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

niwrap_afni/afni/afni_open.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 AFNI_OPEN_METADATA = Metadata(
-    id="87c5cb2a1fc95478c838202fe74a9d66e957b97d.boutiques",
+    id="951fa387ec070337460df2310e677499f20a1408.boutiques",
     name="afni_open",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,25 @@ AFNI_OPEN_METADATA = Metadata(
 
 
 AfniOpenParameters = typing.TypedDict('AfniOpenParameters', {
-    "__STYXTYPE__": typing.Literal["afni_open"],
+    "@type": typing.NotRequired[typing.Literal["afni/afni_open"]],
+    "files": list[InputPathType],
+    "method": typing.NotRequired[str | None],
+    "editor": bool,
+    "downloader": bool,
+    "examinexmat": bool,
+    "browser": bool,
+    "readme": bool,
+    "afniweb": bool,
+    "global_help": bool,
+    "gopts_help": bool,
+    "help": bool,
+    "mini_help": bool,
+    "extreme_help": bool,
+    "h_view": bool,
+    "h_web": bool,
+})
+AfniOpenParametersTagged = typing.TypedDict('AfniOpenParametersTagged', {
+    "@type": typing.Literal["afni/afni_open"],
     "files": list[InputPathType],
     "method": typing.NotRequired[str | None],
     "editor": bool,
@@ -31,42 +49,11 @@ AfniOpenParameters = typing.TypedDict('AfniOpenParameters', {
     "h_view": bool,
     "h_web": 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_open": afni_open_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 AfniOpenOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `afni_open(...)`.
+    Output object returned when calling `AfniOpenParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -88,7 +75,7 @@ def afni_open_params(
     extreme_help: bool = False,
     h_view: bool = False,
     h_web: bool = False,
-) -> AfniOpenParameters:
+) -> AfniOpenParametersTagged:
     """
     Build parameters.
     
@@ -113,7 +100,7 @@ def afni_open_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "afni_open",
+        "@type": "afni/afni_open",
         "files": files,
         "editor": editor,
         "downloader": downloader,
@@ -149,37 +136,37 @@ def afni_open_cargs(
     """
     cargs = []
     cargs.append("afni_open")
-    cargs.extend([execution.input_file(f) for f in params.get("files")])
-    if params.get("method") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("files", None)])
+    if params.get("method", None) is not None:
         cargs.extend([
             "-w",
-            params.get("method")
+            params.get("method", None)
         ])
-    if params.get("editor"):
+    if params.get("editor", False):
         cargs.append("-e")
-    if params.get("downloader"):
+    if params.get("downloader", False):
         cargs.append("-d")
-    if params.get("examinexmat"):
+    if params.get("examinexmat", False):
         cargs.append("-x")
-    if params.get("browser"):
+    if params.get("browser", False):
         cargs.append("-b")
-    if params.get("readme"):
+    if params.get("readme", False):
         cargs.append("-r")
-    if params.get("afniweb"):
+    if params.get("afniweb", False):
         cargs.append("-aw")
-    if params.get("global_help"):
+    if params.get("global_help", False):
         cargs.append("-global_help")
-    if params.get("gopts_help"):
+    if params.get("gopts_help", False):
         cargs.append("-gopts_help")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("mini_help"):
+    if params.get("mini_help", False):
         cargs.append("-h")
-    if params.get("extreme_help"):
+    if params.get("extreme_help", False):
         cargs.append("-HELP")
-    if params.get("h_view"):
+    if params.get("h_view", False):
         cargs.append("-h_view")
-    if params.get("h_web"):
+    if params.get("h_web", False):
         cargs.append("-h_web")
     return cargs
 
@@ -205,9 +192,11 @@ def afni_open_outputs(
 
 def afni_open_execute(
     params: AfniOpenParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AfniOpenOutputs:
     """
+    afni_open
+    
     A program to open various AFNI/SUMA files.
     
     Author: AFNI Developers
@@ -216,10 +205,12 @@ def afni_open_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AfniOpenOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AFNI_OPEN_METADATA)
     params = execution.params(params)
     cargs = afni_open_cargs(params, execution)
     ret = afni_open_outputs(params, execution)
@@ -246,6 +237,8 @@ def afni_open(
     runner: Runner | None = None,
 ) -> AfniOpenOutputs:
     """
+    afni_open
+    
     A program to open various AFNI/SUMA files.
     
