Optimizations, closes #1070

.github/workflows/build_cython_extensions.yml

@@ -0,0 +1,111 @@
+name: Build Cython extensions
+
+permissions:
+  contents: write
+
+on:
+  push:
+    paths:
+      - "cellacdc/**/*.pyx"
+      - "precompile_functions.py"
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        working-directory: ${{ github.workspace }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Build extension
+        run: |
+          python -m pip install --upgrade "setuptools>=77" cython numpy
+          # Remove existing binaries so only the freshly built one remains for upload
+          python -c "
+          import os, glob
+          for f in glob.glob('cellacdc/precompiled/*.so') + glob.glob('cellacdc/precompiled/*.pyd'):
+              os.remove(f)
+              print(f'Removed existing: {f}')
+          "
+          python "${{ github.workspace }}/precompile_functions.py" build_ext --inplace --build-temp "${{ github.workspace }}/build/temp"
+          echo "Built binary:"
+          ls cellacdc/precompiled/
+
+      - uses: actions/upload-artifact@v6
+        with:
+          name: precompiled-${{ matrix.os }}-py${{ matrix.python-version }}
+          path: |
+            cellacdc/precompiled/*.so
+            cellacdc/precompiled/*.pyd
+
+  commit:
+      needs: build
+      runs-on: ubuntu-latest
+      permissions:
+        contents: write
+      defaults:
+        run:
+          working-directory: ${{ github.workspace }}
+      steps:
+        - uses: actions/checkout@v6
+          with:
+            ref: ${{ github.ref_name }}
+            fetch-depth: 0
+
+        - uses: actions/download-artifact@v6
+          with:
+            path: artifacts/
+
+        - name: Flatten artifacts into precompiled directory
+          run: |
+            mkdir -p cellacdc/precompiled
+            find artifacts -type f \( -name "*.pyd" -o -name "*.so" \) -exec cp {} cellacdc/precompiled/ \;
+            echo "Files copied:"
+            ls -la cellacdc/precompiled/
+            echo ""
+            echo "Total files:"
+            find cellacdc/precompiled/ -type f | grep -E '\.(pyd|so)$' | wc -l
+
+        - name: Validate artifact count
+          run: |
+            EXPECTED_COUNT=12
+            FILE_COUNT=$(find cellacdc/precompiled/ -type f \( -name "*.pyd" -o -name "*.so" \) | wc -l)
+            echo "Expected files: $EXPECTED_COUNT"
+            echo "Found files: $FILE_COUNT"
+            if [ "$FILE_COUNT" -lt "$EXPECTED_COUNT" ]; then
+              echo "Missing binaries: expected at least $EXPECTED_COUNT, found $FILE_COUNT"
+              exit 1
+            fi
+
+        - name: Commit precompiled binaries
+          run: |
+            git config user.name "github-actions[bot]"
+            git config user.email "github-actions[bot]@users.noreply.github.com"
+            find cellacdc/precompiled/ -type f \( -name "*.pyd" -o -name "*.so" \) -print0 | xargs -0 git add -f
+            git add cellacdc/precompiled/__init__.py
+            FILE_COUNT=$(find cellacdc/precompiled/ -type f \( -name "*.pyd" -o -name "*.so" \) | wc -l)
+            echo "Files to commit: $FILE_COUNT"
+            if [ "$FILE_COUNT" -eq 0 ]; then
+              echo "No precompiled files found, skipping commit"
+              exit 0
+            fi
+            if git diff --cached --quiet; then
+              echo "No changes to commit"
+              exit 0
+            fi
+            git commit -m "ci: update precompiled Cython extensions [skip ci]"
+            git pull --rebase origin ${{ github.ref_name }}
+            git push origin HEAD:${{ github.ref_name }}

.gitignore

@@ -26,6 +26,13 @@ requirements_new.txt
 **/weights_location_path.txt
 **/_test
 
+# cython generated files
+*.pyd
+*.so
+!cellacdc/precompiled/
+!cellacdc/precompiled/*.pyd
+!cellacdc/precompiled/*.so
+
 # Test output plots
 tests/_plots/
 
@@ -36,7 +43,6 @@ setup.cfg
 
 # Starting from pip 21.3 setup.py is not needed anymore
 # and we rely only on setup.cfg for env
-setup.py
 environment.yml
 # requirements.txt
 conda_env_list_commands.txt

cellacdc/__init__.py

@@ -806,4 +806,17 @@ def inner_function(self, *args, **kwargs):
 single_pos_index_cols = (
     'experiment_folderpath', 
     'Position_n'
-)
+)
+
+precompiled_import_success = False
+try:
+    from cellacdc.precompiled.precompiled_functions import (
+        find_all_objects_2D,
+        find_all_objects_3D,
+        calc_IoA_matrix_2D,
+        calc_IoA_matrix_3D,
+        most_common_projection_3D,
+    )
+    precompiled_import_success = True
+except Exception:
+    pass

cellacdc/_warnings.py

@@ -32,6 +32,34 @@ def warnTooManyItems(mainWin, numItems, qparent):
     )
     return msg.cancel, msg.clickedButton==switchToLowResButton
 
+def warnTooManyNewItems(mainWin, numItems, qparent):
+    from . import widgets
+    mainWin.logger.info(
+        '[WARNING]: asking user what to do with too many objects...'
+    )
+    msg = widgets.myMessageBox(wrapText=False)
+    txt = html_utils.paragraph(f"""
+        WARNING: The resulting segmentation mask has <b>{numItems} objects</b>.<br><br>
+        Creating <b>high resolution</b> text annotations 
+        for these many objects could take a <b>long time</b>.<br><br>
+        We recommend <b>deactivating text annotations</b> or <b>switching to low resolution</b> annotations.<br><br>
+        You can still try to switch to activate them or switch to high resolution later.<br><br>
+        What do you want to do?
+    """)
+
+    _, switchToLowResButton, deactivateAnnotButton = msg.warning(
+        qparent, 'Too many objects', txt,
+        buttonsTexts=(
+            'Cancel', 
+            widgets.reloadPushButton(' Switch to low resolution '), 
+            widgets.noPushButton(' Deactivate text annotations ')              
+        )
+    )
+    switchToLowRes = msg.clickedButton==switchToLowResButton
+    deactivateAnnot = msg.clickedButton==deactivateAnnotButton
+
+    return msg.cancel, switchToLowRes, deactivateAnnot
+
 def warnRestartCellACDCcolorModeToggled(
         scheme, app_name='Cell-ACDC', parent=None
     ):