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

niwrap_afni/afni/v_3d_mask_to_ascii.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_MASK_TO_ASCII_METADATA = Metadata(
-    id="778a8402c86f1b42b01b3553f5a5396f990949e6.boutiques",
+    id="5690b62c0dc16bb101f03c22d22615f3b255e3a0.boutiques",
     name="3dMaskToASCII",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,22 @@ V_3D_MASK_TO_ASCII_METADATA = Metadata(
 
 
 V3dMaskToAsciiParameters = typing.TypedDict('V3dMaskToAsciiParameters', {
-    "__STYXTYPE__": typing.Literal["3dMaskToASCII"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dMaskToASCII"]],
+    "tobin_flag": bool,
+    "dataset": InputPathType,
+    "outputfile": str,
+})
+V3dMaskToAsciiParametersTagged = typing.TypedDict('V3dMaskToAsciiParametersTagged', {
+    "@type": typing.Literal["afni/3dMaskToASCII"],
     "tobin_flag": bool,
     "dataset": InputPathType,
     "outputfile": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dMaskToASCII": v_3d_mask_to_ascii_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 {
-        "3dMaskToASCII": v_3d_mask_to_ascii_outputs,
-    }.get(t)
 
 
 class V3dMaskToAsciiOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_mask_to_ascii(...)`.
+    Output object returned when calling `V3dMaskToAsciiParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def v_3d_mask_to_ascii_params(
     dataset: InputPathType,
     outputfile: str,
     tobin_flag: bool = False,
-) -> V3dMaskToAsciiParameters:
+) -> V3dMaskToAsciiParametersTagged:
     """
     Build parameters.
     
@@ -81,7 +55,7 @@ def v_3d_mask_to_ascii_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dMaskToASCII",
+        "@type": "afni/3dMaskToASCII",
         "tobin_flag": tobin_flag,
         "dataset": dataset,
         "outputfile": outputfile,
@@ -104,10 +78,10 @@ def v_3d_mask_to_ascii_cargs(
     """
     cargs = []
     cargs.append("3dMaskToASCII")
-    if params.get("tobin_flag"):
+    if params.get("tobin_flag", False):
         cargs.append("-tobin")
-    cargs.append(execution.input_file(params.get("dataset")))
-    cargs.append("> " + params.get("outputfile"))
+    cargs.append(execution.input_file(params.get("dataset", None)))
+    cargs.append("> " + params.get("outputfile", None))
     return cargs
 
 
@@ -126,16 +100,18 @@ def v_3d_mask_to_ascii_outputs(
     """
     ret = V3dMaskToAsciiOutputs(
         root=execution.output_file("."),
-        outputfile=execution.output_file(params.get("outputfile")),
+        outputfile=execution.output_file(params.get("outputfile", None)),
     )
     return ret
 
 
 def v_3d_mask_to_ascii_execute(
     params: V3dMaskToAsciiParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dMaskToAsciiOutputs:
     """
+    3dMaskToASCII
+    
     Converts a byte-valued 0/1 dataset into an ASCII string, or vice versa.
     
     Author: AFNI Developers
@@ -144,10 +120,12 @@ def v_3d_mask_to_ascii_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dMaskToAsciiOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MASK_TO_ASCII_METADATA)
     params = execution.params(params)
     cargs = v_3d_mask_to_ascii_cargs(params, execution)
     ret = v_3d_mask_to_ascii_outputs(params, execution)
@@ -162,6 +140,8 @@ def v_3d_mask_to_ascii(
     runner: Runner | None = None,
 ) -> V3dMaskToAsciiOutputs:
     """
+    3dMaskToASCII
+    
     Converts a byte-valued 0/1 dataset into an ASCII string, or vice versa.
     
