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

niwrap_freesurfer/freesurfer/mri_gtmseg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_GTMSEG_METADATA = Metadata(
-    id="1751da2ccfc8c90c9966c0f60af5462d531c0486.boutiques",
+    id="8cda6aca5ff8ba96d9e6ad44c45f23f2537dda6a.boutiques",
     name="mri_gtmseg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,29 @@ MRI_GTMSEG_METADATA = Metadata(
 
 
 MriGtmsegParameters = typing.TypedDict('MriGtmsegParameters', {
-    "__STYXTYPE__": typing.Literal["mri_gtmseg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_gtmseg"]],
+    "output_volume": str,
+    "source_subject": str,
+    "internal_usf": typing.NotRequired[float | None],
+    "apas_file": typing.NotRequired[InputPathType | None],
+    "context_annotation": typing.NotRequired[list[str] | None],
+    "subseg_wm": bool,
+    "wm_annotation": typing.NotRequired[list[str] | None],
+    "dmax": typing.NotRequired[float | None],
+    "keep_hypo": bool,
+    "keep_cc": bool,
+    "ctab": typing.NotRequired[InputPathType | None],
+    "lhminmax": typing.NotRequired[list[float] | None],
+    "rhminmax": typing.NotRequired[list[float] | None],
+    "output_usf": typing.NotRequired[float | None],
+    "threads": typing.NotRequired[float | None],
+    "threads_max": bool,
+    "threads_max_1": bool,
+    "debug": bool,
+    "check_opts": bool,
+})
+MriGtmsegParametersTagged = typing.TypedDict('MriGtmsegParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_gtmseg"],
     "output_volume": str,
     "source_subject": str,
     "internal_usf": typing.NotRequired[float | None],
@@ -35,42 +57,11 @@ MriGtmsegParameters = typing.TypedDict('MriGtmsegParameters', {
     "debug": bool,
     "check_opts": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_gtmseg": mri_gtmseg_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 MriGtmsegOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_gtmseg(...)`.
+    Output object returned when calling `MriGtmsegParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -96,7 +87,7 @@ def mri_gtmseg_params(
     threads_max_1: bool = False,
     debug: bool = False,
     check_opts: bool = False,
-) -> MriGtmsegParameters:
+) -> MriGtmsegParametersTagged:
     """
     Build parameters.
     
@@ -134,7 +125,7 @@ def mri_gtmseg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_gtmseg",
+        "@type": "freesurfer/mri_gtmseg",
         "output_volume": output_volume,
         "source_subject": source_subject,
         "subseg_wm": subseg_wm,
@@ -185,75 +176,75 @@ def mri_gtmseg_cargs(
     cargs.append("mri_gtmseg")
     cargs.extend([
         "--o",
-        params.get("output_volume")
+        params.get("output_volume", None)
     ])
     cargs.extend([
         "--s",
-        params.get("source_subject")
+        params.get("source_subject", None)
     ])
-    if params.get("internal_usf") is not None:
+    if params.get("internal_usf", None) is not None:
         cargs.extend([
             "--internal-usf",
-            str(params.get("internal_usf"))
+            str(params.get("internal_usf", None))
         ])
-    if params.get("apas_file") is not None:
+    if params.get("apas_file", None) is not None:
         cargs.extend([
             "--apas",
-            execution.input_file(params.get("apas_file"))
+            execution.input_file(params.get("apas_file", None))
         ])
-    if params.get("context_annotation") is not None:
+    if params.get("context_annotation", None) is not None:
         cargs.extend([
             "--ctx-annot",
-            *params.get("context_annotation")
+            *params.get("context_annotation", None)
         ])
-    if params.get("subseg_wm"):
+    if params.get("subseg_wm", False):
         cargs.append("--subseg-wm")
-    if params.get("wm_annotation") is not None:
+    if params.get("wm_annotation", None) is not None:
         cargs.extend([
             "--wm-annot",
-            *params.get("wm_annotation")
+            *params.get("wm_annotation", None)
         ])
-    if params.get("dmax") is not None:
+    if params.get("dmax", None) is not None:
         cargs.extend([
             "--dmax",
-            str(params.get("dmax"))
+            str(params.get("dmax", None))
         ])
-    if params.get("keep_hypo"):
+    if params.get("keep_hypo", False):
         cargs.append("--keep-hypo")
-    if params.get("keep_cc"):
+    if params.get("keep_cc", False):
         cargs.append("--keep-cc")
-    if params.get("ctab") is not None:
+    if params.get("ctab", None) is not None:
         cargs.extend([
             "--ctab",
-            execution.input_file(params.get("ctab"))
+            execution.input_file(params.get("ctab", None))
         ])
-    if params.get("lhminmax") is not None:
+    if params.get("lhminmax", None) is not None:
         cargs.extend([
             "--lhminmax",
-            *map(str, params.get("lhminmax"))
+            *map(str, params.get("lhminmax", None))
         ])
-    if params.get("rhminmax") is not None:
+    if params.get("rhminmax", None) is not None:
         cargs.extend([
             "--rhminmax",
-            *map(str, params.get("rhminmax"))
+            *map(str, params.get("rhminmax", None))
         ])
-    if params.get("output_usf") is not None:
+    if params.get("output_usf", None) is not None:
         cargs.extend([
             "--output-usf",
-            str(params.get("output_usf"))
+            str(params.get("output_usf", None))
         ])
-    if params.get("threads") is not None:
+    if params.get("threads", None) is not None:
         cargs.extend([
             "--threads",
-            str(params.get("threads"))
+            str(params.get("threads", None))
         ])
-    if params.get("threads_max"):
+    if params.get("threads_max", False):
         cargs.append("--threads-max")
-    if params.get("threads_max_1"):
+    if params.get("threads_max_1", False):
         cargs.append("--threads-max-1")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("check_opts"):
+    if params.get("check_opts", False):
         cargs.append("--checkopts")
     return cargs
 
