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

niwrap_freesurfer/freesurfer/mris_apply_reg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_APPLY_REG_METADATA = Metadata(
-    id="d83a6dd6faa7d3c0b5d21dce1759961d05ea7655.boutiques",
+    id="3962ba14a9e4039c0dcaa147f07352b32b491d36.boutiques",
     name="mris_apply_reg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,33 @@ MRIS_APPLY_REG_METADATA = Metadata(
 
 
 MrisApplyRegParameters = typing.TypedDict('MrisApplyRegParameters', {
-    "__STYXTYPE__": typing.Literal["mris_apply_reg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_apply_reg"]],
+    "src_input": InputPathType,
+    "trg_output": str,
+    "streg_pair": str,
+    "src_label": typing.NotRequired[InputPathType | None],
+    "src_annotation": typing.NotRequired[InputPathType | None],
+    "src_xyz": typing.NotRequired[InputPathType | None],
+    "jacobian": bool,
+    "no_reverse": bool,
+    "rand_noise": bool,
+    "replace_ones": bool,
+    "center_output": bool,
+    "curv_format": bool,
+    "lta_transform": typing.NotRequired[str | None],
+    "lta_patch_transform": typing.NotRequired[str | None],
+    "reverse_surface": typing.NotRequired[str | None],
+    "patch_apply": typing.NotRequired[str | None],
+    "save_vertex_pair": typing.NotRequired[InputPathType | None],
+    "m3z_transform": typing.NotRequired[str | None],
+    "inv_m3z_transform": typing.NotRequired[str | None],
+    "src_reg_scale": typing.NotRequired[float | None],
+    "trg_reg_scale": typing.NotRequired[float | None],
+    "debug_mode": bool,
+    "check_options": bool,
+})
+MrisApplyRegParametersTagged = typing.TypedDict('MrisApplyRegParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_apply_reg"],
     "src_input": InputPathType,
     "trg_output": str,
     "streg_pair": str,
@@ -39,43 +65,11 @@ MrisApplyRegParameters = typing.TypedDict('MrisApplyRegParameters', {
     "debug_mode": bool,
     "check_options": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_apply_reg": mris_apply_reg_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 {
-        "mris_apply_reg": mris_apply_reg_outputs,
-    }.get(t)
 
 
 class MrisApplyRegOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_apply_reg(...)`.
+    Output object returned when calling `MrisApplyRegParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -107,7 +101,7 @@ def mris_apply_reg_params(
     trg_reg_scale: float | None = None,
     debug_mode: bool = False,
     check_options: bool = False,
-) -> MrisApplyRegParameters:
+) -> MrisApplyRegParametersTagged:
     """
     Build parameters.
     
