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

niwrap_afni/afni/v_3d_unifize.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_UNIFIZE_METADATA = Metadata(
-    id="6277d1cde4dea26d7a71d4b0fc2e2e04b1054790.boutiques",
+    id="9fab3ba8f4e528c3b3fe2bdcd3fc9fd6c7cd2841.boutiques",
     name="3dUnifize",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ V_3D_UNIFIZE_METADATA = Metadata(
 
 
 V3dUnifizeParameters = typing.TypedDict('V3dUnifizeParameters', {
-    "__STYXTYPE__": typing.Literal["3dUnifize"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dUnifize"]],
+    "cl_frac": typing.NotRequired[float | None],
+    "epi": bool,
+    "gm": bool,
+    "no_duplo": bool,
+    "num_threads": typing.NotRequired[int | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "quiet": bool,
+    "rbt": typing.NotRequired[list[float] | None],
+    "prefix": typing.NotRequired[str | None],
+    "scale_file": typing.NotRequired[InputPathType | None],
+    "t2": bool,
+    "t2_up": typing.NotRequired[float | None],
+    "urad": typing.NotRequired[float | None],
+    "in_file": InputPathType,
+})
+V3dUnifizeParametersTagged = typing.TypedDict('V3dUnifizeParametersTagged', {
+    "@type": typing.Literal["afni/3dUnifize"],
     "cl_frac": typing.NotRequired[float | None],
     "epi": bool,
     "gm": bool,
@@ -30,43 +47,11 @@ V3dUnifizeParameters = typing.TypedDict('V3dUnifizeParameters', {
     "urad": typing.NotRequired[float | None],
     "in_file": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dUnifize": v_3d_unifize_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 {
-        "3dUnifize": v_3d_unifize_outputs,
-    }.get(t)
 
 
 class V3dUnifizeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_unifize(...)`.
+    Output object returned when calling `V3dUnifizeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -91,7 +76,7 @@ def v_3d_unifize_params(
     t2: bool = False,
     t2_up: float | None = None,
     urad: float | None = None,
-) -> V3dUnifizeParameters:
+) -> V3dUnifizeParametersTagged:
     """
     Build parameters.
     
@@ -136,7 +121,7 @@ def v_3d_unifize_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dUnifize",
+        "@type": "afni/3dUnifize",
         "epi": epi,
         "gm": gm,
         "no_duplo": no_duplo,
@@ -178,53 +163,53 @@ def v_3d_unifize_cargs(
     """
     cargs = []
     cargs.append("3dUnifize")
-    if params.get("cl_frac") is not None:
+    if params.get("cl_frac", None) is not None:
         cargs.extend([
             "-clfrac",
-            str(params.get("cl_frac"))
+            str(params.get("cl_frac", None))
         ])
-    if params.get("epi"):
+    if params.get("epi", False):
         cargs.append("-EPI")
-    if params.get("gm"):
+    if params.get("gm", False):
         cargs.append("-GM")
-    if params.get("no_duplo"):
+    if params.get("no_duplo", False):
         cargs.append("-noduplo")
-    if params.get("num_threads") is not None:
-        cargs.append(str(params.get("num_threads")))
-    if params.get("outputtype") is not None:
-        cargs.append(params.get("outputtype"))
-    if params.get("quiet"):
+    if params.get("num_threads", None) is not None:
+        cargs.append(str(params.get("num_threads", None)))
+    if params.get("outputtype", None) is not None:
+        cargs.append(params.get("outputtype", None))
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("rbt") is not None:
+    if params.get("rbt", None) is not None:
         cargs.extend([
             "-rbt",
-            *map(str, params.get("rbt"))
+            *map(str, params.get("rbt", None))
         ])
-    if params.get("prefix") is not None:
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("scale_file") is not None:
+    if params.get("scale_file", None) is not None:
         cargs.extend([
             "-ssave",
-            execution.input_file(params.get("scale_file"))
+            execution.input_file(params.get("scale_file", None))
         ])
-    if params.get("t2"):
+    if params.get("t2", False):
         cargs.append("-T2")
-    if params.get("t2_up") is not None:
+    if params.get("t2_up", None) is not None:
         cargs.extend([
             "-T2up",
-            str(params.get("t2_up"))
+            str(params.get("t2_up", None))
         ])
-    if params.get("urad") is not None:
+    if params.get("urad", None) is not None:
         cargs.extend([
             "-Urad",
-            str(params.get("urad"))
+            str(params.get("urad", None))
         ])
     cargs.extend([
         "-input",
-        execution.input_file(params.get("in_file"))
+        execution.input_file(params.get("in_file", None))
     ])
     return cargs
 
