Merge pull request #46 from yibeichan/redo-split

Redo split

Author: djarecka

.gitignore

@@ -1,11 +1,4 @@
 .DS_Store
-*/.DS_Store
-*/*/.DS_Store
-*/*/*/.DS_Store
-*/.DS_Store
-*/*/*/*/.DS_Store
-*/*/*/*/*/.DS_Store
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

pydra/tasks/fsl/_version.py

@@ -0,0 +1,4 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+__version__ = version = '0.1.dev123+gd6b46a1.d20230502'
+__version_tuple__ = version_tuple = (0, 1, 'dev123', 'gd6b46a1.d20230502')

pydra/tasks/fsl/utils/split.py

@@ -2,6 +2,14 @@
 from pydra import ShellCommandTask
 import typing as ty
 
+
+def Split_output(inputs):
+    import os, glob
+
+    output_dir = os.getcwd()
+    return sorted(glob.glob(os.path.join(output_dir, f"{inputs.output_basename}*.*")))
+
+
 input_fields = [
     (
         "in_file",
@@ -14,9 +22,9 @@
         },
     ),
     (
-        "out_base_name",
+        "output_basename",
         str,
-        {"help_string": "outputs prefix", "argstr": "{out_base_name}", "position": 1},
+        {"help_string": "outputs prefix", "argstr": "{output_basename}", "position": 1},
     ),
     (
         "dimension",
@@ -31,13 +39,34 @@
 ]
 Split_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
 
-output_fields = []
+output_fields = [
+    (
+        "out_files",
+        specs.MultiOutputFile,
+        {
+            "help_string": "output files",
+            "requires": ["in_file", "output_basename", "dimension"],
+            "callable": Split_output,
+        },
+    )
+]
 Split_output_spec = specs.SpecInfo(
     name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
 )
 
 
 class Split(ShellCommandTask):
+    """
+    Example
+    -------
+    >>> task = Split()
+    >>> task.inputs.in_file = "test.nii.gz"
+    >>> task.inputs.output_basename = "test_split"
+    >>> task.inputs.dimension = "t"
+    >>> task.cmdline
+    'fslsplit test.nii.gz test_split -t'
+    """
+
     input_spec = Split_input_spec
     output_spec = Split_output_spec
     executable = "fslsplit"

pydra/tasks/fsl/utils/tests/test_run_split.py

@@ -4,7 +4,19 @@
 
 
 @pytest.mark.xfail("FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError)
-@pytest.mark.parametrize("inputs, outputs", [])
+@pytest.mark.parametrize(
+    "inputs, outputs",
+    [
+        (
+            {
+                "in_file": "test.nii.gz",
+                "output_basename": "test_split",
+                "dimension": "t",
+            },
+            ["out_files"],
+        )
+    ],
+)
 def test_Split(test_data, inputs, outputs):
     if inputs is None:
         in_file = Path(test_data) / "test.nii.gz"
@@ -39,34 +51,3 @@ def test_Split(test_data, inputs, outputs):
             assert [os.path.exists(x) for x in getattr(res.output, out_nm)]
         else:
             assert os.path.exists(getattr(res.output, out_nm))
-
-
-@pytest.mark.parametrize("inputs, error", [(None, "AttributeError")])
-def test_Split_exception(test_data, inputs, error):
-    if inputs is None:
-        in_file = Path(test_data) / "test.nii.gz"
-        task = Split(in_file=in_file)
-    else:
-        for key, val in inputs.items():
-            try:
-                pattern = r"\.[a-zA-Z]*"
-                if isinstance(val, str):
-                    if re.findall(pattern, val) != []:
-                        inputs[key] = Path(test_data) / val
-                    elif "_dir" in key:
-                        dirpath = Path(test_data) / val
-                        if dirpath.exists() and dirpath.is_dir():
-                            shutil.rmtree(dirpath)
-                        inputs[key] = Path(test_data) / val
-                    else:
-                        inputs[key] = eval(val)
-                elif isinstance(val, list):
-                    if all(re.findall(pattern, _) != [] for _ in val):
-                        inputs[key] = [Path(test_data) / _ for _ in val]
-                else:
-                    inputs[key] = eval(val)
-            except:
-                pass
-        task = Split(**inputs)
-    with pytest.raises(eval(error)):
-        task.generated_output_names

