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

niwrap_afni/afni/v_1d_dw_grad_o_mat__.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_1D_DW_GRAD_O_MAT___METADATA = Metadata(
-    id="c0c48de32d7854081b446062bfdcf407dd49efef.boutiques",
+    id="089c358fdaa8a6343f360bc42573e573155fe1b0.boutiques",
     name="1dDW_Grad_o_Mat++",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,31 @@ V_1D_DW_GRAD_O_MAT___METADATA = Metadata(
 
 
 V1dDwGradOMatParameters = typing.TypedDict('V1dDwGradOMatParameters', {
-    "__STYXTYPE__": typing.Literal["1dDW_Grad_o_Mat++"],
+    "@type": typing.NotRequired[typing.Literal["afni/1dDW_Grad_o_Mat++"]],
+    "in_row_vec": InputPathType,
+    "in_col_vec": InputPathType,
+    "in_col_matA": InputPathType,
+    "in_col_matT": InputPathType,
+    "flip_x": bool,
+    "flip_y": bool,
+    "flip_z": bool,
+    "no_flip": bool,
+    "out_row_vec": str,
+    "out_col_vec": str,
+    "out_col_matA": str,
+    "out_col_matT": str,
+    "in_bvals": typing.NotRequired[InputPathType | None],
+    "out_col_bval": bool,
+    "out_row_bval_sep": typing.NotRequired[str | None],
+    "out_col_bval_sep": typing.NotRequired[str | None],
+    "unit_mag_out": bool,
+    "check_abs_min": typing.NotRequired[float | None],
+    "bref_mean_top": bool,
+    "put_zeros_top": bool,
+    "bmax_ref": typing.NotRequired[float | None],
+})
+V1dDwGradOMatParametersTagged = typing.TypedDict('V1dDwGradOMatParametersTagged', {
+    "@type": typing.Literal["afni/1dDW_Grad_o_Mat++"],
     "in_row_vec": InputPathType,
     "in_col_vec": InputPathType,
     "in_col_matA": InputPathType,
@@ -37,43 +61,11 @@ V1dDwGradOMatParameters = typing.TypedDict('V1dDwGradOMatParameters', {
     "put_zeros_top": bool,
     "bmax_ref": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "1dDW_Grad_o_Mat++": v_1d_dw_grad_o_mat___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 {
-        "1dDW_Grad_o_Mat++": v_1d_dw_grad_o_mat___outputs,
-    }.get(t)
 
 
 class V1dDwGradOMatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_1d_dw_grad_o_mat__(...)`.
+    Output object returned when calling `V1dDwGradOMatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -107,7 +99,7 @@ def v_1d_dw_grad_o_mat___params(
     bref_mean_top: bool = False,
     put_zeros_top: bool = False,
     bmax_ref: float | None = None,
-) -> V1dDwGradOMatParameters:
+) -> V1dDwGradOMatParametersTagged:
     """
     Build parameters.
     