@@ -139,7 +133,7 @@ def mris_apply_reg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_apply_reg",
+        "@type": "freesurfer/mris_apply_reg",
         "src_input": src_input,
         "trg_output": trg_output,
         "streg_pair": streg_pair,
@@ -196,91 +190,91 @@ def mris_apply_reg_cargs(
     cargs.append("mris_apply_reg")
     cargs.extend([
         "--src",
-        execution.input_file(params.get("src_input"))
+        execution.input_file(params.get("src_input", None))
     ])
     cargs.extend([
         "--trg",
-        params.get("trg_output")
+        params.get("trg_output", None)
     ])
     cargs.extend([
         "--streg",
-        params.get("streg_pair")
+        params.get("streg_pair", None)
     ])
-    if params.get("src_label") is not None:
+    if params.get("src_label", None) is not None:
         cargs.extend([
             "--src-label",
-            execution.input_file(params.get("src_label"))
+            execution.input_file(params.get("src_label", None))
         ])
-    if params.get("src_annotation") is not None:
+    if params.get("src_annotation", None) is not None:
         cargs.extend([
             "--src-annot",
-            execution.input_file(params.get("src_annotation"))
+            execution.input_file(params.get("src_annotation", None))
         ])
-    if params.get("src_xyz") is not None:
+    if params.get("src_xyz", None) is not None:
         cargs.extend([
             "--src-xyz",
-            execution.input_file(params.get("src_xyz"))
+            execution.input_file(params.get("src_xyz", None))
         ])
-    if params.get("jacobian"):
+    if params.get("jacobian", False):
         cargs.append("--jac")
-    if params.get("no_reverse"):
+    if params.get("no_reverse", False):
         cargs.append("--no-rev")
-    if params.get("rand_noise"):
+    if params.get("rand_noise", False):
         cargs.append("--randn")
-    if params.get("replace_ones"):
+    if params.get("replace_ones", False):
         cargs.append("--ones")
-    if params.get("center_output"):
+    if params.get("center_output", False):
         cargs.append("--center")
-    if params.get("curv_format"):
+    if params.get("curv_format", False):
         cargs.append("--curv")
-    if params.get("lta_transform") is not None:
+    if params.get("lta_transform", None) is not None:
         cargs.extend([
             "--lta",
-            params.get("lta_transform")
+            params.get("lta_transform", None)
         ])
-    if params.get("lta_patch_transform") is not None:
+    if params.get("lta_patch_transform", None) is not None:
         cargs.extend([
             "--lta-patch",
-            params.get("lta_patch_transform")
+            params.get("lta_patch_transform", None)
         ])
-    if params.get("reverse_surface") is not None:
+    if params.get("reverse_surface", None) is not None:
         cargs.extend([
             "--reverse",
-            params.get("reverse_surface")
+            params.get("reverse_surface", None)
         ])
-    if params.get("patch_apply") is not None:
+    if params.get("patch_apply", None) is not None:
         cargs.extend([
             "--patch",
-            params.get("patch_apply")
+            params.get("patch_apply", None)
         ])
-    if params.get("save_vertex_pair") is not None:
+    if params.get("save_vertex_pair", None) is not None:
         cargs.extend([
             "--stvpair",
-            execution.input_file(params.get("save_vertex_pair"))
+            execution.input_file(params.get("save_vertex_pair", None))
         ])
-    if params.get("m3z_transform") is not None:
+    if params.get("m3z_transform", None) is not None:
         cargs.extend([
             "--m3z",
-            params.get("m3z_transform")
+            params.get("m3z_transform", None)
         ])
-    if params.get("inv_m3z_transform") is not None:
+    if params.get("inv_m3z_transform", None) is not None:
         cargs.extend([
             "--inv-m3z",
-            params.get("inv_m3z_transform")
+            params.get("inv_m3z_transform", None)
         ])
-    if params.get("src_reg_scale") is not None:
+    if params.get("src_reg_scale", None) is not None:
         cargs.extend([
             "--src-reg-scale",
-            str(params.get("src_reg_scale"))
+            str(params.get("src_reg_scale", None))
         ])
-    if params.get("trg_reg_scale") is not None:
+    if params.get("trg_reg_scale", None) is not None:
         cargs.extend([
             "--trg-reg-scale",
-            str(params.get("trg_reg_scale"))
+            str(params.get("trg_reg_scale", None))
         ])
-    if params.get("debug_mode"):
+    if params.get("debug_mode", False):
         cargs.append("--debug")
-    if params.get("check_options"):
+    if params.get("check_options", False):
         cargs.append("--checkopts")
     return cargs
 
@@ -300,16 +294,18 @@ def mris_apply_reg_outputs(
     """
     ret = MrisApplyRegOutputs(
         root=execution.output_file("."),
-        output_result=execution.output_file(params.get("trg_output")),
+        output_result=execution.output_file(params.get("trg_output", None)),
     )
     return ret
 
 
 def mris_apply_reg_execute(
     params: MrisApplyRegParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisApplyRegOutputs:
     """
+    mris_apply_reg
+    
     Apply surface registration in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -318,10 +314,12 @@ def mris_apply_reg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisApplyRegOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_APPLY_REG_METADATA)
     params = execution.params(params)
     cargs = mris_apply_reg_cargs(params, execution)
     ret = mris_apply_reg_outputs(params, execution)
@@ -356,6 +354,8 @@ def mris_apply_reg(
     runner: Runner | None = None,
 ) -> MrisApplyRegOutputs:
     """
+    mris_apply_reg
+    
     Apply surface registration in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -390,8 +390,6 @@ def mris_apply_reg(
     Returns:
         NamedTuple of outputs (described in `MrisApplyRegOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_APPLY_REG_METADATA)
     params = mris_apply_reg_params(
         src_input=src_input,
         trg_output=trg_output,
@@ -417,13 +415,13 @@ def mris_apply_reg(
         debug_mode=debug_mode,
         check_options=check_options,
     )
-    return mris_apply_reg_execute(params, execution)
+    return mris_apply_reg_execute(params, runner)
 
