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

niwrap_afni/afni/v_3d_synthesize.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_SYNTHESIZE_METADATA = Metadata(
-    id="511fc920fd2752d59d3de694c69c73bdde72a942.boutiques",
+    id="79cfbd97a99e59a5c391e1bda50527a214e73fad.boutiques",
     name="3dSynthesize",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ V_3D_SYNTHESIZE_METADATA = Metadata(
 
 
 V3dSynthesizeParameters = typing.TypedDict('V3dSynthesizeParameters', {
-    "__STYXTYPE__": typing.Literal["3dSynthesize"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dSynthesize"]],
+    "c_bucket": InputPathType,
+    "matrix": InputPathType,
+    "select": str,
+    "prefix": str,
+    "dry_flag": bool,
+    "tr": typing.NotRequired[float | None],
+    "cenfill": typing.NotRequired[typing.Literal["zero", "nbhr", "none"] | None],
+})
+V3dSynthesizeParametersTagged = typing.TypedDict('V3dSynthesizeParametersTagged', {
+    "@type": typing.Literal["afni/3dSynthesize"],
     "c_bucket": InputPathType,
     "matrix": InputPathType,
     "select": str,
@@ -23,42 +33,11 @@ V3dSynthesizeParameters = typing.TypedDict('V3dSynthesizeParameters', {
     "tr": typing.NotRequired[float | None],
     "cenfill": typing.NotRequired[typing.Literal["zero", "nbhr", "none"] | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dSynthesize": v_3d_synthesize_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 V3dSynthesizeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_synthesize(...)`.
+    Output object returned when calling `V3dSynthesizeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,7 +51,7 @@ def v_3d_synthesize_params(
     dry_flag: bool = False,
     tr: float | None = None,
     cenfill: typing.Literal["zero", "nbhr", "none"] | None = None,
-) -> V3dSynthesizeParameters:
+) -> V3dSynthesizeParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +70,7 @@ def v_3d_synthesize_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dSynthesize",
+        "@type": "afni/3dSynthesize",
         "c_bucket": c_bucket,
         "matrix": matrix,
         "select": select_,
@@ -122,31 +101,31 @@ def v_3d_synthesize_cargs(
     cargs.append("3dSynthesize")
     cargs.extend([
         "-cbucket",
-        execution.input_file(params.get("c_bucket"))
+        execution.input_file(params.get("c_bucket", None))
     ])
     cargs.extend([
         "-matrix",
-        execution.input_file(params.get("matrix"))
+        execution.input_file(params.get("matrix", None))
     ])
     cargs.extend([
         "-select",
-        params.get("select")
+        params.get("select", None)
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("dry_flag"):
+    if params.get("dry_flag", False):
         cargs.append("-dry")
-    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("cenfill") is not None:
+    if params.get("cenfill", None) is not None:
         cargs.extend([
             "-cenfill",
-            params.get("cenfill")
+            params.get("cenfill", None)
         ])
     return cargs
 
@@ -172,9 +151,11 @@ def v_3d_synthesize_outputs(
 
 def v_3d_synthesize_execute(
     params: V3dSynthesizeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dSynthesizeOutputs:
     """
+    3dSynthesize
+    
     Reads a '-cbucket' dataset and a '.xmat.1D' matrix from 3dDeconvolve, and
     synthesizes a fit dataset using selected sub-bricks and matrix columns.
     
@@ -184,10 +165,12 @@ def v_3d_synthesize_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dSynthesizeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SYNTHESIZE_METADATA)
     params = execution.params(params)
     cargs = v_3d_synthesize_cargs(params, execution)
     ret = v_3d_synthesize_outputs(params, execution)
@@ -206,6 +189,8 @@ def v_3d_synthesize(
     runner: Runner | None = None,
 ) -> V3dSynthesizeOutputs:
     """
+    3dSynthesize
+    
     Reads a '-cbucket' dataset and a '.xmat.1D' matrix from 3dDeconvolve, and
     synthesizes a fit dataset using selected sub-bricks and matrix columns.
     
