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

niwrap_freesurfer/freesurfer/mri_compute_distances.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_COMPUTE_DISTANCES_METADATA = Metadata(
-    id="b297f3d1325dc93819a91d335166f60fa8370173.boutiques",
+    id="34a89e8327c7da60b1c1a8d6250254274b2847d1.boutiques",
     name="mri_compute_distances",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRI_COMPUTE_DISTANCES_METADATA = Metadata(
 
 
 MriComputeDistancesParameters = typing.TypedDict('MriComputeDistancesParameters', {
-    "__STYXTYPE__": typing.Literal["mri_compute_distances"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_compute_distances"]],
+    "source": InputPathType,
+    "target": InputPathType,
+    "output_xform": str,
+})
+MriComputeDistancesParametersTagged = typing.TypedDict('MriComputeDistancesParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_compute_distances"],
     "source": InputPathType,
     "target": InputPathType,
     "output_xform": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_compute_distances": mri_compute_distances_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 {
-        "mri_compute_distances": mri_compute_distances_outputs,
-    }.get(t)
 
 
 class MriComputeDistancesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_compute_distances(...)`.
+    Output object returned when calling `MriComputeDistancesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def mri_compute_distances_params(
     source: InputPathType,
     target: InputPathType,
     output_xform: str,
-) -> MriComputeDistancesParameters:
+) -> MriComputeDistancesParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +54,7 @@ def mri_compute_distances_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_compute_distances",
+        "@type": "freesurfer/mri_compute_distances",
         "source": source,
         "target": target,
         "output_xform": output_xform,
@@ -103,9 +77,9 @@ def mri_compute_distances_cargs(
     """
     cargs = []
     cargs.append("mri_compute_distances")
-    cargs.append(execution.input_file(params.get("source")))
-    cargs.append(execution.input_file(params.get("target")))
-    cargs.append(params.get("output_xform"))
+    cargs.append(execution.input_file(params.get("source", None)))
+    cargs.append(execution.input_file(params.get("target", None)))
+    cargs.append(params.get("output_xform", None))
     return cargs
 
 
@@ -124,16 +98,18 @@ def mri_compute_distances_outputs(
     """
     ret = MriComputeDistancesOutputs(
         root=execution.output_file("."),
-        output_xform_file=execution.output_file(params.get("output_xform")),
+        output_xform_file=execution.output_file(params.get("output_xform", None)),
     )
     return ret
 
 
 def mri_compute_distances_execute(
     params: MriComputeDistancesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriComputeDistancesOutputs:
     """
+    mri_compute_distances
+    
     A tool to compute distances between source and target images.
     
     Author: FreeSurfer Developers
@@ -142,10 +118,12 @@ def mri_compute_distances_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriComputeDistancesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_COMPUTE_DISTANCES_METADATA)
     params = execution.params(params)
     cargs = mri_compute_distances_cargs(params, execution)
     ret = mri_compute_distances_outputs(params, execution)
@@ -160,6 +138,8 @@ def mri_compute_distances(
     runner: Runner | None = None,
 ) -> MriComputeDistancesOutputs:
     """
+    mri_compute_distances
+    
     A tool to compute distances between source and target images.
     
     Author: FreeSurfer Developers
@@ -175,20 +155,18 @@ def mri_compute_distances(
     Returns:
         NamedTuple of outputs (described in `MriComputeDistancesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_COMPUTE_DISTANCES_METADATA)
     params = mri_compute_distances_params(
         source=source,
         target=target,
         output_xform=output_xform,
     )
-    return mri_compute_distances_execute(params, execution)
+    return mri_compute_distances_execute(params, runner)
 
 
 __all__ = [
     "MRI_COMPUTE_DISTANCES_METADATA",
     "MriComputeDistancesOutputs",
-    "MriComputeDistancesParameters",
     "mri_compute_distances",
+    "mri_compute_distances_execute",
     "mri_compute_distances_params",
 ]

niwrap_freesurfer/freesurfer/mri_compute_layer_fractions.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_COMPUTE_LAYER_FRACTIONS_METADATA = Metadata(
-    id="a8146683627b1832ed56bcd730a4888fd71017d9.boutiques",
+    id="8e237dcf475aabd98621f6fc5f16a5b4ffec92cc.boutiques",
     name="mri_compute_layer_fractions",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,24 @@ MRI_COMPUTE_LAYER_FRACTIONS_METADATA = Metadata(
 
