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

niwrap_freesurfer/freesurfer/dmri_match.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_MATCH_METADATA = Metadata(
-    id="08636d4bb6e04e9a20b447a24991c89c1b588731.boutiques",
+    id="3e19241fdc2d436026c2b1e5858939e139f1083c.boutiques",
     name="dmri_match",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,21 @@ DMRI_MATCH_METADATA = Metadata(
 
 
 DmriMatchParameters = typing.TypedDict('DmriMatchParameters', {
-    "__STYXTYPE__": typing.Literal["dmri_match"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dmri_match"]],
+    "parcellation1": InputPathType,
+    "parcellation2": InputPathType,
+    "num_clusters": float,
+    "clustering_path1": InputPathType,
+    "clustering_path2": InputPathType,
+    "labels": bool,
+    "euclidean": bool,
+    "bounding_box": bool,
+    "symmetry": bool,
+    "inter_hemi_ratio_removal": typing.NotRequired[str | None],
+    "output": str,
+})
+DmriMatchParametersTagged = typing.TypedDict('DmriMatchParametersTagged', {
+    "@type": typing.Literal["freesurfer/dmri_match"],
     "parcellation1": InputPathType,
     "parcellation2": InputPathType,
     "num_clusters": float,
@@ -27,43 +41,11 @@ DmriMatchParameters = typing.TypedDict('DmriMatchParameters', {
     "inter_hemi_ratio_removal": typing.NotRequired[str | None],
     "output": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "dmri_match": dmri_match_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 {
-        "dmri_match": dmri_match_outputs,
-    }.get(t)
 
 
 class DmriMatchOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dmri_match(...)`.
+    Output object returned when calling `DmriMatchParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -83,7 +65,7 @@ def dmri_match_params(
     bounding_box: bool = False,
     symmetry: bool = False,
     inter_hemi_ratio_removal: str | None = None,
-) -> DmriMatchParameters:
+) -> DmriMatchParametersTagged:
     """
     Build parameters.
     
@@ -105,7 +87,7 @@ def dmri_match_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dmri_match",
+        "@type": "freesurfer/dmri_match",
         "parcellation1": parcellation1,
         "parcellation2": parcellation2,
         "num_clusters": num_clusters,
@@ -139,37 +121,37 @@ def dmri_match_cargs(
     cargs.append("dmri_match")
     cargs.extend([
         "-s1",
-        execution.input_file(params.get("parcellation1"))
+        execution.input_file(params.get("parcellation1", None))
     ])
     cargs.extend([
         "-s2",
-        execution.input_file(params.get("parcellation2"))
+        execution.input_file(params.get("parcellation2", None))
     ])
     cargs.extend([
         "-c",
-        str(params.get("num_clusters"))
+        str(params.get("num_clusters", None))
     ])
     cargs.extend([
         "-h1",
-        execution.input_file(params.get("clustering_path1"))
+        execution.input_file(params.get("clustering_path1", None))
     ])
     cargs.extend([
         "-h2",
-        execution.input_file(params.get("clustering_path2"))
+        execution.input_file(params.get("clustering_path2", None))
     ])
-    if params.get("labels"):
+    if params.get("labels", False):
         cargs.append("-labels")
-    if params.get("euclidean"):
+    if params.get("euclidean", False):
         cargs.append("-euclid")
-    if params.get("bounding_box"):
+    if params.get("bounding_box", False):
         cargs.append("-bb")
-    if params.get("symmetry"):
+    if params.get("symmetry", False):
         cargs.append("-sym")
-    if params.get("inter_hemi_ratio_removal") is not None:
-        cargs.append(params.get("inter_hemi_ratio_removal"))
+    if params.get("inter_hemi_ratio_removal", None) is not None:
+        cargs.append(params.get("inter_hemi_ratio_removal", None))
     cargs.extend([
         "-o",
-        params.get("output")
+        params.get("output", None)
     ])
     return cargs
 
@@ -189,16 +171,18 @@ def dmri_match_outputs(
     """
     ret = DmriMatchOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output")),
+        output_file=execution.output_file(params.get("output", None)),
     )
     return ret
 
 
 def dmri_match_execute(
     params: DmriMatchParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DmriMatchOutputs:
     """
+    dmri_match
+    
     Tool for matching diffusion MRI parcellations.
     
