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

niwrap_freesurfer/freesurfer/unpacksdcmdir.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 UNPACKSDCMDIR_METADATA = Metadata(
-    id="6006998b82cae3564b1f7b4f079673c72b20cd58.boutiques",
+    id="f2d2973173264580381ae83a48a3fe0e5aa0e05d.boutiques",
     name="unpacksdcmdir",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ UNPACKSDCMDIR_METADATA = Metadata(
 
 
 UnpacksdcmdirParameters = typing.TypedDict('UnpacksdcmdirParameters', {
-    "__STYXTYPE__": typing.Literal["unpacksdcmdir"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/unpacksdcmdir"]],
+    "input_directory": str,
+    "output_directory": str,
+})
+UnpacksdcmdirParametersTagged = typing.TypedDict('UnpacksdcmdirParametersTagged', {
+    "@type": typing.Literal["freesurfer/unpacksdcmdir"],
     "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 {
-        "unpacksdcmdir": unpacksdcmdir_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 {
-        "unpacksdcmdir": unpacksdcmdir_outputs,
-    }.get(t)
 
 
 class UnpacksdcmdirOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `unpacksdcmdir(...)`.
+    Output object returned when calling `UnpacksdcmdirParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class UnpacksdcmdirOutputs(typing.NamedTuple):
 def unpacksdcmdir_params(
     input_directory: str,
     output_directory: str,
-) -> UnpacksdcmdirParameters:
+) -> UnpacksdcmdirParametersTagged:
     """
     Build parameters.
     
@@ -77,7 +50,7 @@ def unpacksdcmdir_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "unpacksdcmdir",
+        "@type": "freesurfer/unpacksdcmdir",
         "input_directory": input_directory,
         "output_directory": output_directory,
     }
@@ -99,8 +72,8 @@ def unpacksdcmdir_cargs(
     """
     cargs = []
     cargs.append("unpacksdcmdir")
-    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
 
 
@@ -119,16 +92,18 @@ def unpacksdcmdir_outputs(
     """
     ret = UnpacksdcmdirOutputs(
         root=execution.output_file("."),
-        unpacked_data=execution.output_file(params.get("output_directory") + "/unpacked_data"),
+        unpacked_data=execution.output_file(params.get("output_directory", None) + "/unpacked_data"),
     )
     return ret
 
 
 def unpacksdcmdir_execute(
     params: UnpacksdcmdirParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> UnpacksdcmdirOutputs:
     """
+    unpacksdcmdir
+    
     A tool for unpacking SD card directories, typically used in neuroimaging
     workflows. It seems to have a dependency on Tcl, as indicated by the error
     messages.
@@ -139,10 +114,12 @@ def unpacksdcmdir_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `UnpacksdcmdirOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UNPACKSDCMDIR_METADATA)
     params = execution.params(params)
     cargs = unpacksdcmdir_cargs(params, execution)
     ret = unpacksdcmdir_outputs(params, execution)
@@ -156,6 +133,8 @@ def unpacksdcmdir(
     runner: Runner | None = None,
 ) -> UnpacksdcmdirOutputs:
     """
+    unpacksdcmdir
+    
     A tool for unpacking SD card directories, typically used in neuroimaging
     workflows. It seems to have a dependency on Tcl, as indicated by the error
     messages.
@@ -172,19 +151,17 @@ def unpacksdcmdir(
     Returns:
         NamedTuple of outputs (described in `UnpacksdcmdirOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(UNPACKSDCMDIR_METADATA)
     params = unpacksdcmdir_params(
         input_directory=input_directory,
         output_directory=output_directory,
     )
-    return unpacksdcmdir_execute(params, execution)
+    return unpacksdcmdir_execute(params, runner)
 
 
 __all__ = [
     "UNPACKSDCMDIR_METADATA",
     "UnpacksdcmdirOutputs",
-    "UnpacksdcmdirParameters",
     "unpacksdcmdir",
+    "unpacksdcmdir_execute",
     "unpacksdcmdir_params",
 ]

niwrap_freesurfer/freesurfer/update_needed.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 UPDATE_NEEDED_METADATA = Metadata(
-    id="bbeff96a804ee5f7f839128e9a8f2889e0e27e42.boutiques",
+    id="db8c9232b3360e24abd621ee1ace6d7a22a54132.boutiques",
     name="UpdateNeeded",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,22 @@ UPDATE_NEEDED_METADATA = Metadata(
 