     Author: AFNI Developers
@@ -273,8 +266,6 @@ def afni_open(
     Returns:
         NamedTuple of outputs (described in `AfniOpenOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(AFNI_OPEN_METADATA)
     params = afni_open_params(
         files=files,
         method=method,
@@ -292,13 +283,13 @@ def afni_open(
         h_view=h_view,
         h_web=h_web,
     )
-    return afni_open_execute(params, execution)
+    return afni_open_execute(params, runner)
 
 
 __all__ = [
     "AFNI_OPEN_METADATA",
     "AfniOpenOutputs",
-    "AfniOpenParameters",
     "afni_open",
+    "afni_open_execute",
     "afni_open_params",
 ]

niwrap_afni/afni/afni_proc_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 AFNI_PROC_PY_METADATA = Metadata(
-    id="7969059f0ff122f045207188e28f2aea49969161.boutiques",
+    id="23fb1b7014142256e76715fd30000630ec9139af.boutiques",
     name="afni_proc.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,21 @@ AFNI_PROC_PY_METADATA = Metadata(
 
 
 AfniProcPyParameters = typing.TypedDict('AfniProcPyParameters', {
-    "__STYXTYPE__": typing.Literal["afni_proc.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/afni_proc.py"]],
+    "dsets": list[InputPathType],
+    "subj_id": str,
+    "out_dir": typing.NotRequired[str | None],
+    "blocks": typing.NotRequired[list[str] | None],
+    "anat": InputPathType,
+    "echo_times": typing.NotRequired[list[float] | None],
+    "stim_times": typing.NotRequired[list[InputPathType] | None],
+    "stim_files": typing.NotRequired[list[InputPathType] | None],
+    "copy_files": typing.NotRequired[list[InputPathType] | None],
+    "copy_anat": typing.NotRequired[InputPathType | None],
+    "regress_params": typing.NotRequired[list[str] | None],
+})
+AfniProcPyParametersTagged = typing.TypedDict('AfniProcPyParametersTagged', {
+    "@type": typing.Literal["afni/afni_proc.py"],
     "dsets": list[InputPathType],
     "subj_id": str,
     "out_dir": typing.NotRequired[str | None],
@@ -27,47 +41,15 @@ AfniProcPyParameters = typing.TypedDict('AfniProcPyParameters', {
     "copy_anat": typing.NotRequired[InputPathType | None],
     "regress_params": typing.NotRequired[list[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 {
-        "afni_proc.py": afni_proc_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 {
-        "afni_proc.py": afni_proc_py_outputs,
-    }.get(t)
 
 
 class AfniProcPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `afni_proc_py(...)`.
+    Output object returned when calling `AfniProcPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    output_files: OutputPathType | None
+    output_directory: OutputPathType | None
     """All output files stored in the specified output directory."""
 
 
@@ -83,7 +65,7 @@ def afni_proc_py_params(
     copy_files: list[InputPathType] | None = None,
     copy_anat: InputPathType | None = None,
     regress_params: list[str] | None = None,
-) -> AfniProcPyParameters:
+) -> AfniProcPyParametersTagged:
     """
     Build parameters.
     
@@ -107,7 +89,7 @@ def afni_proc_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "afni_proc.py",
+        "@type": "afni/afni_proc.py",
         "dsets": dsets,
         "subj_id": subj_id,
         "anat": anat,
@@ -146,27 +128,27 @@ def afni_proc_py_cargs(
     """
     cargs = []
     cargs.append("afni_proc.py")
-    cargs.extend([execution.input_file(f) for f in params.get("dsets")])
-    cargs.append(params.get("subj_id"))
-    if params.get("out_dir") is not None:
-        cargs.append(params.get("out_dir"))
-    if params.get("blocks") is not None:
-        cargs.extend(params.get("blocks"))
-    cargs.append(execution.input_file(params.get("anat")))
-    if params.get("echo_times") is not None:
-        cargs.extend(map(str, params.get("echo_times")))
-    if params.get("stim_times") is not None:
-        cargs.extend([execution.input_file(f) for f in params.get("stim_times")])
-    if params.get("stim_files") is not None:
-        cargs.extend([execution.input_file(f) for f in params.get("stim_files")])
-    if params.get("copy_files") is not None:
-        cargs.extend([execution.input_file(f) for f in params.get("copy_files")])
-    if params.get("copy_anat") is not None:
-        cargs.append(execution.input_file(params.get("copy_anat")))
-    if params.get("regress_params") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("dsets", None)])
+    cargs.append(params.get("subj_id", None))
+    if params.get("out_dir", None) is not None:
+        cargs.append(params.get("out_dir", None))
+    if params.get("blocks", None) is not None:
+        cargs.extend(params.get("blocks", None))
+    cargs.append(execution.input_file(params.get("anat", None)))
+    if params.get("echo_times", None) is not None:
+        cargs.extend(map(str, params.get("echo_times", None)))
+    if params.get("stim_times", None) is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("stim_times", None)])
+    if params.get("stim_files", None) is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("stim_files", None)])
+    if params.get("copy_files", None) is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("copy_files", None)])
+    if params.get("copy_anat", None) is not None:
+        cargs.append(execution.input_file(params.get("copy_anat", None)))
+    if params.get("regress_params", None) is not None:
         cargs.extend([
             "-regress_opts_3dD",
-            *params.get("regress_params")
+            *params.get("regress_params", None)
         ])
     return cargs
 
@@ -186,16 +168,18 @@ def afni_proc_py_outputs(
     """
     ret = AfniProcPyOutputs(
         root=execution.output_file("."),
-        output_files=execution.output_file(params.get("out_dir") + "/*") if (params.get("out_dir") is not None) else None,
+        output_directory=execution.output_file(params.get("out_dir", None)) if (params.get("out_dir") is not None) else None,
     )
     return ret
 
 
 def afni_proc_py_execute(
     params: AfniProcPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AfniProcPyOutputs:
     """
+    afni_proc.py
+    
     Generate a tcsh script for an AFNI single subject processing stream.
     