 
 __all__ = [
     "MRIS_APPLY_REG_METADATA",
     "MrisApplyRegOutputs",
-    "MrisApplyRegParameters",
     "mris_apply_reg",
+    "mris_apply_reg_execute",
     "mris_apply_reg_params",
 ]

niwrap_freesurfer/freesurfer/mris_autodet_gwstats.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_AUTODET_GWSTATS_METADATA = Metadata(
-    id="7859ad8de8d5de83b72535b7fa4be46c7e06a198.boutiques",
+    id="70fa91a99fbbf9df5a0a9b3f753747e6cbdf864b.boutiques",
     name="mris_autodet_gwstats",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,25 @@ MRIS_AUTODET_GWSTATS_METADATA = Metadata(
 
 
 MrisAutodetGwstatsParameters = typing.TypedDict('MrisAutodetGwstatsParameters', {
-    "__STYXTYPE__": typing.Literal["mris_autodet_gwstats"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_autodet_gwstats"]],
+    "output_file": str,
+    "t1w_volume": InputPathType,
+    "wm_volume": InputPathType,
+    "surf": InputPathType,
+    "lhsurf": typing.NotRequired[InputPathType | None],
+    "rhsurf": typing.NotRequired[InputPathType | None],
+    "subject": str,
+    "subjects_dir": str,
+    "min_border_white": typing.NotRequired[float | None],
+    "max_border_white": typing.NotRequired[float | None],
+    "min_gray_at_white_border": typing.NotRequired[float | None],
+    "max_gray": typing.NotRequired[float | None],
+    "max_gray_at_csf_border": typing.NotRequired[float | None],
+    "min_gray_at_csf_border": typing.NotRequired[float | None],
+    "max_csf": typing.NotRequired[float | None],
+})
+MrisAutodetGwstatsParametersTagged = typing.TypedDict('MrisAutodetGwstatsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_autodet_gwstats"],
     "output_file": str,
     "t1w_volume": InputPathType,
     "wm_volume": InputPathType,
@@ -31,43 +49,11 @@ MrisAutodetGwstatsParameters = typing.TypedDict('MrisAutodetGwstatsParameters',
     "min_gray_at_csf_border": typing.NotRequired[float | None],
     "max_csf": 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 {
-        "mris_autodet_gwstats": mris_autodet_gwstats_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 {
-        "mris_autodet_gwstats": mris_autodet_gwstats_outputs,
-    }.get(t)
 
 
 class MrisAutodetGwstatsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_autodet_gwstats(...)`.
+    Output object returned when calling `MrisAutodetGwstatsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -91,7 +77,7 @@ def mris_autodet_gwstats_params(
     max_gray_at_csf_border: float | None = None,
     min_gray_at_csf_border: float | None = None,
     max_csf: float | None = None,
-) -> MrisAutodetGwstatsParameters:
+) -> MrisAutodetGwstatsParametersTagged:
     """
     Build parameters.
     