 
 UpdateNeededParameters = typing.TypedDict('UpdateNeededParameters', {
-    "__STYXTYPE__": typing.Literal["UpdateNeeded"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/UpdateNeeded"]],
+    "target_file": InputPathType,
+    "source_file": InputPathType,
+    "additional_source_files": typing.NotRequired[list[InputPathType] | None],
+})
+UpdateNeededParametersTagged = typing.TypedDict('UpdateNeededParametersTagged', {
+    "@type": typing.Literal["freesurfer/UpdateNeeded"],
     "target_file": InputPathType,
     "source_file": InputPathType,
     "additional_source_files": typing.NotRequired[list[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 {
-        "UpdateNeeded": update_needed_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 UpdateNeededOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `update_needed(...)`.
+    Output object returned when calling `UpdateNeededParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +39,7 @@ def update_needed_params(
     target_file: InputPathType,
     source_file: InputPathType,
     additional_source_files: list[InputPathType] | None = None,
-) -> UpdateNeededParameters:
+) -> UpdateNeededParametersTagged:
     """
     Build parameters.
     
@@ -77,7 +52,7 @@ def update_needed_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "UpdateNeeded",
+        "@type": "freesurfer/UpdateNeeded",
         "target_file": target_file,
         "source_file": source_file,
     }
@@ -101,10 +76,10 @@ def update_needed_cargs(
     """
     cargs = []
     cargs.append("UpdateNeeded")
-    cargs.append(execution.input_file(params.get("target_file")))
-    cargs.append(execution.input_file(params.get("source_file")))
-    if params.get("additional_source_files") is not None:
-        cargs.extend([execution.input_file(f) for f in params.get("additional_source_files")])
+    cargs.append(execution.input_file(params.get("target_file", None)))
+    cargs.append(execution.input_file(params.get("source_file", None)))
+    if params.get("additional_source_files", None) is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("additional_source_files", None)])
     return cargs
 
 
@@ -129,10 +104,13 @@ def update_needed_outputs(
 
 def update_needed_execute(
     params: UpdateNeededParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> UpdateNeededOutputs:
     """
-    A command-line tool to update a target file based on one or more source files.
+    UpdateNeeded
+    
+    A command-line tool to update a target file based on one or more source
+    files.
     
     Author: FreeSurfer Developers
     
@@ -140,10 +118,12 @@ def update_needed_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `UpdateNeededOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UPDATE_NEEDED_METADATA)
     params = execution.params(params)
     cargs = update_needed_cargs(params, execution)
     ret = update_needed_outputs(params, execution)
@@ -158,7 +138,10 @@ def update_needed(
     runner: Runner | None = None,
 ) -> UpdateNeededOutputs:
     """
-    A command-line tool to update a target file based on one or more source files.
+    UpdateNeeded
+    
+    A command-line tool to update a target file based on one or more source
+    files.
     
     Author: FreeSurfer Developers
     
@@ -173,20 +156,18 @@ def update_needed(
     Returns:
         NamedTuple of outputs (described in `UpdateNeededOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(UPDATE_NEEDED_METADATA)
     params = update_needed_params(
         target_file=target_file,
         source_file=source_file,
         additional_source_files=additional_source_files,
     )
-    return update_needed_execute(params, execution)
+    return update_needed_execute(params, runner)
 
 
 __all__ = [
     "UPDATE_NEEDED_METADATA",
     "UpdateNeededOutputs",
-    "UpdateNeededParameters",
     "update_needed",
+    "update_needed_execute",
     "update_needed_params",
 ]

niwrap_freesurfer/freesurfer/v_3dvolreg_afni.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DVOLREG_AFNI_METADATA = Metadata(
-    id="a987f8d62b507b62d7469f463040360283d6fc83.boutiques",
+    id="f05024124f93d18d98ace7dc462475521ea11012.boutiques",
     name="3dvolreg.afni",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ V_3DVOLREG_AFNI_METADATA = Metadata(
 
