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

niwrap_afni/afni/v__afni_refacer_make_onebig_a12.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__AFNI_REFACER_MAKE_ONEBIG_A12_METADATA = Metadata(
-    id="f03df11cce5321951f2161a48a9756c76bd1cf4e.boutiques",
+    id="0bc73fd2469df279796b8de9f4bc8643932c82f1.boutiques",
     name="@afni_refacer_make_onebigA12",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,46 +14,18 @@ V__AFNI_REFACER_MAKE_ONEBIG_A12_METADATA = Metadata(
 
 
 VAfniRefacerMakeOnebigA12Parameters = typing.TypedDict('VAfniRefacerMakeOnebigA12Parameters', {
-    "__STYXTYPE__": typing.Literal["@afni_refacer_make_onebigA12"],
+    "@type": typing.NotRequired[typing.Literal["afni/@afni_refacer_make_onebigA12"]],
+    "t1w_dataset": InputPathType,
+})
+VAfniRefacerMakeOnebigA12ParametersTagged = typing.TypedDict('VAfniRefacerMakeOnebigA12ParametersTagged', {
+    "@type": typing.Literal["afni/@afni_refacer_make_onebigA12"],
     "t1w_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 {
-        "@afni_refacer_make_onebigA12": v__afni_refacer_make_onebig_a12_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_onebigA12": v__afni_refacer_make_onebig_a12_outputs,
-    }.get(t)
 
 
 class VAfniRefacerMakeOnebigA12Outputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__afni_refacer_make_onebig_a12(...)`.
+    Output object returned when calling `VAfniRefacerMakeOnebigA12Parameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -63,7 +35,7 @@ class VAfniRefacerMakeOnebigA12Outputs(typing.NamedTuple):
 
 def v__afni_refacer_make_onebig_a12_params(
     t1w_dataset: InputPathType,
-) -> VAfniRefacerMakeOnebigA12Parameters:
+) -> VAfniRefacerMakeOnebigA12ParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +45,7 @@ def v__afni_refacer_make_onebig_a12_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@afni_refacer_make_onebigA12",
+        "@type": "afni/@afni_refacer_make_onebigA12",
         "t1w_dataset": t1w_dataset,
     }
     return params
@@ -94,7 +66,7 @@ def v__afni_refacer_make_onebig_a12_cargs(
     """
     cargs = []
     cargs.append("@afni_refacer_make_onebigA12")
-    cargs.append(execution.input_file(params.get("t1w_dataset")))
+    cargs.append(execution.input_file(params.get("t1w_dataset", None)))
     return cargs
 
 
@@ -113,16 +85,18 @@ def v__afni_refacer_make_onebig_a12_outputs(
     """
     ret = VAfniRefacerMakeOnebigA12Outputs(
         root=execution.output_file("."),
-        aligned_output=execution.output_file(pathlib.Path(params.get("t1w_dataset")).name + "_aligned_to_MNI.nii.gz"),
+        aligned_output=execution.output_file(pathlib.Path(params.get("t1w_dataset", None)).name + "_aligned_to_MNI.nii.gz"),
     )
     return ret
 
 
 def v__afni_refacer_make_onebig_a12_execute(
     params: VAfniRefacerMakeOnebigA12Parameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VAfniRefacerMakeOnebigA12Outputs:
     """
+    @afni_refacer_make_onebigA12
+    
     Script to align a single T1w dataset to the MNI template and expand it to a
     'big' grid.
     
@@ -132,10 +106,12 @@ def v__afni_refacer_make_onebig_a12_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VAfniRefacerMakeOnebigA12Outputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__AFNI_REFACER_MAKE_ONEBIG_A12_METADATA)
     params = execution.params(params)
     cargs = v__afni_refacer_make_onebig_a12_cargs(params, execution)
     ret = v__afni_refacer_make_onebig_a12_outputs(params, execution)
@@ -148,6 +124,8 @@ def v__afni_refacer_make_onebig_a12(
     runner: Runner | None = None,
 ) -> VAfniRefacerMakeOnebigA12Outputs:
     """
+    @afni_refacer_make_onebigA12
+    
     Script to align a single T1w dataset to the MNI template and expand it to a
     'big' grid.
     
