corrections to find_centre_pc and remove cucim dependencies

Author: dkazanc

.github/workflows/httomolibgpu_doc_conda.yml

@@ -0,0 +1,44 @@
+name: HTTomolibgpu docs
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+        - name: Checkout repository code
+          uses: actions/checkout@v3
+
+        - name: Setup Python 3.10
+          uses: actions/setup-python@v3
+          with:
+            python-version: "3.10"
+
+        - name: httomolib
+          uses: conda-incubator/setup-miniconda@v2
+          with:
+            auto-update-conda: false
+            activate-environment: httomolibgpu
+            environment-file: ./docs/source/doc-conda-requirements.yml
+
+        - name: Build api docs
+          run: sphinx-apidoc -feT -t=./docs/source/_templates -o ./docs/source/api ./httomolibgpu
+
+        - name: Build html
+          run: sphinx-build -a -E -b html ./docs/source/ ./docs/build/
+
+        - name: Run ghp-import
+          run: ghp-import -n -p -f ./docs/build
+          env:
+            GITHUB_TOKEN: ${{ github.token }}            
+          

.github/workflows/nightly_build.yml …workflows/httomolibgpu_nightly_build.yml.github/workflows/nightly_build.yml renamed to .github/workflows/httomolibgpu_nightly_build.yml .github/workflows/nightly_build.yml renamed to .github/workflows/httomolibgpu_nightly_build.yml

@@ -1,12 +1,12 @@
-name: httomolibgpu nightly dev conda package build + upload
+name: httomolibgpu nightly dev
 
 on:
   schedule:
     # Run at midnight every day
     - cron: '0 0 * * *'
 
 jobs:
-  build-linux:
+  main-conda-build:
     runs-on: ubuntu-20.04
 
     defaults:
@@ -20,11 +20,11 @@ jobs:
           ref: "main"
           fetch-depth: 0
 
-      # setup Python 3.9
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v2
+      # setup Python 3.10
+      - name: Setup Python 3.10
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: '3.10'
 
       - name: Decrypt a secret
         run: ./.scripts/decrypt_secret.sh

.github/workflows/tests_run.yml …orkflows/httomolibgpu_tests_run_iris.yml.github/workflows/tests_run.yml renamed to .github/workflows/httomolibgpu_tests_run_iris.yml .github/workflows/tests_run.yml renamed to .github/workflows/httomolibgpu_tests_run_iris.yml

@@ -1,5 +1,4 @@
-name: httomolibgpu tests on Iris
-
+name: httomolibgpu tests
 on:
   push:
     branches:
@@ -9,7 +8,7 @@ on:
       - main
 
 jobs:
-  build-linux:
+  iris-gpu:
     runs-on: iris-gpu
     container:
       image: nvidia/cuda:11.6.2-devel-ubi8
@@ -40,20 +39,3 @@ jobs:
       - name: Run tests
         run: |
           pytest tests/
-
-      - name: Install docs dependencies
-        run: |
-          micromamba install -c conda-forge sphinx sphinx-book-theme jinja2 sphinx-panels sphinx-copybutton sphinxcontrib-bibtex nbsphinx pyyaml ghp-import
-          micromamba list
-
-      - name: Build api docs
-        run: |
-          sphinx-apidoc -feT -t=./docs/source/_templates -o ./docs/source/api ./httomolibgpu
-
-      - name: Build html
-        run: sphinx-build -a -E -b html ./docs/source/ ./docs/build/
-
-      - name: Run ghp-import
-        run: ghp-import -n -p -f ./docs/build
-        env:
-          GITHUB_TOKEN: ${{ github.token }}

.github/workflows/conda_upload.yml …b/workflows/httomolibgpu_version_tag.yml.github/workflows/conda_upload.yml renamed to .github/workflows/httomolibgpu_version_tag.yml .github/workflows/conda_upload.yml renamed to .github/workflows/httomolibgpu_version_tag.yml

@@ -1,4 +1,4 @@
-name: httomolibgpu conda upload
+name: httomolibgpu version tag pushed
 
 # Run the workflow whenever a tag beginning with `v` is pushed to any branch
 on:
@@ -7,7 +7,7 @@ on:
       - v*
 
 jobs:
-  build-linux:
+  conda-upload-main:
     runs-on: ubuntu-20.04
 
     defaults:
@@ -21,11 +21,11 @@ jobs:
           fetch-depth: 0
           ref: ${{ github.ref_name }}
 
