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

niwrap_freesurfer/freesurfer/trac_all.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TRAC_ALL_METADATA = Metadata(
-    id="4b02da6d23bbdf1aadba4f7ad8effbf91cb48ef5.boutiques",
+    id="530692c9924a90e814f01e102b101913b4b800ea.boutiques",
     name="trac-all",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,44 @@ TRAC_ALL_METADATA = Metadata(
 
 
 TracAllParameters = typing.TypedDict('TracAllParameters', {
-    "__STYXTYPE__": typing.Literal["trac-all"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/trac-all"]],
+    "config_file": typing.NotRequired[InputPathType | None],
+    "subject_name": typing.NotRequired[str | None],
+    "dicom_file": typing.NotRequired[InputPathType | None],
+    "pre_processing": bool,
+    "bedpost": bool,
+    "pathway_reconstruction": bool,
+    "assemble_measures": bool,
+    "image_corrections": bool,
+    "no_image_corrections": bool,
+    "image_quality_assessment": bool,
+    "no_image_quality_assessment": bool,
+    "intra_registration": bool,
+    "no_intra_registration": bool,
+    "tensor_fit": bool,
+    "no_tensor_fit": bool,
+    "inter_registration": bool,
+    "no_inter_registration": bool,
+    "pathway_priors": bool,
+    "no_pathway_priors": bool,
+    "infant_options": bool,
+    "job_file": typing.NotRequired[InputPathType | None],
+    "log_file": typing.NotRequired[str | None],
+    "no_append_log": bool,
+    "cmd_file": typing.NotRequired[str | None],
+    "no_is_running": bool,
+    "subjects_directory": typing.NotRequired[str | None],
+    "umask": typing.NotRequired[str | None],
+    "group_id": typing.NotRequired[str | None],
+    "allow_core_dump": bool,
+    "debug_mode": bool,
+    "dont_run": bool,
+    "only_versions": bool,
+    "version_info": bool,
+    "help": bool,
+})
+TracAllParametersTagged = typing.TypedDict('TracAllParametersTagged', {
+    "@type": typing.Literal["freesurfer/trac-all"],
     "config_file": typing.NotRequired[InputPathType | None],
     "subject_name": typing.NotRequired[str | None],
     "dicom_file": typing.NotRequired[InputPathType | None],
@@ -50,43 +87,11 @@ TracAllParameters = typing.TypedDict('TracAllParameters', {
     "version_info": 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 {
-        "trac-all": trac_all_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 {
-        "trac-all": trac_all_outputs,
-    }.get(t)
 
 
 class TracAllOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `trac_all(...)`.
+    Output object returned when calling `TracAllParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -131,7 +136,7 @@ def trac_all_params(
     only_versions: bool = False,
     version_info: bool = False,
     help_: bool = False,
-) -> TracAllParameters:
+) -> TracAllParametersTagged:
     """
     Build parameters.
     