     Author: FreeSurfer Developers
@@ -207,10 +191,12 @@ def dmri_match_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DmriMatchOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DMRI_MATCH_METADATA)
     params = execution.params(params)
     cargs = dmri_match_cargs(params, execution)
     ret = dmri_match_outputs(params, execution)
@@ -233,6 +219,8 @@ def dmri_match(
     runner: Runner | None = None,
 ) -> DmriMatchOutputs:
     """
+    dmri_match
+    
     Tool for matching diffusion MRI parcellations.
     
     Author: FreeSurfer Developers
@@ -257,8 +245,6 @@ def dmri_match(
     Returns:
         NamedTuple of outputs (described in `DmriMatchOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DMRI_MATCH_METADATA)
     params = dmri_match_params(
         parcellation1=parcellation1,
         parcellation2=parcellation2,
@@ -272,13 +258,13 @@ def dmri_match(
         inter_hemi_ratio_removal=inter_hemi_ratio_removal,
         output=output,
     )
-    return dmri_match_execute(params, execution)
+    return dmri_match_execute(params, runner)
 
 
 __all__ = [
     "DMRI_MATCH_METADATA",
     "DmriMatchOutputs",
-    "DmriMatchParameters",
     "dmri_match",
+    "dmri_match_execute",
     "dmri_match_params",
 ]

niwrap_freesurfer/freesurfer/dmri_mergepaths.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_MERGEPATHS_METADATA = Metadata(
-    id="a806a559aa7a4e196c0f4f692e84bf6c75a34049.boutiques",
+    id="d09f39b5969ca1e494eb59099da10470db2c3ada.boutiques",
     name="dmri_mergepaths",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ DMRI_MERGEPATHS_METADATA = Metadata(
 
 
 DmriMergepathsParameters = typing.TypedDict('DmriMergepathsParameters', {
-    "__STYXTYPE__": typing.Literal["dmri_mergepaths"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dmri_mergepaths"]],
+    "input_volumes": list[InputPathType],
+    "input_directory": typing.NotRequired[str | None],
+    "output_volume": str,
+    "color_table": InputPathType,
+    "threshold": float,
+    "debug": bool,
+    "check_opts": bool,
+})
+DmriMergepathsParametersTagged = typing.TypedDict('DmriMergepathsParametersTagged', {
+    "@type": typing.Literal["freesurfer/dmri_mergepaths"],
     "input_volumes": list[InputPathType],
     "input_directory": typing.NotRequired[str | None],
     "output_volume": str,
@@ -23,42 +33,11 @@ DmriMergepathsParameters = typing.TypedDict('DmriMergepathsParameters', {
     "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 {
-        "dmri_mergepaths": dmri_mergepaths_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 DmriMergepathsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dmri_mergepaths(...)`.
+    Output object returned when calling `DmriMergepathsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,7 +51,7 @@ def dmri_mergepaths_params(
     input_directory: str | None = None,
     debug: bool = False,
     check_opts: bool = False,
-) -> DmriMergepathsParameters:
+) -> DmriMergepathsParametersTagged:
     """
     Build parameters.
     
@@ -89,7 +68,7 @@ def dmri_mergepaths_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dmri_mergepaths",
+        "@type": "freesurfer/dmri_mergepaths",
         "input_volumes": input_volumes,
         "output_volume": output_volume,
         "color_table": color_table,
@@ -117,27 +96,27 @@ def dmri_mergepaths_cargs(
     """
     cargs = []
     cargs.append("dmri_mergepaths")
-    cargs.extend([execution.input_file(f) for f in params.get("input_volumes")])
-    if params.get("input_directory") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("input_volumes", None)])
+    if params.get("input_directory", None) is not None:
         cargs.extend([
             "--indir",
-            params.get("input_directory")
+            params.get("input_directory", None)
         ])
     cargs.extend([
         "--out",
-        params.get("output_volume")
+        params.get("output_volume", None)
     ])
     cargs.extend([
         "--ctab",
-        execution.input_file(params.get("color_table"))
+        execution.input_file(params.get("color_table", None))
     ])
     cargs.extend([
         "--thresh",
-        str(params.get("threshold"))
+        str(params.get("threshold", None))
     ])
-    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
 
@@ -163,9 +142,11 @@ def dmri_mergepaths_outputs(
 
 def dmri_mergepaths_execute(
     params: DmriMergepathsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DmriMergepathsOutputs:
     """
+    dmri_mergepaths
+    
     A tool for merging diffusion MRI path data.
     
