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

niwrap_freesurfer/freesurfer/fs_spmreg_glnxa64.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FS_SPMREG_GLNXA64_METADATA = Metadata(
-    id="9ed2398015232e130c8d384ec8da69f776b63c1c.boutiques",
+    id="5a9193dabec6a736cf37d773fb6396ea21a54ffa.boutiques",
     name="fs_spmreg.glnxa64",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ FS_SPMREG_GLNXA64_METADATA = Metadata(
 
 
 FsSpmregGlnxa64Parameters = typing.TypedDict('FsSpmregGlnxa64Parameters', {
-    "__STYXTYPE__": typing.Literal["fs_spmreg.glnxa64"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fs_spmreg.glnxa64"]],
+    "input_volume": InputPathType,
+    "output_matrix": str,
+})
+FsSpmregGlnxa64ParametersTagged = typing.TypedDict('FsSpmregGlnxa64ParametersTagged', {
+    "@type": typing.Literal["freesurfer/fs_spmreg.glnxa64"],
     "input_volume": InputPathType,
     "output_matrix": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fs_spmreg.glnxa64": fs_spmreg_glnxa64_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 {
-        "fs_spmreg.glnxa64": fs_spmreg_glnxa64_outputs,
-    }.get(t)
 
 
 class FsSpmregGlnxa64Outputs(typing.NamedTuple):
     """
-    Output object returned when calling `fs_spmreg_glnxa64(...)`.
+    Output object returned when calling `FsSpmregGlnxa64Parameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class FsSpmregGlnxa64Outputs(typing.NamedTuple):
 def fs_spmreg_glnxa64_params(
     input_volume: InputPathType,
     output_matrix: str = "output.mat",
-) -> FsSpmregGlnxa64Parameters:
+) -> FsSpmregGlnxa64ParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def fs_spmreg_glnxa64_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fs_spmreg.glnxa64",
+        "@type": "freesurfer/fs_spmreg.glnxa64",
         "input_volume": input_volume,
         "output_matrix": output_matrix,
     }
@@ -98,8 +71,8 @@ def fs_spmreg_glnxa64_cargs(
     """
     cargs = []
     cargs.append("fs_spmreg.glnxa64")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(params.get("output_matrix"))
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(params.get("output_matrix", "output.mat"))
     return cargs
 
 
@@ -118,16 +91,18 @@ def fs_spmreg_glnxa64_outputs(
     """
     ret = FsSpmregGlnxa64Outputs(
         root=execution.output_file("."),
-        output_matrix_file=execution.output_file(params.get("output_matrix")),
+        output_matrix_file=execution.output_file(params.get("output_matrix", "output.mat")),
     )
     return ret
 
 
 def fs_spmreg_glnxa64_execute(
     params: FsSpmregGlnxa64Parameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FsSpmregGlnxa64Outputs:
     """
+    fs_spmreg.glnxa64
+    
     fs_spmreg is a tool for registration using SPM within FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -136,10 +111,12 @@ def fs_spmreg_glnxa64_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsSpmregGlnxa64Outputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FS_SPMREG_GLNXA64_METADATA)
     params = execution.params(params)
     cargs = fs_spmreg_glnxa64_cargs(params, execution)
     ret = fs_spmreg_glnxa64_outputs(params, execution)
@@ -153,6 +130,8 @@ def fs_spmreg_glnxa64(
     runner: Runner | None = None,
 ) -> FsSpmregGlnxa64Outputs:
     """
+    fs_spmreg.glnxa64
+    
     fs_spmreg is a tool for registration using SPM within FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -166,19 +145,17 @@ def fs_spmreg_glnxa64(
     Returns:
         NamedTuple of outputs (described in `FsSpmregGlnxa64Outputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FS_SPMREG_GLNXA64_METADATA)
     params = fs_spmreg_glnxa64_params(
         input_volume=input_volume,
         output_matrix=output_matrix,
     )
-    return fs_spmreg_glnxa64_execute(params, execution)
+    return fs_spmreg_glnxa64_execute(params, runner)
 