@@ -161,18 +139,16 @@ def v__afni_refacer_make_onebig_a12(
     Returns:
         NamedTuple of outputs (described in `VAfniRefacerMakeOnebigA12Outputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__AFNI_REFACER_MAKE_ONEBIG_A12_METADATA)
     params = v__afni_refacer_make_onebig_a12_params(
         t1w_dataset=t1w_dataset,
     )
-    return v__afni_refacer_make_onebig_a12_execute(params, execution)
+    return v__afni_refacer_make_onebig_a12_execute(params, runner)
 
 
 __all__ = [
     "VAfniRefacerMakeOnebigA12Outputs",
-    "VAfniRefacerMakeOnebigA12Parameters",
     "V__AFNI_REFACER_MAKE_ONEBIG_A12_METADATA",
     "v__afni_refacer_make_onebig_a12",
+    "v__afni_refacer_make_onebig_a12_execute",
     "v__afni_refacer_make_onebig_a12_params",
 ]

niwrap_afni/afni/v__afni_refacer_run.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__AFNI_REFACER_RUN_METADATA = Metadata(
-    id="4e275d528a8a916f8bf15e461ab3aaee99ba8b52.boutiques",
+    id="07064724b60b6bb54543b62652b26b267f3ac91b.boutiques",
     name="@afni_refacer_run",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,23 @@ V__AFNI_REFACER_RUN_METADATA = Metadata(
 
 
 VAfniRefacerRunParameters = typing.TypedDict('VAfniRefacerRunParameters', {
-    "__STYXTYPE__": typing.Literal["@afni_refacer_run"],
+    "@type": typing.NotRequired[typing.Literal["afni/@afni_refacer_run"]],
+    "input_file": InputPathType,
+    "mode_deface": bool,
+    "mode_reface": bool,
+    "mode_reface_plus": bool,
+    "mode_all": bool,
+    "prefix": str,
+    "anonymize_output": bool,
+    "cost_function": typing.NotRequired[str | None],
+    "shell_option": typing.NotRequired[str | None],
+    "no_clean": bool,
+    "no_images": bool,
+    "overwrite": bool,
+    "verbose": bool,
+})
+VAfniRefacerRunParametersTagged = typing.TypedDict('VAfniRefacerRunParametersTagged', {
+    "@type": typing.Literal["afni/@afni_refacer_run"],
     "input_file": InputPathType,
     "mode_deface": bool,
     "mode_reface": bool,
@@ -29,43 +45,11 @@ VAfniRefacerRunParameters = typing.TypedDict('VAfniRefacerRunParameters', {
     "overwrite": bool,
     "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 {
-        "@afni_refacer_run": v__afni_refacer_run_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_run": v__afni_refacer_run_outputs,
-    }.get(t)
 
 
 class VAfniRefacerRunOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__afni_refacer_run(...)`.
+    Output object returned when calling `VAfniRefacerRunParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -95,7 +79,7 @@ def v__afni_refacer_run_params(
     no_images: bool = False,
     overwrite: bool = False,
     verbose: bool = False,
-) -> VAfniRefacerRunParameters:
+) -> VAfniRefacerRunParametersTagged:
     """
     Build parameters.
     