     Author: FreeSurfer Developers
@@ -174,10 +155,12 @@ def dmri_mergepaths_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DmriMergepathsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DMRI_MERGEPATHS_METADATA)
     params = execution.params(params)
     cargs = dmri_mergepaths_cargs(params, execution)
     ret = dmri_mergepaths_outputs(params, execution)
@@ -196,6 +179,8 @@ def dmri_mergepaths(
     runner: Runner | None = None,
 ) -> DmriMergepathsOutputs:
     """
+    dmri_mergepaths
+    
     A tool for merging diffusion MRI path data.
     
     Author: FreeSurfer Developers
@@ -215,8 +200,6 @@ def dmri_mergepaths(
     Returns:
         NamedTuple of outputs (described in `DmriMergepathsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DMRI_MERGEPATHS_METADATA)
     params = dmri_mergepaths_params(
         input_volumes=input_volumes,
         input_directory=input_directory,
@@ -226,13 +209,13 @@ def dmri_mergepaths(
         debug=debug,
         check_opts=check_opts,
     )
-    return dmri_mergepaths_execute(params, execution)
+    return dmri_mergepaths_execute(params, runner)
 
 
 __all__ = [
     "DMRI_MERGEPATHS_METADATA",
     "DmriMergepathsOutputs",
-    "DmriMergepathsParameters",
     "dmri_mergepaths",
+    "dmri_mergepaths_execute",
     "dmri_mergepaths_params",
 ]

niwrap_freesurfer/freesurfer/dmri_motion.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_MOTION_METADATA = Metadata(
-    id="cab0386753362d60558aa9f8bff96a94f4b5b4f2.boutiques",
+    id="ada06263395e23a1b2f1d44d26c8631a89c17b54.boutiques",
     name="dmri_motion",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,21 @@ DMRI_MOTION_METADATA = Metadata(
 
 
 DmriMotionParameters = typing.TypedDict('DmriMotionParameters', {
-    "__STYXTYPE__": typing.Literal["dmri_motion"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dmri_motion"]],
+    "outfile": InputPathType,
+    "outf": typing.NotRequired[InputPathType | None],
+    "mat": typing.NotRequired[InputPathType | None],
+    "dwi": typing.NotRequired[list[InputPathType] | None],
+    "bval": typing.NotRequired[list[InputPathType] | None],
+    "threshold": typing.NotRequired[float | None],
+    "diffusivity": typing.NotRequired[float | None],
+    "debug": bool,
+    "checkopts": bool,
+    "help": bool,
+    "version": bool,
+})
+DmriMotionParametersTagged = typing.TypedDict('DmriMotionParametersTagged', {
+    "@type": typing.Literal["freesurfer/dmri_motion"],
     "outfile": InputPathType,
     "outf": typing.NotRequired[InputPathType | None],
     "mat": typing.NotRequired[InputPathType | None],
@@ -27,43 +41,11 @@ DmriMotionParameters = typing.TypedDict('DmriMotionParameters', {
     "help": bool,
     "version": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "dmri_motion": dmri_motion_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 {
-        "dmri_motion": dmri_motion_outputs,
-    }.get(t)
 
 
 class DmriMotionOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dmri_motion(...)`.
+    Output object returned when calling `DmriMotionParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,13 +61,13 @@ def dmri_motion_params(
     mat: InputPathType | None = None,
     dwi: list[InputPathType] | None = None,
     bval: list[InputPathType] | None = None,
-    threshold: float | None = 100,
-    diffusivity: float | None = 0.001,
+    threshold: float | None = None,
+    diffusivity: float | None = None,
     debug: bool = False,
     checkopts: bool = False,
     help_: bool = False,
     version: bool = False,
-) -> DmriMotionParameters:
+) -> DmriMotionParametersTagged:
     """
     Build parameters.
     
