Vtkvolume correction of dimensions order (#2818)

* vtkvolume correction of dimensions order

* add end line

Co-authored-by: ARTUSI <xavier.artusi@cea.fr>

panel/pane/vtk/vtk.py

@@ -679,9 +679,9 @@ def register_serializer(cls, class_type, serializer):
         cls._serializers.update({class_type:serializer})
 
     def _volume_from_array(self, sub_array):
-        return dict(buffer=base64encode(sub_array.ravel(order='F' if sub_array.flags['F_CONTIGUOUS'] else 'C')),
-                    dims=sub_array.shape if sub_array.flags['F_CONTIGUOUS'] else sub_array.shape[::-1],
-                    spacing=self._sub_spacing if sub_array.flags['F_CONTIGUOUS'] else self._sub_spacing[::-1],
+        return dict(buffer=base64encode(sub_array.ravel(order='F')),
+                    dims=sub_array.shape,
+                    spacing=self._sub_spacing,
                     origin=self.origin,
                     data_range=(sub_array.min(), sub_array.max()),
                     dtype=sub_array.dtype.name)
@@ -700,10 +700,10 @@ def _get_volume_data(self):
                 def volume_serializer(inst):
                     imageData = inst.object
                     array = numpy_support.vtk_to_numpy(imageData.GetPointData().GetScalars())
-                    dims = imageData.GetDimensions()[::-1]
-                    inst.spacing = imageData.GetSpacing()[::-1]
+                    dims = imageData.GetDimensions()
+                    inst.spacing = imageData.GetSpacing()
                     inst.origin = imageData.GetOrigin()
-                    return inst._volume_from_array(inst._subsample_array(array.reshape(dims, order='C')))
+                    return inst._volume_from_array(inst._subsample_array(array.reshape(dims, order='F')))
 
                 VTKVolume.register_serializer(vtk.vtkImageData, volume_serializer)
                 serializer = volume_serializer
@@ -722,7 +722,7 @@ def _subsample_array(self, array):
         if any([d_f > 1 for d_f in dowsnscale_factor]):
             try:
                 import scipy.ndimage as nd
-                sub_array = nd.interpolation.zoom(array, zoom=[1 / d_f for d_f in dowsnscale_factor], order=0)
+                sub_array = nd.interpolation.zoom(array, zoom=[1 / d_f for d_f in dowsnscale_factor], order=0, mode="nearest")
             except ImportError:
                 sub_array = array[::int(np.ceil(dowsnscale_factor[0])),
                                   ::int(np.ceil(dowsnscale_factor[1])),

panel/tests/pane/test_vtk.py

@@ -370,3 +370,46 @@ def test_vtkvol_pane_from_image_data(document, comm):
     # Cleanup
     pane._cleanup(model)
     assert pane._models == {}
+
+@vtk_available
+def test_vtkvol_serialization_coherence(document, comm):
+    from vtk.util import numpy_support
+
+    data_matrix = np.zeros([50, 75, 100], dtype=np.uint8)
+    data_matrix[0:35, 0:35, 0:35] = 50
+    data_matrix[25:50, 25:55, 25:55] = 100
+    data_matrix[45:50, 45:74, 45:100] = 150
+
+    origin = (0, 10, 20)
+    spacing = (3,2,1)
+
+    data_matrix_c = np.ascontiguousarray(data_matrix)
+    data_matrix_f = np.asfortranarray(data_matrix)
+    image_data = vtk.vtkImageData()
+    image_data.SetDimensions(*data_matrix.shape)
+    image_data.SetOrigin(*origin)
+    image_data.SetSpacing(*spacing)
+    vtk_arr = numpy_support.numpy_to_vtk(data_matrix.ravel(order='F'))
+    image_data.GetPointData().SetScalars(vtk_arr)
+
+    p_c = VTKVolume(data_matrix_c, origin=origin, spacing=spacing)
+    p_f = VTKVolume(data_matrix_f, origin=origin, spacing=spacing)
+    p_id = VTKVolume(image_data)
+    assert p_c._sub_spacing == p_f._sub_spacing == p_id._sub_spacing == spacing
+    vd_c = p_c._get_volume_data()
+    vd_f = p_f._get_volume_data()
+    vd_id = p_id._get_volume_data()
+    data_decoded = np.frombuffer(base64.b64decode(vd_c["buffer"]), dtype=vd_c["dtype"]).reshape(vd_c["dims"], order="F")
+    assert np.alltrue(data_decoded==data_matrix)
+    assert vd_id == vd_c == vd_f
+
+
+
+    p_c_ds = VTKVolume(data_matrix_c, origin=origin, spacing=spacing, max_data_size=0.1)
+    p_f_ds = VTKVolume(data_matrix_f, origin=origin, spacing=spacing, max_data_size=0.1)
+    p_id_ds = VTKVolume(image_data, max_data_size=0.1)
+    assert p_c_ds._sub_spacing == p_f_ds._sub_spacing == p_id_ds._sub_spacing != spacing
+    vd_c_ds = p_c_ds._get_volume_data()
+    vd_f_ds = p_f_ds._get_volume_data()
+    vd_id_ds = p_id_ds._get_volume_data()
+    assert vd_id_ds == vd_c_ds == vd_f_ds