FIX: pytest and doctest pass

Author: yibeichan

pydra/tasks/fsl/model/cluster.py

@@ -3,17 +3,35 @@
 import typing as ty
 
 
-def Cluster_output(inputs):
-    import attr
+def Cluster_output(field, inputs):
+    import os, attr
     from pydra.engine.helpers_file import split_filename
 
     in_file = inputs.in_file
+    name = field.name
+    pth, fname, ext = split_filename(in_file)
+
+    if name == "out_index_file":
+        return os.path.join(pth, f"{fname}_index{ext}")
+    elif name == "out_localmax_txt_file":
+        return os.path.join(pth, f"{fname}_localmax.txt")
+    elif name == "out_localmax_vol_file":
+        return os.path.join(pth, f"{fname}_localmax{ext}")
+    elif name == "out_max_file":
+        return os.path.join(pth, f"{fname}_max{ext}")
+    elif name == "out_mean_file":
+        return os.path.join(pth, f"{fname}_mean{ext}")
+    elif name == "out_pval_file":
+        return os.path.join(pth, f"{fname}_pval{ext}")
+    elif name == "out_size_file":
+        return os.path.join(pth, f"{fname}_size{ext}")
+    elif name == "out_threshold_file":
+        return os.path.join(pth, f"{fname}_threshold{ext}")
 
-    if in_file not in [None, attr.NOTHING]:
-        pth, fname, ext = split_filename(in_file)
-        return f"{fname}_localmax.txt"
     else:
-        raise Exception(f"this function should be run only for out_localmax_txt_file not {name}")
+        raise Exception(
+            f"this function should be run only for index_file, localmax_txt_file, localmax_vol_file, max_file, mean_file, pval_file, size_file, or threshold_file not {name}"
+        )
 
 
 input_fields = [
@@ -33,74 +51,66 @@ def Cluster_output(inputs):
     ),
     (
         "out_index_file",
-        str,
+        ty.Any,
         {
             "help_string": "output of cluster index (in size order)",
             "argstr": "--oindex={out_index_file}",
-            "output_file_template": "{in_file}_index",
         },
     ),
     (
         "out_threshold_file",
-        str,
+        ty.Any,
         {
             "help_string": "thresholded image",
             "argstr": "--othresh={out_threshold_file}",
-            "output_file_template": "{in_file}_threshold",
         },
     ),
     (
         "out_localmax_txt_file",
-        str,
+        ty.Any,
         {
             "help_string": "local maxima text file",
             "argstr": "--olmax={out_localmax_txt_file}",
-            "output_file_template": Cluster_output,
         },
     ),
     (
         "out_localmax_vol_file",
-        str,
+        ty.Any,
         {
             "help_string": "output of local maxima volume",
             "argstr": "--olmaxim={out_localmax_vol_file}",
-            "output_file_template": "{in_file}_localmax",
         },
     ),
     (
         "out_size_file",
-        str,
+        ty.Any,
         {
             "help_string": "filename for output of size image",
             "argstr": "--osize={out_size_file}",
-            "output_file_template": "{in_file}_size",
         },
     ),
     (
         "out_max_file",
-        str,
+        ty.Any,
         {
             "help_string": "filename for output of max image",
             "argstr": "--omax={out_max_file}",
-            "output_file_template": "{in_file}_max",
         },
     ),
     (
         "out_mean_file",
-        str,
+        ty.Any,
         {
             "help_string": "filename for output of mean image",
             "argstr": "--omean={out_mean_file}",
-            "output_file_template": "{in_file}_mean",
         },
     ),
     (
         "out_pval_file",
-        str,
+        ty.Any,
         {
             "help_string": "filename for image output of log pvals",
             "argstr": "--opvals={out_pval_file}",
-            "output_file_template": "{in_file}_pval",
         },
     ),
     (
@@ -211,9 +221,84 @@ def Cluster_output(inputs):
         },
     ),
 ]
-Cluster_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
+Cluster_input_spec = specs.SpecInfo(
+    name="Input", fields=input_fields, bases=(specs.ShellSpec,)
+)
 
