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

niwrap_freesurfer/freesurfer/tkregisterfv.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TKREGISTERFV_METADATA = Metadata(
-    id="cfc3de5a8f9a77e456ae1e8dd4af7247e9567b9c.boutiques",
+    id="3afbd4404404be4a43cf7e1f0f6bab7eaea59449.boutiques",
     name="tkregisterfv",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,42 @@ TKREGISTERFV_METADATA = Metadata(
 
 
 TkregisterfvParameters = typing.TypedDict('TkregisterfvParameters', {
-    "__STYXTYPE__": typing.Literal["tkregisterfv"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/tkregisterfv"]],
+    "mov": typing.NotRequired[InputPathType | None],
+    "targ": typing.NotRequired[InputPathType | None],
+    "reg": InputPathType,
+    "subject": typing.NotRequired[str | None],
+    "fstarg": typing.NotRequired[InputPathType | None],
+    "sd": typing.NotRequired[str | None],
+    "seg": typing.NotRequired[InputPathType | None],
+    "aseg_flag": bool,
+    "aparc_aseg_flag": bool,
+    "opacity": typing.NotRequired[float | None],
+    "surfs_flag": bool,
+    "pial_surfs_flag": bool,
+    "all_surfs_flag": bool,
+    "no_surfs_flag": bool,
+    "lh_only_flag": bool,
+    "rh_only_flag": bool,
+    "surf": typing.NotRequired[InputPathType | None],
+    "aux_s": typing.NotRequired[InputPathType | None],
+    "plane": typing.NotRequired[str | None],
+    "no_config_flag": bool,
+    "mov2": typing.NotRequired[InputPathType | None],
+    "reg2": typing.NotRequired[InputPathType | None],
+    "mov3": typing.NotRequired[InputPathType | None],
+    "reg3": typing.NotRequired[InputPathType | None],
+    "heat_flag": bool,
+    "regheader_flag": bool,
+    "params": typing.NotRequired[list[float] | None],
+    "flip_x_flag": bool,
+    "flip_y_flag": bool,
+    "flip_z_flag": bool,
+    "fstal": bool,
+    "aux": typing.NotRequired[InputPathType | None],
+})
+TkregisterfvParametersTagged = typing.TypedDict('TkregisterfvParametersTagged', {
+    "@type": typing.Literal["freesurfer/tkregisterfv"],
     "mov": typing.NotRequired[InputPathType | None],
     "targ": typing.NotRequired[InputPathType | None],
     "reg": InputPathType,
@@ -48,42 +83,11 @@ TkregisterfvParameters = typing.TypedDict('TkregisterfvParameters', {
     "fstal": bool,
     "aux": typing.NotRequired[InputPathType | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "tkregisterfv": tkregisterfv_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 TkregisterfvOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `tkregisterfv(...)`.
+    Output object returned when calling `TkregisterfvParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -122,7 +126,7 @@ def tkregisterfv_params(
     flip_z_flag: bool = False,
     fstal: bool = False,
     aux: InputPathType | None = None,
-) -> TkregisterfvParameters:
+) -> TkregisterfvParametersTagged:
     """
     Build parameters.
     
