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

niwrap_afni/afni/{align_epi_anat.py → align_epi_anat_py.py}

@@ -5,16 +5,36 @@ import typing
 import pathlib
 from styxdefs import *
 
-ALIGN_EPI_ANAT_METADATA = Metadata(
-    id="f8698b45584333a566a4ac7a702d9045fad24911.boutiques",
-    name="align_epi_anat",
+ALIGN_EPI_ANAT_PY_METADATA = Metadata(
+    id="1196723b5074ff83caa433d170999d4f8b1ef074.boutiques",
+    name="align_epi_anat.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
 )
 
 
-AlignEpiAnatParameters = typing.TypedDict('AlignEpiAnatParameters', {
-    "__STYXTYPE__": typing.Literal["align_epi_anat"],
+AlignEpiAnatPyParameters = typing.TypedDict('AlignEpiAnatPyParameters', {
+    "@type": typing.NotRequired[typing.Literal["afni/align_epi_anat.py"]],
+    "epi": InputPathType,
+    "anat": InputPathType,
+    "epi_base": str,
+    "anat2epi": bool,
+    "epi2anat": bool,
+    "suffix": typing.NotRequired[str | None],
+    "AddEdge": bool,
+    "big_move": bool,
+    "giant_move": bool,
+    "ginormous_move": bool,
+    "keep_rm_files": bool,
+    "prep_only": bool,
+    "ana_has_skull": typing.NotRequired[typing.Literal["yes", "no"] | None],
+    "epi_strip": typing.NotRequired[typing.Literal["3dSkullStrip", "3dAutomask", "None"] | None],
+    "volreg_method": typing.NotRequired[typing.Literal["3dvolreg", "3dWarpDrive", "3dAllineate"] | None],
+    "ex_mode": typing.NotRequired[typing.Literal["quiet", "echo", "dry_run", "script"] | None],
+    "overwrite": bool,
+})
+AlignEpiAnatPyParametersTagged = typing.TypedDict('AlignEpiAnatPyParametersTagged', {
+    "@type": typing.Literal["afni/align_epi_anat.py"],
     "epi": InputPathType,
     "anat": InputPathType,
     "epi_base": str,
@@ -35,41 +55,9 @@ AlignEpiAnatParameters = typing.TypedDict('AlignEpiAnatParameters', {
 })
 
 
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "align_epi_anat": align_epi_anat_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 {
-        "align_epi_anat": align_epi_anat_outputs,
-    }.get(t)
-
-
-class AlignEpiAnatOutputs(typing.NamedTuple):
+class AlignEpiAnatPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `align_epi_anat(...)`.
+    Output object returned when calling `AlignEpiAnatPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +67,7 @@ class AlignEpiAnatOutputs(typing.NamedTuple):
     """A version of the EPI dataset aligned to the Anatomy"""
 
 
-def align_epi_anat_params(
+def align_epi_anat_py_params(
     epi: InputPathType,
     anat: InputPathType,
     epi_base: str,
@@ -97,7 +85,7 @@ def align_epi_anat_params(
     volreg_method: typing.Literal["3dvolreg", "3dWarpDrive", "3dAllineate"] | None = None,
     ex_mode: typing.Literal["quiet", "echo", "dry_run", "script"] | None = None,
     overwrite: bool = False,
-) -> AlignEpiAnatParameters:
+) -> AlignEpiAnatPyParametersTagged:
     """
     Build parameters.
     
