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

niwrap_freesurfer/freesurfer/listsubj.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LISTSUBJ_METADATA = Metadata(
-    id="88334c9a683da47d52746d6bf16968b8b1d17667.boutiques",
+    id="85f9cf28110636d5950e47d02ab32ecf402ab492.boutiques",
     name="listsubj",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,20 @@ LISTSUBJ_METADATA = Metadata(
 
 
 ListsubjParameters = typing.TypedDict('ListsubjParameters', {
-    "__STYXTYPE__": typing.Literal["listsubj"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/listsubj"]],
+    "subject_dir": str,
+    "cross": bool,
+    "base": bool,
+    "long": bool,
+    "done": bool,
+    "error": bool,
+    "running": bool,
+    "full_path": bool,
+    "count": bool,
+    "help": bool,
+})
+ListsubjParametersTagged = typing.TypedDict('ListsubjParametersTagged', {
+    "@type": typing.Literal["freesurfer/listsubj"],
     "subject_dir": str,
     "cross": bool,
     "base": bool,
@@ -26,42 +39,11 @@ ListsubjParameters = typing.TypedDict('ListsubjParameters', {
     "count": bool,
     "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 {
-        "listsubj": listsubj_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 ListsubjOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `listsubj(...)`.
+    Output object returned when calling `ListsubjParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -78,7 +60,7 @@ def listsubj_params(
     full_path: bool = False,
     count: bool = False,
     help_: bool = False,
-) -> ListsubjParameters:
+) -> ListsubjParametersTagged:
     """
     Build parameters.
     
@@ -97,7 +79,7 @@ def listsubj_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "listsubj",
+        "@type": "freesurfer/listsubj",
         "subject_dir": subject_dir,
         "cross": cross,
         "base": base,
@@ -127,24 +109,24 @@ def listsubj_cargs(
     """
     cargs = []
     cargs.append("listsubj")
-    cargs.append(params.get("subject_dir"))
-    if params.get("cross"):
+    cargs.append(params.get("subject_dir", None))
+    if params.get("cross", False):
         cargs.append("-c")
-    if params.get("base"):
+    if params.get("base", False):
         cargs.append("-b")
-    if params.get("long"):
+    if params.get("long", False):
         cargs.append("-l")
-    if params.get("done"):
+    if params.get("done", False):
         cargs.append("-d")
-    if params.get("error"):
+    if params.get("error", False):
         cargs.append("-e")
-    if params.get("running"):
+    if params.get("running", False):
         cargs.append("-r")
-    if params.get("full_path"):
+    if params.get("full_path", False):
         cargs.append("-f")
-    if params.get("count"):
+    if params.get("count", False):
         cargs.append("-n")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-h")
     return cargs
 
@@ -170,9 +152,11 @@ def listsubj_outputs(
 
 def listsubj_execute(
     params: ListsubjParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ListsubjOutputs:
     """
+    listsubj
+    
     List subject IDs in SUBJECT_DIR.
     
     Author: FreeSurfer Developers
@@ -181,10 +165,12 @@ def listsubj_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ListsubjOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LISTSUBJ_METADATA)
     params = execution.params(params)
     cargs = listsubj_cargs(params, execution)
     ret = listsubj_outputs(params, execution)
@@ -206,6 +192,8 @@ def listsubj(
     runner: Runner | None = None,
 ) -> ListsubjOutputs:
     """
+    listsubj
+    
     List subject IDs in SUBJECT_DIR.
     
     Author: FreeSurfer Developers
@@ -227,8 +215,6 @@ def listsubj(
     Returns:
         NamedTuple of outputs (described in `ListsubjOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LISTSUBJ_METADATA)
     params = listsubj_params(
         subject_dir=subject_dir,
         cross=cross,
@@ -241,13 +227,13 @@ def listsubj(
         count=count,
         help_=help_,
     )
-    return listsubj_execute(params, execution)
+    return listsubj_execute(params, runner)
 
