change to ty.Union[bool, str] for cluster

Author: yibeichan

pydra/tasks/fsl/model/cluster.py

@@ -3,35 +3,14 @@
 import typing as ty
 
 
-def Cluster_output(field, inputs):
+def Cluster_output(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}")
-
-    else:
-        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}"
-        )
+    return os.path.join(pth, f"{fname}_localmax.txt")
 
 
 input_fields = [
@@ -51,66 +30,83 @@ def Cluster_output(field, inputs):
     ),
     (
         "out_index_file",
-        ty.Any,
+        ty.Union[bool, str],
+        False,
         {
             "help_string": "output of cluster index (in size order)",
             "argstr": "--oindex={out_index_file}",
+            "output_file_template": "{in_file}_index",
         },
     ),
     (
         "out_threshold_file",
-        ty.Any,
+        ty.Union[bool, str],
+        False,
         {
             "help_string": "thresholded image",
             "argstr": "--othresh={out_threshold_file}",
+            "output_file_template": "{in_file}_threshold",
         },
     ),
     (
         "out_localmax_txt_file",
-        ty.Any,
+        ty.Union[bool, str],
+        False,
         {
             "help_string": "local maxima text file",
             "argstr": "--olmax={out_localmax_txt_file}",
+            "output_file_template": Cluster_output,
         },
     ),
     (
         "out_localmax_vol_file",
-        ty.Any,
+        ty.Union[bool, str],
+        False,
         {
             "help_string": "output of local maxima volume",
             "argstr": "--olmaxim={out_localmax_vol_file}",
+            "output_file_template":  "{in_file}_localmax",
+
         },
     ),
     (
         "out_size_file",
-        ty.Any,
+        ty.Union[bool, str],
+        False,
         {
             "help_string": "filename for output of size image",
             "argstr": "--osize={out_size_file}",
+            "output_file_template":  "{in_file}_size"
         },
     ),
     (
         "out_max_file",
-        ty.Any,
+        ty.Union[bool, str],
+        False,
         {
             "help_string": "filename for output of max image",
             "argstr": "--omax={out_max_file}",
+            "output_file_template":  "{in_file}_max"
         },
     ),
     (
         "out_mean_file",
-        ty.Any,
+        ty.Union[bool, str],
+        False,
         {
             "help_string": "filename for output of mean image",
             "argstr": "--omean={out_mean_file}",
+            "output_file_template":  "{in_file}_mean"
         },
     ),
     (
         "out_pval_file",
-        ty.Any,
+        ty.Union[bool, str],
+        False,
         {
             "help_string": "filename for image output of log pvals",
             "argstr": "--opvals={out_pval_file}",
+            "output_file_template":  "{in_file}_pval"
         },
     ),
     (
@@ -221,81 +217,12 @@ def Cluster_output(field, 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 = [
-    (
-        "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,)
@@ -308,20 +235,13 @@ class Cluster(ShellCommandTask):
     -------
     >>> task = Cluster()
     >>> task.inputs.in_file = "zstat1.nii.gz"
+    >>> task.inputs.out_localmax_txt_file = True
     >>> task.inputs.threshold = 2.3
     >>> task.inputs.use_mm = True
-    >>> 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'
+    'cluster --in=zstat1.nii.gz --olmax=zstat1_localmax.txt --thresh=2.3000000000 --mm'
     """
 
     input_spec = Cluster_input_spec
     output_spec = Cluster_output_spec
-    executable = "cluster"
+    executable = "cluster"

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

@@ -12,14 +12,7 @@
                 "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": True,
             },
             [
                 "out_index_file",

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

@@ -11,14 +11,7 @@
                 "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": True
             },
             [
                 "out_index_file",