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

niwrap_afni/afni/v_3d_intracranial.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_INTRACRANIAL_METADATA = Metadata(
-    id="684ca9fab6f781de1e41403ff411216ba16a42b4.boutiques",
+    id="5071c8eb886f4586580d6adc004176db2d6abdeb.boutiques",
     name="3dIntracranial",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ V_3D_INTRACRANIAL_METADATA = Metadata(
 
 
 V3dIntracranialParameters = typing.TypedDict('V3dIntracranialParameters', {
-    "__STYXTYPE__": typing.Literal["3dIntracranial"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dIntracranial"]],
+    "infile": InputPathType,
+    "prefix": str,
+    "min_val": typing.NotRequired[float | None],
+    "max_val": typing.NotRequired[float | None],
+    "min_conn": typing.NotRequired[float | None],
+    "max_conn": typing.NotRequired[float | None],
+    "no_smooth": bool,
+    "mask": bool,
+    "quiet": bool,
+})
+V3dIntracranialParametersTagged = typing.TypedDict('V3dIntracranialParametersTagged', {
+    "@type": typing.Literal["afni/3dIntracranial"],
     "infile": InputPathType,
     "prefix": str,
     "min_val": typing.NotRequired[float | None],
@@ -25,43 +37,11 @@ V3dIntracranialParameters = typing.TypedDict('V3dIntracranialParameters', {
     "mask": bool,
     "quiet": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dIntracranial": v_3d_intracranial_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 {
-        "3dIntracranial": v_3d_intracranial_outputs,
-    }.get(t)
 
 
 class V3dIntracranialOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_intracranial(...)`.
+    Output object returned when calling `V3dIntracranialParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +59,7 @@ def v_3d_intracranial_params(
     no_smooth: bool = False,
     mask: bool = False,
     quiet: bool = False,
-) -> V3dIntracranialParameters:
+) -> V3dIntracranialParametersTagged:
     """
     Build parameters.
     
@@ -100,7 +80,7 @@ def v_3d_intracranial_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dIntracranial",
+        "@type": "afni/3dIntracranial",
         "infile": infile,
         "prefix": prefix,
         "no_smooth": no_smooth,
@@ -135,37 +115,37 @@ def v_3d_intracranial_cargs(
     cargs.append("3dIntracranial")
     cargs.extend([
         "-anat",
-        execution.input_file(params.get("infile"))
+        execution.input_file(params.get("infile", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("min_val") is not None:
+    if params.get("min_val", None) is not None:
         cargs.extend([
             "-min_val",
-            str(params.get("min_val"))
+            str(params.get("min_val", None))
         ])
-    if params.get("max_val") is not None:
+    if params.get("max_val", None) is not None:
         cargs.extend([
             "-max_val",
-            str(params.get("max_val"))
+            str(params.get("max_val", None))
         ])
-    if params.get("min_conn") is not None:
+    if params.get("min_conn", None) is not None:
         cargs.extend([
             "-min_conn",
-            str(params.get("min_conn"))
+            str(params.get("min_conn", None))
         ])
-    if params.get("max_conn") is not None:
+    if params.get("max_conn", None) is not None:
         cargs.extend([
             "-max_conn",
-            str(params.get("max_conn"))
+            str(params.get("max_conn", None))
         ])
-    if params.get("no_smooth"):
+    if params.get("no_smooth", False):
         cargs.append("-nosmooth")
-    if params.get("mask"):
+    if params.get("mask", False):
         cargs.append("-mask")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
     return cargs
 
@@ -185,16 +165,18 @@ def v_3d_intracranial_outputs(
     """
     ret = V3dIntracranialOutputs(
         root=execution.output_file("."),
-        segmented_image=execution.output_file(params.get("prefix") + "+orig"),
+        segmented_image=execution.output_file(params.get("prefix", None) + "+orig"),
     )
     return ret
 
 
 def v_3d_intracranial_execute(
     params: V3dIntracranialParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dIntracranialOutputs:
     """
+    3dIntracranial
+    
     Performs automatic segmentation of intracranial region.
     
     Author: AFNI Developers
@@ -203,10 +185,12 @@ def v_3d_intracranial_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dIntracranialOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_INTRACRANIAL_METADATA)
     params = execution.params(params)
     cargs = v_3d_intracranial_cargs(params, execution)
     ret = v_3d_intracranial_outputs(params, execution)
@@ -227,6 +211,8 @@ def v_3d_intracranial(
     runner: Runner | None = None,
 ) -> V3dIntracranialOutputs:
     """
+    3dIntracranial
+    
     Performs automatic segmentation of intracranial region.
     