@@ -228,8 +213,6 @@ def v_3d_synthesize(
     Returns:
         NamedTuple of outputs (described in `V3dSynthesizeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_SYNTHESIZE_METADATA)
     params = v_3d_synthesize_params(
         c_bucket=c_bucket,
         matrix=matrix,
@@ -239,13 +222,13 @@ def v_3d_synthesize(
         tr=tr,
         cenfill=cenfill,
     )
-    return v_3d_synthesize_execute(params, execution)
+    return v_3d_synthesize_execute(params, runner)
 
 
 __all__ = [
     "V3dSynthesizeOutputs",
-    "V3dSynthesizeParameters",
     "V_3D_SYNTHESIZE_METADATA",
     "v_3d_synthesize",
+    "v_3d_synthesize_execute",
     "v_3d_synthesize_params",
 ]

niwrap_afni/afni/v_3d_tagalign.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TAGALIGN_METADATA = Metadata(
-    id="475b53c4b6432ecad79b017ae32826c765d7c00c.boutiques",
+    id="9b9bddb3a6de929defedf353ef13f73e77d162d8.boutiques",
     name="3dTagalign",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,25 @@ V_3D_TAGALIGN_METADATA = Metadata(
 
 
 V3dTagalignParameters = typing.TypedDict('V3dTagalignParameters', {
-    "__STYXTYPE__": typing.Literal["3dTagalign"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dTagalign"]],
+    "input_dataset": InputPathType,
+    "master_dataset": InputPathType,
+    "tagset_file": typing.NotRequired[InputPathType | None],
+    "no_keep_tags": bool,
+    "matvec_file": typing.NotRequired[str | None],
+    "rotate": bool,
+    "affine": bool,
+    "rotscl": bool,
+    "prefix": typing.NotRequired[str | None],
+    "verbose": bool,
+    "dummy": bool,
+    "linear_interpolation": bool,
+    "cubic_interpolation": bool,
+    "nearest_neighbor_interpolation": bool,
+    "quintic_interpolation": bool,
+})
+V3dTagalignParametersTagged = typing.TypedDict('V3dTagalignParametersTagged', {
+    "@type": typing.Literal["afni/3dTagalign"],
     "input_dataset": InputPathType,
     "master_dataset": InputPathType,
     "tagset_file": typing.NotRequired[InputPathType | None],
@@ -31,43 +49,11 @@ V3dTagalignParameters = typing.TypedDict('V3dTagalignParameters', {
     "nearest_neighbor_interpolation": bool,
     "quintic_interpolation": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dTagalign": v_3d_tagalign_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 {
-        "3dTagalign": v_3d_tagalign_outputs,
-    }.get(t)
 
 
 class V3dTagalignOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_tagalign(...)`.
+    Output object returned when calling `V3dTagalignParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -95,7 +81,7 @@ def v_3d_tagalign_params(
     cubic_interpolation: bool = False,
     nearest_neighbor_interpolation: bool = False,
     quintic_interpolation: bool = False,
-) -> V3dTagalignParameters:
+) -> V3dTagalignParametersTagged:
     """
     Build parameters.
     
@@ -128,7 +114,7 @@ def v_3d_tagalign_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dTagalign",
+        "@type": "afni/3dTagalign",
         "input_dataset": input_dataset,
         "master_dataset": master_dataset,
         "no_keep_tags": no_keep_tags,
@@ -166,45 +152,45 @@ def v_3d_tagalign_cargs(
     """
     cargs = []
     cargs.append("3dTagalign")
-    cargs.append(execution.input_file(params.get("input_dataset")))
+    cargs.append(execution.input_file(params.get("input_dataset", None)))
     cargs.extend([
         "-master",
-        execution.input_file(params.get("master_dataset"))
+        execution.input_file(params.get("master_dataset", None))
     ])
-    if params.get("tagset_file") is not None:
+    if params.get("tagset_file", None) is not None:
         cargs.extend([
             "-tagset",
-            execution.input_file(params.get("tagset_file"))
+            execution.input_file(params.get("tagset_file", None))
         ])
-    if params.get("no_keep_tags"):
+    if params.get("no_keep_tags", False):
         cargs.append("-nokeeptags")
-    if params.get("matvec_file") is not None:
+    if params.get("matvec_file", None) is not None:
         cargs.extend([
             "-matvec",
-            params.get("matvec_file")
+            params.get("matvec_file", None)
         ])
-    if params.get("rotate"):
+    if params.get("rotate", False):
         cargs.append("-rotate")
-    if params.get("affine"):
+    if params.get("affine", False):
         cargs.append("-affine")
-    if params.get("rotscl"):
+    if params.get("rotscl", False):
         cargs.append("-rotscl")
-    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("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
-    if params.get("dummy"):
+    if params.get("dummy", False):
         cargs.append("-dummy")
-    if params.get("linear_interpolation"):
+    if params.get("linear_interpolation", False):
         cargs.append("-linear")
-    if params.get("cubic_interpolation"):
+    if params.get("cubic_interpolation", False):
         cargs.append("-cubic")
-    if params.get("nearest_neighbor_interpolation"):
+    if params.get("nearest_neighbor_interpolation", False):
         cargs.append("-NN")
-    if params.get("quintic_interpolation"):
+    if params.get("quintic_interpolation", False):
         cargs.append("-quintic")
     return cargs
 