@@ -105,7 +87,7 @@ def dmri_motion_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dmri_motion",
+        "@type": "freesurfer/dmri_motion",
         "outfile": outfile,
         "debug": debug,
         "checkopts": checkopts,
@@ -144,45 +126,45 @@ def dmri_motion_cargs(
     cargs.append("dmri_motion")
     cargs.extend([
         "--out",
-        execution.input_file(params.get("outfile"))
+        execution.input_file(params.get("outfile", None))
     ])
-    if params.get("outf") is not None:
+    if params.get("outf", None) is not None:
         cargs.extend([
             "--outf",
-            execution.input_file(params.get("outf"))
+            execution.input_file(params.get("outf", None))
         ])
-    if params.get("mat") is not None:
+    if params.get("mat", None) is not None:
         cargs.extend([
             "--mat",
-            execution.input_file(params.get("mat"))
+            execution.input_file(params.get("mat", None))
         ])
-    if params.get("dwi") is not None:
+    if params.get("dwi", None) is not None:
         cargs.extend([
             "--dwi",
-            *[execution.input_file(f) for f in params.get("dwi")]
+            *[execution.input_file(f) for f in params.get("dwi", None)]
         ])
-    if params.get("bval") is not None:
+    if params.get("bval", None) is not None:
         cargs.extend([
             "--bval",
-            *[execution.input_file(f) for f in params.get("bval")]
+            *[execution.input_file(f) for f in params.get("bval", None)]
         ])
-    if params.get("threshold") is not None:
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "--T",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    if params.get("diffusivity") is not None:
+    if params.get("diffusivity", None) is not None:
         cargs.extend([
             "--D",
-            str(params.get("diffusivity"))
+            str(params.get("diffusivity", None))
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("checkopts"):
+    if params.get("checkopts", False):
         cargs.append("--checkopts")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
     return cargs
 
@@ -202,17 +184,19 @@ def dmri_motion_outputs(
     """
     ret = DmriMotionOutputs(
         root=execution.output_file("."),
-        motion_measures_out=execution.output_file(pathlib.Path(params.get("outfile")).name),
-        frame_by_frame_out=execution.output_file(pathlib.Path(params.get("outf")).name) if (params.get("outf") is not None) else None,
+        motion_measures_out=execution.output_file(pathlib.Path(params.get("outfile", None)).name),
+        frame_by_frame_out=execution.output_file(pathlib.Path(params.get("outf", None)).name) if (params.get("outf") is not None) else None,
     )
     return ret
 
 
 def dmri_motion_execute(
     params: DmriMotionParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DmriMotionOutputs:
     """
+    dmri_motion
+    
     A tool for calculating motion measures from DWI scans.
     
     Author: FreeSurfer Developers
@@ -221,10 +205,12 @@ def dmri_motion_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DmriMotionOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DMRI_MOTION_METADATA)
     params = execution.params(params)
     cargs = dmri_motion_cargs(params, execution)
     ret = dmri_motion_outputs(params, execution)
@@ -238,8 +224,8 @@ def dmri_motion(
     mat: InputPathType | None = None,
     dwi: list[InputPathType] | None = None,
     bval: list[InputPathType] | None = None,
-    threshold: float | None = 100,
-    diffusivity: float | None = 0.001,
+    threshold: float | None = None,
+    diffusivity: float | None = None,
     debug: bool = False,
     checkopts: bool = False,
     help_: bool = False,
@@ -247,6 +233,8 @@ def dmri_motion(
     runner: Runner | None = None,
 ) -> DmriMotionOutputs:
     """
+    dmri_motion
+    
     A tool for calculating motion measures from DWI scans.
     
     Author: FreeSurfer Developers
@@ -269,8 +257,6 @@ def dmri_motion(
     Returns:
         NamedTuple of outputs (described in `DmriMotionOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DMRI_MOTION_METADATA)
     params = dmri_motion_params(
         outfile=outfile,
         outf=outf,
@@ -284,13 +270,13 @@ def dmri_motion(
         help_=help_,
         version=version,
     )
-    return dmri_motion_execute(params, execution)
+    return dmri_motion_execute(params, runner)
 
 
 __all__ = [
     "DMRI_MOTION_METADATA",
     "DmriMotionOutputs",
-    "DmriMotionParameters",
     "dmri_motion",
+    "dmri_motion_execute",
     "dmri_motion_params",
 ]