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

niwrap_afni/afni/v_3d_cruiseto_afni.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_CRUISETO_AFNI_METADATA = Metadata(
-    id="ecced7561c452fa6014dcc10bbbbd514bae7282a.boutiques",
+    id="a0d718d69b1cc124137138a300055a2430043a08.boutiques",
     name="3dCRUISEtoAFNI",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,14 +14,31 @@ V_3D_CRUISETO_AFNI_METADATA = Metadata(
 
 
 V3dCruisetoAfniTraceParameters = typing.TypedDict('V3dCruisetoAfniTraceParameters', {
-    "__STYXTYPE__": typing.Literal["trace"],
+    "@type": typing.NotRequired[typing.Literal["trace"]],
+    "trace": bool,
+    "TRACE": bool,
+})
+V3dCruisetoAfniTraceParametersTagged = typing.TypedDict('V3dCruisetoAfniTraceParametersTagged', {
+    "@type": typing.Literal["trace"],
     "trace": bool,
     "TRACE": bool,
 })
 
 
 V3dCruisetoAfniParameters = typing.TypedDict('V3dCruisetoAfniParameters', {
-    "__STYXTYPE__": typing.Literal["3dCRUISEtoAFNI"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dCRUISEtoAFNI"]],
+    "input": InputPathType,
+    "novolreg": bool,
+    "noxform": bool,
+    "setenv": typing.NotRequired[str | None],
+    "trace": typing.NotRequired[V3dCruisetoAfniTraceParameters | None],
+    "nomall": bool,
+    "yesmall": bool,
+    "help": bool,
+    "h": bool,
+})
+V3dCruisetoAfniParametersTagged = typing.TypedDict('V3dCruisetoAfniParametersTagged', {
+    "@type": typing.Literal["afni/3dCRUISEtoAFNI"],
     "input": InputPathType,
     "novolreg": bool,
     "noxform": bool,
@@ -32,44 +49,12 @@ V3dCruisetoAfniParameters = typing.TypedDict('V3dCruisetoAfniParameters', {
     "help": bool,
     "h": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dCRUISEtoAFNI": v_3d_cruiseto_afni_cargs,
-        "trace": v_3d_cruiseto_afni_trace_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 {
-    }.get(t)
 
 
 def v_3d_cruiseto_afni_trace_params(
     trace_: bool = False,
     trace_2: bool = False,
-) -> V3dCruisetoAfniTraceParameters:
+) -> V3dCruisetoAfniTraceParametersTagged:
     """
     Build parameters.
     
@@ -81,7 +66,7 @@ def v_3d_cruiseto_afni_trace_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "trace",
+        "@type": "trace",
         "trace": trace_,
         "TRACE": trace_2,
     }
@@ -102,16 +87,16 @@ def v_3d_cruiseto_afni_trace_cargs(
         Command-line arguments.
     """
     cargs = []
-    if params.get("trace"):
+    if params.get("trace", False):
         cargs.append("-trace")
-    if params.get("TRACE"):
+    if params.get("TRACE", False):
         cargs.append("-TRACE")
     return cargs
 
 
 class V3dCruisetoAfniOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_cruiseto_afni(...)`.
+    Output object returned when calling `V3dCruisetoAfniParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -127,7 +112,7 @@ def v_3d_cruiseto_afni_params(
     yesmall: bool = False,
     help_: bool = False,
     h: bool = False,
-) -> V3dCruisetoAfniParameters:
+) -> V3dCruisetoAfniParametersTagged:
     """
     Build parameters.
     