 
 __all__ = [
     "FS_SPMREG_GLNXA64_METADATA",
     "FsSpmregGlnxa64Outputs",
-    "FsSpmregGlnxa64Parameters",
     "fs_spmreg_glnxa64",
+    "fs_spmreg_glnxa64_execute",
     "fs_spmreg_glnxa64_params",
 ]

niwrap_freesurfer/freesurfer/fs_temp_dir.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FS_TEMP_DIR_METADATA = Metadata(
-    id="d9debad2d46dec10deffc0f2440d01543333ec6a.boutiques",
+    id="527e55a39dc28f0c9acdbccf0047fb17ab363432.boutiques",
     name="fs_temp_dir",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ FS_TEMP_DIR_METADATA = Metadata(
 
 
 FsTempDirParameters = typing.TypedDict('FsTempDirParameters', {
-    "__STYXTYPE__": typing.Literal["fs_temp_dir"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fs_temp_dir"]],
+    "base_directory": typing.NotRequired[str | None],
+    "scratch": bool,
+})
+FsTempDirParametersTagged = typing.TypedDict('FsTempDirParametersTagged', {
+    "@type": typing.Literal["freesurfer/fs_temp_dir"],
     "base_directory": typing.NotRequired[str | None],
     "scratch": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fs_temp_dir": fs_temp_dir_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 {
-        "fs_temp_dir": fs_temp_dir_outputs,
-    }.get(t)
 
 
 class FsTempDirOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fs_temp_dir(...)`.
+    Output object returned when calling `FsTempDirParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class FsTempDirOutputs(typing.NamedTuple):
 def fs_temp_dir_params(
     base_directory: str | None = None,
     scratch: bool = False,
-) -> FsTempDirParameters:
+) -> FsTempDirParametersTagged:
     """
     Build parameters.
     
@@ -77,7 +50,7 @@ def fs_temp_dir_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fs_temp_dir",
+        "@type": "freesurfer/fs_temp_dir",
         "scratch": scratch,
     }
     if base_directory is not None:
@@ -100,12 +73,12 @@ def fs_temp_dir_cargs(
     """
     cargs = []
     cargs.append("fs_temp_dir")
-    if params.get("base_directory") is not None:
+    if params.get("base_directory", None) is not None:
         cargs.extend([
             "-b",
-            params.get("base_directory")
+            params.get("base_directory", None)
         ])
-    if params.get("scratch"):
+    if params.get("scratch", False):
         cargs.append("--scratch")
     return cargs
 
@@ -132,9 +105,11 @@ def fs_temp_dir_outputs(
 
 def fs_temp_dir_execute(
     params: FsTempDirParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FsTempDirOutputs:
     """
+    fs_temp_dir
+    
     Generates and creates an empty temporary directory.
     
     Author: FreeSurfer Developers
@@ -143,10 +118,12 @@ def fs_temp_dir_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsTempDirOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FS_TEMP_DIR_METADATA)
     params = execution.params(params)
     cargs = fs_temp_dir_cargs(params, execution)
     ret = fs_temp_dir_outputs(params, execution)
@@ -160,6 +137,8 @@ def fs_temp_dir(
     runner: Runner | None = None,
 ) -> FsTempDirOutputs:
     """
+    fs_temp_dir
+    
     Generates and creates an empty temporary directory.
     
     Author: FreeSurfer Developers
@@ -174,19 +153,17 @@ def fs_temp_dir(
     Returns:
         NamedTuple of outputs (described in `FsTempDirOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FS_TEMP_DIR_METADATA)
     params = fs_temp_dir_params(
         base_directory=base_directory,
         scratch=scratch,
     )
-    return fs_temp_dir_execute(params, execution)
+    return fs_temp_dir_execute(params, runner)
 
 
 __all__ = [
     "FS_TEMP_DIR_METADATA",
     "FsTempDirOutputs",
-    "FsTempDirParameters",
     "fs_temp_dir",
+    "fs_temp_dir_execute",
     "fs_temp_dir_params",
 ]

niwrap_freesurfer/freesurfer/fs_temp_file.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FS_TEMP_FILE_METADATA = Metadata(
-    id="0af9f914376b0b96f8401ddfbac1babb938c4e65.boutiques",
+    id="e13f522a68dfa61e1b1658e6733c2322a574a1cc.boutiques",
     name="fs_temp_file",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ FS_TEMP_FILE_METADATA = Metadata(
 
