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

niwrap_freesurfer/freesurfer/fsl_sub_mgh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FSL_SUB_MGH_METADATA = Metadata(
-    id="4015aeacaae283d33f0b4ca8406dbe45c4046304.boutiques",
+    id="aaa5591e718a6ff9223763df97592b37eb4d5fc1.boutiques",
     name="fsl_sub_mgh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,23 @@ FSL_SUB_MGH_METADATA = Metadata(
 
 
 FslSubMghParameters = typing.TypedDict('FslSubMghParameters', {
-    "__STYXTYPE__": typing.Literal["fsl_sub_mgh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fsl_sub_mgh"]],
+    "estimated_time": typing.NotRequired[int | None],
+    "queue_name": typing.NotRequired[str | None],
+    "architecture": typing.NotRequired[str | None],
+    "job_priority": typing.NotRequired[int | None],
+    "email_address": typing.NotRequired[str | None],
+    "hold_job": typing.NotRequired[str | None],
+    "task_file": typing.NotRequired[InputPathType | None],
+    "job_name": typing.NotRequired[str | None],
+    "log_dir": typing.NotRequired[str | None],
+    "mail_options": typing.NotRequired[str | None],
+    "flags_in_scripts": bool,
+    "verbose": bool,
+    "shell_path": typing.NotRequired[str | None],
+})
+FslSubMghParametersTagged = typing.TypedDict('FslSubMghParametersTagged', {
+    "@type": typing.Literal["freesurfer/fsl_sub_mgh"],
     "estimated_time": typing.NotRequired[int | None],
     "queue_name": typing.NotRequired[str | None],
     "architecture": typing.NotRequired[str | None],
@@ -29,42 +45,11 @@ FslSubMghParameters = typing.TypedDict('FslSubMghParameters', {
     "verbose": bool,
     "shell_path": 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 {
-        "fsl_sub_mgh": fsl_sub_mgh_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 FslSubMghOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fsl_sub_mgh(...)`.
+    Output object returned when calling `FslSubMghParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,10 +57,10 @@ class FslSubMghOutputs(typing.NamedTuple):
 
 def fsl_sub_mgh_params(
     estimated_time: int | None = None,
-    queue_name: str | None = "long.q",
+    queue_name: str | None = None,
     architecture: str | None = None,
-    job_priority: int | None = 0,
-    email_address: str | None = "root@fmrib.ox.ac.uk",
+    job_priority: int | None = None,
+    email_address: str | None = None,
     hold_job: str | None = None,
     task_file: InputPathType | None = None,
     job_name: str | None = None,
@@ -84,7 +69,7 @@ def fsl_sub_mgh_params(
     flags_in_scripts: bool = False,
     verbose: bool = False,
     shell_path: str | None = None,
-) -> FslSubMghParameters:
+) -> FslSubMghParametersTagged:
     """
     Build parameters.
     
@@ -110,7 +95,7 @@ def fsl_sub_mgh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fsl_sub_mgh",
+        "@type": "freesurfer/fsl_sub_mgh",
         "flags_in_scripts": flags_in_scripts,
         "verbose": verbose,
     }
@@ -154,64 +139,64 @@ def fsl_sub_mgh_cargs(
     """
     cargs = []
     cargs.append("fsl_sub_mgh")
-    if params.get("estimated_time") is not None:
+    if params.get("estimated_time", None) is not None:
         cargs.extend([
             "-T",
-            str(params.get("estimated_time"))
+            str(params.get("estimated_time", None))
         ])
-    if params.get("queue_name") is not None:
+    if params.get("queue_name", None) is not None:
         cargs.extend([
             "-q",
-            params.get("queue_name")
+            params.get("queue_name", None)
         ])
-    if params.get("architecture") is not None:
+    if params.get("architecture", None) is not None:
         cargs.extend([
             "-a",
-            params.get("architecture")
+            params.get("architecture", None)
         ])
-    if params.get("job_priority") is not None:
+    if params.get("job_priority", None) is not None:
         cargs.extend([
             "-p",
-            str(params.get("job_priority"))
+            str(params.get("job_priority", None))
         ])
-    if params.get("email_address") is not None:
+    if params.get("email_address", None) is not None:
         cargs.extend([
             "-M",
-            params.get("email_address")
+            params.get("email_address", None)
         ])
-    if params.get("hold_job") is not None:
+    if params.get("hold_job", None) is not None:
         cargs.extend([
             "-j",
-            params.get("hold_job")
+            params.get("hold_job", None)
         ])
-    if params.get("task_file") is not None:
+    if params.get("task_file", None) is not None:
         cargs.extend([
             "-t",
-            execution.input_file(params.get("task_file"))
+            execution.input_file(params.get("task_file", None))
         ])
-    if params.get("job_name") is not None:
+    if params.get("job_name", None) is not None:
         cargs.extend([
             "-N",
-            params.get("job_name")
+            params.get("job_name", None)
         ])
-    if params.get("log_dir") is not None:
+    if params.get("log_dir", None) is not None:
         cargs.extend([
             "-l",
-            params.get("log_dir")
+            params.get("log_dir", None)
         ])
-    if params.get("mail_options") is not None:
+    if params.get("mail_options", None) is not None:
         cargs.extend([
             "-m",
-            params.get("mail_options")
+            params.get("mail_options", None)
         ])
-    if params.get("flags_in_scripts"):
+    if params.get("flags_in_scripts", False):
         cargs.append("-F")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-v")
-    if params.get("shell_path") is not None:
+    if params.get("shell_path", None) is not None:
         cargs.extend([
             "-s",
-            params.get("shell_path")
+            params.get("shell_path", None)
         ])
     return cargs
 
