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

niwrap_afni/afni/v_3d_notes.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_NOTES_METADATA = Metadata(
-    id="05aa91a825b65166c425b7ec0eb4409fe3f5ad64.boutiques",
+    id="1756987bc517c02b04ed29f17cd59746f7a1e6a8.boutiques",
     name="3dNotes",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ V_3D_NOTES_METADATA = Metadata(
 
 
 V3dNotesParameters = typing.TypedDict('V3dNotesParameters', {
-    "__STYXTYPE__": typing.Literal["3dNotes"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dNotes"]],
+    "add_note": typing.NotRequired[str | None],
+    "append_history": typing.NotRequired[str | None],
+    "replace_history": typing.NotRequired[str | None],
+    "delete_note": typing.NotRequired[float | None],
+    "print_notes": bool,
+    "help": bool,
+    "dataset": InputPathType,
+})
+V3dNotesParametersTagged = typing.TypedDict('V3dNotesParametersTagged', {
+    "@type": typing.Literal["afni/3dNotes"],
     "add_note": typing.NotRequired[str | None],
     "append_history": typing.NotRequired[str | None],
     "replace_history": typing.NotRequired[str | None],
@@ -23,42 +33,11 @@ V3dNotesParameters = typing.TypedDict('V3dNotesParameters', {
     "help": bool,
     "dataset": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dNotes": v_3d_notes_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)
 
 
 class V3dNotesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_notes(...)`.
+    Output object returned when calling `V3dNotesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,7 +51,7 @@ def v_3d_notes_params(
     delete_note: float | None = None,
     print_notes: bool = False,
     help_: bool = False,
-) -> V3dNotesParameters:
+) -> V3dNotesParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +69,7 @@ def v_3d_notes_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dNotes",
+        "@type": "afni/3dNotes",
         "print_notes": print_notes,
         "help": help_,
         "dataset": dataset,
@@ -121,31 +100,31 @@ def v_3d_notes_cargs(
     """
     cargs = []
     cargs.append("3dNotes")
-    if params.get("add_note") is not None:
+    if params.get("add_note", None) is not None:
         cargs.extend([
             "-a",
-            params.get("add_note")
+            params.get("add_note", None)
         ])
-    if params.get("append_history") is not None:
+    if params.get("append_history", None) is not None:
         cargs.extend([
             "-h",
-            params.get("append_history")
+            params.get("append_history", None)
         ])
-    if params.get("replace_history") is not None:
+    if params.get("replace_history", None) is not None:
         cargs.extend([
             "-HH",
-            params.get("replace_history")
+            params.get("replace_history", None)
         ])
-    if params.get("delete_note") is not None:
+    if params.get("delete_note", None) is not None:
         cargs.extend([
             "-d",
-            str(params.get("delete_note"))
+            str(params.get("delete_note", None))
         ])
-    if params.get("print_notes"):
+    if params.get("print_notes", False):
         cargs.append("-ses")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    cargs.append(execution.input_file(params.get("dataset")))
+    cargs.append(execution.input_file(params.get("dataset", None)))
     return cargs
 
 
@@ -170,9 +149,11 @@ def v_3d_notes_outputs(
 
 def v_3d_notes_execute(
     params: V3dNotesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dNotesOutputs:
     """
+    3dNotes
+    
     A program to add, delete and show notes for AFNI datasets.
     
     Author: AFNI Developers
@@ -181,10 +162,12 @@ def v_3d_notes_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dNotesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_NOTES_METADATA)
     params = execution.params(params)
     cargs = v_3d_notes_cargs(params, execution)
     ret = v_3d_notes_outputs(params, execution)
@@ -203,6 +186,8 @@ def v_3d_notes(
     runner: Runner | None = None,
 ) -> V3dNotesOutputs:
     """
+    3dNotes
+    
     A program to add, delete and show notes for AFNI datasets.
     
