From 6cca4df0bc31daa14f25d140d53fbbb28cec9786 Mon Sep 17 00:00:00 2001
From: Mathias Goncalves <goncalves.mathias@gmail.com>
Date: Thu, 18 Jul 2024 13:21:12 -0400
Subject: [PATCH 1/3] ADD: Make template dimensions support T2w as well

---
 niworkflows/interfaces/images.py | 28 ++++++++++++++++++++--------
 1 file changed, 20 insertions(+), 8 deletions(-)

diff --git a/niworkflows/interfaces/images.py b/niworkflows/interfaces/images.py
index c1b2eaee76c..66b45f78248 100644
--- a/niworkflows/interfaces/images.py
+++ b/niworkflows/interfaces/images.py
@@ -365,7 +365,7 @@ def _run_interface(self, runtime):
 
 CONFORMATION_TEMPLATE = """\t\t<h3 class="elem-title">Anatomical Conformation</h3>
 \t\t<ul class="elem-desc">
-\t\t\t<li>Input T1w images: {n_t1w}</li>
+\t\t\t<li>Input {anat} images: {n_anat}</li>
 \t\t\t<li>Output orientation: RAS</li>
 \t\t\t<li>Output dimensions: {dims}</li>
 \t\t\t<li>Output voxel size: {zooms}</li>
@@ -378,8 +378,14 @@ def _run_interface(self, runtime):
 
 
 class _TemplateDimensionsInputSpec(BaseInterfaceInputSpec):
+    anat_type = traits.Enum("T1w", "T2w", usedefault=True, desc="Anatomical image type")
+    anat_list = InputMultiObject(
+        File(exists=True), xor="t1w_list", desc="input anatomical images"
+    )
     t1w_list = InputMultiObject(
-        File(exists=True), mandatory=True, desc="input T1w images"
+        xor="anat_list",
+        deprecated="1.14.0",
+        new_name="anat_list",
     )
     max_scale = traits.Float(
         3.0, usedefault=True, desc="Maximum scaling factor in images to accept"
@@ -387,7 +393,8 @@ class _TemplateDimensionsInputSpec(BaseInterfaceInputSpec):
 
 
 class _TemplateDimensionsOutputSpec(TraitedSpec):
-    t1w_valid_list = OutputMultiObject(exists=True, desc="valid T1w images")
+    t1w_valid_list = OutputMultiObject(exists=True, deprecated="1.14.0", desc="valid T1w images")
+    anat_valid_list = OutputMultiObject(exists=True, desc="valid anatomical images")
     target_zooms = traits.Tuple(
         traits.Float, traits.Float, traits.Float, desc="Target zoom information"
     )
@@ -399,8 +406,8 @@ class _TemplateDimensionsOutputSpec(TraitedSpec):
 
 class TemplateDimensions(SimpleInterface):
     """
-    Finds template target dimensions for a series of T1w images, filtering low-resolution images,
-    if necessary.
+    Finds template target dimensions for a series of anatomical images, filtering low-resolution
+    images, if necessary.
 
     Along each axis, the minimum voxel size (zoom) and the maximum number of voxels (shape) are
     found across images.
@@ -426,7 +433,8 @@ def _generate_segment(self, discards, dims, zooms):
         )
         zoom_fmt = "{:.02g}mm x {:.02g}mm x {:.02g}mm".format(*zooms)
         return CONFORMATION_TEMPLATE.format(
-            n_t1w=len(self.inputs.t1w_list),
+            anat=self.inputs.anat_type,
+            n_anat=len(self.inputs.anat_list),
             dims="x".join(map(str, dims)),
             zooms=zoom_fmt,
             n_discards=len(discards),
@@ -435,7 +443,10 @@ def _generate_segment(self, discards, dims, zooms):
 
     def _run_interface(self, runtime):
         # Load images, orient as RAS, collect shape and zoom data
-        in_names = np.array(self.inputs.t1w_list)
+        if not self.inputs.anat_list:  # Deprecate: 1.14.0
+            self.inputs.anat_list = self.inputs.t1w_list
+
+        in_names = np.array(self.inputs.anat_list)
         orig_imgs = np.vectorize(nb.load)(in_names)
         reoriented = np.vectorize(nb.as_closest_canonical)(orig_imgs)
         all_zooms = np.array([img.header.get_zooms()[:3] for img in reoriented])
@@ -452,7 +463,8 @@ def _run_interface(self, runtime):
 
