Add support for reading and writing TIFF files

DIAGNijmegen · Dec 22, 2023 · 0773cc8 · 0773cc8
1 parent bbc9a76
commit 0773cc8
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/...enge_forge/partials/example-algorithm/example-algorithm{{cookiecutter._}}/inference.py.j2 b/...enge_forge/partials/example-algorithm/example-algorithm{{cookiecutter._}}/inference.py.j2
@@ -107,7 +107,7 @@ def write_json_file(*, location, content):
 
 def load_image_file_as_array(*, location):
     # Use SimpleITK to read a file
-    input_files = glob(str(location / "*"))
+    input_files = glob(str(location / "*.tiff")) + glob(str(location / "*.mha"))
     result = SimpleITK.ReadImage(input_files[0])
 
     # Convert it to a Numpy array
@@ -119,10 +119,13 @@ def load_image_file_as_array(*, location):
 def write_array_as_image_file(*, location, array):
     location.mkdir(parents=True, exist_ok=True)
 
+    # You may need to change the suffix to .tiff to match the expected output
+    suffix = ".mha"
+
     image = SimpleITK.GetImageFromArray(array)
     SimpleITK.WriteImage(
         image,
-        location / "output.mha",
+        location / f"output{suffix}",
         useCompression=True,
     )
 {%- endif %}

diff --git a/...ials/example-evaluation-method/example-evaluation-method{{cookiecutter._}}/evaluate.py.j2 b/...ials/example-evaluation-method/example-evaluation-method{{cookiecutter._}}/evaluate.py.j2
@@ -177,7 +177,7 @@ def load_json_file(*, location):
 
 def load_image_file(*, location):
     # Use SimpleITK to read a file
-    input_files = glob(str(location / "*"))
+    input_files = glob(str(location / "*.tiff")) + glob(str(location / "*.mha"))
     result = SimpleITK.ReadImage(input_files[0])
 
     # Convert it to a Numpy array