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
+from scipy import ndimage
 import matplotlib.pyplot as plt
-import matplotlib as mpl
-import numpy as np
-%matplotlib inline
 ```
 
-%% Cell type:code id: tags:
+qim3d.io.logger.level("info")
 
-``` python
-# Load 2D example image
-img = qim3d.examples.blobs_256x256
-
-# Display image
-plt.imshow(img)
-plt.show()
 ```
 
-%% Cell type:code id: tags:
+# Load example image
+img = qim3d.examples.bone_128x128x128
 
-``` 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)
 ```
 
-%% 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()
+#interface.launch()
+interface.launch(ndimage.zoom(img[0], 3, order=0))
 ```