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

niwrap_afni/afni/uber_subject_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 UBER_SUBJECT_PY_METADATA = Metadata(
-    id="530df676c8d2b6020a3d36b7074940b4993bef60.boutiques",
+    id="bfef0d988515d01a9441002cb166324b59a66ee2.boutiques",
     name="uber_subject.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,53 @@ UBER_SUBJECT_PY_METADATA = Metadata(
 
 
 UberSubjectPyParameters = typing.TypedDict('UberSubjectPyParameters', {
-    "__STYXTYPE__": typing.Literal["uber_subject.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/uber_subject.py"]],
+    "qt_opts": typing.NotRequired[str | None],
+    "svar": typing.NotRequired[str | None],
+    "cvar": typing.NotRequired[str | None],
+    "no_gui": bool,
+    "print_ap_command": bool,
+    "save_ap_command": typing.NotRequired[str | None],
+    "exec_ap_command": bool,
+    "exec_proc_script": bool,
+    "align_cost": typing.NotRequired[str | None],
+    "align_giant_move": typing.NotRequired[str | None],
+    "align_opts_aea": typing.NotRequired[str | None],
+    "anal_domain": typing.NotRequired[str | None],
+    "anal_type": typing.NotRequired[str | None],
+    "anat": typing.NotRequired[InputPathType | None],
+    "anat_has_skull": typing.NotRequired[str | None],
+    "blocks": typing.NotRequired[str | None],
+    "blur_size": typing.NotRequired[float | None],
+    "epi": typing.NotRequired[str | None],
+    "epi_wildcard": typing.NotRequired[str | None],
+    "gid": typing.NotRequired[str | None],
+    "gltsym": typing.NotRequired[str | None],
+    "gltsym_label": typing.NotRequired[str | None],
+    "motion_limit": typing.NotRequired[float | None],
+    "outlier_limit": typing.NotRequired[float | None],
+    "regress_GOFORIT": typing.NotRequired[float | None],
+    "regress_bandpass": typing.NotRequired[str | None],
+    "regress_jobs": typing.NotRequired[float | None],
+    "regress_mot_deriv": typing.NotRequired[str | None],
+    "regress_opts_3dD": typing.NotRequired[str | None],
+    "reml_exec": typing.NotRequired[str | None],
+    "run_clustsim": typing.NotRequired[str | None],
+    "sid": typing.NotRequired[str | None],
+    "stim": typing.NotRequired[InputPathType | None],
+    "stim_basis": typing.NotRequired[str | None],
+    "stim_label": typing.NotRequired[str | None],
+    "stim_type": typing.NotRequired[str | None],
+    "stim_wildcard": typing.NotRequired[str | None],
+    "tcat_nfirst": typing.NotRequired[float | None],
+    "tlrc_base": typing.NotRequired[str | None],
+    "tlrc_ok_maxite": typing.NotRequired[str | None],
+    "tlrc_opts_at": typing.NotRequired[str | None],
+    "volreg_base": typing.NotRequired[str | None],
+    "verb": typing.NotRequired[str | None],
+})
+UberSubjectPyParametersTagged = typing.TypedDict('UberSubjectPyParametersTagged', {
+    "@type": typing.Literal["afni/uber_subject.py"],
     "qt_opts": typing.NotRequired[str | None],
     "svar": typing.NotRequired[str | None],
     "cvar": typing.NotRequired[str | None],
@@ -59,42 +105,11 @@ UberSubjectPyParameters = typing.TypedDict('UberSubjectPyParameters', {
     "volreg_base": typing.NotRequired[str | None],
     "verb": 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 {
-        "uber_subject.py": uber_subject_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 UberSubjectPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `uber_subject_py(...)`.
+    Output object returned when calling `UberSubjectPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -144,7 +159,7 @@ def uber_subject_py_params(
     tlrc_opts_at: str | None = None,
     volreg_base: str | None = None,
     verb: str | None = None,
-) -> UberSubjectPyParameters:
+) -> UberSubjectPyParametersTagged:
     """
     Build parameters.
     