@@ -178,7 +183,7 @@ def trac_all_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "trac-all",
+        "@type": "freesurfer/trac-all",
         "pre_processing": pre_processing,
         "bedpost": bedpost,
         "pathway_reconstruction": pathway_reconstruction,
@@ -241,100 +246,100 @@ def trac_all_cargs(
     """
     cargs = []
     cargs.append("trac-all")
-    if params.get("config_file") is not None:
+    if params.get("config_file", None) is not None:
         cargs.extend([
             "-c",
-            execution.input_file(params.get("config_file"))
+            execution.input_file(params.get("config_file", None))
         ])
-    if params.get("subject_name") is not None:
+    if params.get("subject_name", None) is not None:
         cargs.extend([
             "-s",
-            params.get("subject_name")
+            params.get("subject_name", None)
         ])
-    if params.get("dicom_file") is not None:
+    if params.get("dicom_file", None) is not None:
         cargs.extend([
             "-i",
-            execution.input_file(params.get("dicom_file"))
+            execution.input_file(params.get("dicom_file", None))
         ])
-    if params.get("pre_processing"):
+    if params.get("pre_processing", False):
         cargs.append("-prep")
-    if params.get("bedpost"):
+    if params.get("bedpost", False):
         cargs.append("-bedp")
-    if params.get("pathway_reconstruction"):
+    if params.get("pathway_reconstruction", False):
         cargs.append("-path")
-    if params.get("assemble_measures"):
+    if params.get("assemble_measures", False):
         cargs.append("-stat")
-    if params.get("image_corrections"):
+    if params.get("image_corrections", False):
         cargs.append("-corr")
-    if params.get("no_image_corrections"):
+    if params.get("no_image_corrections", False):
         cargs.append("-nocorr")
-    if params.get("image_quality_assessment"):
+    if params.get("image_quality_assessment", False):
         cargs.append("-qa")
-    if params.get("no_image_quality_assessment"):
+    if params.get("no_image_quality_assessment", False):
         cargs.append("-noqa")
-    if params.get("intra_registration"):
+    if params.get("intra_registration", False):
         cargs.append("-intra")
-    if params.get("no_intra_registration"):
+    if params.get("no_intra_registration", False):
         cargs.append("-nointra")
-    if params.get("tensor_fit"):
+    if params.get("tensor_fit", False):
         cargs.append("-tensor")
-    if params.get("no_tensor_fit"):
+    if params.get("no_tensor_fit", False):
         cargs.append("-notensor")
-    if params.get("inter_registration"):
+    if params.get("inter_registration", False):
         cargs.append("-inter")
-    if params.get("no_inter_registration"):
+    if params.get("no_inter_registration", False):
         cargs.append("-nointer")
-    if params.get("pathway_priors"):
+    if params.get("pathway_priors", False):
         cargs.append("-prior")
-    if params.get("no_pathway_priors"):
+    if params.get("no_pathway_priors", False):
         cargs.append("-noprior")
-    if params.get("infant_options"):
+    if params.get("infant_options", False):
         cargs.append("-infant")
-    if params.get("job_file") is not None:
+    if params.get("job_file", None) is not None:
         cargs.extend([
             "-jobs",
-            execution.input_file(params.get("job_file"))
+            execution.input_file(params.get("job_file", None))
         ])
-    if params.get("log_file") is not None:
+    if params.get("log_file", None) is not None:
         cargs.extend([
             "-log",
-            params.get("log_file")
+            params.get("log_file", None)
         ])
-    if params.get("no_append_log"):
+    if params.get("no_append_log", False):
         cargs.append("-noappendlog")
-    if params.get("cmd_file") is not None:
+    if params.get("cmd_file", None) is not None:
         cargs.extend([
             "-cmd",
-            params.get("cmd_file")
+            params.get("cmd_file", None)
         ])
-    if params.get("no_is_running"):
+    if params.get("no_is_running", False):
         cargs.append("-no-isrunning")
-    if params.get("subjects_directory") is not None:
+    if params.get("subjects_directory", None) is not None:
         cargs.extend([
             "-sd",
-            params.get("subjects_directory")
+            params.get("subjects_directory", None)
         ])
-    if params.get("umask") is not None:
+    if params.get("umask", None) is not None:
         cargs.extend([
             "-umask",
-            params.get("umask")
+            params.get("umask", None)
         ])
-    if params.get("group_id") is not None:
+    if params.get("group_id", None) is not None:
         cargs.extend([
             "-grp",
-            params.get("group_id")
+            params.get("group_id", None)
         ])
-    if params.get("allow_core_dump"):
+    if params.get("allow_core_dump", False):
         cargs.append("-allowcoredump")
-    if params.get("debug_mode"):
+    if params.get("debug_mode", False):
         cargs.append("-debug")
-    if params.get("dont_run"):
+    if params.get("dont_run", False):
         cargs.append("-dontrun")
-    if params.get("only_versions"):
+    if params.get("only_versions", False):
         cargs.append("-onlyversions")
-    if params.get("version_info"):
+    if params.get("version_info", False):
         cargs.append("-version")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -362,9 +367,11 @@ def trac_all_outputs(
 
 def trac_all_execute(
     params: TracAllParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TracAllOutputs:
     """
+    trac-all
+    
     Reconstruct white-matter pathways using an atlas of the underlying anatomy.
     
     Author: FreeSurfer Developers
@@ -373,10 +380,12 @@ def trac_all_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TracAllOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TRAC_ALL_METADATA)
     params = execution.params(params)
     cargs = trac_all_cargs(params, execution)
     ret = trac_all_outputs(params, execution)
@@ -422,6 +431,8 @@ def trac_all(
     runner: Runner | None = None,
 ) -> TracAllOutputs:
     """
+    trac-all
+    
     Reconstruct white-matter pathways using an atlas of the underlying anatomy.
     
     Author: FreeSurfer Developers
@@ -471,8 +482,6 @@ def trac_all(
     Returns:
         NamedTuple of outputs (described in `TracAllOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TRAC_ALL_METADATA)
     params = trac_all_params(
         config_file=config_file,
         subject_name=subject_name,
@@ -509,13 +518,13 @@ def trac_all(
         version_info=version_info,
         help_=help_,
     )
-    return trac_all_execute(params, execution)
+    return trac_all_execute(params, runner)
 
 
 __all__ = [
     "TRAC_ALL_METADATA",
     "TracAllOutputs",
-    "TracAllParameters",
     "trac_all",
+    "trac_all_execute",
     "trac_all_params",
 ]

niwrap_freesurfer/freesurfer/trac_paths.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TRAC_PATHS_METADATA = Metadata(
-    id="f085abb25cd93831e33301f753fc93e1f37fab3b.boutiques",
+    id="e6e0a90c1596483e2f89bd23a9b38b773f7b3348.boutiques",
     name="trac-paths",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,23 @@ TRAC_PATHS_METADATA = Metadata(
 