 
 V3dvolregAfniParameters = typing.TypedDict('V3dvolregAfniParameters', {
-    "__STYXTYPE__": typing.Literal["3dvolreg.afni"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/3dvolreg.afni"]],
+    "input_file": InputPathType,
+    "output_file": str,
+    "options": typing.NotRequired[str | None],
+})
+V3dvolregAfniParametersTagged = typing.TypedDict('V3dvolregAfniParametersTagged', {
+    "@type": typing.Literal["freesurfer/3dvolreg.afni"],
     "input_file": InputPathType,
     "output_file": str,
     "options": 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 {
-        "3dvolreg.afni": v_3dvolreg_afni_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 {
-        "3dvolreg.afni": v_3dvolreg_afni_outputs,
-    }.get(t)
 
 
 class V3dvolregAfniOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dvolreg_afni(...)`.
+    Output object returned when calling `V3dvolregAfniParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def v_3dvolreg_afni_params(
     input_file: InputPathType,
     output_file: str,
     options: str | None = None,
-) -> V3dvolregAfniParameters:
+) -> V3dvolregAfniParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def v_3dvolreg_afni_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dvolreg.afni",
+        "@type": "freesurfer/3dvolreg.afni",
         "input_file": input_file,
         "output_file": output_file,
     }
@@ -103,10 +77,10 @@ def v_3dvolreg_afni_cargs(
     """
     cargs = []
     cargs.append("3dvolreg.afni")
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(params.get("output_file"))
-    if params.get("options") is not None:
-        cargs.append(params.get("options"))
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    cargs.append(params.get("output_file", None))
+    if params.get("options", None) is not None:
+        cargs.append(params.get("options", None))
     return cargs
 
 
@@ -125,16 +99,18 @@ def v_3dvolreg_afni_outputs(
     """
     ret = V3dvolregAfniOutputs(
         root=execution.output_file("."),
-        registered_output=execution.output_file(params.get("output_file") + ".nii"),
+        registered_output=execution.output_file(params.get("output_file", None) + ".nii"),
     )
     return ret
 
 
 def v_3dvolreg_afni_execute(
     params: V3dvolregAfniParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dvolregAfniOutputs:
     """
+    3dvolreg.afni
+    
     AFNI program for volume registration.
     
     Author: FreeSurfer Developers
@@ -143,10 +119,12 @@ def v_3dvolreg_afni_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dvolregAfniOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DVOLREG_AFNI_METADATA)
     params = execution.params(params)
     cargs = v_3dvolreg_afni_cargs(params, execution)
     ret = v_3dvolreg_afni_outputs(params, execution)
@@ -161,6 +139,8 @@ def v_3dvolreg_afni(
     runner: Runner | None = None,
 ) -> V3dvolregAfniOutputs:
     """
+    3dvolreg.afni
+    
     AFNI program for volume registration.
     
     Author: FreeSurfer Developers
@@ -175,20 +155,18 @@ def v_3dvolreg_afni(
     Returns:
         NamedTuple of outputs (described in `V3dvolregAfniOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DVOLREG_AFNI_METADATA)
     params = v_3dvolreg_afni_params(
         input_file=input_file,
         output_file=output_file,
         options=options,
     )
-    return v_3dvolreg_afni_execute(params, execution)
+    return v_3dvolreg_afni_execute(params, runner)
 
 
 __all__ = [
     "V3dvolregAfniOutputs",
-    "V3dvolregAfniParameters",
     "V_3DVOLREG_AFNI_METADATA",
     "v_3dvolreg_afni",
+    "v_3dvolreg_afni_execute",
     "v_3dvolreg_afni_params",
 ]

niwrap_freesurfer/freesurfer/v_4dfptoanalyze.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_4DFPTOANALYZE_METADATA = Metadata(
-    id="080e23daf4f3437b96205f8c01ae61740cf84a3b.boutiques",
+    id="01dad5264225d1f3d1b436c8973cc2f791b5cdb2.boutiques",
     name="4dfptoanalyze",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ V_4DFPTOANALYZE_METADATA = Metadata(
 
