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

niwrap_freesurfer/freesurfer/stattablediff.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 STATTABLEDIFF_METADATA = Metadata(
-    id="3d94abfc9639ba1d887cf8a29a5610dc79fd89d8.boutiques",
+    id="0d32fce001061fdd4d4df206d102f4e4d60f9666.boutiques",
     name="stattablediff",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,22 @@ STATTABLEDIFF_METADATA = Metadata(
 
 
 StattablediffParameters = typing.TypedDict('StattablediffParameters', {
-    "__STYXTYPE__": typing.Literal["stattablediff"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/stattablediff"]],
+    "t1": InputPathType,
+    "t2": InputPathType,
+    "output": str,
+    "percent_diff": bool,
+    "percent_diff_t1": bool,
+    "percent_diff_t2": bool,
+    "multiply": typing.NotRequired[float | None],
+    "divide": typing.NotRequired[float | None],
+    "common": bool,
+    "remove_exvivo": bool,
+    "diff_subjects": bool,
+    "noreplace53": bool,
+})
+StattablediffParametersTagged = typing.TypedDict('StattablediffParametersTagged', {
+    "@type": typing.Literal["freesurfer/stattablediff"],
     "t1": InputPathType,
     "t2": InputPathType,
     "output": str,
@@ -28,43 +43,11 @@ StattablediffParameters = typing.TypedDict('StattablediffParameters', {
     "diff_subjects": bool,
     "noreplace53": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "stattablediff": stattablediff_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 {
-        "stattablediff": stattablediff_outputs,
-    }.get(t)
 
 
 class StattablediffOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `stattablediff(...)`.
+    Output object returned when calling `StattablediffParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -85,7 +68,7 @@ def stattablediff_params(
     remove_exvivo: bool = False,
     diff_subjects: bool = False,
     noreplace53: bool = False,
-) -> StattablediffParameters:
+) -> StattablediffParametersTagged:
     """
     Build parameters.
     
@@ -106,7 +89,7 @@ def stattablediff_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "stattablediff",
+        "@type": "freesurfer/stattablediff",
         "t1": t1,
         "t2": t2,
         "output": output,
@@ -140,32 +123,32 @@ def stattablediff_cargs(
     """
     cargs = []
     cargs.append("stattablediff")
-    cargs.append(execution.input_file(params.get("t1")))
-    cargs.append(execution.input_file(params.get("t2")))
-    cargs.append(params.get("output"))
-    if params.get("percent_diff"):
+    cargs.append(execution.input_file(params.get("t1", None)))
+    cargs.append(execution.input_file(params.get("t2", None)))
+    cargs.append(params.get("output", None))
+    if params.get("percent_diff", False):
         cargs.append("--percent")
-    if params.get("percent_diff_t1"):
+    if params.get("percent_diff_t1", False):
         cargs.append("--percent1")
-    if params.get("percent_diff_t2"):
+    if params.get("percent_diff_t2", False):
         cargs.append("--percent2")
-    if params.get("multiply") is not None:
+    if params.get("multiply", None) is not None:
         cargs.extend([
             "--mul",
-            str(params.get("multiply"))
+            str(params.get("multiply", None))
         ])
-    if params.get("divide") is not None:
+    if params.get("divide", None) is not None:
         cargs.extend([
             "--div",
-            str(params.get("divide"))
+            str(params.get("divide", None))
         ])
-    if params.get("common"):
+    if params.get("common", False):
         cargs.append("--common")
-    if params.get("remove_exvivo"):
+    if params.get("remove_exvivo", False):
         cargs.append("--rm-exvivo")
-    if params.get("diff_subjects"):
+    if params.get("diff_subjects", False):
         cargs.append("--diff-subjs")
-    if params.get("noreplace53"):
+    if params.get("noreplace53", False):
         cargs.append("--noreplace53")
     return cargs
 
@@ -185,16 +168,18 @@ def stattablediff_outputs(
     """
     ret = StattablediffOutputs(
         root=execution.output_file("."),
-        output_diff_table=execution.output_file(params.get("output")),
+        output_diff_table=execution.output_file(params.get("output", None)),
     )
     return ret
 
 
 def stattablediff_execute(
     params: StattablediffParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> StattablediffOutputs:
     """
+    stattablediff
+    
     Creates a table of the differences between two stats tables.
     
