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

niwrap_afni/afni/v__afni_orient2_raimap.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__AFNI_ORIENT2_RAIMAP_METADATA = Metadata(
-    id="ade1258888a2ab4d7104b72e6f2921d74eaf281c.boutiques",
+    id="febf1cf266ecd5b8f67d7b9d8795b382c26c3672.boutiques",
     name="@AfniOrient2RAImap",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,45 +14,18 @@ V__AFNI_ORIENT2_RAIMAP_METADATA = Metadata(
 
 
 VAfniOrient2RaimapParameters = typing.TypedDict('VAfniOrient2RaimapParameters', {
-    "__STYXTYPE__": typing.Literal["@AfniOrient2RAImap"],
+    "@type": typing.NotRequired[typing.Literal["afni/@AfniOrient2RAImap"]],
+    "orientation_code": str,
+})
+VAfniOrient2RaimapParametersTagged = typing.TypedDict('VAfniOrient2RaimapParametersTagged', {
+    "@type": typing.Literal["afni/@AfniOrient2RAImap"],
     "orientation_code": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@AfniOrient2RAImap": v__afni_orient2_raimap_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 VAfniOrient2RaimapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__afni_orient2_raimap(...)`.
+    Output object returned when calling `VAfniOrient2RaimapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class VAfniOrient2RaimapOutputs(typing.NamedTuple):
 
 def v__afni_orient2_raimap_params(
     orientation_code: str,
-) -> VAfniOrient2RaimapParameters:
+) -> VAfniOrient2RaimapParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def v__afni_orient2_raimap_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@AfniOrient2RAImap",
+        "@type": "afni/@AfniOrient2RAImap",
         "orientation_code": orientation_code,
     }
     return params
@@ -91,7 +64,7 @@ def v__afni_orient2_raimap_cargs(
     """
     cargs = []
     cargs.append("@AfniOrient2RAImap")
-    cargs.append(params.get("orientation_code"))
+    cargs.append(params.get("orientation_code", None))
     return cargs
 
 
@@ -116,9 +89,11 @@ def v__afni_orient2_raimap_outputs(
 
 def v__afni_orient2_raimap_execute(
     params: VAfniOrient2RaimapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VAfniOrient2RaimapOutputs:
     """
+    @AfniOrient2RAImap
+    
     Returns the index map for the RAI directions.
     
     Author: AFNI Developers
@@ -127,10 +102,12 @@ def v__afni_orient2_raimap_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VAfniOrient2RaimapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__AFNI_ORIENT2_RAIMAP_METADATA)
     params = execution.params(params)
     cargs = v__afni_orient2_raimap_cargs(params, execution)
     ret = v__afni_orient2_raimap_outputs(params, execution)
@@ -143,6 +120,8 @@ def v__afni_orient2_raimap(
     runner: Runner | None = None,
 ) -> VAfniOrient2RaimapOutputs:
     """
+    @AfniOrient2RAImap
+    
     Returns the index map for the RAI directions.
     
     Author: AFNI Developers
@@ -155,18 +134,16 @@ def v__afni_orient2_raimap(
     Returns:
         NamedTuple of outputs (described in `VAfniOrient2RaimapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__AFNI_ORIENT2_RAIMAP_METADATA)
     params = v__afni_orient2_raimap_params(
         orientation_code=orientation_code,
     )
-    return v__afni_orient2_raimap_execute(params, execution)
+    return v__afni_orient2_raimap_execute(params, runner)
 
 
 __all__ = [
     "VAfniOrient2RaimapOutputs",
-    "VAfniOrient2RaimapParameters",
     "V__AFNI_ORIENT2_RAIMAP_METADATA",
     "v__afni_orient2_raimap",
+    "v__afni_orient2_raimap_execute",
     "v__afni_orient2_raimap_params",
 ]

niwrap_afni/afni/v__afni_orient_sign.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__AFNI_ORIENT_SIGN_METADATA = Metadata(
-    id="0406b1e6aa362529e558b94d8db55d746378a55d.boutiques",
+    id="17bacac61b3bbe671dbec1441539bb30e688fabb.boutiques",
     name="@AfniOrientSign",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,46 +14,18 @@ V__AFNI_ORIENT_SIGN_METADATA = Metadata(
 
