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

niwrap_afni/afni/v_3d_overlap.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_OVERLAP_METADATA = Metadata(
-    id="93e1b7f69d98cd0c2b6369179b0a77d2fb5b72a4.boutiques",
+    id="ad1c98bd4c72aa7f30bc88ed21611a0807942438.boutiques",
     name="3dOverlap",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,22 @@ V_3D_OVERLAP_METADATA = Metadata(
 
 
 V3dOverlapParameters = typing.TypedDict('V3dOverlapParameters', {
-    "__STYXTYPE__": typing.Literal["3dOverlap"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dOverlap"]],
+    "dataset1": InputPathType,
+    "dataset2": list[InputPathType],
+    "save_prefix": typing.NotRequired[str | None],
+})
+V3dOverlapParametersTagged = typing.TypedDict('V3dOverlapParametersTagged', {
+    "@type": typing.Literal["afni/3dOverlap"],
     "dataset1": InputPathType,
     "dataset2": list[InputPathType],
     "save_prefix": 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 {
-        "3dOverlap": v_3d_overlap_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 {
-        "3dOverlap": v_3d_overlap_outputs,
-    }.get(t)
 
 
 class V3dOverlapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_overlap(...)`.
+    Output object returned when calling `V3dOverlapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +43,7 @@ def v_3d_overlap_params(
     dataset1: InputPathType,
     dataset2: list[InputPathType],
     save_prefix: str | None = None,
-) -> V3dOverlapParameters:
+) -> V3dOverlapParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +56,7 @@ def v_3d_overlap_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dOverlap",
+        "@type": "afni/3dOverlap",
         "dataset1": dataset1,
         "dataset2": dataset2,
     }
@@ -106,12 +80,12 @@ def v_3d_overlap_cargs(
     """
     cargs = []
     cargs.append("3dOverlap")
-    cargs.append(execution.input_file(params.get("dataset1")))
-    cargs.extend([execution.input_file(f) for f in params.get("dataset2")])
-    if params.get("save_prefix") is not None:
+    cargs.append(execution.input_file(params.get("dataset1", None)))
+    cargs.extend([execution.input_file(f) for f in params.get("dataset2", None)])
+    if params.get("save_prefix", None) is not None:
         cargs.extend([
             "-save",
-            params.get("save_prefix")
+            params.get("save_prefix", None)
         ])
     return cargs
 
@@ -131,17 +105,19 @@ def v_3d_overlap_outputs(
     """
     ret = V3dOverlapOutputs(
         root=execution.output_file("."),
-        output_brik=execution.output_file(params.get("save_prefix") + "+orig.BRIK") if (params.get("save_prefix") is not None) else None,
-        output_head=execution.output_file(params.get("save_prefix") + "+orig.HEAD") if (params.get("save_prefix") is not None) else None,
+        output_brik=execution.output_file(params.get("save_prefix", None) + "+orig.BRIK") if (params.get("save_prefix") is not None) else None,
+        output_head=execution.output_file(params.get("save_prefix", None) + "+orig.HEAD") if (params.get("save_prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_overlap_execute(
     params: V3dOverlapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dOverlapOutputs:
     """
+    3dOverlap
+    
     Counts the number of voxels that are nonzero in all input datasets.
     
     Author: AFNI Developers
@@ -150,10 +126,12 @@ def v_3d_overlap_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dOverlapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_OVERLAP_METADATA)
     params = execution.params(params)
     cargs = v_3d_overlap_cargs(params, execution)
     ret = v_3d_overlap_outputs(params, execution)
@@ -168,6 +146,8 @@ def v_3d_overlap(
     runner: Runner | None = None,
 ) -> V3dOverlapOutputs:
     """
+    3dOverlap
+    
     Counts the number of voxels that are nonzero in all input datasets.
     
     Author: AFNI Developers
@@ -183,20 +163,18 @@ def v_3d_overlap(
     Returns:
         NamedTuple of outputs (described in `V3dOverlapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_OVERLAP_METADATA)
     params = v_3d_overlap_params(
         dataset1=dataset1,
         dataset2=dataset2,
         save_prefix=save_prefix,
     )
-    return v_3d_overlap_execute(params, execution)
+    return v_3d_overlap_execute(params, runner)
 
