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

niwrap_afni/afni/v_3d_pfm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_PFM_METADATA = Metadata(
-    id="d084aee5c4e75cf817ad2d01aebd36c373c18a2d.boutiques",
+    id="b71b9519322ff10a9267702a56f4f728f16c0bac.boutiques",
     name="3dPFM",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,25 @@ V_3D_PFM_METADATA = Metadata(
 
 
 V3dPfmParameters = typing.TypedDict('V3dPfmParameters', {
-    "__STYXTYPE__": typing.Literal["3dPFM"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dPFM"]],
+    "input": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "algorithm": typing.NotRequired[str | None],
+    "criteria": typing.NotRequired[str | None],
+    "nonzeros": typing.NotRequired[float | None],
+    "maxiter": typing.NotRequired[float | None],
+    "maxiterfactor": typing.NotRequired[float | None],
+    "tr": typing.NotRequired[float | None],
+    "hrf": typing.NotRequired[str | None],
+    "hrf_vol": typing.NotRequired[InputPathType | None],
+    "idx_hrf": typing.NotRequired[InputPathType | None],
+    "LHS": typing.NotRequired[list[InputPathType] | None],
+    "jobs": typing.NotRequired[float | None],
+    "nSeg": typing.NotRequired[float | None],
+    "verb": typing.NotRequired[float | None],
+})
+V3dPfmParametersTagged = typing.TypedDict('V3dPfmParametersTagged', {
+    "@type": typing.Literal["afni/3dPFM"],
     "input": InputPathType,
     "mask": typing.NotRequired[InputPathType | None],
     "algorithm": typing.NotRequired[str | None],
@@ -31,43 +49,11 @@ V3dPfmParameters = typing.TypedDict('V3dPfmParameters', {
     "nSeg": typing.NotRequired[float | None],
     "verb": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dPFM": v_3d_pfm_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 {
-        "3dPFM": v_3d_pfm_outputs,
-    }.get(t)
 
 
 class V3dPfmOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_pfm(...)`.
+    Output object returned when calling `V3dPfmParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -143,7 +129,7 @@ def v_3d_pfm_params(
     jobs: float | None = None,
     n_seg: float | None = None,
     verb: float | None = None,
-) -> V3dPfmParameters:
+) -> V3dPfmParametersTagged:
     """
     Build parameters.
     
@@ -170,7 +156,7 @@ def v_3d_pfm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dPFM",
+        "@type": "afni/3dPFM",
         "input": input_,
     }
     if mask is not None:
@@ -221,77 +207,77 @@ def v_3d_pfm_cargs(
     cargs.append("3dPFM")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input"))
+        execution.input_file(params.get("input", 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("algorithm") is not None:
+    if params.get("algorithm", None) is not None:
         cargs.extend([
             "-algorithm",
-            params.get("algorithm")
+            params.get("algorithm", None)
         ])
-    if params.get("criteria") is not None:
+    if params.get("criteria", None) is not None:
         cargs.extend([
             "-criteria",
-            params.get("criteria")
+            params.get("criteria", None)
         ])
-    if params.get("nonzeros") is not None:
+    if params.get("nonzeros", None) is not None:
         cargs.extend([
             "-nonzeros",
-            str(params.get("nonzeros"))
+            str(params.get("nonzeros", None))
         ])
-    if params.get("maxiter") is not None:
+    if params.get("maxiter", None) is not None:
         cargs.extend([
             "-maxiter",
-            str(params.get("maxiter"))
+            str(params.get("maxiter", None))
         ])
-    if params.get("maxiterfactor") is not None:
+    if params.get("maxiterfactor", None) is not None:
         cargs.extend([
             "-maxiterfactor",
-            str(params.get("maxiterfactor"))
+            str(params.get("maxiterfactor", None))
         ])
-    if params.get("tr") is not None:
+    if params.get("tr", None) is not None:
         cargs.extend([
             "-TR",
-            str(params.get("tr"))
+            str(params.get("tr", None))
         ])
-    if params.get("hrf") is not None:
+    if params.get("hrf", None) is not None:
         cargs.extend([
             "-hrf",
-            params.get("hrf")
+            params.get("hrf", None)
         ])
-    if params.get("hrf_vol") is not None:
+    if params.get("hrf_vol", None) is not None:
         cargs.extend([
             "-hrf_vol",
-            execution.input_file(params.get("hrf_vol"))
+            execution.input_file(params.get("hrf_vol", None))
         ])
-    if params.get("idx_hrf") is not None:
+    if params.get("idx_hrf", None) is not None:
         cargs.extend([
             "-idx_hrf",
-            execution.input_file(params.get("idx_hrf"))
+            execution.input_file(params.get("idx_hrf", None))
         ])
-    if params.get("LHS") is not None:
+    if params.get("LHS", None) is not None:
         cargs.extend([
             "-LHS",
-            *[execution.input_file(f) for f in params.get("LHS")]
+            *[execution.input_file(f) for f in params.get("LHS", None)]
         ])
-    if params.get("jobs") is not None:
+    if params.get("jobs", None) is not None:
         cargs.extend([
             "-jobs",
-            str(params.get("jobs"))
+            str(params.get("jobs", None))
         ])
-    if params.get("nSeg") is not None:
+    if params.get("nSeg", None) is not None:
         cargs.extend([
             "-nSeg",
-            str(params.get("nSeg"))
+            str(params.get("nSeg", None))
         ])
-    if params.get("verb") is not None:
+    if params.get("verb", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verb"))
+            str(params.get("verb", None))
         ])
     return cargs
 
