examples/image_visu.py: exemplify differences between 'XYZ' and 'ZYX' conventions

examples/image_visu.py

@@ -6,73 +6,106 @@ import os
 from vt import vtImage
 
 
-def plot_3D_array_z_slice(arr, z_slice=None, cmap='gray', title=""):
-    """Plot a z-slice of a given 3D array.
+def plot_2D_array(arr, cmap='gray', order='ZYX', title=""):
+    """Plot a 2D array.
 
     Parameters
     ----------
     arr : np.ndarray
         The array to represent.
-    z_slice : int, optional
-        The index of the z-sclice to represent.
     cmap : str in {'gray', 'viridis'}, optional
         Colormap name, all those known by matplolib works. By default use 'gray'.
+    title :
 
     """
-    import matplotlib.pyplot as plt
-    sh = arr.shape
-    if z_slice is None:
-        z_slice = sh[2]//2
-
-    plt.figure()
-    plt.imshow(arr[:, :, z_slice], cmap=cmap)
-    plt.suptitle(title)
-    plt.title("Z-slice: {}/{}".format(z_slice, sh[2]))
-    plt.xlabel('Y-axis')
-    plt.ylabel('X-axis')
+
+    if arr.flags.c_contiguous is True or order is 'ZYX':
+        import matplotlib.pyplot as plt
+        plt.figure()
+        plt.imshow(arr, cmap=cmap)
+        ltitle = title + " - ZYX-ordered"
+    elif arr.flags.f_contiguous is True or order is 'XYZ':
+        import matplotlib.pyplot as plt
+        plt.figure()
+        plt.imshow(np.transpose(arr), cmap=cmap)
+        ltitle = title + " - XYZ-ordered"
+    else:
+        print("do not know how to plot image")
+        return
+
+    plt.suptitle(ltitle)
+
+    plt.xlabel('X-axis')
+    plt.ylabel('Y-axis')
+
     plt.colorbar()
     plt.show()
 
 
-def plot_2D_array(arr, cmap='gray', title=""):
-    """Plot a 2D array.
+def plot_3D_array_z_slice(arr, z_slice=None, cmap='gray', order='ZYX', title=""):
+    """Plot a z-slice of a given 3D array.
 
     Parameters
     ----------
     arr : np.ndarray
         The array to represent.
+    z_slice : int, optional
+        The index of the z-sclice to represent.
     cmap : str in {'gray', 'viridis'}, optional
         Colormap name, all those known by matplolib works. By default use 'gray'.
+    title :
 
     """
-    import matplotlib.pyplot as plt
 
-    plt.figure()
-    plt.imshow(arr, cmap=cmap)
-    plt.suptitle(title)
-    plt.xlabel('Y-axis')
-    plt.ylabel('X-axis')
-    plt.colorbar()
-    plt.show()
+    if arr.ndim <= 1:
+        print("not an image")
+    elif arr.ndim == 2:
+        plot_2D_array(arr, cmap=cmap, title=title)
+    elif arr.ndim == 3:
+        if order is 'ZYX':
+            if z_slice is None:
+                z_slice = arr.shape[0] // 2
+            extarr = arr[z_slice, :, :]
+        elif order is 'XYZ':
+            if z_slice is None:
+                z_slice = arr.shape[2] // 2
+            extarr = arr[:, :, z_slice]
+        else:
+            print("do not know how to plot image")
+            return
+        plot_2D_array(extarr, cmap=cmap, order=order, title=title+" - "+str(z_slice)+"-slice")
+    else:
+        print("not an image")
+
+
 
 
 # ------------------------------------------------------------------------------
 # Test plotting function with a handmade 3D example:
 # ------------------------------------------------------------------------------
-def _plot_handmade_3D():
+def _plot_handmade_3D(order='XYZ'):
 
     xy_shape = 10
     mid_xy = xy_shape//2
     z_shape = 5
 
-    # - Create a 2D array with a diagonal at max value (255):
-    arr_2d = np.diag(np.repeat(255, xy_shape))
-    # - For all rows at middle column, replace by 200:
-    arr_2d[:, mid_xy] = 200
-    # - For all columns at middle row, replace by 100:
-    arr_2d[mid_xy, :] = 100
-    # - Repeat this 2D array `z_shape` times along new dimension to get a 3D array:
-    arr_3d = np.repeat(arr_2d[:, :, np.newaxis], z_shape, axis=2)
+    if order is 'XYZ':
+        # - Create a 2D array with a diagonal at max value (255):
+        arr_2d = np.diag(np.repeat(255, xy_shape))
+        # - For all rows at middle column, replace by 200:
+        arr_2d[:, mid_xy] = 200
+        # - For all columns at middle row, replace by 100:
+        arr_2d[mid_xy, :] = 100
+        # - Repeat this 2D array `z_shape` times along new dimension to get a 3D array:
+        arr_3d = np.repeat(arr_2d[:, :, np.newaxis], z_shape, axis=2)
+        lorder=order
+    else:
+        arr_2d = np.diag(np.repeat(255, xy_shape))
+        arr_2d[mid_xy, :] = 200
+        arr_2d[:, mid_xy] = 100
+        arr_3d = np.repeat(arr_2d[np.newaxis, :, :], z_shape, axis=0)
+        lorder = 'ZYX'
+
 
     print("2D array is C-contiguous:", arr_2d.flags.c_contiguous)
     print("3D array is C-contiguous:", arr_3d.flags.c_contiguous)
@@ -81,14 +114,14 @@ def _plot_handmade_3D():
 
     print("- type q to quit")
 