@@ -279,9 +270,11 @@ def mri_gtmseg_outputs(
 
 def mri_gtmseg_execute(
     params: MriGtmsegParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriGtmsegOutputs:
     """
+    mri_gtmseg
+    
     Creates a segmentation that can be used with the geometric transfer matrix
     (GTM).
     
@@ -291,10 +284,12 @@ def mri_gtmseg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriGtmsegOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_GTMSEG_METADATA)
     params = execution.params(params)
     cargs = mri_gtmseg_cargs(params, execution)
     ret = mri_gtmseg_outputs(params, execution)
@@ -325,6 +320,8 @@ def mri_gtmseg(
     runner: Runner | None = None,
 ) -> MriGtmsegOutputs:
     """
+    mri_gtmseg
+    
     Creates a segmentation that can be used with the geometric transfer matrix
     (GTM).
     
@@ -366,8 +363,6 @@ def mri_gtmseg(
     Returns:
         NamedTuple of outputs (described in `MriGtmsegOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_GTMSEG_METADATA)
     params = mri_gtmseg_params(
         output_volume=output_volume,
         source_subject=source_subject,
@@ -389,13 +384,13 @@ def mri_gtmseg(
         debug=debug,
         check_opts=check_opts,
     )
-    return mri_gtmseg_execute(params, execution)
+    return mri_gtmseg_execute(params, runner)
 
 
 __all__ = [
     "MRI_GTMSEG_METADATA",
     "MriGtmsegOutputs",
-    "MriGtmsegParameters",
     "mri_gtmseg",
+    "mri_gtmseg_execute",
     "mri_gtmseg_params",
 ]

niwrap_freesurfer/freesurfer/mri_hausdorff_dist.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_HAUSDORFF_DIST_METADATA = Metadata(
-    id="bdcef721bb6481f0dd0eb1df21b37c8534448bd6.boutiques",
+    id="4fa8ca2966a7439e3b6f607d5e00c90b1cb0c790.boutiques",
     name="mri_hausdorff_dist",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ MRI_HAUSDORFF_DIST_METADATA = Metadata(
 
