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

niwrap_afni/afni/v__clip_volume.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__CLIP_VOLUME_METADATA = Metadata(
-    id="0999d3039fac00d441e01a61ca33ad8ceb36a238.boutiques",
+    id="7c7d598a3972fa11983862ca7a48415ad15d22ac.boutiques",
     name="@clip_volume",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,28 @@ V__CLIP_VOLUME_METADATA = Metadata(
 
 
 VClipVolumeParameters = typing.TypedDict('VClipVolumeParameters', {
-    "__STYXTYPE__": typing.Literal["@clip_volume"],
+    "@type": typing.NotRequired[typing.Literal["afni/@clip_volume"]],
+    "input_volume": InputPathType,
+    "below_zmm": typing.NotRequired[float | None],
+    "above_zmm": typing.NotRequired[float | None],
+    "left_xmm": typing.NotRequired[float | None],
+    "right_xmm": typing.NotRequired[float | None],
+    "anterior_ymm": typing.NotRequired[float | None],
+    "posterior_ymm": typing.NotRequired[float | None],
+    "box": typing.NotRequired[list[float] | None],
+    "mask_box": typing.NotRequired[list[float] | None],
+    "and_logic": bool,
+    "or_logic": bool,
+    "verbosity": bool,
+    "crop_allzero": bool,
+    "crop_greedy": bool,
+    "crop": bool,
+    "crop_npad": typing.NotRequired[float | None],
+    "output_prefix": typing.NotRequired[str | None],
+    "followers": typing.NotRequired[list[InputPathType] | None],
+})
+VClipVolumeParametersTagged = typing.TypedDict('VClipVolumeParametersTagged', {
+    "@type": typing.Literal["afni/@clip_volume"],
     "input_volume": InputPathType,
     "below_zmm": typing.NotRequired[float | None],
     "above_zmm": typing.NotRequired[float | None],
@@ -34,43 +55,11 @@ VClipVolumeParameters = typing.TypedDict('VClipVolumeParameters', {
     "output_prefix": typing.NotRequired[str | None],
     "followers": typing.NotRequired[list[InputPathType] | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@clip_volume": v__clip_volume_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 {
-        "@clip_volume": v__clip_volume_outputs,
-    }.get(t)
 
 
 class VClipVolumeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__clip_volume(...)`.
+    Output object returned when calling `VClipVolumeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -99,7 +88,7 @@ def v__clip_volume_params(
     crop_npad: float | None = None,
     output_prefix: str | None = None,
     followers: list[InputPathType] | None = None,
-) -> VClipVolumeParameters:
+) -> VClipVolumeParametersTagged:
     """
     Build parameters.
     
