Merge pull request #39 from LCAV/fix/pycsou_v2

Pycsou v2

.github/workflows/python.yml → .github/workflows/python_no_pycsou.yml

@@ -11,7 +11,7 @@ jobs:
       max-parallel: 12
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.8, 3.9, "3.10"]
+        python-version: [3.8, "3.11"]
     steps:
     - uses: actions/checkout@v3
     - name: Checkout submodules

.github/workflows/python_pycsou.yml

@@ -0,0 +1,52 @@
+name: lensless
+
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      max-parallel: 12
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: [3.9, "3.10"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Checkout submodules
+      shell: bash
+      run: |
+        auth_header="$(git config --local --get http.https://github.com/.extraheader)"
+        git submodule sync --recursive
+        git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies and build package
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install -e .
+    - name: Lint with flake8
+      run: |
+        pip install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=B,C,E,F,W,T4,B9 --show-source --statistics --max-complexity=18 --max-line-length=100 --ignore=E203,E266,E501,W503,F403,F401,C901 --exclude=profile,scripts,docs
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Format with black
+      run: |
+        pip install black
+        black *.py -l 100
+        black lensless/*.py -l 100
+        black scripts/*.py -l 100
+        black scripts/recon/*.py -l 100
+        black profile/*.py -l 100
+        black test/*.py -l 100
+    - name: Test with pytest
+      run: |
+        pip install -U pytest
+        pip install -r recon_requirements.txt
+        pip install git+https://github.com/matthieumeo/pycsou.git@v2-dev
+        pytest

CHANGELOG.rst

@@ -22,11 +22,12 @@ Changed
 -  CONTRIBUTING and CHANGELOG, to .rst for documentation.
 -  Shorten README to separate contents in different pages of docs.
 -  Fix typo in GradientDescent class name.
+-  Updated to Pycsou V2, as ``pip install pycsou`` (Pycsou V1) may not work on some machines.
 
 Bugfix
 ~~~~~~
 
--  Loading grayscale PSFs would cause an dimension error when removing the background pixels
+-  Loading grayscale PSFs would cause an dimension error when removing the background pixels.
 
 1.0.2 - (2022-05-31)
 --------------------

README.rst

@@ -79,10 +79,23 @@ install the library locally.
    python scripts/recon/admm.py
 
 
-Note (as of 19-04-2023), there is a problem setting up Pycsou via ``pip`` as 
-the `setup file <https://github.com/matthieumeo/pycsou/blob/master/requirements.txt>`__
-uses asterisks with greater than or equal requirements, which is no longer supported.
-Therefore ``pycsou>=1.0.6`` has been removed from ``recon_requirements.txt``.
+Note (25-04-2023): for using reconstruction method based on Pycsou ``lensless.apgd.APGD``,
+V2 has to be installed:
+
+.. code:: bash
+
+   pip install git+https://github.com/matthieumeo/pycsou.git@v2-dev
+
+If PyTorch is installed, you will need to be sure to have PyTorch 2.0 or higher, 
+as Pycsou V2 is not compatible with earlier versions of PyTorch. Moreover, 
+Pycsou requires Python within 
+`[3.9, 3.11) <https://github.com/matthieumeo/pycsou/blob/v2-dev/setup.cfg#L28>`__.
+
+Moreover, ``numba`` (requirement for Pycsou V2) may require an older version of NumPy:
+
+.. code:: bash
+
+   pip install numpy==1.23.5
 
 **Raspberry Pi**
 

configs/defaults_recon.yaml

@@ -60,4 +60,19 @@ admm:
   mu1: 1e-6
   mu2: 1e-5
   mu3: 4e-5
-  tau: 0.0001
+  tau: 0.0001
+
+apgd:
+  # Stopping criteria
+  max_iter: 1000
+  rel_error: 1e-6
+  acceleration: True     
+  # Differentiable prior / regularization: l2, null
+  diff_penalty: null
+  diff_lambda: 0.001
+  # Proximal prior / regularization: nonneg, l1, null
+  prox_penalty: nonneg
+  prox_lambda: 0.001
+  # Lipschitz
+  lipschitz_tight: True
+  lipschitz_tol: 1.0