 
 __all__ = [
     "V3dOverlapOutputs",
-    "V3dOverlapParameters",
     "V_3D_OVERLAP_METADATA",
     "v_3d_overlap",
+    "v_3d_overlap_execute",
     "v_3d_overlap_params",
 ]

niwrap_afni/afni/{v_3d_par2_afni.py → v_3d_par2_afni_pl.py}

@@ -5,16 +5,29 @@ import typing
 import pathlib
 from styxdefs import *
 
-V_3D_PAR2_AFNI_METADATA = Metadata(
-    id="8a1625af0dec0ca42ff6be27e5b3b994d19a0b23.boutiques",
-    name="3dPAR2AFNI",
+V_3D_PAR2_AFNI_PL_METADATA = Metadata(
+    id="c8cf3333bffe3eef06c654ed6247416c719f0d74.boutiques",
+    name="3dPAR2AFNI.pl",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
 )
 
 
-V3dPar2AfniParameters = typing.TypedDict('V3dPar2AfniParameters', {
-    "__STYXTYPE__": typing.Literal["3dPAR2AFNI"],
+V3dPar2AfniPlParameters = typing.TypedDict('V3dPar2AfniPlParameters', {
+    "@type": typing.NotRequired[typing.Literal["afni/3dPAR2AFNI.pl"]],
+    "input_file": InputPathType,
+    "skip_outliers_test": bool,
+    "output_nifti": bool,
+    "output_analyze": bool,
+    "output_dir": typing.NotRequired[str | None],
+    "verbose_flag": bool,
+    "gzip_files": bool,
+    "byte_swap_2": bool,
+    "byte_swap_4": bool,
+    "help_flag": bool,
+})
+V3dPar2AfniPlParametersTagged = typing.TypedDict('V3dPar2AfniPlParametersTagged', {
+    "@type": typing.Literal["afni/3dPAR2AFNI.pl"],
     "input_file": InputPathType,
     "skip_outliers_test": bool,
     "output_nifti": bool,
@@ -28,41 +41,9 @@ V3dPar2AfniParameters = typing.TypedDict('V3dPar2AfniParameters', {
 })
 
 
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dPAR2AFNI": v_3d_par2_afni_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 {
-        "3dPAR2AFNI": v_3d_par2_afni_outputs,
-    }.get(t)
-
-
-class V3dPar2AfniOutputs(typing.NamedTuple):
+class V3dPar2AfniPlOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_par2_afni(...)`.
+    Output object returned when calling `V3dPar2AfniPlParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +51,7 @@ class V3dPar2AfniOutputs(typing.NamedTuple):
     """Converted output files"""
 
 
-def v_3d_par2_afni_params(
+def v_3d_par2_afni_pl_params(
     input_file: InputPathType,
     skip_outliers_test: bool = False,
     output_nifti: bool = False,
@@ -81,7 +62,7 @@ def v_3d_par2_afni_params(
     byte_swap_2: bool = False,
     byte_swap_4: bool = False,
     help_flag: bool = False,
-) -> V3dPar2AfniParameters:
+) -> V3dPar2AfniPlParametersTagged:
     """
     Build parameters.
     
@@ -107,7 +88,7 @@ def v_3d_par2_afni_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dPAR2AFNI",
+        "@type": "afni/3dPAR2AFNI.pl",
         "input_file": input_file,
         "skip_outliers_test": skip_outliers_test,
         "output_nifti": output_nifti,
@@ -123,8 +104,8 @@ def v_3d_par2_afni_params(
     return params
 
 
-def v_3d_par2_afni_cargs(
-    params: V3dPar2AfniParameters,
+def v_3d_par2_afni_pl_cargs(
+    params: V3dPar2AfniPlParameters,
     execution: Execution,
 ) -> list[str]:
     """
@@ -138,35 +119,35 @@ def v_3d_par2_afni_cargs(
     """
     cargs = []
     cargs.append("3dPAR2AFNI.pl")
-    cargs.append(execution.input_file(params.get("input_file")))
-    if params.get("skip_outliers_test"):
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    if params.get("skip_outliers_test", False):
         cargs.append("-s")
-    if params.get("output_nifti"):
+    if params.get("output_nifti", False):
         cargs.append("-n")
-    if params.get("output_analyze"):
+    if params.get("output_analyze", False):
         cargs.append("-a")
-    if params.get("output_dir") is not None:
+    if params.get("output_dir", None) is not None:
         cargs.extend([
             "-o",
-            params.get("output_dir")
+            params.get("output_dir", None)
         ])
-    if params.get("verbose_flag"):
+    if params.get("verbose_flag", False):
         cargs.append("-v")
-    if params.get("gzip_files"):
+    if params.get("gzip_files", False):
         cargs.append("-g")
-    if params.get("byte_swap_2"):
+    if params.get("byte_swap_2", False):
         cargs.append("-2")
-    if params.get("byte_swap_4"):
+    if params.get("byte_swap_4", False):
         cargs.append("-4")
-    if params.get("help_flag"):
+    if params.get("help_flag", False):
         cargs.append("-h")
     return cargs
 
 
-def v_3d_par2_afni_outputs(
-    params: V3dPar2AfniParameters,
+def v_3d_par2_afni_pl_outputs(
+    params: V3dPar2AfniPlParameters,
     execution: Execution,
-) -> V3dPar2AfniOutputs:
+) -> V3dPar2AfniPlOutputs:
     """
     Build outputs object containing output file paths and possibly stdout/stderr.
     