@@ -131,7 +115,7 @@ def v__afni_refacer_run_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@afni_refacer_run",
+        "@type": "afni/@afni_refacer_run",
         "input_file": input_file,
         "mode_deface": mode_deface,
         "mode_reface": mode_reface,
@@ -168,39 +152,39 @@ def v__afni_refacer_run_cargs(
     cargs.append("@afni_refacer_run")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
-    if params.get("mode_deface"):
+    if params.get("mode_deface", False):
         cargs.append("-mode_deface")
-    if params.get("mode_reface"):
+    if params.get("mode_reface", False):
         cargs.append("-mode_reface")
-    if params.get("mode_reface_plus"):
+    if params.get("mode_reface_plus", False):
         cargs.append("-mode_reface_plus")
-    if params.get("mode_all"):
+    if params.get("mode_all", False):
         cargs.append("-mode_all")
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("anonymize_output"):
+    if params.get("anonymize_output", False):
         cargs.append("-anonymize_output")
-    if params.get("cost_function") is not None:
+    if params.get("cost_function", None) is not None:
         cargs.extend([
             "-cost",
-            params.get("cost_function")
+            params.get("cost_function", None)
         ])
-    if params.get("shell_option") is not None:
+    if params.get("shell_option", None) is not None:
         cargs.extend([
             "-shell",
-            params.get("shell_option")
+            params.get("shell_option", None)
         ])
-    if params.get("no_clean"):
+    if params.get("no_clean", False):
         cargs.append("-no_clean")
-    if params.get("no_images"):
+    if params.get("no_images", False):
         cargs.append("-no_images")
-    if params.get("overwrite"):
+    if params.get("overwrite", False):
         cargs.append("-overwrite")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb_allin")
     return cargs
 
@@ -220,22 +204,24 @@ def v__afni_refacer_run_outputs(
     """
     ret = VAfniRefacerRunOutputs(
         root=execution.output_file("."),
-        output_deface=execution.output_file(params.get("prefix") + ".deface.nii.gz"),
-        output_reface=execution.output_file(params.get("prefix") + ".reface.nii.gz"),
-        output_reface_plus=execution.output_file(params.get("prefix") + ".reface_plus.nii.gz"),
-        output_face=execution.output_file(params.get("prefix") + ".face.nii.gz"),
-        output_face_plus=execution.output_file(params.get("prefix") + ".face_plus.nii.gz"),
+        output_deface=execution.output_file(params.get("prefix", None) + ".deface.nii.gz"),
+        output_reface=execution.output_file(params.get("prefix", None) + ".reface.nii.gz"),
+        output_reface_plus=execution.output_file(params.get("prefix", None) + ".reface_plus.nii.gz"),
+        output_face=execution.output_file(params.get("prefix", None) + ".face.nii.gz"),
+        output_face_plus=execution.output_file(params.get("prefix", None) + ".face_plus.nii.gz"),
     )
     return ret
 
 
 def v__afni_refacer_run_execute(
     params: VAfniRefacerRunParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VAfniRefacerRunOutputs:
     """
-    This script re-faces one input dataset, using a master shell dataset to write
-    over the subject's 'face' region.
+    @afni_refacer_run
+    
+    This script re-faces one input dataset, using a master shell dataset to
+    write over the subject's 'face' region.
     
     Author: AFNI Developers
     
@@ -243,10 +229,12 @@ def v__afni_refacer_run_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VAfniRefacerRunOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__AFNI_REFACER_RUN_METADATA)
     params = execution.params(params)
     cargs = v__afni_refacer_run_cargs(params, execution)
     ret = v__afni_refacer_run_outputs(params, execution)
@@ -271,8 +259,10 @@ def v__afni_refacer_run(
     runner: Runner | None = None,
 ) -> VAfniRefacerRunOutputs:
     """
-    This script re-faces one input dataset, using a master shell dataset to write
-    over the subject's 'face' region.
+    @afni_refacer_run
+    
+    This script re-faces one input dataset, using a master shell dataset to
+    write over the subject's 'face' region.
     