@@ -165,7 +169,7 @@ def tkregisterfv_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tkregisterfv",
+        "@type": "freesurfer/tkregisterfv",
         "reg": reg,
         "aseg_flag": aseg_flag,
         "aparc_aseg_flag": aparc_aseg_flag,
@@ -233,119 +237,119 @@ def tkregisterfv_cargs(
     """
     cargs = []
     cargs.append("tkregisterfv")
-    if params.get("mov") is not None:
+    if params.get("mov", None) is not None:
         cargs.extend([
             "--mov",
-            execution.input_file(params.get("mov"))
+            execution.input_file(params.get("mov", None))
         ])
-    if params.get("targ") is not None:
+    if params.get("targ", None) is not None:
         cargs.extend([
             "--targ",
-            execution.input_file(params.get("targ"))
+            execution.input_file(params.get("targ", None))
         ])
     cargs.extend([
         "--reg",
-        execution.input_file(params.get("reg"))
+        execution.input_file(params.get("reg", None))
     ])
-    if params.get("subject") is not None:
+    if params.get("subject", None) is not None:
         cargs.extend([
             "--s",
-            params.get("subject")
+            params.get("subject", None)
         ])
-    if params.get("fstarg") is not None:
+    if params.get("fstarg", None) is not None:
         cargs.extend([
             "--fstarg",
-            execution.input_file(params.get("fstarg"))
+            execution.input_file(params.get("fstarg", None))
         ])
-    if params.get("sd") is not None:
+    if params.get("sd", None) is not None:
         cargs.extend([
             "--sd",
-            params.get("sd")
+            params.get("sd", None)
         ])
-    if params.get("seg") is not None:
+    if params.get("seg", None) is not None:
         cargs.extend([
             "--seg",
-            execution.input_file(params.get("seg"))
+            execution.input_file(params.get("seg", None))
         ])
-    if params.get("aseg_flag"):
+    if params.get("aseg_flag", False):
         cargs.append("--aseg")
-    if params.get("aparc_aseg_flag"):
+    if params.get("aparc_aseg_flag", False):
         cargs.append("--aparc+aseg")
-    if params.get("opacity") is not None:
+    if params.get("opacity", None) is not None:
         cargs.extend([
             "--opacity",
-            str(params.get("opacity"))
+            str(params.get("opacity", None))
         ])
-    if params.get("surfs_flag"):
+    if params.get("surfs_flag", False):
         cargs.append("--surfs")
-    if params.get("pial_surfs_flag"):
+    if params.get("pial_surfs_flag", False):
         cargs.append("--pial-surfs")
-    if params.get("all_surfs_flag"):
+    if params.get("all_surfs_flag", False):
         cargs.append("--all-surfs")
-    if params.get("no_surfs_flag"):
+    if params.get("no_surfs_flag", False):
         cargs.append("--no-surfs")
-    if params.get("lh_only_flag"):
+    if params.get("lh_only_flag", False):
         cargs.append("--lh-only")
-    if params.get("rh_only_flag"):
+    if params.get("rh_only_flag", False):
         cargs.append("--rh-only")
-    if params.get("surf") is not None:
+    if params.get("surf", None) is not None:
         cargs.extend([
             "--surf",
-            execution.input_file(params.get("surf"))
+            execution.input_file(params.get("surf", None))
         ])
-    if params.get("aux_s") is not None:
+    if params.get("aux_s", None) is not None:
         cargs.extend([
             "--aux-surf",
-            execution.input_file(params.get("aux_s"))
+            execution.input_file(params.get("aux_s", None))
         ])
-    if params.get("plane") is not None:
+    if params.get("plane", None) is not None:
         cargs.extend([
             "--plane",
-            params.get("plane")
+            params.get("plane", None)
         ])
-    if params.get("no_config_flag"):
+    if params.get("no_config_flag", False):
         cargs.append("--no-config")
-    if params.get("mov2") is not None:
+    if params.get("mov2", None) is not None:
         cargs.extend([
             "--mov2",
-            execution.input_file(params.get("mov2"))
+            execution.input_file(params.get("mov2", None))
         ])
-    if params.get("reg2") is not None:
+    if params.get("reg2", None) is not None:
         cargs.extend([
             "--reg2",
-            execution.input_file(params.get("reg2"))
+            execution.input_file(params.get("reg2", None))
         ])
-    if params.get("mov3") is not None:
+    if params.get("mov3", None) is not None:
         cargs.extend([
             "--mov3",
-            execution.input_file(params.get("mov3"))
+            execution.input_file(params.get("mov3", None))
         ])
-    if params.get("reg3") is not None:
+    if params.get("reg3", None) is not None:
         cargs.extend([
             "--reg3",
-            execution.input_file(params.get("reg3"))
+            execution.input_file(params.get("reg3", None))
         ])
-    if params.get("heat_flag"):
+    if params.get("heat_flag", False):
         cargs.append("--heat")
-    if params.get("regheader_flag"):
+    if params.get("regheader_flag", False):
         cargs.append("--regheader")
-    if params.get("params") is not None:
+    if params.get("params", None) is not None:
         cargs.extend([
             "--params",
-            *map(str, params.get("params"))
+            *map(str, params.get("params", None))
         ])
-    if params.get("flip_x_flag"):
+    if params.get("flip_x_flag", False):
         cargs.append("--flip-x")
-    if params.get("flip_y_flag"):
+    if params.get("flip_y_flag", False):
         cargs.append("--flip-y")
-    if params.get("flip_z_flag"):
+    if params.get("flip_z_flag", False):
         cargs.append("--flip-z")
-    if params.get("fstal"):
+    if params.get("fstal", False):
         cargs.append("--fstal")
-    if params.get("aux") is not None:
+    if params.get("aux", None) is not None:
         cargs.extend([
             "--aux",
-            execution.input_file(params.get("aux"))
+            execution.input_file(params.get("aux", None))
         ])
     return cargs
 
