Feature/python numpy

.github/workflows/build_and_test.yml

@@ -118,12 +118,6 @@ jobs:
         with:
           name: agave-linux
           path: ./build/install/Release/agave-install
-      - name: Install and test agave_pyvk
-        working-directory: agave_pyvk
-        run: |
-          python -m pip install -e ".[test]"
-          python -c "from agave_pyvk import AgaveRenderer; import agave_pyvk._native"
-          python -m pytest tests
 
   macos-build:
     runs-on: macos-15
@@ -170,12 +164,6 @@ jobs:
         with:
           name: agave-macos-arm64
           path: ./build/agave-macos-arm64.dmg
-      - name: Install and test agave_pyvk
-        working-directory: agave_pyvk
-        run: |
-          python -m pip install -e ".[test]"
-          python -c "from agave_pyvk import AgaveRenderer; import agave_pyvk._native"
-          python -m pytest tests
 
   windows-build:
     runs-on: windows-latest
@@ -225,15 +213,113 @@ jobs:
         with:
           name: agave-win
           path: ./build/agave-win.exe
-      - name: Install and test agave_pyvk
-        working-directory: agave_pyvk
+
+  linux-pyvk-build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          submodules: "recursive"
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+      - uses: jakoch/install-vulkan-sdk-action@37effcfa045411f8bfbbda26df2fd1b3bf3436fa
+        with:
+          vulkan_version: 1.4.350.1
+          cache: true
+      - name: Install dependencies
+        run: sudo apt-get install libspdlog-dev libglm-dev libgl1-mesa-dev libegl1-mesa-dev libtiff-dev libzstd-dev libcurl4-openssl-dev nasm
+      - run: python -m pip install cibuildwheel==3.3.0
+      - name: Build agave_pyvk wheels
+        run: python -m cibuildwheel agave_pyvk --output-dir wheelhouse
+      - name: Install and test the Python 3.12 wheel
+        run: |
+          python -m pip install pytest wheelhouse/*cp312*.whl
+          python -c "from agave_pyvk import AgaveRenderer; import agave_pyvk._native"
+          python -m pytest agave_pyvk/tests
+      - uses: actions/upload-artifact@v6
+        with:
+          name: agave-pyvk-agave-linux
+          path: wheelhouse/*.whl
+          if-no-files-found: error
+
+  macos-pyvk-build:
+    runs-on: macos-15
+    env:
+      CC: clang
+      CXX: clang++
+      MACOSX_DEPLOYMENT_TARGET: "15.0"
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          submodules: "recursive"
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+      - uses: jakoch/install-vulkan-sdk-action@37effcfa045411f8bfbbda26df2fd1b3bf3436fa
+        with:
+          vulkan_version: 1.4.350.1
+          cache: true
+      - name: Install dependencies
+        run: |
+          brew install spdlog nasm curl
+          if [ -d /usr/local/include/openssl ]; then
+            mv /usr/local/include/openssl /usr/local/include/openssl.bak
+          fi
+      - run: python -m pip install cibuildwheel==3.3.0
+      - name: Build agave_pyvk wheels
+        run: python -m cibuildwheel agave_pyvk --output-dir wheelhouse
+      - name: Install and test the Python 3.12 wheel
+        run: |
+          python -m pip install pytest wheelhouse/*cp312*.whl
+          python -c "from agave_pyvk import AgaveRenderer; import agave_pyvk._native"
+          python -m pytest agave_pyvk/tests
+      - uses: actions/upload-artifact@v6
+        with:
+          name: agave-pyvk-agave-macos-arm64
+          path: wheelhouse/*.whl
+          if-no-files-found: error
+
+  windows-pyvk-build:
+    runs-on: windows-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          submodules: "recursive"
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+      - uses: jakoch/install-vulkan-sdk-action@37effcfa045411f8bfbbda26df2fd1b3bf3436fa
+        with:
+          vulkan_version: 1.4.350.0
+          cache: true
+      - name: Install dependencies
         shell: cmd
         run: |
+          choco install nasm -y
           call "C:\Program Files\Microsoft Visual Studio\18\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
-          python -m pip install -e ".[test]"
-          if errorlevel 1 exit /b %errorlevel%
+          vcpkg install --triplet x64-windows tiff glm zlib libjpeg-turbo liblzma spdlog zstd curl
+      - name: Remove bad Strawberry Perl patch binary in search path
+        run: echo "C:\Program Files\git\usr\bin" >> $env:GITHUB_PATH
+      - run: python -m pip install cibuildwheel==3.3.0
+      - name: Build agave_pyvk wheels with MSVC 18
+        shell: cmd
+        run: |
+          call "C:\Program Files\Microsoft Visual Studio\18\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
+          python -m cibuildwheel agave_pyvk --output-dir wheelhouse
+      - name: Install and test the Python 3.12 wheel
+        shell: pwsh
+        run: |
+          python -m pip install pytest
+          $wheel = Get-ChildItem wheelhouse/*cp312*.whl | Select-Object -First 1
+          python -m pip install $wheel.FullName
           python -c "from agave_pyvk import AgaveRenderer; import agave_pyvk._native"
-          python -m pytest tests
+          python -m pytest agave_pyvk/tests
+      - uses: actions/upload-artifact@v6
+        with:
+          name: agave-pyvk-agave-win
+          path: wheelhouse/*.whl
+          if-no-files-found: error
 
