New Layered Surface Segmentation

All documentation is here https://www.notion.so/qim-dtu/layered_surface_segmentation-704a14494e4a437a9f3311e06eea8e69

qim3d/viz/layers2d.py

+""" Provides a collection of visualisation functions for the Layers2d class."""
+import matplotlib.pyplot as plt
+import numpy as np
+from qim3d.process import layers2d as l2d
+
+def create_subplot_from_2d_arrays(data, m_rows = 1, n_cols = 1, figsize = (10, 10)):
+    '''
+    Creates a subplot from a collection of 2d arrays.
+    
+    Args:
+        data (list of 2d numpy.ndarray): A list of 2d numpy.ndarray.
+        m_rows (int): The number of rows in the subplot grid.
+        n_cols (int): The number of columns in the subplot grid.
+
+    Raises:
+        ValueError: If the product of m_rows and n_cols is not equal to the number of 2d arrays in data.
+
+    Notes:
+    - Subplots are organized in a m rows x n columns Grid.
+    - The total number of subplots is equal to the product of m_rows and n_cols.
+    '''
+    total = m_rows * n_cols
+    
+    if total != len(data):
+        raise ValueError("The product of m_rows and n_cols must be equal to the number of 2d arrays in data.\nCurrently, m_rows * n_cols = {}, while arrays in data = {}".format(m_rows * n_cols, len(data)))
+    
+    pos_idx = range(1, total + 1)
+    
+    fig = plt.figure(figsize = figsize)
+    
+    for k in range(total):
+        ax = fig.add_subplot(m_rows, n_cols, pos_idx[k])
+        ax.imshow(data[k], cmap = "gray")
+
+import os
+from skimage.io import imread
+
+if __name__ == "__main__":
+    path = os.path.join(os.getcwd(), "qim3d", "img_examples", "slice_218x193.png")
+    data = imread(path).astype(np.int32)
+    
+    l2d_obj = l2d.Layers2d()
+    l2d_obj.prepare_update(
+        data = data, 
+        is_inverted=False,
+        delta=1,
+        min_margin=10,
+        n_layers=3
+        ) 
+    l2d_obj.update()    
+    
+    data = []
+    for i in range(len(l2d_obj.get_segmentations())):
+        data.append(l2d_obj.get_segmentations()[i])
+    
+    # Create a subplot
+    create_subplot_from_2d_arrays(data, m_rows = 1, n_cols = 3, figsize = (10, 10))
+    
+    # Display the plot
+    plt.show()
+