niwrap-afni 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/v_3d_afnito_niml.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_AFNITO_NIML_METADATA = Metadata(
-    id="95aceaf6a84ca94fe976a820712d66c290312cfe.boutiques",
+    id="229e46c8f508be2928f7052893ed55235b23d00a.boutiques",
     name="3dAFNItoNIML",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,24 @@ V_3D_AFNITO_NIML_METADATA = Metadata(
 
 
 V3dAfnitoNimlParameters = typing.TypedDict('V3dAfnitoNimlParameters', {
-    "__STYXTYPE__": typing.Literal["3dAFNItoNIML"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dAFNItoNIML"]],
+    "dset": InputPathType,
+    "data": bool,
+    "ascii": bool,
+    "tcp": typing.NotRequired[str | None],
+})
+V3dAfnitoNimlParametersTagged = typing.TypedDict('V3dAfnitoNimlParametersTagged', {
+    "@type": typing.Literal["afni/3dAFNItoNIML"],
     "dset": InputPathType,
     "data": bool,
     "ascii": bool,
     "tcp": 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 {
-        "3dAFNItoNIML": v_3d_afnito_niml_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 V3dAfnitoNimlOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_afnito_niml(...)`.
+    Output object returned when calling `V3dAfnitoNimlParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def v_3d_afnito_niml_params(
     data: bool = False,
     ascii_: bool = False,
     tcp: str | None = None,
-) -> V3dAfnitoNimlParameters:
+) -> V3dAfnitoNimlParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +56,7 @@ def v_3d_afnito_niml_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dAFNItoNIML",
+        "@type": "afni/3dAFNItoNIML",
         "dset": dset,
         "data": data,
         "ascii": ascii_,
@@ -105,15 +81,15 @@ def v_3d_afnito_niml_cargs(
     """
     cargs = []
     cargs.append("3dAFNItoNIML")
-    cargs.append(execution.input_file(params.get("dset")))
-    if params.get("data"):
+    cargs.append(execution.input_file(params.get("dset", None)))
+    if params.get("data", False):
         cargs.append("-data")
-    if params.get("ascii"):
+    if params.get("ascii", False):
         cargs.append("-ascii")
-    if params.get("tcp") is not None:
+    if params.get("tcp", None) is not None:
         cargs.extend([
             "-tcp",
-            params.get("tcp")
+            params.get("tcp", None)
         ])
     return cargs
 
@@ -139,9 +115,11 @@ def v_3d_afnito_niml_outputs(
 
 def v_3d_afnito_niml_execute(
     params: V3dAfnitoNimlParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dAfnitoNimlOutputs:
     """
+    3dAFNItoNIML
+    
     Dumps AFNI dataset header information to stdout in NIML format. Mostly for
     debugging and testing purposes!.
     
@@ -151,10 +129,12 @@ def v_3d_afnito_niml_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dAfnitoNimlOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_AFNITO_NIML_METADATA)
     params = execution.params(params)
     cargs = v_3d_afnito_niml_cargs(params, execution)
     ret = v_3d_afnito_niml_outputs(params, execution)
@@ -170,6 +150,8 @@ def v_3d_afnito_niml(
     runner: Runner | None = None,
 ) -> V3dAfnitoNimlOutputs:
     """
+    3dAFNItoNIML
+    
     Dumps AFNI dataset header information to stdout in NIML format. Mostly for
     debugging and testing purposes!.
     