 
 MriHausdorffDistParameters = typing.TypedDict('MriHausdorffDistParameters', {
-    "__STYXTYPE__": typing.Literal["mri_hausdorff_dist"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_hausdorff_dist"]],
+    "vol1": InputPathType,
+    "vol2": InputPathType,
+    "output_text_file": str,
+    "threshold": typing.NotRequired[float | None],
+    "input_file_flag": bool,
+    "blur_sigma": typing.NotRequired[float | None],
+    "max_flag": bool,
+    "label_index": typing.NotRequired[float | None],
+})
+MriHausdorffDistParametersTagged = typing.TypedDict('MriHausdorffDistParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_hausdorff_dist"],
     "vol1": InputPathType,
     "vol2": InputPathType,
     "output_text_file": str,
@@ -24,43 +35,11 @@ MriHausdorffDistParameters = typing.TypedDict('MriHausdorffDistParameters', {
     "max_flag": bool,
     "label_index": 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 {
-        "mri_hausdorff_dist": mri_hausdorff_dist_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 {
-        "mri_hausdorff_dist": mri_hausdorff_dist_outputs,
-    }.get(t)
 
 
 class MriHausdorffDistOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_hausdorff_dist(...)`.
+    Output object returned when calling `MriHausdorffDistParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -78,7 +57,7 @@ def mri_hausdorff_dist_params(
     blur_sigma: float | None = None,
     max_flag: bool = False,
     label_index: float | None = None,
-) -> MriHausdorffDistParameters:
+) -> MriHausdorffDistParametersTagged:
     """
     Build parameters.
     
@@ -97,7 +76,7 @@ def mri_hausdorff_dist_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_hausdorff_dist",
+        "@type": "freesurfer/mri_hausdorff_dist",
         "vol1": vol1,
         "vol2": vol2,
         "output_text_file": output_text_file,
@@ -128,27 +107,27 @@ def mri_hausdorff_dist_cargs(
     """
     cargs = []
     cargs.append("mri_hausdorff_dist")
-    cargs.append(execution.input_file(params.get("vol1")))
-    cargs.append(execution.input_file(params.get("vol2")))
-    cargs.append(params.get("output_text_file"))
-    if params.get("threshold") is not None:
+    cargs.append(execution.input_file(params.get("vol1", None)))
+    cargs.append(execution.input_file(params.get("vol2", None)))
+    cargs.append(params.get("output_text_file", None))
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "-b",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    if params.get("input_file_flag"):
+    if params.get("input_file_flag", False):
         cargs.append("-F")
-    if params.get("blur_sigma") is not None:
+    if params.get("blur_sigma", None) is not None:
         cargs.extend([
             "-g",
-            str(params.get("blur_sigma"))
+            str(params.get("blur_sigma", None))
         ])
-    if params.get("max_flag"):
+    if params.get("max_flag", False):
         cargs.append("-max")
-    if params.get("label_index") is not None:
+    if params.get("label_index", None) is not None:
         cargs.extend([
             "-l",
-            str(params.get("label_index"))
+            str(params.get("label_index", None))
         ])
     return cargs
 
@@ -168,18 +147,20 @@ def mri_hausdorff_dist_outputs(
     """
     ret = MriHausdorffDistOutputs(
         root=execution.output_file("."),
-        output_text=execution.output_file(params.get("output_text_file")),
+        output_text=execution.output_file(params.get("output_text_file", None)),
     )
     return ret
 
 
 def mri_hausdorff_dist_execute(
     params: MriHausdorffDistParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriHausdorffDistOutputs:
     """
-    Tool for computing the mean or max of the minimum distances between point sets
-    in 3D volumes.
+    mri_hausdorff_dist
+    
+    Tool for computing the mean or max of the minimum distances between point
+    sets in 3D volumes.
     
     Author: FreeSurfer Developers
     
@@ -187,10 +168,12 @@ def mri_hausdorff_dist_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriHausdorffDistOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_HAUSDORFF_DIST_METADATA)
     params = execution.params(params)
     cargs = mri_hausdorff_dist_cargs(params, execution)
     ret = mri_hausdorff_dist_outputs(params, execution)
@@ -210,8 +193,10 @@ def mri_hausdorff_dist(
     runner: Runner | None = None,
 ) -> MriHausdorffDistOutputs:
     """
-    Tool for computing the mean or max of the minimum distances between point sets
-    in 3D volumes.
+    mri_hausdorff_dist
+    
+    Tool for computing the mean or max of the minimum distances between point
+    sets in 3D volumes.
     