 
 MriComputeLayerFractionsParameters = typing.TypedDict('MriComputeLayerFractionsParameters', {
-    "__STYXTYPE__": typing.Literal["mri_compute_layer_fractions"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_compute_layer_fractions"]],
+    "reg_file": InputPathType,
+    "input_volume": InputPathType,
+    "output_stem": str,
+    "output_directory": typing.NotRequired[str | None],
+    "aseg_file": typing.NotRequired[InputPathType | None],
+    "target_volume": typing.NotRequired[InputPathType | None],
+    "hemi_flag": bool,
+    "fs_names_flag": bool,
+    "subject_id": typing.NotRequired[str | None],
+    "n_layers": typing.NotRequired[float | None],
+    "synth_flag": bool,
+    "thickness": typing.NotRequired[float | None],
+    "random_file": typing.NotRequired[InputPathType | None],
+    "identity_file": typing.NotRequired[str | None],
+})
+MriComputeLayerFractionsParametersTagged = typing.TypedDict('MriComputeLayerFractionsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_compute_layer_fractions"],
     "reg_file": InputPathType,
     "input_volume": InputPathType,
     "output_stem": str,
@@ -30,43 +47,11 @@ MriComputeLayerFractionsParameters = typing.TypedDict('MriComputeLayerFractionsP
     "random_file": typing.NotRequired[InputPathType | None],
     "identity_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 {
-        "mri_compute_layer_fractions": mri_compute_layer_fractions_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 {
-        "mri_compute_layer_fractions": mri_compute_layer_fractions_outputs,
-    }.get(t)
 
 
 class MriComputeLayerFractionsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_compute_layer_fractions(...)`.
+    Output object returned when calling `MriComputeLayerFractionsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -91,7 +76,7 @@ def mri_compute_layer_fractions_params(
     thickness: float | None = None,
     random_file: InputPathType | None = None,
     identity_file: str | None = None,
-) -> MriComputeLayerFractionsParameters:
+) -> MriComputeLayerFractionsParametersTagged:
     """
     Build parameters.
     
@@ -115,7 +100,7 @@ def mri_compute_layer_fractions_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_compute_layer_fractions",
+        "@type": "freesurfer/mri_compute_layer_fractions",
         "reg_file": reg_file,
         "input_volume": input_volume,
         "output_stem": output_stem,
@@ -157,49 +142,49 @@ def mri_compute_layer_fractions_cargs(
     """
     cargs = []
     cargs.append("mri_compute_layer_fractions")
-    cargs.append(execution.input_file(params.get("reg_file")))
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(params.get("output_stem"))
-    if params.get("output_directory") is not None:
+    cargs.append(execution.input_file(params.get("reg_file", None)))
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(params.get("output_stem", None))
+    if params.get("output_directory", None) is not None:
         cargs.extend([
             "-SDIR",
-            params.get("output_directory")
+            params.get("output_directory", None)
         ])
-    if params.get("aseg_file") is not None:
+    if params.get("aseg_file", None) is not None:
         cargs.extend([
             "-a",
-            execution.input_file(params.get("aseg_file"))
+            execution.input_file(params.get("aseg_file", None))
         ])
-    if params.get("target_volume") is not None:
-        cargs.append(execution.input_file(params.get("target_volume")))
-    if params.get("hemi_flag"):
+    if params.get("target_volume", None) is not None:
+        cargs.append(execution.input_file(params.get("target_volume", None)))
+    if params.get("hemi_flag", False):
         cargs.append("-hemi")
-    if params.get("fs_names_flag"):
+    if params.get("fs_names_flag", False):
         cargs.append("-FS_names")
-    if params.get("subject_id") is not None:
+    if params.get("subject_id", None) is not None:
         cargs.extend([
             "-s",
-            params.get("subject_id")
+            params.get("subject_id", None)
         ])
-    if params.get("n_layers") is not None:
+    if params.get("n_layers", None) is not None:
         cargs.extend([
             "-nlayers",
-            str(params.get("n_layers"))
+            str(params.get("n_layers", None))
         ])
-    if params.get("synth_flag"):
+    if params.get("synth_flag", False):
         cargs.append("-synth")
-    if params.get("thickness") is not None:
+    if params.get("thickness", None) is not None:
         cargs.extend([
             "-r",
-            str(params.get("thickness"))
+            str(params.get("thickness", None))
         ])
-    if params.get("random_file") is not None:
+    if params.get("random_file", None) is not None:
         cargs.extend([
             "-n",
-            execution.input_file(params.get("random_file"))
+            execution.input_file(params.get("random_file", None))
         ])
-    if params.get("identity_file") is not None:
-        cargs.append(params.get("identity_file"))
+    if params.get("identity_file", None) is not None:
+        cargs.append(params.get("identity_file", None))
     return cargs
 