@@ -196,7 +211,7 @@ def uber_subject_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "uber_subject.py",
+        "@type": "afni/uber_subject.py",
         "no_gui": no_gui,
         "print_ap_command": print_ap_command,
         "exec_ap_command": exec_ap_command,
@@ -298,208 +313,208 @@ def uber_subject_py_cargs(
     """
     cargs = []
     cargs.append("uber_subject.py")
-    if params.get("qt_opts") is not None:
+    if params.get("qt_opts", None) is not None:
         cargs.extend([
             "-qt_opts",
-            params.get("qt_opts")
+            params.get("qt_opts", None)
         ])
-    if params.get("svar") is not None:
+    if params.get("svar", None) is not None:
         cargs.extend([
             "-svar",
-            params.get("svar")
+            params.get("svar", None)
         ])
-    if params.get("cvar") is not None:
+    if params.get("cvar", None) is not None:
         cargs.extend([
             "-cvar",
-            params.get("cvar")
+            params.get("cvar", None)
         ])
-    if params.get("no_gui"):
+    if params.get("no_gui", False):
         cargs.append("-no_gui")
-    if params.get("print_ap_command"):
+    if params.get("print_ap_command", False):
         cargs.append("-print_ap_command")
-    if params.get("save_ap_command") is not None:
+    if params.get("save_ap_command", None) is not None:
         cargs.extend([
             "-save_ap_command",
-            params.get("save_ap_command")
+            params.get("save_ap_command", None)
         ])
-    if params.get("exec_ap_command"):
+    if params.get("exec_ap_command", False):
         cargs.append("-exec_ap_command")
-    if params.get("exec_proc_script"):
+    if params.get("exec_proc_script", False):
         cargs.append("-exec_proc_script")
-    if params.get("align_cost") is not None:
+    if params.get("align_cost", None) is not None:
         cargs.extend([
             "-align_cost",
-            params.get("align_cost")
+            params.get("align_cost", None)
         ])
-    if params.get("align_giant_move") is not None:
+    if params.get("align_giant_move", None) is not None:
         cargs.extend([
             "-align_giant_move",
-            params.get("align_giant_move")
+            params.get("align_giant_move", None)
         ])
-    if params.get("align_opts_aea") is not None:
+    if params.get("align_opts_aea", None) is not None:
         cargs.extend([
             "-align_opts_aea",
-            params.get("align_opts_aea")
+            params.get("align_opts_aea", None)
         ])
-    if params.get("anal_domain") is not None:
+    if params.get("anal_domain", None) is not None:
         cargs.extend([
             "-anal_domain",
-            params.get("anal_domain")
+            params.get("anal_domain", None)
         ])
-    if params.get("anal_type") is not None:
+    if params.get("anal_type", None) is not None:
         cargs.extend([
             "-anal_type",
-            params.get("anal_type")
+            params.get("anal_type", None)
         ])
-    if params.get("anat") is not None:
+    if params.get("anat", None) is not None:
         cargs.extend([
             "-anat",
-            execution.input_file(params.get("anat"))
+            execution.input_file(params.get("anat", None))
         ])
-    if params.get("anat_has_skull") is not None:
+    if params.get("anat_has_skull", None) is not None:
         cargs.extend([
             "-anat_has_skull",
-            params.get("anat_has_skull")
+            params.get("anat_has_skull", None)
         ])
-    if params.get("blocks") is not None:
+    if params.get("blocks", None) is not None:
         cargs.extend([
             "-blocks",
-            params.get("blocks")
+            params.get("blocks", None)
         ])
-    if params.get("blur_size") is not None:
+    if params.get("blur_size", None) is not None:
         cargs.extend([
             "-blur_size",
-            str(params.get("blur_size"))
+            str(params.get("blur_size", None))
         ])
-    if params.get("epi") is not None:
+    if params.get("epi", None) is not None:
         cargs.extend([
             "-epi",
-            params.get("epi")
+            params.get("epi", None)
         ])
-    if params.get("epi_wildcard") is not None:
+    if params.get("epi_wildcard", None) is not None:
         cargs.extend([
             "-epi_wildcard",
-            params.get("epi_wildcard")
+            params.get("epi_wildcard", None)
         ])
-    if params.get("gid") is not None:
+    if params.get("gid", None) is not None:
         cargs.extend([
             "-gid",
-            params.get("gid")
+            params.get("gid", None)
         ])
-    if params.get("gltsym") is not None:
+    if params.get("gltsym", None) is not None:
         cargs.extend([
             "-gltsym",
-            params.get("gltsym")
+            params.get("gltsym", None)
         ])
-    if params.get("gltsym_label") is not None:
+    if params.get("gltsym_label", None) is not None:
         cargs.extend([
             "-gltsym_label",
-            params.get("gltsym_label")
+            params.get("gltsym_label", None)
         ])
-    if params.get("motion_limit") is not None:
