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

niwrap_freesurfer/freesurfer/irepifitvol_glnx64.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 IREPIFITVOL_GLNX64_METADATA = Metadata(
-    id="844a98eac80577b9cd78380d611cc940c14cec64.boutiques",
+    id="a086fe8ba3cbfd5163cdfddf0cd873ea526cb155.boutiques",
     name="irepifitvol.glnx64",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ IREPIFITVOL_GLNX64_METADATA = Metadata(
 
 
 IrepifitvolGlnx64Parameters = typing.TypedDict('IrepifitvolGlnx64Parameters', {
-    "__STYXTYPE__": typing.Literal["irepifitvol.glnx64"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/irepifitvol.glnx64"]],
+    "input_file": InputPathType,
+    "output_file": str,
+})
+IrepifitvolGlnx64ParametersTagged = typing.TypedDict('IrepifitvolGlnx64ParametersTagged', {
+    "@type": typing.Literal["freesurfer/irepifitvol.glnx64"],
     "input_file": InputPathType,
     "output_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 {
-        "irepifitvol.glnx64": irepifitvol_glnx64_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 {
-        "irepifitvol.glnx64": irepifitvol_glnx64_outputs,
-    }.get(t)
 
 
 class IrepifitvolGlnx64Outputs(typing.NamedTuple):
     """
-    Output object returned when calling `irepifitvol_glnx64(...)`.
+    Output object returned when calling `IrepifitvolGlnx64Parameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class IrepifitvolGlnx64Outputs(typing.NamedTuple):
 def irepifitvol_glnx64_params(
     input_file: InputPathType,
     output_file: str,
-) -> IrepifitvolGlnx64Parameters:
+) -> IrepifitvolGlnx64ParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def irepifitvol_glnx64_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "irepifitvol.glnx64",
+        "@type": "freesurfer/irepifitvol.glnx64",
         "input_file": input_file,
         "output_file": output_file,
     }
@@ -98,8 +71,8 @@ def irepifitvol_glnx64_cargs(
     """
     cargs = []
     cargs.append("irepifitvol.glnx64")
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(params.get("output_file"))
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    cargs.append(params.get("output_file", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def irepifitvol_glnx64_outputs(
     """
     ret = IrepifitvolGlnx64Outputs(
         root=execution.output_file("."),
-        output_volume=execution.output_file(params.get("output_file")),
+        output_volume=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def irepifitvol_glnx64_execute(
     params: IrepifitvolGlnx64Parameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> IrepifitvolGlnx64Outputs:
     """
+    irepifitvol.glnx64
+    
     This tool is a part of the FreeSurfer toolkit, designed for certain volume
     fitting tasks.
     
@@ -137,10 +112,12 @@ def irepifitvol_glnx64_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `IrepifitvolGlnx64Outputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IREPIFITVOL_GLNX64_METADATA)
     params = execution.params(params)
     cargs = irepifitvol_glnx64_cargs(params, execution)
     ret = irepifitvol_glnx64_outputs(params, execution)
@@ -154,6 +131,8 @@ def irepifitvol_glnx64(
     runner: Runner | None = None,
 ) -> IrepifitvolGlnx64Outputs:
     """
+    irepifitvol.glnx64
+    
     This tool is a part of the FreeSurfer toolkit, designed for certain volume
     fitting tasks.
     
@@ -168,19 +147,17 @@ def irepifitvol_glnx64(
     Returns:
         NamedTuple of outputs (described in `IrepifitvolGlnx64Outputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(IREPIFITVOL_GLNX64_METADATA)
     params = irepifitvol_glnx64_params(
         input_file=input_file,
         output_file=output_file,
     )
-    return irepifitvol_glnx64_execute(params, execution)
+    return irepifitvol_glnx64_execute(params, runner)
 
 
 __all__ = [
     "IREPIFITVOL_GLNX64_METADATA",
     "IrepifitvolGlnx64Outputs",
-    "IrepifitvolGlnx64Parameters",
     "irepifitvol_glnx64",
+    "irepifitvol_glnx64_execute",
     "irepifitvol_glnx64_params",
 ]

niwrap_freesurfer/freesurfer/is_lta.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 IS_LTA_METADATA = Metadata(
-    id="a9d22638bdece2ba3d66169a55affcf047517108.boutiques",
+    id="5b9882c3525933a7e40833c3e89a1444ba13a395.boutiques",
     name="IsLTA",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ IS_LTA_METADATA = Metadata(
 
