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

niwrap_freesurfer/freesurfer/export_gcam.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 EXPORT_GCAM_METADATA = Metadata(
-    id="433fb1878c30c38bab33359daa220e7ac52950c8.boutiques",
+    id="3b19d60cb17d730d36308a8cf56655ae554738ff.boutiques",
     name="exportGcam",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ EXPORT_GCAM_METADATA = Metadata(
 
 
 ExportGcamParameters = typing.TypedDict('ExportGcamParameters', {
-    "__STYXTYPE__": typing.Literal["exportGcam"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/exportGcam"]],
+    "fixed": InputPathType,
+    "moving": InputPathType,
+    "morph": InputPathType,
+    "out_gcam": str,
+    "zlib_buffer": typing.NotRequired[float | None],
+    "bbox_threshold": typing.NotRequired[float | None],
+    "interp_method": typing.NotRequired[typing.Literal["linear", "nearest"] | None],
+    "test": bool,
+})
+ExportGcamParametersTagged = typing.TypedDict('ExportGcamParametersTagged', {
+    "@type": typing.Literal["freesurfer/exportGcam"],
     "fixed": InputPathType,
     "moving": InputPathType,
     "morph": InputPathType,
@@ -24,43 +35,11 @@ ExportGcamParameters = typing.TypedDict('ExportGcamParameters', {
     "interp_method": typing.NotRequired[typing.Literal["linear", "nearest"] | None],
     "test": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "exportGcam": export_gcam_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 {
-        "exportGcam": export_gcam_outputs,
-    }.get(t)
 
 
 class ExportGcamOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `export_gcam(...)`.
+    Output object returned when calling `ExportGcamParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,9 +54,9 @@ def export_gcam_params(
     out_gcam: str,
     zlib_buffer: float | None = None,
     bbox_threshold: float | None = None,
-    interp_method: typing.Literal["linear", "nearest"] | None = "linear",
+    interp_method: typing.Literal["linear", "nearest"] | None = None,
     test: bool = False,
-) -> ExportGcamParameters:
+) -> ExportGcamParametersTagged:
     """
     Build parameters.
     
@@ -97,7 +76,7 @@ def export_gcam_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "exportGcam",
+        "@type": "freesurfer/exportGcam",
         "fixed": fixed,
         "moving": moving,
         "morph": morph,
@@ -130,36 +109,36 @@ def export_gcam_cargs(
     cargs.append("exportGcam")
     cargs.extend([
         "--fixed",
-        execution.input_file(params.get("fixed"))
+        execution.input_file(params.get("fixed", None))
     ])
     cargs.extend([
         "--moving",
-        execution.input_file(params.get("moving"))
+        execution.input_file(params.get("moving", None))
     ])
     cargs.extend([
         "--morph",
-        execution.input_file(params.get("morph"))
+        execution.input_file(params.get("morph", None))
     ])
     cargs.extend([
         "--out_gcam",
-        params.get("out_gcam")
+        params.get("out_gcam", None)
     ])
-    if params.get("zlib_buffer") is not None:
+    if params.get("zlib_buffer", None) is not None:
         cargs.extend([
             "--zlib_buffer",
-            str(params.get("zlib_buffer"))
+            str(params.get("zlib_buffer", None))
         ])
-    if params.get("bbox_threshold") is not None:
+    if params.get("bbox_threshold", None) is not None:
         cargs.extend([
             "--bbox_threshold",
-            str(params.get("bbox_threshold"))
+            str(params.get("bbox_threshold", None))
         ])
-    if params.get("interp_method") is not None:
+    if params.get("interp_method", None) is not None:
         cargs.extend([
             "--interp",
-            params.get("interp_method")
+            params.get("interp_method", None)
         ])
-    if params.get("test"):
+    if params.get("test", False):
         cargs.append("--test")
     return cargs
 
@@ -179,17 +158,20 @@ def export_gcam_outputs(
     """
     ret = ExportGcamOutputs(
         root=execution.output_file("."),
-        output_gcam_file=execution.output_file(params.get("out_gcam")),
+        output_gcam_file=execution.output_file(params.get("out_gcam", None)),
     )
     return ret
 
 
 def export_gcam_execute(
     params: ExportGcamParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ExportGcamOutputs:
     """
-    A tool for exporting GCAM (Geodesic Coordinate-based Anatomic Mapping) morphs.
+    exportGcam
+    
+    A tool for exporting GCAM (Geodesic Coordinate-based Anatomic Mapping)
+    morphs.
     