     Author: AFNI Developers
     
@@ -310,8 +300,6 @@ def v__afni_refacer_run(
     Returns:
         NamedTuple of outputs (described in `VAfniRefacerRunOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__AFNI_REFACER_RUN_METADATA)
     params = v__afni_refacer_run_params(
         input_file=input_file,
         mode_deface=mode_deface,
@@ -327,13 +315,13 @@ def v__afni_refacer_run(
         overwrite=overwrite,
         verbose=verbose,
     )
-    return v__afni_refacer_run_execute(params, execution)
+    return v__afni_refacer_run_execute(params, runner)
 
 
 __all__ = [
     "VAfniRefacerRunOutputs",
-    "VAfniRefacerRunParameters",
     "V__AFNI_REFACER_RUN_METADATA",
     "v__afni_refacer_run",
+    "v__afni_refacer_run_execute",
     "v__afni_refacer_run_params",
 ]

niwrap_afni/afni/v__afni_run_me.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__AFNI_RUN_ME_METADATA = Metadata(
-    id="759b988e9e66475876e7186709f05a39cd909fce.boutiques",
+    id="7696aecb792a6bb84c18a52039218c06a81327eb.boutiques",
     name="@afni.run.me",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,47 +14,22 @@ V__AFNI_RUN_ME_METADATA = Metadata(
 
 
 VAfniRunMeParameters = typing.TypedDict('VAfniRunMeParameters', {
-    "__STYXTYPE__": typing.Literal["@afni.run.me"],
+    "@type": typing.NotRequired[typing.Literal["afni/@afni.run.me"]],
+    "go": bool,
+    "curl": bool,
+    "help": bool,
+})
+VAfniRunMeParametersTagged = typing.TypedDict('VAfniRunMeParametersTagged', {
+    "@type": typing.Literal["afni/@afni.run.me"],
     "go": bool,
     "curl": bool,
     "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.run.me": v__afni_run_me_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 VAfniRunMeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__afni_run_me(...)`.
+    Output object returned when calling `VAfniRunMeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +39,7 @@ def v__afni_run_me_params(
     go: bool = False,
     curl: bool = False,
     help_: bool = False,
-) -> VAfniRunMeParameters:
+) -> VAfniRunMeParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +51,7 @@ def v__afni_run_me_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@afni.run.me",
+        "@type": "afni/@afni.run.me",
         "go": go,
         "curl": curl,
         "help": help_,
@@ -99,11 +74,11 @@ def v__afni_run_me_cargs(
     """
     cargs = []
     cargs.append("@afni.run.me")
-    if params.get("go"):
+    if params.get("go", False):
         cargs.append("-go")
-    if params.get("curl"):
+    if params.get("curl", False):
         cargs.append("-curl")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -129,9 +104,11 @@ def v__afni_run_me_outputs(
 
 def v__afni_run_me_execute(
     params: VAfniRunMeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VAfniRunMeOutputs:
     """
+    @afni.run.me
+    
     A tool to execute a specific command.
     
     Author: AFNI Developers
@@ -140,10 +117,12 @@ def v__afni_run_me_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VAfniRunMeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__AFNI_RUN_ME_METADATA)
     params = execution.params(params)
     cargs = v__afni_run_me_cargs(params, execution)
     ret = v__afni_run_me_outputs(params, execution)
@@ -158,6 +137,8 @@ def v__afni_run_me(
     runner: Runner | None = None,
 ) -> VAfniRunMeOutputs:
     """
+    @afni.run.me
+    
     A tool to execute a specific command.
     
     Author: AFNI Developers
@@ -172,20 +153,18 @@ def v__afni_run_me(
     Returns:
         NamedTuple of outputs (described in `VAfniRunMeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__AFNI_RUN_ME_METADATA)
     params = v__afni_run_me_params(
         go=go,
         curl=curl,
         help_=help_,
     )
-    return v__afni_run_me_execute(params, execution)
+    return v__afni_run_me_execute(params, runner)
 
 
 __all__ = [
     "VAfniRunMeOutputs",
-    "VAfniRunMeParameters",
     "V__AFNI_RUN_ME_METADATA",
     "v__afni_run_me",
+    "v__afni_run_me_execute",
     "v__afni_run_me_params",
 ]