-output_fields = []
+output_fields = [
+    (
+        "out_index_file",
+        specs.File,
+        {
+            "help_string": "output of cluster index (in size order)",
+            "requires": ["in_file", "out_index_file"],
+            "callable": Cluster_output,
+        },
+    ),
+    (
+        "out_threshold_file",
+        specs.File,
+        {
+            "help_string": "thresholded image",
+            "requires": ["in_file", "out_threshold_file"],
+            "callable": Cluster_output,
+        },
+    ),
+    (
+        "out_localmax_txt_file",
+        specs.File,
+        {
+            "help_string": "local maxima text file",
+            "requires": ["in_file", "out_localmax_txt_file"],
+            "callable": Cluster_output,
+        },
+    ),
+    (
+        "out_localmax_vol_file",
+        specs.File,
+        {
+            "help_string": "output of local maxima volume",
+            "requires": ["in_file", "out_localmax_vol_file"],
+            "callable": Cluster_output,
+        },
+    ),
+    (
+        "out_size_file",
+        specs.File,
+        {
+            "help_string": "filename for output of size image",
+            "requires": ["in_file", "out_size_file"],
+            "callable": Cluster_output,
+        },
+    ),
+    (
+        "out_max_file",
+        specs.File,
+        {
+            "help_string": "filename for output of max image",
+            "requires": ["in_file", "out_max_file"],
+            "callable": Cluster_output,
+        },
+    ),
+    (
+        "out_mean_file",
+        specs.File,
+        {
+            "help_string": "filename for output of mean image",
+            "requires": ["in_file", "out_mean_file"],
+            "callable": Cluster_output,
+        },
+    ),
+    (
+        "out_pval_file",
+        specs.File,
+        {
+            "help_string": "filename for image output of log pvals",
+            "requires": ["in_file", "out_pval_file"],
+            "callable": Cluster_output,
+        },
+    ),
+]
 Cluster_output_spec = specs.SpecInfo(
     name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
 )
@@ -227,8 +312,16 @@ class Cluster(ShellCommandTask):
     >>> task.inputs.in_file = "zstat1.nii.gz"
     >>> task.inputs.threshold = 2.3
     >>> task.inputs.use_mm = True
-    >>> task.cmdline # doctest: +SKIP
-    'cluster --in=zstat1.nii.gz --thresh=2.3000000000 --mm'
+    >>> task.inputs.out_index_file = "zstat1_index.nii.gz"
+    >>> task.inputs.out_threshold_file = "zstat1_threshold.nii.gz"
+    >>> task.inputs.out_localmax_txt_file = "zstat1_localmax.txt"
+    >>> task.inputs.out_localmax_vol_file = "zstat1_localmax.nii.gz"
+    >>> task.inputs.out_size_file = "zstat1_size.nii.gz"
+    >>> task.inputs.out_max_file = "zstat1_max.nii.gz"
+    >>> task.inputs.out_mean_file = "zstat1_mean.nii.gz"
+    >>> task.inputs.out_pval_file = "zstat1_pval.nii.gz"
+    >>> task.cmdline
+    'cluster --in=zstat1.nii.gz --thresh=2.3000000000 --oindex=zstat1_index.nii.gz --othresh=zstat1_threshold.nii.gz --olmax=zstat1_localmax.txt --olmaxim=zstat1_localmax.nii.gz --osize=zstat1_size.nii.gz --omax=zstat1_max.nii.gz --omean=zstat1_mean.nii.gz --opvals=zstat1_pval.nii.gz --mm'
     """
 