pydra/tasks/fsl/utils/tests/test_spec_split.py

@@ -3,7 +3,19 @@
 from ..split import Split
 
 
-@pytest.mark.parametrize("inputs, outputs", [])
+@pytest.mark.parametrize(
+    "inputs, outputs",
+    [
+        (
+            {
+                "in_file": "test.nii.gz",
+                "output_basename": "test_split",
+                "dimension": "t",
+            },
+            ["out_files"],
+        )
+    ],
+)
 def test_Split(test_data, inputs, outputs):
     if inputs is None:
         in_file = Path(test_data) / "test.nii.gz"
@@ -31,34 +43,3 @@ def test_Split(test_data, inputs, outputs):
                 pass
         task = Split(**inputs)
     assert set(task.generated_output_names) == set(["return_code", "stdout", "stderr"] + outputs)
-
-
-@pytest.mark.parametrize("inputs, error", [(None, "AttributeError")])
-def test_Split_exception(test_data, inputs, error):
-    if inputs is None:
-        in_file = Path(test_data) / "test.nii.gz"
-        task = Split(in_file=in_file)
-    else:
-        for key, val in inputs.items():
-            try:
-                pattern = r"\.[a-zA-Z]*"
-                if isinstance(val, str):
-                    if re.findall(pattern, val) != []:
-                        inputs[key] = Path(test_data) / val
-                    elif "_dir" in key:
-                        dirpath = Path(test_data) / val
-                        if dirpath.exists() and dirpath.is_dir():
-                            shutil.rmtree(dirpath)
-                        inputs[key] = Path(test_data) / val
-                    else:
-                        inputs[key] = eval(val)
-                elif isinstance(val, list):
-                    if all(re.findall(pattern, _) != [] for _ in val):
-                        inputs[key] = [Path(test_data) / _ for _ in val]
-                else:
-                    inputs[key] = eval(val)
-            except:
-                pass
-        task = Split(**inputs)
-    with pytest.raises(eval(error)):
-        task.generated_output_names

specs/callables.py

@@ -392,13 +392,20 @@ def MELODIC_output(field, inputs):
     return outputs
 
 
-def SLICE_output(inputs):
-    import glob
+# def SLICE_output(inputs):
+#     import glob
 
-    suffix = "slice_*"
-    if inputs.out_base_name:
-        fname_template = f"{inputs.out_base_name}_{suffix}"
-    else:
-        fname_template = f"{inputs.in_file}_{suffix}"
+#     suffix = "slice_*"
+#     if inputs.out_base_name:
+#         fname_template = f"{inputs.out_base_name}_{suffix}"
+#     else:
+#         fname_template = f"{inputs.in_file}_{suffix}"
+
+#     return sorted(glob(fname_template))
+
+
+def Split_output(inputs):
+    import os, glob
 
-    return sorted(glob(fname_template))
+    output_dir = os.getcwd()
+    return sorted(glob.glob(os.path.join(output_dir, f"{inputs.output_basename}*.*")))

specs/fsl_utils_param.yml

@@ -332,13 +332,21 @@ Smooth:
 
 Split:
   output_requirements:
-    out_file: [in_file, dimension]
-  output_templates:
+    out_files: [in_file, output_basename, dimension]
+  output_callables:
+    out_files: Split_output
   doctest:
+    in_file: test.nii.gz
+    output_basename: test_split
+    dimension: t
+    cmdline: fslsplit test.nii.gz test_split -t
+
   tests_inputs:
-    -
+    - in_file: test.nii.gz
+      output_basename: test_split
+      dimension: t
   tests_outputs:
-    - AttributeError
+    - out_files
 
 SwapDimensions:
   output_requirements: