Merge branch 'main' into haesleinhuepf-patch-2

.github/workflows/comment-on-issue.yml

@@ -21,6 +21,11 @@ jobs:
         echo "Organization - ${{ github.repository_owner }}"
         echo "Repository Name - ${{ github.repository }}"
 
+    - name: Print Job details
+      run: |  
+        echo "Run ID - ${{ github.run_id }}"
+        echo "Job ID - ${{ github.job }}"
+
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
@@ -33,9 +38,11 @@ jobs:
 
     - name: Run Python
       env:
-        #ANTHROPIC_API_KEY: "${{ secrets.ANTHROPIC_API_KEY }}"
-        GIT_BOB_LLM_NAME: "gpt-4o-2024-05-13"
+        ANTHROPIC_API_KEY: "${{ secrets.ANTHROPIC_API_KEY }}"
+        GOOGLE_API_KEY: "${{ secrets.GOOGLE_API_KEY }}"
+        GIT_BOB_LLM_NAME: "${{ secrets.GIT_BOB_LLM_NAME }}"
         OPENAI_API_KEY: "${{ secrets.OPENAI_API_KEY }}"
         GITHUB_API_KEY: "${{ secrets.GITHUB_TOKEN }}"
+        GITHUB_RUN_ID: "${{ github.run_id }}"
       run: |
         git-bob comment-on-issue-action ${{ github.repository }} ${{ github.event.pull_request.number }} ${{ github.event.issue.number }}

.github/workflows/review-pull-request.yml

@@ -20,6 +20,11 @@ jobs:
         echo "Organization - ${{ github.repository_owner }}"
         echo "Repository Name - ${{ github.repository }}"
 
+    - name: Print Job details
+      run: |  
+        echo "Run ID - ${{ github.run_id }}"
+        echo "Job ID - ${{ github.job }}"
+
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
@@ -32,10 +37,12 @@ jobs:
 
     - name: Run Python
       env:
-        #ANTHROPIC_API_KEY: "${{ secrets.ANTHROPIC_API_KEY }}"
-        GIT_BOB_LLM_NAME: "gpt-4o-2024-05-13"
+        ANTHROPIC_API_KEY: "${{ secrets.ANTHROPIC_API_KEY }}"
+        GOOGLE_API_KEY: "${{ secrets.GOOGLE_API_KEY }}"
+        GIT_BOB_LLM_NAME: "${{ secrets.GIT_BOB_LLM_NAME }}"
         OPENAI_API_KEY: "${{ secrets.OPENAI_API_KEY }}"
         GITHUB_API_KEY: "${{ secrets.GITHUB_TOKEN }}"
+        GITHUB_RUN_ID: "${{ github.run_id }}"
       run: |
         git-bob review-pull-request-action ${{ github.repository }} ${{ github.event.pull_request.number }}
 

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="stackview",
-    version="0.8.0",
+    version="0.9.0",
     author="Robert Haase",
     author_email="robert.haase@uni-leipzig.de",
     description="Interactive image stack viewing in jupyter notebooks",

stackview/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.8.0"
+__version__ = "0.9.0"
 
 from ._static_view import jupyter_displayable_output, insight
 from ._utilities import merge_rgb

stackview/_animate.py

@@ -35,6 +35,9 @@ def animate(timelapse, filename:str=None, overwrite_file:bool=True, frame_delay_
     from stackview._image_widget import _img_to_rgb
     from ._utilities import numpy_to_gif_bytestream, _gif_to_html
 
+    if isinstance(timelapse, list):
+        timelapse = np.asarray(timelapse)
+
     if 0 <= timelapse.min() <= 1 and 0 <= timelapse.max() <= 1:
         warnings.warn("The timelapse has a small intensity range between 0 and 1. Consider normalizing it to the range between 0 and 255.")
     if timelapse.min() < 0 or timelapse.max() > 255:
@@ -115,6 +118,13 @@ def animate_curtain(timelapse, timelapse_curtain,
     import numpy as np
     from ._image_widget import _img_to_rgb
 
+
+    if isinstance(timelapse, list):
+        timelapse = np.asarray(timelapse)
+
+    if isinstance(timelapse_curtain, list):
+        timelapse_curtain = np.asarray(timelapse_curtain)
+
     max_size = timelapse.shape[1]
 
     images = []

stackview/_clusterplot.py

@@ -42,6 +42,8 @@ def clusterplot(df, labels, column_x:str="x", column_y:str="y", column_selection
     from ._scatterplot import scatterplot
     import functools
 
+    labels = np.asarray(labels)
+
     if column_selection in df.columns:
         selection = df["selection"].tolist()
 
@@ -72,6 +74,7 @@ def update(selection, label_image, selected_image, widget):
 
     return grid([[
         image_display,
-        scatterplot
+        scatterplot,
+
     ]])
 

stackview/_image_widget.py

@@ -72,7 +72,7 @@ def _img_to_rgb(image,
                 display_max=None):
     from ._colormaps import _labels_lut, create_colormap
 
-    if len(image.shape) > 2 and image.shape[-1] == 3:
+    if len(image.shape) > 2 and (image.shape[-1] == 3 or image.shape[-1] == 4):
         return image
 
     if image.dtype == bool:

stackview/_scatterplot.py

@@ -120,7 +120,9 @@ def __init__(self, df, column_x, column_y, column_selection, figsize, selection_
         manager = Gcf.get_active()
         Gcf.figs.pop(manager.num, None)
 
-        self.selector = Selector(self.fig, self.ax, self.plotted_points, callback=self.set_selection)
+        self.selector = None
+        #self.selector = Selector(self.fig, self.ax, self.plotted_points, callback=self.set_selection)
+        self.update()
 
         # show selection if defined
         if column_selection in df.columns:

stackview/_static_view.py

@@ -46,6 +46,10 @@ def __array_finalize__(self, obj):
         if obj is None: return
         self.library_name = getattr(obj, 'library_name', None)
         self.help_url = getattr(obj, 'help_url', None)
+        self.obj = obj
+
+    def __getitem__(self, index):
+        return self.obj.__getitem__(index)
 
     def _repr_html_(self):
         """HTML representation of the image object for IPython.