@@ -371,9 +375,11 @@ def tkregisterfv_outputs(
 
 def tkregisterfv_execute(
     params: TkregisterfvParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TkregisterfvOutputs:
     """
+    tkregisterfv
+    
     A script that runs freeview with arguments like tkregister, focusing on LTA
     files.
     
@@ -383,10 +389,12 @@ def tkregisterfv_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TkregisterfvOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TKREGISTERFV_METADATA)
     params = execution.params(params)
     cargs = tkregisterfv_cargs(params, execution)
     ret = tkregisterfv_outputs(params, execution)
@@ -430,6 +438,8 @@ def tkregisterfv(
     runner: Runner | None = None,
 ) -> TkregisterfvOutputs:
     """
+    tkregisterfv
+    
     A script that runs freeview with arguments like tkregister, focusing on LTA
     files.
     
@@ -476,8 +486,6 @@ def tkregisterfv(
     Returns:
         NamedTuple of outputs (described in `TkregisterfvOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TKREGISTERFV_METADATA)
     params = tkregisterfv_params(
         mov=mov,
         targ=targ,
@@ -512,13 +520,13 @@ def tkregisterfv(
         fstal=fstal,
         aux=aux,
     )
-    return tkregisterfv_execute(params, execution)
+    return tkregisterfv_execute(params, runner)
 
 
 __all__ = [
     "TKREGISTERFV_METADATA",
     "TkregisterfvOutputs",
-    "TkregisterfvParameters",
     "tkregisterfv",
+    "tkregisterfv_execute",
     "tkregisterfv_params",
 ]

niwrap_freesurfer/freesurfer/tksurfer.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TKSURFER_METADATA = Metadata(
-    id="603cb4c673862d6704782330c4df67ab125e67dd.boutiques",
+    id="b02b5bf307c6379fb8e881e8e4042e5a2fb7f3f9.boutiques",
     name="tksurfer",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,24 @@ TKSURFER_METADATA = Metadata(
 
 
 TksurferParameters = typing.TypedDict('TksurferParameters', {
-    "__STYXTYPE__": typing.Literal["tksurfer"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/tksurfer"]],
+    "subject_id": str,
+    "hemisphere": str,
+    "surface_name": str,
+    "options": typing.NotRequired[str | None],
+})
+TksurferParametersTagged = typing.TypedDict('TksurferParametersTagged', {
+    "@type": typing.Literal["freesurfer/tksurfer"],
     "subject_id": str,
     "hemisphere": str,
     "surface_name": str,
     "options": 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 {
-        "tksurfer": tksurfer_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 TksurferOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `tksurfer(...)`.
+    Output object returned when calling `TksurferParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def tksurfer_params(
     hemisphere: str,
     surface_name: str,
     options: str | None = None,
-) -> TksurferParameters:
+) -> TksurferParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +55,7 @@ def tksurfer_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tksurfer",
+        "@type": "freesurfer/tksurfer",
         "subject_id": subject_id,
         "hemisphere": hemisphere,
         "surface_name": surface_name,
@@ -104,11 +80,11 @@ def tksurfer_cargs(
     """
     cargs = []
     cargs.append("tksurfer")
-    cargs.append(params.get("subject_id"))
-    cargs.append(params.get("hemisphere"))
-    cargs.append(params.get("surface_name"))
-    if params.get("options") is not None:
-        cargs.append(params.get("options"))
+    cargs.append(params.get("subject_id", None))
+    cargs.append(params.get("hemisphere", None))
+    cargs.append(params.get("surface_name", None))
+    if params.get("options", None) is not None:
+        cargs.append(params.get("options", None))
     return cargs
 
 
@@ -133,9 +109,11 @@ def tksurfer_outputs(
 
 def tksurfer_execute(
     params: TksurferParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TksurferOutputs:
     """
+    tksurfer
+    
     3D visualization tool for cortical surface models (part of FreeSurfer).
     
     Author: FreeSurfer Developers
@@ -144,10 +122,12 @@ def tksurfer_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TksurferOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TKSURFER_METADATA)
     params = execution.params(params)
     cargs = tksurfer_cargs(params, execution)
     ret = tksurfer_outputs(params, execution)
@@ -163,6 +143,8 @@ def tksurfer(
     runner: Runner | None = None,
 ) -> TksurferOutputs:
     """
+    tksurfer
+    
     3D visualization tool for cortical surface models (part of FreeSurfer).
     
     Author: FreeSurfer Developers
@@ -178,21 +160,19 @@ def tksurfer(
     Returns:
         NamedTuple of outputs (described in `TksurferOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TKSURFER_METADATA)
     params = tksurfer_params(
         subject_id=subject_id,
         hemisphere=hemisphere,
         surface_name=surface_name,
         options=options,
     )
-    return tksurfer_execute(params, execution)
+    return tksurfer_execute(params, runner)
 
 
 __all__ = [
     "TKSURFER_METADATA",
     "TksurferOutputs",
-    "TksurferParameters",
     "tksurfer",
+    "tksurfer_execute",
     "tksurfer_params",
 ]

niwrap_freesurfer/freesurfer/tksurferfv.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TKSURFERFV_METADATA = Metadata(
-    id="cd3fd7dabbb53c8172ce7700f1ac133b0f1b3603.boutiques",
+    id="3630571b1df098223ac9e1925a90b830452d6684.boutiques",
     name="tksurferfv",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,21 @@ TKSURFERFV_METADATA = Metadata(
 
 
 TksurferfvParameters = typing.TypedDict('TksurferfvParameters', {
-    "__STYXTYPE__": typing.Literal["tksurferfv"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/tksurferfv"]],
+    "subject": str,
+    "hemi": str,
+    "surface": str,
+    "tksurfer": bool,
+    "all_surfaces": bool,
+    "vgl": bool,
+    "no_vgl": bool,
+    "no_outline": bool,
+    "neuro_orientation": bool,
+    "rotate_around_cursor": bool,
+    "heat_scale": typing.NotRequired[str | None],
+})
+TksurferfvParametersTagged = typing.TypedDict('TksurferfvParametersTagged', {
+    "@type": typing.Literal["freesurfer/tksurferfv"],
     "subject": str,
     "hemi": str,
     "surface": str,
@@ -27,42 +41,11 @@ TksurferfvParameters = typing.TypedDict('TksurferfvParameters', {
     "rotate_around_cursor": bool,
     "heat_scale": 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 {
-        "tksurferfv": tksurferfv_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 TksurferfvOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `tksurferfv(...)`.
+    Output object returned when calling `TksurferfvParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,8 +62,8 @@ def tksurferfv_params(
     no_outline: bool = False,
     neuro_orientation: bool = False,
     rotate_around_cursor: bool = False,
-    heat_scale: str | None = "min_to_max",
-) -> TksurferfvParameters:
+    heat_scale: str | None = None,
+) -> TksurferfvParametersTagged:
     """
     Build parameters.
     
