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

niwrap_freesurfer/freesurfer/dmri_bset.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_BSET_METADATA = Metadata(
-    id="91724c14abdc0abe94c9b096e04494e0a0e000cf.boutiques",
+    id="641aa41b2faa626fd3cc64d311c4ac9f03729e4c.boutiques",
     name="dmri_bset",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,20 @@ DMRI_BSET_METADATA = Metadata(
 
 
 DmriBsetParameters = typing.TypedDict('DmriBsetParameters', {
-    "__STYXTYPE__": typing.Literal["dmri_bset"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dmri_bset"]],
+    "input_dwi": InputPathType,
+    "output_dwi": str,
+    "b_values": typing.NotRequired[list[float] | None],
+    "btol": typing.NotRequired[float | None],
+    "bsort": bool,
+    "bmax": typing.NotRequired[float | None],
+    "input_b_table": typing.NotRequired[InputPathType | None],
+    "input_g_table": typing.NotRequired[InputPathType | None],
+    "output_b_table": typing.NotRequired[str | None],
+    "output_g_table": typing.NotRequired[str | None],
+})
+DmriBsetParametersTagged = typing.TypedDict('DmriBsetParametersTagged', {
+    "@type": typing.Literal["freesurfer/dmri_bset"],
     "input_dwi": InputPathType,
     "output_dwi": str,
     "b_values": typing.NotRequired[list[float] | None],
@@ -26,43 +39,11 @@ DmriBsetParameters = typing.TypedDict('DmriBsetParameters', {
     "output_b_table": typing.NotRequired[str | None],
     "output_g_table": 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 {
-        "dmri_bset": dmri_bset_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_bset": dmri_bset_outputs,
-    }.get(t)
 
 
 class DmriBsetOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dmri_bset(...)`.
+    Output object returned when calling `DmriBsetParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -78,14 +59,14 @@ def dmri_bset_params(
     input_dwi: InputPathType,
     output_dwi: str,
     b_values: list[float] | None = None,
-    btol: float | None = 0.05,
+    btol: float | None = None,
     bsort: bool = False,
     bmax: float | None = None,
     input_b_table: InputPathType | None = None,
     input_g_table: InputPathType | None = None,
     output_b_table: str | None = None,
     output_g_table: str | None = None,
-) -> DmriBsetParameters:
+) -> DmriBsetParametersTagged:
     """
     Build parameters.
     
@@ -109,7 +90,7 @@ def dmri_bset_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dmri_bset",
+        "@type": "freesurfer/dmri_bset",
         "input_dwi": input_dwi,
         "output_dwi": output_dwi,
         "bsort": bsort,
@@ -146,44 +127,44 @@ def dmri_bset_cargs(
     """
     cargs = []
     cargs.append("dmri_bset")
-    cargs.append(execution.input_file(params.get("input_dwi")))
-    cargs.append(params.get("output_dwi"))
-    if params.get("b_values") is not None:
+    cargs.append(execution.input_file(params.get("input_dwi", None)))
+    cargs.append(params.get("output_dwi", None))
+    if params.get("b_values", None) is not None:
         cargs.extend([
             "--b",
-            *map(str, params.get("b_values"))
+            *map(str, params.get("b_values", None))
         ])
-    if params.get("btol") is not None:
+    if params.get("btol", None) is not None:
         cargs.extend([
             "--btol",
-            str(params.get("btol"))
+            str(params.get("btol", None))
         ])
-    if params.get("bsort"):
+    if params.get("bsort", False):
         cargs.append("--bsort")
-    if params.get("bmax") is not None:
+    if params.get("bmax", None) is not None:
         cargs.extend([
             "--bmax",
-            str(params.get("bmax"))
+            str(params.get("bmax", None))
         ])
-    if params.get("input_b_table") is not None:
+    if params.get("input_b_table", None) is not None:
         cargs.extend([
             "--inb",
-            execution.input_file(params.get("input_b_table"))
+            execution.input_file(params.get("input_b_table", None))
         ])
-    if params.get("input_g_table") is not None:
+    if params.get("input_g_table", None) is not None:
         cargs.extend([
             "--ing",
-            execution.input_file(params.get("input_g_table"))
+            execution.input_file(params.get("input_g_table", None))
         ])
-    if params.get("output_b_table") is not None:
+    if params.get("output_b_table", None) is not None:
         cargs.extend([
             "--outb",
-            params.get("output_b_table")
+            params.get("output_b_table", None)
         ])
-    if params.get("output_g_table") is not None:
+    if params.get("output_g_table", None) is not None:
         cargs.extend([
             "--outg",
-            params.get("output_g_table")
+            params.get("output_g_table", None)
         ])
     return cargs
 