     Author: FreeSurfer Developers
@@ -203,10 +188,12 @@ def stattablediff_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `StattablediffOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(STATTABLEDIFF_METADATA)
     params = execution.params(params)
     cargs = stattablediff_cargs(params, execution)
     ret = stattablediff_outputs(params, execution)
@@ -230,6 +217,8 @@ def stattablediff(
     runner: Runner | None = None,
 ) -> StattablediffOutputs:
     """
+    stattablediff
+    
     Creates a table of the differences between two stats tables.
     
     Author: FreeSurfer Developers
@@ -253,8 +242,6 @@ def stattablediff(
     Returns:
         NamedTuple of outputs (described in `StattablediffOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(STATTABLEDIFF_METADATA)
     params = stattablediff_params(
         t1=t1,
         t2=t2,
@@ -269,13 +256,13 @@ def stattablediff(
         diff_subjects=diff_subjects,
         noreplace53=noreplace53,
     )
-    return stattablediff_execute(params, execution)
+    return stattablediff_execute(params, runner)
 
 
 __all__ = [
     "STATTABLEDIFF_METADATA",
     "StattablediffOutputs",
-    "StattablediffParameters",
     "stattablediff",
+    "stattablediff_execute",
     "stattablediff_params",
 ]

niwrap_freesurfer/freesurfer/stem2fname.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 STEM2FNAME_METADATA = Metadata(
-    id="ce5df98144f893b253582c44f3afd7f923d0d33d.boutiques",
+    id="9cf1f5f7cd0129324c326a089231814995dc912b.boutiques",
     name="stem2fname",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,18 @@ STEM2FNAME_METADATA = Metadata(
 
 
 Stem2fnameParameters = typing.TypedDict('Stem2fnameParameters', {
-    "__STYXTYPE__": typing.Literal["stem2fname"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/stem2fname"]],
+    "stem": str,
+})
+Stem2fnameParametersTagged = typing.TypedDict('Stem2fnameParametersTagged', {
+    "@type": typing.Literal["freesurfer/stem2fname"],
     "stem": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "stem2fname": stem2fname_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 {
-        "stem2fname": stem2fname_outputs,
-    }.get(t)
 
 
 class Stem2fnameOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `stem2fname(...)`.
+    Output object returned when calling `Stem2fnameParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +36,7 @@ class Stem2fnameOutputs(typing.NamedTuple):
 
 def stem2fname_params(
     stem: str,
-) -> Stem2fnameParameters:
+) -> Stem2fnameParametersTagged:
     """
     Build parameters.
     
@@ -74,7 +46,7 @@ def stem2fname_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "stem2fname",
+        "@type": "freesurfer/stem2fname",
         "stem": stem,
     }
     return params
@@ -95,7 +67,7 @@ def stem2fname_cargs(
     """
     cargs = []
     cargs.append("stem2fname")
-    cargs.append(params.get("stem"))
+    cargs.append(params.get("stem", None))
     return cargs
 
 
@@ -114,18 +86,20 @@ def stem2fname_outputs(
     """
     ret = Stem2fnameOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("stem") + ".[FORMAT]"),
+        output_file=execution.output_file(params.get("stem", None) + ".[FORMAT]"),
     )
     return ret
 
 
 def stem2fname_execute(
     params: Stem2fnameParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Stem2fnameOutputs:
     """
-    Determines the full filename with extension for a given file stem by checking
-    various formats.
+    stem2fname
+    
+    Determines the full filename with extension for a given file stem by
+    checking various formats.
     
     Author: FreeSurfer Developers
     
@@ -133,10 +107,12 @@ def stem2fname_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Stem2fnameOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(STEM2FNAME_METADATA)
     params = execution.params(params)
     cargs = stem2fname_cargs(params, execution)
     ret = stem2fname_outputs(params, execution)
@@ -149,8 +125,10 @@ def stem2fname(
     runner: Runner | None = None,
 ) -> Stem2fnameOutputs:
     """
-    Determines the full filename with extension for a given file stem by checking
-    various formats.
+    stem2fname
+    
+    Determines the full filename with extension for a given file stem by
+    checking various formats.
     