@@ -131,7 +120,7 @@ def v__clip_volume_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@clip_volume",
+        "@type": "afni/@clip_volume",
         "input_volume": input_volume,
         "and_logic": and_logic,
         "or_logic": or_logic,
@@ -180,73 +169,73 @@ def v__clip_volume_cargs(
     """
     cargs = []
     cargs.append("@clip_volume")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    if params.get("below_zmm") is not None:
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    if params.get("below_zmm", None) is not None:
         cargs.extend([
             "-below",
-            str(params.get("below_zmm"))
+            str(params.get("below_zmm", None))
         ])
-    if params.get("above_zmm") is not None:
+    if params.get("above_zmm", None) is not None:
         cargs.extend([
             "-above",
-            str(params.get("above_zmm"))
+            str(params.get("above_zmm", None))
         ])
-    if params.get("left_xmm") is not None:
+    if params.get("left_xmm", None) is not None:
         cargs.extend([
             "-left",
-            str(params.get("left_xmm"))
+            str(params.get("left_xmm", None))
         ])
-    if params.get("right_xmm") is not None:
+    if params.get("right_xmm", None) is not None:
         cargs.extend([
             "-right",
-            str(params.get("right_xmm"))
+            str(params.get("right_xmm", None))
         ])
-    if params.get("anterior_ymm") is not None:
+    if params.get("anterior_ymm", None) is not None:
         cargs.extend([
             "-anterior",
-            str(params.get("anterior_ymm"))
+            str(params.get("anterior_ymm", None))
         ])
-    if params.get("posterior_ymm") is not None:
+    if params.get("posterior_ymm", None) is not None:
         cargs.extend([
             "-posterior",
-            str(params.get("posterior_ymm"))
+            str(params.get("posterior_ymm", None))
         ])
-    if params.get("box") is not None:
+    if params.get("box", None) is not None:
         cargs.extend([
             "-box",
-            *map(str, params.get("box"))
+            *map(str, params.get("box", None))
         ])
-    if params.get("mask_box") is not None:
+    if params.get("mask_box", None) is not None:
         cargs.extend([
             "-mask_box",
-            *map(str, params.get("mask_box"))
+            *map(str, params.get("mask_box", None))
         ])
-    if params.get("and_logic"):
+    if params.get("and_logic", False):
         cargs.append("-and")
-    if params.get("or_logic"):
+    if params.get("or_logic", False):
         cargs.append("-or")
-    if params.get("verbosity"):
+    if params.get("verbosity", False):
         cargs.append("-verb")
-    if params.get("crop_allzero"):
+    if params.get("crop_allzero", False):
         cargs.append("-crop_allzero")
-    if params.get("crop_greedy"):
+    if params.get("crop_greedy", False):
         cargs.append("-crop_greedy")
-    if params.get("crop"):
+    if params.get("crop", False):
         cargs.append("-crop")
-    if params.get("crop_npad") is not None:
+    if params.get("crop_npad", None) is not None:
         cargs.extend([
             "-crop_npad",
-            str(params.get("crop_npad"))
+            str(params.get("crop_npad", None))
         ])
-    if params.get("output_prefix") is not None:
+    if params.get("output_prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("output_prefix")
+            params.get("output_prefix", None)
         ])
-    if params.get("followers") is not None:
+    if params.get("followers", None) is not None:
         cargs.extend([
             "-followers",
-            *[execution.input_file(f) for f in params.get("followers")]
+            *[execution.input_file(f) for f in params.get("followers", None)]
         ])
     return cargs
 
@@ -266,19 +255,21 @@ def v__clip_volume_outputs(
     """
     ret = VClipVolumeOutputs(
         root=execution.output_file("."),
-        output_clipped_volume=execution.output_file(params.get("output_prefix") + "_clp.nii.gz") if (params.get("output_prefix") is not None) else None,
-        output_followers=execution.output_file(params.get("output_prefix") + "_follow_clp.nii.gz") if (params.get("output_prefix") is not None) else None,
+        output_clipped_volume=execution.output_file(params.get("output_prefix", None) + "_clp.nii.gz") if (params.get("output_prefix") is not None) else None,
+        output_followers=execution.output_file(params.get("output_prefix", None) + "_follow_clp.nii.gz") if (params.get("output_prefix") is not None) else None,
     )
     return ret
 
 
 def v__clip_volume_execute(
     params: VClipVolumeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VClipVolumeOutputs:
     """
-    A tool to clip regions of a volume in various ways, such as above/below certain
-    coordinates or within a specified box.
+    @clip_volume
+    
+    A tool to clip regions of a volume in various ways, such as above/below
+    certain coordinates or within a specified box.
     
     Author: AFNI Developers
     
@@ -286,10 +277,12 @@ def v__clip_volume_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VClipVolumeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__CLIP_VOLUME_METADATA)
     params = execution.params(params)
     cargs = v__clip_volume_cargs(params, execution)
     ret = v__clip_volume_outputs(params, execution)
@@ -319,8 +312,10 @@ def v__clip_volume(
     runner: Runner | None = None,
 ) -> VClipVolumeOutputs:
     """
-    A tool to clip regions of a volume in various ways, such as above/below certain
-    coordinates or within a specified box.
+    @clip_volume
+    
+    A tool to clip regions of a volume in various ways, such as above/below
+    certain coordinates or within a specified box.
     
