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

niwrap_afni/afni/v_3d_dteig.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_DTEIG_METADATA = Metadata(
-    id="36a3abb6b11f17e33956cdaa9d15a0c2d499739b.boutiques",
+    id="96580e3014e6c3c304ee3899de8f8b2be948c0fe.boutiques",
     name="3dDTeig",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,50 +14,26 @@ V_3D_DTEIG_METADATA = Metadata(
 
 
 V3dDteigParameters = typing.TypedDict('V3dDteigParameters', {
-    "__STYXTYPE__": typing.Literal["3dDTeig"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dDTeig"]],
+    "input_dataset": str,
+    "prefix": typing.NotRequired[str | None],
+    "datum": typing.NotRequired[typing.Literal["byte", "short", "float"] | None],
+    "sep_dsets": bool,
+    "uddata": bool,
+})
+V3dDteigParametersTagged = typing.TypedDict('V3dDteigParametersTagged', {
+    "@type": typing.Literal["afni/3dDTeig"],
     "input_dataset": str,
     "prefix": typing.NotRequired[str | None],
     "datum": typing.NotRequired[typing.Literal["byte", "short", "float"] | None],
     "sep_dsets": bool,
     "uddata": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dDTeig": v_3d_dteig_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 {
-        "3dDTeig": v_3d_dteig_outputs,
-    }.get(t)
 
 
 class V3dDteigOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_dteig(...)`.
+    Output object returned when calling `V3dDteigParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +55,7 @@ def v_3d_dteig_params(
     datum: typing.Literal["byte", "short", "float"] | None = None,
     sep_dsets: bool = False,
     uddata: bool = False,
-) -> V3dDteigParameters:
+) -> V3dDteigParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +71,7 @@ def v_3d_dteig_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dDTeig",
+        "@type": "afni/3dDTeig",
         "input_dataset": input_dataset,
         "sep_dsets": sep_dsets,
         "uddata": uddata,
@@ -122,20 +98,20 @@ def v_3d_dteig_cargs(
     """
     cargs = []
     cargs.append("3dDTeig")
-    cargs.append(params.get("input_dataset"))
-    if params.get("prefix") is not None:
+    cargs.append(params.get("input_dataset", None))
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("datum") is not None:
+    if params.get("datum", None) is not None:
         cargs.extend([
             "-datum",
-            params.get("datum")
+            params.get("datum", None)
         ])
-    if params.get("sep_dsets"):
+    if params.get("sep_dsets", False):
         cargs.append("-sep_dsets")
-    if params.get("uddata"):
+    if params.get("uddata", False):
         cargs.append("-uddata")
     return cargs
 
@@ -155,20 +131,22 @@ def v_3d_dteig_outputs(
     """
     ret = V3dDteigOutputs(
         root=execution.output_file("."),
-        output_dataset=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
-        output_lambda=execution.output_file(params.get("prefix") + "_lambda.nii.gz") if (params.get("prefix") is not None) else None,
-        output_eigvec=execution.output_file(params.get("prefix") + "_eigvec.nii.gz") if (params.get("prefix") is not None) else None,
-        output_fa=execution.output_file(params.get("prefix") + "_FA.nii.gz") if (params.get("prefix") is not None) else None,
-        output_md=execution.output_file(params.get("prefix") + "_MD.nii.gz") if (params.get("prefix") is not None) else None,
+        output_dataset=execution.output_file(params.get("prefix", None) + ".nii.gz") if (params.get("prefix") is not None) else None,
+        output_lambda=execution.output_file(params.get("prefix", None) + "_lambda.nii.gz") if (params.get("prefix") is not None) else None,
+        output_eigvec=execution.output_file(params.get("prefix", None) + "_eigvec.nii.gz") if (params.get("prefix") is not None) else None,
+        output_fa=execution.output_file(params.get("prefix", None) + "_FA.nii.gz") if (params.get("prefix") is not None) else None,
+        output_md=execution.output_file(params.get("prefix", None) + "_MD.nii.gz") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_dteig_execute(
     params: V3dDteigParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dDteigOutputs:
     """
+    3dDTeig
+    
     Computes eigenvalues and eigenvectors for an input dataset of tensors.
     