     Author: AFNI Developers
@@ -250,8 +236,6 @@ def v_3d_intracranial(
     Returns:
         NamedTuple of outputs (described in `V3dIntracranialOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_INTRACRANIAL_METADATA)
     params = v_3d_intracranial_params(
         infile=infile,
         prefix=prefix,
@@ -263,13 +247,13 @@ def v_3d_intracranial(
         mask=mask,
         quiet=quiet,
     )
-    return v_3d_intracranial_execute(params, execution)
+    return v_3d_intracranial_execute(params, runner)
 
 
 __all__ = [
     "V3dIntracranialOutputs",
-    "V3dIntracranialParameters",
     "V_3D_INTRACRANIAL_METADATA",
     "v_3d_intracranial",
+    "v_3d_intracranial_execute",
     "v_3d_intracranial_params",
 ]

niwrap_afni/afni/v_3d_inv_fmri.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_INV_FMRI_METADATA = Metadata(
-    id="25a087e9b21c2aecd11168bed959695342cab5e2.boutiques",
+    id="b0190aecac1be10981936d10e919bae5418e8d9a.boutiques",
     name="3dInvFMRI",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,21 @@ V_3D_INV_FMRI_METADATA = Metadata(
 
 
 V3dInvFmriParameters = typing.TypedDict('V3dInvFmriParameters', {
-    "__STYXTYPE__": typing.Literal["3dInvFMRI"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dInvFMRI"]],
+    "input_file": InputPathType,
+    "activation_map": InputPathType,
+    "map_weight": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "baseline_file": typing.NotRequired[list[InputPathType] | None],
+    "polynom_order": typing.NotRequired[float | None],
+    "output_file": typing.NotRequired[str | None],
+    "method": typing.NotRequired[str | None],
+    "alpha": typing.NotRequired[float | None],
+    "smooth_fir": bool,
+    "smooth_median": bool,
+})
+V3dInvFmriParametersTagged = typing.TypedDict('V3dInvFmriParametersTagged', {
+    "@type": typing.Literal["afni/3dInvFMRI"],
     "input_file": InputPathType,
     "activation_map": InputPathType,
     "map_weight": typing.NotRequired[InputPathType | None],
@@ -27,43 +41,11 @@ V3dInvFmriParameters = typing.TypedDict('V3dInvFmriParameters', {
     "smooth_fir": bool,
     "smooth_median": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dInvFMRI": v_3d_inv_fmri_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 {
-        "3dInvFMRI": v_3d_inv_fmri_outputs,
-    }.get(t)
 
 
 class V3dInvFmriOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_inv_fmri(...)`.
+    Output object returned when calling `V3dInvFmriParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -83,7 +65,7 @@ def v_3d_inv_fmri_params(
     alpha: float | None = None,
     smooth_fir: bool = False,
     smooth_median: bool = False,
-) -> V3dInvFmriParameters:
+) -> V3dInvFmriParametersTagged:
     """
     Build parameters.
     
@@ -111,7 +93,7 @@ def v_3d_inv_fmri_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dInvFMRI",
+        "@type": "afni/3dInvFMRI",
         "input_file": input_file,
         "activation_map": activation_map,
         "smooth_fir": smooth_fir,
@@ -151,50 +133,50 @@ def v_3d_inv_fmri_cargs(
     cargs.append("3dInvFMRI")
     cargs.extend([
         "-data",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "-map",
-        execution.input_file(params.get("activation_map"))
+        execution.input_file(params.get("activation_map", None))
     ])
-    if params.get("map_weight") is not None:
+    if params.get("map_weight", None) is not None:
         cargs.extend([
             "-mapwt",
-            execution.input_file(params.get("map_weight"))
+            execution.input_file(params.get("map_weight", 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("baseline_file") is not None:
+    if params.get("baseline_file", None) is not None:
         cargs.extend([
             "-base",
-            *[execution.input_file(f) for f in params.get("baseline_file")]
+            *[execution.input_file(f) for f in params.get("baseline_file", None)]
         ])
-    if params.get("polynom_order") is not None:
+    if params.get("polynom_order", None) is not None:
         cargs.extend([
             "-polort",
-            str(params.get("polynom_order"))
+            str(params.get("polynom_order", None))
         ])
-    if params.get("output_file") is not None:
+    if params.get("output_file", None) is not None:
         cargs.extend([
             "-out",
-            params.get("output_file")
+            params.get("output_file", None)
         ])
-    if params.get("method") is not None:
+    if params.get("method", None) is not None:
         cargs.extend([
             "-method",
-            params.get("method")
+            params.get("method", None)
         ])
-    if params.get("alpha") is not None:
+    if params.get("alpha", None) is not None:
         cargs.extend([
             "-alpha",
-            str(params.get("alpha"))
+            str(params.get("alpha", None))
         ])
-    if params.get("smooth_fir"):
+    if params.get("smooth_fir", False):
         cargs.append("-fir5")
-    if params.get("smooth_median"):
+    if params.get("smooth_median", False):
         cargs.append("-median5")
     return cargs
 