@@ -151,7 +143,7 @@ def v_1d_dw_grad_o_mat___params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "1dDW_Grad_o_Mat++",
+        "@type": "afni/1dDW_Grad_o_Mat++",
         "in_row_vec": in_row_vec,
         "in_col_vec": in_col_vec,
         "in_col_matA": in_col_mat_a,
@@ -199,76 +191,76 @@ def v_1d_dw_grad_o_mat___cargs(
     cargs.append("1dDW_Grad_o_Mat++")
     cargs.extend([
         "-in_row_vec",
-        execution.input_file(params.get("in_row_vec"))
+        execution.input_file(params.get("in_row_vec", None))
     ])
     cargs.extend([
         "-in_col_vec",
-        execution.input_file(params.get("in_col_vec"))
+        execution.input_file(params.get("in_col_vec", None))
     ])
     cargs.extend([
         "-in_col_matA",
-        execution.input_file(params.get("in_col_matA"))
+        execution.input_file(params.get("in_col_matA", None))
     ])
     cargs.extend([
         "-in_col_matT",
-        execution.input_file(params.get("in_col_matT"))
+        execution.input_file(params.get("in_col_matT", None))
     ])
-    if params.get("flip_x"):
+    if params.get("flip_x", False):
         cargs.append("-flip_x")
-    if params.get("flip_y"):
+    if params.get("flip_y", False):
         cargs.append("-flip_y")
-    if params.get("flip_z"):
+    if params.get("flip_z", False):
         cargs.append("-flip_z")
-    if params.get("no_flip"):
+    if params.get("no_flip", False):
         cargs.append("-no_flip")
     cargs.extend([
         "-out_row_vec",
-        params.get("out_row_vec")
+        params.get("out_row_vec", None)
     ])
     cargs.extend([
         "-out_col_vec",
-        params.get("out_col_vec")
+        params.get("out_col_vec", None)
     ])
     cargs.extend([
         "-out_col_matA",
-        params.get("out_col_matA")
+        params.get("out_col_matA", None)
     ])
     cargs.extend([
         "-out_col_matT",
-        params.get("out_col_matT")
+        params.get("out_col_matT", None)
     ])
-    if params.get("in_bvals") is not None:
+    if params.get("in_bvals", None) is not None:
         cargs.extend([
             "-in_bvals",
-            execution.input_file(params.get("in_bvals"))
+            execution.input_file(params.get("in_bvals", None))
         ])
-    if params.get("out_col_bval"):
+    if params.get("out_col_bval", False):
         cargs.append("-out_col_bval")
-    if params.get("out_row_bval_sep") is not None:
+    if params.get("out_row_bval_sep", None) is not None:
         cargs.extend([
             "-out_row_bval_sep",
-            params.get("out_row_bval_sep")
+            params.get("out_row_bval_sep", None)
         ])
-    if params.get("out_col_bval_sep") is not None:
+    if params.get("out_col_bval_sep", None) is not None:
         cargs.extend([
             "-out_col_bval_sep",
-            params.get("out_col_bval_sep")
+            params.get("out_col_bval_sep", None)
         ])
-    if params.get("unit_mag_out"):
+    if params.get("unit_mag_out", False):
         cargs.append("-unit_mag_out")
-    if params.get("check_abs_min") is not None:
+    if params.get("check_abs_min", None) is not None:
         cargs.extend([
             "-check_abs_min",
-            str(params.get("check_abs_min"))
+            str(params.get("check_abs_min", None))
         ])
-    if params.get("bref_mean_top"):
+    if params.get("bref_mean_top", False):
         cargs.append("-bref_mean_top")
-    if params.get("put_zeros_top"):
+    if params.get("put_zeros_top", False):
         cargs.append("-put_zeros_top")
-    if params.get("bmax_ref") is not None:
+    if params.get("bmax_ref", None) is not None:
         cargs.extend([
             "-bmax_ref",
-            str(params.get("bmax_ref"))
+            str(params.get("bmax_ref", None))
         ])
     return cargs
 
@@ -288,20 +280,22 @@ def v_1d_dw_grad_o_mat___outputs(
     """
     ret = V1dDwGradOMatOutputs(
         root=execution.output_file("."),
-        outfile=execution.output_file(params.get("out_row_vec")),
-        out_row_bval_file=execution.output_file(params.get("out_row_bval_sep")) if (params.get("out_row_bval_sep") is not None) else None,
-        out_col_bval_file=execution.output_file(params.get("out_row_bval_sep")) if (params.get("out_row_bval_sep") is not None) else None,
+        outfile=execution.output_file(params.get("out_row_vec", None)),
+        out_row_bval_file=execution.output_file(params.get("out_row_bval_sep", None)) if (params.get("out_row_bval_sep") is not None) else None,
+        out_col_bval_file=execution.output_file(params.get("out_row_bval_sep", None)) if (params.get("out_row_bval_sep") is not None) else None,
     )
     return ret
 
 
 def v_1d_dw_grad_o_mat___execute(
     params: V1dDwGradOMatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V1dDwGradOMatOutputs:
     """
-    Manipulation of diffusion-weighted (DW) gradient vector files, b-value files,
-    and b- or g-matrices with various input and output configurations.
+    1dDW_Grad_o_Mat++
+    
+    Manipulation of diffusion-weighted (DW) gradient vector files, b-value
+    files, and b- or g-matrices with various input and output configurations.
     
     Author: AFNI Developers
     
@@ -309,10 +303,12 @@ def v_1d_dw_grad_o_mat___execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V1dDwGradOMatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_DW_GRAD_O_MAT___METADATA)
     params = execution.params(params)
     cargs = v_1d_dw_grad_o_mat___cargs(params, execution)
     ret = v_1d_dw_grad_o_mat___outputs(params, execution)
@@ -345,8 +341,10 @@ def v_1d_dw_grad_o_mat__(
     runner: Runner | None = None,
 ) -> V1dDwGradOMatOutputs:
     """
-    Manipulation of diffusion-weighted (DW) gradient vector files, b-value files,
-    and b- or g-matrices with various input and output configurations.
+    1dDW_Grad_o_Mat++
+    
+    Manipulation of diffusion-weighted (DW) gradient vector files, b-value
+    files, and b- or g-matrices with various input and output configurations.
     