@@ -148,7 +133,7 @@ def v_3d_cruiseto_afni_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dCRUISEtoAFNI",
+        "@type": "afni/3dCRUISEtoAFNI",
         "input": input_,
         "novolreg": novolreg,
         "noxform": noxform,
@@ -181,26 +166,26 @@ def v_3d_cruiseto_afni_cargs(
     cargs.append("3dCRUISEtoAFNI")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input"))
+        execution.input_file(params.get("input", None))
     ])
-    if params.get("novolreg"):
+    if params.get("novolreg", False):
         cargs.append("-novolreg")
-    if params.get("noxform"):
+    if params.get("noxform", False):
         cargs.append("-noxform")
-    if params.get("setenv") is not None:
+    if params.get("setenv", None) is not None:
         cargs.extend([
             "-setenv",
-            params.get("setenv")
+            params.get("setenv", None)
         ])
-    if params.get("trace") is not None:
-        cargs.extend(dyn_cargs(params.get("trace")["__STYXTYPE__"])(params.get("trace"), execution))
-    if params.get("nomall"):
+    if params.get("trace", None) is not None:
+        cargs.extend(v_3d_cruiseto_afni_trace_cargs(params.get("trace", None), execution))
+    if params.get("nomall", False):
         cargs.append("-nomall")
-    if params.get("yesmall"):
+    if params.get("yesmall", False):
         cargs.append("-yesmall")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("h"):
+    if params.get("h", False):
         cargs.append("-h")
     return cargs
 
@@ -226,9 +211,11 @@ def v_3d_cruiseto_afni_outputs(
 
 def v_3d_cruiseto_afni_execute(
     params: V3dCruisetoAfniParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dCruisetoAfniOutputs:
     """
+    3dCRUISEtoAFNI
+    
     Converts a CRUISE dataset defined by a header in OpenDX format.
     
     Author: AFNI Developers
@@ -237,10 +224,12 @@ def v_3d_cruiseto_afni_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dCruisetoAfniOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_CRUISETO_AFNI_METADATA)
     params = execution.params(params)
     cargs = v_3d_cruiseto_afni_cargs(params, execution)
     ret = v_3d_cruiseto_afni_outputs(params, execution)
@@ -261,6 +250,8 @@ def v_3d_cruiseto_afni(
     runner: Runner | None = None,
 ) -> V3dCruisetoAfniOutputs:
     """
+    3dCRUISEtoAFNI
+    
     Converts a CRUISE dataset defined by a header in OpenDX format.
     
     Author: AFNI Developers
@@ -284,8 +275,6 @@ def v_3d_cruiseto_afni(
     Returns:
         NamedTuple of outputs (described in `V3dCruisetoAfniOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_CRUISETO_AFNI_METADATA)
     params = v_3d_cruiseto_afni_params(
         input_=input_,
         novolreg=novolreg,
@@ -297,15 +286,14 @@ def v_3d_cruiseto_afni(
         help_=help_,
         h=h,
     )
-    return v_3d_cruiseto_afni_execute(params, execution)
+    return v_3d_cruiseto_afni_execute(params, runner)
 
 
 __all__ = [
     "V3dCruisetoAfniOutputs",
-    "V3dCruisetoAfniParameters",
-    "V3dCruisetoAfniTraceParameters",
     "V_3D_CRUISETO_AFNI_METADATA",
     "v_3d_cruiseto_afni",
+    "v_3d_cruiseto_afni_execute",
     "v_3d_cruiseto_afni_params",
     "v_3d_cruiseto_afni_trace_params",
 ]

niwrap_afni/afni/v_3d_deconvolve.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_DECONVOLVE_METADATA = Metadata(
-    id="225d407793b7fcf83484f3e230794ff1d08c27df.boutiques",
+    id="08b4eeadd57ceed9e4f25bde7f18f8c07ac59916.boutiques",
     name="3dDeconvolve",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,25 @@ V_3D_DECONVOLVE_METADATA = Metadata(
 