     Author: FreeSurfer Developers
     
@@ -197,10 +179,12 @@ def export_gcam_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ExportGcamOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(EXPORT_GCAM_METADATA)
     params = execution.params(params)
     cargs = export_gcam_cargs(params, execution)
     ret = export_gcam_outputs(params, execution)
@@ -215,12 +199,15 @@ def export_gcam(
     out_gcam: str,
     zlib_buffer: float | None = None,
     bbox_threshold: float | None = None,
-    interp_method: typing.Literal["linear", "nearest"] | None = "linear",
+    interp_method: typing.Literal["linear", "nearest"] | None = None,
     test: bool = False,
     runner: Runner | None = None,
 ) -> ExportGcamOutputs:
     """
-    A tool for exporting GCAM (Geodesic Coordinate-based Anatomic Mapping) morphs.
+    exportGcam
+    
+    A tool for exporting GCAM (Geodesic Coordinate-based Anatomic Mapping)
+    morphs.
     
     Author: FreeSurfer Developers
     
@@ -242,8 +229,6 @@ def export_gcam(
     Returns:
         NamedTuple of outputs (described in `ExportGcamOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(EXPORT_GCAM_METADATA)
     params = export_gcam_params(
         fixed=fixed,
         moving=moving,
@@ -254,13 +239,13 @@ def export_gcam(
         interp_method=interp_method,
         test=test,
     )
-    return export_gcam_execute(params, execution)
+    return export_gcam_execute(params, runner)
 
 
 __all__ = [
     "EXPORT_GCAM_METADATA",
     "ExportGcamOutputs",
-    "ExportGcamParameters",
     "export_gcam",
+    "export_gcam_execute",
     "export_gcam_params",
 ]

niwrap_freesurfer/freesurfer/extract_seg_waveform.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 EXTRACT_SEG_WAVEFORM_METADATA = Metadata(
-    id="1e8d726c7b2975eda55d107c6a157a6568cc1f02.boutiques",
+    id="0c14a7e22cc624b467246c753b26e8a0c353711a.boutiques",
     name="extract_seg_waveform",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ EXTRACT_SEG_WAVEFORM_METADATA = Metadata(
 
 
 ExtractSegWaveformParameters = typing.TypedDict('ExtractSegWaveformParameters', {
-    "__STYXTYPE__": typing.Literal["extract_seg_waveform"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/extract_seg_waveform"]],
+    "seg_file": InputPathType,
+    "seg_indices": list[float],
+    "input_volume": InputPathType,
+    "reg_file": InputPathType,
+    "vsm_file": typing.NotRequired[InputPathType | None],
+    "regheader_flag": bool,
+    "demean_flag": bool,
+    "output_file": str,
+})
+ExtractSegWaveformParametersTagged = typing.TypedDict('ExtractSegWaveformParametersTagged', {
+    "@type": typing.Literal["freesurfer/extract_seg_waveform"],
     "seg_file": InputPathType,
     "seg_indices": list[float],
     "input_volume": InputPathType,
@@ -24,42 +35,11 @@ ExtractSegWaveformParameters = typing.TypedDict('ExtractSegWaveformParameters',
     "demean_flag": bool,
     "output_file": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "extract_seg_waveform": extract_seg_waveform_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 ExtractSegWaveformOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `extract_seg_waveform(...)`.
+    Output object returned when calling `ExtractSegWaveformParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,7 +54,7 @@ def extract_seg_waveform_params(
     vsm_file: InputPathType | None = None,
     regheader_flag: bool = False,
     demean_flag: bool = False,
-) -> ExtractSegWaveformParameters:
+) -> ExtractSegWaveformParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +71,7 @@ def extract_seg_waveform_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "extract_seg_waveform",
+        "@type": "freesurfer/extract_seg_waveform",
         "seg_file": seg_file,
         "seg_indices": seg_indices,
         "input_volume": input_volume,
@@ -122,32 +102,32 @@ def extract_seg_waveform_cargs(
     cargs.append("extract_seg_waveform")
     cargs.extend([
         "--seg",
-        execution.input_file(params.get("seg_file"))
+        execution.input_file(params.get("seg_file", None))
     ])
     cargs.extend([
         "--id",
-        *map(str, params.get("seg_indices"))
+        *map(str, params.get("seg_indices", None))
     ])
     cargs.extend([
         "--i",
-        execution.input_file(params.get("input_volume"))
+        execution.input_file(params.get("input_volume", None))
     ])
     cargs.extend([
         "--reg",
-        execution.input_file(params.get("reg_file"))
+        execution.input_file(params.get("reg_file", None))
     ])
-    if params.get("vsm_file") is not None:
+    if params.get("vsm_file", None) is not None:
         cargs.extend([
             "--vsm",
-            execution.input_file(params.get("vsm_file"))
+            execution.input_file(params.get("vsm_file", None))
         ])
-    if params.get("regheader_flag"):
+    if params.get("regheader_flag", False):
         cargs.append("--regheader")
-    if params.get("demean_flag"):
+    if params.get("demean_flag", False):
         cargs.append("--demean")
     cargs.extend([
         "--o",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
     return cargs
 