 
 __all__ = [
     "LISTSUBJ_METADATA",
     "ListsubjOutputs",
-    "ListsubjParameters",
     "listsubj",
+    "listsubj_execute",
     "listsubj_params",
 ]

niwrap_freesurfer/freesurfer/long_create_base_sigma.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LONG_CREATE_BASE_SIGMA_METADATA = Metadata(
-    id="359af0d6b57993950b3f756ef93dd6df37402a88.boutiques",
+    id="4c6141a217c61baf0c141da4a8f2865bd36f37dd.boutiques",
     name="long_create_base_sigma",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ LONG_CREATE_BASE_SIGMA_METADATA = Metadata(
 
 
 LongCreateBaseSigmaParameters = typing.TypedDict('LongCreateBaseSigmaParameters', {
-    "__STYXTYPE__": typing.Literal["long_create_base_sigma"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/long_create_base_sigma"]],
+    "base_id": str,
+    "sigma": int,
+})
+LongCreateBaseSigmaParametersTagged = typing.TypedDict('LongCreateBaseSigmaParametersTagged', {
+    "@type": typing.Literal["freesurfer/long_create_base_sigma"],
     "base_id": str,
     "sigma": int,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "long_create_base_sigma": long_create_base_sigma_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 LongCreateBaseSigmaOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `long_create_base_sigma(...)`.
+    Output object returned when calling `LongCreateBaseSigmaParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class LongCreateBaseSigmaOutputs(typing.NamedTuple):
 def long_create_base_sigma_params(
     base_id: str,
     sigma: int,
-) -> LongCreateBaseSigmaParameters:
+) -> LongCreateBaseSigmaParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def long_create_base_sigma_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "long_create_base_sigma",
+        "@type": "freesurfer/long_create_base_sigma",
         "base_id": base_id,
         "sigma": sigma,
     }
@@ -95,8 +69,8 @@ def long_create_base_sigma_cargs(
     """
     cargs = []
     cargs.append("long_create_base_sigma")
-    cargs.append(params.get("base_id"))
-    cargs.append(str(params.get("sigma")))
+    cargs.append(params.get("base_id", None))
+    cargs.append(str(params.get("sigma", None)))
     return cargs
 
 
@@ -121,9 +95,11 @@ def long_create_base_sigma_outputs(
 
 def long_create_base_sigma_execute(
     params: LongCreateBaseSigmaParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> LongCreateBaseSigmaOutputs:
     """
+    long_create_base_sigma
+    
     Performs a joint normalization and atlas renormalization at a specific sigma
     smoothing level. This is usually done as part of the base stream but can be
     performed to add files for a different sigma level to an existing base.
@@ -134,10 +110,12 @@ def long_create_base_sigma_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `LongCreateBaseSigmaOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LONG_CREATE_BASE_SIGMA_METADATA)
     params = execution.params(params)
     cargs = long_create_base_sigma_cargs(params, execution)
     ret = long_create_base_sigma_outputs(params, execution)
@@ -151,6 +129,8 @@ def long_create_base_sigma(
     runner: Runner | None = None,
 ) -> LongCreateBaseSigmaOutputs:
     """
+    long_create_base_sigma
+    
     Performs a joint normalization and atlas renormalization at a specific sigma
     smoothing level. This is usually done as part of the base stream but can be
     performed to add files for a different sigma level to an existing base.
@@ -166,19 +146,17 @@ def long_create_base_sigma(
     Returns:
         NamedTuple of outputs (described in `LongCreateBaseSigmaOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LONG_CREATE_BASE_SIGMA_METADATA)
     params = long_create_base_sigma_params(
         base_id=base_id,
         sigma=sigma,
     )
-    return long_create_base_sigma_execute(params, execution)
+    return long_create_base_sigma_execute(params, runner)
 
 
 __all__ = [
     "LONG_CREATE_BASE_SIGMA_METADATA",
     "LongCreateBaseSigmaOutputs",
-    "LongCreateBaseSigmaParameters",
     "long_create_base_sigma",
+    "long_create_base_sigma_execute",
     "long_create_base_sigma_params",
 ]

niwrap_freesurfer/freesurfer/long_create_orig.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LONG_CREATE_ORIG_METADATA = Metadata(
-    id="b5bf312a7f38bd0a0811e93327cd17069c91c260.boutiques",
+    id="ab4e59774c02e65ea0d6e83e65869f67ba49bb38.boutiques",
     name="long_create_orig",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,59 +14,31 @@ LONG_CREATE_ORIG_METADATA = Metadata(
 