 
 V3dDeconvolveParameters = typing.TypedDict('V3dDeconvolveParameters', {
-    "__STYXTYPE__": typing.Literal["3dDeconvolve"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dDeconvolve"]],
+    "input_dataset": InputPathType,
+    "mask_dataset": typing.NotRequired[InputPathType | None],
+    "num_stimts": typing.NotRequired[int | None],
+    "stim_file": typing.NotRequired[str | None],
+    "stim_label": typing.NotRequired[str | None],
+    "stim_base": bool,
+    "stim_times": typing.NotRequired[str | None],
+    "iresp": typing.NotRequired[str | None],
+    "fitts": typing.NotRequired[str | None],
+    "fout": bool,
+    "tout": bool,
+    "bucket": typing.NotRequired[str | None],
+    "cbucket": typing.NotRequired[str | None],
+    "x1D": typing.NotRequired[str | None],
+    "jobs": typing.NotRequired[int | None],
+})
+V3dDeconvolveParametersTagged = typing.TypedDict('V3dDeconvolveParametersTagged', {
+    "@type": typing.Literal["afni/3dDeconvolve"],
     "input_dataset": InputPathType,
     "mask_dataset": typing.NotRequired[InputPathType | None],
     "num_stimts": typing.NotRequired[int | None],
@@ -31,43 +49,11 @@ V3dDeconvolveParameters = typing.TypedDict('V3dDeconvolveParameters', {
     "x1D": typing.NotRequired[str | None],
     "jobs": 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 {
-        "3dDeconvolve": v_3d_deconvolve_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 {
-        "3dDeconvolve": v_3d_deconvolve_outputs,
-    }.get(t)
 
 
 class V3dDeconvolveOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_deconvolve(...)`.
+    Output object returned when calling `V3dDeconvolveParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -99,7 +85,7 @@ def v_3d_deconvolve_params(
     cbucket: str | None = None,
     x1_d: str | None = None,
     jobs: int | None = None,
-) -> V3dDeconvolveParameters:
+) -> V3dDeconvolveParametersTagged:
     """
     Build parameters.
     
@@ -127,7 +113,7 @@ def v_3d_deconvolve_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dDeconvolve",
+        "@type": "afni/3dDeconvolve",
         "input_dataset": input_dataset,
         "stim_base": stim_base,
         "fout": fout,
@@ -175,68 +161,68 @@ def v_3d_deconvolve_cargs(
     cargs.append("3dDeconvolve")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_dataset"))
+        execution.input_file(params.get("input_dataset", None))
     ])
-    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("num_stimts") is not None:
+    if params.get("num_stimts", None) is not None:
         cargs.extend([
             "-num_stimts",
-            str(params.get("num_stimts"))
+            str(params.get("num_stimts", None))
         ])
-    if params.get("stim_file") is not None:
+    if params.get("stim_file", None) is not None:
         cargs.extend([
             "-stim_file",
-            params.get("stim_file")
+            params.get("stim_file", None)
         ])
-    if params.get("stim_label") is not None:
+    if params.get("stim_label", None) is not None:
         cargs.extend([
             "-stim_label",
-            params.get("stim_label")
+            params.get("stim_label", None)
         ])
-    if params.get("stim_base"):
+    if params.get("stim_base", False):
         cargs.append("-stim_base")
-    if params.get("stim_times") is not None:
+    if params.get("stim_times", None) is not None:
         cargs.extend([
             "-stim_times",
-            params.get("stim_times")
+            params.get("stim_times", None)
         ])
-    if params.get("iresp") is not None:
+    if params.get("iresp", None) is not None:
         cargs.extend([
             "-iresp",
-            params.get("iresp")
+            params.get("iresp", None)
         ])
-    if params.get("fitts") is not None:
+    if params.get("fitts", None) is not None:
         cargs.extend([
             "-fitts",
-            params.get("fitts")
+            params.get("fitts", None)
         ])
-    if params.get("fout"):
+    if params.get("fout", False):
         cargs.append("-fout")
-    if params.get("tout"):
+    if params.get("tout", False):
         cargs.append("-tout")
-    if params.get("bucket") is not None:
+    if params.get("bucket", None) is not None:
         cargs.extend([
             "-bucket",
-            params.get("bucket")
+            params.get("bucket", None)
         ])
-    if params.get("cbucket") is not None:
+    if params.get("cbucket", None) is not None:
         cargs.extend([
             "-cbucket",
-            params.get("cbucket")
+            params.get("cbucket", None)
         ])
-    if params.get("x1D") is not None:
+    if params.get("x1D", None) is not None:
         cargs.extend([
             "-x1D",
-            params.get("x1D")
+            params.get("x1D", 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))
         ])
     return cargs
 