 
 IsLtaParameters = typing.TypedDict('IsLtaParameters', {
-    "__STYXTYPE__": typing.Literal["IsLTA"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/IsLTA"]],
+    "candidate_file": InputPathType,
+    "outfile": str,
+})
+IsLtaParametersTagged = typing.TypedDict('IsLtaParametersTagged', {
+    "@type": typing.Literal["freesurfer/IsLTA"],
     "candidate_file": InputPathType,
     "outfile": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "IsLTA": is_lta_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 {
-        "IsLTA": is_lta_outputs,
-    }.get(t)
 
 
 class IsLtaOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `is_lta(...)`.
+    Output object returned when calling `IsLtaParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class IsLtaOutputs(typing.NamedTuple):
 def is_lta_params(
     candidate_file: InputPathType,
     outfile: str,
-) -> IsLtaParameters:
+) -> IsLtaParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def is_lta_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "IsLTA",
+        "@type": "freesurfer/IsLTA",
         "candidate_file": candidate_file,
         "outfile": outfile,
     }
@@ -100,11 +73,11 @@ def is_lta_cargs(
     cargs.append("IsLTA")
     cargs.extend([
         "--r",
-        execution.input_file(params.get("candidate_file"))
+        execution.input_file(params.get("candidate_file", None))
     ])
     cargs.extend([
         "--o",
-        params.get("outfile")
+        params.get("outfile", None)
     ])
     return cargs
 
@@ -124,18 +97,20 @@ def is_lta_outputs(
     """
     ret = IsLtaOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("outfile")),
+        output_file=execution.output_file(params.get("outfile", None)),
     )
     return ret
 
 
 def is_lta_execute(
     params: IsLtaParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> IsLtaOutputs:
     """
-    Determines if a given file is an LTA (Linear Transform Array) file. Outputs 1 if
-    true, otherwise outputs 0.
+    IsLTA
+    
+    Determines if a given file is an LTA (Linear Transform Array) file. Outputs
+    1 if true, otherwise outputs 0.
     
     Author: FreeSurfer Developers
     
@@ -143,10 +118,12 @@ def is_lta_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `IsLtaOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IS_LTA_METADATA)
     params = execution.params(params)
     cargs = is_lta_cargs(params, execution)
     ret = is_lta_outputs(params, execution)
@@ -160,8 +137,10 @@ def is_lta(
     runner: Runner | None = None,
 ) -> IsLtaOutputs:
     """
-    Determines if a given file is an LTA (Linear Transform Array) file. Outputs 1 if
-    true, otherwise outputs 0.
+    IsLTA
+    
+    Determines if a given file is an LTA (Linear Transform Array) file. Outputs
+    1 if true, otherwise outputs 0.
     
     Author: FreeSurfer Developers
     
@@ -174,19 +153,17 @@ def is_lta(
     Returns:
         NamedTuple of outputs (described in `IsLtaOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(IS_LTA_METADATA)
     params = is_lta_params(
         candidate_file=candidate_file,
         outfile=outfile,
     )
-    return is_lta_execute(params, execution)
+    return is_lta_execute(params, runner)
 
 
 __all__ = [
     "IS_LTA_METADATA",
     "IsLtaOutputs",
-    "IsLtaParameters",
     "is_lta",
+    "is_lta_execute",
     "is_lta_params",
 ]

niwrap_freesurfer/freesurfer/is_surface.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 IS_SURFACE_METADATA = Metadata(
-    id="86c411bc39041a8b3eae45962259ad09e76de3b1.boutiques",
+    id="035e166500ca11119ee6ff6e44628cacf5feb50e.boutiques",
     name="is-surface",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ IS_SURFACE_METADATA = Metadata(
 
 
 IsSurfaceParameters = typing.TypedDict('IsSurfaceParameters', {
-    "__STYXTYPE__": typing.Literal["is-surface"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/is-surface"]],
+    "infile": InputPathType,
+})
+IsSurfaceParametersTagged = typing.TypedDict('IsSurfaceParametersTagged', {
+    "@type": typing.Literal["freesurfer/is-surface"],
     "infile": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "is-surface": is_surface_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 IsSurfaceOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `is_surface(...)`.
+    Output object returned when calling `IsSurfaceParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class IsSurfaceOutputs(typing.NamedTuple):
 
 def is_surface_params(
     infile: InputPathType,
-) -> IsSurfaceParameters:
+) -> IsSurfaceParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def is_surface_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "is-surface",
+        "@type": "freesurfer/is-surface",
         "infile": infile,
     }
     return params
@@ -93,7 +66,7 @@ def is_surface_cargs(
     cargs.append("is-surface")
     cargs.extend([
         "-surface",
-        execution.input_file(params.get("infile"))
+        execution.input_file(params.get("infile", None))
     ])
     return cargs
 
@@ -119,9 +92,11 @@ def is_surface_outputs(
 
 def is_surface_execute(
     params: IsSurfaceParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> IsSurfaceOutputs:
     """
+    is-surface
+    
     Determines whether a file is a volume-encoded surface file by examining its
     dimensions.
     