@@ -203,20 +184,22 @@ def dmri_bset_outputs(
     """
     ret = DmriBsetOutputs(
         root=execution.output_file("."),
-        output_dwi_file=execution.output_file(params.get("output_dwi")),
-        output_b_table_file=execution.output_file(params.get("output_b_table")) if (params.get("output_b_table") is not None) else None,
-        output_g_table_file=execution.output_file(params.get("output_g_table")) if (params.get("output_g_table") is not None) else None,
+        output_dwi_file=execution.output_file(params.get("output_dwi", None)),
+        output_b_table_file=execution.output_file(params.get("output_b_table", None)) if (params.get("output_b_table") is not None) else None,
+        output_g_table_file=execution.output_file(params.get("output_g_table", None)) if (params.get("output_g_table") is not None) else None,
     )
     return ret
 
 
 def dmri_bset_execute(
     params: DmriBsetParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DmriBsetOutputs:
     """
-    This tool extracts a subset of volumes, b-values, and gradient directions from a
-    diffusion MRI data set.
+    dmri_bset
+    
+    This tool extracts a subset of volumes, b-values, and gradient directions
+    from a diffusion MRI data set.
     
     Author: FreeSurfer Developers
     
@@ -224,10 +207,12 @@ def dmri_bset_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DmriBsetOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DMRI_BSET_METADATA)
     params = execution.params(params)
     cargs = dmri_bset_cargs(params, execution)
     ret = dmri_bset_outputs(params, execution)
@@ -239,7 +224,7 @@ def dmri_bset(
     input_dwi: InputPathType,
     output_dwi: str,
     b_values: list[float] | None = None,
-    btol: float | None = 0.05,
+    btol: float | None = None,
     bsort: bool = False,
     bmax: float | None = None,
     input_b_table: InputPathType | None = None,
@@ -249,8 +234,10 @@ def dmri_bset(
     runner: Runner | None = None,
 ) -> DmriBsetOutputs:
     """
-    This tool extracts a subset of volumes, b-values, and gradient directions from a
-    diffusion MRI data set.
+    dmri_bset
+    
+    This tool extracts a subset of volumes, b-values, and gradient directions
+    from a diffusion MRI data set.
     
     Author: FreeSurfer Developers
     
@@ -276,8 +263,6 @@ def dmri_bset(
     Returns:
         NamedTuple of outputs (described in `DmriBsetOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DMRI_BSET_METADATA)
     params = dmri_bset_params(
         input_dwi=input_dwi,
         output_dwi=output_dwi,
@@ -290,13 +275,13 @@ def dmri_bset(
         output_b_table=output_b_table,
         output_g_table=output_g_table,
     )
-    return dmri_bset_execute(params, execution)
+    return dmri_bset_execute(params, runner)
 
 
 __all__ = [
     "DMRI_BSET_METADATA",
     "DmriBsetOutputs",
-    "DmriBsetParameters",
     "dmri_bset",
+    "dmri_bset_execute",
     "dmri_bset_params",
 ]

niwrap_freesurfer/freesurfer/dmri_colored_fa.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_COLORED_FA_METADATA = Metadata(
-    id="46a4473ad7a91ae9adbdb875b3792b8a983b19dc.boutiques",
+    id="718feafd2d16e543f6009bc9e147cd221438c40e.boutiques",
     name="dmri_coloredFA",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ DMRI_COLORED_FA_METADATA = Metadata(
 