@@ -256,22 +242,24 @@ def v_3d_deconvolve_outputs(
     """
     ret = V3dDeconvolveOutputs(
         root=execution.output_file("."),
-        bucket_output=execution.output_file(params.get("bucket") + ".HEAD") if (params.get("bucket") is not None) else None,
-        cbucket_output=execution.output_file(params.get("cbucket") + ".HEAD") if (params.get("cbucket") is not None) else None,
-        iresp_output=execution.output_file(params.get("iresp") + ".HEAD") if (params.get("iresp") is not None) else None,
-        fitts_output=execution.output_file(params.get("fitts") + ".HEAD") if (params.get("fitts") is not None) else None,
-        x1d_file=execution.output_file(params.get("x1D") + ".1D") if (params.get("x1D") is not None) else None,
+        bucket_output=execution.output_file(params.get("bucket", None) + ".HEAD") if (params.get("bucket") is not None) else None,
+        cbucket_output=execution.output_file(params.get("cbucket", None) + ".HEAD") if (params.get("cbucket") is not None) else None,
+        iresp_output=execution.output_file(params.get("iresp", None) + ".HEAD") if (params.get("iresp") is not None) else None,
+        fitts_output=execution.output_file(params.get("fitts", None) + ".HEAD") if (params.get("fitts") is not None) else None,
+        x1d_file=execution.output_file(params.get("x1D", None) + ".1D") if (params.get("x1D") is not None) else None,
     )
     return ret
 
 
 def v_3d_deconvolve_execute(
     params: V3dDeconvolveParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dDeconvolveOutputs:
     """
-    Program to calculate the deconvolution of a measurement 3D+time dataset with a
-    specified input stimulus time series.
+    3dDeconvolve
+    
+    Program to calculate the deconvolution of a measurement 3D+time dataset with
+    a specified input stimulus time series.
     
     Author: AFNI Developers
     
@@ -279,10 +267,12 @@ def v_3d_deconvolve_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dDeconvolveOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DECONVOLVE_METADATA)
     params = execution.params(params)
     cargs = v_3d_deconvolve_cargs(params, execution)
     ret = v_3d_deconvolve_outputs(params, execution)
@@ -309,8 +299,10 @@ def v_3d_deconvolve(
     runner: Runner | None = None,
 ) -> V3dDeconvolveOutputs:
     """
-    Program to calculate the deconvolution of a measurement 3D+time dataset with a
-    specified input stimulus time series.
+    3dDeconvolve
+    
+    Program to calculate the deconvolution of a measurement 3D+time dataset with
+    a specified input stimulus time series.
     
     Author: AFNI Developers
     
@@ -340,8 +332,6 @@ def v_3d_deconvolve(
     Returns:
         NamedTuple of outputs (described in `V3dDeconvolveOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_DECONVOLVE_METADATA)
     params = v_3d_deconvolve_params(
         input_dataset=input_dataset,
         mask_dataset=mask_dataset,
@@ -359,13 +349,13 @@ def v_3d_deconvolve(
         x1_d=x1_d,
         jobs=jobs,
     )
-    return v_3d_deconvolve_execute(params, execution)
+    return v_3d_deconvolve_execute(params, runner)
 
 
 __all__ = [
     "V3dDeconvolveOutputs",
-    "V3dDeconvolveParameters",
     "V_3D_DECONVOLVE_METADATA",
     "v_3d_deconvolve",
+    "v_3d_deconvolve_execute",
     "v_3d_deconvolve_params",
 ]