niwrap-freesurfer 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/tridec.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TRIDEC_METADATA = Metadata(
-    id="b02273ae065ddda351360aefaa95dc302ac759eb.boutiques",
+    id="17d2ba140c1142170644182d8abc8ce2ba86d70e.boutiques",
     name="tridec",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ TRIDEC_METADATA = Metadata(
 
 
 TridecParameters = typing.TypedDict('TridecParameters', {
-    "__STYXTYPE__": typing.Literal["tridec"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/tridec"]],
+    "subject_name": str,
+    "fine_file": InputPathType,
+    "ico_file": InputPathType,
+    "out_file": str,
+})
+TridecParametersTagged = typing.TypedDict('TridecParametersTagged', {
+    "@type": typing.Literal["freesurfer/tridec"],
     "subject_name": str,
     "fine_file": InputPathType,
     "ico_file": InputPathType,
     "out_file": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "tridec": tridec_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "tridec": tridec_outputs,
-    }.get(t)
 
 
 class TridecOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `tridec(...)`.
+    Output object returned when calling `TridecParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def tridec_params(
     fine_file: InputPathType,
     ico_file: InputPathType,
     out_file: str,
-) -> TridecParameters:
+) -> TridecParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def tridec_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tridec",
+        "@type": "freesurfer/tridec",
         "subject_name": subject_name,
         "fine_file": fine_file,
         "ico_file": ico_file,
@@ -106,10 +81,10 @@ def tridec_cargs(
     """
     cargs = []
     cargs.append("tridec")
-    cargs.append(params.get("subject_name"))
-    cargs.append(execution.input_file(params.get("fine_file")))
-    cargs.append(execution.input_file(params.get("ico_file")))
-    cargs.append(params.get("out_file"))
+    cargs.append(params.get("subject_name", None))
+    cargs.append(execution.input_file(params.get("fine_file", None)))
+    cargs.append(execution.input_file(params.get("ico_file", None)))
+    cargs.append(params.get("out_file", None))
     return cargs
 
 
@@ -128,16 +103,18 @@ def tridec_outputs(
     """
     ret = TridecOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("out_file")),
+        output_file=execution.output_file(params.get("out_file", None)),
     )
     return ret
 
 
 def tridec_execute(
     params: TridecParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TridecOutputs:
     """
+    tridec
+    
     Tridec tool for processing brain images.
     
     Author: FreeSurfer Developers
@@ -146,10 +123,12 @@ def tridec_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TridecOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TRIDEC_METADATA)
     params = execution.params(params)
     cargs = tridec_cargs(params, execution)
     ret = tridec_outputs(params, execution)
@@ -165,6 +144,8 @@ def tridec(
     runner: Runner | None = None,
 ) -> TridecOutputs:
     """
+    tridec
+    
     Tridec tool for processing brain images.
     
     Author: FreeSurfer Developers
@@ -180,21 +161,19 @@ def tridec(
     Returns:
         NamedTuple of outputs (described in `TridecOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TRIDEC_METADATA)
     params = tridec_params(
         subject_name=subject_name,
         fine_file=fine_file,
         ico_file=ico_file,
         out_file=out_file,
     )
-    return tridec_execute(params, execution)
+    return tridec_execute(params, runner)
 
 
 __all__ = [
     "TRIDEC_METADATA",
     "TridecOutputs",
-    "TridecParameters",
     "tridec",
+    "tridec_execute",
     "tridec_params",
 ]

niwrap_freesurfer/freesurfer/trk_tools.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TRK_TOOLS_METADATA = Metadata(
-    id="e8662b8aa4556e166a6c80f8f4ea3e413af139aa.boutiques",
+    id="113c2ab5e4181b985d590456b9c41a26b1525c4f.boutiques",
     name="trk_tools",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ TRK_TOOLS_METADATA = Metadata(
 