     Author: FreeSurfer Developers
     
@@ -162,18 +140,16 @@ def stem2fname(
     Returns:
         NamedTuple of outputs (described in `Stem2fnameOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(STEM2FNAME_METADATA)
     params = stem2fname_params(
         stem=stem,
     )
-    return stem2fname_execute(params, execution)
+    return stem2fname_execute(params, runner)
 
 
 __all__ = [
     "STEM2FNAME_METADATA",
     "Stem2fnameOutputs",
-    "Stem2fnameParameters",
     "stem2fname",
+    "stem2fname_execute",
     "stem2fname_params",
 ]

niwrap_freesurfer/freesurfer/surf2vol.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SURF2VOL_METADATA = Metadata(
-    id="cb9d30b60e852e42d3af84e07bf8e781d39d6242.boutiques",
+    id="2f13e7b99130c1abcbecb98db3d3979f7a4aec03.boutiques",
     name="surf2vol",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,27 @@ SURF2VOL_METADATA = Metadata(
 
 
 Surf2volParameters = typing.TypedDict('Surf2volParameters', {
-    "__STYXTYPE__": typing.Literal["surf2vol"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/surf2vol"]],
+    "fixed_surface": InputPathType,
+    "moving_surface": InputPathType,
+    "fixed_mri": InputPathType,
+    "moving_mri": InputPathType,
+    "output_file": typing.NotRequired[str | None],
+    "output_field": typing.NotRequired[str | None],
+    "output_affine": typing.NotRequired[str | None],
+    "output_surf": typing.NotRequired[str | None],
+    "output_surf_affine": typing.NotRequired[str | None],
+    "output_mesh": typing.NotRequired[str | None],
+    "spacing_x": typing.NotRequired[float | None],
+    "spacing_y": typing.NotRequired[float | None],
+    "spacing_z": typing.NotRequired[float | None],
+    "poisson_ratio": typing.NotRequired[float | None],
+    "dirty_factor": typing.NotRequired[float | None],
+    "debug_output": bool,
+    "cache_transform": typing.NotRequired[str | None],
+})
+Surf2volParametersTagged = typing.TypedDict('Surf2volParametersTagged', {
+    "@type": typing.Literal["freesurfer/surf2vol"],
     "fixed_surface": InputPathType,
     "moving_surface": InputPathType,
     "fixed_mri": InputPathType,
@@ -33,43 +53,11 @@ Surf2volParameters = typing.TypedDict('Surf2volParameters', {
     "debug_output": bool,
     "cache_transform": 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 {
-        "surf2vol": surf2vol_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 {
-        "surf2vol": surf2vol_outputs,
-    }.get(t)
 
 
 class Surf2volOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `surf2vol(...)`.
+    Output object returned when calling `Surf2volParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -84,8 +72,8 @@ def surf2vol_params(
     moving_surface: InputPathType,
     fixed_mri: InputPathType,
     moving_mri: InputPathType,
-    output_file: str | None = "out.mgz",
-    output_field: str | None = "out_field.mgz",
+    output_file: str | None = None,
+    output_field: str | None = None,
     output_affine: str | None = None,
     output_surf: str | None = None,
     output_surf_affine: str | None = None,
@@ -97,7 +85,7 @@ def surf2vol_params(
     dirty_factor: float | None = None,
     debug_output: bool = False,
     cache_transform: str | None = None,
-) -> Surf2volParameters:
+) -> Surf2volParametersTagged:
     """
     Build parameters.
     