 
 FsTempFileParameters = typing.TypedDict('FsTempFileParameters', {
-    "__STYXTYPE__": typing.Literal["fs_temp_file"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fs_temp_file"]],
+    "base_dir": typing.NotRequired[str | None],
+    "base_dir_alt": typing.NotRequired[str | None],
+    "suffix": typing.NotRequired[str | None],
+    "suffix_alt": typing.NotRequired[str | None],
+    "scratch": bool,
+    "help": bool,
+    "help_alt": bool,
+})
+FsTempFileParametersTagged = typing.TypedDict('FsTempFileParametersTagged', {
+    "@type": typing.Literal["freesurfer/fs_temp_file"],
     "base_dir": typing.NotRequired[str | None],
     "base_dir_alt": typing.NotRequired[str | None],
     "suffix": typing.NotRequired[str | None],
@@ -23,42 +33,11 @@ FsTempFileParameters = typing.TypedDict('FsTempFileParameters', {
     "help": bool,
     "help_alt": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fs_temp_file": fs_temp_file_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 FsTempFileOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fs_temp_file(...)`.
+    Output object returned when calling `FsTempFileParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,7 +51,7 @@ def fs_temp_file_params(
     scratch: bool = False,
     help_: bool = False,
     help_alt: bool = False,
-) -> FsTempFileParameters:
+) -> FsTempFileParametersTagged:
     """
     Build parameters.
     
@@ -89,7 +68,7 @@ def fs_temp_file_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fs_temp_file",
+        "@type": "freesurfer/fs_temp_file",
         "scratch": scratch,
         "help": help_,
         "help_alt": help_alt,
@@ -120,31 +99,31 @@ def fs_temp_file_cargs(
     """
     cargs = []
     cargs.append("fs_temp_file")
-    if params.get("base_dir") is not None:
+    if params.get("base_dir", None) is not None:
         cargs.extend([
             "-b",
-            params.get("base_dir")
+            params.get("base_dir", None)
         ])
-    if params.get("base_dir_alt") is not None:
+    if params.get("base_dir_alt", None) is not None:
         cargs.extend([
             "--base",
-            params.get("base_dir_alt")
+            params.get("base_dir_alt", None)
         ])
-    if params.get("suffix") is not None:
+    if params.get("suffix", None) is not None:
         cargs.extend([
             "-s",
-            params.get("suffix")
+            params.get("suffix", None)
         ])
-    if params.get("suffix_alt") is not None:
+    if params.get("suffix_alt", None) is not None:
         cargs.extend([
             "--suffix",
-            params.get("suffix_alt")
+            params.get("suffix_alt", None)
         ])
-    if params.get("scratch"):
+    if params.get("scratch", False):
         cargs.append("--scratch")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-h")
-    if params.get("help_alt"):
+    if params.get("help_alt", False):
         cargs.append("--help")
     return cargs
 
@@ -170,11 +149,13 @@ def fs_temp_file_outputs(
 
 def fs_temp_file_execute(
     params: FsTempFileParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FsTempFileOutputs:
     """
-    Generates and creates an empty temporary file, printing the resulting path to
-    stdout.
+    fs_temp_file
+    
+    Generates and creates an empty temporary file, printing the resulting path
+    to stdout.
     
     Author: FreeSurfer Developers
     
@@ -182,10 +163,12 @@ def fs_temp_file_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsTempFileOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FS_TEMP_FILE_METADATA)
     params = execution.params(params)
     cargs = fs_temp_file_cargs(params, execution)
     ret = fs_temp_file_outputs(params, execution)
@@ -204,8 +187,10 @@ def fs_temp_file(
     runner: Runner | None = None,
 ) -> FsTempFileOutputs:
     """
-    Generates and creates an empty temporary file, printing the resulting path to
-    stdout.
+    fs_temp_file
+    
+    Generates and creates an empty temporary file, printing the resulting path
+    to stdout.
     
     Author: FreeSurfer Developers
     
@@ -224,8 +209,6 @@ def fs_temp_file(
     Returns:
         NamedTuple of outputs (described in `FsTempFileOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FS_TEMP_FILE_METADATA)
     params = fs_temp_file_params(
         base_dir=base_dir,
         base_dir_alt=base_dir_alt,
@@ -235,13 +218,13 @@ def fs_temp_file(
         help_=help_,
         help_alt=help_alt,
     )
-    return fs_temp_file_execute(params, execution)
+    return fs_temp_file_execute(params, runner)
 