@@ -176,18 +157,20 @@ def v_3d_par2_afni_outputs(
     Returns:
         Outputs object.
     """
-    ret = V3dPar2AfniOutputs(
+    ret = V3dPar2AfniPlOutputs(
         root=execution.output_file("."),
-        output_files=execution.output_file(pathlib.Path(params.get("input_file")).name + "_converted"),
+        output_files=execution.output_file(pathlib.Path(params.get("input_file", None)).name + "_converted"),
     )
     return ret
 
 
-def v_3d_par2_afni_execute(
-    params: V3dPar2AfniParameters,
-    execution: Execution,
-) -> V3dPar2AfniOutputs:
+def v_3d_par2_afni_pl_execute(
+    params: V3dPar2AfniPlParameters,
+    runner: Runner | None = None,
+) -> V3dPar2AfniPlOutputs:
     """
+    3dPAR2AFNI.pl
+    
     Convert Philips PAR/REC files to AFNI's BRIK/HEAD, NIfTI, or ANALYZE format.
     
     Author: AFNI Developers
@@ -196,18 +179,20 @@ def v_3d_par2_afni_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `V3dPar2AfniOutputs`).
+        NamedTuple of outputs (described in `V3dPar2AfniPlOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_PAR2_AFNI_PL_METADATA)
     params = execution.params(params)
-    cargs = v_3d_par2_afni_cargs(params, execution)
-    ret = v_3d_par2_afni_outputs(params, execution)
+    cargs = v_3d_par2_afni_pl_cargs(params, execution)
+    ret = v_3d_par2_afni_pl_outputs(params, execution)
     execution.run(cargs)
     return ret
 
 
-def v_3d_par2_afni(
+def v_3d_par2_afni_pl(
     input_file: InputPathType,
     skip_outliers_test: bool = False,
     output_nifti: bool = False,
@@ -219,8 +204,10 @@ def v_3d_par2_afni(
     byte_swap_4: bool = False,
     help_flag: bool = False,
     runner: Runner | None = None,
-) -> V3dPar2AfniOutputs:
+) -> V3dPar2AfniPlOutputs:
     """
+    3dPAR2AFNI.pl
+    
     Convert Philips PAR/REC files to AFNI's BRIK/HEAD, NIfTI, or ANALYZE format.
     
     Author: AFNI Developers
@@ -247,11 +234,9 @@ def v_3d_par2_afni(
         help_flag: Display help message.
         runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `V3dPar2AfniOutputs`).
+        NamedTuple of outputs (described in `V3dPar2AfniPlOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_PAR2_AFNI_METADATA)
-    params = v_3d_par2_afni_params(
+    params = v_3d_par2_afni_pl_params(
         input_file=input_file,
         skip_outliers_test=skip_outliers_test,
         output_nifti=output_nifti,
@@ -263,13 +248,13 @@ def v_3d_par2_afni(
         byte_swap_4=byte_swap_4,
         help_flag=help_flag,
     )
-    return v_3d_par2_afni_execute(params, execution)
+    return v_3d_par2_afni_pl_execute(params, runner)
 
 
 __all__ = [
-    "V3dPar2AfniOutputs",
-    "V3dPar2AfniParameters",
-    "V_3D_PAR2_AFNI_METADATA",
-    "v_3d_par2_afni",
-    "v_3d_par2_afni_params",
+    "V3dPar2AfniPlOutputs",
+    "V_3D_PAR2_AFNI_PL_METADATA",
+    "v_3d_par2_afni_pl",
+    "v_3d_par2_afni_pl_execute",
+    "v_3d_par2_afni_pl_params",
 ]

niwrap_afni/afni/v_3d_periodogram.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_PERIODOGRAM_METADATA = Metadata(
-    id="6103fc4ec1736b577ce1d3b54eaf5ff203d3fbf7.boutiques",
+    id="93dde3ca0345979135760163670cbc2ca38a4193.boutiques",
     name="3dPeriodogram",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ V_3D_PERIODOGRAM_METADATA = Metadata(
 