@@ -187,21 +169,19 @@ def v_3d_afnito_niml(
     Returns:
         NamedTuple of outputs (described in `V3dAfnitoNimlOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_AFNITO_NIML_METADATA)
     params = v_3d_afnito_niml_params(
         dset=dset,
         data=data,
         ascii_=ascii_,
         tcp=tcp,
     )
-    return v_3d_afnito_niml_execute(params, execution)
+    return v_3d_afnito_niml_execute(params, runner)
 
 
 __all__ = [
     "V3dAfnitoNimlOutputs",
-    "V3dAfnitoNimlParameters",
     "V_3D_AFNITO_NIML_METADATA",
     "v_3d_afnito_niml",
+    "v_3d_afnito_niml_execute",
     "v_3d_afnito_niml_params",
 ]

niwrap_afni/afni/v_3d_afnito_raw.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_AFNITO_RAW_METADATA = Metadata(
-    id="fbf9965fdc0f2095a41d56980e48457852926f51.boutiques",
+    id="60eca0941c9d95cfbd0d412e769b819823aa38bf.boutiques",
     name="3dAFNItoRaw",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,47 +14,22 @@ V_3D_AFNITO_RAW_METADATA = Metadata(
 
 
 V3dAfnitoRawParameters = typing.TypedDict('V3dAfnitoRawParameters', {
-    "__STYXTYPE__": typing.Literal["3dAFNItoRaw"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dAFNItoRaw"]],
+    "output_file": typing.NotRequired[str | None],
+    "force_float": bool,
+    "dataset": str,
+})
+V3dAfnitoRawParametersTagged = typing.TypedDict('V3dAfnitoRawParametersTagged', {
+    "@type": typing.Literal["afni/3dAFNItoRaw"],
     "output_file": typing.NotRequired[str | None],
     "force_float": bool,
     "dataset": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dAFNItoRaw": v_3d_afnito_raw_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 V3dAfnitoRawOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_afnito_raw(...)`.
+    Output object returned when calling `V3dAfnitoRawParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +39,7 @@ def v_3d_afnito_raw_params(
     dataset: str,
     output_file: str | None = None,
     force_float: bool = False,
-) -> V3dAfnitoRawParameters:
+) -> V3dAfnitoRawParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +54,7 @@ def v_3d_afnito_raw_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dAFNItoRaw",
+        "@type": "afni/3dAFNItoRaw",
         "force_float": force_float,
         "dataset": dataset,
     }
@@ -103,14 +78,14 @@ def v_3d_afnito_raw_cargs(
     """
     cargs = []
     cargs.append("3dAFNItoRaw")
-    if params.get("output_file") is not None:
+    if params.get("output_file", None) is not None:
         cargs.extend([
             "-output",
-            params.get("output_file")
+            params.get("output_file", None)
         ])
-    if params.get("force_float"):
+    if params.get("force_float", False):
         cargs.append("-datum float")
-    cargs.append(params.get("dataset"))
+    cargs.append(params.get("dataset", None))
     return cargs
 
 
@@ -135,9 +110,11 @@ def v_3d_afnito_raw_outputs(
 
 def v_3d_afnito_raw_execute(
     params: V3dAfnitoRawParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dAfnitoRawOutputs:
     """
+    3dAFNItoRaw
+    
     Convert an AFNI brik file with multiple sub-briks to a raw file with each
     sub-brik voxel concatenated voxel-wise.
     
@@ -147,10 +124,12 @@ def v_3d_afnito_raw_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dAfnitoRawOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_AFNITO_RAW_METADATA)
     params = execution.params(params)
     cargs = v_3d_afnito_raw_cargs(params, execution)
     ret = v_3d_afnito_raw_outputs(params, execution)
@@ -165,6 +144,8 @@ def v_3d_afnito_raw(
     runner: Runner | None = None,
 ) -> V3dAfnitoRawOutputs:
     """
+    3dAFNItoRaw
+    
     Convert an AFNI brik file with multiple sub-briks to a raw file with each
     sub-brik voxel concatenated voxel-wise.
     