     Author: AFNI Developers
@@ -177,10 +155,12 @@ def v_3d_dteig_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dDteigOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DTEIG_METADATA)
     params = execution.params(params)
     cargs = v_3d_dteig_cargs(params, execution)
     ret = v_3d_dteig_outputs(params, execution)
@@ -197,6 +177,8 @@ def v_3d_dteig(
     runner: Runner | None = None,
 ) -> V3dDteigOutputs:
     """
+    3dDTeig
+    
     Computes eigenvalues and eigenvectors for an input dataset of tensors.
     
     Author: AFNI Developers
@@ -215,8 +197,6 @@ def v_3d_dteig(
     Returns:
         NamedTuple of outputs (described in `V3dDteigOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_DTEIG_METADATA)
     params = v_3d_dteig_params(
         input_dataset=input_dataset,
         prefix=prefix,
@@ -224,13 +204,13 @@ def v_3d_dteig(
         sep_dsets=sep_dsets,
         uddata=uddata,
     )
-    return v_3d_dteig_execute(params, execution)
+    return v_3d_dteig_execute(params, runner)
 
 
 __all__ = [
     "V3dDteigOutputs",
-    "V3dDteigParameters",
     "V_3D_DTEIG_METADATA",
     "v_3d_dteig",
+    "v_3d_dteig_execute",
     "v_3d_dteig_params",
 ]

niwrap_afni/afni/v_3d_dtto_dwi.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_DTTO_DWI_METADATA = Metadata(
-    id="1fb2551331e4f3894dddfd8963dc18afa2c8a38e.boutiques",
+    id="b9cff0e8b3a61102a8410407fc0ea2e75ea382d6.boutiques",
     name="3dDTtoDWI",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V_3D_DTTO_DWI_METADATA = Metadata(
 
 
 V3dDttoDwiParameters = typing.TypedDict('V3dDttoDwiParameters', {
-    "__STYXTYPE__": typing.Literal["3dDTtoDWI"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dDTtoDWI"]],
+    "gradient_file": InputPathType,
+    "i0_dataset": InputPathType,
+    "dt_dataset": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "automask": bool,
+    "datum_type": typing.NotRequired[str | None],
+    "scale_out_1000": bool,
+    "help": bool,
+})
+V3dDttoDwiParametersTagged = typing.TypedDict('V3dDttoDwiParametersTagged', {
+    "@type": typing.Literal["afni/3dDTtoDWI"],
     "gradient_file": InputPathType,
     "i0_dataset": InputPathType,
     "dt_dataset": InputPathType,
@@ -24,43 +35,11 @@ V3dDttoDwiParameters = typing.TypedDict('V3dDttoDwiParameters', {
     "scale_out_1000": bool,
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dDTtoDWI": v_3d_dtto_dwi_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 {
-        "3dDTtoDWI": v_3d_dtto_dwi_outputs,
-    }.get(t)
 
 
 class V3dDttoDwiOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_dtto_dwi(...)`.
+    Output object returned when calling `V3dDttoDwiParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def v_3d_dtto_dwi_params(
     datum_type: str | None = None,
     scale_out_1000: bool = False,
     help_: bool = False,
-) -> V3dDttoDwiParameters:
+) -> V3dDttoDwiParametersTagged:
     """
     Build parameters.
     
@@ -97,7 +76,7 @@ def v_3d_dtto_dwi_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dDTtoDWI",
+        "@type": "afni/3dDTtoDWI",
         "gradient_file": gradient_file,
         "i0_dataset": i0_dataset,
         "dt_dataset": dt_dataset,
@@ -127,24 +106,24 @@ def v_3d_dtto_dwi_cargs(
     """
     cargs = []
     cargs.append("3dDTtoDWI")
-    cargs.append(execution.input_file(params.get("gradient_file")))
-    cargs.append(execution.input_file(params.get("i0_dataset")))
-    cargs.append(execution.input_file(params.get("dt_dataset")))
-    if params.get("prefix") is not None:
+    cargs.append(execution.input_file(params.get("gradient_file", None)))
+    cargs.append(execution.input_file(params.get("i0_dataset", None)))
+    cargs.append(execution.input_file(params.get("dt_dataset", None)))
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
-    if params.get("datum_type") is not None:
+    if params.get("datum_type", None) is not None:
         cargs.extend([
             "-datum",
-            params.get("datum_type")
+            params.get("datum_type", None)
         ])
-    if params.get("scale_out_1000"):
+    if params.get("scale_out_1000", False):
         cargs.append("-scale_out_1000")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -164,16 +143,18 @@ def v_3d_dtto_dwi_outputs(
     """
     ret = V3dDttoDwiOutputs(
         root=execution.output_file("."),
-        output_dwi=execution.output_file(params.get("prefix") + "*.HEAD") if (params.get("prefix") is not None) else None,
+        output_dwi=execution.output_file(params.get("prefix", None) + ".HEAD") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_dtto_dwi_execute(
     params: V3dDttoDwiParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dDttoDwiOutputs:
     """
+    3dDTtoDWI
+    
     Tool to compute multiple gradient images from tensors and gradient vector
     coordinates applied to the I0-dataset.
     
