Added ApplyXFM interface

README.md

@@ -83,7 +83,7 @@ Below is a list of all planned interfaces, with completed interfaces checked. Th
 ### Preprocess
 
 - [x] ApplyWarp (`applywarp`)
-- [ ] ApplyXFM (`flirt`)
+- [X] ApplyXFM (`flirt`)
 - [x] BET (`bet`)
 - [x] FAST (`fast`)
 - [x] FIRST (`first`)

pydra/tasks/fsl/preprocess/applyxfm.py

@@ -0,0 +1,75 @@
+from pydra.engine import specs
+from .flirt import FLIRT
+
+input_fields = [
+    (
+        "in_file",
+        specs.File,
+        {
+            "help_string": "input file",
+            "argstr": "-in {in_file}",
+            "mandatory": True,
+            "position": 0,
+        },
+    ),
+    (
+        "reference",
+        specs.File,
+        {
+            "help_string": "reference file",
+            "argstr": "-ref {reference}",
+            "mandatory": True,
+            "position": 1,
+        },
+    ),
+    (
+        "apply_xfm",
+        bool,
+        True,
+        {
+            "help_string": "apply transformation supplied by in_matrix_file or uses_qform to use the affine matrix stored in the reference header",
+            "argstr": "-applyxfm",
+        },
+    ),
+    (
+        "in_matrix_file",
+        str,
+        {
+            "help_string": "input 4x4 affine matrix",
+            "argstr": "-init {in_matrix_file}",
+            "mandatory": True,
+        },
+    ),
+    (
+        "out_file",
+        str,
+        {
+            "help_string": "registered output file",
+            "argstr": "-out {out_file}",
+            "position": 2,
+            "output_file_template": "{in_file}_flirt",
+        },
+    ),
+]
+
+ApplyXFM_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
+
+
+class ApplyXFM(FLIRT):
+    """
+    Example
+    -------
+    >>> task = ApplyXFM()
+    >>> task.inputs.in_file = 'test.nii.gz'
+    >>> task.inputs.in_matrix_file = 'transform.mat'
+    >>> task.inputs.reference = 'dest.nii.gz'
+    >>> task.cmdline # doctest: +ELLIPSIS
+    'flirt -in test.nii.gz -ref dest.nii.gz -out .../test_flirt.nii.gz -applyxfm -init transform.mat'
+
+    # using a custom outfile
+    >>> task.inputs.out_file = 'custom_outfile.nii.gz'
+    >>> task.cmdline
+    'flirt -in test.nii.gz -ref dest.nii.gz -out custom_outfile.nii.gz -applyxfm -init transform.mat'
+    """
+
+    input_spec = ApplyXFM_input_spec

pydra/tasks/fsl/preprocess/tests/test_run_applyxfm.py

@@ -0,0 +1,38 @@
+import os, pytest
+from pathlib import Path
+from ..applyxfm import ApplyXFM
+
+
+@pytest.mark.xfail("FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError)
+@pytest.mark.parametrize("inputs, outputs", [(None, ["out_file"])])
+def test_ApplyXFM(test_data, inputs, outputs):
+    in_file = Path(test_data) / "test.nii.gz"
+    reference = Path(test_data) / "test.nii.gz"
+    in_matrix_file = Path(test_data) / "transform.mat"
+    if inputs is None:
+        inputs = {}
+    for key, val in inputs.items():
+        try:
+            inputs[key] = eval(val)
+        except:
+            pass
+    task = ApplyXFM(in_file=in_file, reference=reference, in_matrix_file=in_matrix_file, **inputs)
+    assert set(task.generated_output_names) == set(["return_code", "stdout", "stderr"] + outputs)
+    res = task()
+    print("RESULT: ", res)
+    for out_nm in outputs:
+        assert getattr(res.output, out_nm).exists()
+
+
+@pytest.mark.parametrize("inputs, error", [(None, "AttributeError")])
+def test_ApplyXFM_exception(test_data, inputs, error):
+    if inputs is None:
+        inputs = {}
+    for key, val in inputs.items():
+        try:
+            inputs[key] = eval(val)
+        except:
+            pass
+    task = ApplyXFM(**inputs)
+    with pytest.raises(eval(error)):
+        task.generated_output_names

pydra/tasks/fsl/tests/data/transform.mat

@@ -0,0 +1,4 @@
+1  0.0001371992403  0  -0.01404274377
+0  1  0.0003819660051  -0.04808253666
+0  0  1  0
+0  0  0  1