 
 V4dfptoanalyzeParameters = typing.TypedDict('V4dfptoanalyzeParameters', {
-    "__STYXTYPE__": typing.Literal["4dfptoanalyze"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/4dfptoanalyze"]],
+    "input_file": InputPathType,
+    "scale_factor": typing.NotRequired[float | None],
+    "output_8bit": bool,
+    "spm99": bool,
+    "endianness": typing.NotRequired[str | None],
+})
+V4dfptoanalyzeParametersTagged = typing.TypedDict('V4dfptoanalyzeParametersTagged', {
+    "@type": typing.Literal["freesurfer/4dfptoanalyze"],
     "input_file": InputPathType,
     "scale_factor": typing.NotRequired[float | None],
     "output_8bit": bool,
     "spm99": bool,
     "endianness": 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 {
-        "4dfptoanalyze": v_4dfptoanalyze_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 {
-        "4dfptoanalyze": v_4dfptoanalyze_outputs,
-    }.get(t)
 
 
 class V4dfptoanalyzeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_4dfptoanalyze(...)`.
+    Output object returned when calling `V4dfptoanalyzeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +49,7 @@ def v_4dfptoanalyze_params(
     output_8bit: bool = False,
     spm99: bool = False,
     endianness: str | None = None,
-) -> V4dfptoanalyzeParameters:
+) -> V4dfptoanalyzeParametersTagged:
     """
     Build parameters.
     
@@ -87,7 +63,7 @@ def v_4dfptoanalyze_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "4dfptoanalyze",
+        "@type": "freesurfer/4dfptoanalyze",
         "input_file": input_file,
         "output_8bit": output_8bit,
         "spm99": spm99,
@@ -114,20 +90,20 @@ def v_4dfptoanalyze_cargs(
     """
     cargs = []
     cargs.append("4dfptoanalyze")
-    cargs.append(execution.input_file(params.get("input_file")))
-    if params.get("scale_factor") is not None:
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    if params.get("scale_factor", None) is not None:
         cargs.extend([
             "-c",
-            str(params.get("scale_factor"))
+            str(params.get("scale_factor", None))
         ])
-    if params.get("output_8bit"):
+    if params.get("output_8bit", False):
         cargs.append("-8")
-    if params.get("spm99"):
+    if params.get("spm99", False):
         cargs.append("-SPM99")
-    if params.get("endianness") is not None:
+    if params.get("endianness", None) is not None:
         cargs.extend([
             "-@",
-            params.get("endianness")
+            params.get("endianness", None)
         ])
     return cargs
 
@@ -147,17 +123,19 @@ def v_4dfptoanalyze_outputs(
     """
     ret = V4dfptoanalyzeOutputs(
         root=execution.output_file("."),
-        analyze_hdr=execution.output_file(pathlib.Path(params.get("input_file")).name + "_analyze.hdr"),
-        analyze_img=execution.output_file(pathlib.Path(params.get("input_file")).name + "_analyze.img"),
+        analyze_hdr=execution.output_file(pathlib.Path(params.get("input_file", None)).name + "_analyze.hdr"),
+        analyze_img=execution.output_file(pathlib.Path(params.get("input_file", None)).name + "_analyze.img"),
     )
     return ret
 
 
 def v_4dfptoanalyze_execute(
     params: V4dfptoanalyzeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V4dfptoanalyzeOutputs:
     """
+    4dfptoanalyze
+    
     Converts 4dfp formatted files to Analyze format.
     
     Author: FreeSurfer Developers
@@ -166,10 +144,12 @@ def v_4dfptoanalyze_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V4dfptoanalyzeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_4DFPTOANALYZE_METADATA)
     params = execution.params(params)
     cargs = v_4dfptoanalyze_cargs(params, execution)
     ret = v_4dfptoanalyze_outputs(params, execution)
@@ -186,6 +166,8 @@ def v_4dfptoanalyze(
     runner: Runner | None = None,
 ) -> V4dfptoanalyzeOutputs:
     """
+    4dfptoanalyze
+    
     Converts 4dfp formatted files to Analyze format.
     
     Author: FreeSurfer Developers
@@ -202,8 +184,6 @@ def v_4dfptoanalyze(
     Returns:
         NamedTuple of outputs (described in `V4dfptoanalyzeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_4DFPTOANALYZE_METADATA)
     params = v_4dfptoanalyze_params(
         input_file=input_file,
         scale_factor=scale_factor,
@@ -211,13 +191,13 @@ def v_4dfptoanalyze(
         spm99=spm99,
         endianness=endianness,
     )
-    return v_4dfptoanalyze_execute(params, execution)
+    return v_4dfptoanalyze_execute(params, runner)
 
 
 __all__ = [
     "V4dfptoanalyzeOutputs",
-    "V4dfptoanalyzeParameters",
     "V_4DFPTOANALYZE_METADATA",
     "v_4dfptoanalyze",
+    "v_4dfptoanalyze_execute",
     "v_4dfptoanalyze_params",
 ]