 
@@ -218,19 +203,21 @@ def mri_compute_layer_fractions_outputs(
     """
     ret = MriComputeLayerFractionsOutputs(
         root=execution.output_file("."),
-        layer_fractions_output=execution.output_file(params.get("output_stem") + "_layer_fractions.mgz"),
-        synth_output=execution.output_file(params.get("output_stem") + "_synth.mgz"),
+        layer_fractions_output=execution.output_file(params.get("output_stem", None) + "_layer_fractions.mgz"),
+        synth_output=execution.output_file(params.get("output_stem", None) + "_synth.mgz"),
     )
     return ret
 
 
 def mri_compute_layer_fractions_execute(
     params: MriComputeLayerFractionsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriComputeLayerFractionsOutputs:
     """
-    This program computes volumetric partial volume fractions from laminar surfaces
-    using FreeSurfer.
+    mri_compute_layer_fractions
+    
+    This program computes volumetric partial volume fractions from laminar
+    surfaces using FreeSurfer.
     
     Author: FreeSurfer Developers
     
@@ -238,10 +225,12 @@ def mri_compute_layer_fractions_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriComputeLayerFractionsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_COMPUTE_LAYER_FRACTIONS_METADATA)
     params = execution.params(params)
     cargs = mri_compute_layer_fractions_cargs(params, execution)
     ret = mri_compute_layer_fractions_outputs(params, execution)
@@ -267,8 +256,10 @@ def mri_compute_layer_fractions(
     runner: Runner | None = None,
 ) -> MriComputeLayerFractionsOutputs:
     """
-    This program computes volumetric partial volume fractions from laminar surfaces
-    using FreeSurfer.
+    mri_compute_layer_fractions
+    
+    This program computes volumetric partial volume fractions from laminar
+    surfaces using FreeSurfer.
     
     Author: FreeSurfer Developers
     
@@ -294,8 +285,6 @@ def mri_compute_layer_fractions(
     Returns:
         NamedTuple of outputs (described in `MriComputeLayerFractionsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_COMPUTE_LAYER_FRACTIONS_METADATA)
     params = mri_compute_layer_fractions_params(
         reg_file=reg_file,
         input_volume=input_volume,
@@ -312,13 +301,13 @@ def mri_compute_layer_fractions(
         random_file=random_file,
         identity_file=identity_file,
     )
-    return mri_compute_layer_fractions_execute(params, execution)
+    return mri_compute_layer_fractions_execute(params, runner)
 
 
 __all__ = [
     "MRI_COMPUTE_LAYER_FRACTIONS_METADATA",
     "MriComputeLayerFractionsOutputs",
-    "MriComputeLayerFractionsParameters",
     "mri_compute_layer_fractions",
+    "mri_compute_layer_fractions_execute",
     "mri_compute_layer_fractions_params",
 ]

niwrap_freesurfer/freesurfer/mri_compute_overlap.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_COMPUTE_OVERLAP_METADATA = Metadata(
-    id="89394442cf520ee4ec9dd5ada3c18bd5fdb4dfe4.boutiques",
+    id="0c5ac0119d70b24a0fee21a86463fd0232db9009.boutiques",
     name="mri_compute_overlap",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,21 @@ MRI_COMPUTE_OVERLAP_METADATA = Metadata(
 
 
 MriComputeOverlapParameters = typing.TypedDict('MriComputeOverlapParameters', {
-    "__STYXTYPE__": typing.Literal["mri_compute_overlap"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_compute_overlap"]],
+    "volumes": list[InputPathType],
+    "label_numbers": typing.NotRequired[list[str] | None],
+    "all_labels": bool,
+    "show_label": bool,
+    "total_overlap": bool,
+    "no_summary": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "output_file": typing.NotRequired[str | None],
+    "quiet_mode": bool,
+    "translate_label": typing.NotRequired[list[float] | None],
+    "help": bool,
+})
+MriComputeOverlapParametersTagged = typing.TypedDict('MriComputeOverlapParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_compute_overlap"],
     "volumes": list[InputPathType],
     "label_numbers": typing.NotRequired[list[str] | None],
     "all_labels": bool,
@@ -27,42 +41,11 @@ MriComputeOverlapParameters = typing.TypedDict('MriComputeOverlapParameters', {
     "translate_label": typing.NotRequired[list[float] | None],
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_compute_overlap": mri_compute_overlap_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 MriComputeOverlapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_compute_overlap(...)`.
+    Output object returned when calling `MriComputeOverlapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -80,7 +63,7 @@ def mri_compute_overlap_params(
     quiet_mode: bool = False,
     translate_label: list[float] | None = None,
     help_: bool = False,
-) -> MriComputeOverlapParameters:
+) -> MriComputeOverlapParametersTagged:
     """
     Build parameters.
     