@@ -116,7 +102,7 @@ def mris_autodet_gwstats_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_autodet_gwstats",
+        "@type": "freesurfer/mris_autodet_gwstats",
         "output_file": output_file,
         "t1w_volume": t1w_volume,
         "wm_volume": wm_volume,
@@ -162,72 +148,72 @@ def mris_autodet_gwstats_cargs(
     cargs.append("mris_autodet_gwstats")
     cargs.extend([
         "--o",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
     cargs.extend([
         "--i",
-        execution.input_file(params.get("t1w_volume"))
+        execution.input_file(params.get("t1w_volume", None))
     ])
     cargs.extend([
         "--wm",
-        execution.input_file(params.get("wm_volume"))
+        execution.input_file(params.get("wm_volume", None))
     ])
     cargs.extend([
         "--surf",
-        execution.input_file(params.get("surf"))
+        execution.input_file(params.get("surf", None))
     ])
-    if params.get("lhsurf") is not None:
+    if params.get("lhsurf", None) is not None:
         cargs.extend([
             "--lh-surf",
-            execution.input_file(params.get("lhsurf"))
+            execution.input_file(params.get("lhsurf", None))
         ])
-    if params.get("rhsurf") is not None:
+    if params.get("rhsurf", None) is not None:
         cargs.extend([
             "--rh-surf",
-            execution.input_file(params.get("rhsurf"))
+            execution.input_file(params.get("rhsurf", None))
         ])
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
     cargs.extend([
         "--sd",
-        params.get("subjects_dir")
+        params.get("subjects_dir", None)
     ])
-    if params.get("min_border_white") is not None:
+    if params.get("min_border_white", None) is not None:
         cargs.extend([
             "--min_border_white",
-            str(params.get("min_border_white"))
+            str(params.get("min_border_white", None))
         ])
-    if params.get("max_border_white") is not None:
+    if params.get("max_border_white", None) is not None:
         cargs.extend([
             "--max_border_white",
-            str(params.get("max_border_white"))
+            str(params.get("max_border_white", None))
         ])
-    if params.get("min_gray_at_white_border") is not None:
+    if params.get("min_gray_at_white_border", None) is not None:
         cargs.extend([
             "--min_gray_at_white_border",
-            str(params.get("min_gray_at_white_border"))
+            str(params.get("min_gray_at_white_border", None))
         ])
-    if params.get("max_gray") is not None:
+    if params.get("max_gray", None) is not None:
         cargs.extend([
             "--max_gray",
-            str(params.get("max_gray"))
+            str(params.get("max_gray", None))
         ])
-    if params.get("max_gray_at_csf_border") is not None:
+    if params.get("max_gray_at_csf_border", None) is not None:
         cargs.extend([
             "--max_gray_at_csf_border",
-            str(params.get("max_gray_at_csf_border"))
+            str(params.get("max_gray_at_csf_border", None))
         ])
-    if params.get("min_gray_at_csf_border") is not None:
+    if params.get("min_gray_at_csf_border", None) is not None:
         cargs.extend([
             "--min_gray_at_csf_border",
-            str(params.get("min_gray_at_csf_border"))
+            str(params.get("min_gray_at_csf_border", None))
         ])
-    if params.get("max_csf") is not None:
+    if params.get("max_csf", None) is not None:
         cargs.extend([
             "--max_csf",
-            str(params.get("max_csf"))
+            str(params.get("max_csf", None))
         ])
     return cargs
 
@@ -247,18 +233,20 @@ def mris_autodet_gwstats_outputs(
     """
     ret = MrisAutodetGwstatsOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_file")),
+        output_file=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def mris_autodet_gwstats_execute(
     params: MrisAutodetGwstatsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisAutodetGwstatsOutputs:
     """
-    Manages the computation of the gray/white statistics used to place the white and
-    pial surfaces.
+    mris_autodet_gwstats
+    
+    Manages the computation of the gray/white statistics used to place the white
+    and pial surfaces.
     
     Author: FreeSurfer Developers
     
@@ -266,10 +254,12 @@ def mris_autodet_gwstats_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisAutodetGwstatsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_AUTODET_GWSTATS_METADATA)
     params = execution.params(params)
     cargs = mris_autodet_gwstats_cargs(params, execution)
     ret = mris_autodet_gwstats_outputs(params, execution)
@@ -296,8 +286,10 @@ def mris_autodet_gwstats(
     runner: Runner | None = None,
 ) -> MrisAutodetGwstatsOutputs:
     """
-    Manages the computation of the gray/white statistics used to place the white and
-    pial surfaces.
+    mris_autodet_gwstats
+    
+    Manages the computation of the gray/white statistics used to place the white
+    and pial surfaces.
     
     Author: FreeSurfer Developers
     
@@ -324,8 +316,6 @@ def mris_autodet_gwstats(
     Returns:
         NamedTuple of outputs (described in `MrisAutodetGwstatsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_AUTODET_GWSTATS_METADATA)
     params = mris_autodet_gwstats_params(
         output_file=output_file,
         t1w_volume=t1w_volume,
@@ -343,13 +333,13 @@ def mris_autodet_gwstats(
         min_gray_at_csf_border=min_gray_at_csf_border,
         max_csf=max_csf,
     )
-    return mris_autodet_gwstats_execute(params, execution)
+    return mris_autodet_gwstats_execute(params, runner)
 
 
 __all__ = [
     "MRIS_AUTODET_GWSTATS_METADATA",
     "MrisAutodetGwstatsOutputs",
-    "MrisAutodetGwstatsParameters",
     "mris_autodet_gwstats",
+    "mris_autodet_gwstats_execute",
     "mris_autodet_gwstats_params",
 ]