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

niwrap_afni/afni/v_3d_lrflip.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_LRFLIP_METADATA = Metadata(
-    id="57b905fab9f06f442859815c246d2b61d1ef0e9b.boutiques",
+    id="958d124c668f02051ee45f4c019b87646e6b14ab.boutiques",
     name="3dLRflip",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V_3D_LRFLIP_METADATA = Metadata(
 
 
 V3dLrflipParameters = typing.TypedDict('V3dLrflipParameters', {
-    "__STYXTYPE__": typing.Literal["3dLRflip"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dLRflip"]],
+    "flip_lr": bool,
+    "flip_ap": bool,
+    "flip_is": bool,
+    "flip_x": bool,
+    "flip_y": bool,
+    "flip_z": bool,
+    "output_prefix": typing.NotRequired[str | None],
+    "datasets": list[InputPathType],
+})
+V3dLrflipParametersTagged = typing.TypedDict('V3dLrflipParametersTagged', {
+    "@type": typing.Literal["afni/3dLRflip"],
     "flip_lr": bool,
     "flip_ap": bool,
     "flip_is": bool,
@@ -24,48 +35,14 @@ V3dLrflipParameters = typing.TypedDict('V3dLrflipParameters', {
     "output_prefix": typing.NotRequired[str | None],
     "datasets": list[InputPathType],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dLRflip": v_3d_lrflip_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 {
-        "3dLRflip": v_3d_lrflip_outputs,
-    }.get(t)
 
 
 class V3dLrflipOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_lrflip(...)`.
+    Output object returned when calling `V3dLrflipParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    flipped_output: OutputPathType | None
-    """Output dataset after flipping"""
 
 
 def v_3d_lrflip_params(
@@ -77,7 +54,7 @@ def v_3d_lrflip_params(
     flip_y: bool = False,
     flip_z: bool = False,
     output_prefix: str | None = None,
-) -> V3dLrflipParameters:
+) -> V3dLrflipParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +72,7 @@ def v_3d_lrflip_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dLRflip",
+        "@type": "afni/3dLRflip",
         "flip_lr": flip_lr,
         "flip_ap": flip_ap,
         "flip_is": flip_is,
@@ -124,24 +101,24 @@ def v_3d_lrflip_cargs(
     """
     cargs = []
     cargs.append("3dLRflip")
-    if params.get("flip_lr"):
+    if params.get("flip_lr", False):
         cargs.append("-LR")
-    if params.get("flip_ap"):
+    if params.get("flip_ap", False):
         cargs.append("-AP")
-    if params.get("flip_is"):
+    if params.get("flip_is", False):
         cargs.append("-IS")
-    if params.get("flip_x"):
+    if params.get("flip_x", False):
         cargs.append("-X")
-    if params.get("flip_y"):
+    if params.get("flip_y", False):
         cargs.append("-Y")
-    if params.get("flip_z"):
+    if params.get("flip_z", False):
         cargs.append("-Z")
-    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)
         ])
-    cargs.extend([execution.input_file(f) for f in params.get("datasets")])
+    cargs.extend([execution.input_file(f) for f in params.get("datasets", None)])
     return cargs
 
 
@@ -160,16 +137,17 @@ def v_3d_lrflip_outputs(
     """
     ret = V3dLrflipOutputs(
         root=execution.output_file("."),
-        flipped_output=execution.output_file(params.get("output_prefix") + "*") if (params.get("output_prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_lrflip_execute(
     params: V3dLrflipParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dLrflipOutputs:
     """
+    3dLRflip
+    
     Flips the rows of a dataset along one of the three axes to correct dataset
     direction labeling errors.
     
@@ -179,10 +157,12 @@ def v_3d_lrflip_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dLrflipOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LRFLIP_METADATA)
     params = execution.params(params)
     cargs = v_3d_lrflip_cargs(params, execution)
     ret = v_3d_lrflip_outputs(params, execution)
@@ -202,6 +182,8 @@ def v_3d_lrflip(
     runner: Runner | None = None,
 ) -> V3dLrflipOutputs:
     """
+    3dLRflip
+    
     Flips the rows of a dataset along one of the three axes to correct dataset
     direction labeling errors.
     
