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

niwrap_afni/afni/v_1d_sem.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_1D_SEM_METADATA = Metadata(
-    id="aeff1d057462eede99aff722b7dd6ab414847e03.boutiques",
+    id="6575bee84394160db744d2f6c5c4fb4c754de905.boutiques",
     name="1dSEM",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,26 @@ V_1D_SEM_METADATA = Metadata(
 
 
 V1dSemParameters = typing.TypedDict('V1dSemParameters', {
-    "__STYXTYPE__": typing.Literal["1dSEM"],
+    "@type": typing.NotRequired[typing.Literal["afni/1dSEM"]],
+    "theta": InputPathType,
+    "correlation_matrix": InputPathType,
+    "residual_variance": InputPathType,
+    "degrees_of_freedom": float,
+    "max_iterations": typing.NotRequired[int | None],
+    "number_random_trials": typing.NotRequired[int | None],
+    "limits": typing.NotRequired[list[float] | None],
+    "calculate_cost": bool,
+    "verbose": typing.NotRequired[int | None],
+    "tree_growth": bool,
+    "model_search": bool,
+    "max_paths": typing.NotRequired[int | None],
+    "stop_cost": typing.NotRequired[float | None],
+    "forest_growth": bool,
+    "grow_all": bool,
+    "leafpicker": bool,
+})
+V1dSemParametersTagged = typing.TypedDict('V1dSemParametersTagged', {
+    "@type": typing.Literal["afni/1dSEM"],
     "theta": InputPathType,
     "correlation_matrix": InputPathType,
     "residual_variance": InputPathType,
@@ -32,43 +51,11 @@ V1dSemParameters = typing.TypedDict('V1dSemParameters', {
     "grow_all": bool,
     "leafpicker": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "1dSEM": v_1d_sem_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 {
-        "1dSEM": v_1d_sem_outputs,
-    }.get(t)
 
 
 class V1dSemOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_1d_sem(...)`.
+    Output object returned when calling `V1dSemParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -93,7 +80,7 @@ def v_1d_sem_params(
     forest_growth: bool = False,
     grow_all: bool = False,
     leafpicker: bool = False,
-) -> V1dSemParameters:
+) -> V1dSemParametersTagged:
     """
     Build parameters.
     
@@ -130,7 +117,7 @@ def v_1d_sem_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "1dSEM",
+        "@type": "afni/1dSEM",
         "theta": theta,
         "correlation_matrix": correlation_matrix,
         "residual_variance": residual_variance,
@@ -174,61 +161,61 @@ def v_1d_sem_cargs(
     cargs.append("1dSEM")
     cargs.extend([
         "-theta",
-        execution.input_file(params.get("theta"))
+        execution.input_file(params.get("theta", None))
     ])
     cargs.extend([
         "-C",
-        execution.input_file(params.get("correlation_matrix"))
+        execution.input_file(params.get("correlation_matrix", None))
     ])
     cargs.extend([
         "-psi",
-        execution.input_file(params.get("residual_variance"))
+        execution.input_file(params.get("residual_variance", None))
     ])
     cargs.extend([
         "-DF",
-        str(params.get("degrees_of_freedom"))
+        str(params.get("degrees_of_freedom", None))
     ])
-    if params.get("max_iterations") is not None:
+    if params.get("max_iterations", None) is not None:
         cargs.extend([
             "-max_iter",
-            str(params.get("max_iterations"))
+            str(params.get("max_iterations", None))
         ])
-    if params.get("number_random_trials") is not None:
+    if params.get("number_random_trials", None) is not None:
         cargs.extend([
             "-nrand",
-            str(params.get("number_random_trials"))
+            str(params.get("number_random_trials", None))
         ])
-    if params.get("limits") is not None:
+    if params.get("limits", None) is not None:
         cargs.extend([
             "-limits",
-            *map(str, params.get("limits"))
+            *map(str, params.get("limits", None))
         ])
-    if params.get("calculate_cost"):
+    if params.get("calculate_cost", False):
         cargs.append("-calccost")
-    if params.get("verbose") is not None:
+    if params.get("verbose", None) is not None:
         cargs.extend([
             "-verbose",
-            str(params.get("verbose"))
+            str(params.get("verbose", None))
         ])
-    if params.get("tree_growth"):
+    if params.get("tree_growth", False):
         cargs.append("-tree_growth")
-    if params.get("model_search"):
+    if params.get("model_search", False):
         cargs.append("-model_search")
-    if params.get("max_paths") is not None:
+    if params.get("max_paths", None) is not None:
         cargs.extend([
             "-max_paths",
-            str(params.get("max_paths"))
+            str(params.get("max_paths", None))
         ])
-    if params.get("stop_cost") is not None:
+    if params.get("stop_cost", None) is not None:
         cargs.extend([
             "-stop_cost",
-            str(params.get("stop_cost"))
+            str(params.get("stop_cost", None))
         ])
-    if params.get("forest_growth"):
+    if params.get("forest_growth", False):
         cargs.append("-forest_growth")
-    if params.get("grow_all"):
+    if params.get("grow_all", False):
         cargs.append("-grow_all")
-    if params.get("leafpicker"):
+    if params.get("leafpicker", False):
         cargs.append("-leafpicker")
     return cargs
 
