Fix timepoints determination

HISTORY.md

@@ -1,5 +1,9 @@
 # History
 
+## 0.13.1 (2023-07-19)
+
+* Fix timepoints determination
+
 ## 0.13.0 (2023-07-17)
 
 * Increased maximum number of segments to 64

panimg/models.py

@@ -3,6 +3,7 @@
 import re
 import shutil
 from enum import Enum
+from functools import cached_property
 from pathlib import Path
 from typing import Any, Dict, FrozenSet, List, NamedTuple, Optional, Set, Tuple
 from uuid import UUID, uuid4
@@ -230,8 +231,9 @@ def window_width(self) -> Optional[float]:
 
     @property
     def timepoints(self) -> Optional[int]:
-        if self.image.GetDimension() == 4:
-            return int(self.image.GetSize()[-1])
+        if self.image.GetDimension() == 4 and self.segments is None:
+            # Only 4D files that are non-segmentations have timepoints
+            return int(self.image.GetSize()[3])
         else:
             return None
 
@@ -262,7 +264,7 @@ def add_value_range_meta_data(cls, image: Image):  # noqa: B902, N805
 
         return image
 
-    @property
+    @cached_property
     def segments(self) -> Optional[FrozenSet[int]]:
         if (
             self.image.GetNumberOfComponentsPerPixel() != 1

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "panimg"
-version = "0.13.0"
+version = "0.13.1"
 description = "Conversion of medical images to MHA and TIFF."
 license = "Apache-2.0"
 authors = ["James Meakin <[email protected]>"]

tests/resources/image10x11x12x13.mhd

@@ -3,12 +3,12 @@ NDims = 4
 BinaryData = True
 BinaryDataByteOrderMSB = False
 CompressedData = True
-CompressedDataSize = 39
+CompressedDataSize = 40
 TransformMatrix = 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1
 Offset = -131 -99 -917 0
 CenterOfRotation = 0 0 0 0
 ElementSpacing = 0.429 0.429 0.5 1
 DimSize = 10 11 12 13
-AnatomicalOrientation = RAI
+AnatomicalOrientation = ????
 ElementType = MET_UCHAR
 ElementDataFile = image10x11x12x13.zraw

tests/test_background_tasks.py

@@ -66,6 +66,7 @@ def test_staged_4d_mha_and_4d_mhd_upload(images, tmpdir_factory):
     assert len(result.new_images) == 1
 
     image = result.new_images.pop()
+
     assert image.timepoints == 13
     assert image.depth == 12
     assert image.height == 11

tests/test_mhd.py

@@ -26,11 +26,11 @@ def test_parse_header_valid_4d_mhd():
         "BinaryData": "True",
         "BinaryDataByteOrderMSB": "False",
         "CompressedData": "True",
-        "CompressedDataSize": "39",
+        "CompressedDataSize": "40",
         "TransformMatrix": "1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1",
         "Offset": "-131 -99 -917 0",
         "CenterOfRotation": "0 0 0 0",
-        "AnatomicalOrientation": "RAI",
+        "AnatomicalOrientation": "????",
         "ElementSpacing": "0.429 0.429 0.5 1",
         "DimSize": "10 11 12 13",
         "ElementType": "MET_UCHAR",

tests/test_models.py

@@ -133,8 +133,8 @@ def test_built_image_extra_metadata_defaults(tmpdir, caplog):
         ),
         (  # 4D image
             "image10x11x12x13.mha",
-            0,
-            0,
+            2,
+            2,
         ),
     ],
 )
@@ -245,3 +245,16 @@ def test_invalid_4d(tmp_path_factory):
             )
         ]
     }
+
+
+def test_4d_segmentation_none_timepoints(tmp_path_factory):
+    result = _build_files(
+        builder=image_builders.image_builder_mhd,
+        files={RESOURCE_PATH / "segments" / "4D_1_1_1_5_UInt8.mha"},
+        output_directory=tmp_path_factory.mktemp("output"),
+    )
+
+    new_image = result.new_images.pop()
+
+    assert new_image.segments == frozenset({1, 2, 3, 4, 5})
+    assert new_image.timepoints is None