 
 VAfniOrientSignParameters = typing.TypedDict('VAfniOrientSignParameters', {
-    "__STYXTYPE__": typing.Literal["@AfniOrientSign"],
+    "@type": typing.NotRequired[typing.Literal["afni/@AfniOrientSign"]],
+    "infile": InputPathType,
+})
+VAfniOrientSignParametersTagged = typing.TypedDict('VAfniOrientSignParametersTagged', {
+    "@type": typing.Literal["afni/@AfniOrientSign"],
     "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 {
-        "@AfniOrientSign": v__afni_orient_sign_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 {
-        "@AfniOrientSign": v__afni_orient_sign_outputs,
-    }.get(t)
 
 
 class VAfniOrientSignOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__afni_orient_sign(...)`.
+    Output object returned when calling `VAfniOrientSignParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -63,7 +35,7 @@ class VAfniOrientSignOutputs(typing.NamedTuple):
 
 def v__afni_orient_sign_params(
     infile: InputPathType,
-) -> VAfniOrientSignParameters:
+) -> VAfniOrientSignParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +45,7 @@ def v__afni_orient_sign_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@AfniOrientSign",
+        "@type": "afni/@AfniOrientSign",
         "infile": infile,
     }
     return params
@@ -96,7 +68,7 @@ def v__afni_orient_sign_cargs(
     cargs.append("@AfniOrientSign")
     cargs.extend([
         "-orient",
-        execution.input_file(params.get("infile"))
+        execution.input_file(params.get("infile", None))
     ])
     return cargs
 
@@ -116,16 +88,18 @@ def v__afni_orient_sign_outputs(
     """
     ret = VAfniOrientSignOutputs(
         root=execution.output_file("."),
-        outfile=execution.output_file(pathlib.Path(params.get("infile")).name + "_orient.txt"),
+        outfile=execution.output_file(pathlib.Path(params.get("infile", None)).name + "_orient.txt"),
     )
     return ret
 
 
 def v__afni_orient_sign_execute(
     params: VAfniOrientSignParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VAfniOrientSignOutputs:
     """
+    @AfniOrientSign
+    
     A tool within the AFNI suite to determine the orientation signs of datasets.
     
     Author: AFNI Developers
@@ -134,10 +108,12 @@ def v__afni_orient_sign_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VAfniOrientSignOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__AFNI_ORIENT_SIGN_METADATA)
     params = execution.params(params)
     cargs = v__afni_orient_sign_cargs(params, execution)
     ret = v__afni_orient_sign_outputs(params, execution)
@@ -150,6 +126,8 @@ def v__afni_orient_sign(
     runner: Runner | None = None,
 ) -> VAfniOrientSignOutputs:
     """
+    @AfniOrientSign
+    
     A tool within the AFNI suite to determine the orientation signs of datasets.
     
     Author: AFNI Developers
@@ -162,18 +140,16 @@ def v__afni_orient_sign(
     Returns:
         NamedTuple of outputs (described in `VAfniOrientSignOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__AFNI_ORIENT_SIGN_METADATA)
     params = v__afni_orient_sign_params(
         infile=infile,
     )
-    return v__afni_orient_sign_execute(params, execution)
+    return v__afni_orient_sign_execute(params, runner)
 
 
 __all__ = [
     "VAfniOrientSignOutputs",
-    "VAfniOrientSignParameters",
     "V__AFNI_ORIENT_SIGN_METADATA",
     "v__afni_orient_sign",
+    "v__afni_orient_sign_execute",
     "v__afni_orient_sign_params",
 ]

niwrap_afni/afni/v__afni_r_package_install.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__AFNI_R_PACKAGE_INSTALL_METADATA = Metadata(
-    id="cbebf13217e6c26c27782fa62a21100bbdcabaf7.boutiques",
+    id="207907acfab1da0bfd8b8c768ead9047dfc66aa7.boutiques",
     name="@afni_R_package_install",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ V__AFNI_R_PACKAGE_INSTALL_METADATA = Metadata(
 
