Annotation tool 4 0

This merge finished the MVP version of the annotation tool

docs/notebooks/annotation_tool.ipynb

 %% Cell type:markdown id: tags:
 
 # Image annotation tool
 This notebook shows how the annotation interface can be used to create masks for images
 
 %% Cell type:code id: tags:
 
 ``` python
 import qim3d
-import matplotlib.pyplot as plt
-import matplotlib as mpl
-import numpy as np
-%matplotlib inline
 ```
 
-%% Cell type:code id: tags:
 
-``` python
-# Load 2D example image
-img = qim3d.examples.blobs_256x256
+# Load example image
+img = qim3d.examples.bone_128x128x128
 
 # Display image
-plt.imshow(img)
-plt.show()
 ```
 
-%% Cell type:code id: tags:
+qim3d.viz.slices(img)
 
-``` python
 # Start annotation tool
 interface = qim3d.gui.annotation_tool.Interface()
-interface.max_masks = 4
+
 
 # We can directly pass the image we loaded to the interface
-interface.launch(img=img)
+interface.launch(img[0])
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 # When 'prepare mask for download' is pressed once, the mask can be retrieved with the get_result() method
 mask = interface.get_result()
 ```
 
 %% Cell type:markdown id: tags:
 
 ## Check the obtained mask
 
 %% Cell type:code id: tags:
 
 ``` python
 print (f"Original image shape..: {img.shape}")
 print (f"Mask image shape......: {mask.shape}")
 print (f"\nNumber of masks: {np.max(mask)}")
 ```
 
 %% Cell type:markdown id: tags:
 
 ## Show the masked regions
 
 %% Cell type:code id: tags:
 
 ``` python
 %matplotlib inline
 
 nmasks = np.max(mask)
 fig, axs = plt.subplots(nrows=1, ncols=nmasks+2, figsize=(12,3))
 
 # Show original image
 axs[0].imshow(img)
 axs[0].set_title("Original")
 axs[0].axis('off')
 
 
 # Show masks
 cmap = mpl.colormaps["rainbow"].copy()
 cmap.set_under(color='black') # Sets the background to black
 axs[1].imshow(mask, interpolation='none', cmap=cmap, vmin=1, vmax=nmasks+1)
 axs[1].set_title("Masks")
 axs[1].axis('off')
 
 # Show masked regions
 for idx in np.arange(2, nmasks+2):
     mask_id = idx-1
     submask = mask.copy()
     submask[submask != mask_id] = 0
 
     masked_img = img.copy()
     masked_img[submask==0] = 0
     axs[idx].imshow(masked_img)
     axs[idx].set_title(f"Mask {mask_id}")
 
     axs[idx].axis('off')
 
 plt.show()
 ```