@@ -214,16 +196,18 @@ def v_3d_inv_fmri_outputs(
     """
     ret = V3dInvFmriOutputs(
         root=execution.output_file("."),
-        outfile=execution.output_file(params.get("output_file")) if (params.get("output_file") is not None) else None,
+        outfile=execution.output_file(params.get("output_file", None)) if (params.get("output_file") is not None) else None,
     )
     return ret
 
 
 def v_3d_inv_fmri_execute(
     params: V3dInvFmriParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dInvFmriOutputs:
     """
+    3dInvFMRI
+    
     Program to compute stimulus time series, given a 3D+time dataset and an
     activation map (the inverse of the usual FMRI analysis problem).
     
@@ -233,10 +217,12 @@ def v_3d_inv_fmri_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dInvFmriOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_INV_FMRI_METADATA)
     params = execution.params(params)
     cargs = v_3d_inv_fmri_cargs(params, execution)
     ret = v_3d_inv_fmri_outputs(params, execution)
@@ -259,6 +245,8 @@ def v_3d_inv_fmri(
     runner: Runner | None = None,
 ) -> V3dInvFmriOutputs:
     """
+    3dInvFMRI
+    
     Program to compute stimulus time series, given a 3D+time dataset and an
     activation map (the inverse of the usual FMRI analysis problem).
     
@@ -290,8 +278,6 @@ def v_3d_inv_fmri(
     Returns:
         NamedTuple of outputs (described in `V3dInvFmriOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_INV_FMRI_METADATA)
     params = v_3d_inv_fmri_params(
         input_file=input_file,
         activation_map=activation_map,
@@ -305,13 +291,13 @@ def v_3d_inv_fmri(
         smooth_fir=smooth_fir,
         smooth_median=smooth_median,
     )
-    return v_3d_inv_fmri_execute(params, execution)
+    return v_3d_inv_fmri_execute(params, runner)
 
 
 __all__ = [
     "V3dInvFmriOutputs",
-    "V3dInvFmriParameters",
     "V_3D_INV_FMRI_METADATA",
     "v_3d_inv_fmri",
+    "v_3d_inv_fmri_execute",
     "v_3d_inv_fmri_params",
 ]

niwrap_afni/afni/v_3d_isc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_ISC_METADATA = Metadata(
-    id="f357d26d08e0fd1804a232fb9dcfe38bcb751a49.boutiques",
+    id="d3b5a8dbd0deceefb7a05348177e13e4a8e37bdc.boutiques",
     name="3dISC",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ V_3D_ISC_METADATA = Metadata(
 
 
 V3dIscParameters = typing.TypedDict('V3dIscParameters', {
-    "__STYXTYPE__": typing.Literal["3dISC"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dISC"]],
+    "outfile_prefix": str,
+    "num_jobs": typing.NotRequired[float | None],
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "model_structure": str,
+    "qvar_centers": typing.NotRequired[str | None],
+    "quantitative_vars": typing.NotRequired[str | None],
+    "fisher_transform": bool,
+    "io_functions": typing.NotRequired[typing.Literal["AFNI", "R"] | None],
+    "data_table": str,
+})
+V3dIscParametersTagged = typing.TypedDict('V3dIscParametersTagged', {
+    "@type": typing.Literal["afni/3dISC"],
     "outfile_prefix": str,
     "num_jobs": typing.NotRequired[float | None],
     "mask_file": typing.NotRequired[InputPathType | None],
@@ -25,43 +37,11 @@ V3dIscParameters = typing.TypedDict('V3dIscParameters', {
     "io_functions": typing.NotRequired[typing.Literal["AFNI", "R"] | None],
     "data_table": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dISC": v_3d_isc_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 {
-        "3dISC": v_3d_isc_outputs,
-    }.get(t)
 
 
 class V3dIscOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_isc(...)`.
+    Output object returned when calling `V3dIscParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +61,7 @@ def v_3d_isc_params(
     quantitative_vars: str | None = None,
     fisher_transform: bool = False,
     io_functions: typing.Literal["AFNI", "R"] | None = None,
-) -> V3dIscParameters:
+) -> V3dIscParametersTagged:
     """
     Build parameters.
     