@@ -173,14 +153,16 @@ def extract_seg_waveform_outputs(
 
 def extract_seg_waveform_execute(
     params: ExtractSegWaveformParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ExtractSegWaveformOutputs:
     """
-    This program extracts an average waveform from an input volume where the average
-    is computed over the voxels in the given segmentation indices. The input volume
-    is mapped to the space of the segmentation given the registration, and if a
-    voxel shift map (VSM) is supplied, it is applied simultaneously as part of the
-    transform.
+    extract_seg_waveform
+    
+    This program extracts an average waveform from an input volume where the
+    average is computed over the voxels in the given segmentation indices. The
+    input volume is mapped to the space of the segmentation given the
+    registration, and if a voxel shift map (VSM) is supplied, it is applied
+    simultaneously as part of the transform.
     
     Author: FreeSurfer Developers
     
@@ -188,10 +170,12 @@ def extract_seg_waveform_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ExtractSegWaveformOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(EXTRACT_SEG_WAVEFORM_METADATA)
     params = execution.params(params)
     cargs = extract_seg_waveform_cargs(params, execution)
     ret = extract_seg_waveform_outputs(params, execution)
@@ -211,11 +195,13 @@ def extract_seg_waveform(
     runner: Runner | None = None,
 ) -> ExtractSegWaveformOutputs:
     """
-    This program extracts an average waveform from an input volume where the average
-    is computed over the voxels in the given segmentation indices. The input volume
-    is mapped to the space of the segmentation given the registration, and if a
-    voxel shift map (VSM) is supplied, it is applied simultaneously as part of the
-    transform.
+    extract_seg_waveform
+    
+    This program extracts an average waveform from an input volume where the
+    average is computed over the voxels in the given segmentation indices. The
+    input volume is mapped to the space of the segmentation given the
+    registration, and if a voxel shift map (VSM) is supplied, it is applied
+    simultaneously as part of the transform.
     
     Author: FreeSurfer Developers
     
@@ -234,8 +220,6 @@ def extract_seg_waveform(
     Returns:
         NamedTuple of outputs (described in `ExtractSegWaveformOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(EXTRACT_SEG_WAVEFORM_METADATA)
     params = extract_seg_waveform_params(
         seg_file=seg_file,
         seg_indices=seg_indices,
@@ -246,13 +230,13 @@ def extract_seg_waveform(
         demean_flag=demean_flag,
         output_file=output_file,
     )
-    return extract_seg_waveform_execute(params, execution)
+    return extract_seg_waveform_execute(params, runner)
 
 
 __all__ = [
     "EXTRACT_SEG_WAVEFORM_METADATA",
     "ExtractSegWaveformOutputs",
-    "ExtractSegWaveformParameters",
     "extract_seg_waveform",
+    "extract_seg_waveform_execute",
     "extract_seg_waveform_params",
 ]

niwrap_freesurfer/freesurfer/exvivo_hemi_proc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 EXVIVO_HEMI_PROC_METADATA = Metadata(
-    id="cb414a078e8d94e5c45d97713e59b5d051d0f4fb.boutiques",
+    id="29085991345ac22aea975305bede128ac6b2e321.boutiques",
     name="exvivo-hemi-proc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,25 @@ EXVIVO_HEMI_PROC_METADATA = Metadata(
 
 
 ExvivoHemiProcParameters = typing.TypedDict('ExvivoHemiProcParameters', {
-    "__STYXTYPE__": typing.Literal["exvivo-hemi-proc"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/exvivo-hemi-proc"]],
+    "flashdir": str,
+    "outdir": str,
+    "subject": str,
+    "left_hemi": bool,
+    "right_hemi": bool,
+    "suptent": bool,
+    "no_rotate": bool,
+    "t1thresh": typing.NotRequired[float | None],
+    "threads": typing.NotRequired[float | None],
+    "check_only": bool,
+    "prep_only": bool,
+    "mask_only": bool,
+    "samseg_only": bool,
+    "stop_mmppsp_after": typing.NotRequired[str | None],
+    "force": bool,
+})
+ExvivoHemiProcParametersTagged = typing.TypedDict('ExvivoHemiProcParametersTagged', {
+    "@type": typing.Literal["freesurfer/exvivo-hemi-proc"],
     "flashdir": str,
     "outdir": str,
     "subject": str,
@@ -31,42 +49,11 @@ ExvivoHemiProcParameters = typing.TypedDict('ExvivoHemiProcParameters', {
     "stop_mmppsp_after": typing.NotRequired[str | None],
     "force": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "exvivo-hemi-proc": exvivo_hemi_proc_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 ExvivoHemiProcOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `exvivo_hemi_proc(...)`.
+    Output object returned when calling `ExvivoHemiProcParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -88,7 +75,7 @@ def exvivo_hemi_proc_params(
     samseg_only: bool = False,
     stop_mmppsp_after: str | None = None,
     force: bool = False,
-) -> ExvivoHemiProcParameters:
+) -> ExvivoHemiProcParametersTagged:
     """
     Build parameters.
     
