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

niwrap_afni/afni/apsearch.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 APSEARCH_METADATA = Metadata(
-    id="cd2ec5b2b99155700676e65bd9c04ed3a27a09dc.boutiques",
+    id="7c240b20ea8614826dd26b9ef855f0eba347b56c.boutiques",
     name="apsearch",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,22 @@ APSEARCH_METADATA = Metadata(
 
 
 ApsearchParameters = typing.TypedDict('ApsearchParameters', {
-    "__STYXTYPE__": typing.Literal["apsearch"],
+    "@type": typing.NotRequired[typing.Literal["afni/apsearch"]],
+    "search_term": str,
+    "file_output": typing.NotRequired[str | None],
+    "verbose": bool,
+})
+ApsearchParametersTagged = typing.TypedDict('ApsearchParametersTagged', {
+    "@type": typing.Literal["afni/apsearch"],
     "search_term": str,
     "file_output": typing.NotRequired[str | 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 {
-        "apsearch": apsearch_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 {
-        "apsearch": apsearch_outputs,
-    }.get(t)
 
 
 class ApsearchOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `apsearch(...)`.
+    Output object returned when calling `ApsearchParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def apsearch_params(
     search_term: str,
     file_output: str | None = None,
     verbose: bool = False,
-) -> ApsearchParameters:
+) -> ApsearchParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def apsearch_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "apsearch",
+        "@type": "afni/apsearch",
         "search_term": search_term,
         "verbose": verbose,
     }
@@ -103,10 +77,10 @@ def apsearch_cargs(
     """
     cargs = []
     cargs.append("apsearch")
-    cargs.append(params.get("search_term"))
-    if params.get("file_output") is not None:
-        cargs.append(params.get("file_output"))
-    if params.get("verbose"):
+    cargs.append(params.get("search_term", None))
+    if params.get("file_output", None) is not None:
+        cargs.append(params.get("file_output", None))
+    if params.get("verbose", False):
         cargs.append("-v")
     return cargs
 
@@ -126,16 +100,18 @@ def apsearch_outputs(
     """
     ret = ApsearchOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("file_output")) if (params.get("file_output") is not None) else None,
+        output_file=execution.output_file(params.get("file_output", None)) if (params.get("file_output") is not None) else None,
     )
     return ret
 
 
 def apsearch_execute(
     params: ApsearchParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ApsearchOutputs:
     """
+    apsearch
+    
     A tool for searching applications.
     
     Author: AFNI Developers
@@ -144,10 +120,12 @@ def apsearch_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ApsearchOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(APSEARCH_METADATA)
     params = execution.params(params)
     cargs = apsearch_cargs(params, execution)
     ret = apsearch_outputs(params, execution)
@@ -162,6 +140,8 @@ def apsearch(
     runner: Runner | None = None,
 ) -> ApsearchOutputs:
     """
+    apsearch
+    
     A tool for searching applications.
     
     Author: AFNI Developers
@@ -176,20 +156,18 @@ def apsearch(
     Returns:
         NamedTuple of outputs (described in `ApsearchOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(APSEARCH_METADATA)
     params = apsearch_params(
         search_term=search_term,
         file_output=file_output,
         verbose=verbose,
     )
-    return apsearch_execute(params, execution)
+    return apsearch_execute(params, runner)
 
 
 __all__ = [
     "APSEARCH_METADATA",
     "ApsearchOutputs",
-    "ApsearchParameters",
     "apsearch",
+    "apsearch_execute",
     "apsearch_params",
 ]

niwrap_afni/afni/auto_warp_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 AUTO_WARP_PY_METADATA = Metadata(
-    id="0544bfd6f7c98eb7f7b9e3942033737cca834e31.boutiques",
+    id="9d62ac70156fc0e15439602dbb70dde9a4663939.boutiques",
     name="auto_warp.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,43 @@ AUTO_WARP_PY_METADATA = Metadata(
 