 
 TracPathsParameters = typing.TypedDict('TracPathsParameters', {
-    "__STYXTYPE__": typing.Literal["trac-paths"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/trac-paths"]],
+    "dmrirc_file": InputPathType,
+    "log_file": typing.NotRequired[str | None],
+    "no_log": bool,
+    "cmd_file": typing.NotRequired[str | None],
+    "no_cmd": bool,
+    "no_isrunning": bool,
+    "umask": typing.NotRequired[str | None],
+    "group_id": typing.NotRequired[str | None],
+    "allow_core_dump": bool,
+    "debug": bool,
+    "dontrun": bool,
+    "version": bool,
+    "help": bool,
+})
+TracPathsParametersTagged = typing.TypedDict('TracPathsParametersTagged', {
+    "@type": typing.Literal["freesurfer/trac-paths"],
     "dmrirc_file": InputPathType,
     "log_file": typing.NotRequired[str | None],
     "no_log": bool,
@@ -29,42 +45,11 @@ TracPathsParameters = typing.TypedDict('TracPathsParameters', {
     "version": 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 {
-        "trac-paths": trac_paths_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 TracPathsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `trac_paths(...)`.
+    Output object returned when calling `TracPathsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -84,7 +69,7 @@ def trac_paths_params(
     dontrun: bool = False,
     version: bool = False,
     help_: bool = False,
-) -> TracPathsParameters:
+) -> TracPathsParametersTagged:
     """
     Build parameters.
     
@@ -109,7 +94,7 @@ def trac_paths_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "trac-paths",
+        "@type": "freesurfer/trac-paths",
         "dmrirc_file": dmrirc_file,
         "no_log": no_log,
         "no_cmd": no_cmd,
@@ -148,43 +133,43 @@ def trac_paths_cargs(
     cargs.append("trac-paths")
     cargs.extend([
         "-c",
-        execution.input_file(params.get("dmrirc_file"))
+        execution.input_file(params.get("dmrirc_file", None))
     ])
-    if params.get("log_file") is not None:
+    if params.get("log_file", None) is not None:
         cargs.extend([
             "-log",
-            params.get("log_file")
+            params.get("log_file", None)
         ])
-    if params.get("no_log"):
+    if params.get("no_log", False):
         cargs.append("-nolog")
-    if params.get("cmd_file") is not None:
+    if params.get("cmd_file", None) is not None:
         cargs.extend([
             "-cmd",
-            params.get("cmd_file")
+            params.get("cmd_file", None)
         ])
-    if params.get("no_cmd"):
+    if params.get("no_cmd", False):
         cargs.append("-nocmd")
-    if params.get("no_isrunning"):
+    if params.get("no_isrunning", False):
         cargs.append("-no-isrunning")
-    if params.get("umask") is not None:
+    if params.get("umask", None) is not None:
         cargs.extend([
             "-umask",
-            params.get("umask")
+            params.get("umask", None)
         ])
-    if params.get("group_id") is not None:
+    if params.get("group_id", None) is not None:
         cargs.extend([
             "-grp",
-            params.get("group_id")
+            params.get("group_id", None)
         ])
-    if params.get("allow_core_dump"):
+    if params.get("allow_core_dump", False):
         cargs.append("-allowcoredump")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-debug")
-    if params.get("dontrun"):
+    if params.get("dontrun", False):
         cargs.append("-dontrun")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-version")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -210,9 +195,11 @@ def trac_paths_outputs(
 
 def trac_paths_execute(
     params: TracPathsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TracPathsOutputs:
     """
+    trac-paths
+    
     Tractography for a single subject.
     
     Author: FreeSurfer Developers
@@ -221,10 +208,12 @@ def trac_paths_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TracPathsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TRAC_PATHS_METADATA)
     params = execution.params(params)
     cargs = trac_paths_cargs(params, execution)
     ret = trac_paths_outputs(params, execution)
@@ -249,6 +238,8 @@ def trac_paths(
     runner: Runner | None = None,
 ) -> TracPathsOutputs:
     """
+    trac-paths
+    
     Tractography for a single subject.
     
     Author: FreeSurfer Developers
@@ -276,8 +267,6 @@ def trac_paths(
     Returns:
         NamedTuple of outputs (described in `TracPathsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TRAC_PATHS_METADATA)
     params = trac_paths_params(
         dmrirc_file=dmrirc_file,
         log_file=log_file,
@@ -293,13 +282,13 @@ def trac_paths(
         version=version,
         help_=help_,
     )
-    return trac_paths_execute(params, execution)
+    return trac_paths_execute(params, runner)
 
 
 __all__ = [
     "TRAC_PATHS_METADATA",
     "TracPathsOutputs",
-    "TracPathsParameters",
     "trac_paths",
+    "trac_paths_execute",
     "trac_paths_params",
 ]