 
 DmriColoredFaParameters = typing.TypedDict('DmriColoredFaParameters', {
-    "__STYXTYPE__": typing.Literal["dmri_coloredFA"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dmri_coloredFA"]],
+    "input_volume": InputPathType,
+    "output_volume": str,
+})
+DmriColoredFaParametersTagged = typing.TypedDict('DmriColoredFaParametersTagged', {
+    "@type": typing.Literal["freesurfer/dmri_coloredFA"],
     "input_volume": InputPathType,
     "output_volume": 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_coloredFA": dmri_colored_fa_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_coloredFA": dmri_colored_fa_outputs,
-    }.get(t)
 
 
 class DmriColoredFaOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dmri_colored_fa(...)`.
+    Output object returned when calling `DmriColoredFaParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class DmriColoredFaOutputs(typing.NamedTuple):
 def dmri_colored_fa_params(
     input_volume: InputPathType,
     output_volume: str = "colored_FA",
-) -> DmriColoredFaParameters:
+) -> DmriColoredFaParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def dmri_colored_fa_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dmri_coloredFA",
+        "@type": "freesurfer/dmri_coloredFA",
         "input_volume": input_volume,
         "output_volume": output_volume,
     }
@@ -98,8 +71,8 @@ def dmri_colored_fa_cargs(
     """
     cargs = []
     cargs.append("dmri_coloredFA")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(params.get("output_volume"))
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(params.get("output_volume", "colored_FA"))
     return cargs
 
 
@@ -118,16 +91,18 @@ def dmri_colored_fa_outputs(
     """
     ret = DmriColoredFaOutputs(
         root=execution.output_file("."),
-        output_colored_fa=execution.output_file(params.get("output_volume") + ".nii.gz"),
+        output_colored_fa=execution.output_file(params.get("output_volume", "colored_FA") + ".nii.gz"),
     )
     return ret
 
 
 def dmri_colored_fa_execute(
     params: DmriColoredFaParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DmriColoredFaOutputs:
     """
+    dmri_coloredFA
+    
     Tool for generating colored FA maps from diffusion MRI data.
     
     Author: FreeSurfer Developers
@@ -136,10 +111,12 @@ def dmri_colored_fa_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DmriColoredFaOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DMRI_COLORED_FA_METADATA)
     params = execution.params(params)
     cargs = dmri_colored_fa_cargs(params, execution)
     ret = dmri_colored_fa_outputs(params, execution)
@@ -153,6 +130,8 @@ def dmri_colored_fa(
     runner: Runner | None = None,
 ) -> DmriColoredFaOutputs:
     """
+    dmri_coloredFA
+    
     Tool for generating colored FA maps from diffusion MRI data.
     
     Author: FreeSurfer Developers
@@ -166,19 +145,17 @@ def dmri_colored_fa(
     Returns:
         NamedTuple of outputs (described in `DmriColoredFaOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DMRI_COLORED_FA_METADATA)
     params = dmri_colored_fa_params(
         input_volume=input_volume,
         output_volume=output_volume,
     )
-    return dmri_colored_fa_execute(params, execution)
+    return dmri_colored_fa_execute(params, runner)
 
 
 __all__ = [
     "DMRI_COLORED_FA_METADATA",
     "DmriColoredFaOutputs",
-    "DmriColoredFaParameters",
     "dmri_colored_fa",
+    "dmri_colored_fa_execute",
     "dmri_colored_fa_params",
 ]

niwrap_freesurfer/freesurfer/dmri_extract_surface_measurements.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_EXTRACT_SURFACE_MEASUREMENTS_METADATA = Metadata(
-    id="1571ae7852c5d0ff3bb69988315d8db4d363f2a7.boutiques",
+    id="ba58cc768fedfd8c0bd03df98664733dd0e1a4e1.boutiques",
     name="dmri_extractSurfaceMeasurements",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,23 @@ DMRI_EXTRACT_SURFACE_MEASUREMENTS_METADATA = Metadata(
 