 
 LongCreateOrigParameters = typing.TypedDict('LongCreateOrigParameters', {
-    "__STYXTYPE__": typing.Literal["long_create_orig"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/long_create_orig"]],
+    "base_id": str,
+    "tp_id": typing.NotRequired[str | None],
+})
+LongCreateOrigParametersTagged = typing.TypedDict('LongCreateOrigParametersTagged', {
+    "@type": typing.Literal["freesurfer/long_create_orig"],
     "base_id": str,
     "tp_id": 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 {
-        "long_create_orig": long_create_orig_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 {
-        "long_create_orig": long_create_orig_outputs,
-    }.get(t)
 
 
 class LongCreateOrigOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `long_create_orig(...)`.
+    Output object returned when calling `LongCreateOrigParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    output_directory: OutputPathType
-    """Output directory for processed time point data. Defaults to the specified
-    path."""
+    output_directory: OutputPathType | None
+    """Output directory within <SUBJECTS_DIR> for processed time point data."""
 
 
 def long_create_orig_params(
     base_id: str,
     tp_id: str | None = None,
-) -> LongCreateOrigParameters:
+) -> LongCreateOrigParametersTagged:
     """
     Build parameters.
     
@@ -77,7 +49,7 @@ def long_create_orig_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "long_create_orig",
+        "@type": "freesurfer/long_create_orig",
         "base_id": base_id,
     }
     if tp_id is not None:
@@ -100,9 +72,9 @@ def long_create_orig_cargs(
     """
     cargs = []
     cargs.append("long_create_orig")
-    cargs.append(params.get("base_id"))
-    if params.get("tp_id") is not None:
-        cargs.append(params.get("tp_id"))
+    cargs.append(params.get("base_id", None))
+    if params.get("tp_id", None) is not None:
+        cargs.append(params.get("tp_id", None))
     return cargs
 
 
@@ -121,16 +93,18 @@ def long_create_orig_outputs(
     """
     ret = LongCreateOrigOutputs(
         root=execution.output_file("."),
-        output_directory=execution.output_file("<SUBJECTS_DIR>/<base-id>/longtp/<tp-id>"),
+        output_directory=execution.output_file(params.get("base_id", None) + "/longtp/" + params.get("tp_id", None)) if (params.get("tp_id") is not None) else None,
     )
     return ret
 
 
 def long_create_orig_execute(
     params: LongCreateOrigParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> LongCreateOrigOutputs:
     """
+    long_create_orig
+    
     Maps, conforms and averages (motioncorrect) raw inputs from cross-sectional
     directory to base space in Freesurfer.
     
@@ -140,10 +114,12 @@ def long_create_orig_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `LongCreateOrigOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LONG_CREATE_ORIG_METADATA)
     params = execution.params(params)
     cargs = long_create_orig_cargs(params, execution)
     ret = long_create_orig_outputs(params, execution)
@@ -157,6 +133,8 @@ def long_create_orig(
     runner: Runner | None = None,
 ) -> LongCreateOrigOutputs:
     """
+    long_create_orig
+    
     Maps, conforms and averages (motioncorrect) raw inputs from cross-sectional
     directory to base space in Freesurfer.
     
@@ -171,19 +149,17 @@ def long_create_orig(
     Returns:
         NamedTuple of outputs (described in `LongCreateOrigOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LONG_CREATE_ORIG_METADATA)
     params = long_create_orig_params(
         base_id=base_id,
         tp_id=tp_id,
     )
-    return long_create_orig_execute(params, execution)
+    return long_create_orig_execute(params, runner)
 
 
 __all__ = [
     "LONG_CREATE_ORIG_METADATA",
     "LongCreateOrigOutputs",
-    "LongCreateOrigParameters",
     "long_create_orig",
+    "long_create_orig_execute",
     "long_create_orig_params",
 ]