@@ -183,20 +164,18 @@ def v_3d_afnito_raw(
     Returns:
         NamedTuple of outputs (described in `V3dAfnitoRawOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_AFNITO_RAW_METADATA)
     params = v_3d_afnito_raw_params(
         output_file=output_file,
         force_float=force_float,
         dataset=dataset,
     )
-    return v_3d_afnito_raw_execute(params, execution)
+    return v_3d_afnito_raw_execute(params, runner)
 
 
 __all__ = [
     "V3dAfnitoRawOutputs",
-    "V3dAfnitoRawParameters",
     "V_3D_AFNITO_RAW_METADATA",
     "v_3d_afnito_raw",
+    "v_3d_afnito_raw_execute",
     "v_3d_afnito_raw_params",
 ]

niwrap_afni/afni/v_3d_allineate.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_ALLINEATE_METADATA = Metadata(
-    id="05acda1bcc694397c89e84c0f214f9da9cbb22ef.boutiques",
+    id="9ce154d883bf2de1c0766bcc756cdff4dc6a028d.boutiques",
     name="3dAllineate",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ V_3D_ALLINEATE_METADATA = Metadata(
 
 
 V3dAllineateParameters = typing.TypedDict('V3dAllineateParameters', {
-    "__STYXTYPE__": typing.Literal["3dAllineate"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dAllineate"]],
+    "source": InputPathType,
+    "base": typing.NotRequired[InputPathType | None],
+    "prefix": str,
+    "param_save": typing.NotRequired[str | None],
+    "param_apply": typing.NotRequired[str | None],
+    "matrix_save": typing.NotRequired[str | None],
+    "matrix_apply": typing.NotRequired[str | None],
+    "cost": typing.NotRequired[str | None],
+    "interp": typing.NotRequired[str | None],
+    "final": typing.NotRequired[str | None],
+    "nmatch": typing.NotRequired[float | None],
+    "nopad": bool,
+    "verbose": bool,
+    "quiet": bool,
+})
+V3dAllineateParametersTagged = typing.TypedDict('V3dAllineateParametersTagged', {
+    "@type": typing.Literal["afni/3dAllineate"],
     "source": InputPathType,
     "base": typing.NotRequired[InputPathType | None],
     "prefix": str,
@@ -30,43 +47,11 @@ V3dAllineateParameters = typing.TypedDict('V3dAllineateParameters', {
     "verbose": bool,
     "quiet": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dAllineate": v_3d_allineate_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 {
-        "3dAllineate": v_3d_allineate_outputs,
-    }.get(t)
 
 
 class V3dAllineateOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_allineate(...)`.
+    Output object returned when calling `V3dAllineateParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -95,7 +80,7 @@ def v_3d_allineate_params(
     nopad: bool = False,
     verbose: bool = False,
     quiet: bool = False,
-) -> V3dAllineateParameters:
+) -> V3dAllineateParametersTagged:
     """
     Build parameters.
     
@@ -122,7 +107,7 @@ def v_3d_allineate_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dAllineate",
+        "@type": "afni/3dAllineate",
         "source": source,
         "prefix": prefix,
         "nopad": nopad,
@@ -165,61 +150,61 @@ def v_3d_allineate_cargs(
     """
     cargs = []
     cargs.append("3dAllineate")
-    cargs.append(execution.input_file(params.get("source")))
-    if params.get("base") is not None:
+    cargs.append(execution.input_file(params.get("source", None)))
+    if params.get("base", None) is not None:
         cargs.extend([
             "-base",
-            execution.input_file(params.get("base"))
+            execution.input_file(params.get("base", None))
         ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("param_save") is not None:
+    if params.get("param_save", None) is not None:
         cargs.extend([
             "-1Dparam_save",
-            params.get("param_save")
+            params.get("param_save", None)
         ])
-    if params.get("param_apply") is not None:
+    if params.get("param_apply", None) is not None:
         cargs.extend([
             "-1Dparam_apply",
-            params.get("param_apply")
+            params.get("param_apply", None)
         ])
-    if params.get("matrix_save") is not None:
+    if params.get("matrix_save", None) is not None:
         cargs.extend([
             "-1Dmatrix_save",
-            params.get("matrix_save")
+            params.get("matrix_save", None)
         ])
-    if params.get("matrix_apply") is not None:
+    if params.get("matrix_apply", None) is not None:
         cargs.extend([
             "-1Dmatrix_apply",
-            params.get("matrix_apply")
+            params.get("matrix_apply", None)
         ])
-    if params.get("cost") is not None:
+    if params.get("cost", None) is not None:
         cargs.extend([
             "-cost",
-            params.get("cost")
+            params.get("cost", None)
         ])
-    if params.get("interp") is not None:
+    if params.get("interp", None) is not None:
         cargs.extend([
             "-interp",
-            params.get("interp")
+            params.get("interp", None)
         ])
-    if params.get("final") is not None:
+    if params.get("final", None) is not None:
         cargs.extend([
             "-final",
-            params.get("final")
+            params.get("final", None)
         ])
-    if params.get("nmatch") is not None:
+    if params.get("nmatch", None) is not None:
         cargs.extend([
             "-nmatch",
-            str(params.get("nmatch"))
+            str(params.get("nmatch", None))
         ])
-    if params.get("nopad"):
+    if params.get("nopad", False):
         cargs.append("-nopad")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
     return cargs
 