 
 VAfniRPackageInstallParameters = typing.TypedDict('VAfniRPackageInstallParameters', {
-    "__STYXTYPE__": typing.Literal["@afni_R_package_install"],
+    "@type": typing.NotRequired[typing.Literal["afni/@afni_R_package_install"]],
+    "afni": bool,
+    "shiny": bool,
+    "bayes_view": bool,
+    "circos": bool,
+    "custom_packages": typing.NotRequired[str | None],
+    "mirror": typing.NotRequired[str | None],
+    "help": bool,
+})
+VAfniRPackageInstallParametersTagged = typing.TypedDict('VAfniRPackageInstallParametersTagged', {
+    "@type": typing.Literal["afni/@afni_R_package_install"],
     "afni": bool,
     "shiny": bool,
     "bayes_view": bool,
@@ -23,43 +33,11 @@ VAfniRPackageInstallParameters = typing.TypedDict('VAfniRPackageInstallParameter
     "mirror": typing.NotRequired[str | None],
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@afni_R_package_install": v__afni_r_package_install_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 {
-        "@afni_R_package_install": v__afni_r_package_install_outputs,
-    }.get(t)
 
 
 class VAfniRPackageInstallOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__afni_r_package_install(...)`.
+    Output object returned when calling `VAfniRPackageInstallParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def v__afni_r_package_install_params(
     custom_packages: str | None = None,
     mirror: str | None = None,
     help_: bool = False,
-) -> VAfniRPackageInstallParameters:
+) -> VAfniRPackageInstallParametersTagged:
     """
     Build parameters.
     
@@ -92,7 +70,7 @@ def v__afni_r_package_install_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@afni_R_package_install",
+        "@type": "afni/@afni_R_package_install",
         "afni": afni,
         "shiny": shiny,
         "bayes_view": bayes_view,
@@ -121,25 +99,25 @@ def v__afni_r_package_install_cargs(
     """
     cargs = []
     cargs.append("@afni_R_package_install")
-    if params.get("afni"):
+    if params.get("afni", False):
         cargs.append("-afni")
-    if params.get("shiny"):
+    if params.get("shiny", False):
         cargs.append("-shiny")
-    if params.get("bayes_view"):
+    if params.get("bayes_view", False):
         cargs.append("-bayes_view")
-    if params.get("circos"):
+    if params.get("circos", False):
         cargs.append("-circos")
-    if params.get("custom_packages") is not None:
+    if params.get("custom_packages", None) is not None:
         cargs.extend([
             "-custom",
-            params.get("custom_packages")
+            params.get("custom_packages", None)
         ])
-    if params.get("mirror") is not None:
+    if params.get("mirror", None) is not None:
         cargs.extend([
             "-mirror",
-            params.get("mirror")
+            params.get("mirror", None)
         ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -166,9 +144,11 @@ def v__afni_r_package_install_outputs(
 
 def v__afni_r_package_install_execute(
     params: VAfniRPackageInstallParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VAfniRPackageInstallOutputs:
     """
+    @afni_R_package_install
+    
     Helper script to install R packages for various afni-ish purposes.
     
     Author: AFNI Developers
@@ -177,10 +157,12 @@ def v__afni_r_package_install_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VAfniRPackageInstallOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__AFNI_R_PACKAGE_INSTALL_METADATA)
     params = execution.params(params)
     cargs = v__afni_r_package_install_cargs(params, execution)
     ret = v__afni_r_package_install_outputs(params, execution)
@@ -199,6 +181,8 @@ def v__afni_r_package_install(
     runner: Runner | None = None,
 ) -> VAfniRPackageInstallOutputs:
     """
+    @afni_R_package_install
+    
     Helper script to install R packages for various afni-ish purposes.
     
     Author: AFNI Developers
@@ -218,8 +202,6 @@ def v__afni_r_package_install(
     Returns:
         NamedTuple of outputs (described in `VAfniRPackageInstallOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__AFNI_R_PACKAGE_INSTALL_METADATA)
     params = v__afni_r_package_install_params(
         afni=afni,
         shiny=shiny,
@@ -229,13 +211,13 @@ def v__afni_r_package_install(
         mirror=mirror,
         help_=help_,
     )
-    return v__afni_r_package_install_execute(params, execution)
+    return v__afni_r_package_install_execute(params, runner)
 