@@ -131,10 +106,12 @@ def is_surface_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `IsSurfaceOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IS_SURFACE_METADATA)
     params = execution.params(params)
     cargs = is_surface_cargs(params, execution)
     ret = is_surface_outputs(params, execution)
@@ -147,6 +124,8 @@ def is_surface(
     runner: Runner | None = None,
 ) -> IsSurfaceOutputs:
     """
+    is-surface
+    
     Determines whether a file is a volume-encoded surface file by examining its
     dimensions.
     
@@ -160,18 +139,16 @@ def is_surface(
     Returns:
         NamedTuple of outputs (described in `IsSurfaceOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(IS_SURFACE_METADATA)
     params = is_surface_params(
         infile=infile,
     )
-    return is_surface_execute(params, execution)
+    return is_surface_execute(params, runner)
 
 
 __all__ = [
     "IS_SURFACE_METADATA",
     "IsSurfaceOutputs",
-    "IsSurfaceParameters",
     "is_surface",
+    "is_surface_execute",
     "is_surface_params",
 ]

niwrap_freesurfer/freesurfer/isanalyze.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ISANALYZE_METADATA = Metadata(
-    id="3d8f8ed4f2f6a0e189b0b47b6a3b1fc896553e24.boutiques",
+    id="aa58d8228bd180bd56d730927dfa201442c71e68.boutiques",
     name="isanalyze",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ ISANALYZE_METADATA = Metadata(
 
 
 IsanalyzeParameters = typing.TypedDict('IsanalyzeParameters', {
-    "__STYXTYPE__": typing.Literal["isanalyze"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/isanalyze"]],
+    "input_file": InputPathType,
+})
+IsanalyzeParametersTagged = typing.TypedDict('IsanalyzeParametersTagged', {
+    "@type": typing.Literal["freesurfer/isanalyze"],
     "input_file": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "isanalyze": isanalyze_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 IsanalyzeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `isanalyze(...)`.
+    Output object returned when calling `IsanalyzeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class IsanalyzeOutputs(typing.NamedTuple):
 
 def isanalyze_params(
     input_file: InputPathType,
-) -> IsanalyzeParameters:
+) -> IsanalyzeParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def isanalyze_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "isanalyze",
+        "@type": "freesurfer/isanalyze",
         "input_file": input_file,
     }
     return params
@@ -91,7 +64,7 @@ def isanalyze_cargs(
     """
     cargs = []
     cargs.append("isanalyze")
-    cargs.append(execution.input_file(params.get("input_file")))
+    cargs.append(execution.input_file(params.get("input_file", None)))
     return cargs
 
 
@@ -116,9 +89,11 @@ def isanalyze_outputs(
 
 def isanalyze_execute(
     params: IsanalyzeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> IsanalyzeOutputs:
     """
+    isanalyze
+    
     A tool to analyze and process IS files.
     
     Author: FreeSurfer Developers
@@ -127,10 +102,12 @@ def isanalyze_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `IsanalyzeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ISANALYZE_METADATA)
     params = execution.params(params)
     cargs = isanalyze_cargs(params, execution)
     ret = isanalyze_outputs(params, execution)
@@ -143,6 +120,8 @@ def isanalyze(
     runner: Runner | None = None,
 ) -> IsanalyzeOutputs:
     """
+    isanalyze
+    
     A tool to analyze and process IS files.
     
     Author: FreeSurfer Developers
@@ -155,18 +134,16 @@ def isanalyze(
     Returns:
         NamedTuple of outputs (described in `IsanalyzeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ISANALYZE_METADATA)
     params = isanalyze_params(
         input_file=input_file,
     )
-    return isanalyze_execute(params, execution)
+    return isanalyze_execute(params, runner)
 
 
 __all__ = [
     "ISANALYZE_METADATA",
     "IsanalyzeOutputs",
-    "IsanalyzeParameters",
     "isanalyze",
+    "isanalyze_execute",
     "isanalyze_params",
 ]