     Author: AFNI Developers
@@ -178,20 +158,18 @@ def v_3d_mask_to_ascii(
     Returns:
         NamedTuple of outputs (described in `V3dMaskToAsciiOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_MASK_TO_ASCII_METADATA)
     params = v_3d_mask_to_ascii_params(
         tobin_flag=tobin_flag,
         dataset=dataset,
         outputfile=outputfile,
     )
-    return v_3d_mask_to_ascii_execute(params, execution)
+    return v_3d_mask_to_ascii_execute(params, runner)
 
 
 __all__ = [
     "V3dMaskToAsciiOutputs",
-    "V3dMaskToAsciiParameters",
     "V_3D_MASK_TO_ASCII_METADATA",
     "v_3d_mask_to_ascii",
+    "v_3d_mask_to_ascii_execute",
     "v_3d_mask_to_ascii_params",
 ]

niwrap_afni/afni/v_3d_match.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_MATCH_METADATA = Metadata(
-    id="5a9b48cc507b88f6620f1b745b682a96b9bb92f5.boutiques",
+    id="9348cabab9fad8b570461c663d6f7926fc341f05.boutiques",
     name="3dMatch",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ V_3D_MATCH_METADATA = Metadata(
 
 
 V3dMatchParameters = typing.TypedDict('V3dMatchParameters', {
-    "__STYXTYPE__": typing.Literal["3dMatch"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dMatch"]],
+    "inset": InputPathType,
+    "refset": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "in_min": typing.NotRequired[float | None],
+    "in_max": typing.NotRequired[float | None],
+    "ref_min": typing.NotRequired[float | None],
+    "ref_max": typing.NotRequired[float | None],
+    "prefix": str,
+    "only_dice_thr": bool,
+})
+V3dMatchParametersTagged = typing.TypedDict('V3dMatchParametersTagged', {
+    "@type": typing.Literal["afni/3dMatch"],
     "inset": InputPathType,
     "refset": InputPathType,
     "mask": typing.NotRequired[InputPathType | None],
@@ -25,43 +37,11 @@ V3dMatchParameters = typing.TypedDict('V3dMatchParameters', {
     "prefix": str,
     "only_dice_thr": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dMatch": v_3d_match_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 {
-        "3dMatch": v_3d_match_outputs,
-    }.get(t)
 
 
 class V3dMatchOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_match(...)`.
+    Output object returned when calling `V3dMatchParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -87,7 +67,7 @@ def v_3d_match_params(
     ref_min: float | None = None,
     ref_max: float | None = None,
     only_dice_thr: bool = False,
-) -> V3dMatchParameters:
+) -> V3dMatchParametersTagged:
     """
     Build parameters.
     
@@ -111,7 +91,7 @@ def v_3d_match_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dMatch",
+        "@type": "afni/3dMatch",
         "inset": inset,
         "refset": refset,
         "prefix": prefix,
@@ -147,42 +127,42 @@ def v_3d_match_cargs(
     cargs.append("3dMatch")
     cargs.extend([
         "-inset",
-        execution.input_file(params.get("inset"))
+        execution.input_file(params.get("inset", None))
     ])
     cargs.extend([
         "-refset",
-        execution.input_file(params.get("refset"))
+        execution.input_file(params.get("refset", 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_min") is not None:
+    if params.get("in_min", None) is not None:
         cargs.extend([
             "-in_min",
-            str(params.get("in_min"))
+            str(params.get("in_min", None))
         ])
-    if params.get("in_max") is not None:
+    if params.get("in_max", None) is not None:
         cargs.extend([
             "-in_max",
-            str(params.get("in_max"))
+            str(params.get("in_max", None))
         ])
-    if params.get("ref_min") is not None:
+    if params.get("ref_min", None) is not None:
         cargs.extend([
             "-ref_min",
-            str(params.get("ref_min"))
+            str(params.get("ref_min", None))
         ])
-    if params.get("ref_max") is not None:
+    if params.get("ref_max", None) is not None:
         cargs.extend([
             "-ref_max",
-            str(params.get("ref_max"))
+            str(params.get("ref_max", None))
         ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("only_dice_thr"):
+    if params.get("only_dice_thr", False):
         cargs.append("-only_dice_thr")
     return cargs
 
