From e4a0d3f8ed3513e2a386bd6386303d2497378667 Mon Sep 17 00:00:00 2001
From: Sam Gerber <95931209+sgerber-hf@users.noreply.github.com>
Date: Thu, 21 Nov 2024 05:51:17 -0500
Subject: [PATCH] [utils] Support MetaImage files with unspecified HeaderSize
 (#149)

---
 src/deepali/utils/imageio/meta.py | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/src/deepali/utils/imageio/meta.py b/src/deepali/utils/imageio/meta.py
index 68df4a4..6b99ba5 100644
--- a/src/deepali/utils/imageio/meta.py
+++ b/src/deepali/utils/imageio/meta.py
@@ -218,12 +218,13 @@ def read_meta_image_from_fileobj(f: io.BufferedReader) -> Tuple[np.ndarray, Meta
             "ElementDataFile",
         ):
             meta[key] = value
+        elif key == "HeaderSize":
+            meta[key] = np.intp(value)
         elif key in (
             "NDims",
             "ID",
             "ParentID",
             "CompressedDataSize",
-            "HeaderSize",
             "HeaderSizePerSlice",
             "ElementNumberOfChannels",
         ):
@@ -268,8 +269,18 @@ def read_meta_image_from_fileobj(f: io.BufferedReader) -> Tuple[np.ndarray, Meta
     element_size = np.dtype(meta["ElementType"]).itemsize
     increment = np.prod(shape[1:], dtype=int) * element_size
 
-    f.seek(meta_size, 0)
-    f.seek((meta.get("HeaderSize") or 0), 1)
+    header_size = int( meta.get("HeaderSize") or 0 )
+    if header_size == -1:
+        #See https://github.com/Kitware/MetaIO/blob/1a031fd8223c4846e2f90f50216cbcb415d52018/src/metaImage.cxx#L2601 for reference
+        data_quantity = int(np.prod(meta["DimSize"])) #type: ignore
+        element_size = int(np.dtype(meta["ElementType"]).itemsize)
+        read_size = data_quantity * int(meta["ElementNumberOfChannels"]) * element_size #type: ignore
+        f.seek(-read_size, 2)
+    elif header_size >= 0:
+        f.seek(meta_size + header_size, 0)
+    else:
+        raise ValueError(f"Invalid HeaderSize {header_size}")
+
     if meta.get("CompressedData"):
         if meta["CompressedDataSize"] is None:
             raise ValueError("CompressedDataSize needs to be specified when using CompressedData")