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

niwrap_freesurfer/freesurfer/gca_apply.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 GCA_APPLY_METADATA = Metadata(
-    id="3eeb1cba1d7c8f0e6b004894e26c4716c5d93e5d.boutiques",
+    id="694182fb584f9038ebca1a169c46117c3e0d43c0.boutiques",
     name="gca-apply",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,28 @@ GCA_APPLY_METADATA = Metadata(
 
 
 GcaApplyParameters = typing.TypedDict('GcaApplyParameters', {
-    "__STYXTYPE__": typing.Literal["gca-apply"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/gca-apply"]],
+    "gcafile": InputPathType,
+    "subject": str,
+    "nthreads": typing.NotRequired[float | None],
+    "base": typing.NotRequired[str | None],
+    "no_segstats": bool,
+    "subjects_dir": typing.NotRequired[str | None],
+    "dice_seg": typing.NotRequired[str | None],
+    "dice_file": typing.NotRequired[str | None],
+    "lta": typing.NotRequired[InputPathType | None],
+    "norm": typing.NotRequired[InputPathType | None],
+    "input_mgz": typing.NotRequired[InputPathType | None],
+    "brainmask": typing.NotRequired[InputPathType | None],
+    "output_dir": typing.NotRequired[str | None],
+    "no_v6labopts": bool,
+    "m3z_file": typing.NotRequired[InputPathType | None],
+    "gca_rb_2016": bool,
+    "force_update": bool,
+    "gcareg_iters": typing.NotRequired[float | None],
+})
+GcaApplyParametersTagged = typing.TypedDict('GcaApplyParametersTagged', {
+    "@type": typing.Literal["freesurfer/gca-apply"],
     "gcafile": InputPathType,
     "subject": str,
     "nthreads": typing.NotRequired[float | None],
@@ -34,43 +55,11 @@ GcaApplyParameters = typing.TypedDict('GcaApplyParameters', {
     "force_update": bool,
     "gcareg_iters": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "gca-apply": gca_apply_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 {
-        "gca-apply": gca_apply_outputs,
-    }.get(t)
 
 
 class GcaApplyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `gca_apply(...)`.
+    Output object returned when calling `GcaApplyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -105,7 +94,7 @@ def gca_apply_params(
     gca_rb_2016: bool = False,
     force_update: bool = False,
     gcareg_iters: float | None = None,
-) -> GcaApplyParameters:
+) -> GcaApplyParametersTagged:
     """
     Build parameters.
     