+    if params.get("motion_limit", None) is not None:
         cargs.extend([
             "-motion_limit",
-            str(params.get("motion_limit"))
+            str(params.get("motion_limit", None))
         ])
-    if params.get("outlier_limit") is not None:
+    if params.get("outlier_limit", None) is not None:
         cargs.extend([
             "-outlier_limit",
-            str(params.get("outlier_limit"))
+            str(params.get("outlier_limit", None))
         ])
-    if params.get("regress_GOFORIT") is not None:
+    if params.get("regress_GOFORIT", None) is not None:
         cargs.extend([
             "-regress_GOFORIT",
-            str(params.get("regress_GOFORIT"))
+            str(params.get("regress_GOFORIT", None))
         ])
-    if params.get("regress_bandpass") is not None:
+    if params.get("regress_bandpass", None) is not None:
         cargs.extend([
             "-regress_bandpass",
-            params.get("regress_bandpass")
+            params.get("regress_bandpass", None)
         ])
-    if params.get("regress_jobs") is not None:
+    if params.get("regress_jobs", None) is not None:
         cargs.extend([
             "-regress_jobs",
-            str(params.get("regress_jobs"))
+            str(params.get("regress_jobs", None))
         ])
-    if params.get("regress_mot_deriv") is not None:
+    if params.get("regress_mot_deriv", None) is not None:
         cargs.extend([
             "-regress_mot_deriv",
-            params.get("regress_mot_deriv")
+            params.get("regress_mot_deriv", None)
         ])
-    if params.get("regress_opts_3dD") is not None:
+    if params.get("regress_opts_3dD", None) is not None:
         cargs.extend([
             "-regress_opts_3dD",
-            params.get("regress_opts_3dD")
+            params.get("regress_opts_3dD", None)
         ])
-    if params.get("reml_exec") is not None:
+    if params.get("reml_exec", None) is not None:
         cargs.extend([
             "-reml_exec",
-            params.get("reml_exec")
+            params.get("reml_exec", None)
         ])
-    if params.get("run_clustsim") is not None:
+    if params.get("run_clustsim", None) is not None:
         cargs.extend([
             "-run_clustsim",
-            params.get("run_clustsim")
+            params.get("run_clustsim", None)
         ])
-    if params.get("sid") is not None:
+    if params.get("sid", None) is not None:
         cargs.extend([
             "-sid",
-            params.get("sid")
+            params.get("sid", None)
         ])
-    if params.get("stim") is not None:
+    if params.get("stim", None) is not None:
         cargs.extend([
             "-stim",
-            execution.input_file(params.get("stim"))
+            execution.input_file(params.get("stim", None))
         ])
-    if params.get("stim_basis") is not None:
+    if params.get("stim_basis", None) is not None:
         cargs.extend([
             "-stim_basis",
-            params.get("stim_basis")
+            params.get("stim_basis", None)
         ])
-    if params.get("stim_label") is not None:
+    if params.get("stim_label", None) is not None:
         cargs.extend([
             "-stim_label",
-            params.get("stim_label")
+            params.get("stim_label", None)
         ])
-    if params.get("stim_type") is not None:
+    if params.get("stim_type", None) is not None:
         cargs.extend([
             "-stim_type",
-            params.get("stim_type")
+            params.get("stim_type", None)
         ])
-    if params.get("stim_wildcard") is not None:
+    if params.get("stim_wildcard", None) is not None:
         cargs.extend([
             "-stim_wildcard",
-            params.get("stim_wildcard")
+            params.get("stim_wildcard", None)
         ])
-    if params.get("tcat_nfirst") is not None:
+    if params.get("tcat_nfirst", None) is not None:
         cargs.extend([
             "-tcat_nfirst",
-            str(params.get("tcat_nfirst"))
+            str(params.get("tcat_nfirst", None))
         ])
-    if params.get("tlrc_base") is not None:
+    if params.get("tlrc_base", None) is not None:
         cargs.extend([
             "-tlrc_base",
-            params.get("tlrc_base")
+            params.get("tlrc_base", None)
         ])
-    if params.get("tlrc_ok_maxite") is not None:
+    if params.get("tlrc_ok_maxite", None) is not None:
         cargs.extend([
             "-tlrc_ok_maxite",
-            params.get("tlrc_ok_maxite")
+            params.get("tlrc_ok_maxite", None)
         ])
-    if params.get("tlrc_opts_at") is not None:
+    if params.get("tlrc_opts_at", None) is not None:
         cargs.extend([
             "-tlrc_opts_at",
-            params.get("tlrc_opts_at")
+            params.get("tlrc_opts_at", None)
         ])
-    if params.get("volreg_base") is not None:
+    if params.get("volreg_base", None) is not None:
         cargs.extend([
             "-volreg_base",
-            params.get("volreg_base")
+            params.get("volreg_base", None)
         ])
-    if params.get("verb") is not None:
+    if params.get("verb", None) is not None:
         cargs.extend([
             "-verb",
-            params.get("verb")
+            params.get("verb", None)
         ])
     return cargs
 