-      # setup Python 3.9
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v2
+      # setup Python 3.10
+      - name: Setup Python 3.10
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: '3.10'
 
       # install dependencies with conda
       - name: Install dependencies with conda

.scripts/conda_upload.sh

@@ -13,7 +13,7 @@ export CONDA_BLD_PATH=~/conda-bld
 $CONDA/bin/conda install conda-build
 $CONDA/bin/conda install -c conda-forge anaconda-client
 
-$CONDA/bin/conda build . -c conda-forge -c httomo -c rapidsai --no-test
+$CONDA/bin/conda build . -c conda-forge -c httomo --no-test
 
 # upload packages to conda
 find $CONDA_BLD_PATH/$OS -name *.tar.bz2 | while read file

README.rst

@@ -20,9 +20,7 @@ Install HTTomolibGPU as a pre-built conda Python package
 
    $ conda create --name httomolibgpu # create a fresh conda environment
    $ conda activate httomolibgpu # activate the environment
-   $ conda install -c httomo httomolibgpu -c rapidsai -c conda-forge # for linux users
-   $ conda install -c httomo httomolibgpu -c jplumail -c conda-forge # for windows users
-
+   $ conda install -c httomo httomolibgpu -c conda-forge # for linux users
 
 Setup the development environment:
 ==================================
@@ -39,5 +37,5 @@ Build HTTomolibGPU as a conda Python package
 
 .. code-block:: console
 
-   $ conda build conda/recipe/ -c conda-forge -c httomo -c rapidsai
+   $ conda build conda/recipe/ -c conda-forge -c httomo
 

conda/environment.yml

@@ -2,7 +2,6 @@ name: httomolibgpu
 channels:
   - conda-forge
   - httomo
-  - rapidsai
 dependencies:
   - conda-forge::cupy=12.3.0
   - conda-forge::numpy<=1.25
@@ -21,5 +20,4 @@ dependencies:
   - conda-forge::h5py
   - conda-forge::astra-toolbox
   - httomo::tomobar
-  - rapidsai::cucim
   - conda-forge::scikit-image

conda/recipe/meta.yaml

@@ -24,7 +24,6 @@ requirements:
     - python
     - numpy>= 1.20, <= 1.25
     - cupy=12.3.0
-    - cucim
     - astra-toolbox
     - nvtx
     - tomobar

httomolibgpu/misc/morph.py

@@ -28,8 +28,6 @@
 nvtx = cupywrapper.nvtx
 from typing import Literal
 
-from cupyx.scipy.interpolate import interpn
-
 __all__ = [
     "sino_360_to_180",
     "data_resampler",
@@ -126,7 +124,7 @@ def data_resampler(
     Returns:
         cp.ndarray: Up/Down-scaled 3D cupy array
     """
-    if cupywrapper.cupy_run:
+    if cupywrapper.cupy_run:        
         return __data_resampler(data, newshape, axis, interpolation)
     else:
         print("data_resampler won't be executed because CuPy is not installed")
@@ -137,6 +135,8 @@ def data_resampler(
 def __data_resampler(
     data: cp.ndarray, newshape: list, axis: int = 1, interpolation: str = "linear"
 ) -> cp.ndarray:
+    from cupyx.scipy.interpolate import interpn
+    
     if data.ndim != 3:
         raise ValueError("only 3D data is supported")
 

httomolibgpu/recon/rotation.py

@@ -767,7 +767,7 @@ def __find_center_pc(
     rotc_guess: Union[float, Optional[str]] = None,
 ) -> float:
     from cupyx.scipy.ndimage import shift
-    from cucim.skimage.registration import phase_cross_correlation
+    from skimage.registration import phase_cross_correlation
 
     imgshift = 0.0 if rotc_guess is None else rotc_guess - (proj1.shape[1] - 1.0) / 2.0
 
@@ -777,9 +777,9 @@ def __find_center_pc(
     # create reflection of second projection
     proj2 = cp.fliplr(proj2)
 
-    # using cucim of rapids to do phase cross correlation between two images
+    # do phase cross correlation between two images
     shiftr = phase_cross_correlation(
-        reference_image=proj1, moving_image=proj2, upsample_factor=1.0 / tol
+        reference_image=proj1.get(), moving_image=proj2.get(), upsample_factor=1.0 / tol
     )
 
     # Compute center of rotation as the center of first image and the