@@ -244,17 +229,19 @@ def v_3d_unifize_outputs(
     """
     ret = V3dUnifizeOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
-        scale_file_outfile=execution.output_file(pathlib.Path(params.get("scale_file")).name) if (params.get("scale_file") is not None) else None,
+        out_file=execution.output_file(params.get("prefix", None)) if (params.get("prefix") is not None) else None,
+        scale_file_outfile=execution.output_file(pathlib.Path(params.get("scale_file", None)).name) if (params.get("scale_file") is not None) else None,
     )
     return ret
 
 
 def v_3d_unifize_execute(
     params: V3dUnifizeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dUnifizeOutputs:
     """
+    3dUnifize
+    
     3dUnifize - for uniformizing image intensity
     * The input dataset is supposed to be a T1-weighted volume, possibly already
     skull-stripped (e.g., via 3dSkullStrip). However, this program can be a
@@ -280,10 +267,12 @@ def v_3d_unifize_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dUnifizeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_UNIFIZE_METADATA)
     params = execution.params(params)
     cargs = v_3d_unifize_cargs(params, execution)
     ret = v_3d_unifize_outputs(params, execution)
@@ -309,6 +298,8 @@ def v_3d_unifize(
     runner: Runner | None = None,
 ) -> V3dUnifizeOutputs:
     """
+    3dUnifize
+    
     3dUnifize - for uniformizing image intensity
     * The input dataset is supposed to be a T1-weighted volume, possibly already
     skull-stripped (e.g., via 3dSkullStrip). However, this program can be a
@@ -373,8 +364,6 @@ def v_3d_unifize(
     Returns:
         NamedTuple of outputs (described in `V3dUnifizeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_UNIFIZE_METADATA)
     params = v_3d_unifize_params(
         cl_frac=cl_frac,
         epi=epi,
@@ -391,13 +380,13 @@ def v_3d_unifize(
         urad=urad,
         in_file=in_file,
     )
-    return v_3d_unifize_execute(params, execution)
+    return v_3d_unifize_execute(params, runner)
 
 
 __all__ = [
     "V3dUnifizeOutputs",
-    "V3dUnifizeParameters",
     "V_3D_UNIFIZE_METADATA",
     "v_3d_unifize",
+    "v_3d_unifize_execute",
     "v_3d_unifize_params",
 ]

niwrap_afni/afni/v_3d_upsample.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_UPSAMPLE_METADATA = Metadata(
-    id="1517c44535a12e8aed86c6a112d119fc406a90b4.boutiques",
+    id="8787a10a03c7df64a9f923eb157688d9ad60ac0f.boutiques",
     name="3dUpsample",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V_3D_UPSAMPLE_METADATA = Metadata(
 
 
 V3dUpsampleParameters = typing.TypedDict('V3dUpsampleParameters', {
-    "__STYXTYPE__": typing.Literal["3dUpsample"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dUpsample"]],
+    "upsample_factor": int,
+    "input_dataset": str,
+    "linear_interpolation": bool,
+    "output_prefix": typing.NotRequired[str | None],
+    "verbose_flag": bool,
+    "datatype": typing.NotRequired[str | None],
+})
+V3dUpsampleParametersTagged = typing.TypedDict('V3dUpsampleParametersTagged', {
+    "@type": typing.Literal["afni/3dUpsample"],
     "upsample_factor": int,
     "input_dataset": str,
     "linear_interpolation": bool,
@@ -22,43 +31,11 @@ V3dUpsampleParameters = typing.TypedDict('V3dUpsampleParameters', {
     "verbose_flag": bool,
     "datatype": 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 {
-        "3dUpsample": v_3d_upsample_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 {
-        "3dUpsample": v_3d_upsample_outputs,
-    }.get(t)
 
 
 class V3dUpsampleOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_upsample(...)`.
+    Output object returned when calling `V3dUpsampleParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +52,7 @@ def v_3d_upsample_params(
     output_prefix: str | None = None,
     verbose_flag: bool = False,
     datatype: str | None = None,
-) -> V3dUpsampleParameters:
+) -> V3dUpsampleParametersTagged:
     """
     Build parameters.
     