 
 AutoWarpPyParameters = typing.TypedDict('AutoWarpPyParameters', {
-    "__STYXTYPE__": typing.Literal["auto_warp.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/auto_warp.py"]],
+    "base": InputPathType,
+    "input": InputPathType,
+    "skull_strip_input": bool,
+    "qblur": typing.NotRequired[str | None],
+    "qworkhard": typing.NotRequired[str | None],
+    "qw_opts": typing.NotRequired[str | None],
+    "keep_rm_files": bool,
+    "prep_only": bool,
+    "help": bool,
+    "hview": bool,
+    "limited_help": bool,
+    "option_help": bool,
+    "version": bool,
+    "ver": bool,
+    "verb": bool,
+    "save_script": bool,
+    "skip_affine": bool,
+    "skull_strip_base": bool,
+    "ex_mode": typing.NotRequired[str | None],
+    "overwrite": bool,
+    "suffix": typing.NotRequired[str | None],
+    "child_anat": typing.NotRequired[str | None],
+    "warp_dxyz": typing.NotRequired[float | None],
+    "affine_dxyz": typing.NotRequired[float | None],
+    "affine_input_xmat": typing.NotRequired[str | None],
+    "smooth_anat": bool,
+    "smooth_base": bool,
+    "unifize_input": bool,
+    "output_dir": typing.NotRequired[str | None],
+    "followers": typing.NotRequired[str | None],
+    "affine_followers_xmat": typing.NotRequired[str | None],
+    "skullstrip_opts": typing.NotRequired[str | None],
+    "at_opts": typing.NotRequired[str | None],
+})
+AutoWarpPyParametersTagged = typing.TypedDict('AutoWarpPyParametersTagged', {
+    "@type": typing.Literal["afni/auto_warp.py"],
     "base": InputPathType,
     "input": InputPathType,
     "skull_strip_input": bool,
@@ -49,42 +85,11 @@ AutoWarpPyParameters = typing.TypedDict('AutoWarpPyParameters', {
     "skullstrip_opts": typing.NotRequired[str | None],
     "at_opts": 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 {
-        "auto_warp.py": auto_warp_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 {
-    }.get(t)
 
 
 class AutoWarpPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `auto_warp_py(...)`.
+    Output object returned when calling `AutoWarpPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -124,7 +129,7 @@ def auto_warp_py_params(
     affine_followers_xmat: str | None = None,
     skullstrip_opts: str | None = None,
     at_opts: str | None = None,
-) -> AutoWarpPyParameters:
+) -> AutoWarpPyParametersTagged:
     """
     Build parameters.
     
@@ -169,7 +174,7 @@ def auto_warp_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "auto_warp.py",
+        "@type": "afni/auto_warp.py",
         "base": base,
         "input": input_,
         "skull_strip_input": skull_strip_input,
@@ -238,115 +243,115 @@ def auto_warp_py_cargs(
     cargs.append("auto_warp.py")
     cargs.extend([
         "-base",
-        execution.input_file(params.get("base"))
+        execution.input_file(params.get("base", None))
     ])
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input"))
+        execution.input_file(params.get("input", None))
     ])
-    if params.get("skull_strip_input"):
+    if params.get("skull_strip_input", False):
         cargs.append("-skull_strip_input")
-    if params.get("qblur") is not None:
+    if params.get("qblur", None) is not None:
         cargs.extend([
             "-qblur",
-            params.get("qblur")
+            params.get("qblur", None)
         ])
-    if params.get("qworkhard") is not None:
+    if params.get("qworkhard", None) is not None:
         cargs.extend([
             "-qworkhard",
-            params.get("qworkhard")
+            params.get("qworkhard", None)
         ])
-    if params.get("qw_opts") is not None:
+    if params.get("qw_opts", None) is not None:
         cargs.extend([
             "-qw_opts",
-            params.get("qw_opts")
+            params.get("qw_opts", None)
         ])
-    if params.get("keep_rm_files"):
+    if params.get("keep_rm_files", False):
         cargs.append("-keep_rm_files")
-    if params.get("prep_only"):
+    if params.get("prep_only", False):
         cargs.append("-prep_only")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("hview"):
+    if params.get("hview", False):
         cargs.append("-hview")
-    if params.get("limited_help"):
+    if params.get("limited_help", False):
         cargs.append("-limited_help")
-    if params.get("option_help"):
+    if params.get("option_help", False):
         cargs.append("-option_help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-version")
-    if params.get("ver"):
+    if params.get("ver", False):
         cargs.append("-ver")
-    if params.get("verb"):
+    if params.get("verb", False):
         cargs.append("-verb")
-    if params.get("save_script"):
+    if params.get("save_script", False):
         cargs.append("-save_script")
-    if params.get("skip_affine"):
+    if params.get("skip_affine", False):
         cargs.append("-skip_affine")
-    if params.get("skull_strip_base"):
+    if params.get("skull_strip_base", False):
         cargs.append("-skull_strip_base")
-    if params.get("ex_mode") is not None:
+    if params.get("ex_mode", None) is not None:
         cargs.extend([
             "-ex_mode",
-            params.get("ex_mode")
+            params.get("ex_mode", None)
         ])
-    if params.get("overwrite"):
+    if params.get("overwrite", False):
         cargs.append("-overwrite")
-    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("child_anat") is not None:
+    if params.get("child_anat", None) is not None:
         cargs.extend([
             "-child_anat",
-            params.get("child_anat")
+            params.get("child_anat", None)
         ])
-    if params.get("warp_dxyz") is not None:
+    if params.get("warp_dxyz", None) is not None:
         cargs.extend([
             "-warp_dxyz",
-            str(params.get("warp_dxyz"))
+            str(params.get("warp_dxyz", None))
         ])
-    if params.get("affine_dxyz") is not None:
+    if params.get("affine_dxyz", None) is not None:
         cargs.extend([
             "-affine_dxyz",
-            str(params.get("affine_dxyz"))
+            str(params.get("affine_dxyz", None))
         ])
-    if params.get("affine_input_xmat") is not None:
+    if params.get("affine_input_xmat", None) is not None:
         cargs.extend([
             "-affine_input_xmat",
-            params.get("affine_input_xmat")
+            params.get("affine_input_xmat", None)
         ])
-    if params.get("smooth_anat"):
+    if params.get("smooth_anat", False):
         cargs.append("-smooth_anat")
-    if params.get("smooth_base"):
+    if params.get("smooth_base", False):
         cargs.append("-smooth_base")
-    if params.get("unifize_input"):
+    if params.get("unifize_input", False):
         cargs.append("-unifize_input")
-    if params.get("output_dir") is not None:
+    if params.get("output_dir", None) is not None:
         cargs.extend([
             "-output_dir",
-            params.get("output_dir")
+            params.get("output_dir", None)
         ])
-    if params.get("followers") is not None:
+    if params.get("followers", None) is not None:
         cargs.extend([
             "-followers",
-            params.get("followers")
+            params.get("followers", None)
         ])
-    if params.get("affine_followers_xmat") is not None:
+    if params.get("affine_followers_xmat", None) is not None:
         cargs.extend([
             "-affine_followers_xmat",
-            params.get("affine_followers_xmat")
+            params.get("affine_followers_xmat", None)
         ])
-    if params.get("skullstrip_opts") is not None:
+    if params.get("skullstrip_opts", None) is not None:
         cargs.extend([
             "-skullstrip_opts",
-            params.get("skullstrip_opts")
+            params.get("skullstrip_opts", None)
         ])
-    if params.get("at_opts") is not None:
+    if params.get("at_opts", None) is not None:
         cargs.extend([
             "-at_opts",
-            params.get("at_opts")
+            params.get("at_opts", None)
         ])
     return cargs
 
@@ -372,9 +377,11 @@ def auto_warp_py_outputs(
 
 def auto_warp_py_execute(
     params: AutoWarpPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AutoWarpPyOutputs:
     """
+    auto_warp.py
+    
     Nonlinear registration tool.
     
     Author: AFNI Developers
@@ -383,10 +390,12 @@ def auto_warp_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AutoWarpPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AUTO_WARP_PY_METADATA)
     params = execution.params(params)
     cargs = auto_warp_py_cargs(params, execution)
     ret = auto_warp_py_outputs(params, execution)
@@ -431,6 +440,8 @@ def auto_warp_py(
     runner: Runner | None = None,
 ) -> AutoWarpPyOutputs:
     """
+    auto_warp.py
+    
     Nonlinear registration tool.
     
     Author: AFNI Developers
@@ -478,8 +489,6 @@ def auto_warp_py(
     Returns:
         NamedTuple of outputs (described in `AutoWarpPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(AUTO_WARP_PY_METADATA)
     params = auto_warp_py_params(
         base=base,
         input_=input_,
@@ -515,13 +524,13 @@ def auto_warp_py(
         skullstrip_opts=skullstrip_opts,
         at_opts=at_opts,
     )
-    return auto_warp_py_execute(params, execution)
+    return auto_warp_py_execute(params, runner)
 
 
 __all__ = [
     "AUTO_WARP_PY_METADATA",
     "AutoWarpPyOutputs",
-    "AutoWarpPyParameters",
     "auto_warp_py",
+    "auto_warp_py_execute",
     "auto_warp_py_params",
 ]

niwrap_afni/afni/balloon.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BALLOON_METADATA = Metadata(
-    id="efa704edebd4da856d63213685c5a8439a31d101.boutiques",
+    id="0a7d4282856d71f09868e8b468d6ca3effe21796.boutiques",
     name="balloon",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ BALLOON_METADATA = Metadata(
 
 
 BalloonParameters = typing.TypedDict('BalloonParameters', {
-    "__STYXTYPE__": typing.Literal["balloon"],
+    "@type": typing.NotRequired[typing.Literal["afni/balloon"]],
+    "tr": float,
+    "num_scans": int,
+    "event_times": InputPathType,
+    "t_rise": typing.NotRequired[list[float] | None],
+    "t_fall": typing.NotRequired[list[float] | None],
+    "t_sustain": typing.NotRequired[list[float] | None],
+})
+BalloonParametersTagged = typing.TypedDict('BalloonParametersTagged', {
+    "@type": typing.Literal["afni/balloon"],
     "tr": float,
     "num_scans": int,
     "event_times": InputPathType,
@@ -22,42 +31,11 @@ BalloonParameters = typing.TypedDict('BalloonParameters', {
     "t_fall": typing.NotRequired[list[float] | None],
     "t_sustain": typing.NotRequired[list[float] | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "balloon": balloon_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 BalloonOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `balloon(...)`.
+    Output object returned when calling `BalloonParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def balloon_params(
     t_rise: list[float] | None = None,
     t_fall: list[float] | None = None,
     t_sustain: list[float] | None = None,
-) -> BalloonParameters:
+) -> BalloonParametersTagged:
     """
     Build parameters.
     
@@ -92,7 +70,7 @@ def balloon_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "balloon",
+        "@type": "afni/balloon",
         "tr": tr,
         "num_scans": num_scans,
         "event_times": event_times,
@@ -121,15 +99,15 @@ def balloon_cargs(
     """
     cargs = []
     cargs.append("balloon")
-    cargs.append(str(params.get("tr")))
-    cargs.append(str(params.get("num_scans")))
-    cargs.append(execution.input_file(params.get("event_times")))
-    if params.get("t_rise") is not None:
-        cargs.extend(map(str, params.get("t_rise")))
-    if params.get("t_fall") is not None:
-        cargs.extend(map(str, params.get("t_fall")))
-    if params.get("t_sustain") is not None:
-        cargs.extend(map(str, params.get("t_sustain")))
+    cargs.append(str(params.get("tr", None)))
+    cargs.append(str(params.get("num_scans", None)))
+    cargs.append(execution.input_file(params.get("event_times", None)))
+    if params.get("t_rise", None) is not None:
+        cargs.extend(map(str, params.get("t_rise", None)))
+    if params.get("t_fall", None) is not None:
+        cargs.extend(map(str, params.get("t_fall", None)))
+    if params.get("t_sustain", None) is not None:
+        cargs.extend(map(str, params.get("t_sustain", None)))
     return cargs
 
 
@@ -154,9 +132,11 @@ def balloon_outputs(
 
 def balloon_execute(
     params: BalloonParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> BalloonOutputs:
     """
+    balloon
+    
     Simulation of haemodynamic response using the balloon model. Based on the
     theoretical model proposed by Buxton et al. (1998).
     
@@ -166,10 +146,12 @@ def balloon_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `BalloonOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(BALLOON_METADATA)
     params = execution.params(params)
     cargs = balloon_cargs(params, execution)
     ret = balloon_outputs(params, execution)
@@ -187,6 +169,8 @@ def balloon(
     runner: Runner | None = None,
 ) -> BalloonOutputs:
     """
+    balloon
+    
     Simulation of haemodynamic response using the balloon model. Based on the
     theoretical model proposed by Buxton et al. (1998).
     
@@ -212,8 +196,6 @@ def balloon(
     Returns:
         NamedTuple of outputs (described in `BalloonOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(BALLOON_METADATA)
     params = balloon_params(
         tr=tr,
         num_scans=num_scans,
@@ -222,13 +204,13 @@ def balloon(
         t_fall=t_fall,
         t_sustain=t_sustain,
     )
-    return balloon_execute(params, execution)
+    return balloon_execute(params, runner)
 
 
 __all__ = [
     "BALLOON_METADATA",
     "BalloonOutputs",
-    "BalloonParameters",
     "balloon",
+    "balloon_execute",
     "balloon_params",
 ]