 
 __all__ = [
     "FS_TEMP_FILE_METADATA",
     "FsTempFileOutputs",
-    "FsTempFileParameters",
     "fs_temp_file",
+    "fs_temp_file_execute",
     "fs_temp_file_params",
 ]

niwrap_freesurfer/freesurfer/fs_time.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FS_TIME_METADATA = Metadata(
-    id="897824286c7098dc9c88cb3bcaf0654aece28325.boutiques",
+    id="ebe69ebd0ffd307fd6b99269db6880b8aacee0d9.boutiques",
     name="fs_time",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ FS_TIME_METADATA = Metadata(
 
 
 FsTimeParameters = typing.TypedDict('FsTimeParameters', {
-    "__STYXTYPE__": typing.Literal["fs_time"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fs_time"]],
+    "output_file": typing.NotRequired[str | None],
+    "key": typing.NotRequired[str | None],
+    "load_avg": bool,
+    "command": str,
+    "args": typing.NotRequired[list[str] | None],
+})
+FsTimeParametersTagged = typing.TypedDict('FsTimeParametersTagged', {
+    "@type": typing.Literal["freesurfer/fs_time"],
     "output_file": typing.NotRequired[str | None],
     "key": typing.NotRequired[str | None],
     "load_avg": bool,
     "command": str,
     "args": typing.NotRequired[list[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 {
-        "fs_time": fs_time_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 {
-        "fs_time": fs_time_outputs,
-    }.get(t)
 
 
 class FsTimeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fs_time(...)`.
+    Output object returned when calling `FsTimeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def fs_time_params(
     key: str | None = None,
     load_avg: bool = False,
     args: list[str] | None = None,
-) -> FsTimeParameters:
+) -> FsTimeParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +61,7 @@ def fs_time_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fs_time",
+        "@type": "freesurfer/fs_time",
         "load_avg": load_avg,
         "command": command,
     }
@@ -113,21 +89,21 @@ def fs_time_cargs(
     """
     cargs = []
     cargs.append("fs_time")
-    if params.get("output_file") is not None:
+    if params.get("output_file", None) is not None:
         cargs.extend([
             "-o",
-            params.get("output_file")
+            params.get("output_file", None)
         ])
-    if params.get("key") is not None:
+    if params.get("key", None) is not None:
         cargs.extend([
             "-k",
-            params.get("key")
+            params.get("key", None)
         ])
-    if params.get("load_avg"):
+    if params.get("load_avg", False):
         cargs.append("-l")
-    cargs.append(params.get("command"))
-    if params.get("args") is not None:
-        cargs.extend(params.get("args"))
+    cargs.append(params.get("command", None))
+    if params.get("args", None) is not None:
+        cargs.extend(params.get("args", None))
     return cargs
 
 
@@ -146,16 +122,18 @@ def fs_time_outputs(
     """
     ret = FsTimeOutputs(
         root=execution.output_file("."),
-        resource_output=execution.output_file(params.get("output_file")) if (params.get("output_file") is not None) else None,
+        resource_output=execution.output_file(params.get("output_file", None)) if (params.get("output_file") is not None) else None,
     )
     return ret
 
 
 def fs_time_execute(
     params: FsTimeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FsTimeOutputs:
     """
+    fs_time
+    
     A frontend for the unix /usr/bin/time program to track resource usage by a
     process.
     
@@ -165,10 +143,12 @@ def fs_time_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsTimeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FS_TIME_METADATA)
     params = execution.params(params)
     cargs = fs_time_cargs(params, execution)
     ret = fs_time_outputs(params, execution)
@@ -185,6 +165,8 @@ def fs_time(
     runner: Runner | None = None,
 ) -> FsTimeOutputs:
     """
+    fs_time
+    
     A frontend for the unix /usr/bin/time program to track resource usage by a
     process.
     
@@ -202,8 +184,6 @@ def fs_time(
     Returns:
         NamedTuple of outputs (described in `FsTimeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FS_TIME_METADATA)
     params = fs_time_params(
         output_file=output_file,
         key=key,
@@ -211,13 +191,13 @@ def fs_time(
         command=command,
         args=args,
     )
-    return fs_time_execute(params, execution)
+    return fs_time_execute(params, runner)
 
 
 __all__ = [
     "FS_TIME_METADATA",
     "FsTimeOutputs",
-    "FsTimeParameters",
     "fs_time",
+    "fs_time_execute",
     "fs_time_params",
 ]