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

niwrap_freesurfer/freesurfer/mri_label_volume.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_LABEL_VOLUME_METADATA = Metadata(
-    id="ee89fc69a4f2636ea1f0a072d5cd1e5cd8d3081c.boutiques",
+    id="99198f949ed98f95d26d4d6070c2f37caba7c4ac.boutiques",
     name="mri_label_volume",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,26 @@ MRI_LABEL_VOLUME_METADATA = Metadata(
 
 
 MriLabelVolumeParameters = typing.TypedDict('MriLabelVolumeParameters', {
-    "__STYXTYPE__": typing.Literal["mri_label_volume"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_label_volume"]],
+    "volume": InputPathType,
+    "labels": list[str],
+    "partial_volume_effects": typing.NotRequired[InputPathType | None],
+    "intracranial_volume": typing.NotRequired[InputPathType | None],
+    "spreadsheet_subject": typing.NotRequired[str | None],
+    "non_zero_voxels": bool,
+    "replace_label_in": typing.NotRequired[str | None],
+    "replace_label_out": typing.NotRequired[str | None],
+    "brain_volume": typing.NotRequired[InputPathType | None],
+    "percentage": bool,
+    "log_results": typing.NotRequired[InputPathType | None],
+    "atlas_transform_file": typing.NotRequired[InputPathType | None],
+    "atlas_scalefactor": typing.NotRequired[float | None],
+    "etiv_transform_file": typing.NotRequired[InputPathType | None],
+    "etiv_scalefactor": typing.NotRequired[float | None],
+    "etiv_subject": typing.NotRequired[str | None],
+})
+MriLabelVolumeParametersTagged = typing.TypedDict('MriLabelVolumeParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_label_volume"],
     "volume": InputPathType,
     "labels": list[str],
     "partial_volume_effects": typing.NotRequired[InputPathType | None],
@@ -32,43 +51,11 @@ MriLabelVolumeParameters = typing.TypedDict('MriLabelVolumeParameters', {
     "etiv_scalefactor": typing.NotRequired[float | None],
     "etiv_subject": 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_label_volume": mri_label_volume_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_label_volume": mri_label_volume_outputs,
-    }.get(t)
 
 
 class MriLabelVolumeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_label_volume(...)`.
+    Output object returned when calling `MriLabelVolumeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -95,7 +82,7 @@ def mri_label_volume_params(
     etiv_transform_file: InputPathType | None = None,
     etiv_scalefactor: float | None = None,
     etiv_subject: str | None = None,
-) -> MriLabelVolumeParameters:
+) -> MriLabelVolumeParametersTagged:
     """
     Build parameters.
     
@@ -126,7 +113,7 @@ def mri_label_volume_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_label_volume",
+        "@type": "freesurfer/mri_label_volume",
         "volume": volume,
         "labels": labels,
         "non_zero_voxels": non_zero_voxels,
@@ -174,62 +161,62 @@ def mri_label_volume_cargs(
     """
     cargs = []
     cargs.append("mri_label_volume")
-    cargs.append(execution.input_file(params.get("volume")))
-    cargs.extend(params.get("labels"))
-    if params.get("partial_volume_effects") is not None:
+    cargs.append(execution.input_file(params.get("volume", None)))
+    cargs.extend(params.get("labels", None))
+    if params.get("partial_volume_effects", None) is not None:
         cargs.extend([
             "-pv",
-            execution.input_file(params.get("partial_volume_effects"))
+            execution.input_file(params.get("partial_volume_effects", None))
         ])
-    if params.get("intracranial_volume") is not None:
+    if params.get("intracranial_volume", None) is not None:
         cargs.extend([
             "-icv",
-            execution.input_file(params.get("intracranial_volume"))
+            execution.input_file(params.get("intracranial_volume", None))
         ])
-    if params.get("spreadsheet_subject") is not None:
+    if params.get("spreadsheet_subject", None) is not None:
         cargs.extend([
             "-s",
-            params.get("spreadsheet_subject")
+            params.get("spreadsheet_subject", None)
         ])
-    if params.get("non_zero_voxels"):
+    if params.get("non_zero_voxels", False):
         cargs.append("-a")
-    if params.get("replace_label_in") is not None:
+    if params.get("replace_label_in", None) is not None:
         cargs.extend([
             "-t",
-            params.get("replace_label_in")
+            params.get("replace_label_in", None)
         ])
-    if params.get("replace_label_out") is not None:
-        cargs.append(params.get("replace_label_out"))
-    if params.get("brain_volume") is not None:
+    if params.get("replace_label_out", None) is not None:
+        cargs.append(params.get("replace_label_out", None))
+    if params.get("brain_volume", None) is not None:
         cargs.extend([
             "-b",
-            execution.input_file(params.get("brain_volume"))
+            execution.input_file(params.get("brain_volume", None))
         ])
-    if params.get("percentage"):
+    if params.get("percentage", False):
         cargs.append("-p")
-    if params.get("log_results") is not None:
+    if params.get("log_results", None) is not None:
         cargs.extend([
             "-l",
-            execution.input_file(params.get("log_results"))
+            execution.input_file(params.get("log_results", None))
         ])
-    if params.get("atlas_transform_file") is not None:
+    if params.get("atlas_transform_file", None) is not None:
         cargs.extend([
             "-atlas_icv",
-            execution.input_file(params.get("atlas_transform_file"))
+            execution.input_file(params.get("atlas_transform_file", None))
         ])
-    if params.get("atlas_scalefactor") is not None:
-        cargs.append(str(params.get("atlas_scalefactor")))
-    if params.get("etiv_transform_file") is not None:
+    if params.get("atlas_scalefactor", None) is not None:
+        cargs.append(str(params.get("atlas_scalefactor", None)))
+    if params.get("etiv_transform_file", None) is not None:
         cargs.extend([
             "-eTIV",
-            execution.input_file(params.get("etiv_transform_file"))
+            execution.input_file(params.get("etiv_transform_file", None))
         ])
-    if params.get("etiv_scalefactor") is not None:
-        cargs.append(str(params.get("etiv_scalefactor")))
-    if params.get("etiv_subject") is not None:
+    if params.get("etiv_scalefactor", None) is not None:
+        cargs.append(str(params.get("etiv_scalefactor", None)))
+    if params.get("etiv_subject", None) is not None:
         cargs.extend([
             "-eTIV_matdat",
-            params.get("etiv_subject")
+            params.get("etiv_subject", None)
         ])
     return cargs
 
