Further segmentation efficiency improvements

src/highdicom/content.py

@@ -6,6 +6,7 @@
 
 import numpy as np
 from pydicom.dataset import Dataset
+from pydicom import DataElement
 from pydicom.sequence import Sequence as DataElementSequence
 from pydicom.sr.coding import Code
 from pydicom.sr.codedict import codes
@@ -469,18 +470,27 @@ def __init__(
                     'Position in Pixel Matrix must be specified for '
                     'slide coordinate system.'
                 )
-            col_position, row_position = pixel_matrix_position
             x, y, z = image_position
-            item.XOffsetInSlideCoordinateSystem = DS(x, auto_format=True)
-            item.YOffsetInSlideCoordinateSystem = DS(y, auto_format=True)
-            item.ZOffsetInSlideCoordinateSystem = DS(z, auto_format=True)
+            col_position, row_position = pixel_matrix_position
             if row_position < 0 or col_position < 0:
                 raise ValueError(
                     'Both items in "pixel_matrix_position" must be positive '
                     'integers.'
                 )
-            item.RowPositionInTotalImagePixelMatrix = row_position
-            item.ColumnPositionInTotalImagePixelMatrix = col_position
+
+            # Use hard-coded tags to avoid the keywork dictionary lookup
+            # (this constructor is called a large number of times in large
+            # multiframe images, so some optimization makes sense)
+            x_tag = 0x0040072a  # XOffsetInSlideCoordinateSystem
+            y_tag = 0x0040073a  # YOffsetInSlideCoordinateSystem
+            z_tag = 0x0040074a  # ZOffsetInSlideCoordinateSystem
+            row_tag = 0x0048021f  # RowPositionInTotalImagePixelMatrix
+            column_tag = 0x0048021e  # ColumnPositionInTotalImagePixelMatrix
+            item.add(DataElement(x_tag, 'DS', DS(x, auto_format=True)))
+            item.add(DataElement(y_tag, 'DS', DS(y, auto_format=True)))
+            item.add(DataElement(z_tag, 'DS', DS(z, auto_format=True)))
+            item.add(DataElement(row_tag, 'SL', int(row_position)))
+            item.add(DataElement(column_tag, 'SL', int(col_position)))
         elif coordinate_system == CoordinateSystemNames.PATIENT:
             item.ImagePositionPatient = [
                 DS(ip, auto_format=True) for ip in image_position

src/highdicom/seg/pyramid.py

@@ -336,16 +336,16 @@ def create_segmentation_pyramid(
         if n_pix_arrays > 1:
             pixel_array = pixel_arrays[output_level]
         else:
-            need_resize = True
-            if n_sources > 1:
-                output_size = (
-                    source_image.TotalPixelMatrixColumns,
-                    source_image.TotalPixelMatrixRows
-                )
+            if output_level == 0:
+                pixel_array = pixel_arrays[0]
+                need_resize = False
             else:
-                if output_level == 0:
-                    pixel_array = pixel_arrays[0]
-                    need_resize = False
+                need_resize = True
+                if n_sources > 1:
+                    output_size = (
+                        source_image.TotalPixelMatrixColumns,
+                        source_image.TotalPixelMatrixRows
+                    )
                 else:
                     f = downsample_factors[output_level - 1]
                     output_size = (