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

niwrap_afni/afni/v_3d_fdr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_FDR_METADATA = Metadata(
-    id="aabaf1707d0311895de132618ad782f134d28f72.boutiques",
+    id="350aa41ff9a5dcdf52caeed1110a7921f9ec4220.boutiques",
     name="3dFDR",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ V_3D_FDR_METADATA = Metadata(
 
 
 V3dFdrParameters = typing.TypedDict('V3dFdrParameters', {
-    "__STYXTYPE__": typing.Literal["3dFDR"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dFDR"]],
+    "input_file": InputPathType,
+    "input1d_file": typing.NotRequired[InputPathType | None],
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "mask_threshold": typing.NotRequired[float | None],
+    "constant_type": typing.NotRequired[typing.Literal["cind", "cdep"] | None],
+    "quiet": bool,
+    "list": bool,
+    "prefix": str,
+    "mode_option": typing.NotRequired[typing.Literal["old", "new"] | None],
+    "pmask": bool,
+    "nopmask": bool,
+    "force": bool,
+    "float": bool,
+    "qval": bool,
+})
+V3dFdrParametersTagged = typing.TypedDict('V3dFdrParametersTagged', {
+    "@type": typing.Literal["afni/3dFDR"],
     "input_file": InputPathType,
     "input1d_file": typing.NotRequired[InputPathType | None],
     "mask_file": typing.NotRequired[InputPathType | None],
@@ -30,43 +47,11 @@ V3dFdrParameters = typing.TypedDict('V3dFdrParameters', {
     "float": bool,
     "qval": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dFDR": v_3d_fdr_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 {
-        "3dFDR": v_3d_fdr_outputs,
-    }.get(t)
 
 
 class V3dFdrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_fdr(...)`.
+    Output object returned when calling `V3dFdrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -93,7 +78,7 @@ def v_3d_fdr_params(
     force: bool = False,
     float_: bool = False,
     qval: bool = False,
-) -> V3dFdrParameters:
+) -> V3dFdrParametersTagged:
     """
     Build parameters.
     
@@ -122,7 +107,7 @@ def v_3d_fdr_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dFDR",
+        "@type": "afni/3dFDR",
         "input_file": input_file,
         "quiet": quiet,
         "list": list_,
@@ -163,50 +148,50 @@ def v_3d_fdr_cargs(
     cargs.append("3dFDR")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
-    if params.get("input1d_file") is not None:
+    if params.get("input1d_file", None) is not None:
         cargs.extend([
             "-input1D",
-            execution.input_file(params.get("input1d_file"))
+            execution.input_file(params.get("input1d_file", None))
         ])
-    if params.get("mask_file") is not None:
+    if params.get("mask_file", None) is not None:
         cargs.extend([
             "-mask_file",
-            execution.input_file(params.get("mask_file"))
+            execution.input_file(params.get("mask_file", None))
         ])
-    if params.get("mask_threshold") is not None:
+    if params.get("mask_threshold", None) is not None:
         cargs.extend([
             "-mask_thr",
-            str(params.get("mask_threshold"))
+            str(params.get("mask_threshold", None))
         ])
-    if params.get("constant_type") is not None:
+    if params.get("constant_type", None) is not None:
         cargs.extend([
             "-c",
-            params.get("constant_type")
+            params.get("constant_type", None)
         ])
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("list"):
+    if params.get("list", False):
         cargs.append("-list")
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("mode_option") is not None:
+    if params.get("mode_option", None) is not None:
         cargs.extend([
             "-",
-            params.get("mode_option")
+            params.get("mode_option", None)
         ])
-    if params.get("pmask"):
+    if params.get("pmask", False):
         cargs.append("-pmask")
-    if params.get("nopmask"):
+    if params.get("nopmask", False):
         cargs.append("-nopmask")
-    if params.get("force"):
+    if params.get("force", False):
         cargs.append("-force")
-    if params.get("float"):
+    if params.get("float", False):
         cargs.append("-float")
-    if params.get("qval"):
+    if params.get("qval", False):
         cargs.append("-qval")
     return cargs
 