@@ -105,7 +88,7 @@ def mri_compute_overlap_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_compute_overlap",
+        "@type": "freesurfer/mri_compute_overlap",
         "volumes": volumes,
         "all_labels": all_labels,
         "show_label": show_label,
@@ -140,35 +123,35 @@ def mri_compute_overlap_cargs(
     """
     cargs = []
     cargs.append("mri_compute_overlap")
-    cargs.extend([execution.input_file(f) for f in params.get("volumes")])
-    if params.get("label_numbers") is not None:
-        cargs.extend(params.get("label_numbers"))
-    if params.get("all_labels"):
+    cargs.extend([execution.input_file(f) for f in params.get("volumes", None)])
+    if params.get("label_numbers", None) is not None:
+        cargs.extend(params.get("label_numbers", None))
+    if params.get("all_labels", False):
         cargs.append("-a")
-    if params.get("show_label"):
+    if params.get("show_label", False):
         cargs.append("-s")
-    if params.get("total_overlap"):
+    if params.get("total_overlap", False):
         cargs.append("-total")
-    if params.get("no_summary"):
+    if params.get("no_summary", False):
         cargs.append("-nosummary")
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
-    if params.get("output_file") is not None:
+    if params.get("output_file", None) is not None:
         cargs.extend([
             "-l",
-            params.get("output_file")
+            params.get("output_file", None)
         ])
-    if params.get("quiet_mode"):
+    if params.get("quiet_mode", False):
         cargs.append("-q")
-    if params.get("translate_label") is not None:
+    if params.get("translate_label", None) is not None:
         cargs.extend([
             "-t",
-            *map(str, params.get("translate_label"))
+            *map(str, params.get("translate_label", None))
         ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-h")
     return cargs
 
@@ -194,10 +177,13 @@ def mri_compute_overlap_outputs(
 
 def mri_compute_overlap_execute(
     params: MriComputeOverlapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriComputeOverlapOutputs:
     """
-    Computes three different types of overlap measures for labels in input volumes.
+    mri_compute_overlap
+    
+    Computes three different types of overlap measures for labels in input
+    volumes.
     
     Author: FreeSurfer Developers
     
@@ -205,10 +191,12 @@ def mri_compute_overlap_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriComputeOverlapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_COMPUTE_OVERLAP_METADATA)
     params = execution.params(params)
     cargs = mri_compute_overlap_cargs(params, execution)
     ret = mri_compute_overlap_outputs(params, execution)
@@ -231,7 +219,10 @@ def mri_compute_overlap(
     runner: Runner | None = None,
 ) -> MriComputeOverlapOutputs:
     """
-    Computes three different types of overlap measures for labels in input volumes.
+    mri_compute_overlap
+    
+    Computes three different types of overlap measures for labels in input
+    volumes.
     
     Author: FreeSurfer Developers
     
@@ -258,8 +249,6 @@ def mri_compute_overlap(
     Returns:
         NamedTuple of outputs (described in `MriComputeOverlapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_COMPUTE_OVERLAP_METADATA)
     params = mri_compute_overlap_params(
         volumes=volumes,
         label_numbers=label_numbers,
@@ -273,13 +262,13 @@ def mri_compute_overlap(
         translate_label=translate_label,
         help_=help_,
     )
-    return mri_compute_overlap_execute(params, execution)
+    return mri_compute_overlap_execute(params, runner)
 
 
 __all__ = [
     "MRI_COMPUTE_OVERLAP_METADATA",
     "MriComputeOverlapOutputs",
-    "MriComputeOverlapParameters",
     "mri_compute_overlap",
+    "mri_compute_overlap_execute",
     "mri_compute_overlap_params",
 ]