     input_spec = Cluster_input_spec

pydra/tasks/fsl/model/tests/test_run_cluster.py

@@ -3,12 +3,26 @@
 from ..cluster import Cluster
 
 
-@pytest.mark.xfail("FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError)
+@pytest.mark.xfail(
+    "FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError
+)
 @pytest.mark.parametrize(
     "inputs, outputs",
     [
         (
-            {"in_file": "zstat1.nii.gz", "threshold": 2.3, "use_mm": True},
+            {
+                "in_file": "zstat1.nii.gz",
+                "threshold": 2.3,
+                "use_mm": True,
+                "out_index_file": "zstat1_index.nii.gz",
+                "out_threshold_file": "zstat1_threshold.nii.gz",
+                "out_localmax_txt_file": "zstat1_localmax.txt",
+                "out_localmax_vol_file": "zstat1_localmax.nii.gz",
+                "out_size_file": "zstat1_size.nii.gz",
+                "out_max_file": "zstat1_max.nii.gz",
+                "out_mean_file": "zstat1_mean.nii.gz",
+                "out_pval_file": "zstat1_pval.nii.gz",
+            },
             [
                 "out_index_file",
                 "out_localmax_txt_file",
@@ -49,7 +63,9 @@ def test_Cluster(test_data, inputs, outputs):
             except:
                 pass
         task = Cluster(**inputs)
-    assert set(task.generated_output_names) == set(["return_code", "stdout", "stderr"] + outputs)
+    assert set(task.generated_output_names) == set(
+        ["return_code", "stdout", "stderr"] + outputs
+    )
     res = task()
     print("RESULT: ", res)
     for out_nm in outputs:

pydra/tasks/fsl/model/tests/test_spec_cluster.py

@@ -7,7 +7,19 @@
     "inputs, outputs",
     [
         (
-            {"in_file": "zstat1.nii.gz", "threshold": 2.3, "use_mm": True},
+            {
+                "in_file": "zstat1.nii.gz",
+                "threshold": 2.3,
+                "use_mm": True,
+                "out_index_file": "zstat1_index.nii.gz",
+                "out_threshold_file": "zstat1_threshold.nii.gz",
+                "out_localmax_txt_file": "zstat1_localmax.txt",
+                "out_localmax_vol_file": "zstat1_localmax.nii.gz",
+                "out_size_file": "zstat1_size.nii.gz",
+                "out_max_file": "zstat1_max.nii.gz",
+                "out_mean_file": "zstat1_mean.nii.gz",
+                "out_pval_file": "zstat1_pval.nii.gz",
+            },
             [
                 "out_index_file",
                 "out_localmax_txt_file",
@@ -48,4 +60,6 @@ def test_Cluster(test_data, inputs, outputs):
             except:
                 pass
         task = Cluster(**inputs)
-    assert set(task.generated_output_names) == set(["return_code", "stdout", "stderr"] + outputs)
+    assert set(task.generated_output_names) == set(
+        ["return_code", "stdout", "stderr"] + outputs
+    )

specs/callables.py

@@ -1,14 +1,30 @@
-def Cluster_output(inputs):
-    import attr
+def Cluster_output(field, inputs):
+    import os, attr
     from pydra.engine.helpers_file import split_filename
 
     in_file = inputs.in_file
+    name = field.name
+    pth, fname, ext = split_filename(in_file)
+    
+    if name == "index_file":
+        return os.path.join(pth, f"{fname}_index{ext}")
+    elif name == "localmax_txt_file":
+        return os.path.join(pth, f"{fname}_localmax.txt")
+    elif name == "localmax_vol_file":
+        return os.path.join(pth, f"{fname}_localmax{ext}")
+    elif name == "max_file":
+        return os.path.join(pth, f"{fname}_max{ext}")
+    elif name == "mean_file":
+        return os.path.join(pth, f"{fname}_mean{ext}")
+    elif name == "pval_file":
+        return os.path.join(pth, f"{fname}_pval{ext}")
+    elif name == "size_file":
+        return os.path.join(pth, f"{fname}_size{ext}")
+    elif name == "threshold_file":
+        return os.path.join(pth, f"{fname}_threshold{ext}")
 
-    if in_file not in [None, attr.NOTHING]:
-        pth, fname, ext = split_filename(in_file)
-        return f"{fname}_localmax.txt"
     else:
-        raise Exception(f"this function should be run only for out_localmax_txt_file not {name}")
+        raise Exception(f"this function should be run only for index_file, localmax_txt_file, localmax_vol_file, max_file, mean_file, pval_file, size_file, or threshold_file not {name}")
 
 
 def Complex_output(inputs):