@@ -255,11 +242,13 @@ def v_1d_sem_outputs(
 
 def v_1d_sem_execute(
     params: V1dSemParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V1dSemOutputs:
     """
-    Computes path coefficients for connection matrix in Structural Equation Modeling
-    (SEM).
+    1dSEM
+    
+    Computes path coefficients for connection matrix in Structural Equation
+    Modeling (SEM).
     
     Author: AFNI Developers
     
@@ -267,10 +256,12 @@ def v_1d_sem_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V1dSemOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_SEM_METADATA)
     params = execution.params(params)
     cargs = v_1d_sem_cargs(params, execution)
     ret = v_1d_sem_outputs(params, execution)
@@ -298,8 +289,10 @@ def v_1d_sem(
     runner: Runner | None = None,
 ) -> V1dSemOutputs:
     """
-    Computes path coefficients for connection matrix in Structural Equation Modeling
-    (SEM).
+    1dSEM
+    
+    Computes path coefficients for connection matrix in Structural Equation
+    Modeling (SEM).
     
     Author: AFNI Developers
     
@@ -338,8 +331,6 @@ def v_1d_sem(
     Returns:
         NamedTuple of outputs (described in `V1dSemOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_1D_SEM_METADATA)
     params = v_1d_sem_params(
         theta=theta,
         correlation_matrix=correlation_matrix,
@@ -358,13 +349,13 @@ def v_1d_sem(
         grow_all=grow_all,
         leafpicker=leafpicker,
     )
-    return v_1d_sem_execute(params, execution)
+    return v_1d_sem_execute(params, runner)
 
 
 __all__ = [
     "V1dSemOutputs",
-    "V1dSemParameters",
     "V_1D_SEM_METADATA",
     "v_1d_sem",
+    "v_1d_sem_execute",
     "v_1d_sem_params",
 ]

niwrap_afni/afni/v_1d_tool_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_1D_TOOL_PY_METADATA = Metadata(
-    id="518c0251ec5c51cc40ce28708b52c3282abb8107.boutiques",
+    id="d9ce647eaf11266f160d869e7be6ab7a3f504bcf.boutiques",
     name="1d_tool.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,23 @@ V_1D_TOOL_PY_METADATA = Metadata(
 
 
 V1dToolPyParameters = typing.TypedDict('V1dToolPyParameters', {
-    "__STYXTYPE__": typing.Literal["1d_tool.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/1d_tool.py"]],
+    "infile": InputPathType,
+    "write": typing.NotRequired[str | None],
+    "select_cols": typing.NotRequired[str | None],
+    "select_rows": typing.NotRequired[str | None],
+    "select_groups": typing.NotRequired[str | None],
+    "censor_motion": typing.NotRequired[float | None],
+    "pad_into_many_runs": typing.NotRequired[str | None],
+    "set_nruns": typing.NotRequired[float | None],
+    "set_run_lengths": typing.NotRequired[str | None],
+    "show_rows_cols": bool,
+    "transpose": bool,
+    "reverse": bool,
+    "show_max_displace": bool,
+})
+V1dToolPyParametersTagged = typing.TypedDict('V1dToolPyParametersTagged', {
+    "@type": typing.Literal["afni/1d_tool.py"],
     "infile": InputPathType,
     "write": typing.NotRequired[str | None],
     "select_cols": typing.NotRequired[str | None],
@@ -29,43 +45,11 @@ V1dToolPyParameters = typing.TypedDict('V1dToolPyParameters', {
     "reverse": bool,
     "show_max_displace": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "1d_tool.py": v_1d_tool_py_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 {
-        "1d_tool.py": v_1d_tool_py_outputs,
-    }.get(t)
 
 
 class V1dToolPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_1d_tool_py(...)`.
+    Output object returned when calling `V1dToolPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -87,7 +71,7 @@ def v_1d_tool_py_params(
     transpose: bool = False,
     reverse: bool = False,
     show_max_displace: bool = False,
-) -> V1dToolPyParameters:
+) -> V1dToolPyParametersTagged:
     """
     Build parameters.
     
