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

niwrap_freesurfer/freesurfer/unpack_mnc_tcl.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 UNPACK_MNC_TCL_METADATA = Metadata(
-    id="23b95f229842c6004787027d672c29ea26934516.boutiques",
+    id="94dabaf49b0dbd76599a446af7424766e944571e.boutiques",
     name="unpack_mnc.tcl",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ UNPACK_MNC_TCL_METADATA = Metadata(
 
 
 UnpackMncTclParameters = typing.TypedDict('UnpackMncTclParameters', {
-    "__STYXTYPE__": typing.Literal["unpack_mnc.tcl"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/unpack_mnc.tcl"]],
+    "verbose": bool,
+    "output_dir": typing.NotRequired[str | None],
+    "input_file": typing.NotRequired[InputPathType | None],
+})
+UnpackMncTclParametersTagged = typing.TypedDict('UnpackMncTclParametersTagged', {
+    "@type": typing.Literal["freesurfer/unpack_mnc.tcl"],
     "verbose": bool,
     "output_dir": typing.NotRequired[str | None],
     "input_file": typing.NotRequired[InputPathType | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "unpack_mnc.tcl": unpack_mnc_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_mnc.tcl": unpack_mnc_tcl_outputs,
-    }.get(t)
 
 
 class UnpackMncTclOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `unpack_mnc_tcl(...)`.
+    Output object returned when calling `UnpackMncTclParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def unpack_mnc_tcl_params(
     verbose: bool = False,
     output_dir: str | None = None,
     input_file: InputPathType | None = None,
-) -> UnpackMncTclParameters:
+) -> UnpackMncTclParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def unpack_mnc_tcl_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "unpack_mnc.tcl",
+        "@type": "freesurfer/unpack_mnc.tcl",
         "verbose": verbose,
     }
     if output_dir is not None:
@@ -104,17 +78,17 @@ def unpack_mnc_tcl_cargs(
     """
     cargs = []
     cargs.append("unpack_mnc.tcl")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-v")
-    if params.get("output_dir") is not None:
+    if params.get("output_dir", None) is not None:
         cargs.extend([
             "-o",
-            params.get("output_dir")
+            params.get("output_dir", None)
         ])
-    if params.get("input_file") is not None:
+    if params.get("input_file", None) is not None:
         cargs.extend([
             "-i",
-            execution.input_file(params.get("input_file"))
+            execution.input_file(params.get("input_file", None))
         ])
     return cargs
 
@@ -134,16 +108,18 @@ def unpack_mnc_tcl_outputs(
     """
     ret = UnpackMncTclOutputs(
         root=execution.output_file("."),
-        unpacked_file=execution.output_file(params.get("output_dir") + "/unpacked_data.mnc") if (params.get("output_dir") is not None) else None,
+        unpacked_file=execution.output_file(params.get("output_dir", None) + "/unpacked_data.mnc") if (params.get("output_dir") is not None) else None,
     )
     return ret
 
 
 def unpack_mnc_tcl_execute(
     params: UnpackMncTclParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> UnpackMncTclOutputs:
     """
+    unpack_mnc.tcl
+    
     A tool for unpacking MINC format images.
     
     Author: FreeSurfer Developers
@@ -152,10 +128,12 @@ def unpack_mnc_tcl_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `UnpackMncTclOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UNPACK_MNC_TCL_METADATA)
     params = execution.params(params)
     cargs = unpack_mnc_tcl_cargs(params, execution)
     ret = unpack_mnc_tcl_outputs(params, execution)
@@ -170,6 +148,8 @@ def unpack_mnc_tcl(
     runner: Runner | None = None,
 ) -> UnpackMncTclOutputs:
     """
+    unpack_mnc.tcl
+    
     A tool for unpacking MINC format images.
     