@@ -127,7 +115,7 @@ def surf2vol_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "surf2vol",
+        "@type": "freesurfer/surf2vol",
         "fixed_surface": fixed_surface,
         "moving_surface": moving_surface,
         "fixed_mri": fixed_mri,
@@ -178,81 +166,81 @@ def surf2vol_cargs(
     cargs.append("surf2vol")
     cargs.extend([
         "-fixed_surf",
-        execution.input_file(params.get("fixed_surface"))
+        execution.input_file(params.get("fixed_surface", None))
     ])
     cargs.extend([
         "-moving_surf",
-        execution.input_file(params.get("moving_surface"))
+        execution.input_file(params.get("moving_surface", None))
     ])
     cargs.extend([
         "-fixed_mri",
-        execution.input_file(params.get("fixed_mri"))
+        execution.input_file(params.get("fixed_mri", None))
     ])
     cargs.extend([
         "-moving_mri",
-        execution.input_file(params.get("moving_mri"))
+        execution.input_file(params.get("moving_mri", None))
     ])
-    if params.get("output_file") is not None:
+    if params.get("output_file", None) is not None:
         cargs.extend([
             "-out",
-            params.get("output_file")
+            params.get("output_file", None)
         ])
-    if params.get("output_field") is not None:
+    if params.get("output_field", None) is not None:
         cargs.extend([
             "-out_field",
-            params.get("output_field")
+            params.get("output_field", None)
         ])
-    if params.get("output_affine") is not None:
+    if params.get("output_affine", None) is not None:
         cargs.extend([
             "-out_affine",
-            params.get("output_affine")
+            params.get("output_affine", None)
         ])
-    if params.get("output_surf") is not None:
+    if params.get("output_surf", None) is not None:
         cargs.extend([
             "-out_surf",
-            params.get("output_surf")
+            params.get("output_surf", None)
         ])
-    if params.get("output_surf_affine") is not None:
+    if params.get("output_surf_affine", None) is not None:
         cargs.extend([
             "-out_surf_affine",
-            params.get("output_surf_affine")
+            params.get("output_surf_affine", None)
         ])
-    if params.get("output_mesh") is not None:
+    if params.get("output_mesh", None) is not None:
         cargs.extend([
             "-out_mesh",
-            params.get("output_mesh")
+            params.get("output_mesh", None)
         ])
-    if params.get("spacing_x") is not None:
+    if params.get("spacing_x", None) is not None:
         cargs.extend([
             "-spacing_x",
-            str(params.get("spacing_x"))
+            str(params.get("spacing_x", None))
         ])
-    if params.get("spacing_y") is not None:
+    if params.get("spacing_y", None) is not None:
         cargs.extend([
             "-spacing_y",
-            str(params.get("spacing_y"))
+            str(params.get("spacing_y", None))
         ])
-    if params.get("spacing_z") is not None:
+    if params.get("spacing_z", None) is not None:
         cargs.extend([
             "-spacing_z",
-            str(params.get("spacing_z"))
+            str(params.get("spacing_z", None))
         ])
-    if params.get("poisson_ratio") is not None:
+    if params.get("poisson_ratio", None) is not None:
         cargs.extend([
             "-poisson",
-            str(params.get("poisson_ratio"))
+            str(params.get("poisson_ratio", None))
         ])
-    if params.get("dirty_factor") is not None:
+    if params.get("dirty_factor", None) is not None:
         cargs.extend([
             "-dirty",
-            str(params.get("dirty_factor"))
+            str(params.get("dirty_factor", None))
         ])
-    if params.get("debug_output"):
+    if params.get("debug_output", False):
         cargs.append("-dbg_output")
-    if params.get("cache_transform") is not None:
+    if params.get("cache_transform", None) is not None:
         cargs.extend([
             "-cache_transform",
-            params.get("cache_transform")
+            params.get("cache_transform", None)
         ])
     return cargs
 
@@ -272,17 +260,19 @@ def surf2vol_outputs(
     """
     ret = Surf2volOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_file")) if (params.get("output_file") is not None) else None,
-        output_field=execution.output_file(params.get("output_field")) if (params.get("output_field") is not None) else None,
+        output_file=execution.output_file(params.get("output_file", None)) if (params.get("output_file") is not None) else None,
+        output_field=execution.output_file(params.get("output_field", None)) if (params.get("output_field") is not None) else None,
     )
     return ret
 
 
 def surf2vol_execute(
     params: Surf2volParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Surf2volOutputs:
     """
+    surf2vol
+    
     Diffuse surface deformation to volumes using surface and MRI data.
     
     Author: FreeSurfer Developers
@@ -291,10 +281,12 @@ def surf2vol_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Surf2volOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF2VOL_METADATA)
     params = execution.params(params)
     cargs = surf2vol_cargs(params, execution)
     ret = surf2vol_outputs(params, execution)
@@ -307,8 +299,8 @@ def surf2vol(
     moving_surface: InputPathType,
     fixed_mri: InputPathType,
     moving_mri: InputPathType,
-    output_file: str | None = "out.mgz",
-    output_field: str | None = "out_field.mgz",
+    output_file: str | None = None,
+    output_field: str | None = None,
     output_affine: str | None = None,
     output_surf: str | None = None,
     output_surf_affine: str | None = None,
@@ -323,6 +315,8 @@ def surf2vol(
     runner: Runner | None = None,
 ) -> Surf2volOutputs:
     """
+    surf2vol
+    
     Diffuse surface deformation to volumes using surface and MRI data.
     
     Author: FreeSurfer Developers
@@ -355,8 +349,6 @@ def surf2vol(
     Returns:
         NamedTuple of outputs (described in `Surf2volOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SURF2VOL_METADATA)
     params = surf2vol_params(
         fixed_surface=fixed_surface,
         moving_surface=moving_surface,
@@ -376,13 +368,13 @@ def surf2vol(
         debug_output=debug_output,
         cache_transform=cache_transform,
     )
-    return surf2vol_execute(params, execution)
+    return surf2vol_execute(params, runner)
 
 
 __all__ = [
     "SURF2VOL_METADATA",
     "Surf2volOutputs",
-    "Surf2volParameters",
     "surf2vol",
+    "surf2vol_execute",
     "surf2vol_params",
 ]