109 macos installer

.github/workflows/build_installers.yaml

@@ -1,7 +1,10 @@
 name: build_installers
 
 on:
+  workflow_dispatch:
   push:
+    branches:
+      - "**"
     tags:
       - '**'
 
@@ -72,14 +75,13 @@ jobs:
         run: |
           cd deployment
           micromamba activate base
-          micromamba install -y -c conda-forge python=3.10
-          micromamba install -y -c conda-forge constructor
-          micromamba install -y -c conda-forge ruamel.yaml
           micromamba install -y -c conda-forge mamba
           mamba env create --file=env.yaml
-          python version_getter.py
-          mkdir ./${{ matrix.os }}_x86_64
-          constructor --conda-exe=$(which mamba) --output-dir ./${{ matrix.os }}_x86_64 .
+          micromamba activate __MICROSAM_BUILD_ENV__
+          mamba install -y -c conda-forge pyinstaller
+          source ./build_pyinstaller_app.sh
+          mv ./dist/annotator ./${{ matrix.os }}_x86_64
+
 
       - name: upload installer
         uses: actions/upload-artifact@v3

deployment/build_pyinstaller_app.sh

@@ -0,0 +1,43 @@
+#!/bin/bash
+rm -rf dist
+rm -f annotator.py
+echo "from micro_sam.sam_annotator.annotator import main" >> annotator.py
+echo "main()" >> annotator.py
+PYTHON_SITE=$(python -c "import site; print(''.join(site.getsitepackages()))")
+echo $PYTHON_SITE
+ls $PYTHON_SITE
+pyinstaller --log-level=DEBUG \
+--hidden-import=napari_svg \
+--hidden-import=napari_plugin_engine \
+--hidden-import=napari_console \
+--hidden-import=napari_builtins \
+--hidden-import=napari._event_loop \
+--hidden-import=vispy.app.backends._pyqt5 \
+--hidden-import=fontconfig \
+--hidden-import=magicgui.backends._qtpy \
+--hidden-import=imagecodecs._shared \
+--hidden-import=torchvision.io \
+--hidden-import=pytorch.jit \
+--hidden-import=torchtriton \
+--hidden-import=imagecodecs._imcd \
+--hidden-import=jpeg \
+--hidden-import=libnvjpeg \
+--hidden-import=openjpeg \
+--hidden-import=libpng \
+--hidden-import=micro_sam \
+--add-data "${PYTHON_SITE}/napari/resources/icons:napari/resources/icons" \
+--add-data "${PYTHON_SITE}/napari/_qt/qt_resources/styles:napari/_qt/qt_resources/styles" \
+--add-data "${PYTHON_SITE}/vispy/io/_data:vispy/io/_data" \
+--add-data "${PYTHON_SITE}/vispy/util/fonts/data:vispy/util/fonts/data" \
+--add-data "${PYTHON_SITE}/napari_builtins:napari_builtins" \
+--add-data "${PYTHON_SITE}/PIL:PIL" \
+--add-data "${PYTHON_SITE}/torchvision:torchvision" \
+--add-data "${PYTHON_SITE}/torch:torch" \
+--add-data "${PYTHON_SITE}/numpy:numpy" \
+--add-data "${PYTHON_SITE}/vispy/glsl:vispy/glsl" annotator.py
+
+mkdir ./dist/annotator/lib
+ls ./dist/annotator
+#cp ./dist/annotator/libiomp5.dylib ./dist/annotator/lib
+cd ./dist/annotator
+./annotator

micro_sam/sam_annotator/annotator_2d.py

@@ -60,6 +60,7 @@ def _autosegment_widget(
     if AMG is None:
         AMG = instance_segmentation.get_amg(PREDICTOR, is_tiled)
 
+    print("initializing autosegment")
     if not AMG.is_initialized:
         AMG.initialize(v.layers["raw"].data, image_embeddings=IMAGE_EMBEDDINGS, verbose=True)
 
@@ -92,7 +93,7 @@ def _initialize_viewer(raw, segmentation_result, tile_shape, show_embeddings):
     # initialize the viewer and add layers
     #
 
-    v.add_image(raw)
+    v.add_image(raw, name="raw")
     shape = _get_shape(raw)
 
     v.add_labels(data=np.zeros(shape, dtype="uint32"), name="auto_segmentation")

micro_sam/sam_annotator/annotator_3d.py

@@ -239,7 +239,7 @@ def annotator_3d(
 
     v = Viewer()
 
-    v.add_image(raw)
+    v.add_image(raw, name="raw")
     if segmentation_result is None:
         v.add_labels(data=np.zeros(raw.shape, dtype="uint32"), name="committed_objects")
     else:

micro_sam/sam_annotator/annotator_tracking.py

@@ -433,7 +433,7 @@ def annotator_tracking(
 
     v = Viewer()
 
-    v.add_image(raw)
+    v.add_image(raw, name="raw")
     if tracking_result is None:
         v.add_labels(data=np.zeros(raw.shape, dtype="uint32"), name="committed_tracks")
     else: