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

niwrap_freesurfer/freesurfer/long_submit_postproc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LONG_SUBMIT_POSTPROC_METADATA = Metadata(
-    id="9134aeb62a00f2309da855fdc314f3ded0379757.boutiques",
+    id="5a3c5834d2d418103170611462c8bcc41e050e60.boutiques",
     name="long_submit_postproc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ LONG_SUBMIT_POSTPROC_METADATA = Metadata(
 
 
 LongSubmitPostprocParameters = typing.TypedDict('LongSubmitPostprocParameters', {
-    "__STYXTYPE__": typing.Literal["long_submit_postproc"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/long_submit_postproc"]],
+    "qdec": InputPathType,
+    "prog": str,
+    "flags": typing.NotRequired[str | None],
+    "dir": typing.NotRequired[str | None],
+    "simulate": bool,
+    "pause": typing.NotRequired[float | None],
+    "max": typing.NotRequired[float | None],
+    "queue": typing.NotRequired[str | None],
+})
+LongSubmitPostprocParametersTagged = typing.TypedDict('LongSubmitPostprocParametersTagged', {
+    "@type": typing.Literal["freesurfer/long_submit_postproc"],
     "qdec": InputPathType,
     "prog": str,
     "flags": typing.NotRequired[str | None],
@@ -24,42 +35,11 @@ LongSubmitPostprocParameters = typing.TypedDict('LongSubmitPostprocParameters',
     "max": typing.NotRequired[float | None],
     "queue": 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_submit_postproc": long_submit_postproc_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 LongSubmitPostprocOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `long_submit_postproc(...)`.
+    Output object returned when calling `LongSubmitPostprocParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,10 +51,10 @@ def long_submit_postproc_params(
     flags: str | None = None,
     dir_: str | None = None,
     simulate: bool = False,
-    pause: float | None = 13,
-    max_: float | None = 100,
+    pause: float | None = None,
+    max_: float | None = None,
     queue_: str | None = None,
-) -> LongSubmitPostprocParameters:
+) -> LongSubmitPostprocParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +71,7 @@ def long_submit_postproc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "long_submit_postproc",
+        "@type": "freesurfer/long_submit_postproc",
         "qdec": qdec,
         "prog": prog,
         "simulate": simulate,
@@ -126,38 +106,38 @@ def long_submit_postproc_cargs(
     cargs.append("long_submit_postproc")
     cargs.extend([
         "--qdec",
-        execution.input_file(params.get("qdec"))
+        execution.input_file(params.get("qdec", None))
     ])
     cargs.extend([
         "--prog",
-        params.get("prog")
+        params.get("prog", None)
     ])
-    if params.get("flags") is not None:
+    if params.get("flags", None) is not None:
         cargs.extend([
             "--flags",
-            params.get("flags")
+            params.get("flags", None)
         ])
-    if params.get("dir") is not None:
+    if params.get("dir", None) is not None:
         cargs.extend([
             "--dir",
-            params.get("dir")
+            params.get("dir", None)
         ])
-    if params.get("simulate"):
+    if params.get("simulate", False):
         cargs.append("--simulate")
-    if params.get("pause") is not None:
+    if params.get("pause", None) is not None:
         cargs.extend([
             "--pause",
-            str(params.get("pause"))
+            str(params.get("pause", None))
         ])
-    if params.get("max") is not None:
+    if params.get("max", None) is not None:
         cargs.extend([
             "--max",
-            str(params.get("max"))
+            str(params.get("max", None))
         ])
-    if params.get("queue") is not None:
+    if params.get("queue", None) is not None:
         cargs.extend([
             "--queue",
-            params.get("queue")
+            params.get("queue", None)
         ])
     return cargs
 
@@ -183,9 +163,11 @@ def long_submit_postproc_outputs(
 
 def long_submit_postproc_execute(
     params: LongSubmitPostprocParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> LongSubmitPostprocOutputs:
     """
+    long_submit_postproc
+    
     Submits jobs to the cluster (either seychelles or launchpad at NMR) for
     longitudinal post-processing.
     
@@ -195,10 +177,12 @@ def long_submit_postproc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `LongSubmitPostprocOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LONG_SUBMIT_POSTPROC_METADATA)
     params = execution.params(params)
     cargs = long_submit_postproc_cargs(params, execution)
     ret = long_submit_postproc_outputs(params, execution)
@@ -212,12 +196,14 @@ def long_submit_postproc(
     flags: str | None = None,
     dir_: str | None = None,
     simulate: bool = False,
-    pause: float | None = 13,
-    max_: float | None = 100,
+    pause: float | None = None,
+    max_: float | None = None,
     queue_: str | None = None,
     runner: Runner | None = None,
 ) -> LongSubmitPostprocOutputs:
     """
+    long_submit_postproc
+    
     Submits jobs to the cluster (either seychelles or launchpad at NMR) for
     longitudinal post-processing.
     
@@ -238,8 +224,6 @@ def long_submit_postproc(
     Returns:
         NamedTuple of outputs (described in `LongSubmitPostprocOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LONG_SUBMIT_POSTPROC_METADATA)
     params = long_submit_postproc_params(
         qdec=qdec,
         prog=prog,
@@ -250,13 +234,13 @@ def long_submit_postproc(
         max_=max_,
         queue_=queue_,
     )
-    return long_submit_postproc_execute(params, execution)
+    return long_submit_postproc_execute(params, runner)
 
 
 __all__ = [
     "LONG_SUBMIT_POSTPROC_METADATA",
     "LongSubmitPostprocOutputs",
-    "LongSubmitPostprocParameters",
     "long_submit_postproc",
+    "long_submit_postproc_execute",
     "long_submit_postproc_params",
 ]

niwrap_freesurfer/freesurfer/longmc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LONGMC_METADATA = Metadata(
-    id="9c5dbdbd78fd37002556b682f478a737c506908c.boutiques",
+    id="8b8d473dc021d846b6f6add4166697d771e2be94.boutiques",
     name="longmc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ LONGMC_METADATA = Metadata(
 
 
 LongmcParameters = typing.TypedDict('LongmcParameters', {
-    "__STYXTYPE__": typing.Literal["longmc"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/longmc"]],
+    "cross_tp_name": str,
+    "base_name": str,
+    "conform_to_hires": bool,
+    "no_conform_to_hires": bool,
+    "subjects_dir": str,
+    "subject_name": typing.NotRequired[str | None],
+    "no_force_update": bool,
+})
+LongmcParametersTagged = typing.TypedDict('LongmcParametersTagged', {
+    "@type": typing.Literal["freesurfer/longmc"],
     "cross_tp_name": str,
     "base_name": str,
     "conform_to_hires": bool,
@@ -23,42 +33,11 @@ LongmcParameters = typing.TypedDict('LongmcParameters', {
     "subject_name": typing.NotRequired[str | None],
     "no_force_update": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "longmc": longmc_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 LongmcOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `longmc(...)`.
+    Output object returned when calling `LongmcParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,7 +51,7 @@ def longmc_params(
     no_conform_to_hires: bool = False,
     subject_name: str | None = None,
     no_force_update: bool = False,
-) -> LongmcParameters:
+) -> LongmcParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +67,7 @@ def longmc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "longmc",
+        "@type": "freesurfer/longmc",
         "cross_tp_name": cross_tp_name,
         "base_name": base_name,
         "conform_to_hires": conform_to_hires,
@@ -118,23 +97,23 @@ def longmc_cargs(
     cargs.append("longmc")
     cargs.extend([
         "-long",
-        params.get("cross_tp_name")
+        params.get("cross_tp_name", None)
     ])
-    cargs.append(params.get("base_name"))
-    if params.get("conform_to_hires"):
+    cargs.append(params.get("base_name", None))
+    if params.get("conform_to_hires", False):
         cargs.append("-conf2hires")
-    if params.get("no_conform_to_hires"):
+    if params.get("no_conform_to_hires", False):
         cargs.append("-no-conf2hires")
     cargs.extend([
         "-sd",
-        params.get("subjects_dir")
+        params.get("subjects_dir", 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("no_force_update"):
+    if params.get("no_force_update", False):
         cargs.append("-no-force-update")
     return cargs
 
@@ -160,11 +139,13 @@ def longmc_outputs(
 
 def longmc_execute(
     params: LongmcParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> LongmcOutputs:
     """
-    Perform motion correction for the longitudinal recon-all stream when creating
-    the longitudinal timepoint of a subject.
+    longmc
+    
+    Perform motion correction for the longitudinal recon-all stream when
+    creating the longitudinal timepoint of a subject.
     