@@ -126,7 +114,7 @@ def align_epi_anat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "align_epi_anat",
+        "@type": "afni/align_epi_anat.py",
         "epi": epi,
         "anat": anat,
         "epi_base": epi_base,
@@ -153,8 +141,8 @@ def align_epi_anat_params(
     return params
 
 
-def align_epi_anat_cargs(
-    params: AlignEpiAnatParameters,
+def align_epi_anat_py_cargs(
+    params: AlignEpiAnatPyParameters,
     execution: Execution,
 ) -> list[str]:
     """
@@ -170,66 +158,66 @@ def align_epi_anat_cargs(
     cargs.append("align_epi_anat.py")
     cargs.extend([
         "-epi",
-        execution.input_file(params.get("epi"))
+        execution.input_file(params.get("epi", None))
     ])
     cargs.extend([
         "-anat",
-        execution.input_file(params.get("anat"))
+        execution.input_file(params.get("anat", None))
     ])
     cargs.extend([
         "-epi_base",
-        params.get("epi_base")
+        params.get("epi_base", None)
     ])
-    if params.get("anat2epi"):
+    if params.get("anat2epi", False):
         cargs.append("-anat2epi")
-    if params.get("epi2anat"):
+    if params.get("epi2anat", False):
         cargs.append("-epi2anat")
-    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("AddEdge"):
+    if params.get("AddEdge", False):
         cargs.append("-AddEdge")
-    if params.get("big_move"):
+    if params.get("big_move", False):
         cargs.append("-big_move")
-    if params.get("giant_move"):
+    if params.get("giant_move", False):
         cargs.append("-giant_move")
-    if params.get("ginormous_move"):
+    if params.get("ginormous_move", False):
         cargs.append("-ginormous_move")
-    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("ana_has_skull") is not None:
+    if params.get("ana_has_skull", None) is not None:
         cargs.extend([
             "-anat_has_skull",
-            params.get("ana_has_skull")
+            params.get("ana_has_skull", None)
         ])
-    if params.get("epi_strip") is not None:
+    if params.get("epi_strip", None) is not None:
         cargs.extend([
             "-epi_strip",
-            params.get("epi_strip")
+            params.get("epi_strip", None)
         ])
-    if params.get("volreg_method") is not None:
+    if params.get("volreg_method", None) is not None:
         cargs.extend([
             "-volreg_method",
-            params.get("volreg_method")
+            params.get("volreg_method", None)
         ])
-    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")
     return cargs
 
 
-def align_epi_anat_outputs(
-    params: AlignEpiAnatParameters,
+def align_epi_anat_py_outputs(
+    params: AlignEpiAnatPyParameters,
     execution: Execution,
-) -> AlignEpiAnatOutputs:
+) -> AlignEpiAnatPyOutputs:
     """
     Build outputs object containing output file paths and possibly stdout/stderr.
     
@@ -239,19 +227,21 @@ def align_epi_anat_outputs(
     Returns:
         Outputs object.
     """
-    ret = AlignEpiAnatOutputs(
+    ret = AlignEpiAnatPyOutputs(
         root=execution.output_file("."),
-        anat_aligned=execution.output_file(pathlib.Path(params.get("anat")).name + "+orig"),
-        epi_aligned=execution.output_file(pathlib.Path(params.get("epi")).name + "+orig"),
+        anat_aligned=execution.output_file(pathlib.Path(params.get("anat", None)).name + "+orig"),
+        epi_aligned=execution.output_file(pathlib.Path(params.get("epi", None)).name + "+orig"),
     )
     return ret
 
 
-def align_epi_anat_execute(
-    params: AlignEpiAnatParameters,
-    execution: Execution,
-) -> AlignEpiAnatOutputs:
+def align_epi_anat_py_execute(
+    params: AlignEpiAnatPyParameters,
+    runner: Runner | None = None,
+) -> AlignEpiAnatPyOutputs:
     """
+    align_epi_anat.py
+    
     Align EPI to anatomical datasets or vice versa.
     
     Author: AFNI Developers
@@ -260,18 +250,20 @@ def align_epi_anat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `AlignEpiAnatOutputs`).
+        NamedTuple of outputs (described in `AlignEpiAnatPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ALIGN_EPI_ANAT_PY_METADATA)
     params = execution.params(params)
-    cargs = align_epi_anat_cargs(params, execution)
-    ret = align_epi_anat_outputs(params, execution)
+    cargs = align_epi_anat_py_cargs(params, execution)
+    ret = align_epi_anat_py_outputs(params, execution)
     execution.run(cargs)
     return ret
 
 
-def align_epi_anat(
+def align_epi_anat_py(
     epi: InputPathType,
     anat: InputPathType,
     epi_base: str,
@@ -290,8 +282,10 @@ def align_epi_anat(
     ex_mode: typing.Literal["quiet", "echo", "dry_run", "script"] | None = None,
     overwrite: bool = False,
     runner: Runner | None = None,
-) -> AlignEpiAnatOutputs:
+) -> AlignEpiAnatPyOutputs:
     """
+    align_epi_anat.py
+    
     Align EPI to anatomical datasets or vice versa.
     