     Author: FreeSurfer Developers
@@ -184,20 +164,18 @@ def unpack_mnc_tcl(
     Returns:
         NamedTuple of outputs (described in `UnpackMncTclOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(UNPACK_MNC_TCL_METADATA)
     params = unpack_mnc_tcl_params(
         verbose=verbose,
         output_dir=output_dir,
         input_file=input_file,
     )
-    return unpack_mnc_tcl_execute(params, execution)
+    return unpack_mnc_tcl_execute(params, runner)
 
 
 __all__ = [
     "UNPACK_MNC_TCL_METADATA",
     "UnpackMncTclOutputs",
-    "UnpackMncTclParameters",
     "unpack_mnc_tcl",
+    "unpack_mnc_tcl_execute",
     "unpack_mnc_tcl_params",
 ]

niwrap_freesurfer/freesurfer/unpackimadir.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 UNPACKIMADIR_METADATA = Metadata(
-    id="6a27f64ee58627da90e1a875d70fa5b839c021e5.boutiques",
+    id="5bc48c2b10587aee2d4de8244a11789fed81bd8a.boutiques",
     name="unpackimadir",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ UNPACKIMADIR_METADATA = Metadata(
 
 
 UnpackimadirParameters = typing.TypedDict('UnpackimadirParameters', {
-    "__STYXTYPE__": typing.Literal["unpackimadir"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/unpackimadir"]],
+    "source_directory": str,
+    "target_directory": str,
+})
+UnpackimadirParametersTagged = typing.TypedDict('UnpackimadirParametersTagged', {
+    "@type": typing.Literal["freesurfer/unpackimadir"],
     "source_directory": str,
     "target_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 {
-        "unpackimadir": unpackimadir_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 UnpackimadirOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `unpackimadir(...)`.
+    Output object returned when calling `UnpackimadirParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class UnpackimadirOutputs(typing.NamedTuple):
 def unpackimadir_params(
     source_directory: str,
     target_directory: str,
-) -> UnpackimadirParameters:
+) -> UnpackimadirParametersTagged:
     """
     Build parameters.
     
@@ -74,7 +48,7 @@ def unpackimadir_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "unpackimadir",
+        "@type": "freesurfer/unpackimadir",
         "source_directory": source_directory,
         "target_directory": target_directory,
     }
@@ -98,11 +72,11 @@ def unpackimadir_cargs(
     cargs.append("unpackimadir")
     cargs.extend([
         "-src",
-        params.get("source_directory")
+        params.get("source_directory", None)
     ])
     cargs.extend([
         "-targ",
-        params.get("target_directory")
+        params.get("target_directory", None)
     ])
     return cargs
 
@@ -128,9 +102,11 @@ def unpackimadir_outputs(
 
 def unpackimadir_execute(
     params: UnpackimadirParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> UnpackimadirOutputs:
     """
+    unpackimadir
+    
     Unpack image directories.
     
     Author: FreeSurfer Developers
@@ -139,10 +115,12 @@ def unpackimadir_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `UnpackimadirOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UNPACKIMADIR_METADATA)
     params = execution.params(params)
     cargs = unpackimadir_cargs(params, execution)
     ret = unpackimadir_outputs(params, execution)
@@ -156,6 +134,8 @@ def unpackimadir(
     runner: Runner | None = None,
 ) -> UnpackimadirOutputs:
     """
+    unpackimadir
+    
     Unpack image directories.
     
     Author: FreeSurfer Developers
@@ -170,19 +150,17 @@ def unpackimadir(
     Returns:
         NamedTuple of outputs (described in `UnpackimadirOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(UNPACKIMADIR_METADATA)
     params = unpackimadir_params(
         source_directory=source_directory,
         target_directory=target_directory,
     )
-    return unpackimadir_execute(params, execution)
+    return unpackimadir_execute(params, runner)
 
 
 __all__ = [
     "UNPACKIMADIR_METADATA",
     "UnpackimadirOutputs",
-    "UnpackimadirParameters",
     "unpackimadir",
+    "unpackimadir_execute",
     "unpackimadir_params",
 ]

niwrap_freesurfer/freesurfer/unpackimadir2.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 UNPACKIMADIR2_METADATA = Metadata(
-    id="bdf6eb9c77635e9326080586e7654d60496c26b4.boutiques",
+    id="a9223f4f9bff668d7fd030c3934c5982e5b81aa3.boutiques",
     name="unpackimadir2",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ UNPACKIMADIR2_METADATA = Metadata(
 
