Fix downsamplers so they take into account number of bytes per element (

#242)

* Make sure size calculation in downsampling takes into account number of bytes per element

* fix issues with extent in hdf5 readers

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## v22.x.x
 * When a new image is loaded on the 3D viewer, reset camera position, slice and volume orientation and visibility, and clipping planes.
+* Fix downsampling of resample readers when working with datatypes other than uint8. Previously resulting size of image was multiple times greater than requested target size as uint8 type was always assumed.
 
 ## v22.1.1
 * Changes released in 22.0.1, but also requires vtk version >= 9.0.3

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

@@ -1131,7 +1131,7 @@ def RequestData(self, request, inInfo, outInfo):
             else:
                 shape = list(readshape)[::-1]
 
-            total_size = shape[0] * shape[1] * shape[2]
+            total_size = shape[0] * shape[1] * shape[2] * self.GetBytesPerElement()
 
             max_size = self.GetTargetSize()
 
@@ -1334,10 +1334,8 @@ def _GetInternalChunkReader(self):
         # Here we read just the chunk from the hdf5 file:
         cropped_reader = HDF5SubsetReader()
         cropped_reader.SetInputConnection(reader.GetOutputPort())
-        dims = self.GetStoredArrayShape()
         # Set default extent to full extent:
-        cropped_reader.SetUpdateExtent(
-            (0, dims[0]-1, 0, dims[1]-1, 0, dims[2]-1))
+        cropped_reader.SetUpdateExtent((0, -1, 0, -1, 0, -1))
         self._ChunkReader = cropped_reader
         return cropped_reader
 
@@ -1346,6 +1344,9 @@ def UpdateChunkToRead(self, start_slice):
         start_slice in the z direction'''
         num_slices_per_chunk = self._GetNumSlicesPerChunk()
         end_slice = start_slice + num_slices_per_chunk - 1
+        end_z_value = self.GetStoredArrayShape()[2]-1
+        if end_slice > end_z_value:
+            end_slice = end_z_value
         if start_slice < 0:
             raise ValueError('{} ERROR: Start slice cannot be negative.'
                              .format(self.__class__.__name__))
@@ -1654,6 +1655,8 @@ def RequestData(self, request, inInfo, outInfo):
         read_data = reader.GetOutput()
         outData.ShallowCopy(read_data)
 
+        return 1
+
 
 # ------------ RESAMPLE FROM MEMORY: ------------------------------------------------------------------------------
 
@@ -1701,6 +1704,11 @@ def GetTargetSize(self):
         ''' Get the total target size to downsample image to, in bytes.'''
         return self._TargetSize
 
+    def GetBytesPerElement(self):
+        ''' Get number of bytes per element'''
+        if hasattr(self, '_BytesPerElement'):
+            return self._BytesPerElement
+
     def GetOutput(self):
         return self.GetOutputDataObject(0)
 
@@ -1709,6 +1717,7 @@ def ReadDataSetInfo(self, inData):
         self._Origin = inData.GetOrigin()
         self._Extent = inData.GetExtent()
         self._StoredArrayShape = (self._Extent[1]+1, (self._Extent[3]+1), (self._Extent[5]+1))
+        self._BytesPerElement = Converter.vtkType_to_bytes[inData.GetScalarType()]
 
     def GetElementSpacing(self):
         ''' Returns the spacing of the input dataset as a tuple'''
@@ -1736,7 +1745,7 @@ def RequestData(self, request, inInfo, outInfo):
         extent = self.GetExtent()
         shape = self.GetStoredArrayShape()
 
-        total_size = shape[0] * shape[1] * shape[2]
+        total_size = shape[0] * shape[1] * shape[2] * self.GetBytesPerElement()
 
         max_size = self.GetTargetSize()
 

Wrappers/Python/ccpi/viewer/utils/hdf5_io.py

@@ -219,20 +219,21 @@ def RequestUpdateExtent(self, request, inInfo, outInfo):
                 vtk.vtkStreamingDemandDrivenPipeline.WHOLE_EXTENT())
             set_extent = list(info.Get(
                 vtk.vtkStreamingDemandDrivenPipeline.UPDATE_EXTENT()))
+
             for i, value in enumerate(set_extent):
                 if value == -1:
                     set_extent[i] = whole_extent[i]
                 else:
                     if i % 2 == 0:
                         if value < whole_extent[i]:
                             raise ValueError("Requested extent {}\
-                                is outside of original image extent {}".format(
-                                set_extent, whole_extent))
+                                is outside of original image extent {} as {}<{}".format(
+                                set_extent, whole_extent, value, whole_extent[i]))
                     else:
                         if value > whole_extent[i]:
                             raise ValueError("Requested extent {}\
-                                is outside of original image extent {}".format(
-                                set_extent, whole_extent))
+                                is outside of original image extent {} as {}>{}".format(
+                                set_extent, whole_extent, value, whole_extent[i]))
 
             self.SetUpdateExtent(set_extent)
 

Wrappers/Python/test/test_hdf5.py

@@ -65,7 +65,7 @@ def test_read_hdf5_channel(self):
         np.testing.assert_array_equal(
             self.input_4D_array[channel_index], read_array)
 