 
 TrkToolsParameters = typing.TypedDict('TrkToolsParameters', {
-    "__STYXTYPE__": typing.Literal["trk_tools"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/trk_tools"]],
+    "reference_image": InputPathType,
+    "input_trk": InputPathType,
+    "output_trk": typing.NotRequired[str | None],
+    "output_image": typing.NotRequired[str | None],
+    "update_header": bool,
+    "output_vtk": typing.NotRequired[str | None],
+})
+TrkToolsParametersTagged = typing.TypedDict('TrkToolsParametersTagged', {
+    "@type": typing.Literal["freesurfer/trk_tools"],
     "reference_image": InputPathType,
     "input_trk": InputPathType,
     "output_trk": typing.NotRequired[str | None],
@@ -22,43 +31,11 @@ TrkToolsParameters = typing.TypedDict('TrkToolsParameters', {
     "update_header": bool,
     "output_vtk": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "trk_tools": trk_tools_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "trk_tools": trk_tools_outputs,
-    }.get(t)
 
 
 class TrkToolsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `trk_tools(...)`.
+    Output object returned when calling `TrkToolsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +54,7 @@ def trk_tools_params(
     output_image: str | None = None,
     update_header: bool = False,
     output_vtk: str | None = None,
-) -> TrkToolsParameters:
+) -> TrkToolsParametersTagged:
     """
     Build parameters.
     
@@ -92,7 +69,7 @@ def trk_tools_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "trk_tools",
+        "@type": "freesurfer/trk_tools",
         "reference_image": reference_image,
         "input_trk": input_trk,
         "update_header": update_header,
@@ -123,28 +100,28 @@ def trk_tools_cargs(
     cargs.append("trk_tools")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("reference_image"))
+        execution.input_file(params.get("reference_image", None))
     ])
     cargs.extend([
         "-f",
-        execution.input_file(params.get("input_trk"))
+        execution.input_file(params.get("input_trk", None))
     ])
-    if params.get("output_trk") is not None:
+    if params.get("output_trk", None) is not None:
         cargs.extend([
             "-o",
-            params.get("output_trk")
+            params.get("output_trk", None)
         ])
-    if params.get("output_image") is not None:
+    if params.get("output_image", None) is not None:
         cargs.extend([
             "-e",
-            params.get("output_image")
+            params.get("output_image", None)
         ])
-    if params.get("update_header"):
+    if params.get("update_header", False):
         cargs.append("-u")
-    if params.get("output_vtk") is not None:
+    if params.get("output_vtk", None) is not None:
         cargs.extend([
             "-v",
-            params.get("output_vtk")
+            params.get("output_vtk", None)
         ])
     return cargs
 
@@ -164,18 +141,20 @@ def trk_tools_outputs(
     """
     ret = TrkToolsOutputs(
         root=execution.output_file("."),
-        trk_output_file=execution.output_file(params.get("output_trk")) if (params.get("output_trk") is not None) else None,
-        image_output_file=execution.output_file(params.get("output_image")) if (params.get("output_image") is not None) else None,
-        vtk_output_file=execution.output_file(params.get("output_vtk")) if (params.get("output_vtk") is not None) else None,
+        trk_output_file=execution.output_file(params.get("output_trk", None)) if (params.get("output_trk") is not None) else None,
+        image_output_file=execution.output_file(params.get("output_image", None)) if (params.get("output_image") is not None) else None,
+        vtk_output_file=execution.output_file(params.get("output_vtk", None)) if (params.get("output_vtk") is not None) else None,
     )
     return ret
 
 
 def trk_tools_execute(
     params: TrkToolsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TrkToolsOutputs:
     """
+    trk_tools
+    
     Tool for processing TRK files.
     
     Author: FreeSurfer Developers
@@ -184,10 +163,12 @@ def trk_tools_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TrkToolsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TRK_TOOLS_METADATA)
     params = execution.params(params)
     cargs = trk_tools_cargs(params, execution)
     ret = trk_tools_outputs(params, execution)
@@ -205,6 +186,8 @@ def trk_tools(
     runner: Runner | None = None,
 ) -> TrkToolsOutputs:
     """
+    trk_tools
+    
     Tool for processing TRK files.
     