 
 __all__ = [
     "VAfniRPackageInstallOutputs",
-    "VAfniRPackageInstallParameters",
     "V__AFNI_R_PACKAGE_INSTALL_METADATA",
     "v__afni_r_package_install",
+    "v__afni_r_package_install_execute",
     "v__afni_r_package_install_params",
 ]

niwrap_afni/afni/v__afni_refacer_make_master.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__AFNI_REFACER_MAKE_MASTER_METADATA = Metadata(
-    id="754d45612350ae723d8b3264a150b211e0e4c0e8.boutiques",
+    id="eceacc4cfbc7ea186554f5192a5cba27bc45f891.boutiques",
     name="@afni_refacer_make_master",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,46 +14,18 @@ V__AFNI_REFACER_MAKE_MASTER_METADATA = Metadata(
 
 
 VAfniRefacerMakeMasterParameters = typing.TypedDict('VAfniRefacerMakeMasterParameters', {
-    "__STYXTYPE__": typing.Literal["@afni_refacer_make_master"],
+    "@type": typing.NotRequired[typing.Literal["afni/@afni_refacer_make_master"]],
+    "input_datasets": list[InputPathType],
+})
+VAfniRefacerMakeMasterParametersTagged = typing.TypedDict('VAfniRefacerMakeMasterParametersTagged', {
+    "@type": typing.Literal["afni/@afni_refacer_make_master"],
     "input_datasets": list[InputPathType],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@afni_refacer_make_master": v__afni_refacer_make_master_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 {
-        "@afni_refacer_make_master": v__afni_refacer_make_master_outputs,
-    }.get(t)
 
 
 class VAfniRefacerMakeMasterOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__afni_refacer_make_master(...)`.
+    Output object returned when calling `VAfniRefacerMakeMasterParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -63,7 +35,7 @@ class VAfniRefacerMakeMasterOutputs(typing.NamedTuple):
 
 def v__afni_refacer_make_master_params(
     input_datasets: list[InputPathType],
-) -> VAfniRefacerMakeMasterParameters:
+) -> VAfniRefacerMakeMasterParametersTagged:
     """
     Build parameters.
     
@@ -74,7 +46,7 @@ def v__afni_refacer_make_master_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@afni_refacer_make_master",
+        "@type": "afni/@afni_refacer_make_master",
         "input_datasets": input_datasets,
     }
     return params
@@ -95,7 +67,7 @@ def v__afni_refacer_make_master_cargs(
     """
     cargs = []
     cargs.append("@afni_refacer_make_master")
-    cargs.extend([execution.input_file(f) for f in params.get("input_datasets")])
+    cargs.extend([execution.input_file(f) for f in params.get("input_datasets", None)])
     return cargs
 
 
@@ -121,9 +93,11 @@ def v__afni_refacer_make_master_outputs(
 
 def v__afni_refacer_make_master_execute(
     params: VAfniRefacerMakeMasterParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VAfniRefacerMakeMasterOutputs:
     """
+    @afni_refacer_make_master
+    
     This script makes a new mask/shell dataset for use with @afni_refacer_run by
     averaging 'faces' (non-brain tissue) from input datasets.
     
@@ -133,10 +107,12 @@ def v__afni_refacer_make_master_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VAfniRefacerMakeMasterOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__AFNI_REFACER_MAKE_MASTER_METADATA)
     params = execution.params(params)
     cargs = v__afni_refacer_make_master_cargs(params, execution)
     ret = v__afni_refacer_make_master_outputs(params, execution)
@@ -149,6 +125,8 @@ def v__afni_refacer_make_master(
     runner: Runner | None = None,
 ) -> VAfniRefacerMakeMasterOutputs:
     """
+    @afni_refacer_make_master
+    
     This script makes a new mask/shell dataset for use with @afni_refacer_run by
     averaging 'faces' (non-brain tissue) from input datasets.
     
@@ -163,18 +141,16 @@ def v__afni_refacer_make_master(
     Returns:
         NamedTuple of outputs (described in `VAfniRefacerMakeMasterOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__AFNI_REFACER_MAKE_MASTER_METADATA)
     params = v__afni_refacer_make_master_params(
         input_datasets=input_datasets,
     )
-    return v__afni_refacer_make_master_execute(params, execution)
+    return v__afni_refacer_make_master_execute(params, runner)
 
 
 __all__ = [
     "VAfniRefacerMakeMasterOutputs",
-    "VAfniRefacerMakeMasterParameters",
     "V__AFNI_REFACER_MAKE_MASTER_METADATA",
     "v__afni_refacer_make_master",
+    "v__afni_refacer_make_master_execute",
     "v__afni_refacer_make_master_params",
 ]