@@ -113,7 +100,7 @@ def exvivo_hemi_proc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "exvivo-hemi-proc",
+        "@type": "freesurfer/exvivo-hemi-proc",
         "flashdir": flashdir,
         "outdir": outdir,
         "subject": subject,
@@ -153,48 +140,48 @@ def exvivo_hemi_proc_cargs(
     cargs.append("exvivo-hemi-proc")
     cargs.extend([
         "--i",
-        params.get("flashdir")
+        params.get("flashdir", None)
     ])
     cargs.extend([
         "--o",
-        params.get("outdir")
+        params.get("outdir", None)
     ])
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("left_hemi"):
+    if params.get("left_hemi", False):
         cargs.append("--lh")
-    if params.get("right_hemi"):
+    if params.get("right_hemi", False):
         cargs.append("--rh")
-    if params.get("suptent"):
+    if params.get("suptent", False):
         cargs.append("--suptent")
-    if params.get("no_rotate"):
+    if params.get("no_rotate", False):
         cargs.append("--no-rotate")
-    if params.get("t1thresh") is not None:
+    if params.get("t1thresh", None) is not None:
         cargs.extend([
             "--t1thresh",
-            str(params.get("t1thresh"))
+            str(params.get("t1thresh", None))
         ])
-    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))
         ])
-    if params.get("check_only"):
+    if params.get("check_only", False):
         cargs.append("--check-only")
-    if params.get("prep_only"):
+    if params.get("prep_only", False):
         cargs.append("--prep-only")
-    if params.get("mask_only"):
+    if params.get("mask_only", False):
         cargs.append("--mask-only")
-    if params.get("samseg_only"):
+    if params.get("samseg_only", False):
         cargs.append("--samseg-only")
-    if params.get("stop_mmppsp_after") is not None:
+    if params.get("stop_mmppsp_after", None) is not None:
         cargs.extend([
             "--stop-mmppsp-after",
-            params.get("stop_mmppsp_after")
+            params.get("stop_mmppsp_after", None)
         ])
-    if params.get("force"):
+    if params.get("force", False):
         cargs.append("--force")
     return cargs
 
@@ -220,10 +207,13 @@ def exvivo_hemi_proc_outputs(
 
 def exvivo_hemi_proc_execute(
     params: ExvivoHemiProcParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ExvivoHemiProcOutputs:
     """
-    Processes whole hemisphere data for Jeans entorhinal subfield labeling project.
+    exvivo-hemi-proc
+    
+    Processes whole hemisphere data for Jeans entorhinal subfield labeling
+    project.
     
     Author: FreeSurfer Developers
     
@@ -231,10 +221,12 @@ def exvivo_hemi_proc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ExvivoHemiProcOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(EXVIVO_HEMI_PROC_METADATA)
     params = execution.params(params)
     cargs = exvivo_hemi_proc_cargs(params, execution)
     ret = exvivo_hemi_proc_outputs(params, execution)
@@ -261,7 +253,10 @@ def exvivo_hemi_proc(
     runner: Runner | None = None,
 ) -> ExvivoHemiProcOutputs:
     """
-    Processes whole hemisphere data for Jeans entorhinal subfield labeling project.
+    exvivo-hemi-proc
+    
+    Processes whole hemisphere data for Jeans entorhinal subfield labeling
+    project.
     
     Author: FreeSurfer Developers
     
@@ -288,8 +283,6 @@ def exvivo_hemi_proc(
     Returns:
         NamedTuple of outputs (described in `ExvivoHemiProcOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(EXVIVO_HEMI_PROC_METADATA)
     params = exvivo_hemi_proc_params(
         flashdir=flashdir,
         outdir=outdir,
@@ -307,13 +300,13 @@ def exvivo_hemi_proc(
         stop_mmppsp_after=stop_mmppsp_after,
         force=force,
     )
-    return exvivo_hemi_proc_execute(params, execution)
+    return exvivo_hemi_proc_execute(params, runner)
 
 
 __all__ = [
     "EXVIVO_HEMI_PROC_METADATA",
     "ExvivoHemiProcOutputs",
-    "ExvivoHemiProcParameters",
     "exvivo_hemi_proc",
+    "exvivo_hemi_proc_execute",
     "exvivo_hemi_proc_params",
 ]