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

niwrap_freesurfer/freesurfer/xcerebralseg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 XCEREBRALSEG_METADATA = Metadata(
-    id="5fb80211d047813ad88a87144a02240628a74311.boutiques",
+    id="cc6ba028a87f397d827eb7c7af93eafd8d88d4d3.boutiques",
     name="xcerebralseg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,20 @@ XCEREBRALSEG_METADATA = Metadata(
 
 
 XcerebralsegParameters = typing.TypedDict('XcerebralsegParameters', {
-    "__STYXTYPE__": typing.Literal["xcerebralseg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/xcerebralseg"]],
+    "subject": str,
+    "output_volume": typing.NotRequired[str | None],
+    "atlas": typing.NotRequired[str | None],
+    "mergevol": typing.NotRequired[str | None],
+    "source_volume": typing.NotRequired[str | None],
+    "no_stats": bool,
+    "seg1_name": typing.NotRequired[str | None],
+    "no_pons": bool,
+    "no_vermis": bool,
+    "threads": typing.NotRequired[float | None],
+})
+XcerebralsegParametersTagged = typing.TypedDict('XcerebralsegParametersTagged', {
+    "@type": typing.Literal["freesurfer/xcerebralseg"],
     "subject": str,
     "output_volume": typing.NotRequired[str | None],
     "atlas": typing.NotRequired[str | None],
@@ -26,43 +39,11 @@ XcerebralsegParameters = typing.TypedDict('XcerebralsegParameters', {
     "no_vermis": bool,
     "threads": 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 {
-        "xcerebralseg": xcerebralseg_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 {
-        "xcerebralseg": xcerebralseg_outputs,
-    }.get(t)
 
 
 class XcerebralsegOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `xcerebralseg(...)`.
+    Output object returned when calling `XcerebralsegParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,16 +53,16 @@ class XcerebralsegOutputs(typing.NamedTuple):
 
 def xcerebralseg_params(
     subject: str,
-    output_volume: str | None = "apas+head.mgz",
-    atlas: str | None = "/usr/local/freesurfer/average/aseg+spmhead+vermis+pons.ixi.gca",
-    mergevol: str | None = "aparc+aseg.mgz",
-    source_volume: str | None = "nu.mgz",
+    output_volume: str | None = None,
+    atlas: str | None = None,
+    mergevol: str | None = None,
+    source_volume: str | None = None,
     no_stats: bool = False,
     seg1_name: str | None = None,
     no_pons: bool = False,
     no_vermis: bool = False,
     threads: float | None = None,
-) -> XcerebralsegParameters:
+) -> XcerebralsegParametersTagged:
     """
     Build parameters.
     
@@ -102,7 +83,7 @@ def xcerebralseg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "xcerebralseg",
+        "@type": "freesurfer/xcerebralseg",
         "subject": subject,
         "no_stats": no_stats,
         "no_pons": no_pons,
@@ -140,43 +121,43 @@ def xcerebralseg_cargs(
     cargs.append("xcerebralseg")
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("output_volume") is not None:
+    if params.get("output_volume", None) is not None:
         cargs.extend([
             "--o",
-            params.get("output_volume")
+            params.get("output_volume", None)
         ])
-    if params.get("atlas") is not None:
+    if params.get("atlas", None) is not None:
         cargs.extend([
             "--atlas",
-            params.get("atlas")
+            params.get("atlas", None)
         ])
-    if params.get("mergevol") is not None:
+    if params.get("mergevol", None) is not None:
         cargs.extend([
             "--m",
-            params.get("mergevol")
+            params.get("mergevol", None)
         ])
-    if params.get("source_volume") is not None:
+    if params.get("source_volume", None) is not None:
         cargs.extend([
             "--srcvol",
-            params.get("source_volume")
+            params.get("source_volume", None)
         ])
-    if params.get("no_stats"):
+    if params.get("no_stats", False):
         cargs.append("--no-stats")
-    if params.get("seg1_name") is not None:
+    if params.get("seg1_name", None) is not None:
         cargs.extend([
             "--seg1",
-            params.get("seg1_name")
+            params.get("seg1_name", None)
         ])
-    if params.get("no_pons"):
+    if params.get("no_pons", False):
         cargs.append("--no-pons")
-    if params.get("no_vermis"):
+    if params.get("no_vermis", False):
         cargs.append("--no-vermis")
-    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))
         ])
     return cargs
 