     Author: AFNI Developers
     
@@ -392,8 +390,6 @@ def v_1d_dw_grad_o_mat__(
     Returns:
         NamedTuple of outputs (described in `V1dDwGradOMatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_1D_DW_GRAD_O_MAT___METADATA)
     params = v_1d_dw_grad_o_mat___params(
         in_row_vec=in_row_vec,
         in_col_vec=in_col_vec,
@@ -417,13 +413,13 @@ def v_1d_dw_grad_o_mat__(
         put_zeros_top=put_zeros_top,
         bmax_ref=bmax_ref,
     )
-    return v_1d_dw_grad_o_mat___execute(params, execution)
+    return v_1d_dw_grad_o_mat___execute(params, runner)
 
 
 __all__ = [
     "V1dDwGradOMatOutputs",
-    "V1dDwGradOMatParameters",
     "V_1D_DW_GRAD_O_MAT___METADATA",
     "v_1d_dw_grad_o_mat__",
+    "v_1d_dw_grad_o_mat___execute",
     "v_1d_dw_grad_o_mat___params",
 ]

niwrap_afni/afni/v_1d_flag_motion.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_1D_FLAG_MOTION_METADATA = Metadata(
-    id="3cccb4c8c9ef53bdcbc8db52f5600d6320db213e.boutiques",
+    id="50cd14d6c955325b397090100d74d78dcd0f657a.boutiques",
     name="1dFlagMotion",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,22 @@ V_1D_FLAG_MOTION_METADATA = Metadata(
 
 
 V1dFlagMotionParameters = typing.TypedDict('V1dFlagMotionParameters', {
-    "__STYXTYPE__": typing.Literal["1dFlagMotion"],
+    "@type": typing.NotRequired[typing.Literal["afni/1dFlagMotion"]],
+    "input_motion_file": InputPathType,
+    "max_translation": typing.NotRequired[float | None],
+    "max_rotation": typing.NotRequired[float | None],
+})
+V1dFlagMotionParametersTagged = typing.TypedDict('V1dFlagMotionParametersTagged', {
+    "@type": typing.Literal["afni/1dFlagMotion"],
     "input_motion_file": InputPathType,
     "max_translation": typing.NotRequired[float | None],
     "max_rotation": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "1dFlagMotion": v_1d_flag_motion_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 {
-        "1dFlagMotion": v_1d_flag_motion_outputs,
-    }.get(t)
 
 
 class V1dFlagMotionOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_1d_flag_motion(...)`.
+    Output object returned when calling `V1dFlagMotionParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def v_1d_flag_motion_params(
     input_motion_file: InputPathType,
     max_translation: float | None = None,
     max_rotation: float | None = None,
-) -> V1dFlagMotionParameters:
+) -> V1dFlagMotionParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +57,7 @@ def v_1d_flag_motion_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "1dFlagMotion",
+        "@type": "afni/1dFlagMotion",
         "input_motion_file": input_motion_file,
     }
     if max_translation is not None:
@@ -108,16 +82,16 @@ def v_1d_flag_motion_cargs(
     """
     cargs = []
     cargs.append("1dFlagMotion")
-    cargs.append(execution.input_file(params.get("input_motion_file")))
-    if params.get("max_translation") is not None:
+    cargs.append(execution.input_file(params.get("input_motion_file", None)))
+    if params.get("max_translation", None) is not None:
         cargs.extend([
             "-MaxTrans",
-            str(params.get("max_translation"))
+            str(params.get("max_translation", None))
         ])
-    if params.get("max_rotation") is not None:
+    if params.get("max_rotation", None) is not None:
         cargs.extend([
             "-MaxRot",
-            str(params.get("max_rotation"))
+            str(params.get("max_rotation", None))
         ])
     return cargs
 
@@ -144,11 +118,13 @@ def v_1d_flag_motion_outputs(
 
 def v_1d_flag_motion_execute(
     params: V1dFlagMotionParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V1dFlagMotionOutputs:
     """
-    Produces a list of time points with excessive motion relative to the previous
-    time point.
+    1dFlagMotion
+    
+    Produces a list of time points with excessive motion relative to the
+    previous time point.
     
     Author: AFNI Developers
     
@@ -156,10 +132,12 @@ def v_1d_flag_motion_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V1dFlagMotionOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_FLAG_MOTION_METADATA)
     params = execution.params(params)
     cargs = v_1d_flag_motion_cargs(params, execution)
     ret = v_1d_flag_motion_outputs(params, execution)
@@ -174,8 +152,10 @@ def v_1d_flag_motion(
     runner: Runner | None = None,
 ) -> V1dFlagMotionOutputs:
     """
-    Produces a list of time points with excessive motion relative to the previous
-    time point.
+    1dFlagMotion
+    
+    Produces a list of time points with excessive motion relative to the
+    previous time point.
     