@@ -133,7 +122,7 @@ def gca_apply_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "gca-apply",
+        "@type": "freesurfer/gca-apply",
         "gcafile": gcafile,
         "subject": subject,
         "no_segstats": no_segstats,
@@ -185,73 +174,73 @@ def gca_apply_cargs(
     cargs.append("gca-apply")
     cargs.extend([
         "-apply",
-        execution.input_file(params.get("gcafile"))
+        execution.input_file(params.get("gcafile", None))
     ])
-    cargs.append(params.get("subject"))
-    if params.get("nthreads") is not None:
+    cargs.append(params.get("subject", None))
+    if params.get("nthreads", None) is not None:
         cargs.extend([
             "--nthreads",
-            str(params.get("nthreads"))
+            str(params.get("nthreads", None))
         ])
-    if params.get("base") is not None:
+    if params.get("base", None) is not None:
         cargs.extend([
             "--base",
-            params.get("base")
+            params.get("base", None)
         ])
-    if params.get("no_segstats"):
+    if params.get("no_segstats", False):
         cargs.append("--no-segstats")
-    if params.get("subjects_dir") is not None:
+    if params.get("subjects_dir", None) is not None:
         cargs.extend([
             "--sd",
-            params.get("subjects_dir")
+            params.get("subjects_dir", None)
         ])
-    if params.get("dice_seg") is not None:
+    if params.get("dice_seg", None) is not None:
         cargs.extend([
             "--dice",
-            params.get("dice_seg")
+            params.get("dice_seg", None)
         ])
-    if params.get("dice_file") is not None:
-        cargs.append(params.get("dice_file"))
-    if params.get("lta") is not None:
+    if params.get("dice_file", None) is not None:
+        cargs.append(params.get("dice_file", None))
+    if params.get("lta", None) is not None:
         cargs.extend([
             "--lta",
-            execution.input_file(params.get("lta"))
+            execution.input_file(params.get("lta", None))
         ])
-    if params.get("norm") is not None:
+    if params.get("norm", None) is not None:
         cargs.extend([
             "--norm",
-            execution.input_file(params.get("norm"))
+            execution.input_file(params.get("norm", None))
         ])
-    if params.get("input_mgz") is not None:
+    if params.get("input_mgz", None) is not None:
         cargs.extend([
             "--input",
-            execution.input_file(params.get("input_mgz"))
+            execution.input_file(params.get("input_mgz", None))
         ])
-    if params.get("brainmask") is not None:
+    if params.get("brainmask", None) is not None:
         cargs.extend([
             "--brainmask",
-            execution.input_file(params.get("brainmask"))
+            execution.input_file(params.get("brainmask", None))
         ])
-    if params.get("output_dir") is not None:
+    if params.get("output_dir", None) is not None:
         cargs.extend([
             "--o",
-            params.get("output_dir")
+            params.get("output_dir", None)
         ])
-    if params.get("no_v6labopts"):
+    if params.get("no_v6labopts", False):
         cargs.append("--no-v6labopts")
-    if params.get("m3z_file") is not None:
+    if params.get("m3z_file", None) is not None:
         cargs.extend([
             "--m3z",
-            execution.input_file(params.get("m3z_file"))
+            execution.input_file(params.get("m3z_file", None))
         ])
-    if params.get("gca_rb_2016"):
+    if params.get("gca_rb_2016", False):
         cargs.append("--gca-rb-2016")
-    if params.get("force_update"):
+    if params.get("force_update", False):
         cargs.append("--force-update")
-    if params.get("gcareg_iters") is not None:
+    if params.get("gcareg_iters", None) is not None:
         cargs.extend([
             "--gcareg-iters",
-            str(params.get("gcareg_iters"))
+            str(params.get("gcareg_iters", None))
         ])
     return cargs
 
@@ -271,20 +260,22 @@ def gca_apply_outputs(
     """
     ret = GcaApplyOutputs(
         root=execution.output_file("."),
-        output_lta=execution.output_file(params.get("base") + ".lta") if (params.get("base") is not None) else None,
-        output_m3z=execution.output_file(params.get("base") + ".m3z") if (params.get("base") is not None) else None,
-        normalized_gca=execution.output_file("norm." + params.get("base") + ".mgz") if (params.get("base") is not None) else None,
-        segmented_gca=execution.output_file(params.get("base") + ".aseg.mgz") if (params.get("base") is not None) else None,
-        stats_output=execution.output_file(params.get("base") + ".stats") if (params.get("base") is not None) else None,
+        output_lta=execution.output_file(params.get("base", None) + ".lta") if (params.get("base") is not None) else None,
+        output_m3z=execution.output_file(params.get("base", None) + ".m3z") if (params.get("base") is not None) else None,
+        normalized_gca=execution.output_file("norm." + params.get("base", None) + ".mgz") if (params.get("base") is not None) else None,
+        segmented_gca=execution.output_file(params.get("base", None) + ".aseg.mgz") if (params.get("base") is not None) else None,
+        stats_output=execution.output_file(params.get("base", None) + ".stats") if (params.get("base") is not None) else None,
     )
     return ret
 