     Author: AFNI Developers
@@ -223,8 +208,6 @@ def v_3d_notes(
     Returns:
         NamedTuple of outputs (described in `V3dNotesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_NOTES_METADATA)
     params = v_3d_notes_params(
         add_note=add_note,
         append_history=append_history,
@@ -234,13 +217,13 @@ def v_3d_notes(
         help_=help_,
         dataset=dataset,
     )
-    return v_3d_notes_execute(params, execution)
+    return v_3d_notes_execute(params, runner)
 
 
 __all__ = [
     "V3dNotesOutputs",
-    "V3dNotesParameters",
     "V_3D_NOTES_METADATA",
     "v_3d_notes",
+    "v_3d_notes_execute",
     "v_3d_notes_params",
 ]

niwrap_afni/afni/v_3d_nwarp_adjust.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_NWARP_ADJUST_METADATA = Metadata(
-    id="01d507ebaf57c706c49cc3bf6e04158f3b035085.boutiques",
+    id="2b1c9bcb47b87bb26653dff4b575bf7dc8439ce3.boutiques",
     name="3dNwarpAdjust",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,22 @@ V_3D_NWARP_ADJUST_METADATA = Metadata(
 
 
 V3dNwarpAdjustParameters = typing.TypedDict('V3dNwarpAdjustParameters', {
-    "__STYXTYPE__": typing.Literal["3dNwarpAdjust"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dNwarpAdjust"]],
+    "input_warps": list[InputPathType],
+    "source_datasets": typing.NotRequired[list[InputPathType] | None],
+    "output_prefix": typing.NotRequired[str | None],
+})
+V3dNwarpAdjustParametersTagged = typing.TypedDict('V3dNwarpAdjustParametersTagged', {
+    "@type": typing.Literal["afni/3dNwarpAdjust"],
     "input_warps": list[InputPathType],
     "source_datasets": typing.NotRequired[list[InputPathType] | None],
     "output_prefix": 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 {
-        "3dNwarpAdjust": v_3d_nwarp_adjust_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 {
-        "3dNwarpAdjust": v_3d_nwarp_adjust_outputs,
-    }.get(t)
 
 
 class V3dNwarpAdjustOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_nwarp_adjust(...)`.
+    Output object returned when calling `V3dNwarpAdjustParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +43,7 @@ def v_3d_nwarp_adjust_params(
     input_warps: list[InputPathType],
     source_datasets: list[InputPathType] | None = None,
     output_prefix: str | None = None,
-) -> V3dNwarpAdjustParameters:
+) -> V3dNwarpAdjustParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +58,7 @@ def v_3d_nwarp_adjust_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dNwarpAdjust",
+        "@type": "afni/3dNwarpAdjust",
         "input_warps": input_warps,
     }
     if source_datasets is not None:
@@ -111,17 +85,17 @@ def v_3d_nwarp_adjust_cargs(
     cargs.append("3dNwarpAdjust")
     cargs.extend([
         "-nwarp",
-        *[execution.input_file(f) for f in params.get("input_warps")]
+        *[execution.input_file(f) for f in params.get("input_warps", None)]
     ])
-    if params.get("source_datasets") is not None:
+    if params.get("source_datasets", None) is not None:
         cargs.extend([
             "-source",
-            *[execution.input_file(f) for f in params.get("source_datasets")]
+            *[execution.input_file(f) for f in params.get("source_datasets", 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)
         ])
     return cargs
 
@@ -141,20 +115,22 @@ def v_3d_nwarp_adjust_outputs(
     """
     ret = V3dNwarpAdjustOutputs(
         root=execution.output_file("."),
-        output_brik=execution.output_file(params.get("output_prefix") + "+tlrc.BRIK") if (params.get("output_prefix") is not None) else None,
-        output_head=execution.output_file(params.get("output_prefix") + "+tlrc.HEAD") if (params.get("output_prefix") is not None) else None,
+        output_brik=execution.output_file(params.get("output_prefix", None) + "+tlrc.BRIK") if (params.get("output_prefix") is not None) else None,
+        output_head=execution.output_file(params.get("output_prefix", None) + "+tlrc.HEAD") if (params.get("output_prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_nwarp_adjust_execute(
     params: V3dNwarpAdjustParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dNwarpAdjustOutputs:
     """
-    Program to adjust 3D warp datasets by composing them with the inverse of their
-    average, optionally warping input datasets and generating an output mean
-    dataset.
+    3dNwarpAdjust
+    
+    Program to adjust 3D warp datasets by composing them with the inverse of
+    their average, optionally warping input datasets and generating an output
+    mean dataset.
     