@@ -203,9 +184,11 @@ def xcerebralseg_outputs(
 
 def xcerebralseg_execute(
     params: XcerebralsegParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> XcerebralsegOutputs:
     """
+    xcerebralseg
+    
     Tool for labeling extracerebral structures including sulcal CSF, skull/bone,
     head soft tissue, and air inside the head, merged with aparc+aseg.mgz
     segmentation for a whole head segmentation.
@@ -216,10 +199,12 @@ def xcerebralseg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `XcerebralsegOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(XCEREBRALSEG_METADATA)
     params = execution.params(params)
     cargs = xcerebralseg_cargs(params, execution)
     ret = xcerebralseg_outputs(params, execution)
@@ -229,10 +214,10 @@ def xcerebralseg_execute(
 
 def xcerebralseg(
     subject: str,
-    output_volume: str | None = "apas+head.mgz",
-    atlas: str | None = "/usr/local/freesurfer/average/aseg+spmhead+vermis+pons.ixi.gca",
-    mergevol: str | None = "aparc+aseg.mgz",
-    source_volume: str | None = "nu.mgz",
+    output_volume: str | None = None,
+    atlas: str | None = None,
+    mergevol: str | None = None,
+    source_volume: str | None = None,
     no_stats: bool = False,
     seg1_name: str | None = None,
     no_pons: bool = False,
@@ -241,6 +226,8 @@ def xcerebralseg(
     runner: Runner | None = None,
 ) -> XcerebralsegOutputs:
     """
+    xcerebralseg
+    
     Tool for labeling extracerebral structures including sulcal CSF, skull/bone,
     head soft tissue, and air inside the head, merged with aparc+aseg.mgz
     segmentation for a whole head segmentation.
@@ -266,8 +253,6 @@ def xcerebralseg(
     Returns:
         NamedTuple of outputs (described in `XcerebralsegOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(XCEREBRALSEG_METADATA)
     params = xcerebralseg_params(
         subject=subject,
         output_volume=output_volume,
@@ -280,13 +265,13 @@ def xcerebralseg(
         no_vermis=no_vermis,
         threads=threads,
     )
-    return xcerebralseg_execute(params, execution)
+    return xcerebralseg_execute(params, runner)
 
 
 __all__ = [
     "XCEREBRALSEG_METADATA",
     "XcerebralsegOutputs",
-    "XcerebralsegParameters",
     "xcerebralseg",
+    "xcerebralseg_execute",
     "xcerebralseg_params",
 ]

niwrap_freesurfer/freesurfer/xcorr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 XCORR_METADATA = Metadata(
-    id="a7f1ff8dc4d4bbe9012bab5846d66d5b73222d26.boutiques",
+    id="f8b9dd638b9f5e8810aaa75fbf39dd6dbf704d0c.boutiques",
     name="xcorr",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ XCORR_METADATA = Metadata(
 
 
 XcorrParameters = typing.TypedDict('XcorrParameters', {
-    "__STYXTYPE__": typing.Literal["xcorr"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/xcorr"]],
+    "input1": InputPathType,
+    "input2": InputPathType,
+    "output": str,
+    "log_file": typing.NotRequired[str | None],
+    "tmp_dir": typing.NotRequired[str | None],
+    "no_cleanup": bool,
+})
+XcorrParametersTagged = typing.TypedDict('XcorrParametersTagged', {
+    "@type": typing.Literal["freesurfer/xcorr"],
     "input1": InputPathType,
     "input2": InputPathType,
     "output": str,
@@ -22,43 +31,11 @@ XcorrParameters = typing.TypedDict('XcorrParameters', {
     "tmp_dir": typing.NotRequired[str | None],
     "no_cleanup": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "xcorr": xcorr_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 {
-        "xcorr": xcorr_outputs,
-    }.get(t)
 