-    def test_read_cropped_hdf5(self):
+    def test_hdf5_subset_reader(self):
         # With the subset reader: -----------------------------
         # Test cropping the extent of a dataset
         cropped_array = self.input_3D_array[1:3, 3:6, 0:3]
@@ -81,7 +81,10 @@ def test_read_cropped_hdf5(self):
         array_image_data = cropped_reader.GetOutputDataObject(0)
         read_cropped_array = Converter.vtk2numpy(array_image_data)
         np.testing.assert_array_equal(cropped_array, read_cropped_array)
-        # With the Cropped reader: -----------------------------
+
+    def test_read_cropped_hdf5_reader(self):
+        # # With the Cropped reader: -----------------------------
+        cropped_array = self.input_3D_array[1:3, 3:6, 0:3]
         reader = cilHDF5CroppedReader()
         reader.SetFileName(self.hdf5_filename_3D)
         reader.SetDatasetName("ImageData")
@@ -154,7 +157,7 @@ def test_hdf5_resample_reader(self):
         resulting_shape = (extent[1]+1, (extent[3]+1), (extent[5]+1))
         og_shape = np.shape(self.input_3D_array)
         og_shape = (og_shape[2], og_shape[1], og_shape[0])
-        og_size = og_shape[0]*og_shape[1]*og_shape[2]
+        og_size = og_shape[0]*og_shape[1]*og_shape[2]*readerhdf5.GetBytesPerElement()
         expected_shape = calculate_target_downsample_shape(
             target_size, og_size, og_shape)
         self.assertEqual(resulting_shape, expected_shape)

Wrappers/Python/test/test_resample_readers.py

@@ -28,15 +28,17 @@ class TestResampleReaders(unittest.TestCase):
     def setUp(self):
         # Generate random 3D array and write to HDF5:
         np.random.seed(1)
-        self.input_3D_array = np.random.randint(10, size=(5, 10, 6), dtype=np.uint8)
+        bits = 16
+        self.bytes_per_element = int(bits/8)
+        self.input_3D_array = np.random.randint(10, size=(5, 10, 6), dtype=eval(f"np.uint{bits}"))
         bytes_3D_array = bytes(self.input_3D_array)
         self.raw_filename_3D = 'test_3D_data.raw'
         with open(self.raw_filename_3D, 'wb') as f:
             f.write(bytes_3D_array)
 
         # write header to go with raw file
         self.mhd_filename_3D = 'raw_header.mhd'
-        typecode = 'uint8'
+        typecode = f'uint{bits}'
         big_endian = False
         header_length = 0
         shape = np.shape(self.input_3D_array)
@@ -77,7 +79,7 @@ def test_raw_resample_reader(self):
         extent = image.GetExtent()
         resulting_shape = (extent[1]+1, (extent[3]+1), (extent[5]+1))
         og_shape = (og_shape[2], og_shape[1], og_shape[0])
-        og_size = og_shape[0]*og_shape[1]*og_shape[2]
+        og_size = og_shape[0]*og_shape[1]*og_shape[2]*self.bytes_per_element
         expected_shape = calculate_target_downsample_shape(
             target_size, og_size, og_shape)
         self.assertEqual(resulting_shape, expected_shape)
@@ -105,10 +107,10 @@ def test_raw_resample_reader(self):
         reader.Update()
         image = reader.GetOutput()
         extent = image.GetExtent()
-        shape_not_acquisition = calculate_target_downsample_shape(
+        shape_acquisition = calculate_target_downsample_shape(
             target_size, og_size, og_shape, acq=True)
-        expected_size = shape_not_acquisition[0] * \
-            shape_not_acquisition[1]*shape_not_acquisition[2]
+        expected_size = shape_acquisition[0] * \
+            shape_acquisition[1]*shape_acquisition[2]
         resulting_shape = (extent[1]+1, (extent[3]+1), (extent[5]+1))
         resulting_size = resulting_shape[0] * \
             resulting_shape[1]*resulting_shape[2]
@@ -140,7 +142,7 @@ def test_meta_and_numpy_resample_readers(self):
                 extent = image.GetExtent()
                 resulting_shape = (extent[1]+1, (extent[3]+1), (extent[5]+1))
                 og_shape = (og_shape[2], og_shape[1], og_shape[0])
-                og_size = og_shape[0]*og_shape[1]*og_shape[2]
+                og_size = og_shape[0]*og_shape[1]*og_shape[2]*self.bytes_per_element
                 expected_shape = calculate_target_downsample_shape(
                     target_size, og_size, og_shape)
                 self.assertEqual(resulting_shape, expected_shape)

Wrappers/Python/test/test_vtk_image_resampler.py

@@ -24,7 +24,9 @@ class TestVTKImageResampler(unittest.TestCase):
     def setUp(self):
         # Generate random 3D array and convert to VTK Image Data:
         np.random.seed(1)
-        self.input_3D_array = np.random.randint(10, size=(50, 10, 60), dtype=np.uint8)
+        bits = 16
+        self.bytes_per_element = int(bits/8)
+        self.input_3D_array = np.random.randint(10, size=(50, 10, 60), dtype=eval(f"np.uint{bits}"))
         self.input_vtk_image = Converter.numpy2vtkImage(self.input_3D_array)
 
 
@@ -44,7 +46,7 @@ def test_vtk_resample_reader(self):
         og_shape = np.shape(self.input_3D_array)
         resulting_shape = (extent[1]+1, (extent[3]+1), (extent[5]+1))
         og_shape = (og_shape[2], og_shape[1], og_shape[0])
-        og_size = og_shape[0]*og_shape[1]*og_shape[2]
+        og_size = og_shape[0]*og_shape[1]*og_shape[2]*self.bytes_per_element
         expected_shape = calculate_target_downsample_shape(
             target_size, og_size, og_shape)
         self.assertEqual(resulting_shape, expected_shape)