 
 Unpackimadir2Parameters = typing.TypedDict('Unpackimadir2Parameters', {
-    "__STYXTYPE__": typing.Literal["unpackimadir2"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/unpackimadir2"]],
+    "directory": InputPathType,
+})
+Unpackimadir2ParametersTagged = typing.TypedDict('Unpackimadir2ParametersTagged', {
+    "@type": typing.Literal["freesurfer/unpackimadir2"],
     "directory": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "unpackimadir2": unpackimadir2_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 Unpackimadir2Outputs(typing.NamedTuple):
     """
-    Output object returned when calling `unpackimadir2(...)`.
+    Output object returned when calling `Unpackimadir2Parameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class Unpackimadir2Outputs(typing.NamedTuple):
 
 def unpackimadir2_params(
     directory: InputPathType,
-) -> Unpackimadir2Parameters:
+) -> Unpackimadir2ParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def unpackimadir2_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "unpackimadir2",
+        "@type": "freesurfer/unpackimadir2",
         "directory": directory,
     }
     return params
@@ -91,7 +64,7 @@ def unpackimadir2_cargs(
     """
     cargs = []
     cargs.append("unpackimadir2")
-    cargs.append(execution.input_file(params.get("directory")))
+    cargs.append(execution.input_file(params.get("directory", None)))
     return cargs
 
 
@@ -116,9 +89,11 @@ def unpackimadir2_outputs(
 
 def unpackimadir2_execute(
     params: Unpackimadir2Parameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Unpackimadir2Outputs:
     """
+    unpackimadir2
+    
     Tool to unpack image directories, from FreeSurfer suite.
     
     Author: FreeSurfer Developers
@@ -127,10 +102,12 @@ def unpackimadir2_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Unpackimadir2Outputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UNPACKIMADIR2_METADATA)
     params = execution.params(params)
     cargs = unpackimadir2_cargs(params, execution)
     ret = unpackimadir2_outputs(params, execution)
@@ -143,6 +120,8 @@ def unpackimadir2(
     runner: Runner | None = None,
 ) -> Unpackimadir2Outputs:
     """
+    unpackimadir2
+    
     Tool to unpack image directories, from FreeSurfer suite.
     
     Author: FreeSurfer Developers
@@ -155,18 +134,16 @@ def unpackimadir2(
     Returns:
         NamedTuple of outputs (described in `Unpackimadir2Outputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(UNPACKIMADIR2_METADATA)
     params = unpackimadir2_params(
         directory=directory,
     )
-    return unpackimadir2_execute(params, execution)
+    return unpackimadir2_execute(params, runner)
 
 
 __all__ = [
     "UNPACKIMADIR2_METADATA",
     "Unpackimadir2Outputs",
-    "Unpackimadir2Parameters",
     "unpackimadir2",
+    "unpackimadir2_execute",
     "unpackimadir2_params",
 ]

niwrap_freesurfer/freesurfer/unpackmincdir.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 UNPACKMINCDIR_METADATA = Metadata(
-    id="2dc1b33b00ea414a122d0a6f9b270fd885e8e3eb.boutiques",
+    id="7110e5930638ffed1d35700999de9827614bdb2e.boutiques",
     name="unpackmincdir",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ UNPACKMINCDIR_METADATA = Metadata(
 
 
 UnpackmincdirParameters = typing.TypedDict('UnpackmincdirParameters', {
-    "__STYXTYPE__": typing.Literal["unpackmincdir"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/unpackmincdir"]],
+    "source_directory": str,
+    "target_directory": str,
+    "scan_sequence_info": typing.NotRequired[str | None],
+    "functional_sequence": typing.NotRequired[str | None],
+    "functional_subdirectory": typing.NotRequired[str | None],
+    "minc_only": bool,
+    "no_copy": bool,
+    "umask": typing.NotRequired[str | None],
+})
+UnpackmincdirParametersTagged = typing.TypedDict('UnpackmincdirParametersTagged', {
+    "@type": typing.Literal["freesurfer/unpackmincdir"],
     "source_directory": str,
     "target_directory": str,
     "scan_sequence_info": typing.NotRequired[str | None],
@@ -24,42 +35,11 @@ UnpackmincdirParameters = typing.TypedDict('UnpackmincdirParameters', {
     "no_copy": bool,
     "umask": 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 {
-        "unpackmincdir": unpackmincdir_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 UnpackmincdirOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `unpackmincdir(...)`.
+    Output object returned when calling `UnpackmincdirParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,7 +54,7 @@ def unpackmincdir_params(
     minc_only: bool = False,
     no_copy: bool = False,
     umask: str | None = None,
-) -> UnpackmincdirParameters:
+) -> UnpackmincdirParametersTagged:
     """
     Build parameters.
     