 
 class XcorrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `xcorr(...)`.
+    Output object returned when calling `XcorrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +52,7 @@ def xcorr_params(
     log_file: str | None = None,
     tmp_dir: str | None = None,
     no_cleanup: bool = False,
-) -> XcorrParameters:
+) -> XcorrParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +67,7 @@ def xcorr_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "xcorr",
+        "@type": "freesurfer/xcorr",
         "input1": input1,
         "input2": input2,
         "output": output,
@@ -120,27 +97,27 @@ def xcorr_cargs(
     cargs.append("xcorr")
     cargs.extend([
         "--i1",
-        execution.input_file(params.get("input1"))
+        execution.input_file(params.get("input1", None))
     ])
     cargs.extend([
         "--i2",
-        execution.input_file(params.get("input2"))
+        execution.input_file(params.get("input2", None))
     ])
     cargs.extend([
         "--o",
-        params.get("output")
+        params.get("output", None)
     ])
-    if params.get("log_file") is not None:
+    if params.get("log_file", None) is not None:
         cargs.extend([
             "--log",
-            params.get("log_file")
+            params.get("log_file", None)
         ])
-    if params.get("tmp_dir") is not None:
+    if params.get("tmp_dir", None) is not None:
         cargs.extend([
             "--tmp",
-            params.get("tmp_dir")
+            params.get("tmp_dir", None)
         ])
-    if params.get("no_cleanup"):
+    if params.get("no_cleanup", False):
         cargs.append("--no-cleanup")
     return cargs
 
@@ -160,17 +137,19 @@ def xcorr_outputs(
     """
     ret = XcorrOutputs(
         root=execution.output_file("."),
-        out_xcorrfile=execution.output_file(params.get("output")),
-        log_output=execution.output_file(params.get("log_file")) if (params.get("log_file") is not None) else None,
+        out_xcorrfile=execution.output_file(params.get("output", None)),
+        log_output=execution.output_file(params.get("log_file", None)) if (params.get("log_file") is not None) else None,
     )
     return ret
 
 
 def xcorr_execute(
     params: XcorrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> XcorrOutputs:
     """
+    xcorr
+    
     Computes the voxel-for-voxel correlation coefficient between two volumes.
     
     Author: FreeSurfer Developers
@@ -179,10 +158,12 @@ def xcorr_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `XcorrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(XCORR_METADATA)
     params = execution.params(params)
     cargs = xcorr_cargs(params, execution)
     ret = xcorr_outputs(params, execution)
@@ -200,6 +181,8 @@ def xcorr(
     runner: Runner | None = None,
 ) -> XcorrOutputs:
     """
+    xcorr
+    
     Computes the voxel-for-voxel correlation coefficient between two volumes.
     
     Author: FreeSurfer Developers
@@ -217,8 +200,6 @@ def xcorr(
     Returns:
         NamedTuple of outputs (described in `XcorrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(XCORR_METADATA)
     params = xcorr_params(
         input1=input1,
         input2=input2,
@@ -227,13 +208,13 @@ def xcorr(
         tmp_dir=tmp_dir,
         no_cleanup=no_cleanup,
     )
-    return xcorr_execute(params, execution)
+    return xcorr_execute(params, runner)
 
 
 __all__ = [
     "XCORR_METADATA",
     "XcorrOutputs",
-    "XcorrParameters",
     "xcorr",
+    "xcorr_execute",
     "xcorr_params",
 ]

niwrap_freesurfer/freesurfer/xfmrot.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 XFMROT_METADATA = Metadata(
-    id="31f4e9f4af4d5258649b001584ed13a30a8aab5e.boutiques",
+    id="8a5ccaa8ac132b29b0a8eb8461062c564cf46d22.boutiques",
     name="xfmrot",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ XFMROT_METADATA = Metadata(
 