@@ -102,7 +85,7 @@ def tksurferfv_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tksurferfv",
+        "@type": "freesurfer/tksurferfv",
         "subject": subject,
         "hemi": hemi,
         "surface": surface,
@@ -134,25 +117,25 @@ def tksurferfv_cargs(
     """
     cargs = []
     cargs.append("tksurferfv")
-    cargs.append(params.get("subject"))
-    cargs.append(params.get("hemi"))
-    cargs.append(params.get("surface"))
-    if params.get("tksurfer"):
+    cargs.append(params.get("subject", None))
+    cargs.append(params.get("hemi", None))
+    cargs.append(params.get("surface", None))
+    if params.get("tksurfer", False):
         cargs.append("-tksurfer")
-    if params.get("all_surfaces"):
+    if params.get("all_surfaces", False):
         cargs.append("-all")
-    if params.get("vgl"):
+    if params.get("vgl", False):
         cargs.append("-vgl")
-    if params.get("no_vgl"):
+    if params.get("no_vgl", False):
         cargs.append("-no-vgl")
-    if params.get("no_outline"):
+    if params.get("no_outline", False):
         cargs.append("-no-outline")
-    if params.get("neuro_orientation"):
+    if params.get("neuro_orientation", False):
         cargs.append("-neuro")
-    if params.get("rotate_around_cursor"):
+    if params.get("rotate_around_cursor", False):
         cargs.append("-rca")
-    if params.get("heat_scale") is not None:
-        cargs.append(params.get("heat_scale"))
+    if params.get("heat_scale", None) is not None:
+        cargs.append(params.get("heat_scale", None))
     return cargs
 
 
@@ -177,9 +160,11 @@ def tksurferfv_outputs(
 
 def tksurferfv_execute(
     params: TksurferfvParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TksurferfvOutputs:
     """
+    tksurferfv
+    
     A script that runs freeview with arguments similar to tksurfer.
     
     Author: FreeSurfer Developers
@@ -188,10 +173,12 @@ def tksurferfv_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TksurferfvOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TKSURFERFV_METADATA)
     params = execution.params(params)
     cargs = tksurferfv_cargs(params, execution)
     ret = tksurferfv_outputs(params, execution)
@@ -210,10 +197,12 @@ def tksurferfv(
     no_outline: bool = False,
     neuro_orientation: bool = False,
     rotate_around_cursor: bool = False,
-    heat_scale: str | None = "min_to_max",
+    heat_scale: str | None = None,
     runner: Runner | None = None,
 ) -> TksurferfvOutputs:
     """
+    tksurferfv
+    
     A script that runs freeview with arguments similar to tksurfer.
     
     Author: FreeSurfer Developers
@@ -238,8 +227,6 @@ def tksurferfv(
     Returns:
         NamedTuple of outputs (described in `TksurferfvOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TKSURFERFV_METADATA)
     params = tksurferfv_params(
         subject=subject,
         hemi=hemi,
@@ -253,13 +240,13 @@ def tksurferfv(
         rotate_around_cursor=rotate_around_cursor,
         heat_scale=heat_scale,
     )
-    return tksurferfv_execute(params, execution)
+    return tksurferfv_execute(params, runner)
 
 
 __all__ = [
     "TKSURFERFV_METADATA",
     "TksurferfvOutputs",
-    "TksurferfvParameters",
     "tksurferfv",
+    "tksurferfv_execute",
     "tksurferfv_params",
 ]