@@ -223,8 +205,6 @@ def v_3d_lrflip(
     Returns:
         NamedTuple of outputs (described in `V3dLrflipOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_LRFLIP_METADATA)
     params = v_3d_lrflip_params(
         flip_lr=flip_lr,
         flip_ap=flip_ap,
@@ -235,13 +215,13 @@ def v_3d_lrflip(
         output_prefix=output_prefix,
         datasets=datasets,
     )
-    return v_3d_lrflip_execute(params, execution)
+    return v_3d_lrflip_execute(params, runner)
 
 
 __all__ = [
     "V3dLrflipOutputs",
-    "V3dLrflipParameters",
     "V_3D_LRFLIP_METADATA",
     "v_3d_lrflip",
+    "v_3d_lrflip_execute",
     "v_3d_lrflip_params",
 ]

niwrap_afni/afni/v_3d_lss.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_LSS_METADATA = Metadata(
-    id="740f5c6d3d107774eb13ee9d6ebced41219d9fe4.boutiques",
+    id="f59c06c71271844acbd9b7f7f4806ab324672634.boutiques",
     name="3dLSS",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V_3D_LSS_METADATA = Metadata(
 
 
 V3dLssParameters = typing.TypedDict('V3dLssParameters', {
-    "__STYXTYPE__": typing.Literal["3dLSS"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dLSS"]],
+    "matrix": InputPathType,
+    "input": typing.NotRequired[InputPathType | None],
+    "nodata": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "prefix": typing.NotRequired[str | None],
+    "save1D": typing.NotRequired[str | None],
+    "verbose": bool,
+})
+V3dLssParametersTagged = typing.TypedDict('V3dLssParametersTagged', {
+    "@type": typing.Literal["afni/3dLSS"],
     "matrix": InputPathType,
     "input": typing.NotRequired[InputPathType | None],
     "nodata": bool,
@@ -24,43 +35,11 @@ V3dLssParameters = typing.TypedDict('V3dLssParameters', {
     "save1D": typing.NotRequired[str | 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 {
-        "3dLSS": v_3d_lss_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 {
-        "3dLSS": v_3d_lss_outputs,
-    }.get(t)
 
 
 class V3dLssOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_lss(...)`.
+    Output object returned when calling `V3dLssParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -80,7 +59,7 @@ def v_3d_lss_params(
     prefix: str | None = None,
     save1_d: str | None = None,
     verbose: bool = False,
-) -> V3dLssParameters:
+) -> V3dLssParametersTagged:
     """
     Build parameters.
     
@@ -104,7 +83,7 @@ def v_3d_lss_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dLSS",
+        "@type": "afni/3dLSS",
         "matrix": matrix,
         "nodata": nodata,
         "automask": automask,
@@ -138,33 +117,33 @@ def v_3d_lss_cargs(
     cargs.append("3dLSS")
     cargs.extend([
         "-matrix",
-        execution.input_file(params.get("matrix"))
+        execution.input_file(params.get("matrix", None))
     ])
-    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("nodata"):
+    if params.get("nodata", False):
         cargs.append("-nodata")
-    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("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
-    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("save1D") is not None:
+    if params.get("save1D", None) is not None:
         cargs.extend([
             "-save1D",
-            params.get("save1D")
+            params.get("save1D", None)
         ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
     return cargs
 
@@ -185,16 +164,18 @@ def v_3d_lss_outputs(
     ret = V3dLssOutputs(
         root=execution.output_file("."),
         output_dataset=execution.output_file("LSSout+orig.HEAD"),
-        save1_d_output=execution.output_file(params.get("save1D")) if (params.get("save1D") is not None) else None,
+        save1_d_output=execution.output_file(params.get("save1D", None)) if (params.get("save1D") is not None) else None,
     )
     return ret
 
 
 def v_3d_lss_execute(
     params: V3dLssParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dLssOutputs:
     """
+    3dLSS
+    
     Least-Squares-Sum (LSS) estimation tool from a -stim_times_IM matrix for
     multivoxel pattern classification analyses.
     
@@ -204,10 +185,12 @@ def v_3d_lss_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dLssOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LSS_METADATA)
     params = execution.params(params)
     cargs = v_3d_lss_cargs(params, execution)
     ret = v_3d_lss_outputs(params, execution)
@@ -227,6 +210,8 @@ def v_3d_lss(
     runner: Runner | None = None,
 ) -> V3dLssOutputs:
     """
+    3dLSS
+    
     Least-Squares-Sum (LSS) estimation tool from a -stim_times_IM matrix for
     multivoxel pattern classification analyses.
     
@@ -254,8 +239,6 @@ def v_3d_lss(
     Returns:
         NamedTuple of outputs (described in `V3dLssOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_LSS_METADATA)
     params = v_3d_lss_params(
         matrix=matrix,
         input_=input_,
@@ -266,13 +249,13 @@ def v_3d_lss(
         save1_d=save1_d,
         verbose=verbose,
     )
-    return v_3d_lss_execute(params, execution)
+    return v_3d_lss_execute(params, runner)
 