 
 DmriExtractSurfaceMeasurementsParameters = typing.TypedDict('DmriExtractSurfaceMeasurementsParameters', {
-    "__STYXTYPE__": typing.Literal["dmri_extractSurfaceMeasurements"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dmri_extractSurfaceMeasurements"]],
+    "streamline_file": InputPathType,
+    "lh_surface_file": InputPathType,
+    "lh_thickness_overlay": InputPathType,
+    "lh_curvature_overlay": InputPathType,
+    "rh_surface_file": InputPathType,
+    "rh_thickness_overlay": InputPathType,
+    "rh_curvature_overlay": InputPathType,
+    "output_directory": str,
+    "reference_image": typing.NotRequired[InputPathType | None],
+    "reference_image_anatomical": typing.NotRequired[InputPathType | None],
+    "transformation": typing.NotRequired[InputPathType | None],
+    "annotation_file": typing.NotRequired[InputPathType | None],
+    "fa_options": typing.NotRequired[list[str] | None],
+})
+DmriExtractSurfaceMeasurementsParametersTagged = typing.TypedDict('DmriExtractSurfaceMeasurementsParametersTagged', {
+    "@type": typing.Literal["freesurfer/dmri_extractSurfaceMeasurements"],
     "streamline_file": InputPathType,
     "lh_surface_file": InputPathType,
     "lh_thickness_overlay": InputPathType,
@@ -29,42 +45,11 @@ DmriExtractSurfaceMeasurementsParameters = typing.TypedDict('DmriExtractSurfaceM
     "annotation_file": typing.NotRequired[InputPathType | None],
     "fa_options": typing.NotRequired[list[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 {
-        "dmri_extractSurfaceMeasurements": dmri_extract_surface_measurements_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 DmriExtractSurfaceMeasurementsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dmri_extract_surface_measurements(...)`.
+    Output object returned when calling `DmriExtractSurfaceMeasurementsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -84,7 +69,7 @@ def dmri_extract_surface_measurements_params(
     transformation: InputPathType | None = None,
     annotation_file: InputPathType | None = None,
     fa_options: list[str] | None = None,
-) -> DmriExtractSurfaceMeasurementsParameters:
+) -> DmriExtractSurfaceMeasurementsParametersTagged:
     """
     Build parameters.
     
