niwrap-afni 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/v_3dfim_.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DFIM__METADATA = Metadata(
-    id="fc1b029ae0a8def8888aac6bc72283bb5b04bcf9.boutiques",
+    id="120206f029effcc24405469fe1eefbde41719998.boutiques",
     name="3dfim+",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,22 @@ V_3DFIM__METADATA = Metadata(
 
 
 V3dfimParameters = typing.TypedDict('V3dfimParameters', {
-    "__STYXTYPE__": typing.Literal["3dfim+"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dfim+"]],
+    "infile": InputPathType,
+    "input1dfile": typing.NotRequired[InputPathType | None],
+    "maskfile": typing.NotRequired[InputPathType | None],
+    "first_image": typing.NotRequired[float | None],
+    "last_image": typing.NotRequired[float | None],
+    "baseline_polynomial": typing.NotRequired[float | None],
+    "threshold": typing.NotRequired[float | None],
+    "cdisp_value": typing.NotRequired[float | None],
+    "ort_file": typing.NotRequired[InputPathType | None],
+    "ideal_file": InputPathType,
+    "output_params": typing.NotRequired[list[str] | None],
+    "output_bucket": typing.NotRequired[str | None],
+})
+V3dfimParametersTagged = typing.TypedDict('V3dfimParametersTagged', {
+    "@type": typing.Literal["afni/3dfim+"],
     "infile": InputPathType,
     "input1dfile": typing.NotRequired[InputPathType | None],
     "maskfile": typing.NotRequired[InputPathType | None],
@@ -28,43 +43,11 @@ V3dfimParameters = typing.TypedDict('V3dfimParameters', {
     "output_params": typing.NotRequired[list[str] | None],
     "output_bucket": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dfim+": v_3dfim__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 {
-        "3dfim+": v_3dfim__outputs,
-    }.get(t)
 
 
 class V3dfimOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dfim_(...)`.
+    Output object returned when calling `V3dfimParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -91,7 +74,7 @@ def v_3dfim__params(
     ort_file: InputPathType | None = None,
     output_params: list[str] | None = None,
     output_bucket: str | None = None,
-) -> V3dfimParameters:
+) -> V3dfimParametersTagged:
     """
     Build parameters.
     
@@ -123,7 +106,7 @@ def v_3dfim__params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dfim+",
+        "@type": "afni/3dfim+",
         "infile": infile,
         "ideal_file": ideal_file,
     }
@@ -165,60 +148,60 @@ def v_3dfim__cargs(
     """
     cargs = []
     cargs.append("3dfim+")
-    cargs.append(execution.input_file(params.get("infile")))
-    if params.get("input1dfile") is not None:
+    cargs.append(execution.input_file(params.get("infile", None)))
+    if params.get("input1dfile", None) is not None:
         cargs.extend([
             "-input1D",
-            execution.input_file(params.get("input1dfile"))
+            execution.input_file(params.get("input1dfile", None))
         ])
-    if params.get("maskfile") is not None:
+    if params.get("maskfile", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("maskfile"))
+            execution.input_file(params.get("maskfile", None))
         ])
-    if params.get("first_image") is not None:
+    if params.get("first_image", None) is not None:
         cargs.extend([
             "-nfirst",
-            str(params.get("first_image"))
+            str(params.get("first_image", None))
         ])
-    if params.get("last_image") is not None:
+    if params.get("last_image", None) is not None:
         cargs.extend([
             "-nlast",
-            str(params.get("last_image"))
+            str(params.get("last_image", None))
         ])
-    if params.get("baseline_polynomial") is not None:
+    if params.get("baseline_polynomial", None) is not None:
         cargs.extend([
             "-polort",
-            str(params.get("baseline_polynomial"))
+            str(params.get("baseline_polynomial", None))
         ])
-    if params.get("threshold") is not None:
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "-fim_thr",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    if params.get("cdisp_value") is not None:
+    if params.get("cdisp_value", None) is not None:
         cargs.extend([
             "-cdisp",
-            str(params.get("cdisp_value"))
+            str(params.get("cdisp_value", None))
         ])
-    if params.get("ort_file") is not None:
+    if params.get("ort_file", None) is not None:
         cargs.extend([
             "-ort_file",
-            execution.input_file(params.get("ort_file"))
+            execution.input_file(params.get("ort_file", None))
         ])
     cargs.extend([
         "-ideal_file",
-        execution.input_file(params.get("ideal_file"))
+        execution.input_file(params.get("ideal_file", None))
     ])
-    if params.get("output_params") is not None:
+    if params.get("output_params", None) is not None:
         cargs.extend([
             "-out",
-            *params.get("output_params")
+            *params.get("output_params", None)
         ])
-    if params.get("output_bucket") is not None:
+    if params.get("output_bucket", None) is not None:
         cargs.extend([
             "-bucket",
-            params.get("output_bucket")
+            params.get("output_bucket", None)
         ])
     return cargs
 