-    plot_3D_array_z_slice(arr_3d, cmap='viridis', title='Test array')
+    plot_3D_array_z_slice(arr_3d, cmap='viridis', order=order, title='Test array')
 
 
 # ------------------------------------------------------------------------------
 # Use plotting function with real data:
 # ------------------------------------------------------------------------------
 
-def _plot_example_data(img_name):
+def _plot_example_data(img_name, order='ZYX'):
 
     # Defines the image to read:
     img_path = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "data", img_name))
@@ -99,48 +132,64 @@ def _plot_example_data(img_name):
     print("Image shape is: {}".format(sh))
     # Extract the array of data:
     arr = vt_im.copy_to_array().copy()
-    # arr =  np.reshape(arr.ravel(), sh, order='C')
     print("Array shape is: {}".format(arr.shape))
     print("- type q to quit")
 
-    plot_3D_array_z_slice(arr, cmap='gray', title=img_name)
+    plot_3D_array_z_slice(arr, cmap='gray', order=order, title=img_name)
 
 # ------------------------------------------------------------------------------
 #
 # ------------------------------------------------------------------------------
 
-def _build_array(x, y, z=1, dtype=np.ubyte, order='C'):
+
+def _build_array(x, y, z=1, dtype=np.ubyte, order='ZYX'):
     a = None
-    if z == 1:
-        a = np.ndarray([y,x], dtype=dtype, order=order)
-        for y in range(a.shape[0]):
-            for x in range(a.shape[1]):
-                a[y][x] = y * a.shape[1] + x
-    elif z > 1:
-        a = np.ndarray([z, y, x], dtype=dtype, order=order)
-        for y in range(a.shape[0]):
+    if order is 'ZYX':
+        if z == 1:
+            a = np.ndarray([y, x], dtype=dtype)
+            for y in range(a.shape[0]):
+                for x in range(a.shape[1]):
+                    a[y][x] = y * a.shape[1] + x
+        elif z > 1:
+            a = np.ndarray([z, y, x], dtype=dtype)
+            for z in range(a.shape[0]):
+                for y in range(a.shape[1]):
+                    for x in range(a.shape[2]):
+                        a[z][y][x] = z * a.shape[1] * a.shape[2] + y * a.shape[2] + x
+    else:
+        if z == 1:
+            a = np.ndarray([x, y], dtype=dtype)
             for y in range(a.shape[1]):
-                for x in range(a.shape[2]):
-                    a[z][y][x] = z * a.shape[1] * a.shape[2] + y * a.shape[2] + x
+                for x in range(a.shape[0]):
+                    a[x][y] = y * a.shape[0] + x
+        elif z > 1:
+            a = np.ndarray([x, y, z], dtype=dtype)
+            for z in range(a.shape[2]):
+                for y in range(a.shape[1]):
+                    for x in range(a.shape[0]):
+                        a[x][y][z] = z * a.shape[1] * a.shape[0] + y * a.shape[0] + x
+
     return a
 
 
-def _plot_build_array(x, y, z=1, dtype=np.ubyte, order='C'):
+def _plot_build_array(x, y, z=1, dtype=np.ubyte, order='ZYX'):
     arr = _build_array(x=x, y=y, z=z, dtype=dtype, order=order)
     print("Array shape is: {}".format(arr.shape))
     print("Array strides is: {}".format(arr.strides))
     print("Array flags are: {}".format(arr.flags))
     if z > 1:
-        plot_3D_array_z_slice(arr, cmap='gray')
+        plot_3D_array_z_slice(arr, cmap='gray', order=order)
     else:
-        plot_2D_array(arr, cmap='gray')
+        plot_2D_array(arr, cmap='gray', order=order)
 
 
 # ------------------------------------------------------------------------------
 # main
 # ------------------------------------------------------------------------------
 _plot_handmade_3D()
+_plot_handmade_3D(order='ZYX')
 _plot_example_data('p58-t0_INT_down_interp_2x.inr')
+# _plot_build_array(19, 9)
 # _plot_build_array(19, 17)
-# _plot_build_array(19, 17, order='F')
-
+_plot_build_array(19, 17, 13)
+_plot_build_array(19, 17, 13, order='XYZ')