     Author: AFNI Developers
@@ -321,11 +315,9 @@ def align_epi_anat(
         overwrite: Overwrite existing files.
         runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `AlignEpiAnatOutputs`).
+        NamedTuple of outputs (described in `AlignEpiAnatPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ALIGN_EPI_ANAT_METADATA)
-    params = align_epi_anat_params(
+    params = align_epi_anat_py_params(
         epi=epi,
         anat=anat,
         epi_base=epi_base,
@@ -344,13 +336,13 @@ def align_epi_anat(
         ex_mode=ex_mode,
         overwrite=overwrite,
     )
-    return align_epi_anat_execute(params, execution)
+    return align_epi_anat_py_execute(params, runner)
 
 
 __all__ = [
-    "ALIGN_EPI_ANAT_METADATA",
-    "AlignEpiAnatOutputs",
-    "AlignEpiAnatParameters",
-    "align_epi_anat",
-    "align_epi_anat_params",
+    "ALIGN_EPI_ANAT_PY_METADATA",
+    "AlignEpiAnatPyOutputs",
+    "align_epi_anat_py",
+    "align_epi_anat_py_execute",
+    "align_epi_anat_py_params",
 ]

niwrap_afni/afni/analyze_trace.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ANALYZE_TRACE_METADATA = Metadata(
-    id="5171e53d12a5707c7fff96e1018d7b6e069c808d.boutiques",
+    id="23ae8fde537591a8258c993870270483cf69dd88.boutiques",
     name="AnalyzeTrace",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,21 @@ ANALYZE_TRACE_METADATA = Metadata(
 
 
 AnalyzeTraceParameters = typing.TypedDict('AnalyzeTraceParameters', {
-    "__STYXTYPE__": typing.Literal["AnalyzeTrace"],
+    "@type": typing.NotRequired[typing.Literal["afni/AnalyzeTrace"]],
+    "tracefile": InputPathType,
+    "max_func_lines": typing.NotRequired[int | None],
+    "suma_c": typing.NotRequired[InputPathType | None],
+    "max_err": typing.NotRequired[int | None],
+    "novolreg": bool,
+    "noxform": bool,
+    "setenv": typing.NotRequired[str | None],
+    "trace": bool,
+    "extreme_trace": bool,
+    "nomall": bool,
+    "yesmall": bool,
+})
+AnalyzeTraceParametersTagged = typing.TypedDict('AnalyzeTraceParametersTagged', {
+    "@type": typing.Literal["afni/AnalyzeTrace"],
     "tracefile": InputPathType,
     "max_func_lines": typing.NotRequired[int | None],
     "suma_c": typing.NotRequired[InputPathType | None],
@@ -27,42 +41,11 @@ AnalyzeTraceParameters = typing.TypedDict('AnalyzeTraceParameters', {
     "nomall": bool,
     "yesmall": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "AnalyzeTrace": analyze_trace_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 AnalyzeTraceOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `analyze_trace(...)`.
+    Output object returned when calling `AnalyzeTraceParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -80,7 +63,7 @@ def analyze_trace_params(
     extreme_trace: bool = False,
     nomall: bool = False,
     yesmall: bool = False,
-) -> AnalyzeTraceParameters:
+) -> AnalyzeTraceParametersTagged:
     """
     Build parameters.
     