@@ -183,10 +164,12 @@ def v_3d_dtto_dwi_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dDttoDwiOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DTTO_DWI_METADATA)
     params = execution.params(params)
     cargs = v_3d_dtto_dwi_cargs(params, execution)
     ret = v_3d_dtto_dwi_outputs(params, execution)
@@ -206,6 +189,8 @@ def v_3d_dtto_dwi(
     runner: Runner | None = None,
 ) -> V3dDttoDwiOutputs:
     """
+    3dDTtoDWI
+    
     Tool to compute multiple gradient images from tensors and gradient vector
     coordinates applied to the I0-dataset.
     
@@ -229,8 +214,6 @@ def v_3d_dtto_dwi(
     Returns:
         NamedTuple of outputs (described in `V3dDttoDwiOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_DTTO_DWI_METADATA)
     params = v_3d_dtto_dwi_params(
         gradient_file=gradient_file,
         i0_dataset=i0_dataset,
@@ -241,13 +224,13 @@ def v_3d_dtto_dwi(
         scale_out_1000=scale_out_1000,
         help_=help_,
     )
-    return v_3d_dtto_dwi_execute(params, execution)
+    return v_3d_dtto_dwi_execute(params, runner)
 
 
 __all__ = [
     "V3dDttoDwiOutputs",
-    "V3dDttoDwiParameters",
     "V_3D_DTTO_DWI_METADATA",
     "v_3d_dtto_dwi",
+    "v_3d_dtto_dwi_execute",
     "v_3d_dtto_dwi_params",
 ]

niwrap_afni/afni/v_3d_dtto_noisy_dwi.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_DTTO_NOISY_DWI_METADATA = Metadata(
-    id="d89d2e3adba6b6e4e6f21f400c343e8140cca0a2.boutiques",
+    id="f0e92e7f32664311e32199aa4c239b82a4ba36c2.boutiques",
     name="3dDTtoNoisyDWI",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V_3D_DTTO_NOISY_DWI_METADATA = Metadata(
 
 
 V3dDttoNoisyDwiParameters = typing.TypedDict('V3dDttoNoisyDwiParameters', {
-    "__STYXTYPE__": typing.Literal["3dDTtoNoisyDWI"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dDTtoNoisyDWI"]],
+    "dt_file": InputPathType,
+    "grad_file": InputPathType,
+    "noise_dwi": float,
+    "noise_b0": typing.NotRequired[float | None],
+    "prefix": str,
+    "mask": typing.NotRequired[InputPathType | None],
+    "bval": typing.NotRequired[float | None],
+    "s0": typing.NotRequired[float | None],
+})
+V3dDttoNoisyDwiParametersTagged = typing.TypedDict('V3dDttoNoisyDwiParametersTagged', {
+    "@type": typing.Literal["afni/3dDTtoNoisyDWI"],
     "dt_file": InputPathType,
     "grad_file": InputPathType,
     "noise_dwi": float,
@@ -24,43 +35,11 @@ V3dDttoNoisyDwiParameters = typing.TypedDict('V3dDttoNoisyDwiParameters', {
     "bval": typing.NotRequired[float | None],
     "s0": 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 {
-        "3dDTtoNoisyDWI": v_3d_dtto_noisy_dwi_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 {
-        "3dDTtoNoisyDWI": v_3d_dtto_noisy_dwi_outputs,
-    }.get(t)
 
 
 class V3dDttoNoisyDwiOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_dtto_noisy_dwi(...)`.
+    Output object returned when calling `V3dDttoNoisyDwiParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -78,7 +57,7 @@ def v_3d_dtto_noisy_dwi_params(
     mask: InputPathType | None = None,
     bval: float | None = None,
     s0: float | None = None,
-) -> V3dDttoNoisyDwiParameters:
+) -> V3dDttoNoisyDwiParametersTagged:
     """
     Build parameters.
     