@@ -237,11 +222,13 @@ def fsl_sub_mgh_outputs(
 
 def fsl_sub_mgh_execute(
     params: FslSubMghParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FslSubMghOutputs:
     """
-    Wrapper for job control system such as SGE, modified for compatibility with the
-    PBS queueing system.
+    fsl_sub_mgh
+    
+    Wrapper for job control system such as SGE, modified for compatibility with
+    the PBS queueing system.
     
     Author: FreeSurfer Developers
     
@@ -249,10 +236,12 @@ def fsl_sub_mgh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FslSubMghOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FSL_SUB_MGH_METADATA)
     params = execution.params(params)
     cargs = fsl_sub_mgh_cargs(params, execution)
     ret = fsl_sub_mgh_outputs(params, execution)
@@ -262,10 +251,10 @@ def fsl_sub_mgh_execute(
 
 def fsl_sub_mgh(
     estimated_time: int | None = None,
-    queue_name: str | None = "long.q",
+    queue_name: str | None = None,
     architecture: str | None = None,
-    job_priority: int | None = 0,
-    email_address: str | None = "root@fmrib.ox.ac.uk",
+    job_priority: int | None = None,
+    email_address: str | None = None,
     hold_job: str | None = None,
     task_file: InputPathType | None = None,
     job_name: str | None = None,
@@ -277,8 +266,10 @@ def fsl_sub_mgh(
     runner: Runner | None = None,
 ) -> FslSubMghOutputs:
     """
-    Wrapper for job control system such as SGE, modified for compatibility with the
-    PBS queueing system.
+    fsl_sub_mgh
+    
+    Wrapper for job control system such as SGE, modified for compatibility with
+    the PBS queueing system.
     
     Author: FreeSurfer Developers
     
@@ -306,8 +297,6 @@ def fsl_sub_mgh(
     Returns:
         NamedTuple of outputs (described in `FslSubMghOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSL_SUB_MGH_METADATA)
     params = fsl_sub_mgh_params(
         estimated_time=estimated_time,
         queue_name=queue_name,
@@ -323,13 +312,13 @@ def fsl_sub_mgh(
         verbose=verbose,
         shell_path=shell_path,
     )
-    return fsl_sub_mgh_execute(params, execution)
+    return fsl_sub_mgh_execute(params, runner)
 
 
 __all__ = [
     "FSL_SUB_MGH_METADATA",
     "FslSubMghOutputs",
-    "FslSubMghParameters",
     "fsl_sub_mgh",
+    "fsl_sub_mgh_execute",
     "fsl_sub_mgh_params",
 ]

niwrap_freesurfer/freesurfer/fslregister.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FSLREGISTER_METADATA = Metadata(
-    id="9ec9754c04caff23125f7deb97b579d2e3e28e25.boutiques",
+    id="6bd3805871440ca11998e2002e3f8711494bc7d6.boutiques",
     name="fslregister",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,40 @@ FSLREGISTER_METADATA = Metadata(
 