@@ -226,18 +211,20 @@ def v_3d_fdr_outputs(
     """
     ret = V3dFdrOutputs(
         root=execution.output_file("."),
-        output_brik=execution.output_file(params.get("prefix") + "+orig.BRIK"),
-        output_head=execution.output_file(params.get("prefix") + "+orig.HEAD"),
-        output_1d=execution.output_file(params.get("prefix") + ".1D"),
+        output_brik=execution.output_file(params.get("prefix", None) + "+orig.BRIK"),
+        output_head=execution.output_file(params.get("prefix", None) + "+orig.HEAD"),
+        output_1d=execution.output_file(params.get("prefix", None) + ".1D"),
     )
     return ret
 
 
 def v_3d_fdr_execute(
     params: V3dFdrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dFdrOutputs:
     """
+    3dFDR
+    
     A tool for applying False Discovery Rate (FDR) thresholding to voxelwise
     statistics in 3D functional datasets.
     
@@ -247,10 +234,12 @@ def v_3d_fdr_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dFdrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_FDR_METADATA)
     params = execution.params(params)
     cargs = v_3d_fdr_cargs(params, execution)
     ret = v_3d_fdr_outputs(params, execution)
@@ -276,6 +265,8 @@ def v_3d_fdr(
     runner: Runner | None = None,
 ) -> V3dFdrOutputs:
     """
+    3dFDR
+    
     A tool for applying False Discovery Rate (FDR) thresholding to voxelwise
     statistics in 3D functional datasets.
     
@@ -308,8 +299,6 @@ def v_3d_fdr(
     Returns:
         NamedTuple of outputs (described in `V3dFdrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_FDR_METADATA)
     params = v_3d_fdr_params(
         input_file=input_file,
         input1d_file=input1d_file,
@@ -326,13 +315,13 @@ def v_3d_fdr(
         float_=float_,
         qval=qval,
     )
-    return v_3d_fdr_execute(params, execution)
+    return v_3d_fdr_execute(params, runner)
 
 
 __all__ = [
     "V3dFdrOutputs",
-    "V3dFdrParameters",
     "V_3D_FDR_METADATA",
     "v_3d_fdr",
+    "v_3d_fdr_execute",
     "v_3d_fdr_params",
 ]

niwrap_afni/afni/v_3d_fft.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_FFT_METADATA = Metadata(
-    id="251cf31407b8d42f4fb6ef0851808d440783f20f.boutiques",
+    id="16383a790fc31c986fad912d46cdaf2dbe9e7423.boutiques",
     name="3dFFT",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,22 @@ V_3D_FFT_METADATA = Metadata(
 
 
 V3dFftParameters = typing.TypedDict('V3dFftParameters', {
-    "__STYXTYPE__": typing.Literal["3dFFT"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dFFT"]],
+    "dataset": InputPathType,
+    "abs": bool,
+    "phase": bool,
+    "complex": bool,
+    "inverse": bool,
+    "Lx": typing.NotRequired[float | None],
+    "Ly": typing.NotRequired[float | None],
+    "Lz": typing.NotRequired[float | None],
+    "altIN": bool,
+    "altOUT": bool,
+    "input": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+})
+V3dFftParametersTagged = typing.TypedDict('V3dFftParametersTagged', {
+    "@type": typing.Literal["afni/3dFFT"],
     "dataset": InputPathType,
     "abs": bool,
     "phase": bool,
@@ -28,43 +43,11 @@ V3dFftParameters = typing.TypedDict('V3dFftParameters', {
     "input": typing.NotRequired[InputPathType | None],
     "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 {
-        "3dFFT": v_3d_fft_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 {
-        "3dFFT": v_3d_fft_outputs,
-    }.get(t)
 
 
 class V3dFftOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_fft(...)`.
+    Output object returned when calling `V3dFftParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -85,7 +68,7 @@ def v_3d_fft_params(
     alt_out: bool = False,
     input_: InputPathType | None = None,
     prefix: str | None = None,
-) -> V3dFftParameters:
+) -> V3dFftParametersTagged:
     """
     Build parameters.
     