@@ -238,21 +221,23 @@ def v_3dfim__outputs(
     """
     ret = V3dfimOutputs(
         root=execution.output_file("."),
-        outfile_tlrc_head=execution.output_file(params.get("output_bucket") + "+tlrc.HEAD") if (params.get("output_bucket") is not None) else None,
-        outfile_tlrc_brk=execution.output_file(params.get("output_bucket") + "+tlrc.BRIK") if (params.get("output_bucket") is not None) else None,
-        outfile_orig_head=execution.output_file(params.get("output_bucket") + "+orig.HEAD") if (params.get("output_bucket") is not None) else None,
-        outfile_orig_brk=execution.output_file(params.get("output_bucket") + "+orig.BRIK") if (params.get("output_bucket") is not None) else None,
+        outfile_tlrc_head=execution.output_file(params.get("output_bucket", None) + "+tlrc.HEAD") if (params.get("output_bucket") is not None) else None,
+        outfile_tlrc_brk=execution.output_file(params.get("output_bucket", None) + "+tlrc.BRIK") if (params.get("output_bucket") is not None) else None,
+        outfile_orig_head=execution.output_file(params.get("output_bucket", None) + "+orig.HEAD") if (params.get("output_bucket") is not None) else None,
+        outfile_orig_brk=execution.output_file(params.get("output_bucket", None) + "+orig.BRIK") if (params.get("output_bucket") is not None) else None,
     )
     return ret
 
 
 def v_3dfim__execute(
     params: V3dfimParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dfimOutputs:
     """
-    Program to calculate the cross-correlation of an ideal reference waveform with
-    the measured FMRI time series for each voxel.
+    3dfim+
+    
+    Program to calculate the cross-correlation of an ideal reference waveform
+    with the measured FMRI time series for each voxel.
     
     Author: AFNI Developers
     
@@ -260,10 +245,12 @@ def v_3dfim__execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dfimOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DFIM__METADATA)
     params = execution.params(params)
     cargs = v_3dfim__cargs(params, execution)
     ret = v_3dfim__outputs(params, execution)
@@ -287,8 +274,10 @@ def v_3dfim_(
     runner: Runner | None = None,
 ) -> V3dfimOutputs:
     """
-    Program to calculate the cross-correlation of an ideal reference waveform with
-    the measured FMRI time series for each voxel.
+    3dfim+
+    
+    Program to calculate the cross-correlation of an ideal reference waveform
+    with the measured FMRI time series for each voxel.
     
     Author: AFNI Developers
     
@@ -322,8 +311,6 @@ def v_3dfim_(
     Returns:
         NamedTuple of outputs (described in `V3dfimOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DFIM__METADATA)
     params = v_3dfim__params(
         infile=infile,
         input1dfile=input1dfile,
@@ -338,13 +325,13 @@ def v_3dfim_(
         output_params=output_params,
         output_bucket=output_bucket,
     )
-    return v_3dfim__execute(params, execution)
+    return v_3dfim__execute(params, runner)
 
 
 __all__ = [
     "V3dfimOutputs",
-    "V3dfimParameters",
     "V_3DFIM__METADATA",
     "v_3dfim_",
+    "v_3dfim__execute",
     "v_3dfim__params",
 ]

niwrap_afni/afni/v_3dfractionize.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DFRACTIONIZE_METADATA = Metadata(
-    id="663b4096f3c27dafe7f1f91756343636456bd9a8.boutiques",
+    id="131e3f310d788f67bb187824b228758d394458e7.boutiques",
     name="3dfractionize",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ V_3DFRACTIONIZE_METADATA = Metadata(
 