 
 def gca_apply_execute(
     params: GcaApplyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> GcaApplyOutputs:
     """
+    gca-apply
+    
     Applies a GCA, performing the steps of mri_em_register, mri_ca_normalize,
     mri_ca_register, and mri_ca_label. This script replicates the stages in
     recon-all without overwriting files.
@@ -295,10 +286,12 @@ def gca_apply_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `GcaApplyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(GCA_APPLY_METADATA)
     params = execution.params(params)
     cargs = gca_apply_cargs(params, execution)
     ret = gca_apply_outputs(params, execution)
@@ -328,6 +321,8 @@ def gca_apply(
     runner: Runner | None = None,
 ) -> GcaApplyOutputs:
     """
+    gca-apply
+    
     Applies a GCA, performing the steps of mri_em_register, mri_ca_normalize,
     mri_ca_register, and mri_ca_label. This script replicates the stages in
     recon-all without overwriting files.
@@ -360,8 +355,6 @@ def gca_apply(
     Returns:
         NamedTuple of outputs (described in `GcaApplyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(GCA_APPLY_METADATA)
     params = gca_apply_params(
         gcafile=gcafile,
         subject=subject,
@@ -382,13 +375,13 @@ def gca_apply(
         force_update=force_update,
         gcareg_iters=gcareg_iters,
     )
-    return gca_apply_execute(params, execution)
+    return gca_apply_execute(params, runner)
 
 
 __all__ = [
     "GCA_APPLY_METADATA",
     "GcaApplyOutputs",
-    "GcaApplyParameters",
     "gca_apply",
+    "gca_apply_execute",
     "gca_apply_params",
 ]

niwrap_freesurfer/freesurfer/gcainit.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 GCAINIT_METADATA = Metadata(
-    id="00dfdd96c6b86f2b1c5b47fc4b41253a5bcd0e9f.boutiques",
+    id="7a2fe85ce0a55a53579f1c2b93d5c87e23c74e9b.boutiques",
     name="gcainit",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ GCAINIT_METADATA = Metadata(
 
 
 GcainitParameters = typing.TypedDict('GcainitParameters', {
-    "__STYXTYPE__": typing.Literal["gcainit"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/gcainit"]],
+    "gcadir": str,
+})
+GcainitParametersTagged = typing.TypedDict('GcainitParametersTagged', {
+    "@type": typing.Literal["freesurfer/gcainit"],
     "gcadir": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "gcainit": gcainit_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 GcainitOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `gcainit(...)`.
+    Output object returned when calling `GcainitParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class GcainitOutputs(typing.NamedTuple):
 
 def gcainit_params(
     gcadir: str,
-) -> GcainitParameters:
+) -> GcainitParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def gcainit_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "gcainit",
+        "@type": "freesurfer/gcainit",
         "gcadir": gcadir,
     }
     return params
@@ -93,7 +66,7 @@ def gcainit_cargs(
     cargs.append("gcainit")
     cargs.extend([
         "--g",
-        params.get("gcadir")
+        params.get("gcadir", None)
     ])
     return cargs
 
@@ -119,9 +92,11 @@ def gcainit_outputs(
 
 def gcainit_execute(
     params: GcainitParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> GcainitOutputs:
     """
+    gcainit
+    
     Initializes the GCA for brain processing tasks.
     
     Author: FreeSurfer Developers
@@ -130,10 +105,12 @@ def gcainit_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `GcainitOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(GCAINIT_METADATA)
     params = execution.params(params)
     cargs = gcainit_cargs(params, execution)
     ret = gcainit_outputs(params, execution)
@@ -146,6 +123,8 @@ def gcainit(
     runner: Runner | None = None,
 ) -> GcainitOutputs:
     """
+    gcainit
+    
     Initializes the GCA for brain processing tasks.
     