     Author: FreeSurfer Developers
@@ -222,8 +205,6 @@ def trk_tools(
     Returns:
         NamedTuple of outputs (described in `TrkToolsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TRK_TOOLS_METADATA)
     params = trk_tools_params(
         reference_image=reference_image,
         input_trk=input_trk,
@@ -232,13 +213,13 @@ def trk_tools(
         update_header=update_header,
         output_vtk=output_vtk,
     )
-    return trk_tools_execute(params, execution)
+    return trk_tools_execute(params, runner)
 
 
 __all__ = [
     "TRK_TOOLS_METADATA",
     "TrkToolsOutputs",
-    "TrkToolsParameters",
     "trk_tools",
+    "trk_tools_execute",
     "trk_tools_params",
 ]

niwrap_freesurfer/freesurfer/unpack_ima1_tcl.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 UNPACK_IMA1_TCL_METADATA = Metadata(
-    id="2f44fce6973250c18da864f8fa4ee59aea5aae9d.boutiques",
+    id="879dfc4e2c1cd294a8c370964cc378f77296eb2a.boutiques",
     name="unpack_ima1.tcl",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,58 +14,31 @@ UNPACK_IMA1_TCL_METADATA = Metadata(
 
 
 UnpackIma1TclParameters = typing.TypedDict('UnpackIma1TclParameters', {
-    "__STYXTYPE__": typing.Literal["unpack_ima1.tcl"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/unpack_ima1.tcl"]],
+    "input_directory": str,
+    "output_directory": str,
+})
+UnpackIma1TclParametersTagged = typing.TypedDict('UnpackIma1TclParametersTagged', {
+    "@type": typing.Literal["freesurfer/unpack_ima1.tcl"],
     "input_directory": str,
     "output_directory": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "unpack_ima1.tcl": unpack_ima1_tcl_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "unpack_ima1.tcl": unpack_ima1_tcl_outputs,
-    }.get(t)
 
 
 class UnpackIma1TclOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `unpack_ima1_tcl(...)`.
+    Output object returned when calling `UnpackIma1TclParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    unpacked_files: OutputPathType
-    """Unpacked files stored in the output directory"""
+    output_directory: OutputPathType
+    """Output directory containing unpacked files"""
 
 
 def unpack_ima1_tcl_params(
     input_directory: str,
     output_directory: str,
-) -> UnpackIma1TclParameters:
+) -> UnpackIma1TclParametersTagged:
     """
     Build parameters.
     
@@ -78,7 +51,7 @@ def unpack_ima1_tcl_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "unpack_ima1.tcl",
+        "@type": "freesurfer/unpack_ima1.tcl",
         "input_directory": input_directory,
         "output_directory": output_directory,
     }
@@ -100,8 +73,8 @@ def unpack_ima1_tcl_cargs(
     """
     cargs = []
     cargs.append("unpack_ima1.tcl")
-    cargs.append(params.get("input_directory"))
-    cargs.append(params.get("output_directory"))
+    cargs.append(params.get("input_directory", None))
+    cargs.append(params.get("output_directory", None))
     return cargs
 
 
@@ -120,16 +93,18 @@ def unpack_ima1_tcl_outputs(
     """
     ret = UnpackIma1TclOutputs(
         root=execution.output_file("."),
-        unpacked_files=execution.output_file(params.get("output_directory") + "/*"),
+        output_directory=execution.output_file(params.get("output_directory", None)),
     )
     return ret
 
 
 def unpack_ima1_tcl_execute(
     params: UnpackIma1TclParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> UnpackIma1TclOutputs:
     """
+    unpack_ima1.tcl
+    
     A tool for unpacking images using FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -138,10 +113,12 @@ def unpack_ima1_tcl_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `UnpackIma1TclOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UNPACK_IMA1_TCL_METADATA)
     params = execution.params(params)
     cargs = unpack_ima1_tcl_cargs(params, execution)
     ret = unpack_ima1_tcl_outputs(params, execution)
@@ -155,6 +132,8 @@ def unpack_ima1_tcl(
     runner: Runner | None = None,
 ) -> UnpackIma1TclOutputs:
     """
+    unpack_ima1.tcl
+    
     A tool for unpacking images using FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -170,19 +149,17 @@ def unpack_ima1_tcl(
     Returns:
         NamedTuple of outputs (described in `UnpackIma1TclOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(UNPACK_IMA1_TCL_METADATA)
     params = unpack_ima1_tcl_params(
         input_directory=input_directory,
         output_directory=output_directory,
     )
-    return unpack_ima1_tcl_execute(params, execution)
+    return unpack_ima1_tcl_execute(params, runner)
 