     Author: AFNI Developers
     
@@ -162,10 +138,12 @@ def v_3d_nwarp_adjust_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dNwarpAdjustOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_NWARP_ADJUST_METADATA)
     params = execution.params(params)
     cargs = v_3d_nwarp_adjust_cargs(params, execution)
     ret = v_3d_nwarp_adjust_outputs(params, execution)
@@ -180,9 +158,11 @@ def v_3d_nwarp_adjust(
     runner: Runner | None = None,
 ) -> V3dNwarpAdjustOutputs:
     """
-    Program to adjust 3D warp datasets by composing them with the inverse of their
-    average, optionally warping input datasets and generating an output mean
-    dataset.
+    3dNwarpAdjust
+    
+    Program to adjust 3D warp datasets by composing them with the inverse of
+    their average, optionally warping input datasets and generating an output
+    mean dataset.
     
     Author: AFNI Developers
     
@@ -199,20 +179,18 @@ def v_3d_nwarp_adjust(
     Returns:
         NamedTuple of outputs (described in `V3dNwarpAdjustOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_NWARP_ADJUST_METADATA)
     params = v_3d_nwarp_adjust_params(
         input_warps=input_warps,
         source_datasets=source_datasets,
         output_prefix=output_prefix,
     )
-    return v_3d_nwarp_adjust_execute(params, execution)
+    return v_3d_nwarp_adjust_execute(params, runner)
 
 
 __all__ = [
     "V3dNwarpAdjustOutputs",
-    "V3dNwarpAdjustParameters",
     "V_3D_NWARP_ADJUST_METADATA",
     "v_3d_nwarp_adjust",
+    "v_3d_nwarp_adjust_execute",
     "v_3d_nwarp_adjust_params",
 ]

niwrap_afni/afni/v_3d_nwarp_apply.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_NWARP_APPLY_METADATA = Metadata(
-    id="482fdd065e612d0faece31b8bc78fd21f004b766.boutiques",
+    id="b697b26d251dbe1445c036c2a8bcc84105820fb1.boutiques",
     name="3dNwarpApply",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ V_3D_NWARP_APPLY_METADATA = Metadata(
 
 
 V3dNwarpApplyParameters = typing.TypedDict('V3dNwarpApplyParameters', {
-    "__STYXTYPE__": typing.Literal["3dNwarpApply"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dNwarpApply"]],
+    "nwarp": str,
+    "iwarp": bool,
+    "source": str,
+    "master": typing.NotRequired[str | None],
+    "newgrid": typing.NotRequired[str | None],
+    "dxyz": typing.NotRequired[str | None],
+    "interp": typing.NotRequired[str | None],
+    "ainterp": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "suffix": typing.NotRequired[str | None],
+    "short": bool,
+    "wprefix": typing.NotRequired[str | None],
+    "quiet": bool,
+    "verb": bool,
+})
+V3dNwarpApplyParametersTagged = typing.TypedDict('V3dNwarpApplyParametersTagged', {
+    "@type": typing.Literal["afni/3dNwarpApply"],
     "nwarp": str,
     "iwarp": bool,
     "source": str,
@@ -30,50 +47,16 @@ V3dNwarpApplyParameters = typing.TypedDict('V3dNwarpApplyParameters', {
     "quiet": bool,
     "verb": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dNwarpApply": v_3d_nwarp_apply_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 {
-        "3dNwarpApply": v_3d_nwarp_apply_outputs,
-    }.get(t)
 
 
 class V3dNwarpApplyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_nwarp_apply(...)`.
+    Output object returned when calling `V3dNwarpApplyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
     warped_output: OutputPathType | None
     """Warped output dataset"""
-    generated_warp: OutputPathType | None
-    """Warp dataset generated during application"""
 
 
 def v_3d_nwarp_apply_params(
@@ -91,7 +74,7 @@ def v_3d_nwarp_apply_params(
     wprefix: str | None = None,
     quiet: bool = False,
     verb: bool = False,
-) -> V3dNwarpApplyParameters:
+) -> V3dNwarpApplyParametersTagged:
     """
     Build parameters.
     