@@ -94,7 +71,7 @@ def v_3d_upsample_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dUpsample",
+        "@type": "afni/3dUpsample",
         "upsample_factor": upsample_factor,
         "input_dataset": input_dataset,
         "linear_interpolation": linear_interpolation,
@@ -124,25 +101,25 @@ def v_3d_upsample_cargs(
     cargs.append("3dUpsample")
     cargs.extend([
         "-n",
-        str(params.get("upsample_factor"))
+        str(params.get("upsample_factor", None))
     ])
     cargs.extend([
         "-input",
-        params.get("input_dataset")
+        params.get("input_dataset", None)
     ])
-    if params.get("linear_interpolation"):
+    if params.get("linear_interpolation", False):
         cargs.append("-1")
-    if params.get("output_prefix") is not None:
+    if params.get("output_prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("output_prefix")
+            params.get("output_prefix", None)
         ])
-    if params.get("verbose_flag"):
+    if params.get("verbose_flag", False):
         cargs.append("-verb")
-    if params.get("datatype") is not None:
+    if params.get("datatype", None) is not None:
         cargs.extend([
             "-datum",
-            params.get("datatype")
+            params.get("datatype", None)
         ])
     return cargs
 
@@ -162,17 +139,19 @@ def v_3d_upsample_outputs(
     """
     ret = V3dUpsampleOutputs(
         root=execution.output_file("."),
-        output_brik=execution.output_file(params.get("output_prefix") + "+orig.BRIK") if (params.get("output_prefix") is not None) else None,
-        output_head=execution.output_file(params.get("output_prefix") + "+orig.HEAD") if (params.get("output_prefix") is not None) else None,
+        output_brik=execution.output_file(params.get("output_prefix", None) + "+orig.BRIK") if (params.get("output_prefix") is not None) else None,
+        output_head=execution.output_file(params.get("output_prefix", None) + "+orig.HEAD") if (params.get("output_prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_upsample_execute(
     params: V3dUpsampleParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dUpsampleOutputs:
     """
+    3dUpsample
+    
     Upsamples a 3D+time dataset in the time direction by a specified factor.
     
     Author: AFNI Developers
@@ -181,10 +160,12 @@ def v_3d_upsample_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dUpsampleOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_UPSAMPLE_METADATA)
     params = execution.params(params)
     cargs = v_3d_upsample_cargs(params, execution)
     ret = v_3d_upsample_outputs(params, execution)
@@ -202,6 +183,8 @@ def v_3d_upsample(
     runner: Runner | None = None,
 ) -> V3dUpsampleOutputs:
     """
+    3dUpsample
+    
     Upsamples a 3D+time dataset in the time direction by a specified factor.
     
     Author: AFNI Developers
@@ -223,8 +206,6 @@ def v_3d_upsample(
     Returns:
         NamedTuple of outputs (described in `V3dUpsampleOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_UPSAMPLE_METADATA)
     params = v_3d_upsample_params(
         upsample_factor=upsample_factor,
         input_dataset=input_dataset,
@@ -233,13 +214,13 @@ def v_3d_upsample(
         verbose_flag=verbose_flag,
         datatype=datatype,
     )
-    return v_3d_upsample_execute(params, execution)
+    return v_3d_upsample_execute(params, runner)
 
 
 __all__ = [
     "V3dUpsampleOutputs",
-    "V3dUpsampleParameters",
     "V_3D_UPSAMPLE_METADATA",
     "v_3d_upsample",
+    "v_3d_upsample_execute",
     "v_3d_upsample_params",
 ]

niwrap_afni/afni/v_3d_vec_rgb_to_hsl.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_VEC_RGB_TO_HSL_METADATA = Metadata(
-    id="05db8a83da7be7436039f9e5ae40fa617ded47cf.boutiques",
+    id="0e76c1c25d1c0286977cb2ffb47e49348642858e.boutiques",
     name="3dVecRGB_to_HSL",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ V_3D_VEC_RGB_TO_HSL_METADATA = Metadata(
 