@@ -343,9 +329,11 @@ def v_3d_pfm_outputs(
 
 def v_3d_pfm_execute(
     params: V3dPfmParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dPfmOutputs:
     """
+    3dPFM
+    
     Program for identifying brief BOLD events in fMRI time series using Paradigm
     Free Mapping.
     
@@ -355,10 +343,12 @@ def v_3d_pfm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dPfmOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_PFM_METADATA)
     params = execution.params(params)
     cargs = v_3d_pfm_cargs(params, execution)
     ret = v_3d_pfm_outputs(params, execution)
@@ -385,6 +375,8 @@ def v_3d_pfm(
     runner: Runner | None = None,
 ) -> V3dPfmOutputs:
     """
+    3dPFM
+    
     Program for identifying brief BOLD events in fMRI time series using Paradigm
     Free Mapping.
     
@@ -415,8 +407,6 @@ def v_3d_pfm(
     Returns:
         NamedTuple of outputs (described in `V3dPfmOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_PFM_METADATA)
     params = v_3d_pfm_params(
         input_=input_,
         mask=mask,
@@ -434,13 +424,13 @@ def v_3d_pfm(
         n_seg=n_seg,
         verb=verb,
     )
-    return v_3d_pfm_execute(params, execution)
+    return v_3d_pfm_execute(params, runner)
 
 
 __all__ = [
     "V3dPfmOutputs",
-    "V3dPfmParameters",
     "V_3D_PFM_METADATA",
     "v_3d_pfm",
+    "v_3d_pfm_execute",
     "v_3d_pfm_params",
 ]

niwrap_afni/afni/v_3d_polyfit.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_POLYFIT_METADATA = Metadata(
-    id="634ca94604006da564db557fefa10ca9d8de9d9c.boutiques",
+    id="0e4fe88ec0cfc1d3aebc6e9308bba232fbca5fc6.boutiques",
     name="3dPolyfit",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ V_3D_POLYFIT_METADATA = Metadata(
 
 
 V3dPolyfitParameters = typing.TypedDict('V3dPolyfitParameters', {
-    "__STYXTYPE__": typing.Literal["3dPolyfit"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dPolyfit"]],
+    "input_dataset": InputPathType,
+    "poly_order": typing.NotRequired[int | None],
+    "blur": typing.NotRequired[float | None],
+    "median_radius": typing.NotRequired[float | None],
+    "output_prefix": typing.NotRequired[str | None],
+    "resid_prefix": typing.NotRequired[str | None],
+    "coeff_output": typing.NotRequired[str | None],
+    "automask": bool,
+    "mask_dataset": typing.NotRequired[InputPathType | None],
+    "mean_scale": bool,
+    "clip_box": bool,
+    "fit_method": typing.NotRequired[int | None],
+    "base_dataset": typing.NotRequired[InputPathType | None],
+    "verbose": bool,
+})
+V3dPolyfitParametersTagged = typing.TypedDict('V3dPolyfitParametersTagged', {
+    "@type": typing.Literal["afni/3dPolyfit"],
     "input_dataset": InputPathType,
     "poly_order": typing.NotRequired[int | None],
     "blur": typing.NotRequired[float | None],
@@ -30,43 +47,11 @@ V3dPolyfitParameters = typing.TypedDict('V3dPolyfitParameters', {
     "base_dataset": typing.NotRequired[InputPathType | None],
     "verbose": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dPolyfit": v_3d_polyfit_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 {
-        "3dPolyfit": v_3d_polyfit_outputs,
-    }.get(t)
 
 
 class V3dPolyfitOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_polyfit(...)`.
+    Output object returned when calling `V3dPolyfitParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -93,7 +78,7 @@ def v_3d_polyfit_params(
     fit_method: int | None = None,
     base_dataset: InputPathType | None = None,
     verbose: bool = False,
-) -> V3dPolyfitParameters:
+) -> V3dPolyfitParametersTagged:
     """
     Build parameters.
     
