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

niwrap_afni/afni/v_3d_detrend.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_DETREND_METADATA = Metadata(
-    id="faca4a9ab4f62b19137fef436e84cc69ec36b7a1.boutiques",
+    id="8103447086a47281a149ad00588e72a68068176d.boutiques",
     name="3dDetrend",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,47 +14,20 @@ V_3D_DETREND_METADATA = Metadata(
 
 
 V3dDetrendParameters = typing.TypedDict('V3dDetrendParameters', {
-    "__STYXTYPE__": typing.Literal["3dDetrend"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dDetrend"]],
+    "in_file": InputPathType,
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+})
+V3dDetrendParametersTagged = typing.TypedDict('V3dDetrendParametersTagged', {
+    "@type": typing.Literal["afni/3dDetrend"],
     "in_file": InputPathType,
     "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dDetrend": v_3d_detrend_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 {
-        "3dDetrend": v_3d_detrend_outputs,
-    }.get(t)
 
 
 class V3dDetrendOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_detrend(...)`.
+    Output object returned when calling `V3dDetrendParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +40,7 @@ class V3dDetrendOutputs(typing.NamedTuple):
 def v_3d_detrend_params(
     in_file: InputPathType,
     outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
-) -> V3dDetrendParameters:
+) -> V3dDetrendParametersTagged:
     """
     Build parameters.
     
@@ -78,7 +51,7 @@ def v_3d_detrend_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dDetrend",
+        "@type": "afni/3dDetrend",
         "in_file": in_file,
     }
     if outputtype is not None:
@@ -101,9 +74,9 @@ def v_3d_detrend_cargs(
     """
     cargs = []
     cargs.append("3dDetrend")
-    cargs.append(execution.input_file(params.get("in_file")))
-    if params.get("outputtype") is not None:
-        cargs.append(params.get("outputtype"))
+    cargs.append(execution.input_file(params.get("in_file", None)))
+    if params.get("outputtype", None) is not None:
+        cargs.append(params.get("outputtype", None))
     return cargs
 
 
@@ -122,7 +95,7 @@ def v_3d_detrend_outputs(
     """
     ret = V3dDetrendOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(pathlib.Path(params.get("in_file")).name + "_detrend"),
+        out_file=execution.output_file(pathlib.Path(params.get("in_file", None)).name + "_detrend"),
         out_file_=execution.output_file("out_file"),
     )
     return ret
@@ -130,9 +103,11 @@ def v_3d_detrend_outputs(
 
 def v_3d_detrend_execute(
     params: V3dDetrendParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dDetrendOutputs:
     """
+    3dDetrend
+    
     This program removes components from voxel time series using linear least
     squares.
     
@@ -142,10 +117,12 @@ def v_3d_detrend_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dDetrendOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DETREND_METADATA)
     params = execution.params(params)
     cargs = v_3d_detrend_cargs(params, execution)
     ret = v_3d_detrend_outputs(params, execution)
@@ -159,6 +136,8 @@ def v_3d_detrend(
     runner: Runner | None = None,
 ) -> V3dDetrendOutputs:
     """
+    3dDetrend
+    
     This program removes components from voxel time series using linear least
     squares.
     
@@ -173,19 +152,17 @@ def v_3d_detrend(
     Returns:
         NamedTuple of outputs (described in `V3dDetrendOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_DETREND_METADATA)
     params = v_3d_detrend_params(
         in_file=in_file,
         outputtype=outputtype,
     )
-    return v_3d_detrend_execute(params, execution)
+    return v_3d_detrend_execute(params, runner)
 
 
 __all__ = [
     "V3dDetrendOutputs",
-    "V3dDetrendParameters",
     "V_3D_DETREND_METADATA",
     "v_3d_detrend",
+    "v_3d_detrend_execute",
     "v_3d_detrend_params",
 ]

niwrap_afni/afni/v_3d_dft.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_DFT_METADATA = Metadata(
-    id="6d9e48bc41131cc9d366a1482d65d7f807be33ce.boutiques",
+    id="2962876f8d44b9744d34d11bb1c8253a9c686b30.boutiques",
     name="3dDFT",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ V_3D_DFT_METADATA = Metadata(
 