   lint-and-test-webclient:
     runs-on: ubuntu-latest

.github/workflows/tagged_master_release.yml

@@ -48,14 +48,6 @@ jobs:
         with:
           name: agave-linux
           path: ./build/install/Release/agave-install
-      - run: python -m pip install cibuildwheel==3.3.0
-      - name: Build agave_pyvk wheels
-        run: python -m cibuildwheel agave_pyvk --output-dir wheelhouse
-      - uses: actions/upload-artifact@v6
-        with:
-          name: agave-pyvk-agave-linux
-          path: wheelhouse/*.whl
-          if-no-files-found: error
 
   macos-build:
     runs-on: macos-15
@@ -102,14 +94,6 @@ jobs:
         with:
           name: agave-macos-arm64
           path: ./build/agave-macos-arm64.dmg
-      - run: python -m pip install cibuildwheel==3.3.0
-      - name: Build agave_pyvk wheels
-        run: python -m cibuildwheel agave_pyvk --output-dir wheelhouse
-      - uses: actions/upload-artifact@v6
-        with:
-          name: agave-pyvk-agave-macos-arm64
-          path: wheelhouse/*.whl
-          if-no-files-found: error
 
   windows-build:
     runs-on: windows-latest
@@ -159,6 +143,78 @@ jobs:
         with:
           name: agave-win
           path: ./build/agave-win.exe
+
+  linux-pyvk-build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          submodules: "recursive"
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+      - run: python -m pip install cibuildwheel==3.3.0
+      - name: Build agave_pyvk wheels
+        run: python -m cibuildwheel agave_pyvk --output-dir wheelhouse
+      - uses: actions/upload-artifact@v6
+        with:
+          name: agave-pyvk-agave-linux
+          path: wheelhouse/*.whl
+          if-no-files-found: error
+
+  macos-pyvk-build:
+    runs-on: macos-15
+    env:
+      CC: clang
+      CXX: clang++
+      MACOSX_DEPLOYMENT_TARGET: "15.0"
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          submodules: "recursive"
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+      - uses: jakoch/install-vulkan-sdk-action@37effcfa045411f8bfbbda26df2fd1b3bf3436fa
+        with:
+          vulkan_version: 1.4.350.1
+          cache: true
+      - name: Install dependencies
+        run: |
+          brew install spdlog nasm curl
+          if [ -d /usr/local/include/openssl ]; then
+            mv /usr/local/include/openssl /usr/local/include/openssl.bak
+          fi
+      - run: python -m pip install cibuildwheel==3.3.0
+      - name: Build agave_pyvk wheels
+        run: python -m cibuildwheel agave_pyvk --output-dir wheelhouse
+      - uses: actions/upload-artifact@v6
+        with:
+          name: agave-pyvk-agave-macos-arm64
+          path: wheelhouse/*.whl
+          if-no-files-found: error
+
+  windows-pyvk-build:
+    runs-on: windows-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          submodules: "recursive"
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+      - uses: jakoch/install-vulkan-sdk-action@37effcfa045411f8bfbbda26df2fd1b3bf3436fa
+        with:
+          vulkan_version: 1.4.350.0
+          cache: true
+      - name: Install dependencies
+        shell: cmd
+        run: |
+          choco install nasm -y
+          call "C:\Program Files\Microsoft Visual Studio\18\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
+          vcpkg install --triplet x64-windows tiff glm zlib libjpeg-turbo liblzma spdlog zstd curl
+      - name: Remove bad Strawberry Perl patch binary in search path
+        run: echo "C:\Program Files\git\usr\bin" >> $env:GITHUB_PATH
       - run: python -m pip install cibuildwheel==3.3.0
       - name: Build agave_pyvk wheels with MSVC 18
         shell: cmd
@@ -243,7 +299,15 @@ jobs:
           verbose: true
 