@@ -93,7 +73,7 @@ def unpackmincdir_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "unpackmincdir",
+        "@type": "freesurfer/unpackmincdir",
         "source_directory": source_directory,
         "target_directory": target_directory,
         "minc_only": minc_only,
@@ -127,35 +107,35 @@ def unpackmincdir_cargs(
     cargs.append("unpackmincdir")
     cargs.extend([
         "-src",
-        params.get("source_directory")
+        params.get("source_directory", None)
     ])
     cargs.extend([
         "-targ",
-        params.get("target_directory")
+        params.get("target_directory", None)
     ])
-    if params.get("scan_sequence_info") is not None:
+    if params.get("scan_sequence_info", None) is not None:
         cargs.extend([
             "-scanseqinfo",
-            params.get("scan_sequence_info")
+            params.get("scan_sequence_info", None)
         ])
-    if params.get("functional_sequence") is not None:
+    if params.get("functional_sequence", None) is not None:
         cargs.extend([
             "-funcseq",
-            params.get("functional_sequence")
+            params.get("functional_sequence", None)
         ])
-    if params.get("functional_subdirectory") is not None:
+    if params.get("functional_subdirectory", None) is not None:
         cargs.extend([
             "-fsd",
-            params.get("functional_subdirectory")
+            params.get("functional_subdirectory", None)
         ])
-    if params.get("minc_only"):
+    if params.get("minc_only", False):
         cargs.append("-minconly")
-    if params.get("no_copy"):
+    if params.get("no_copy", False):
         cargs.append("-nocopy")
-    if params.get("umask") is not None:
+    if params.get("umask", None) is not None:
         cargs.extend([
             "-umask",
-            params.get("umask")
+            params.get("umask", None)
         ])
     return cargs
 
@@ -181,9 +161,11 @@ def unpackmincdir_outputs(
 
 def unpackmincdir_execute(
     params: UnpackmincdirParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> UnpackmincdirOutputs:
     """
+    unpackmincdir
+    
     Tool for unpacking directories with MINC files.
     
     Author: FreeSurfer Developers
@@ -192,10 +174,12 @@ def unpackmincdir_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `UnpackmincdirOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UNPACKMINCDIR_METADATA)
     params = execution.params(params)
     cargs = unpackmincdir_cargs(params, execution)
     ret = unpackmincdir_outputs(params, execution)
@@ -215,6 +199,8 @@ def unpackmincdir(
     runner: Runner | None = None,
 ) -> UnpackmincdirOutputs:
     """
+    unpackmincdir
+    
     Tool for unpacking directories with MINC files.
     
     Author: FreeSurfer Developers
@@ -236,8 +222,6 @@ def unpackmincdir(
     Returns:
         NamedTuple of outputs (described in `UnpackmincdirOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(UNPACKMINCDIR_METADATA)
     params = unpackmincdir_params(
         source_directory=source_directory,
         target_directory=target_directory,
@@ -248,13 +232,13 @@ def unpackmincdir(
         no_copy=no_copy,
         umask=umask,
     )
-    return unpackmincdir_execute(params, execution)
+    return unpackmincdir_execute(params, runner)
 
 
 __all__ = [
     "UNPACKMINCDIR_METADATA",
     "UnpackmincdirOutputs",
-    "UnpackmincdirParameters",
     "unpackmincdir",
+    "unpackmincdir_execute",
     "unpackmincdir_params",
 ]