@@ -109,7 +93,7 @@ def v_1d_tool_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "1d_tool.py",
+        "@type": "afni/1d_tool.py",
         "infile": infile,
         "show_rows_cols": show_rows_cols,
         "transpose": transpose,
@@ -152,55 +136,55 @@ def v_1d_tool_py_cargs(
     cargs.append("1d_tool.py")
     cargs.extend([
         "-infile",
-        execution.input_file(params.get("infile"))
+        execution.input_file(params.get("infile", None))
     ])
-    if params.get("write") is not None:
+    if params.get("write", None) is not None:
         cargs.extend([
             "-write",
-            params.get("write")
+            params.get("write", None)
         ])
-    if params.get("select_cols") is not None:
+    if params.get("select_cols", None) is not None:
         cargs.extend([
             "-select_cols",
-            params.get("select_cols")
+            params.get("select_cols", None)
         ])
-    if params.get("select_rows") is not None:
+    if params.get("select_rows", None) is not None:
         cargs.extend([
             "-select_rows",
-            params.get("select_rows")
+            params.get("select_rows", None)
         ])
-    if params.get("select_groups") is not None:
+    if params.get("select_groups", None) is not None:
         cargs.extend([
             "-select_groups",
-            params.get("select_groups")
+            params.get("select_groups", None)
         ])
-    if params.get("censor_motion") is not None:
+    if params.get("censor_motion", None) is not None:
         cargs.extend([
             "-censor_motion",
-            str(params.get("censor_motion"))
+            str(params.get("censor_motion", None))
         ])
-    if params.get("pad_into_many_runs") is not None:
+    if params.get("pad_into_many_runs", None) is not None:
         cargs.extend([
             "-pad_into_many_runs",
-            params.get("pad_into_many_runs")
+            params.get("pad_into_many_runs", None)
         ])
-    if params.get("set_nruns") is not None:
+    if params.get("set_nruns", None) is not None:
         cargs.extend([
             "-set_nruns",
-            str(params.get("set_nruns"))
+            str(params.get("set_nruns", None))
         ])
-    if params.get("set_run_lengths") is not None:
+    if params.get("set_run_lengths", None) is not None:
         cargs.extend([
             "-set_run_lengths",
-            params.get("set_run_lengths")
+            params.get("set_run_lengths", None)
         ])
-    if params.get("show_rows_cols"):
+    if params.get("show_rows_cols", False):
         cargs.append("-show_rows_cols")
-    if params.get("transpose"):
+    if params.get("transpose", False):
         cargs.append("-transpose")
-    if params.get("reverse"):
+    if params.get("reverse", False):
         cargs.append("-reverse")
-    if params.get("show_max_displace"):
+    if params.get("show_max_displace", False):
         cargs.append("-show_max_displace")
     return cargs
 
@@ -220,16 +204,18 @@ def v_1d_tool_py_outputs(
     """
     ret = V1dToolPyOutputs(
         root=execution.output_file("."),
-        outfile=execution.output_file(params.get("write")) if (params.get("write") is not None) else None,
+        outfile=execution.output_file(params.get("write", None)) if (params.get("write") is not None) else None,
     )
     return ret
 
 
 def v_1d_tool_py_execute(
     params: V1dToolPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V1dToolPyOutputs:
     """
+    1d_tool.py
+    
     A tool for manipulating and evaluating 1D files.
     
     Author: AFNI Developers
@@ -238,10 +224,12 @@ def v_1d_tool_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V1dToolPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_TOOL_PY_METADATA)
     params = execution.params(params)
     cargs = v_1d_tool_py_cargs(params, execution)
     ret = v_1d_tool_py_outputs(params, execution)
@@ -266,6 +254,8 @@ def v_1d_tool_py(
     runner: Runner | None = None,
 ) -> V1dToolPyOutputs:
     """
+    1d_tool.py
+    
     A tool for manipulating and evaluating 1D files.
     