@@ -202,21 +182,23 @@ def v_3d_match_outputs(
     """
     ret = V3dMatchOutputs(
         root=execution.output_file("."),
-        ref_brik=execution.output_file(params.get("prefix") + "_REF+orig.BRIK"),
-        ref_coeff_vals=execution.output_file(params.get("prefix") + "_REF_coeff.vals"),
-        in_brik=execution.output_file(params.get("prefix") + "_IN+orig.BRIK"),
-        in_coeff_vals=execution.output_file(params.get("prefix") + "_IN_coeff.vals"),
+        ref_brik=execution.output_file(params.get("prefix", None) + "_REF+orig.BRIK"),
+        ref_coeff_vals=execution.output_file(params.get("prefix", None) + "_REF_coeff.vals"),
+        in_brik=execution.output_file(params.get("prefix", None) + "_IN+orig.BRIK"),
+        in_coeff_vals=execution.output_file(params.get("prefix", None) + "_IN_coeff.vals"),
     )
     return ret
 
 
 def v_3d_match_execute(
     params: V3dMatchParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dMatchOutputs:
     """
-    Find similar subbricks and rearrange order to ease comparison. Part of FATCAT in
-    AFNI.
+    3dMatch
+    
+    Find similar subbricks and rearrange order to ease comparison. Part of
+    FATCAT in AFNI.
     
     Author: AFNI Developers
     
@@ -224,10 +206,12 @@ def v_3d_match_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dMatchOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MATCH_METADATA)
     params = execution.params(params)
     cargs = v_3d_match_cargs(params, execution)
     ret = v_3d_match_outputs(params, execution)
@@ -248,8 +232,10 @@ def v_3d_match(
     runner: Runner | None = None,
 ) -> V3dMatchOutputs:
     """
-    Find similar subbricks and rearrange order to ease comparison. Part of FATCAT in
-    AFNI.
+    3dMatch
+    
+    Find similar subbricks and rearrange order to ease comparison. Part of
+    FATCAT in AFNI.
     
     Author: AFNI Developers
     
@@ -275,8 +261,6 @@ def v_3d_match(
     Returns:
         NamedTuple of outputs (described in `V3dMatchOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_MATCH_METADATA)
     params = v_3d_match_params(
         inset=inset,
         refset=refset,
@@ -288,13 +272,13 @@ def v_3d_match(
         prefix=prefix,
         only_dice_thr=only_dice_thr,
     )
-    return v_3d_match_execute(params, execution)
+    return v_3d_match_execute(params, runner)
 
 
 __all__ = [
     "V3dMatchOutputs",
-    "V3dMatchParameters",
     "V_3D_MATCH_METADATA",
     "v_3d_match",
+    "v_3d_match_execute",
     "v_3d_match_params",
 ]

niwrap_afni/afni/v_3d_mean.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_MEAN_METADATA = Metadata(
-    id="66db8b2cf4b9457a41b7a29a860b777a3814d4b9.boutiques",
+    id="c3ac13b34415144da277586edf4aa7b38c139609.boutiques",
     name="3dMean",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,29 @@ V_3D_MEAN_METADATA = Metadata(
 
 
 V3dMeanParameters = typing.TypedDict('V3dMeanParameters', {
-    "__STYXTYPE__": typing.Literal["3dMean"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dMean"]],
+    "input_files": list[InputPathType],
+    "verbose": bool,
+    "prefix": typing.NotRequired[str | None],
+    "datum": typing.NotRequired[str | None],
+    "fscale": bool,
+    "gscale": bool,
+    "nscale": bool,
+    "non_zero": bool,
+    "stdev": bool,
+    "sqr": bool,
+    "sum": bool,
+    "count": bool,
+    "max": bool,
+    "min": bool,
+    "absmax": bool,
+    "signed_absmax": bool,
+    "mask_inter": bool,
+    "mask_union": bool,
+    "weightset": typing.NotRequired[InputPathType | None],
+})
+V3dMeanParametersTagged = typing.TypedDict('V3dMeanParametersTagged', {
+    "@type": typing.Literal["afni/3dMean"],
     "input_files": list[InputPathType],
     "verbose": bool,
     "prefix": typing.NotRequired[str | None],
@@ -35,43 +57,11 @@ V3dMeanParameters = typing.TypedDict('V3dMeanParameters', {
     "mask_union": bool,
     "weightset": 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 {
-        "3dMean": v_3d_mean_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 {
-        "3dMean": v_3d_mean_outputs,
-    }.get(t)
 
 
 class V3dMeanOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_mean(...)`.
+    Output object returned when calling `V3dMeanParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -99,7 +89,7 @@ def v_3d_mean_params(
     mask_inter: bool = False,
     mask_union: bool = False,
     weightset: InputPathType | None = None,
-) -> V3dMeanParameters:
+) -> V3dMeanParametersTagged:
     """
     Build parameters.
     