 
 V3dfractionizeParameters = typing.TypedDict('V3dfractionizeParameters', {
-    "__STYXTYPE__": typing.Literal["3dfractionize"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dfractionize"]],
+    "template": InputPathType,
+    "input": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "clip": typing.NotRequired[float | None],
+    "warp": typing.NotRequired[InputPathType | None],
+    "preserve": bool,
+    "vote": bool,
+})
+V3dfractionizeParametersTagged = typing.TypedDict('V3dfractionizeParametersTagged', {
+    "@type": typing.Literal["afni/3dfractionize"],
     "template": InputPathType,
     "input": InputPathType,
     "prefix": typing.NotRequired[str | None],
@@ -23,43 +33,11 @@ V3dfractionizeParameters = typing.TypedDict('V3dfractionizeParameters', {
     "preserve": bool,
     "vote": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dfractionize": v_3dfractionize_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 {
-        "3dfractionize": v_3dfractionize_outputs,
-    }.get(t)
 
 
 class V3dfractionizeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dfractionize(...)`.
+    Output object returned when calling `V3dfractionizeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def v_3dfractionize_params(
     warp: InputPathType | None = None,
     preserve: bool = False,
     vote: bool = False,
-) -> V3dfractionizeParameters:
+) -> V3dfractionizeParametersTagged:
     """
     Build parameters.
     
@@ -97,7 +75,7 @@ def v_3dfractionize_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dfractionize",
+        "@type": "afni/3dfractionize",
         "template": template,
         "input": input_,
         "preserve": preserve,
@@ -129,30 +107,30 @@ def v_3dfractionize_cargs(
     cargs.append("3dfractionize")
     cargs.extend([
         "-template",
-        execution.input_file(params.get("template"))
+        execution.input_file(params.get("template", None))
     ])
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input"))
+        execution.input_file(params.get("input", None))
     ])
-    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("clip") is not None:
+    if params.get("clip", None) is not None:
         cargs.extend([
             "-clip",
-            str(params.get("clip"))
+            str(params.get("clip", None))
         ])
-    if params.get("warp") is not None:
+    if params.get("warp", None) is not None:
         cargs.extend([
             "-warp",
-            execution.input_file(params.get("warp"))
+            execution.input_file(params.get("warp", None))
         ])
-    if params.get("preserve"):
+    if params.get("preserve", False):
         cargs.append("-preserve")
-    if params.get("vote"):
+    if params.get("vote", False):
         cargs.append("-vote")
     return cargs
 
@@ -172,16 +150,18 @@ def v_3dfractionize_outputs(
     """
     ret = V3dfractionizeOutputs(
         root=execution.output_file("."),
-        output=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+        output=execution.output_file(params.get("prefix", None)) if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3dfractionize_execute(
     params: V3dfractionizeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dfractionizeOutputs:
     """
+    3dfractionize
+    
     For each voxel in the output dataset, computes the fraction of it that is
     occupied by nonzero voxels from the input.
     
@@ -191,10 +171,12 @@ def v_3dfractionize_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dfractionizeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DFRACTIONIZE_METADATA)
     params = execution.params(params)
     cargs = v_3dfractionize_cargs(params, execution)
     ret = v_3dfractionize_outputs(params, execution)
@@ -213,6 +195,8 @@ def v_3dfractionize(
     runner: Runner | None = None,
 ) -> V3dfractionizeOutputs:
     """
+    3dfractionize
+    
     For each voxel in the output dataset, computes the fraction of it that is
     occupied by nonzero voxels from the input.
     
@@ -238,8 +222,6 @@ def v_3dfractionize(
     Returns:
         NamedTuple of outputs (described in `V3dfractionizeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DFRACTIONIZE_METADATA)
     params = v_3dfractionize_params(
         template=template,
         input_=input_,
@@ -249,13 +231,13 @@ def v_3dfractionize(
         preserve=preserve,
         vote=vote,
     )
-    return v_3dfractionize_execute(params, execution)
+    return v_3dfractionize_execute(params, runner)
 
 
 __all__ = [
     "V3dfractionizeOutputs",
-    "V3dfractionizeParameters",
     "V_3DFRACTIONIZE_METADATA",
     "v_3dfractionize",
+    "v_3dfractionize_execute",
     "v_3dfractionize_params",
 ]