Merge branch 'master' into change_push

Author: haesleinhuepf

demo/basics/inspecting_3d_images.ipynb

@@ -15,6 +15,7 @@
     create_2d_xy,
     create_2d_yx,
     create_2d_zx,
+    create_2d_xz,
     create_2d_zy,
     create_2d_yz,
     create_none,

pyclesperanto_prototype/_tier0/__init__.py

@@ -1,9 +1,9 @@
 from .._tier0 import execute
-from .._tier0 import create_2d_xy
+from .._tier0 import create_2d_yx
 from .._tier0 import plugin_function
 from .._tier0 import Image
 
-@plugin_function(output_creator=create_2d_xy, categories=['projection'])
+@plugin_function(output_creator=create_2d_yx, categories=['projection'])
 def maximum_z_projection(source :Image, destination_max :Image = None):
     """Determines the maximum intensity projection of an image along Z. 
     

pyclesperanto_prototype/_tier1/_maximum_z_projection.py

@@ -1,9 +1,9 @@
 from .._tier0 import execute
 from .._tier0 import plugin_function
 from .._tier0 import Image
-from .._tier0 import create_2d_zy
+from .._tier0 import create_2d_yz
 
-@plugin_function(output_creator=create_2d_zy, categories=['projection'])
+@plugin_function(output_creator=create_2d_yz, categories=['projection'])
 def mean_x_projection(source : Image, destination : Image):
     """Determines the mean average intensity projection of an image along X. 
     

pyclesperanto_prototype/_tier1/_mean_x_projection.py

@@ -1,9 +1,9 @@
 from .._tier0 import execute
 from .._tier0 import plugin_function
 from .._tier0 import Image
-from .._tier0 import create_2d_xy
+from .._tier0 import create_2d_yx
 
-@plugin_function(output_creator=create_2d_xy, categories=['projection'])
+@plugin_function(output_creator=create_2d_yx, categories=['projection'])
 def mean_z_projection(source : Image, destination : Image):
     """Determines the mean average intensity projection of an image along Z. 
     

pyclesperanto_prototype/_tier1/_mean_z_projection.py

@@ -2,9 +2,9 @@
 from .._tier0 import execute
 from .._tier0 import plugin_function
 from .._tier0 import Image
-from .._tier0 import create_2d_zy
+from .._tier0 import create_2d_yz
 
-@plugin_function(output_creator=create_2d_zy, categories=['projection'])
+@plugin_function(output_creator=create_2d_yz, categories=['projection'])
 def minimum_x_projection(source : Image, destination_min : Image = None):
     """Determines the minimum intensity projection of an image along Y. 
     

pyclesperanto_prototype/_tier1/_minimum_x_projection.py

@@ -2,9 +2,9 @@
 from .._tier0 import execute
 from .._tier0 import plugin_function
 from .._tier0 import Image
-from .._tier0 import create_2d_xy
+from .._tier0 import create_2d_yx
 
-@plugin_function(output_creator=create_2d_xy, categories=['projection'])
+@plugin_function(output_creator=create_2d_yx, categories=['projection'])
 def minimum_z_projection(source : Image, destination_min : Image = None):
     """Determines the minimum intensity projection of an image along Z. 
     

pyclesperanto_prototype/_tier1/_minimum_z_projection.py

@@ -2,9 +2,9 @@
 from .._tier0 import execute
 from .._tier0 import plugin_function
 from .._tier0 import Image
-from .._tier0 import create_2d_zy
+from .._tier0 import create_2d_yz
 
-@plugin_function(output_creator=create_2d_zy, categories=['projection'])
+@plugin_function(output_creator=create_2d_yz, categories=['projection'])
 def sum_x_projection(source : Image, destination : Image = None):
     """Determines the sum intensity projection of an image along Z. 
     

pyclesperanto_prototype/_tier1/_sum_x_projection.py

@@ -1,9 +1,9 @@
 from .._tier0 import execute
 from .._tier0 import plugin_function
 from .._tier0 import Image
-from .._tier0 import create_2d_xy
+from .._tier0 import create_2d_yx
 
-@plugin_function(output_creator=create_2d_xy, categories=['projection'])
+@plugin_function(output_creator=create_2d_yx, categories=['projection'])
 def sum_z_projection(source : Image, destination : Image = None):
     """Determines the sum intensity projection of an image along Z. 
     

pyclesperanto_prototype/_tier1/_sum_z_projection.py

@@ -1,7 +1,7 @@
 from .._tier0 import Image
 
-def imshow(image : Image, title : str = None, labels : bool = False, min_display_intensity : float = None, max_display_intensity : float = None, color_map =None):
-    from .._tier0 import pull
+def imshow(image : Image, title : str = None, labels : bool = False, min_display_intensity : float = None, max_display_intensity : float = None, color_map = None, plot = None):
+    from .._tier0 import pull_zyx
     from .._tier1 import maximum_z_projection
 
     if len(image.shape) == 3:
@@ -15,6 +15,10 @@ def imshow(image : Image, title : str = None, labels : bool = False, min_display
         import numpy as np
         cmap = matplotlib.colors.ListedColormap ( np.random.rand ( 256,3))
 
-    import matplotlib.pyplot as plt
-    plt.imshow(image, cmap=cmap, vmin=min_display_intensity, vmax=max_display_intensity)
-    plt.show()
+    if plot is None:
+        import matplotlib.pyplot as plt
+        plt.imshow(image, cmap=cmap, vmin=min_display_intensity, vmax=max_display_intensity)
+        plt.show()
+    else:
+        plot.imshow(image, cmap=cmap, vmin=min_display_intensity, vmax=max_display_intensity)
+