 
 V3dPeriodogramParameters = typing.TypedDict('V3dPeriodogramParameters', {
-    "__STYXTYPE__": typing.Literal["3dPeriodogram"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dPeriodogram"]],
+    "prefix": typing.NotRequired[str | None],
+    "taper": typing.NotRequired[float | None],
+    "nfft": typing.NotRequired[float | None],
+    "dataset": InputPathType,
+})
+V3dPeriodogramParametersTagged = typing.TypedDict('V3dPeriodogramParametersTagged', {
+    "@type": typing.Literal["afni/3dPeriodogram"],
     "prefix": typing.NotRequired[str | None],
     "taper": typing.NotRequired[float | None],
     "nfft": typing.NotRequired[float | None],
     "dataset": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dPeriodogram": v_3d_periodogram_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 {
-        "3dPeriodogram": v_3d_periodogram_outputs,
-    }.get(t)
 
 
 class V3dPeriodogramOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_periodogram(...)`.
+    Output object returned when calling `V3dPeriodogramParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +46,7 @@ def v_3d_periodogram_params(
     prefix: str | None = None,
     taper: float | None = None,
     nfft: float | None = None,
-) -> V3dPeriodogramParameters:
+) -> V3dPeriodogramParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +59,7 @@ def v_3d_periodogram_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dPeriodogram",
+        "@type": "afni/3dPeriodogram",
         "dataset": dataset,
     }
     if prefix is not None:
@@ -111,22 +86,22 @@ def v_3d_periodogram_cargs(
     """
     cargs = []
     cargs.append("3dPeriodogram")
-    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("taper") is not None:
+    if params.get("taper", None) is not None:
         cargs.extend([
             "-taper",
-            str(params.get("taper"))
+            str(params.get("taper", None))
         ])
-    if params.get("nfft") is not None:
+    if params.get("nfft", None) is not None:
         cargs.extend([
             "-nfft",
-            str(params.get("nfft"))
+            str(params.get("nfft", None))
         ])
-    cargs.append(execution.input_file(params.get("dataset")))
+    cargs.append(execution.input_file(params.get("dataset", None)))
     return cargs
 
 
@@ -145,19 +120,21 @@ def v_3d_periodogram_outputs(
     """
     ret = V3dPeriodogramOutputs(
         root=execution.output_file("."),
-        output_header=execution.output_file(params.get("prefix") + ".HEAD") if (params.get("prefix") is not None) else None,
-        output_brick=execution.output_file(params.get("prefix") + ".BRIK") if (params.get("prefix") is not None) else None,
+        output_header=execution.output_file(params.get("prefix", None) + ".HEAD") if (params.get("prefix") is not None) else None,
+        output_brick=execution.output_file(params.get("prefix", None) + ".BRIK") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_periodogram_execute(
     params: V3dPeriodogramParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dPeriodogramOutputs:
     """
-    Computes the periodogram of each voxel time series. The periodogram is a crude
-    estimate of the power spectrum.
+    3dPeriodogram
+    
+    Computes the periodogram of each voxel time series. The periodogram is a
+    crude estimate of the power spectrum.
     
     Author: AFNI Developers
     
@@ -165,10 +142,12 @@ def v_3d_periodogram_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dPeriodogramOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_PERIODOGRAM_METADATA)
     params = execution.params(params)
     cargs = v_3d_periodogram_cargs(params, execution)
     ret = v_3d_periodogram_outputs(params, execution)
@@ -184,8 +163,10 @@ def v_3d_periodogram(
     runner: Runner | None = None,
 ) -> V3dPeriodogramOutputs:
     """
-    Computes the periodogram of each voxel time series. The periodogram is a crude
-    estimate of the power spectrum.
+    3dPeriodogram
+    
+    Computes the periodogram of each voxel time series. The periodogram is a
+    crude estimate of the power spectrum.
     
     Author: AFNI Developers
     
@@ -200,21 +181,19 @@ def v_3d_periodogram(
     Returns:
         NamedTuple of outputs (described in `V3dPeriodogramOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_PERIODOGRAM_METADATA)
     params = v_3d_periodogram_params(
         prefix=prefix,
         taper=taper,
         nfft=nfft,
         dataset=dataset,
     )
-    return v_3d_periodogram_execute(params, execution)
+    return v_3d_periodogram_execute(params, runner)
 
 
 __all__ = [
     "V3dPeriodogramOutputs",
-    "V3dPeriodogramParameters",
     "V_3D_PERIODOGRAM_METADATA",
     "v_3d_periodogram",
+    "v_3d_periodogram_execute",
     "v_3d_periodogram_params",
 ]