@@ -133,7 +123,7 @@ def v_3d_mean_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dMean",
+        "@type": "afni/3dMean",
         "input_files": input_files,
         "verbose": verbose,
         "fscale": fscale,
@@ -175,51 +165,51 @@ def v_3d_mean_cargs(
     """
     cargs = []
     cargs.append("3dMean")
-    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
-    if params.get("verbose"):
+    cargs.extend([execution.input_file(f) for f in params.get("input_files", None)])
+    if params.get("verbose", False):
         cargs.append("-verbose")
-    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("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("fscale"):
+    if params.get("fscale", False):
         cargs.append("-fscale")
-    if params.get("gscale"):
+    if params.get("gscale", False):
         cargs.append("-gscale")
-    if params.get("nscale"):
+    if params.get("nscale", False):
         cargs.append("-nscale")
-    if params.get("non_zero"):
+    if params.get("non_zero", False):
         cargs.append("-non_zero")
-    if params.get("stdev"):
+    if params.get("stdev", False):
         cargs.append("-sd")
-    if params.get("sqr"):
+    if params.get("sqr", False):
         cargs.append("-sqr")
-    if params.get("sum"):
+    if params.get("sum", False):
         cargs.append("-sum")
-    if params.get("count"):
+    if params.get("count", False):
         cargs.append("-count")
-    if params.get("max"):
+    if params.get("max", False):
         cargs.append("-max")
-    if params.get("min"):
+    if params.get("min", False):
         cargs.append("-min")
-    if params.get("absmax"):
+    if params.get("absmax", False):
         cargs.append("-absmax")
-    if params.get("signed_absmax"):
+    if params.get("signed_absmax", False):
         cargs.append("-signed_absmax")
-    if params.get("mask_inter"):
+    if params.get("mask_inter", False):
         cargs.append("-mask_inter")
-    if params.get("mask_union"):
+    if params.get("mask_union", False):
         cargs.append("-mask_union")
-    if params.get("weightset") is not None:
+    if params.get("weightset", None) is not None:
         cargs.extend([
             "-weightset",
-            execution.input_file(params.get("weightset"))
+            execution.input_file(params.get("weightset", None))
         ])
     return cargs
 
@@ -239,18 +229,20 @@ def v_3d_mean_outputs(
     """
     ret = V3dMeanOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + "<+optional_extension>") if (params.get("prefix") is not None) else None,
+        output_file=execution.output_file(params.get("prefix", None)) if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_mean_execute(
     params: V3dMeanParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dMeanOutputs:
     """
-    Takes the voxel-by-voxel mean of all input datasets; designed to be faster than
-    3dcalc.
+    3dMean
+    
+    Takes the voxel-by-voxel mean of all input datasets; designed to be faster
+    than 3dcalc.
     
     Author: AFNI Developers
     
@@ -258,10 +250,12 @@ def v_3d_mean_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dMeanOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MEAN_METADATA)
     params = execution.params(params)
     cargs = v_3d_mean_cargs(params, execution)
     ret = v_3d_mean_outputs(params, execution)
@@ -292,8 +286,10 @@ def v_3d_mean(
     runner: Runner | None = None,
 ) -> V3dMeanOutputs:
     """
-    Takes the voxel-by-voxel mean of all input datasets; designed to be faster than
-    3dcalc.
+    3dMean
+    
+    Takes the voxel-by-voxel mean of all input datasets; designed to be faster
+    than 3dcalc.
     
     Author: AFNI Developers
     
@@ -329,8 +325,6 @@ def v_3d_mean(
     Returns:
         NamedTuple of outputs (described in `V3dMeanOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_MEAN_METADATA)
     params = v_3d_mean_params(
         input_files=input_files,
         verbose=verbose,
@@ -352,13 +346,13 @@ def v_3d_mean(
         mask_union=mask_union,
         weightset=weightset,
     )
-    return v_3d_mean_execute(params, execution)
+    return v_3d_mean_execute(params, runner)
 
 
 __all__ = [
     "V3dMeanOutputs",
-    "V3dMeanParameters",
     "V_3D_MEAN_METADATA",
     "v_3d_mean",
+    "v_3d_mean_execute",
     "v_3d_mean_params",
 ]