     Author: FreeSurfer Developers
     
@@ -172,10 +153,12 @@ def longmc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `LongmcOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LONGMC_METADATA)
     params = execution.params(params)
     cargs = longmc_cargs(params, execution)
     ret = longmc_outputs(params, execution)
@@ -194,8 +177,10 @@ def longmc(
     runner: Runner | None = None,
 ) -> LongmcOutputs:
     """
-    Perform motion correction for the longitudinal recon-all stream when creating
-    the longitudinal timepoint of a subject.
+    longmc
+    
+    Perform motion correction for the longitudinal recon-all stream when
+    creating the longitudinal timepoint of a subject.
     
     Author: FreeSurfer Developers
     
@@ -213,8 +198,6 @@ def longmc(
     Returns:
         NamedTuple of outputs (described in `LongmcOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LONGMC_METADATA)
     params = longmc_params(
         cross_tp_name=cross_tp_name,
         base_name=base_name,
@@ -224,13 +207,13 @@ def longmc(
         subject_name=subject_name,
         no_force_update=no_force_update,
     )
-    return longmc_execute(params, execution)
+    return longmc_execute(params, runner)
 
 
 __all__ = [
     "LONGMC_METADATA",
     "LongmcOutputs",
-    "LongmcParameters",
     "longmc",
+    "longmc_execute",
     "longmc_params",
 ]

niwrap_freesurfer/freesurfer/lpcregister.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LPCREGISTER_METADATA = Metadata(
-    id="a83effe70fd200096fd005f862df8be1ea3a7e01.boutiques",
+    id="29afa985c94bdbcc43dae3f6ed825e4b0a32c8f9.boutiques",
     name="lpcregister",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,23 @@ LPCREGISTER_METADATA = Metadata(
 
 
 LpcregisterParameters = typing.TypedDict('LpcregisterParameters', {
-    "__STYXTYPE__": typing.Literal["lpcregister"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/lpcregister"]],
+    "subject_id": str,
+    "mov_volume": str,
+    "reg_file": str,
+    "dof_9": bool,
+    "dof_12": bool,
+    "frame_number": typing.NotRequired[float | None],
+    "mid_frame": bool,
+    "fsvol": typing.NotRequired[str | None],
+    "output_volume": typing.NotRequired[str | None],
+    "tmp_dir": typing.NotRequired[str | None],
+    "no_cleanup": bool,
+    "version": bool,
+    "help": bool,
+})
+LpcregisterParametersTagged = typing.TypedDict('LpcregisterParametersTagged', {
+    "@type": typing.Literal["freesurfer/lpcregister"],
     "subject_id": str,
     "mov_volume": str,
     "reg_file": str,
@@ -29,43 +45,11 @@ LpcregisterParameters = typing.TypedDict('LpcregisterParameters', {
     "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 {
-        "lpcregister": lpcregister_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 {
-        "lpcregister": lpcregister_outputs,
-    }.get(t)
 
 
 class LpcregisterOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `lpcregister(...)`.
+    Output object returned when calling `LpcregisterParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -89,7 +73,7 @@ def lpcregister_params(
     no_cleanup: bool = False,
     version: bool = False,
     help_: bool = False,
-) -> LpcregisterParameters:
+) -> LpcregisterParametersTagged:
     """
     Build parameters.
     
