, 1.11.0, 1.12.0, 1.13.0]
exclude:
- python-version: 3.6
pytorch-version: 1.11.0
- python-version: 3.6
pytorch-version: 1.12.0
- python-version: 3.6
pytorch-version: 1.13.0

steps:
- uses: actions/checkout@v1
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}

- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: "Python wheel"

- name: Install dependencies
run: pip install torch==${{ matrix.pytorch-version }} torchvision opencv-python-headless scikit-image pytest
run: pip install torch==${{ matrix.pytorch-version }} torchvision opencv-python-headless scikit-image pytest "numpy<2"

- name: Install wheel
run: pip install --find-links=${{github.workspace}} torchstain-*
Expand Down
21 changes: 11 additions & 10 deletions .github/workflows/tests_quick.yml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
name: tests
name: Quick Tests

on:
push:
Expand All @@ -7,14 +7,15 @@ on:
pull_request:
branches-ignore:
- main
workflow_dispatch:

jobs:
build:
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v1
- uses: actions/checkout@v4
- name: Set up Python 3.6
uses: actions/setup-python@v2
uses: actions/setup-python@v4
with:
python-version: 3.6

Expand All @@ -25,7 +26,7 @@ jobs:
run: python setup.py bdist_wheel

- name: Upload Python wheel
uses: actions/upload-artifact@v2
uses: actions/upload-artifact@v4
with:
name: Python wheel
path: ${{github.workspace}}/dist/torchstain-*.whl
Expand All @@ -36,14 +37,14 @@ jobs:
runs-on: ubuntu-20.04

steps:
- uses: actions/checkout@v1
- uses: actions/checkout@v4
- name: Set up Python 3.8
uses: actions/setup-python@v2
uses: actions/setup-python@v4
with:
python-version: 3.8

- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: "Python wheel"

Expand All @@ -62,14 +63,14 @@ jobs:
runs-on: ubuntu-20.04

steps:
- uses: actions/checkout@v1
- uses: actions/checkout@v4
- name: Set up Python 3.8
uses: actions/setup-python@v2
uses: actions/setup-python@v4
with:
python-version: 3.8

- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: "Python wheel"

Expand Down
6 changes: 2 additions & 4 deletions torchstain/numpy/normalizers/reinhard.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,7 @@ def fit(self, target):
lab = rgb2lab(target)

# get summary statistics
# stack_ = np.apply_along_axis(get_mean_std, 1, lab_split(lab))
stack_ = np.apply_along_axis(get_mean_std, axis=1, arr=lab_split(lab))
stack_ = np.array([get_mean_std(x) for x in lab_split(lab)])

self.target_means = stack_[:, 0]
self.target_stds = stack_[:, 1]
Expand All @@ -40,8 +39,7 @@ def normalize(self, I):
labs = lab_split(lab)

# get summary statistics from LAB
# stack_ = np.apply_along_axis(get_mean_std, 1, labs)
stack_ = np.apply_along_axis(get_mean_std, axis=1, arr=labs)
stack_ = np.array([get_mean_std(x) for x in labs])

mus = stack_[:, 0]
stds = stack_[:, 1]
Expand Down