     Author: FreeSurfer Developers
@@ -158,18 +137,16 @@ def gcainit(
     Returns:
         NamedTuple of outputs (described in `GcainitOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(GCAINIT_METADATA)
     params = gcainit_params(
         gcadir=gcadir,
     )
-    return gcainit_execute(params, execution)
+    return gcainit_execute(params, runner)
 
 
 __all__ = [
     "GCAINIT_METADATA",
     "GcainitOutputs",
-    "GcainitParameters",
     "gcainit",
+    "gcainit_execute",
     "gcainit_params",
 ]

niwrap_freesurfer/freesurfer/gcaprepone.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 GCAPREPONE_METADATA = Metadata(
-    id="fea37ea95fe10bc19c820f21259071fe7046f12d.boutiques",
+    id="940518fccb866cf95e928c8f745beb1878a0cb61.boutiques",
     name="gcaprepone",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ GCAPREPONE_METADATA = Metadata(
 
 
 GcapreponeParameters = typing.TypedDict('GcapreponeParameters', {
-    "__STYXTYPE__": typing.Literal["gcaprepone"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/gcaprepone"]],
+    "gcadir": str,
+    "subject": str,
+    "init_subject": bool,
+    "source_subjects_dir": str,
+    "done_file": str,
+    "no_emreg": bool,
+})
+GcapreponeParametersTagged = typing.TypedDict('GcapreponeParametersTagged', {
+    "@type": typing.Literal["freesurfer/gcaprepone"],
     "gcadir": str,
     "subject": str,
     "init_subject": bool,
@@ -22,42 +31,11 @@ GcapreponeParameters = typing.TypedDict('GcapreponeParameters', {
     "done_file": str,
     "no_emreg": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "gcaprepone": gcaprepone_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 GcapreponeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `gcaprepone(...)`.
+    Output object returned when calling `GcapreponeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def gcaprepone_params(
     done_file: str,
     init_subject: bool = False,
     no_emreg: bool = False,
-) -> GcapreponeParameters:
+) -> GcapreponeParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +63,7 @@ def gcaprepone_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "gcaprepone",
+        "@type": "freesurfer/gcaprepone",
         "gcadir": gcadir,
         "subject": subject,
         "init_subject": init_subject,
@@ -113,23 +91,23 @@ def gcaprepone_cargs(
     cargs.append("gcaprepone")
     cargs.extend([
         "--o",
-        params.get("gcadir")
+        params.get("gcadir", None)
     ])
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("init_subject"):
+    if params.get("init_subject", False):
         cargs.append("--init-subject")
     cargs.extend([
         "--sd",
-        params.get("source_subjects_dir")
+        params.get("source_subjects_dir", None)
     ])
     cargs.extend([
         "--done",
-        params.get("done_file")
+        params.get("done_file", None)
     ])
-    if params.get("no_emreg"):
+    if params.get("no_emreg", False):
         cargs.append("--no-emreg")
     return cargs
 
@@ -155,9 +133,11 @@ def gcaprepone_outputs(
 
 def gcaprepone_execute(
     params: GcapreponeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> GcapreponeOutputs:
     """
+    gcaprepone
+    
     Tool for preparing FreeSurfer subjects for use with group-wise template
     generation.
     
@@ -167,10 +147,12 @@ def gcaprepone_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `GcapreponeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(GCAPREPONE_METADATA)
     params = execution.params(params)
     cargs = gcaprepone_cargs(params, execution)
     ret = gcaprepone_outputs(params, execution)
@@ -188,6 +170,8 @@ def gcaprepone(
     runner: Runner | None = None,
 ) -> GcapreponeOutputs:
     """
+    gcaprepone
+    
     Tool for preparing FreeSurfer subjects for use with group-wise template
     generation.
     
@@ -206,8 +190,6 @@ def gcaprepone(
     Returns:
         NamedTuple of outputs (described in `GcapreponeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(GCAPREPONE_METADATA)
     params = gcaprepone_params(
         gcadir=gcadir,
         subject=subject,
@@ -216,13 +198,13 @@ def gcaprepone(
         done_file=done_file,
         no_emreg=no_emreg,
     )
-    return gcaprepone_execute(params, execution)
+    return gcaprepone_execute(params, runner)
 
 
 __all__ = [
     "GCAPREPONE_METADATA",
     "GcapreponeOutputs",
-    "GcapreponeParameters",
     "gcaprepone",
+    "gcaprepone_execute",
     "gcaprepone_params",
 ]