         # Ignore dropped images
         valid_fnames = np.atleast_1d(in_names[valid]).tolist()
-        self._results["t1w_valid_list"] = valid_fnames
+        self._results["anat_valid_list"] = valid_fnames
+        self._results["t1w_valid_list"] = valid_fnames  # Deprecate: 1.14.0
 
         # Set target shape information
         target_zooms = all_zooms[valid].min(axis=0)

From 30dfc5ba0eaa92adbb7ba40482f6c80237e44b7c Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Fri, 19 Jul 2024 13:38:22 -0400
Subject: [PATCH 2/3] test: Test TemplateDimensions interface

---
 niworkflows/interfaces/tests/test_images.py | 36 +++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/niworkflows/interfaces/tests/test_images.py b/niworkflows/interfaces/tests/test_images.py
index a013a7dcad0..d21ad53eb80 100644
--- a/niworkflows/interfaces/tests/test_images.py
+++ b/niworkflows/interfaces/tests/test_images.py
@@ -22,6 +22,7 @@
 #
 """Test images module."""
 import time
+from pathlib import Path
 import numpy as np
 import nibabel as nb
 from nipype.pipeline import engine as pe
@@ -179,3 +180,38 @@ def test_RobustAverage(tmpdir, shape):
 
     assert out_file.shape == (10, 10, 10)
     assert np.allclose(out_file.get_fdata(), 1.0)
+
+
+def test_TemplateDimensions(tmp_path):
+    """Exercise the various types of inputs."""
+    shapes = [
+        (10, 10, 10),
+        (11, 11, 11),
+    ]
+    zooms = [
+        (1, 1, 1),
+        (0.9, 0.9, 0.9),
+    ]
+
+    for i, (shape, zoom) in enumerate(zip(shapes, zooms)):
+        img = nb.Nifti1Image(np.ones(shape, dtype="float32"), np.eye(4))
+        img.header.set_zooms(zoom)
+        img.to_filename(tmp_path / f"test{i}.nii")
+
+    anat_list = [str(tmp_path / f"test{i}.nii") for i in range(2)]
+    td = im.TemplateDimensions(anat_list=anat_list)
+    res = td.run()
+
+    report = Path(res.outputs.out_report).read_text()
+    assert "Input T1w images: 2" in report
+    assert "Output dimensions: 11x11x11" in report
+    assert "Output voxel size: 0.9mm x 0.9mm x 0.9mm" in report
+    assert "Discarded images: 0" in report
+
+    assert res.outputs.t1w_valid_list == anat_list
+    assert res.outputs.anat_valid_list == anat_list
+    assert np.allclose(res.outputs.target_zooms, (0.9, 0.9, 0.9))
+    assert res.outputs.target_shape == (11, 11, 11)
+
+    with pytest.warns(UserWarning, match="t1w_list .* is deprecated"):
+        im.TemplateDimensions(t1w_list=anat_list)

From 785c40f38ae406032729a5433ce37aa3aff3b992 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Fri, 19 Jul 2024 13:39:06 -0400
Subject: [PATCH 3/3] fix: Update xor type, remove deprecation from output

---
 niworkflows/interfaces/images.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/niworkflows/interfaces/images.py b/niworkflows/interfaces/images.py
index 66b45f78248..2669904196a 100644
--- a/niworkflows/interfaces/images.py
+++ b/niworkflows/interfaces/images.py
@@ -380,10 +380,11 @@ def _run_interface(self, runtime):
 class _TemplateDimensionsInputSpec(BaseInterfaceInputSpec):
     anat_type = traits.Enum("T1w", "T2w", usedefault=True, desc="Anatomical image type")
     anat_list = InputMultiObject(
-        File(exists=True), xor="t1w_list", desc="input anatomical images"
+        File(exists=True), xor=["t1w_list"], desc="input anatomical images"
     )
     t1w_list = InputMultiObject(
-        xor="anat_list",
+        File(exists=True),
+        xor=["anat_list"],
         deprecated="1.14.0",
         new_name="anat_list",
     )
@@ -393,7 +394,7 @@ class _TemplateDimensionsInputSpec(BaseInterfaceInputSpec):
 
 
 class _TemplateDimensionsOutputSpec(TraitedSpec):
-    t1w_valid_list = OutputMultiObject(exists=True, deprecated="1.14.0", desc="valid T1w images")
+    t1w_valid_list = OutputMultiObject(exists=True, desc="valid T1w images")
     anat_valid_list = OutputMultiObject(exists=True, desc="valid anatomical images")
     target_zooms = traits.Tuple(
         traits.Float, traits.Float, traits.Float, desc="Target zoom information"