@@ -111,7 +94,7 @@ def v_3d_fft_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dFFT",
+        "@type": "afni/3dFFT",
         "dataset": dataset,
         "abs": abs_,
         "phase": phase,
@@ -148,43 +131,43 @@ def v_3d_fft_cargs(
     """
     cargs = []
     cargs.append("3dFFT")
-    cargs.append(execution.input_file(params.get("dataset")))
-    if params.get("abs"):
+    cargs.append(execution.input_file(params.get("dataset", None)))
+    if params.get("abs", False):
         cargs.append("--abs")
-    if params.get("phase"):
+    if params.get("phase", False):
         cargs.append("--phase")
-    if params.get("complex"):
+    if params.get("complex", False):
         cargs.append("--complex")
-    if params.get("inverse"):
+    if params.get("inverse", False):
         cargs.append("--inverse")
-    if params.get("Lx") is not None:
+    if params.get("Lx", None) is not None:
         cargs.extend([
             "--Lx",
-            str(params.get("Lx"))
+            str(params.get("Lx", None))
         ])
-    if params.get("Ly") is not None:
+    if params.get("Ly", None) is not None:
         cargs.extend([
             "--Ly",
-            str(params.get("Ly"))
+            str(params.get("Ly", None))
         ])
-    if params.get("Lz") is not None:
+    if params.get("Lz", None) is not None:
         cargs.extend([
             "--Lz",
-            str(params.get("Lz"))
+            str(params.get("Lz", None))
         ])
-    if params.get("altIN"):
+    if params.get("altIN", False):
         cargs.append("--altIN")
-    if params.get("altOUT"):
+    if params.get("altOUT", False):
         cargs.append("--altOUT")
-    if params.get("input") is not None:
+    if params.get("input", None) is not None:
         cargs.extend([
             "--input",
-            execution.input_file(params.get("input"))
+            execution.input_file(params.get("input", 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)
         ])
     return cargs
 
@@ -204,18 +187,20 @@ def v_3d_fft_outputs(
     """
     ret = V3dFftOutputs(
         root=execution.output_file("."),
-        output_dataset=execution.output_file(params.get("prefix") + ".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,
     )
     return ret
 
 
 def v_3d_fft_execute(
     params: V3dFftParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dFftOutputs:
     """
-    Performs the FFT of the input dataset in 3 directions (x, y, z) and produces the
-    output dataset.
+    3dFFT
+    
+    Performs the FFT of the input dataset in 3 directions (x, y, z) and produces
+    the output dataset.
     
     Author: AFNI Developers
     
@@ -223,10 +208,12 @@ def v_3d_fft_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dFftOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_FFT_METADATA)
     params = execution.params(params)
     cargs = v_3d_fft_cargs(params, execution)
     ret = v_3d_fft_outputs(params, execution)
@@ -250,8 +237,10 @@ def v_3d_fft(
     runner: Runner | None = None,
 ) -> V3dFftOutputs:
     """
-    Performs the FFT of the input dataset in 3 directions (x, y, z) and produces the
-    output dataset.
+    3dFFT
+    
+    Performs the FFT of the input dataset in 3 directions (x, y, z) and produces
+    the output dataset.
     
     Author: AFNI Developers
     
@@ -279,8 +268,6 @@ def v_3d_fft(
     Returns:
         NamedTuple of outputs (described in `V3dFftOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_FFT_METADATA)
     params = v_3d_fft_params(
         dataset=dataset,
         abs_=abs_,
@@ -295,13 +282,13 @@ def v_3d_fft(
         input_=input_,
         prefix=prefix,
     )
-    return v_3d_fft_execute(params, execution)
+    return v_3d_fft_execute(params, runner)
 
 
 __all__ = [
     "V3dFftOutputs",
-    "V3dFftParameters",
     "V_3D_FFT_METADATA",
     "v_3d_fft",
+    "v_3d_fft_execute",
     "v_3d_fft_params",
 ]

niwrap_afni/afni/v_3d_friedman.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_FRIEDMAN_METADATA = Metadata(
-    id="f420b1764d2a8c3e67aa44bf4d11906383ad53d6.boutiques",
+    id="a8439d785b86745838dfe4d337513a003ae76358.boutiques",
     name="3dFriedman",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,55 +14,29 @@ V_3D_FRIEDMAN_METADATA = Metadata(
 