 
 V3dDftParameters = typing.TypedDict('V3dDftParameters', {
-    "__STYXTYPE__": typing.Literal["3dDFT"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dDFT"]],
+    "infile": InputPathType,
+    "prefix": str,
+    "abs_output": bool,
+    "nfft": typing.NotRequired[float | None],
+    "detrend": bool,
+    "taper": typing.NotRequired[float | None],
+    "inverse": bool,
+})
+V3dDftParametersTagged = typing.TypedDict('V3dDftParametersTagged', {
+    "@type": typing.Literal["afni/3dDFT"],
     "infile": InputPathType,
     "prefix": str,
     "abs_output": bool,
@@ -23,43 +33,11 @@ V3dDftParameters = typing.TypedDict('V3dDftParameters', {
     "taper": typing.NotRequired[float | None],
     "inverse": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dDFT": v_3d_dft_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 {
-        "3dDFT": v_3d_dft_outputs,
-    }.get(t)
 
 
 class V3dDftOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_dft(...)`.
+    Output object returned when calling `V3dDftParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +55,7 @@ def v_3d_dft_params(
     detrend: bool = False,
     taper: float | None = None,
     inverse: bool = False,
-) -> V3dDftParameters:
+) -> V3dDftParametersTagged:
     """
     Build parameters.
     
@@ -93,7 +71,7 @@ def v_3d_dft_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dDFT",
+        "@type": "afni/3dDFT",
         "infile": infile,
         "prefix": prefix,
         "abs_output": abs_output,
@@ -122,26 +100,26 @@ def v_3d_dft_cargs(
     """
     cargs = []
     cargs.append("3dDFT")
-    cargs.append(execution.input_file(params.get("infile")))
+    cargs.append(execution.input_file(params.get("infile", None)))
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("abs_output"):
+    if params.get("abs_output", False):
         cargs.append("-abs")
-    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))
         ])
-    if params.get("detrend"):
+    if params.get("detrend", False):
         cargs.append("-detrend")
-    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("inverse"):
+    if params.get("inverse", False):
         cargs.append("-inverse")
     return cargs
 
@@ -161,19 +139,21 @@ def v_3d_dft_outputs(
     """
     ret = V3dDftOutputs(
         root=execution.output_file("."),
-        outfile=execution.output_file(params.get("prefix") + "+orig.BRIK"),
-        outheader=execution.output_file(params.get("prefix") + "+orig.HEAD"),
+        outfile=execution.output_file(params.get("prefix", None) + "+orig.BRIK"),
+        outheader=execution.output_file(params.get("prefix", None) + "+orig.HEAD"),
     )
     return ret
 
 
 def v_3d_dft_execute(
     params: V3dDftParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dDftOutputs:
     """
-    Performs Discrete Fourier Transform (DFT) along the time axis of a complex- or
-    float-valued dataset.
+    3dDFT
+    
+    Performs Discrete Fourier Transform (DFT) along the time axis of a complex-
+    or float-valued dataset.
     
     Author: AFNI Developers
     
@@ -181,10 +161,12 @@ def v_3d_dft_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dDftOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DFT_METADATA)
     params = execution.params(params)
     cargs = v_3d_dft_cargs(params, execution)
     ret = v_3d_dft_outputs(params, execution)
@@ -203,8 +185,10 @@ def v_3d_dft(
     runner: Runner | None = None,
 ) -> V3dDftOutputs:
     """
-    Performs Discrete Fourier Transform (DFT) along the time axis of a complex- or
-    float-valued dataset.
+    3dDFT
+    
+    Performs Discrete Fourier Transform (DFT) along the time axis of a complex-
+    or float-valued dataset.
     
     Author: AFNI Developers
     
@@ -222,8 +206,6 @@ def v_3d_dft(
     Returns:
         NamedTuple of outputs (described in `V3dDftOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_DFT_METADATA)
     params = v_3d_dft_params(
         infile=infile,
         prefix=prefix,
@@ -233,13 +215,13 @@ def v_3d_dft(
         taper=taper,
         inverse=inverse,
     )
-    return v_3d_dft_execute(params, execution)
+    return v_3d_dft_execute(params, runner)
 
 
 __all__ = [
     "V3dDftOutputs",
-    "V3dDftParameters",
     "V_3D_DFT_METADATA",
     "v_3d_dft",
+    "v_3d_dft_execute",
     "v_3d_dft_params",
 ]

niwrap_afni/afni/v_3d_diff.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_DIFF_METADATA = Metadata(
-    id="7213e0a8a950ad09edafb5b67833470abda8875b.boutiques",
+    id="8694f200d58e60edf8f8355fa427160988463ac9.boutiques",
     name="3dDiff",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V_3D_DIFF_METADATA = Metadata(
 