@@ -121,7 +104,7 @@ def v_3d_nwarp_apply_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dNwarpApply",
+        "@type": "afni/3dNwarpApply",
         "nwarp": nwarp,
         "iwarp": iwarp,
         "source": source,
@@ -165,59 +148,59 @@ def v_3d_nwarp_apply_cargs(
     cargs.append("3dNwarpApply")
     cargs.extend([
         "-nwarp",
-        params.get("nwarp")
+        params.get("nwarp", None)
     ])
-    if params.get("iwarp"):
+    if params.get("iwarp", False):
         cargs.append("-iwarp")
     cargs.extend([
         "-source",
-        params.get("source")
+        params.get("source", None)
     ])
-    if params.get("master") is not None:
+    if params.get("master", None) is not None:
         cargs.extend([
             "-master",
-            params.get("master")
+            params.get("master", None)
         ])
-    if params.get("newgrid") is not None:
+    if params.get("newgrid", None) is not None:
         cargs.extend([
             "-newgrid",
-            params.get("newgrid")
+            params.get("newgrid", None)
         ])
-    if params.get("dxyz") is not None:
+    if params.get("dxyz", None) is not None:
         cargs.extend([
             "-dxyz",
-            params.get("dxyz")
+            params.get("dxyz", None)
         ])
-    if params.get("interp") is not None:
+    if params.get("interp", None) is not None:
         cargs.extend([
             "-interp",
-            params.get("interp")
+            params.get("interp", None)
         ])
-    if params.get("ainterp") is not None:
+    if params.get("ainterp", None) is not None:
         cargs.extend([
             "-ainterp",
-            params.get("ainterp")
+            params.get("ainterp", 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("suffix") is not None:
+    if params.get("suffix", None) is not None:
         cargs.extend([
             "-suffix",
-            params.get("suffix")
+            params.get("suffix", None)
         ])
-    if params.get("short"):
+    if params.get("short", False):
         cargs.append("-short")
-    if params.get("wprefix") is not None:
+    if params.get("wprefix", None) is not None:
         cargs.extend([
             "-wprefix",
-            params.get("wprefix")
+            params.get("wprefix", None)
         ])
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("verb"):
+    if params.get("verb", False):
         cargs.append("-verb")
     return cargs
 
@@ -237,19 +220,20 @@ def v_3d_nwarp_apply_outputs(
     """
     ret = V3dNwarpApplyOutputs(
         root=execution.output_file("."),
-        warped_output=execution.output_file(params.get("prefix") + "_" + params.get("source") + "_warped.nii.gz") if (params.get("prefix") is not None) else None,
-        generated_warp=execution.output_file(params.get("wprefix") + "_warp_????.nii.gz") if (params.get("wprefix") is not None) else None,
+        warped_output=execution.output_file(params.get("prefix", None) + "_" + params.get("source", None) + "_warped.nii.gz") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_nwarp_apply_execute(
     params: V3dNwarpApplyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dNwarpApplyOutputs:
     """
-    Program to apply a nonlinear 3D warp saved from 3dQwarp (or 3dNwarpCat, etc.) to
-    a 3D dataset, to produce a warped version of the source dataset.
+    3dNwarpApply
+    
+    Program to apply a nonlinear 3D warp saved from 3dQwarp (or 3dNwarpCat,
+    etc.) to a 3D dataset, to produce a warped version of the source dataset.
     
     Author: AFNI Developers
     
@@ -257,10 +241,12 @@ def v_3d_nwarp_apply_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dNwarpApplyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_NWARP_APPLY_METADATA)
     params = execution.params(params)
     cargs = v_3d_nwarp_apply_cargs(params, execution)
     ret = v_3d_nwarp_apply_outputs(params, execution)
@@ -286,8 +272,10 @@ def v_3d_nwarp_apply(
     runner: Runner | None = None,
 ) -> V3dNwarpApplyOutputs:
     """
-    Program to apply a nonlinear 3D warp saved from 3dQwarp (or 3dNwarpCat, etc.) to
-    a 3D dataset, to produce a warped version of the source dataset.
+    3dNwarpApply
+    
+    Program to apply a nonlinear 3D warp saved from 3dQwarp (or 3dNwarpCat,
+    etc.) to a 3D dataset, to produce a warped version of the source dataset.
     
     Author: AFNI Developers
     
@@ -319,8 +307,6 @@ def v_3d_nwarp_apply(
     Returns:
         NamedTuple of outputs (described in `V3dNwarpApplyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_NWARP_APPLY_METADATA)
     params = v_3d_nwarp_apply_params(
         nwarp=nwarp,
         iwarp=iwarp,
@@ -337,13 +323,13 @@ def v_3d_nwarp_apply(
         quiet=quiet,
         verb=verb,
     )
-    return v_3d_nwarp_apply_execute(params, execution)
+    return v_3d_nwarp_apply_execute(params, runner)
 
 
 __all__ = [
     "V3dNwarpApplyOutputs",
-    "V3dNwarpApplyParameters",
     "V_3D_NWARP_APPLY_METADATA",
     "v_3d_nwarp_apply",
+    "v_3d_nwarp_apply_execute",
     "v_3d_nwarp_apply_params",
 ]