@@ -108,7 +93,7 @@ def dmri_extract_surface_measurements_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dmri_extractSurfaceMeasurements",
+        "@type": "freesurfer/dmri_extractSurfaceMeasurements",
         "streamline_file": streamline_file,
         "lh_surface_file": lh_surface_file,
         "lh_thickness_overlay": lh_thickness_overlay,
@@ -148,60 +133,60 @@ def dmri_extract_surface_measurements_cargs(
     cargs.append("dmri_extractSurfaceMeasurements")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("streamline_file"))
+        execution.input_file(params.get("streamline_file", None))
     ])
     cargs.extend([
         "-sl",
-        execution.input_file(params.get("lh_surface_file"))
+        execution.input_file(params.get("lh_surface_file", None))
     ])
     cargs.extend([
         "-tl",
-        execution.input_file(params.get("lh_thickness_overlay"))
+        execution.input_file(params.get("lh_thickness_overlay", None))
     ])
     cargs.extend([
         "-cl",
-        execution.input_file(params.get("lh_curvature_overlay"))
+        execution.input_file(params.get("lh_curvature_overlay", None))
     ])
     cargs.extend([
         "-sr",
-        execution.input_file(params.get("rh_surface_file"))
+        execution.input_file(params.get("rh_surface_file", None))
     ])
     cargs.extend([
         "-tr",
-        execution.input_file(params.get("rh_thickness_overlay"))
+        execution.input_file(params.get("rh_thickness_overlay", None))
     ])
     cargs.extend([
         "-cr",
-        execution.input_file(params.get("rh_curvature_overlay"))
+        execution.input_file(params.get("rh_curvature_overlay", None))
     ])
     cargs.extend([
         "-o",
-        params.get("output_directory")
+        params.get("output_directory", None)
     ])
-    if params.get("reference_image") is not None:
+    if params.get("reference_image", None) is not None:
         cargs.extend([
             "-rid",
-            execution.input_file(params.get("reference_image"))
+            execution.input_file(params.get("reference_image", None))
         ])
-    if params.get("reference_image_anatomical") is not None:
+    if params.get("reference_image_anatomical", None) is not None:
         cargs.extend([
             "-ria",
-            execution.input_file(params.get("reference_image_anatomical"))
+            execution.input_file(params.get("reference_image_anatomical", None))
         ])
-    if params.get("transformation") is not None:
+    if params.get("transformation", None) is not None:
         cargs.extend([
             "-t",
-            execution.input_file(params.get("transformation"))
+            execution.input_file(params.get("transformation", None))
         ])
-    if params.get("annotation_file") is not None:
+    if params.get("annotation_file", None) is not None:
         cargs.extend([
             "-a",
-            execution.input_file(params.get("annotation_file"))
+            execution.input_file(params.get("annotation_file", None))
         ])
-    if params.get("fa_options") is not None:
+    if params.get("fa_options", None) is not None:
         cargs.extend([
             "-fa",
-            *params.get("fa_options")
+            *params.get("fa_options", None)
         ])
     return cargs
 
@@ -227,9 +212,11 @@ def dmri_extract_surface_measurements_outputs(
 
 def dmri_extract_surface_measurements_execute(
     params: DmriExtractSurfaceMeasurementsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DmriExtractSurfaceMeasurementsOutputs:
     """
+    dmri_extractSurfaceMeasurements
+    
     A tool for extracting surface measurements from diffusion MRI data.
     
     Author: FreeSurfer Developers
@@ -238,10 +225,12 @@ def dmri_extract_surface_measurements_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DmriExtractSurfaceMeasurementsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DMRI_EXTRACT_SURFACE_MEASUREMENTS_METADATA)
     params = execution.params(params)
     cargs = dmri_extract_surface_measurements_cargs(params, execution)
     ret = dmri_extract_surface_measurements_outputs(params, execution)
@@ -266,6 +255,8 @@ def dmri_extract_surface_measurements(
     runner: Runner | None = None,
 ) -> DmriExtractSurfaceMeasurementsOutputs:
     """
+    dmri_extractSurfaceMeasurements
+    
     A tool for extracting surface measurements from diffusion MRI data.
     
     Author: FreeSurfer Developers
@@ -292,8 +283,6 @@ def dmri_extract_surface_measurements(
     Returns:
         NamedTuple of outputs (described in `DmriExtractSurfaceMeasurementsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DMRI_EXTRACT_SURFACE_MEASUREMENTS_METADATA)
     params = dmri_extract_surface_measurements_params(
         streamline_file=streamline_file,
         lh_surface_file=lh_surface_file,
@@ -309,13 +298,13 @@ def dmri_extract_surface_measurements(
         annotation_file=annotation_file,
         fa_options=fa_options,
     )
-    return dmri_extract_surface_measurements_execute(params, execution)
+    return dmri_extract_surface_measurements_execute(params, runner)
 
 
 __all__ = [
     "DMRI_EXTRACT_SURFACE_MEASUREMENTS_METADATA",
     "DmriExtractSurfaceMeasurementsOutputs",
-    "DmriExtractSurfaceMeasurementsParameters",
     "dmri_extract_surface_measurements",
+    "dmri_extract_surface_measurements_execute",
     "dmri_extract_surface_measurements_params",
 ]