     Author: AFNI Developers
     
@@ -354,8 +349,6 @@ def v__clip_volume(
     Returns:
         NamedTuple of outputs (described in `VClipVolumeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__CLIP_VOLUME_METADATA)
     params = v__clip_volume_params(
         input_volume=input_volume,
         below_zmm=below_zmm,
@@ -376,13 +369,13 @@ def v__clip_volume(
         output_prefix=output_prefix,
         followers=followers,
     )
-    return v__clip_volume_execute(params, execution)
+    return v__clip_volume_execute(params, runner)
 
 
 __all__ = [
     "VClipVolumeOutputs",
-    "VClipVolumeParameters",
     "V__CLIP_VOLUME_METADATA",
     "v__clip_volume",
+    "v__clip_volume_execute",
     "v__clip_volume_params",
 ]

niwrap_afni/afni/v__clust_exp_cat_lab.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__CLUST_EXP_CAT_LAB_METADATA = Metadata(
-    id="a8c640445d8474e65d913f1c890529556dbc2470.boutiques",
+    id="2ba125157c3f380c072d353eca9d9fd8d9c75735.boutiques",
     name="@ClustExp_CatLab",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,22 @@ V__CLUST_EXP_CAT_LAB_METADATA = Metadata(
 
 
 VClustExpCatLabParameters = typing.TypedDict('VClustExpCatLabParameters', {
-    "__STYXTYPE__": typing.Literal["@ClustExp_CatLab"],
+    "@type": typing.NotRequired[typing.Literal["afni/@ClustExp_CatLab"]],
+    "prefix": str,
+    "input_file": InputPathType,
+    "help": bool,
+})
+VClustExpCatLabParametersTagged = typing.TypedDict('VClustExpCatLabParametersTagged', {
+    "@type": typing.Literal["afni/@ClustExp_CatLab"],
     "prefix": str,
     "input_file": InputPathType,
     "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 {
-        "@ClustExp_CatLab": v__clust_exp_cat_lab_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 {
-        "@ClustExp_CatLab": v__clust_exp_cat_lab_outputs,
-    }.get(t)
 
 
 class VClustExpCatLabOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__clust_exp_cat_lab(...)`.
+    Output object returned when calling `VClustExpCatLabParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def v__clust_exp_cat_lab_params(
     prefix: str,
     input_file: InputPathType,
     help_: bool = False,
-) -> VClustExpCatLabParameters:
+) -> VClustExpCatLabParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +54,7 @@ def v__clust_exp_cat_lab_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@ClustExp_CatLab",
+        "@type": "afni/@ClustExp_CatLab",
         "prefix": prefix,
         "input_file": input_file,
         "help": help_,
@@ -105,13 +79,13 @@ def v__clust_exp_cat_lab_cargs(
     cargs.append("@ClustExp_CatLab")
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -131,16 +105,18 @@ def v__clust_exp_cat_lab_outputs(
     """
     ret = VClustExpCatLabOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + ".nii.gz"),
+        output_file=execution.output_file(params.get("prefix", None) + ".nii.gz"),
     )
     return ret
 
 
 def v__clust_exp_cat_lab_execute(
     params: VClustExpCatLabParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VClustExpCatLabOutputs:
     """
+    @ClustExp_CatLab
+    
     Helper script to concatenate and label a group of data sets.
     
     Author: AFNI Developers
@@ -149,10 +125,12 @@ def v__clust_exp_cat_lab_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VClustExpCatLabOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__CLUST_EXP_CAT_LAB_METADATA)
     params = execution.params(params)
     cargs = v__clust_exp_cat_lab_cargs(params, execution)
     ret = v__clust_exp_cat_lab_outputs(params, execution)
@@ -167,6 +145,8 @@ def v__clust_exp_cat_lab(
     runner: Runner | None = None,
 ) -> VClustExpCatLabOutputs:
     """
+    @ClustExp_CatLab
+    
     Helper script to concatenate and label a group of data sets.
     