 
 V3dFriedmanParameters = typing.TypedDict('V3dFriedmanParameters', {
-    "__STYXTYPE__": typing.Literal["3dFriedman"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dFriedman"]],
+    "levels": int,
+    "datasets": list[InputPathType],
+    "workmem": typing.NotRequired[int | None],
+    "voxel_num": typing.NotRequired[int | None],
+    "output_prefix": str,
+})
+V3dFriedmanParametersTagged = typing.TypedDict('V3dFriedmanParametersTagged', {
+    "@type": typing.Literal["afni/3dFriedman"],
     "levels": int,
     "datasets": list[InputPathType],
     "workmem": typing.NotRequired[int | None],
     "voxel_num": typing.NotRequired[int | None],
     "output_prefix": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dFriedman": v_3d_friedman_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 {
-        "3dFriedman": v_3d_friedman_outputs,
-    }.get(t)
 
 
 class V3dFriedmanOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_friedman(...)`.
+    Output object returned when calling `V3dFriedmanParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    output_file: OutputPathType
-    """Friedman statistics output file"""
 
 
 def v_3d_friedman_params(
@@ -71,7 +45,7 @@ def v_3d_friedman_params(
     output_prefix: str,
     workmem: int | None = None,
     voxel_num: int | None = None,
-) -> V3dFriedmanParameters:
+) -> V3dFriedmanParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +59,7 @@ def v_3d_friedman_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dFriedman",
+        "@type": "afni/3dFriedman",
         "levels": levels,
         "datasets": datasets,
         "output_prefix": output_prefix,
@@ -112,24 +86,24 @@ def v_3d_friedman_cargs(
     """
     cargs = []
     cargs.append("3dFriedman")
-    cargs.append(str(params.get("levels")))
+    cargs.append(str(params.get("levels", None)))
     cargs.extend([
         "-dset",
-        *[execution.input_file(f) for f in params.get("datasets")]
+        *[execution.input_file(f) for f in params.get("datasets", None)]
     ])
-    if params.get("workmem") is not None:
+    if params.get("workmem", None) is not None:
         cargs.extend([
             "-workmem",
-            str(params.get("workmem"))
+            str(params.get("workmem", None))
         ])
-    if params.get("voxel_num") is not None:
+    if params.get("voxel_num", None) is not None:
         cargs.extend([
             "-voxel",
-            str(params.get("voxel_num"))
+            str(params.get("voxel_num", None))
         ])
     cargs.extend([
         "-out",
-        params.get("output_prefix")
+        params.get("output_prefix", None)
     ])
     return cargs
 
@@ -149,16 +123,17 @@ def v_3d_friedman_outputs(
     """
     ret = V3dFriedmanOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_prefix") + "*"),
     )
     return ret
 
 
 def v_3d_friedman_execute(
     params: V3dFriedmanParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dFriedmanOutputs:
     """
+    3dFriedman
+    
     Performs nonparametric Friedman test for randomized complete block design
     experiments.
     
@@ -168,10 +143,12 @@ def v_3d_friedman_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dFriedmanOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_FRIEDMAN_METADATA)
     params = execution.params(params)
     cargs = v_3d_friedman_cargs(params, execution)
     ret = v_3d_friedman_outputs(params, execution)
@@ -188,6 +165,8 @@ def v_3d_friedman(
     runner: Runner | None = None,
 ) -> V3dFriedmanOutputs:
     """
+    3dFriedman
+    
     Performs nonparametric Friedman test for randomized complete block design
     experiments.
     
@@ -205,8 +184,6 @@ def v_3d_friedman(
     Returns:
         NamedTuple of outputs (described in `V3dFriedmanOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_FRIEDMAN_METADATA)
     params = v_3d_friedman_params(
         levels=levels,
         datasets=datasets,
@@ -214,13 +191,13 @@ def v_3d_friedman(
         voxel_num=voxel_num,
         output_prefix=output_prefix,
     )
-    return v_3d_friedman_execute(params, execution)
+    return v_3d_friedman_execute(params, runner)
 
 
 __all__ = [
     "V3dFriedmanOutputs",
-    "V3dFriedmanParameters",
     "V_3D_FRIEDMAN_METADATA",
     "v_3d_friedman",
+    "v_3d_friedman_execute",
     "v_3d_friedman_params",
 ]