@@ -239,21 +224,23 @@ def v_3d_allineate_outputs(
     """
     ret = V3dAllineateOutputs(
         root=execution.output_file("."),
-        out_brik=execution.output_file(params.get("prefix") + "+orig.BRIK"),
-        out_head=execution.output_file(params.get("prefix") + "+orig.HEAD"),
-        out_param_save=execution.output_file(params.get("param_save")) if (params.get("param_save") is not None) else None,
-        out_matrix_save=execution.output_file(params.get("matrix_save")) if (params.get("matrix_save") is not None) else None,
+        out_brik=execution.output_file(params.get("prefix", None) + "+orig.BRIK"),
+        out_head=execution.output_file(params.get("prefix", None) + "+orig.HEAD"),
+        out_param_save=execution.output_file(params.get("param_save", None)) if (params.get("param_save") is not None) else None,
+        out_matrix_save=execution.output_file(params.get("matrix_save", None)) if (params.get("matrix_save") is not None) else None,
     )
     return ret
 
 
 def v_3d_allineate_execute(
     params: V3dAllineateParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dAllineateOutputs:
     """
-    Program to align one dataset (the 'source') to a 'base' dataset using an affine
-    (matrix) transformation of space.
+    3dAllineate
+    
+    Program to align one dataset (the 'source') to a 'base' dataset using an
+    affine (matrix) transformation of space.
     
     Author: AFNI Developers
     
@@ -261,10 +248,12 @@ def v_3d_allineate_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dAllineateOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ALLINEATE_METADATA)
     params = execution.params(params)
     cargs = v_3d_allineate_cargs(params, execution)
     ret = v_3d_allineate_outputs(params, execution)
@@ -290,8 +279,10 @@ def v_3d_allineate(
     runner: Runner | None = None,
 ) -> V3dAllineateOutputs:
     """
-    Program to align one dataset (the 'source') to a 'base' dataset using an affine
-    (matrix) transformation of space.
+    3dAllineate
+    
+    Program to align one dataset (the 'source') to a 'base' dataset using an
+    affine (matrix) transformation of space.
     
     Author: AFNI Developers
     
@@ -320,8 +311,6 @@ def v_3d_allineate(
     Returns:
         NamedTuple of outputs (described in `V3dAllineateOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_ALLINEATE_METADATA)
     params = v_3d_allineate_params(
         source=source,
         base=base,
@@ -338,13 +327,13 @@ def v_3d_allineate(
         verbose=verbose,
         quiet=quiet,
     )
-    return v_3d_allineate_execute(params, execution)
+    return v_3d_allineate_execute(params, runner)
 
 
 __all__ = [
     "V3dAllineateOutputs",
-    "V3dAllineateParameters",
     "V_3D_ALLINEATE_METADATA",
     "v_3d_allineate",
+    "v_3d_allineate_execute",
     "v_3d_allineate_params",
 ]