     Author: AFNI Developers
@@ -182,20 +162,18 @@ def v__clust_exp_cat_lab(
     Returns:
         NamedTuple of outputs (described in `VClustExpCatLabOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__CLUST_EXP_CAT_LAB_METADATA)
     params = v__clust_exp_cat_lab_params(
         prefix=prefix,
         input_file=input_file,
         help_=help_,
     )
-    return v__clust_exp_cat_lab_execute(params, execution)
+    return v__clust_exp_cat_lab_execute(params, runner)
 
 
 __all__ = [
     "VClustExpCatLabOutputs",
-    "VClustExpCatLabParameters",
     "V__CLUST_EXP_CAT_LAB_METADATA",
     "v__clust_exp_cat_lab",
+    "v__clust_exp_cat_lab_execute",
     "v__clust_exp_cat_lab_params",
 ]

niwrap_afni/afni/v__clust_exp_run_shiny.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__CLUST_EXP_RUN_SHINY_METADATA = Metadata(
-    id="d9831cf53b939c4f9cf4a57c2979fe1ccbb9233f.boutiques",
+    id="476038a41888b6b7661d5ea93892295d41d7243a.boutiques",
     name="@ClustExp_run_shiny",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,46 +14,20 @@ V__CLUST_EXP_RUN_SHINY_METADATA = Metadata(
 
 
 VClustExpRunShinyParameters = typing.TypedDict('VClustExpRunShinyParameters', {
-    "__STYXTYPE__": typing.Literal["@ClustExp_run_shiny"],
+    "@type": typing.NotRequired[typing.Literal["afni/@ClustExp_run_shiny"]],
+    "directory": str,
+    "help": bool,
+})
+VClustExpRunShinyParametersTagged = typing.TypedDict('VClustExpRunShinyParametersTagged', {
+    "@type": typing.Literal["afni/@ClustExp_run_shiny"],
     "directory": str,
     "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 {
-        "@ClustExp_run_shiny": v__clust_exp_run_shiny_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 VClustExpRunShinyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__clust_exp_run_shiny(...)`.
+    Output object returned when calling `VClustExpRunShinyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class VClustExpRunShinyOutputs(typing.NamedTuple):
 def v__clust_exp_run_shiny_params(
     directory: str,
     help_: bool = False,
-) -> VClustExpRunShinyParameters:
+) -> VClustExpRunShinyParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def v__clust_exp_run_shiny_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@ClustExp_run_shiny",
+        "@type": "afni/@ClustExp_run_shiny",
         "directory": directory,
         "help": help_,
     }
@@ -95,8 +69,8 @@ def v__clust_exp_run_shiny_cargs(
     """
     cargs = []
     cargs.append("@ClustExp_run_shiny")
-    cargs.append(params.get("directory"))
-    if params.get("help"):
+    cargs.append(params.get("directory", None))
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -122,9 +96,11 @@ def v__clust_exp_run_shiny_outputs(
 
 def v__clust_exp_run_shiny_execute(
     params: VClustExpRunShinyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VClustExpRunShinyOutputs:
     """
+    @ClustExp_run_shiny
+    
     Launch a shiny app that was created by ClustExp_StatParse.py.
     
     Author: AFNI Developers
@@ -133,10 +109,12 @@ def v__clust_exp_run_shiny_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VClustExpRunShinyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__CLUST_EXP_RUN_SHINY_METADATA)
     params = execution.params(params)
     cargs = v__clust_exp_run_shiny_cargs(params, execution)
     ret = v__clust_exp_run_shiny_outputs(params, execution)
@@ -150,6 +128,8 @@ def v__clust_exp_run_shiny(
     runner: Runner | None = None,
 ) -> VClustExpRunShinyOutputs:
     """
+    @ClustExp_run_shiny
+    
     Launch a shiny app that was created by ClustExp_StatParse.py.
     
     Author: AFNI Developers
@@ -163,19 +143,17 @@ def v__clust_exp_run_shiny(
     Returns:
         NamedTuple of outputs (described in `VClustExpRunShinyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__CLUST_EXP_RUN_SHINY_METADATA)
     params = v__clust_exp_run_shiny_params(
         directory=directory,
         help_=help_,
     )
-    return v__clust_exp_run_shiny_execute(params, execution)
+    return v__clust_exp_run_shiny_execute(params, runner)
 
 
 __all__ = [
     "VClustExpRunShinyOutputs",
-    "VClustExpRunShinyParameters",
     "V__CLUST_EXP_RUN_SHINY_METADATA",
     "v__clust_exp_run_shiny",
+    "v__clust_exp_run_shiny_execute",
     "v__clust_exp_run_shiny_params",
 ]