From 9ef5d4d17ec273d7a25d4a9e79030d880a76e3b8 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Thu, 30 May 2024 00:39:30 +0930
Subject: [PATCH] fixed up image dims for 4-D nifti files

---
 .github/workflows/ci-cd.yml                 |  5 ++++-
 extras/fileformats/extras/medimage/nifti.py | 11 +++++++----
 fileformats/medimage/nifti.py               |  4 ++--
 3 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml
index ecb6e9e..8ae5bc0 100644
--- a/.github/workflows/ci-cd.yml
+++ b/.github/workflows/ci-cd.yml
@@ -57,7 +57,10 @@ jobs:
     - name: Install Package
       run: python3 -m pip install -e .[test] -e ./extras[test]
     - name: Pytest
-      run: pytest -vvs --cov fileformats --cov-config .coveragerc --cov-report xml .
+      run: |
+        REPO=$pwd
+        cd ~
+        pytest -vvs --cov fileformats --cov-config .coveragerc --cov-report xml $REPO 
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v2
       with:
diff --git a/extras/fileformats/extras/medimage/nifti.py b/extras/fileformats/extras/medimage/nifti.py
index 2fef5af..40cf74a 100644
--- a/extras/fileformats/extras/medimage/nifti.py
+++ b/extras/fileformats/extras/medimage/nifti.py
@@ -35,14 +35,17 @@ def nifti_data_array(nifti: Nifti) -> np.ndarray:  # noqa
 
 @MedicalImage.vox_sizes.register
 def nifti_vox_sizes(nifti: Nifti) -> ty.Tuple[float, float, float]:
-    # FIXME: This won't work for 4-D files
-    return tuple(float(d) for d in nifti.metadata["pixdim"][1:4])
+    ndims = len(nifti_dims(nifti))
+    return tuple(float(d) for d in nifti.metadata["pixdim"][1 : ndims + 1])
 
 
 @MedicalImage.dims.register
 def nifti_dims(nifti: Nifti) -> ty.Tuple[int, int, int]:
-    # FIXME: This won't work for 4-D files
-    return tuple(int(d) for d in nifti.metadata["dim"][1:4])
+    dim_array = [int(d) for d in nifti.metadata["dim"]]
+    for i in range(1, len(dim_array)):
+        if all(d == 1 for d in dim_array[i:]):
+            break  # Stop when the remaining dimensions are singletons
+    return tuple(dim_array[1:i])
 
 
 @FileSet.generate_sample_data.register
diff --git a/fileformats/medimage/nifti.py b/fileformats/medimage/nifti.py
index 015780b..41f6cb2 100644
--- a/fileformats/medimage/nifti.py
+++ b/fileformats/medimage/nifti.py
@@ -1,9 +1,9 @@
 import typing as ty
 from fileformats.generic import File
 from fileformats.core import hook
-from fileformats.core.mixin import (
-    WithSideCars, WithMagicNumber, WithAdjacentFiles)
+from fileformats.core.mixin import WithSideCars, WithMagicNumber, WithAdjacentFiles
 from fileformats.application import Json
+
 # from fileformats.text import Tsv
 from fileformats.application import Gzip
 from .base import MedicalImage