     Author: AFNI Developers
     
@@ -193,20 +173,18 @@ def v_1d_flag_motion(
     Returns:
         NamedTuple of outputs (described in `V1dFlagMotionOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_1D_FLAG_MOTION_METADATA)
     params = v_1d_flag_motion_params(
         input_motion_file=input_motion_file,
         max_translation=max_translation,
         max_rotation=max_rotation,
     )
-    return v_1d_flag_motion_execute(params, execution)
+    return v_1d_flag_motion_execute(params, runner)
 
 
 __all__ = [
     "V1dFlagMotionOutputs",
-    "V1dFlagMotionParameters",
     "V_1D_FLAG_MOTION_METADATA",
     "v_1d_flag_motion",
+    "v_1d_flag_motion_execute",
     "v_1d_flag_motion_params",
 ]

niwrap_afni/afni/v_1d_marry.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_1D_MARRY_METADATA = Metadata(
-    id="451c2e1e1510e8db86d7d55846288c13e106eaf6.boutiques",
+    id="cc94cabd89bb70b7939757f293061c23f4519b11.boutiques",
     name="1dMarry",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,22 @@ V_1D_MARRY_METADATA = Metadata(
 
 
 V1dMarryParameters = typing.TypedDict('V1dMarryParameters', {
-    "__STYXTYPE__": typing.Literal["1dMarry"],
+    "@type": typing.NotRequired[typing.Literal["afni/1dMarry"]],
+    "sep": typing.NotRequired[str | None],
+    "divorce": bool,
+    "files": list[InputPathType],
+})
+V1dMarryParametersTagged = typing.TypedDict('V1dMarryParametersTagged', {
+    "@type": typing.Literal["afni/1dMarry"],
     "sep": typing.NotRequired[str | None],
     "divorce": bool,
     "files": list[InputPathType],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "1dMarry": v_1d_marry_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 {
-        "1dMarry": v_1d_marry_outputs,
-    }.get(t)
 
 
 class V1dMarryOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_1d_marry(...)`.
+    Output object returned when calling `V1dMarryParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,7 +46,7 @@ def v_1d_marry_params(
     files: list[InputPathType],
     sep: str | None = None,
     divorce: bool = False,
-) -> V1dMarryParameters:
+) -> V1dMarryParametersTagged:
     """
     Build parameters.
     
@@ -86,7 +60,7 @@ def v_1d_marry_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "1dMarry",
+        "@type": "afni/1dMarry",
         "divorce": divorce,
         "files": files,
     }
@@ -110,14 +84,14 @@ def v_1d_marry_cargs(
     """
     cargs = []
     cargs.append("1dMarry")
-    if params.get("sep") is not None:
+    if params.get("sep", None) is not None:
         cargs.extend([
             "-sep",
-            params.get("sep")
+            params.get("sep", None)
         ])
-    if params.get("divorce"):
+    if params.get("divorce", False):
         cargs.append("-divorce")
-    cargs.extend([execution.input_file(f) for f in params.get("files")])
+    cargs.extend([execution.input_file(f) for f in params.get("files", None)])
     return cargs
 
 
@@ -145,9 +119,11 @@ def v_1d_marry_outputs(
 
 def v_1d_marry_execute(
     params: V1dMarryParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V1dMarryOutputs:
     """
+    1dMarry
+    
     Joins together 2 (or more) ragged-right .1D files, for use with 3dDeconvolve
     -stim_times_AM2, or breaks up 1 married file into 2 (or more) single-valued
     files.
@@ -158,10 +134,12 @@ def v_1d_marry_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V1dMarryOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_MARRY_METADATA)
     params = execution.params(params)
     cargs = v_1d_marry_cargs(params, execution)
     ret = v_1d_marry_outputs(params, execution)
@@ -176,6 +154,8 @@ def v_1d_marry(
     runner: Runner | None = None,
 ) -> V1dMarryOutputs:
     """
+    1dMarry
+    
     Joins together 2 (or more) ragged-right .1D files, for use with 3dDeconvolve
     -stim_times_AM2, or breaks up 1 married file into 2 (or more) single-valued
     files.
@@ -194,20 +174,18 @@ def v_1d_marry(
     Returns:
         NamedTuple of outputs (described in `V1dMarryOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_1D_MARRY_METADATA)
     params = v_1d_marry_params(
         sep=sep,
         divorce=divorce,
         files=files,
     )
-    return v_1d_marry_execute(params, execution)
+    return v_1d_marry_execute(params, runner)
 
 
 __all__ = [
     "V1dMarryOutputs",
-    "V1dMarryParameters",
     "V_1D_MARRY_METADATA",
     "v_1d_marry",
+    "v_1d_marry_execute",
     "v_1d_marry_params",
 ]