Merge pull request #41 from haesleinhuepf/conditional_hints

conditional hints for bia-bob depending on what's installed

napari_segment_blobs_and_things_with_membranes/__init__.py

@@ -1,5 +1,5 @@
 
-__version__ = "0.3.9"
+__version__ = "0.3.10"
 __common_alias__ = "nsbatwm"
 
 from napari_plugin_engine import napari_hook_implementation

napari_segment_blobs_and_things_with_membranes/_bia_bob_plugins.py

@@ -1,25 +1,25 @@
 def list_bia_bob_plugins():
     """List of function hints for bia_bob"""
-    return """    ## napari-segment-blobs-and-things-with-membranes (nsbatwm)
-    nsbatwm is a Python library that processes images, mostly using the scikit-image library, but with simpler access.
-    When you use it, you always start by importing the library: `import napari_segment_blobs_and_things_with_membranes as nsbatwm`.
-    When asked for how to use nsbatwm, you can adapt one of the following code snippets:
-  
-    * Splits touching objects in a binary image using an algorithm similar to the ImageJ watershed.
-      nsbatwm.split_touching_objects(binary_image)
-   
+    try:
+        import pyclesperanto
+        good_alternative_installed = True
+    except:
+        pass
+    try:
+        import pyclesperanto_prototype
+        good_alternative_installed = True
+    except:
+        pass
+
+    if not good_alternative_installed:
+        basic_hints = """
+    
     * Applies Otsu's method to binarize an intensity image (also works with yen, isodata, li, mean, minimum, triangle instead of otsu).
       nsbatwm.threshold_otsu(image)
-      
-    * Labels connected components in a binary image.
-      nsbatwm.connected_component_labeling(binary_image)
-      
-    * Applies seeded watershed segmentation using labeled objects, e.g. nuclei, and an image showing bright borders between objects such as cell membranes.
-      nsbatwm.seeded_watershed(image, labeled_objects)
-      
+    
     * Segments blob-like structures using Voronoi-Otsu labeling.
       nsbatwm.voronoi_otsu_labeling(image, spot_sigma=4, outline_sigma=1)
-     
+    
     * Applies a Gaussian blur for noise reduction.
       nsbatwm.gaussian_blur(image, sigma=5)
       
@@ -28,9 +28,6 @@ def list_bia_bob_plugins():
       
     * Smooth a label image using a local most popular intensity (mode) filter.
       nsbatwm.mode_filter(labels)
-      
-    * Applies a percentile filter.
-      nsbatwm.percentile_filter(image)
     
     * Removes background in an image using the top-hat filter.
       nsbatwm.white_tophat(image)
@@ -46,10 +43,30 @@ def list_bia_bob_plugins():
     
     * Expands labels by a specified distance.
       nsbatwm.expand_labels(label_image, distance=2)
+    """
+
+    return f"""    ## napari-segment-blobs-and-things-with-membranes (nsbatwm)
+    nsbatwm is a Python library that processes images, mostly using the scikit-image library, but with simpler access.
+    When you use it, you always start by importing the library: `import napari_segment_blobs_and_things_with_membranes as nsbatwm`.
+    When asked for how to use nsbatwm, you can adapt one of the following code snippets:
+    
+    {basic_hints}
+  
+    * Splits touching objects in a binary image using an algorithm similar to the ImageJ watershed.
+      nsbatwm.split_touching_objects(binary_image)
+      
+    * Labels connected components in a binary image.
+      nsbatwm.connected_component_labeling(binary_image)
+      
+    * Applies seeded watershed segmentation using labeled objects, e.g. nuclei, and an image showing bright borders between objects such as cell membranes.
+      nsbatwm.seeded_watershed(image, labeled_objects)
+      
+    * Applies a percentile filter.
+      nsbatwm.percentile_filter(image)
     
     * Segments using seeded watershed with local minima as seeds.
       nsbatwm.local_minima_seeded_watershed(image, spot_sigma=10, outline_sigma=2)
     
     * Skeletonizes labeled objects.
       nsbatwm.skeletonize(image)
-"""
+    """

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = napari-segment-blobs-and-things-with-membranes
-version = 0.3.9
+version = 0.3.10
 author = Robert Haase
 author_email = robert.haase@tu-dresden.de
 url = https://github.com/haesleinhuepf/napari-segment-blobs-and-things-with-membranes