     Author: AFNI Developers
@@ -290,8 +280,6 @@ def v_1d_tool_py(
     Returns:
         NamedTuple of outputs (described in `V1dToolPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_1D_TOOL_PY_METADATA)
     params = v_1d_tool_py_params(
         infile=infile,
         write=write,
@@ -307,13 +295,13 @@ def v_1d_tool_py(
         reverse=reverse,
         show_max_displace=show_max_displace,
     )
-    return v_1d_tool_py_execute(params, execution)
+    return v_1d_tool_py_execute(params, runner)
 
 
 __all__ = [
     "V1dToolPyOutputs",
-    "V1dToolPyParameters",
     "V_1D_TOOL_PY_METADATA",
     "v_1d_tool_py",
+    "v_1d_tool_py_execute",
     "v_1d_tool_py_params",
 ]

niwrap_afni/afni/v_1d_tsort.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_1D_TSORT_METADATA = Metadata(
-    id="ecc942c1165cb3a80b8962001b4930353b149d14.boutiques",
+    id="e0d377bd316d506a908a41bee8b40bbec2d74713.boutiques",
     name="1dTsort",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V_1D_TSORT_METADATA = Metadata(
 
 
 V1dTsortParameters = typing.TypedDict('V1dTsortParameters', {
-    "__STYXTYPE__": typing.Literal["1dTsort"],
+    "@type": typing.NotRequired[typing.Literal["afni/1dTsort"]],
+    "inc_order": bool,
+    "dec_order": bool,
+    "transpose": bool,
+    "column": typing.NotRequired[float | None],
+    "imode": bool,
+    "infile": InputPathType,
+})
+V1dTsortParametersTagged = typing.TypedDict('V1dTsortParametersTagged', {
+    "@type": typing.Literal["afni/1dTsort"],
     "inc_order": bool,
     "dec_order": bool,
     "transpose": bool,
@@ -22,42 +31,11 @@ V1dTsortParameters = typing.TypedDict('V1dTsortParameters', {
     "imode": bool,
     "infile": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "1dTsort": v_1d_tsort_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 V1dTsortOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_1d_tsort(...)`.
+    Output object returned when calling `V1dTsortParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def v_1d_tsort_params(
     transpose: bool = False,
     column: float | None = None,
     imode: bool = False,
-) -> V1dTsortParameters:
+) -> V1dTsortParametersTagged:
     """
     Build parameters.
     
@@ -87,7 +65,7 @@ def v_1d_tsort_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "1dTsort",
+        "@type": "afni/1dTsort",
         "inc_order": inc_order,
         "dec_order": dec_order,
         "transpose": transpose,
@@ -114,20 +92,20 @@ def v_1d_tsort_cargs(
     """
     cargs = []
     cargs.append("1dTsort")
-    if params.get("inc_order"):
+    if params.get("inc_order", False):
         cargs.append("-inc")
-    if params.get("dec_order"):
+    if params.get("dec_order", False):
         cargs.append("-dec")
-    if params.get("transpose"):
+    if params.get("transpose", False):
         cargs.append("-flip")
-    if params.get("column") is not None:
+    if params.get("column", None) is not None:
         cargs.extend([
             "-col",
-            str(params.get("column"))
+            str(params.get("column", None))
         ])
-    if params.get("imode"):
+    if params.get("imode", False):
         cargs.append("-imode")
-    cargs.append(execution.input_file(params.get("infile")))
+    cargs.append(execution.input_file(params.get("infile", None)))
     return cargs
 
 
@@ -152,9 +130,11 @@ def v_1d_tsort_outputs(
 
 def v_1d_tsort_execute(
     params: V1dTsortParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V1dTsortOutputs:
     """
+    1dTsort
+    
     Sorts each column of the input 1D file and writes result to stdout.
     
     Author: AFNI Developers
@@ -163,10 +143,12 @@ def v_1d_tsort_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V1dTsortOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_TSORT_METADATA)
     params = execution.params(params)
     cargs = v_1d_tsort_cargs(params, execution)
     ret = v_1d_tsort_outputs(params, execution)
@@ -184,6 +166,8 @@ def v_1d_tsort(
     runner: Runner | None = None,
 ) -> V1dTsortOutputs:
     """
+    1dTsort
+    
     Sorts each column of the input 1D file and writes result to stdout.
     
     Author: AFNI Developers
@@ -203,8 +187,6 @@ def v_1d_tsort(
     Returns:
         NamedTuple of outputs (described in `V1dTsortOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_1D_TSORT_METADATA)
     params = v_1d_tsort_params(
         inc_order=inc_order,
         dec_order=dec_order,
@@ -213,13 +195,13 @@ def v_1d_tsort(
         imode=imode,
         infile=infile,
     )
-    return v_1d_tsort_execute(params, execution)
+    return v_1d_tsort_execute(params, runner)
 
 
 __all__ = [
     "V1dTsortOutputs",
-    "V1dTsortParameters",
     "V_1D_TSORT_METADATA",
     "v_1d_tsort",
+    "v_1d_tsort_execute",
     "v_1d_tsort_params",
 ]