@@ -102,7 +81,7 @@ def v_3d_dtto_noisy_dwi_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dDTtoNoisyDWI",
+        "@type": "afni/3dDTtoNoisyDWI",
         "dt_file": dt_file,
         "grad_file": grad_file,
         "noise_dwi": noise_dwi,
@@ -134,35 +113,35 @@ def v_3d_dtto_noisy_dwi_cargs(
     """
     cargs = []
     cargs.append("3dDTtoNoisyDWI")
-    cargs.append(execution.input_file(params.get("dt_file")))
-    cargs.append(execution.input_file(params.get("grad_file")))
+    cargs.append(execution.input_file(params.get("dt_file", None)))
+    cargs.append(execution.input_file(params.get("grad_file", None)))
     cargs.extend([
         "-noise_DWI",
-        str(params.get("noise_dwi"))
+        str(params.get("noise_dwi", None))
     ])
-    if params.get("noise_b0") is not None:
+    if params.get("noise_b0", None) is not None:
         cargs.extend([
             "-noise_B0",
-            str(params.get("noise_b0"))
+            str(params.get("noise_b0", None))
         ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
-    if params.get("bval") is not None:
+    if params.get("bval", None) is not None:
         cargs.extend([
             "-bval",
-            str(params.get("bval"))
+            str(params.get("bval", None))
         ])
-    if params.get("s0") is not None:
+    if params.get("s0", None) is not None:
         cargs.extend([
             "-S0",
-            str(params.get("s0"))
+            str(params.get("s0", None))
         ])
     return cargs
 
@@ -182,18 +161,21 @@ def v_3d_dtto_noisy_dwi_outputs(
     """
     ret = V3dDttoNoisyDwiOutputs(
         root=execution.output_file("."),
-        output_dwi=execution.output_file(params.get("prefix") + "+orig"),
+        output_dwi=execution.output_file(params.get("prefix", None) + "+orig"),
     )
     return ret
 
 
 def v_3d_dtto_noisy_dwi_execute(
     params: V3dDttoNoisyDwiParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dDttoNoisyDwiOutputs:
     """
-    Generate a synthetic set of DWI measures with a given SNR from an AFNI-style DT
-    file and a set of gradients. This can be useful for simulations and testing.
+    3dDTtoNoisyDWI
+    
+    Generate a synthetic set of DWI measures with a given SNR from an AFNI-style
+    DT file and a set of gradients. This can be useful for simulations and
+    testing.
     
     Author: AFNI Developers
     
@@ -201,10 +183,12 @@ def v_3d_dtto_noisy_dwi_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dDttoNoisyDwiOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DTTO_NOISY_DWI_METADATA)
     params = execution.params(params)
     cargs = v_3d_dtto_noisy_dwi_cargs(params, execution)
     ret = v_3d_dtto_noisy_dwi_outputs(params, execution)
@@ -224,8 +208,11 @@ def v_3d_dtto_noisy_dwi(
     runner: Runner | None = None,
 ) -> V3dDttoNoisyDwiOutputs:
     """
-    Generate a synthetic set of DWI measures with a given SNR from an AFNI-style DT
-    file and a set of gradients. This can be useful for simulations and testing.
+    3dDTtoNoisyDWI
+    
+    Generate a synthetic set of DWI measures with a given SNR from an AFNI-style
+    DT file and a set of gradients. This can be useful for simulations and
+    testing.
     
     Author: AFNI Developers
     
@@ -251,8 +238,6 @@ def v_3d_dtto_noisy_dwi(
     Returns:
         NamedTuple of outputs (described in `V3dDttoNoisyDwiOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_DTTO_NOISY_DWI_METADATA)
     params = v_3d_dtto_noisy_dwi_params(
         dt_file=dt_file,
         grad_file=grad_file,
@@ -263,13 +248,13 @@ def v_3d_dtto_noisy_dwi(
         bval=bval,
         s0=s0,
     )
-    return v_3d_dtto_noisy_dwi_execute(params, execution)
+    return v_3d_dtto_noisy_dwi_execute(params, runner)
 
 
 __all__ = [
     "V3dDttoNoisyDwiOutputs",
-    "V3dDttoNoisyDwiParameters",
     "V_3D_DTTO_NOISY_DWI_METADATA",
     "v_3d_dtto_noisy_dwi",
+    "v_3d_dtto_noisy_dwi_execute",
     "v_3d_dtto_noisy_dwi_params",
 ]