@@ -224,18 +210,20 @@ def v_3d_tagalign_outputs(
     """
     ret = V3dTagalignOutputs(
         root=execution.output_file("."),
-        output_dataset_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
-        output_dataset_brick=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
-        output_matvec_file=execution.output_file(params.get("matvec_file")) if (params.get("matvec_file") is not None) else None,
+        output_dataset_head=execution.output_file(params.get("prefix", None) + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        output_dataset_brick=execution.output_file(params.get("prefix", None) + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        output_matvec_file=execution.output_file(params.get("matvec_file", None)) if (params.get("matvec_file") is not None) else None,
     )
     return ret
 
 
 def v_3d_tagalign_execute(
     params: V3dTagalignParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dTagalignOutputs:
     """
+    3dTagalign
+    
     Rotates/translates dataset 'dset' to be aligned with the master using the
     tagsets embedded in their .HEAD files.
     
@@ -245,10 +233,12 @@ def v_3d_tagalign_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dTagalignOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TAGALIGN_METADATA)
     params = execution.params(params)
     cargs = v_3d_tagalign_cargs(params, execution)
     ret = v_3d_tagalign_outputs(params, execution)
@@ -275,6 +265,8 @@ def v_3d_tagalign(
     runner: Runner | None = None,
 ) -> V3dTagalignOutputs:
     """
+    3dTagalign
+    
     Rotates/translates dataset 'dset' to be aligned with the master using the
     tagsets embedded in their .HEAD files.
     
@@ -311,8 +303,6 @@ def v_3d_tagalign(
     Returns:
         NamedTuple of outputs (described in `V3dTagalignOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_TAGALIGN_METADATA)
     params = v_3d_tagalign_params(
         input_dataset=input_dataset,
         master_dataset=master_dataset,
@@ -330,13 +320,13 @@ def v_3d_tagalign(
         nearest_neighbor_interpolation=nearest_neighbor_interpolation,
         quintic_interpolation=quintic_interpolation,
     )
-    return v_3d_tagalign_execute(params, execution)
+    return v_3d_tagalign_execute(params, runner)
 
 
 __all__ = [
     "V3dTagalignOutputs",
-    "V3dTagalignParameters",
     "V_3D_TAGALIGN_METADATA",
     "v_3d_tagalign",
+    "v_3d_tagalign_execute",
     "v_3d_tagalign_params",
 ]

niwrap_afni/afni/v_3d_tcat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TCAT_METADATA = Metadata(
-    id="ba0a2ce95d407a699f2eba057a11a25a96d21814.boutiques",
+    id="dae1d0374caa2f002a062c98157df3b60e781511.boutiques",
     name="3dTcat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V_3D_TCAT_METADATA = Metadata(
 
