Fix error when visualising 2D image (#439)

- Edits the `numpy2vtkImage` converter to delete the extra array which causes the error.
- Adds argument to the calls of `QCILViewerWidget`.
- Adds example to check where the error is raised.

CHANGELOG.md

@@ -8,6 +8,7 @@ Enhancements:
   - Adds methods to CILviewer and CILviewer2D #425
 
 Bugfix:
+  - Fix error when visualising 2D images #439
   - Hides the slider when one image dimension is 1 #432
   - Differentiate 3D and 2D images in the converter `numpy2vtkImage` #437
   - Edit slider min value #420

Wrappers/Python/ccpi/viewer/iviewer.py

@@ -14,7 +14,7 @@ class SingleViewerCenterWidget(QtWidgets.QMainWindow):
     def __init__(self, parent=None, viewer=viewer2D):
         QtWidgets.QMainWindow.__init__(self, parent)
 
-        self.frame = QCILViewerWidget(viewer=viewer, shape=(600, 600))
+        self.frame = QCILViewerWidget(parent, viewer=viewer, shape=(600, 600))
 
         if viewer == viewer3D:
             self.frame.viewer.setVolumeRenderOpacityMethod('scalar')
@@ -41,8 +41,8 @@ def __init__(self, parent=None, viewer1='2D', viewer2='2D'):
             elif viewer == '3D':
                 styles.append(vlink.Linked3DInteractorStyle)
             viewers.append(eval('viewer' + viewer))
-        self.frame1 = QCILViewerWidget(viewer=viewers[0], shape=(600, 600), interactorStyle=styles[0])
-        self.frame2 = QCILViewerWidget(viewer=viewers[1], shape=(600, 600), interactorStyle=styles[1])
+        self.frame1 = QCILViewerWidget(parent, viewer=viewers[0], shape=(600, 600), interactorStyle=styles[0])
+        self.frame2 = QCILViewerWidget(parent, viewer=viewers[1], shape=(600, 600), interactorStyle=styles[1])
 
         # Initially link viewers
         self.linkedViewersSetup()

Wrappers/Python/ccpi/viewer/standalone_viewer.py

@@ -159,4 +159,4 @@ def main():
 
 
 if __name__ == '__main__':
-    main()
+    main()

Wrappers/Python/ccpi/viewer/ui/main_windows.py

@@ -2,7 +2,6 @@
 import sys
 from functools import partial
 from pathlib import Path
-
 import ccpi.viewer.viewerLinker as vlink
 import vtk
 from ccpi.viewer import CILViewer2D, CILViewer
@@ -381,7 +380,6 @@ def updateViewerCoordsDockWidgetWithCoords(self, reader=None):
             The reader used to read the image. This contains some extra info about the
             original image file.
         '''
-
         viewer = self.viewer_coords_dock.viewers[0]
 
         if not isinstance(viewer, (CILViewer2D, CILViewer)):

Wrappers/Python/ccpi/viewer/utils/conversion.py

@@ -90,24 +90,31 @@ class Converter(object):
 
     @staticmethod
     def numpy2vtkImage(nparray, spacing=(1., 1., 1.), origin=(0, 0, 0), deep=0, output=None):
-        """The method converts a numpy array to a vtk image.
-        The vtk extent is set and needs to differentiate between 3D and 2D images."""
+        """
+        The method converts a numpy array to a vtk image.
+
+        Raises an error if the dimension of the image is not 2 or 3.
+        The array is flattened in the correct order, either fortran or C.
+        The vtk extent is set and needs to differentiate between 3D and 2D images.
+        Creates a vtkImageData if `output` is None, otherwise uses the provided empty output.
+        Adds the vtkarray to the image's point data. If an array is already present, it removes it."""
+
         shape = numpy.shape(nparray)
-        if (nparray.flags["FNC"]):
+        num_dims = len(shape)
+        if num_dims not in [2, 3]:
+            raise ValueError("Only 2D or 3D numpy arrays are supported.")
 
+        if nparray.flags["FNC"]:
             order = "F"
-            i = 0
-            k = len(shape) - 1
+            i, k = 0, num_dims - 1
         else:
             order = "C"
-            i = len(shape) - 1
-            k = 0
+            i, k = num_dims - 1, 0
 
         nparray = nparray.ravel(order)
         vtkarray = numpy_support.numpy_to_vtk(num_array=nparray,
                                               deep=deep,
                                               array_type=numpy_support.get_vtk_array_type(nparray.dtype))
-        vtkarray.SetName('vtkarray')
 
         if output is None:
             img_data = vtk.vtkImageData()
@@ -117,12 +124,16 @@ def numpy2vtkImage(nparray, spacing=(1., 1., 1.), origin=(0, 0, 0), deep=0, outp
             else:
                 img_data = output
 