@@ -126,7 +111,7 @@ def v_3d_polyfit_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dPolyfit",
+        "@type": "afni/3dPolyfit",
         "input_dataset": input_dataset,
         "automask": automask,
         "mean_scale": mean_scale,
@@ -169,59 +154,59 @@ def v_3d_polyfit_cargs(
     """
     cargs = []
     cargs.append("3dPolyfit")
-    cargs.append(execution.input_file(params.get("input_dataset")))
-    if params.get("poly_order") is not None:
+    cargs.append(execution.input_file(params.get("input_dataset", None)))
+    if params.get("poly_order", None) is not None:
         cargs.extend([
             "-nord",
-            str(params.get("poly_order"))
+            str(params.get("poly_order", None))
         ])
-    if params.get("blur") is not None:
+    if params.get("blur", None) is not None:
         cargs.extend([
             "-blur",
-            str(params.get("blur"))
+            str(params.get("blur", None))
         ])
-    if params.get("median_radius") is not None:
+    if params.get("median_radius", None) is not None:
         cargs.extend([
             "-mrad",
-            str(params.get("median_radius"))
+            str(params.get("median_radius", None))
         ])
-    if params.get("output_prefix") is not None:
+    if params.get("output_prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("output_prefix")
+            params.get("output_prefix", None)
         ])
-    if params.get("resid_prefix") is not None:
+    if params.get("resid_prefix", None) is not None:
         cargs.extend([
             "-resid",
-            params.get("resid_prefix")
+            params.get("resid_prefix", None)
         ])
-    if params.get("coeff_output") is not None:
+    if params.get("coeff_output", None) is not None:
         cargs.extend([
             "-1Dcoef",
-            params.get("coeff_output")
+            params.get("coeff_output", None)
         ])
-    if params.get("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
-    if params.get("mask_dataset") is not None:
+    if params.get("mask_dataset", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask_dataset"))
+            execution.input_file(params.get("mask_dataset", None))
         ])
-    if params.get("mean_scale"):
+    if params.get("mean_scale", False):
         cargs.append("-mone")
-    if params.get("clip_box"):
+    if params.get("clip_box", False):
         cargs.append("-mclip")
-    if params.get("fit_method") is not None:
+    if params.get("fit_method", None) is not None:
         cargs.extend([
             "-meth",
-            str(params.get("fit_method"))
+            str(params.get("fit_method", None))
         ])
-    if params.get("base_dataset") is not None:
+    if params.get("base_dataset", None) is not None:
         cargs.extend([
             "-base",
-            execution.input_file(params.get("base_dataset"))
+            execution.input_file(params.get("base_dataset", None))
         ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
     return cargs
 
@@ -241,20 +226,22 @@ def v_3d_polyfit_outputs(
     """
     ret = V3dPolyfitOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_prefix") + ".nii.gz") if (params.get("output_prefix") is not None) else None,
-        resid_file=execution.output_file(params.get("resid_prefix") + ".nii.gz") if (params.get("resid_prefix") is not None) else None,
-        coeff_file=execution.output_file(params.get("coeff_output") + ".1D") if (params.get("coeff_output") is not None) else None,
+        output_file=execution.output_file(params.get("output_prefix", None) + ".nii.gz") if (params.get("output_prefix") is not None) else None,
+        resid_file=execution.output_file(params.get("resid_prefix", None) + ".nii.gz") if (params.get("resid_prefix") is not None) else None,
+        coeff_file=execution.output_file(params.get("coeff_output", None) + ".1D") if (params.get("coeff_output") is not None) else None,
     )
     return ret
 
 
 def v_3d_polyfit_execute(
     params: V3dPolyfitParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dPolyfitOutputs:
     """
-    Fits a polynomial in space to the input dataset and outputs that fitted dataset.
-    You can also add your own basis datasets to the fitting mix.
+    3dPolyfit
+    
+    Fits a polynomial in space to the input dataset and outputs that fitted
+    dataset. You can also add your own basis datasets to the fitting mix.
     
     Author: AFNI Developers
     
@@ -262,10 +249,12 @@ def v_3d_polyfit_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dPolyfitOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_POLYFIT_METADATA)
     params = execution.params(params)
     cargs = v_3d_polyfit_cargs(params, execution)
     ret = v_3d_polyfit_outputs(params, execution)
@@ -291,8 +280,10 @@ def v_3d_polyfit(
     runner: Runner | None = None,
 ) -> V3dPolyfitOutputs:
     """
-    Fits a polynomial in space to the input dataset and outputs that fitted dataset.
-    You can also add your own basis datasets to the fitting mix.
+    3dPolyfit
+    
+    Fits a polynomial in space to the input dataset and outputs that fitted
+    dataset. You can also add your own basis datasets to the fitting mix.
     
     Author: AFNI Developers
     
@@ -327,8 +318,6 @@ def v_3d_polyfit(
     Returns:
         NamedTuple of outputs (described in `V3dPolyfitOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_POLYFIT_METADATA)
     params = v_3d_polyfit_params(
         input_dataset=input_dataset,
         poly_order=poly_order,
@@ -345,13 +334,13 @@ def v_3d_polyfit(
         base_dataset=base_dataset,
         verbose=verbose,
     )
-    return v_3d_polyfit_execute(params, execution)
+    return v_3d_polyfit_execute(params, runner)
 
 
 __all__ = [
     "V3dPolyfitOutputs",
-    "V3dPolyfitParameters",
     "V_3D_POLYFIT_METADATA",
     "v_3d_polyfit",
+    "v_3d_polyfit_execute",
     "v_3d_polyfit_params",
 ]