     Author: AFNI Developers
@@ -204,10 +188,12 @@ def afni_proc_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AfniProcPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AFNI_PROC_PY_METADATA)
     params = execution.params(params)
     cargs = afni_proc_py_cargs(params, execution)
     ret = afni_proc_py_outputs(params, execution)
@@ -230,6 +216,8 @@ def afni_proc_py(
     runner: Runner | None = None,
 ) -> AfniProcPyOutputs:
     """
+    afni_proc.py
+    
     Generate a tcsh script for an AFNI single subject processing stream.
     
     Author: AFNI Developers
@@ -256,8 +244,6 @@ def afni_proc_py(
     Returns:
         NamedTuple of outputs (described in `AfniProcPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(AFNI_PROC_PY_METADATA)
     params = afni_proc_py_params(
         dsets=dsets,
         subj_id=subj_id,
@@ -271,13 +257,13 @@ def afni_proc_py(
         copy_anat=copy_anat,
         regress_params=regress_params,
     )
-    return afni_proc_py_execute(params, execution)
+    return afni_proc_py_execute(params, runner)
 
 
 __all__ = [
     "AFNI_PROC_PY_METADATA",
     "AfniProcPyOutputs",
-    "AfniProcPyParameters",
     "afni_proc_py",
+    "afni_proc_py_execute",
     "afni_proc_py_params",
 ]

niwrap_afni/afni/afni_run_r.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 AFNI_RUN_R_METADATA = Metadata(
-    id="c25de8aaab9b4faa0067fa6c9d3361eb1f13f7bf.boutiques",
+    id="b7b1c26a0099d70aa13bea32d8b349365c08955c.boutiques",
     name="afni_run_R",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,46 +14,20 @@ AFNI_RUN_R_METADATA = Metadata(
 
 
 AfniRunRParameters = typing.TypedDict('AfniRunRParameters', {
-    "__STYXTYPE__": typing.Literal["afni_run_R"],
+    "@type": typing.NotRequired[typing.Literal["afni/afni_run_R"]],
+    "r_script": InputPathType,
+    "r_args": list[str],
+})
+AfniRunRParametersTagged = typing.TypedDict('AfniRunRParametersTagged', {
+    "@type": typing.Literal["afni/afni_run_R"],
     "r_script": InputPathType,
     "r_args": list[str],
 })
-
-
-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_R": afni_run_r_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 AfniRunROutputs(typing.NamedTuple):
     """
-    Output object returned when calling `afni_run_r(...)`.
+    Output object returned when calling `AfniRunRParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class AfniRunROutputs(typing.NamedTuple):
 def afni_run_r_params(
     r_script: InputPathType,
     r_args: list[str],
-) -> AfniRunRParameters:
+) -> AfniRunRParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def afni_run_r_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "afni_run_R",
+        "@type": "afni/afni_run_R",
         "r_script": r_script,
         "r_args": r_args,
     }
@@ -95,8 +69,8 @@ def afni_run_r_cargs(
     """
     cargs = []
     cargs.append("afni_run_R")
-    cargs.append(execution.input_file(params.get("r_script")))
-    cargs.extend(params.get("r_args"))
+    cargs.append(execution.input_file(params.get("r_script", None)))
+    cargs.extend(params.get("r_args", None))
     return cargs
 
 
@@ -121,9 +95,11 @@ def afni_run_r_outputs(
 
 def afni_run_r_execute(
     params: AfniRunRParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AfniRunROutputs:
     """
+    afni_run_R
+    
     Run an R script with the specified arguments.
     
     Author: AFNI Developers
@@ -132,10 +108,12 @@ def afni_run_r_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AfniRunROutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AFNI_RUN_R_METADATA)
     params = execution.params(params)
     cargs = afni_run_r_cargs(params, execution)
     ret = afni_run_r_outputs(params, execution)
@@ -149,6 +127,8 @@ def afni_run_r(
     runner: Runner | None = None,
 ) -> AfniRunROutputs:
     """
+    afni_run_R
+    
     Run an R script with the specified arguments.
     
     Author: AFNI Developers
@@ -162,19 +142,17 @@ def afni_run_r(
     Returns:
         NamedTuple of outputs (described in `AfniRunROutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(AFNI_RUN_R_METADATA)
     params = afni_run_r_params(
         r_script=r_script,
         r_args=r_args,
     )
-    return afni_run_r_execute(params, execution)
+    return afni_run_r_execute(params, runner)
 
 
 __all__ = [
     "AFNI_RUN_R_METADATA",
     "AfniRunROutputs",
-    "AfniRunRParameters",
     "afni_run_r",
+    "afni_run_r_execute",
     "afni_run_r_params",
 ]