 
 XfmrotParameters = typing.TypedDict('XfmrotParameters', {
-    "__STYXTYPE__": typing.Literal["xfmrot"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/xfmrot"]],
+    "transform_file": InputPathType,
+    "input_vector_file": InputPathType,
+    "output_vector_file": typing.NotRequired[str | None],
+})
+XfmrotParametersTagged = typing.TypedDict('XfmrotParametersTagged', {
+    "@type": typing.Literal["freesurfer/xfmrot"],
     "transform_file": InputPathType,
     "input_vector_file": InputPathType,
     "output_vector_file": 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 {
-        "xfmrot": xfmrot_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 {
-        "xfmrot": xfmrot_outputs,
-    }.get(t)
 
 
 class XfmrotOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `xfmrot(...)`.
+    Output object returned when calling `XfmrotParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def xfmrot_params(
     transform_file: InputPathType,
     input_vector_file: InputPathType,
     output_vector_file: str | None = None,
-) -> XfmrotParameters:
+) -> XfmrotParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +56,7 @@ def xfmrot_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "xfmrot",
+        "@type": "freesurfer/xfmrot",
         "transform_file": transform_file,
         "input_vector_file": input_vector_file,
     }
@@ -106,10 +80,10 @@ def xfmrot_cargs(
     """
     cargs = []
     cargs.append("xfmrot")
-    cargs.append(execution.input_file(params.get("transform_file")))
-    cargs.append(execution.input_file(params.get("input_vector_file")))
-    if params.get("output_vector_file") is not None:
-        cargs.append(params.get("output_vector_file"))
+    cargs.append(execution.input_file(params.get("transform_file", None)))
+    cargs.append(execution.input_file(params.get("input_vector_file", None)))
+    if params.get("output_vector_file", None) is not None:
+        cargs.append(params.get("output_vector_file", None))
     return cargs
 
 
@@ -128,18 +102,20 @@ def xfmrot_outputs(
     """
     ret = XfmrotOutputs(
         root=execution.output_file("."),
-        transformed_vector=execution.output_file(params.get("output_vector_file")) if (params.get("output_vector_file") is not None) else None,
+        transformed_vector=execution.output_file(params.get("output_vector_file", None)) if (params.get("output_vector_file") is not None) else None,
     )
     return ret
 
 
 def xfmrot_execute(
     params: XfmrotParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> XfmrotOutputs:
     """
-    Tool to apply a transformation defined in a transform file to an input vector
-    file.
+    xfmrot
+    
+    Tool to apply a transformation defined in a transform file to an input
+    vector file.
     
     Author: FreeSurfer Developers
     
@@ -147,10 +123,12 @@ def xfmrot_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `XfmrotOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(XFMROT_METADATA)
     params = execution.params(params)
     cargs = xfmrot_cargs(params, execution)
     ret = xfmrot_outputs(params, execution)
@@ -165,8 +143,10 @@ def xfmrot(
     runner: Runner | None = None,
 ) -> XfmrotOutputs:
     """
-    Tool to apply a transformation defined in a transform file to an input vector
-    file.
+    xfmrot
+    
+    Tool to apply a transformation defined in a transform file to an input
+    vector file.
     
     Author: FreeSurfer Developers
     
@@ -183,20 +163,18 @@ def xfmrot(
     Returns:
         NamedTuple of outputs (described in `XfmrotOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(XFMROT_METADATA)
     params = xfmrot_params(
         transform_file=transform_file,
         input_vector_file=input_vector_file,
         output_vector_file=output_vector_file,
     )
-    return xfmrot_execute(params, execution)
+    return xfmrot_execute(params, runner)
 
 
 __all__ = [
     "XFMROT_METADATA",
     "XfmrotOutputs",
-    "XfmrotParameters",
     "xfmrot",
+    "xfmrot_execute",
     "xfmrot_params",
 ]