 
 __all__ = [
     "UNPACK_IMA1_TCL_METADATA",
     "UnpackIma1TclOutputs",
-    "UnpackIma1TclParameters",
     "unpack_ima1_tcl",
+    "unpack_ima1_tcl_execute",
     "unpack_ima1_tcl_params",
 ]

niwrap_freesurfer/freesurfer/unpack_ima_tcl.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 UNPACK_IMA_TCL_METADATA = Metadata(
-    id="f7bb633c8e2fc57cba56d642be005b58715d8346.boutiques",
+    id="5abb0fa0a5b93ef44cb7fe8eb27edb41e6c27c9c.boutiques",
     name="unpack_ima.tcl",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ UNPACK_IMA_TCL_METADATA = Metadata(
 
 
 UnpackImaTclParameters = typing.TypedDict('UnpackImaTclParameters', {
-    "__STYXTYPE__": typing.Literal["unpack_ima.tcl"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/unpack_ima.tcl"]],
+    "target_dir": str,
+})
+UnpackImaTclParametersTagged = typing.TypedDict('UnpackImaTclParametersTagged', {
+    "@type": typing.Literal["freesurfer/unpack_ima.tcl"],
     "target_dir": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "unpack_ima.tcl": unpack_ima_tcl_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-    }.get(t)
 
 
 class UnpackImaTclOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `unpack_ima_tcl(...)`.
+    Output object returned when calling `UnpackImaTclParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class UnpackImaTclOutputs(typing.NamedTuple):
 
 def unpack_ima_tcl_params(
     target_dir: str = "~",
-) -> UnpackImaTclParameters:
+) -> UnpackImaTclParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def unpack_ima_tcl_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "unpack_ima.tcl",
+        "@type": "freesurfer/unpack_ima.tcl",
         "target_dir": target_dir,
     }
     return params
@@ -91,7 +64,7 @@ def unpack_ima_tcl_cargs(
     """
     cargs = []
     cargs.append("unpack_ima.tcl")
-    cargs.append(params.get("target_dir"))
+    cargs.append(params.get("target_dir", "~"))
     return cargs
 
 
@@ -116,9 +89,11 @@ def unpack_ima_tcl_outputs(
 
 def unpack_ima_tcl_execute(
     params: UnpackImaTclParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> UnpackImaTclOutputs:
     """
+    unpack_ima.tcl
+    
     A tool to unpack MRI DICOM .ima files.
     
     Author: FreeSurfer Developers
@@ -127,10 +102,12 @@ def unpack_ima_tcl_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `UnpackImaTclOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UNPACK_IMA_TCL_METADATA)
     params = execution.params(params)
     cargs = unpack_ima_tcl_cargs(params, execution)
     ret = unpack_ima_tcl_outputs(params, execution)
@@ -143,6 +120,8 @@ def unpack_ima_tcl(
     runner: Runner | None = None,
 ) -> UnpackImaTclOutputs:
     """
+    unpack_ima.tcl
+    
     A tool to unpack MRI DICOM .ima files.
     
     Author: FreeSurfer Developers
@@ -155,18 +134,16 @@ def unpack_ima_tcl(
     Returns:
         NamedTuple of outputs (described in `UnpackImaTclOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(UNPACK_IMA_TCL_METADATA)
     params = unpack_ima_tcl_params(
         target_dir=target_dir,
     )
-    return unpack_ima_tcl_execute(params, execution)
+    return unpack_ima_tcl_execute(params, runner)
 
 
 __all__ = [
     "UNPACK_IMA_TCL_METADATA",
     "UnpackImaTclOutputs",
-    "UnpackImaTclParameters",
     "unpack_ima_tcl",
+    "unpack_ima_tcl_execute",
     "unpack_ima_tcl_params",
 ]