 
 FslregisterParameters = typing.TypedDict('FslregisterParameters', {
-    "__STYXTYPE__": typing.Literal["fslregister"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fslregister"]],
+    "subjid": str,
+    "mov_vol": str,
+    "reg_file": str,
+    "fsl_matrix": typing.NotRequired[str | None],
+    "init_fsl_matrix": typing.NotRequired[str | None],
+    "no_init_xfm": bool,
+    "niters": typing.NotRequired[float | None],
+    "dof": typing.NotRequired[float | None],
+    "bins": typing.NotRequired[float | None],
+    "cost": typing.NotRequired[str | None],
+    "max_angle": typing.NotRequired[float | None],
+    "no_new_schedule": bool,
+    "no_allow_swap": bool,
+    "no_trans": bool,
+    "bet_mov": bool,
+    "bet_fvalue": typing.NotRequired[float | None],
+    "bet_func": bool,
+    "bet_ref": bool,
+    "frame": typing.NotRequired[float | None],
+    "mid_frame": bool,
+    "freesurfer_volume": typing.NotRequired[str | None],
+    "template_output": typing.NotRequired[str | None],
+    "output_volume": typing.NotRequired[str | None],
+    "verbose": typing.NotRequired[float | None],
+    "tmp_dir": typing.NotRequired[str | None],
+    "no_cleanup": bool,
+    "no_log": bool,
+    "version": bool,
+    "help": bool,
+    "lta_format": typing.NotRequired[str | None],
+})
+FslregisterParametersTagged = typing.TypedDict('FslregisterParametersTagged', {
+    "@type": typing.Literal["freesurfer/fslregister"],
     "subjid": str,
     "mov_vol": str,
     "reg_file": str,
@@ -46,43 +79,11 @@ FslregisterParameters = typing.TypedDict('FslregisterParameters', {
     "help": bool,
     "lta_format": 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 {
-        "fslregister": fslregister_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 {
-        "fslregister": fslregister_outputs,
-    }.get(t)
 
 
 class FslregisterOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fslregister(...)`.
+    Output object returned when calling `FslregisterParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -129,7 +130,7 @@ def fslregister_params(
     version: bool = False,
     help_: bool = False,
     lta_format: str | None = None,
-) -> FslregisterParameters:
+) -> FslregisterParametersTagged:
     """
     Build parameters.
     
@@ -169,7 +170,7 @@ def fslregister_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fslregister",
+        "@type": "freesurfer/fslregister",
         "subjid": subjid,
         "mov_vol": mov_vol,
         "reg_file": reg_file,
@@ -236,114 +237,114 @@ def fslregister_cargs(
     cargs.append("fslregister")
     cargs.extend([
         "--s",
-        params.get("subjid")
+        params.get("subjid", None)
     ])
     cargs.extend([
         "--mov",
-        params.get("mov_vol")
+        params.get("mov_vol", None)
     ])
     cargs.extend([
         "--reg",
-        params.get("reg_file")
+        params.get("reg_file", None)
     ])
-    if params.get("fsl_matrix") is not None:
+    if params.get("fsl_matrix", None) is not None:
         cargs.extend([
             "--fslmat",
-            params.get("fsl_matrix")
+            params.get("fsl_matrix", None)
         ])
-    if params.get("init_fsl_matrix") is not None:
+    if params.get("init_fsl_matrix", None) is not None:
         cargs.extend([
             "--initfslmat",
-            params.get("init_fsl_matrix")
+            params.get("init_fsl_matrix", None)
         ])
-    if params.get("no_init_xfm"):
+    if params.get("no_init_xfm", False):
         cargs.append("--noinitxfm")
-    if params.get("niters") is not None:
+    if params.get("niters", None) is not None:
         cargs.extend([
             "--niters",
-            str(params.get("niters"))
+            str(params.get("niters", None))
         ])
-    if params.get("dof") is not None:
+    if params.get("dof", None) is not None:
         cargs.extend([
             "--dof",
-            str(params.get("dof"))
+            str(params.get("dof", None))
         ])
-    if params.get("bins") is not None:
+    if params.get("bins", None) is not None:
         cargs.extend([
             "--bins",
-            str(params.get("bins"))
+            str(params.get("bins", None))
         ])
-    if params.get("cost") is not None:
+    if params.get("cost", None) is not None:
         cargs.extend([
             "--cost",
-            params.get("cost")
+            params.get("cost", None)
         ])
-    if params.get("max_angle") is not None:
+    if params.get("max_angle", None) is not None:
         cargs.extend([
             "--maxangle",
-            str(params.get("max_angle"))
+            str(params.get("max_angle", None))
         ])
-    if params.get("no_new_schedule"):
+    if params.get("no_new_schedule", False):
         cargs.append("--no-new-schedule")
-    if params.get("no_allow_swap"):
+    if params.get("no_allow_swap", False):
         cargs.append("--no-allow-swap")
-    if params.get("no_trans"):
+    if params.get("no_trans", False):
         cargs.append("--no-trans")
-    if params.get("bet_mov"):
+    if params.get("bet_mov", False):
         cargs.append("--betmov")
-    if params.get("bet_fvalue") is not None:
+    if params.get("bet_fvalue", None) is not None:
         cargs.extend([
             "--betfvalue",
-            str(params.get("bet_fvalue"))
+            str(params.get("bet_fvalue", None))
         ])
-    if params.get("bet_func"):
+    if params.get("bet_func", False):
         cargs.append("--betfunc")
-    if params.get("bet_ref"):
+    if params.get("bet_ref", False):
         cargs.append("--betref")
-    if params.get("frame") is not None:
+    if params.get("frame", None) is not None:
         cargs.extend([
             "--frame",
-            str(params.get("frame"))
+            str(params.get("frame", None))
         ])
-    if params.get("mid_frame"):
+    if params.get("mid_frame", False):
         cargs.append("--mid-frame")
-    if params.get("freesurfer_volume") is not None:
+    if params.get("freesurfer_volume", None) is not None:
         cargs.extend([
             "--fsvol",
-            params.get("freesurfer_volume")
+            params.get("freesurfer_volume", None)
         ])
-    if params.get("template_output") is not None:
+    if params.get("template_output", None) is not None:
         cargs.extend([
             "--template-out",
-            params.get("template_output")
+            params.get("template_output", None)
         ])
-    if params.get("output_volume") is not None:
+    if params.get("output_volume", None) is not None:
         cargs.extend([
             "--out",
-            params.get("output_volume")
+            params.get("output_volume", None)
         ])
-    if params.get("verbose") is not None:
+    if params.get("verbose", None) is not None:
         cargs.extend([
             "--verbose",
-            str(params.get("verbose"))
+            str(params.get("verbose", None))
         ])
-    if params.get("tmp_dir") is not None:
+    if params.get("tmp_dir", None) is not None:
         cargs.extend([
             "--tmp",
-            params.get("tmp_dir")
+            params.get("tmp_dir", None)
         ])
-    if params.get("no_cleanup"):
+    if params.get("no_cleanup", False):
         cargs.append("--nocleanup")
-    if params.get("no_log"):
+    if params.get("no_log", False):
         cargs.append("--nolog")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
-    if params.get("lta_format") is not None:
+    if params.get("lta_format", None) is not None:
         cargs.extend([
             "--lta",
-            params.get("lta_format")
+            params.get("lta_format", None)
         ])
     return cargs
 