-        img_data.GetPointData().AddArray(vtkarray)
-        if len(shape) == 3:
+        point_data = img_data.GetPointData()
+        while point_data.GetNumberOfArrays() > 0:
+            point_data.RemoveArray(0)
+        vtkarray.SetName('ImageScalars')
+        point_data.AddArray(vtkarray)
+        img_data.GetPointData().SetScalars(vtkarray)
+        if num_dims == 3:
             img_data.SetExtent(0, shape[i] - 1, 0, shape[1] - 1, 0, shape[k] - 1)
-        elif len(shape) == 2:
+        elif num_dims == 2:
             img_data.SetExtent(0, shape[i] - 1, 0, shape[k] - 1, 0, 0)
-        img_data.GetPointData().SetActiveScalars('vtkarray')
         img_data.SetOrigin(origin)
         img_data.SetSpacing(spacing)
 

Wrappers/Python/examples/2Dimage_reading.py

@@ -0,0 +1,14 @@
+from ccpi.viewer.CILViewer2D import CILViewer2D
+import vtk
+
+# This example imports a 2D tiff image and tests the 2D viewer
+DATASET_TO_READ = [path]  # insert path here
+if DATASET_TO_READ is not None:
+    reader = vtk.vtkTIFFReader()
+    reader.SetFileName(DATASET_TO_READ)
+    reader.Update()
+
+    v = CILViewer2D()
+    print(reader.GetOutput())
+    v.setInputData(reader.GetOutput())
+    v.startRenderLoop()

Wrappers/Python/examples/FourDockableLinkedViewerWidgets.py

@@ -18,7 +18,8 @@ def __init__(self, parent=None, reader=None):
         #self.resize(800,600)
 
         # create the dockable widgets with the viewer inside
-        self.v00 = QCILDockableWidget(viewer=viewer2D,
+        self.v00 = QCILDockableWidget(parent,
+                                      viewer=viewer2D,
                                       shape=(600, 600),
                                       title="X",
                                       interactorStyle=vlink.Linked2DInteractorStyle)

Wrappers/Python/examples/SingleViewerCentralWidget.py

@@ -11,7 +11,7 @@ class SingleViewerCenterWidget(QtWidgets.QMainWindow):
     def __init__(self, parent=None, viewer=viewer2D):
         QtWidgets.QMainWindow.__init__(self, parent)
 
-        self.frame = QCILViewerWidget(viewer=viewer, shape=(600, 600))
+        self.frame = QCILViewerWidget(parent, viewer=viewer, shape=(600, 600))
 
         head = example_data.HEAD.get()
 

Wrappers/Python/examples/SingleViewerCentralWidget2.py

@@ -12,7 +12,7 @@ class SingleViewerCenterWidget(QtWidgets.QMainWindow):
     def __init__(self, parent=None, viewer=viewer2D):
         QtWidgets.QMainWindow.__init__(self, parent)
         self.setGeometry(450, 250, 1000, 1000)
-        self.frame = QCILViewerWidget(viewer=viewer, shape=(2000, 2000))
+        self.frame = QCILViewerWidget(parent, viewer=viewer, shape=(2000, 2000))
 
         head = example_data.HEAD.get()
 

Wrappers/Python/examples/TwoLinkedViewersCentralWidget.py

@@ -16,8 +16,14 @@ def __init__(self, parent=None):
         QtWidgets.QMainWindow.__init__(self, parent)
         #self.resize(800,600)
 
-        self.frame1 = QCILViewerWidget(viewer=viewer2D, shape=(600, 600), interactorStyle=vlink.Linked2DInteractorStyle)
-        self.frame2 = QCILViewerWidget(viewer=viewer3D, shape=(600, 600), interactorStyle=vlink.Linked3DInteractorStyle)
+        self.frame1 = QCILViewerWidget(parent,
+                                       viewer=viewer2D,
+                                       shape=(600, 600),
+                                       interactorStyle=vlink.Linked2DInteractorStyle)
+        self.frame2 = QCILViewerWidget(parent,
+                                       viewer=viewer3D,
+                                       shape=(600, 600),
+                                       interactorStyle=vlink.Linked3DInteractorStyle)
 
         head = example_data.HEAD.get()
 

Wrappers/Python/examples/opacity_in_viewer.py

@@ -23,7 +23,7 @@ class OpacityViewerWidget(SingleViewerCenterWidget):
     def __init__(self, parent=None, viewer=viewer3D):
         SingleViewerCenterWidget.__init__(self, parent)
 
-        self.frame = QCILViewerWidget(viewer=viewer, shape=(600, 600))
+        self.frame = QCILViewerWidget(parent, viewer=viewer, shape=(600, 600))
 
         self.setCentralWidget(self.frame)