@@ -525,9 +540,11 @@ def uber_subject_py_outputs(
 
 def uber_subject_py_execute(
     params: UberSubjectPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> UberSubjectPyOutputs:
     """
+    uber_subject.py
+    
     Graphical interface to afni_proc.py.
     
     Author: AFNI Developers
@@ -536,10 +553,12 @@ def uber_subject_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `UberSubjectPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UBER_SUBJECT_PY_METADATA)
     params = execution.params(params)
     cargs = uber_subject_py_cargs(params, execution)
     ret = uber_subject_py_outputs(params, execution)
@@ -594,6 +613,8 @@ def uber_subject_py(
     runner: Runner | None = None,
 ) -> UberSubjectPyOutputs:
     """
+    uber_subject.py
+    
     Graphical interface to afni_proc.py.
     
     Author: AFNI Developers
@@ -648,8 +669,6 @@ def uber_subject_py(
     Returns:
         NamedTuple of outputs (described in `UberSubjectPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(UBER_SUBJECT_PY_METADATA)
     params = uber_subject_py_params(
         qt_opts=qt_opts,
         svar=svar,
@@ -695,13 +714,13 @@ def uber_subject_py(
         volreg_base=volreg_base,
         verb=verb,
     )
-    return uber_subject_py_execute(params, execution)
+    return uber_subject_py_execute(params, runner)
 
 
 __all__ = [
     "UBER_SUBJECT_PY_METADATA",
     "UberSubjectPyOutputs",
-    "UberSubjectPyParameters",
     "uber_subject_py",
+    "uber_subject_py_execute",
     "uber_subject_py_params",
 ]

niwrap_afni/afni/un_warp_epi_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 UN_WARP_EPI_PY_METADATA = Metadata(
-    id="fc0d8fa1e4c87d01b5598b608c709cf97544808c.boutiques",
+    id="2073ad8540cf4584fe797a4fb911a5cf6c3d80e1.boutiques",
     name="unWarpEPI.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ UN_WARP_EPI_PY_METADATA = Metadata(
 