@@ -363,22 +364,24 @@ def fslregister_outputs(
     """
     ret = FslregisterOutputs(
         root=execution.output_file("."),
-        output_reg_file=execution.output_file(params.get("reg_file")),
-        output_resliced_volume=execution.output_file(params.get("output_volume")) if (params.get("output_volume") is not None) else None,
-        output_fsl_matrix=execution.output_file(params.get("fsl_matrix")) if (params.get("fsl_matrix") is not None) else None,
-        lta_output=execution.output_file(params.get("lta_format")) if (params.get("lta_format") is not None) else None,
-        output_template=execution.output_file(params.get("template_output")) if (params.get("template_output") is not None) else None,
+        output_reg_file=execution.output_file(params.get("reg_file", None)),
+        output_resliced_volume=execution.output_file(params.get("output_volume", None)) if (params.get("output_volume") is not None) else None,
+        output_fsl_matrix=execution.output_file(params.get("fsl_matrix", None)) if (params.get("fsl_matrix") is not None) else None,
+        lta_output=execution.output_file(params.get("lta_format", None)) if (params.get("lta_format") is not None) else None,
+        output_template=execution.output_file(params.get("template_output", None)) if (params.get("template_output") is not None) else None,
     )
     return ret
 
 
 def fslregister_execute(
     params: FslregisterParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FslregisterOutputs:
     """
-    Registers a volume to its FreeSurfer anatomical using FSL's FLIRT and creates a
-    FreeSurfer register.dat file.
+    fslregister
+    
+    Registers a volume to its FreeSurfer anatomical using FSL's FLIRT and
+    creates a FreeSurfer register.dat file.
     
     Author: FreeSurfer Developers
     
@@ -386,10 +389,12 @@ def fslregister_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FslregisterOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FSLREGISTER_METADATA)
     params = execution.params(params)
     cargs = fslregister_cargs(params, execution)
     ret = fslregister_outputs(params, execution)
@@ -431,8 +436,10 @@ def fslregister(
     runner: Runner | None = None,
 ) -> FslregisterOutputs:
     """
-    Registers a volume to its FreeSurfer anatomical using FSL's FLIRT and creates a
-    FreeSurfer register.dat file.
+    fslregister
+    
+    Registers a volume to its FreeSurfer anatomical using FSL's FLIRT and
+    creates a FreeSurfer register.dat file.
     
     Author: FreeSurfer Developers
     
@@ -474,8 +481,6 @@ def fslregister(
     Returns:
         NamedTuple of outputs (described in `FslregisterOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSLREGISTER_METADATA)
     params = fslregister_params(
         subjid=subjid,
         mov_vol=mov_vol,
@@ -508,13 +513,13 @@ def fslregister(
         help_=help_,
         lta_format=lta_format,
     )
-    return fslregister_execute(params, execution)
+    return fslregister_execute(params, runner)
 
 
 __all__ = [
     "FSLREGISTER_METADATA",
     "FslregisterOutputs",
-    "FslregisterParameters",
     "fslregister",
+    "fslregister_execute",
     "fslregister_params",
 ]