   publish_agave_pyvk:
-    needs: [linux-build, macos-build, windows-build]
+    needs:
+      [
+        linux-build,
+        macos-build,
+        windows-build,
+        linux-pyvk-build,
+        macos-pyvk-build,
+        windows-pyvk-build,
+      ]
     runs-on: ubuntu-latest
     steps:
       - name: Download agave_pyvk wheel artifacts

CMake/ConfigureVulkan.cmake

@@ -57,6 +57,8 @@ if(AGAVE_VULKAN_SDK_ROOT)
     set(Vulkan_LIBRARY "${AGAVE_VULKAN_SDK_ROOT}/lib/libvulkan.dylib" CACHE FILEPATH "Vulkan loader library" FORCE)
   elseif(EXISTS "${AGAVE_VULKAN_SDK_ROOT}/lib/libvulkan.so")
     set(Vulkan_LIBRARY "${AGAVE_VULKAN_SDK_ROOT}/lib/libvulkan.so" CACHE FILEPATH "Vulkan loader library" FORCE)
+  elseif(EXISTS "${AGAVE_VULKAN_SDK_ROOT}/lib/VulkanLoader/lib/libvulkan.so")
+    set(Vulkan_LIBRARY "${AGAVE_VULKAN_SDK_ROOT}/lib/VulkanLoader/lib/libvulkan.so" CACHE FILEPATH "Vulkan loader library" FORCE)
   endif()
 endif()
 

agave_pyvk/README.md

@@ -14,6 +14,28 @@ with AgaveRenderer(mode="pathtrace") as renderer:
     renderer.redraw()
 ```
 
+NumPy volumes can also be loaded directly. Three-dimensional arrays use ZYX
+order and four-dimensional arrays use CZYX order:
+
+```python
+import numpy as np
+
+volume = np.zeros((2, 64, 256, 256), dtype=np.uint16)
+with AgaveRenderer(mode="pathtrace") as renderer:
+    info = renderer.load_array(
+        volume,
+        name="example",
+        voxel_size=(0.108, 0.108, 0.29),
+        spatial_units="um",
+        channel_names=("DNA", "membrane"),
+    )
+```
+
+`uint8`, `uint16`, and `float32` arrays are accepted and copied into AGAVE's
+channel-major `uint16` storage. `uint8` values are widened without rescaling;
+each `float32` channel is independently min-max normalized to the full 16-bit
+range. A new call replaces the current volume and represents one time point.
+
 A Vulkan 1.3-capable driver and the Vulkan SDK are required to build. The
 remaining native dependencies are the same ones used by renderlib.
 

agave_pyvk/agave_pyvk/agave.py

@@ -8,7 +8,7 @@
 import json
 import math
 from pathlib import Path
-from typing import List, Optional
+from typing import List, Optional, Sequence
 
 import numpy
 from PIL import Image
@@ -281,6 +281,37 @@ def load_data_and_get_info(
             path, scene, multiresolution_level, time, channels, region
         )
 
+    def load_array(
+        self,
+        data: numpy.ndarray,
+        name: str = "array",
+        voxel_size: Sequence[float] = (1.0, 1.0, 1.0),
+        spatial_units: str = "units",
+        channel_names: Optional[Sequence[str]] = None,
+    ) -> dict:
+        """Replace the current volume with a copied ZYX or CZYX NumPy array."""
+        if self._renderer is None:
+            raise RuntimeError("Renderer is closed")
+
+        array = numpy.asarray(data)
+        if array.dtype not in (
+            numpy.dtype("uint8"),
+            numpy.dtype("uint16"),
+            numpy.dtype("float32"),
+        ):
+            raise TypeError("data dtype must be uint8, uint16, or float32")
+        if array.ndim not in (3, 4):
+            raise ValueError("data must have ZYX or CZYX shape")
+
+        result = self._renderer.load_array(
+            numpy.ascontiguousarray(array),
+            name,
+            list(voxel_size),
+            spatial_units,
+            list(channel_names) if channel_names is not None else [],
+        )
+        return json.loads(result)
+
     def show_scale_bar(self, on: int):
         return self._execute("SHOW_SCALE_BAR", on)