 
 UnWarpEpiPyParameters = typing.TypedDict('UnWarpEpiPyParameters', {
-    "__STYXTYPE__": typing.Literal["unWarpEPI.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/unWarpEPI.py"]],
+    "forward": InputPathType,
+    "reverse": InputPathType,
+    "anat4warp": InputPathType,
+    "data": str,
+    "subjID": str,
+    "giant_move": bool,
+})
+UnWarpEpiPyParametersTagged = typing.TypedDict('UnWarpEpiPyParametersTagged', {
+    "@type": typing.Literal["afni/unWarpEPI.py"],
     "forward": InputPathType,
     "reverse": InputPathType,
     "anat4warp": InputPathType,
@@ -22,42 +31,11 @@ UnWarpEpiPyParameters = typing.TypedDict('UnWarpEpiPyParameters', {
     "subjID": str,
     "giant_move": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "unWarpEPI.py": un_warp_epi_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 UnWarpEpiPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `un_warp_epi_py(...)`.
+    Output object returned when calling `UnWarpEpiPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def un_warp_epi_py_params(
     data: str,
     subj_id: str,
     giant_move: bool = False,
-) -> UnWarpEpiPyParameters:
+) -> UnWarpEpiPyParametersTagged:
     """
     Build parameters.
     
@@ -87,7 +65,7 @@ def un_warp_epi_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "unWarpEPI.py",
+        "@type": "afni/unWarpEPI.py",
         "forward": forward,
         "reverse": reverse,
         "anat4warp": anat4warp,
@@ -115,25 +93,25 @@ def un_warp_epi_py_cargs(
     cargs.append("unWarpEPI.py")
     cargs.extend([
         "-f",
-        execution.input_file(params.get("forward"))
+        execution.input_file(params.get("forward", None))
     ])
     cargs.extend([
         "-r",
-        execution.input_file(params.get("reverse"))
+        execution.input_file(params.get("reverse", None))
     ])
     cargs.extend([
         "-a",
-        execution.input_file(params.get("anat4warp"))
+        execution.input_file(params.get("anat4warp", None))
     ])
     cargs.extend([
         "-d",
-        params.get("data")
+        params.get("data", None)
     ])
     cargs.extend([
         "-s",
-        params.get("subjID")
+        params.get("subjID", None)
     ])
-    if params.get("giant_move"):
+    if params.get("giant_move", False):
         cargs.append("-g")
     return cargs
 
@@ -159,10 +137,13 @@ def un_warp_epi_py_outputs(
 
 def un_warp_epi_py_execute(
     params: UnWarpEpiPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> UnWarpEpiPyOutputs:
     """
-    Routine to unwarp EPI data set using another data set with opposite polarity.
+    unWarpEPI.py
+    
+    Routine to unwarp EPI data set using another data set with opposite
+    polarity.
     
     Author: AFNI Developers
     
@@ -170,10 +151,12 @@ def un_warp_epi_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `UnWarpEpiPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UN_WARP_EPI_PY_METADATA)
     params = execution.params(params)
     cargs = un_warp_epi_py_cargs(params, execution)
     ret = un_warp_epi_py_outputs(params, execution)
@@ -191,7 +174,10 @@ def un_warp_epi_py(
     runner: Runner | None = None,
 ) -> UnWarpEpiPyOutputs:
     """
-    Routine to unwarp EPI data set using another data set with opposite polarity.
+    unWarpEPI.py
+    
+    Routine to unwarp EPI data set using another data set with opposite
+    polarity.
     
     Author: AFNI Developers
     
@@ -210,8 +196,6 @@ def un_warp_epi_py(
     Returns:
         NamedTuple of outputs (described in `UnWarpEpiPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(UN_WARP_EPI_PY_METADATA)
     params = un_warp_epi_py_params(
         forward=forward,
         reverse=reverse,
@@ -220,13 +204,13 @@ def un_warp_epi_py(
         subj_id=subj_id,
         giant_move=giant_move,
     )
-    return un_warp_epi_py_execute(params, execution)
+    return un_warp_epi_py_execute(params, runner)
 
 
 __all__ = [
     "UN_WARP_EPI_PY_METADATA",
     "UnWarpEpiPyOutputs",
-    "UnWarpEpiPyParameters",
     "un_warp_epi_py",
+    "un_warp_epi_py_execute",
     "un_warp_epi_py_params",
 ]