 
 V3dVecRgbToHslParameters = typing.TypedDict('V3dVecRgbToHslParameters', {
-    "__STYXTYPE__": typing.Literal["3dVecRGB_to_HSL"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dVecRGB_to_HSL"]],
+    "prefix": str,
+    "in_vec": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "in_scal": typing.NotRequired[InputPathType | None],
+})
+V3dVecRgbToHslParametersTagged = typing.TypedDict('V3dVecRgbToHslParametersTagged', {
+    "@type": typing.Literal["afni/3dVecRGB_to_HSL"],
     "prefix": str,
     "in_vec": InputPathType,
     "mask": typing.NotRequired[InputPathType | None],
     "in_scal": typing.NotRequired[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 {
-        "3dVecRGB_to_HSL": v_3d_vec_rgb_to_hsl_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 {
-        "3dVecRGB_to_HSL": v_3d_vec_rgb_to_hsl_outputs,
-    }.get(t)
 
 
 class V3dVecRgbToHslOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_vec_rgb_to_hsl(...)`.
+    Output object returned when calling `V3dVecRgbToHslParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def v_3d_vec_rgb_to_hsl_params(
     in_vec: InputPathType,
     mask: InputPathType | None = None,
     in_scal: InputPathType | None = None,
-) -> V3dVecRgbToHslParameters:
+) -> V3dVecRgbToHslParametersTagged:
     """
     Build parameters.
     
@@ -86,7 +61,7 @@ def v_3d_vec_rgb_to_hsl_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dVecRGB_to_HSL",
+        "@type": "afni/3dVecRGB_to_HSL",
         "prefix": prefix,
         "in_vec": in_vec,
     }
@@ -114,21 +89,21 @@ def v_3d_vec_rgb_to_hsl_cargs(
     cargs.append("3dVecRGB_to_HSL")
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
     cargs.extend([
         "-in_vec",
-        execution.input_file(params.get("in_vec"))
+        execution.input_file(params.get("in_vec", 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("in_scal") is not None:
+    if params.get("in_scal", None) is not None:
         cargs.extend([
             "-in_scal",
-            execution.input_file(params.get("in_scal"))
+            execution.input_file(params.get("in_scal", None))
         ])
     return cargs
 
@@ -148,18 +123,20 @@ def v_3d_vec_rgb_to_hsl_outputs(
     """
     ret = V3dVecRgbToHslOutputs(
         root=execution.output_file("."),
-        output_hsl_dataset=execution.output_file(params.get("prefix") + "_HSL+*.HEAD"),
+        output_hsl_dataset=execution.output_file(params.get("prefix", None) + "_HSL.HEAD"),
     )
     return ret
 
 
 def v_3d_vec_rgb_to_hsl_execute(
     params: V3dVecRgbToHslParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dVecRgbToHslOutputs:
     """
-    Convert a 3-brick RGB (red, green, blue) data set to an HSL (hue, saturation,
-    luminance) one.
+    3dVecRGB_to_HSL
+    
+    Convert a 3-brick RGB (red, green, blue) data set to an HSL (hue,
+    saturation, luminance) one.
     
     Author: AFNI Developers
     
@@ -167,10 +144,12 @@ def v_3d_vec_rgb_to_hsl_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dVecRgbToHslOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_VEC_RGB_TO_HSL_METADATA)
     params = execution.params(params)
     cargs = v_3d_vec_rgb_to_hsl_cargs(params, execution)
     ret = v_3d_vec_rgb_to_hsl_outputs(params, execution)
@@ -186,8 +165,10 @@ def v_3d_vec_rgb_to_hsl(
     runner: Runner | None = None,
 ) -> V3dVecRgbToHslOutputs:
     """
-    Convert a 3-brick RGB (red, green, blue) data set to an HSL (hue, saturation,
-    luminance) one.
+    3dVecRGB_to_HSL
+    
+    Convert a 3-brick RGB (red, green, blue) data set to an HSL (hue,
+    saturation, luminance) one.
     
     Author: AFNI Developers
     
@@ -206,21 +187,19 @@ def v_3d_vec_rgb_to_hsl(
     Returns:
         NamedTuple of outputs (described in `V3dVecRgbToHslOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_VEC_RGB_TO_HSL_METADATA)
     params = v_3d_vec_rgb_to_hsl_params(
         prefix=prefix,
         in_vec=in_vec,
         mask=mask,
         in_scal=in_scal,
     )
-    return v_3d_vec_rgb_to_hsl_execute(params, execution)
+    return v_3d_vec_rgb_to_hsl_execute(params, runner)
 
 
 __all__ = [
     "V3dVecRgbToHslOutputs",
-    "V3dVecRgbToHslParameters",
     "V_3D_VEC_RGB_TO_HSL_METADATA",
     "v_3d_vec_rgb_to_hsl",
+    "v_3d_vec_rgb_to_hsl_execute",
     "v_3d_vec_rgb_to_hsl_params",
 ]