 
 V3dTcatParameters = typing.TypedDict('V3dTcatParameters', {
-    "__STYXTYPE__": typing.Literal["3dTcat"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dTcat"]],
+    "rlt": typing.NotRequired[typing.Literal["", "+", "++"] | None],
+    "in_files": InputPathType,
+    "out_file": typing.NotRequired[str | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "num_threads": typing.NotRequired[int | None],
+    "verbose": bool,
+})
+V3dTcatParametersTagged = typing.TypedDict('V3dTcatParametersTagged', {
+    "@type": typing.Literal["afni/3dTcat"],
     "rlt": typing.NotRequired[typing.Literal["", "+", "++"] | None],
     "in_files": InputPathType,
     "out_file": typing.NotRequired[str | None],
@@ -22,43 +31,11 @@ V3dTcatParameters = typing.TypedDict('V3dTcatParameters', {
     "num_threads": typing.NotRequired[int | 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 {
-        "3dTcat": v_3d_tcat_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 {
-        "3dTcat": v_3d_tcat_outputs,
-    }.get(t)
 
 
 class V3dTcatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_tcat(...)`.
+    Output object returned when calling `V3dTcatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def v_3d_tcat_params(
     outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
     num_threads: int | None = None,
     verbose: bool = False,
-) -> V3dTcatParameters:
+) -> V3dTcatParametersTagged:
     """
     Build parameters.
     
@@ -92,7 +69,7 @@ def v_3d_tcat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dTcat",
+        "@type": "afni/3dTcat",
         "in_files": in_files,
         "verbose": verbose,
     }
@@ -122,21 +99,21 @@ def v_3d_tcat_cargs(
     """
     cargs = []
     cargs.append("3dTcat")
-    if params.get("rlt") is not None:
+    if params.get("rlt", None) is not None:
         cargs.extend([
             "-rlt",
-            params.get("rlt") + execution.input_file(params.get("in_files"))
+            params.get("rlt", None) + execution.input_file(params.get("in_files", None))
         ])
-    if params.get("out_file") is not None:
+    if params.get("out_file", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("out_file")
+            params.get("out_file", None)
         ])
-    if params.get("outputtype") is not None:
-        cargs.append(params.get("outputtype"))
-    if params.get("num_threads") is not None:
-        cargs.append(str(params.get("num_threads")))
-    if params.get("verbose"):
+    if params.get("outputtype", None) is not None:
+        cargs.append(params.get("outputtype", None))
+    if params.get("num_threads", None) is not None:
+        cargs.append(str(params.get("num_threads", None)))
+    if params.get("verbose", False):
         cargs.append("-verb")
     return cargs
 
@@ -156,16 +133,18 @@ def v_3d_tcat_outputs(
     """
     ret = V3dTcatOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(pathlib.Path(params.get("in_files")).name + "_tcat"),
+        out_file=execution.output_file(pathlib.Path(params.get("in_files", None)).name + "_tcat"),
     )
     return ret
 
 
 def v_3d_tcat_execute(
     params: V3dTcatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dTcatOutputs:
     """
+    3dTcat
+    
     Concatenate sub-bricks from input datasets into one big 3D+time dataset.
     TODO Replace InputMultiPath in_files with Traits.List, if possible. Current
     version adds extra whitespace.
@@ -176,10 +155,12 @@ def v_3d_tcat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dTcatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TCAT_METADATA)
     params = execution.params(params)
     cargs = v_3d_tcat_cargs(params, execution)
     ret = v_3d_tcat_outputs(params, execution)
@@ -197,6 +178,8 @@ def v_3d_tcat(
     runner: Runner | None = None,
 ) -> V3dTcatOutputs:
     """
+    3dTcat
+    
     Concatenate sub-bricks from input datasets into one big 3D+time dataset.
     TODO Replace InputMultiPath in_files with Traits.List, if possible. Current
     version adds extra whitespace.
@@ -220,8 +203,6 @@ def v_3d_tcat(
     Returns:
         NamedTuple of outputs (described in `V3dTcatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_TCAT_METADATA)
     params = v_3d_tcat_params(
         rlt=rlt,
         in_files=in_files,
@@ -230,13 +211,13 @@ def v_3d_tcat(
         num_threads=num_threads,
         verbose=verbose,
     )
-    return v_3d_tcat_execute(params, execution)
+    return v_3d_tcat_execute(params, runner)
 
 
 __all__ = [
     "V3dTcatOutputs",
-    "V3dTcatParameters",
     "V_3D_TCAT_METADATA",
     "v_3d_tcat",
+    "v_3d_tcat_execute",
     "v_3d_tcat_params",
 ]