     Author: FreeSurfer Developers
     
@@ -232,8 +217,6 @@ def mri_hausdorff_dist(
     Returns:
         NamedTuple of outputs (described in `MriHausdorffDistOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_HAUSDORFF_DIST_METADATA)
     params = mri_hausdorff_dist_params(
         vol1=vol1,
         vol2=vol2,
@@ -244,13 +227,13 @@ def mri_hausdorff_dist(
         max_flag=max_flag,
         label_index=label_index,
     )
-    return mri_hausdorff_dist_execute(params, execution)
+    return mri_hausdorff_dist_execute(params, runner)
 
 
 __all__ = [
     "MRI_HAUSDORFF_DIST_METADATA",
     "MriHausdorffDistOutputs",
-    "MriHausdorffDistParameters",
     "mri_hausdorff_dist",
+    "mri_hausdorff_dist_execute",
     "mri_hausdorff_dist_params",
 ]

niwrap_freesurfer/freesurfer/mri_head.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_HEAD_METADATA = Metadata(
-    id="a9ef6649904a08c5a1b37e6402d0ba5b4265e680.boutiques",
+    id="85959685db5266a614d692c0ad190c777b2f0695.boutiques",
     name="mri_head",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRI_HEAD_METADATA = Metadata(
 
 
 MriHeadParameters = typing.TypedDict('MriHeadParameters', {
-    "__STYXTYPE__": typing.Literal["mri_head"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_head"]],
+    "identify": bool,
+    "read": bool,
+    "filename": typing.NotRequired[str | None],
+    "help": bool,
+    "usage": bool,
+    "question_mark_help": bool,
+})
+MriHeadParametersTagged = typing.TypedDict('MriHeadParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_head"],
     "identify": bool,
     "read": bool,
     "filename": typing.NotRequired[str | None],
@@ -22,42 +31,11 @@ MriHeadParameters = typing.TypedDict('MriHeadParameters', {
     "usage": bool,
     "question_mark_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 {
-        "mri_head": mri_head_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 MriHeadOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_head(...)`.
+    Output object returned when calling `MriHeadParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def mri_head_params(
     help_: bool = False,
     usage: bool = False,
     question_mark_help: bool = False,
-) -> MriHeadParameters:
+) -> MriHeadParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +63,7 @@ def mri_head_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_head",
+        "@type": "freesurfer/mri_head",
         "identify": identify,
         "read": read,
         "help": help_,
@@ -112,17 +90,17 @@ def mri_head_cargs(
     """
     cargs = []
     cargs.append("mri_head")
-    if params.get("identify"):
+    if params.get("identify", False):
         cargs.append("-identify")
-    if params.get("read"):
+    if params.get("read", False):
         cargs.append("-read")
-    if params.get("filename") is not None:
-        cargs.append(params.get("filename"))
-    if params.get("help"):
+    if params.get("filename", None) is not None:
+        cargs.append(params.get("filename", None))
+    if params.get("help", False):
         cargs.append("-h")
-    if params.get("usage"):
+    if params.get("usage", False):
         cargs.append("-u")
-    if params.get("question_mark_help"):
+    if params.get("question_mark_help", False):
         cargs.append("-?")
     return cargs
 
@@ -148,9 +126,11 @@ def mri_head_outputs(
 
 def mri_head_execute(
     params: MriHeadParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriHeadOutputs:
     """
+    mri_head
+    
     No description.
     
     Author: FreeSurfer Developers
@@ -159,10 +139,12 @@ def mri_head_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriHeadOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_HEAD_METADATA)
     params = execution.params(params)
     cargs = mri_head_cargs(params, execution)
     ret = mri_head_outputs(params, execution)
@@ -180,6 +162,8 @@ def mri_head(
     runner: Runner | None = None,
 ) -> MriHeadOutputs:
     """
+    mri_head
+    
     No description.
     
     Author: FreeSurfer Developers
@@ -197,8 +181,6 @@ def mri_head(
     Returns:
         NamedTuple of outputs (described in `MriHeadOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_HEAD_METADATA)
     params = mri_head_params(
         identify=identify,
         read=read,
@@ -207,13 +189,13 @@ def mri_head(
         usage=usage,
         question_mark_help=question_mark_help,
     )
-    return mri_head_execute(params, execution)
+    return mri_head_execute(params, runner)
 
 
 __all__ = [
     "MRI_HEAD_METADATA",
     "MriHeadOutputs",
-    "MriHeadParameters",
     "mri_head",
+    "mri_head_execute",
     "mri_head_params",
 ]