 
 __all__ = [
     "V3dLssOutputs",
-    "V3dLssParameters",
     "V_3D_LSS_METADATA",
     "v_3d_lss",
+    "v_3d_lss_execute",
     "v_3d_lss_params",
 ]

niwrap_afni/afni/v_3d_mann_whitney.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_MANN_WHITNEY_METADATA = Metadata(
-    id="e0fe96cdc7cfcb9551b9f02dac2ae2e304e42627.boutiques",
+    id="fb00db9925fb8e8685faf28f5dd4c98d2b2e2420.boutiques",
     name="3dMannWhitney",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,56 +14,29 @@ V_3D_MANN_WHITNEY_METADATA = Metadata(
 
 
 V3dMannWhitneyParameters = typing.TypedDict('V3dMannWhitneyParameters', {
-    "__STYXTYPE__": typing.Literal["3dMannWhitney"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dMannWhitney"]],
+    "dset1_x": list[str],
+    "dset2_y": list[str],
+    "output_prefix": str,
+    "workmem": typing.NotRequired[int | None],
+    "voxel_num": typing.NotRequired[int | None],
+})
+V3dMannWhitneyParametersTagged = typing.TypedDict('V3dMannWhitneyParametersTagged', {
+    "@type": typing.Literal["afni/3dMannWhitney"],
     "dset1_x": list[str],
     "dset2_y": list[str],
     "output_prefix": str,
     "workmem": typing.NotRequired[int | None],
     "voxel_num": typing.NotRequired[int | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dMannWhitney": v_3d_mann_whitney_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 {
-        "3dMannWhitney": v_3d_mann_whitney_outputs,
-    }.get(t)
 
 
 class V3dMannWhitneyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_mann_whitney(...)`.
+    Output object returned when calling `V3dMannWhitneyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    output_files: OutputPathType
-    """Output files for the estimated population delta and Wilcoxon-Mann-Whitney
-    statistics."""
 
 
 def v_3d_mann_whitney_params(
@@ -72,7 +45,7 @@ def v_3d_mann_whitney_params(
     output_prefix: str,
     workmem: int | None = None,
     voxel_num: int | None = None,
-) -> V3dMannWhitneyParameters:
+) -> V3dMannWhitneyParametersTagged:
     """
     Build parameters.
     
@@ -89,7 +62,7 @@ def v_3d_mann_whitney_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dMannWhitney",
+        "@type": "afni/3dMannWhitney",
         "dset1_x": dset1_x,
         "dset2_y": dset2_y,
         "output_prefix": output_prefix,
@@ -118,25 +91,25 @@ def v_3d_mann_whitney_cargs(
     cargs.append("3dMannWhitney")
     cargs.extend([
         "-dset 1",
-        *params.get("dset1_x")
+        *params.get("dset1_x", None)
     ])
     cargs.extend([
         "-dset 2",
-        *params.get("dset2_y")
+        *params.get("dset2_y", None)
     ])
     cargs.extend([
         "-out",
-        params.get("output_prefix")
+        params.get("output_prefix", 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))
         ])
     return cargs
 
@@ -156,16 +129,17 @@ def v_3d_mann_whitney_outputs(
     """
     ret = V3dMannWhitneyOutputs(
         root=execution.output_file("."),
-        output_files=execution.output_file(params.get("output_prefix") + "*"),
     )
     return ret
 
 
 def v_3d_mann_whitney_execute(
     params: V3dMannWhitneyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dMannWhitneyOutputs:
     """
+    3dMannWhitney
+    
     Performs nonparametric Mann-Whitney two-sample test.
     
     Author: AFNI Developers
@@ -174,10 +148,12 @@ def v_3d_mann_whitney_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dMannWhitneyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MANN_WHITNEY_METADATA)
     params = execution.params(params)
     cargs = v_3d_mann_whitney_cargs(params, execution)
     ret = v_3d_mann_whitney_outputs(params, execution)
@@ -194,6 +170,8 @@ def v_3d_mann_whitney(
     runner: Runner | None = None,
 ) -> V3dMannWhitneyOutputs:
     """
+    3dMannWhitney
+    
     Performs nonparametric Mann-Whitney two-sample test.
     
     Author: AFNI Developers
@@ -213,8 +191,6 @@ def v_3d_mann_whitney(
     Returns:
         NamedTuple of outputs (described in `V3dMannWhitneyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_MANN_WHITNEY_METADATA)
     params = v_3d_mann_whitney_params(
         dset1_x=dset1_x,
         dset2_y=dset2_y,
@@ -222,13 +198,13 @@ def v_3d_mann_whitney(
         workmem=workmem,
         voxel_num=voxel_num,
     )
-    return v_3d_mann_whitney_execute(params, execution)
+    return v_3d_mann_whitney_execute(params, runner)
 
 
 __all__ = [
     "V3dMannWhitneyOutputs",
-    "V3dMannWhitneyParameters",
     "V_3D_MANN_WHITNEY_METADATA",
     "v_3d_mann_whitney",
+    "v_3d_mann_whitney_execute",
     "v_3d_mann_whitney_params",
 ]