 
 V3dDiffParameters = typing.TypedDict('V3dDiffParameters', {
-    "__STYXTYPE__": typing.Literal["3dDiff"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dDiff"]],
+    "dataset_a": InputPathType,
+    "dataset_b": InputPathType,
+    "tolerance": typing.NotRequired[float | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "quiet_mode": bool,
+    "tabular_mode": bool,
+    "brutalist_mode": bool,
+    "long_report_mode": bool,
+})
+V3dDiffParametersTagged = typing.TypedDict('V3dDiffParametersTagged', {
+    "@type": typing.Literal["afni/3dDiff"],
     "dataset_a": InputPathType,
     "dataset_b": InputPathType,
     "tolerance": typing.NotRequired[float | None],
@@ -24,43 +35,11 @@ V3dDiffParameters = typing.TypedDict('V3dDiffParameters', {
     "brutalist_mode": bool,
     "long_report_mode": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dDiff": v_3d_diff_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 {
-        "3dDiff": v_3d_diff_outputs,
-    }.get(t)
 
 
 class V3dDiffOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_diff(...)`.
+    Output object returned when calling `V3dDiffParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def v_3d_diff_params(
     tabular_mode: bool = False,
     brutalist_mode: bool = False,
     long_report_mode: bool = False,
-) -> V3dDiffParameters:
+) -> V3dDiffParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +74,7 @@ def v_3d_diff_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dDiff",
+        "@type": "afni/3dDiff",
         "dataset_a": dataset_a,
         "dataset_b": dataset_b,
         "quiet_mode": quiet_mode,
@@ -127,29 +106,29 @@ def v_3d_diff_cargs(
     cargs.append("3dDiff")
     cargs.extend([
         "-a",
-        execution.input_file(params.get("dataset_a"))
+        execution.input_file(params.get("dataset_a", None))
     ])
     cargs.extend([
         "-b",
-        execution.input_file(params.get("dataset_b"))
+        execution.input_file(params.get("dataset_b", None))
     ])
-    if params.get("tolerance") is not None:
+    if params.get("tolerance", None) is not None:
         cargs.extend([
             "-tol",
-            str(params.get("tolerance"))
+            str(params.get("tolerance", 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("quiet_mode"):
+    if params.get("quiet_mode", False):
         cargs.append("-q")
-    if params.get("tabular_mode"):
+    if params.get("tabular_mode", False):
         cargs.append("-tabular")
-    if params.get("brutalist_mode"):
+    if params.get("brutalist_mode", False):
         cargs.append("-brutalist")
-    if params.get("long_report_mode"):
+    if params.get("long_report_mode", False):
         cargs.append("-long_report")
     return cargs
 
@@ -169,16 +148,18 @@ def v_3d_diff_outputs(
     """
     ret = V3dDiffOutputs(
         root=execution.output_file("."),
-        output_log=execution.output_file(pathlib.Path(params.get("dataset_a")).name + "_vs_" + pathlib.Path(params.get("dataset_b")).name + ".log"),
+        output_log=execution.output_file(pathlib.Path(params.get("dataset_a", None)).name + "_vs_" + pathlib.Path(params.get("dataset_b", None)).name + ".log"),
     )
     return ret
 
 
 def v_3d_diff_execute(
     params: V3dDiffParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dDiffOutputs:
     """
+    3dDiff
+    
     A program to examine element-wise differences between two images.
     
     Author: AFNI Developers
@@ -187,10 +168,12 @@ def v_3d_diff_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dDiffOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DIFF_METADATA)
     params = execution.params(params)
     cargs = v_3d_diff_cargs(params, execution)
     ret = v_3d_diff_outputs(params, execution)
@@ -210,6 +193,8 @@ def v_3d_diff(
     runner: Runner | None = None,
 ) -> V3dDiffOutputs:
     """
+    3dDiff
+    
     A program to examine element-wise differences between two images.
     
     Author: AFNI Developers
@@ -230,8 +215,6 @@ def v_3d_diff(
     Returns:
         NamedTuple of outputs (described in `V3dDiffOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_DIFF_METADATA)
     params = v_3d_diff_params(
         dataset_a=dataset_a,
         dataset_b=dataset_b,
@@ -242,13 +225,13 @@ def v_3d_diff(
         brutalist_mode=brutalist_mode,
         long_report_mode=long_report_mode,
     )
-    return v_3d_diff_execute(params, execution)
+    return v_3d_diff_execute(params, runner)
 
 
 __all__ = [
     "V3dDiffOutputs",
-    "V3dDiffParameters",
     "V_3D_DIFF_METADATA",
     "v_3d_diff",
+    "v_3d_diff_execute",
     "v_3d_diff_params",
 ]