@@ -108,7 +88,7 @@ def v_3d_isc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dISC",
+        "@type": "afni/3dISC",
         "outfile_prefix": outfile_prefix,
         "model_structure": model_structure,
         "fisher_transform": fisher_transform,
@@ -144,42 +124,42 @@ def v_3d_isc_cargs(
     cargs.append("3dISC")
     cargs.extend([
         "-prefix",
-        params.get("outfile_prefix")
+        params.get("outfile_prefix", None)
     ])
-    if params.get("num_jobs") is not None:
+    if params.get("num_jobs", None) is not None:
         cargs.extend([
             "-jobs",
-            str(params.get("num_jobs"))
+            str(params.get("num_jobs", None))
         ])
-    if params.get("mask_file") is not None:
+    if params.get("mask_file", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask_file"))
+            execution.input_file(params.get("mask_file", None))
         ])
     cargs.extend([
         "-model",
-        params.get("model_structure")
+        params.get("model_structure", None)
     ])
-    if params.get("qvar_centers") is not None:
+    if params.get("qvar_centers", None) is not None:
         cargs.extend([
             "-qVarCenters",
-            params.get("qvar_centers")
+            params.get("qvar_centers", None)
         ])
-    if params.get("quantitative_vars") is not None:
+    if params.get("quantitative_vars", None) is not None:
         cargs.extend([
             "-qVars",
-            params.get("quantitative_vars")
+            params.get("quantitative_vars", None)
         ])
-    if params.get("fisher_transform"):
+    if params.get("fisher_transform", False):
         cargs.append("-r2z")
-    if params.get("io_functions") is not None:
+    if params.get("io_functions", None) is not None:
         cargs.extend([
             "-cio",
-            params.get("io_functions")
+            params.get("io_functions", None)
         ])
     cargs.extend([
         "-dataTable",
-        params.get("data_table")
+        params.get("data_table", None)
     ])
     return cargs
 
@@ -199,17 +179,19 @@ def v_3d_isc_outputs(
     """
     ret = V3dIscOutputs(
         root=execution.output_file("."),
-        isc_output=execution.output_file(params.get("outfile_prefix") + "_ISC.nii"),
-        tstat_output=execution.output_file(params.get("outfile_prefix") + "_tstat.nii"),
+        isc_output=execution.output_file(params.get("outfile_prefix", None) + "_ISC.nii"),
+        tstat_output=execution.output_file(params.get("outfile_prefix", None) + "_tstat.nii"),
     )
     return ret
 
 
 def v_3d_isc_execute(
     params: V3dIscParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dIscOutputs:
     """
+    3dISC
+    
     Program for Voxelwise Inter-Subject Correlation (ISC) Analysis using linear
     mixed-effects modeling.
     
@@ -219,10 +201,12 @@ def v_3d_isc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dIscOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ISC_METADATA)
     params = execution.params(params)
     cargs = v_3d_isc_cargs(params, execution)
     ret = v_3d_isc_outputs(params, execution)
@@ -243,6 +227,8 @@ def v_3d_isc(
     runner: Runner | None = None,
 ) -> V3dIscOutputs:
     """
+    3dISC
+    
     Program for Voxelwise Inter-Subject Correlation (ISC) Analysis using linear
     mixed-effects modeling.
     
@@ -273,8 +259,6 @@ def v_3d_isc(
     Returns:
         NamedTuple of outputs (described in `V3dIscOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_ISC_METADATA)
     params = v_3d_isc_params(
         outfile_prefix=outfile_prefix,
         num_jobs=num_jobs,
@@ -286,13 +270,13 @@ def v_3d_isc(
         io_functions=io_functions,
         data_table=data_table,
     )
-    return v_3d_isc_execute(params, execution)
+    return v_3d_isc_execute(params, runner)
 
 
 __all__ = [
     "V3dIscOutputs",
-    "V3dIscParameters",
     "V_3D_ISC_METADATA",
     "v_3d_isc",
+    "v_3d_isc_execute",
     "v_3d_isc_params",
 ]