@@ -106,7 +89,7 @@ def analyze_trace_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "AnalyzeTrace",
+        "@type": "afni/AnalyzeTrace",
         "tracefile": tracefile,
         "novolreg": novolreg,
         "noxform": noxform,
@@ -141,38 +124,38 @@ def analyze_trace_cargs(
     """
     cargs = []
     cargs.append("AnalyzeTrace")
-    cargs.append(execution.input_file(params.get("tracefile")))
-    if params.get("max_func_lines") is not None:
+    cargs.append(execution.input_file(params.get("tracefile", None)))
+    if params.get("max_func_lines", None) is not None:
         cargs.extend([
             "-max_func_lines",
-            str(params.get("max_func_lines"))
+            str(params.get("max_func_lines", None))
         ])
-    if params.get("suma_c") is not None:
+    if params.get("suma_c", None) is not None:
         cargs.extend([
             "-suma_c",
-            execution.input_file(params.get("suma_c"))
+            execution.input_file(params.get("suma_c", None))
         ])
-    if params.get("max_err") is not None:
+    if params.get("max_err", None) is not None:
         cargs.extend([
             "-max_err",
-            str(params.get("max_err"))
+            str(params.get("max_err", None))
         ])
-    if params.get("novolreg"):
+    if params.get("novolreg", False):
         cargs.append("-novolreg")
-    if params.get("noxform"):
+    if params.get("noxform", False):
         cargs.append("-noxform")
-    if params.get("setenv") is not None:
+    if params.get("setenv", None) is not None:
         cargs.extend([
             "-setenv",
-            params.get("setenv")
+            params.get("setenv", None)
         ])
-    if params.get("trace"):
+    if params.get("trace", False):
         cargs.append("-trace")
-    if params.get("extreme_trace"):
+    if params.get("extreme_trace", False):
         cargs.append("-TRACE")
-    if params.get("nomall"):
+    if params.get("nomall", False):
         cargs.append("-nomall")
-    if params.get("yesmall"):
+    if params.get("yesmall", False):
         cargs.append("-yesmall")
     return cargs
 
@@ -198,11 +181,13 @@ def analyze_trace_outputs(
 
 def analyze_trace_execute(
     params: AnalyzeTraceParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AnalyzeTraceOutputs:
     """
-    A program to analyze SUMA (and AFNI's perhaps) stack output for functions that
-    return with RETURN without bothering to go on the stack.
+    AnalyzeTrace
+    
+    A program to analyze SUMA (and AFNI's perhaps) stack output for functions
+    that return with RETURN without bothering to go on the stack.
     
     Author: AFNI Developers
     
@@ -210,10 +195,12 @@ def analyze_trace_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AnalyzeTraceOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ANALYZE_TRACE_METADATA)
     params = execution.params(params)
     cargs = analyze_trace_cargs(params, execution)
     ret = analyze_trace_outputs(params, execution)
@@ -236,8 +223,10 @@ def analyze_trace(
     runner: Runner | None = None,
 ) -> AnalyzeTraceOutputs:
     """
-    A program to analyze SUMA (and AFNI's perhaps) stack output for functions that
-    return with RETURN without bothering to go on the stack.
+    AnalyzeTrace
+    
+    A program to analyze SUMA (and AFNI's perhaps) stack output for functions
+    that return with RETURN without bothering to go on the stack.
     
     Author: AFNI Developers
     
@@ -265,8 +254,6 @@ def analyze_trace(
     Returns:
         NamedTuple of outputs (described in `AnalyzeTraceOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ANALYZE_TRACE_METADATA)
     params = analyze_trace_params(
         tracefile=tracefile,
         max_func_lines=max_func_lines,
@@ -280,13 +267,13 @@ def analyze_trace(
         nomall=nomall,
         yesmall=yesmall,
     )
-    return analyze_trace_execute(params, execution)
+    return analyze_trace_execute(params, runner)
 
 
 __all__ = [
     "ANALYZE_TRACE_METADATA",
     "AnalyzeTraceOutputs",
-    "AnalyzeTraceParameters",
     "analyze_trace",
+    "analyze_trace_execute",
     "analyze_trace_params",
 ]