@@ -118,7 +102,7 @@ def lpcregister_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "lpcregister",
+        "@type": "freesurfer/lpcregister",
         "subject_id": subject_id,
         "mov_volume": mov_volume,
         "reg_file": reg_file,
@@ -157,47 +141,47 @@ def lpcregister_cargs(
     cargs.append("lpcregister")
     cargs.extend([
         "--s",
-        params.get("subject_id")
+        params.get("subject_id", None)
     ])
     cargs.extend([
         "--mov",
-        params.get("mov_volume")
+        params.get("mov_volume", None)
     ])
     cargs.extend([
         "--reg",
-        params.get("reg_file")
+        params.get("reg_file", None)
     ])
-    if params.get("dof_9"):
+    if params.get("dof_9", False):
         cargs.append("--9")
-    if params.get("dof_12"):
+    if params.get("dof_12", False):
         cargs.append("--12")
-    if params.get("frame_number") is not None:
+    if params.get("frame_number", None) is not None:
         cargs.extend([
             "--frame",
-            str(params.get("frame_number"))
+            str(params.get("frame_number", None))
         ])
-    if params.get("mid_frame"):
+    if params.get("mid_frame", False):
         cargs.append("--mid-frame")
-    if params.get("fsvol") is not None:
+    if params.get("fsvol", None) is not None:
         cargs.extend([
             "--fsvol",
-            params.get("fsvol")
+            params.get("fsvol", None)
         ])
-    if params.get("output_volume") is not None:
+    if params.get("output_volume", None) is not None:
         cargs.extend([
             "--o",
-            params.get("output_volume")
+            params.get("output_volume", 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("version"):
+    if params.get("version", False):
         cargs.append("--version")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
     return cargs
 
@@ -218,18 +202,21 @@ def lpcregister_outputs(
     ret = LpcregisterOutputs(
         root=execution.output_file("."),
         output_reg_file=execution.output_file("register.dat"),
-        resampled_volume=execution.output_file(params.get("output_volume")) if (params.get("output_volume") is not None) else None,
+        resampled_volume=execution.output_file(params.get("output_volume", None)) if (params.get("output_volume") is not None) else None,
     )
     return ret
 
 
 def lpcregister_execute(
     params: LpcregisterParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> LpcregisterOutputs:
     """
-    Registers a volume to its FreeSurfer anatomical using Local Pearson Correlation
-    (LPC) (the AFNI lpc_align.py program). Creates a FreeSurfer register.dat file.
+    lpcregister
+    
+    Registers a volume to its FreeSurfer anatomical using Local Pearson
+    Correlation (LPC) (the AFNI lpc_align.py program). Creates a FreeSurfer
+    register.dat file.
     
     Author: FreeSurfer Developers
     
@@ -237,10 +224,12 @@ def lpcregister_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `LpcregisterOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LPCREGISTER_METADATA)
     params = execution.params(params)
     cargs = lpcregister_cargs(params, execution)
     ret = lpcregister_outputs(params, execution)
@@ -265,8 +254,11 @@ def lpcregister(
     runner: Runner | None = None,
 ) -> LpcregisterOutputs:
     """
-    Registers a volume to its FreeSurfer anatomical using Local Pearson Correlation
-    (LPC) (the AFNI lpc_align.py program). Creates a FreeSurfer register.dat file.
+    lpcregister
+    
+    Registers a volume to its FreeSurfer anatomical using Local Pearson
+    Correlation (LPC) (the AFNI lpc_align.py program). Creates a FreeSurfer
+    register.dat file.
     
     Author: FreeSurfer Developers
     
@@ -297,8 +289,6 @@ def lpcregister(
     Returns:
         NamedTuple of outputs (described in `LpcregisterOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LPCREGISTER_METADATA)
     params = lpcregister_params(
         subject_id=subject_id,
         mov_volume=mov_volume,
@@ -314,13 +304,13 @@ def lpcregister(
         version=version,
         help_=help_,
     )
-    return lpcregister_execute(params, execution)
+    return lpcregister_execute(params, runner)
 
 
 __all__ = [
     "LPCREGISTER_METADATA",
     "LpcregisterOutputs",
-    "LpcregisterParameters",
     "lpcregister",
+    "lpcregister_execute",
     "lpcregister_params",
 ]