@@ -257,9 +244,11 @@ def mri_label_volume_outputs(
 
 def mri_label_volume_execute(
     params: MriLabelVolumeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriLabelVolumeOutputs:
     """
+    mri_label_volume
+    
     A tool to compute volumes of labeled voxels within MRI images, often used in
     conjunction with FreeSurfer processed data.
     
@@ -269,10 +258,12 @@ def mri_label_volume_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriLabelVolumeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_LABEL_VOLUME_METADATA)
     params = execution.params(params)
     cargs = mri_label_volume_cargs(params, execution)
     ret = mri_label_volume_outputs(params, execution)
@@ -300,6 +291,8 @@ def mri_label_volume(
     runner: Runner | None = None,
 ) -> MriLabelVolumeOutputs:
     """
+    mri_label_volume
+    
     A tool to compute volumes of labeled voxels within MRI images, often used in
     conjunction with FreeSurfer processed data.
     
@@ -334,8 +327,6 @@ def mri_label_volume(
     Returns:
         NamedTuple of outputs (described in `MriLabelVolumeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_LABEL_VOLUME_METADATA)
     params = mri_label_volume_params(
         volume=volume,
         labels=labels,
@@ -354,13 +345,13 @@ def mri_label_volume(
         etiv_scalefactor=etiv_scalefactor,
         etiv_subject=etiv_subject,
     )
-    return mri_label_volume_execute(params, execution)
+    return mri_label_volume_execute(params, runner)
 
 
 __all__ = [
     "MRI_LABEL_VOLUME_METADATA",
     "MriLabelVolumeOutputs",
-    "MriLabelVolumeParameters",
     "mri_label_volume",
+    "mri_label_volume_execute",
     "mri_label_volume_params",
 ]

niwrap_freesurfer/freesurfer/mri_linear_align.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_LINEAR_ALIGN_METADATA = Metadata(
-    id="e21ce25c91e684ff7b180749c2270d4bd42ef69b.boutiques",
+    id="c2787a45600aa69474da7d62372760a22ffd70d0.boutiques",
     name="mri_linear_align",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,22 @@ MRI_LINEAR_ALIGN_METADATA = Metadata(
 
 
 MriLinearAlignParameters = typing.TypedDict('MriLinearAlignParameters', {
-    "__STYXTYPE__": typing.Literal["mri_linear_align"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_linear_align"]],
+    "source": InputPathType,
+    "target": InputPathType,
+    "output_xform": str,
+})
+MriLinearAlignParametersTagged = typing.TypedDict('MriLinearAlignParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_linear_align"],
     "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_linear_align": mri_linear_align_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 MriLinearAlignOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_linear_align(...)`.
+    Output object returned when calling `MriLinearAlignParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +39,7 @@ def mri_linear_align_params(
     source: InputPathType,
     target: InputPathType,
     output_xform: str,
-) -> MriLinearAlignParameters:
+) -> MriLinearAlignParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +51,7 @@ def mri_linear_align_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_linear_align",
+        "@type": "freesurfer/mri_linear_align",
         "source": source,
         "target": target,
         "output_xform": output_xform,
@@ -99,9 +74,9 @@ def mri_linear_align_cargs(
     """
     cargs = []
     cargs.append("mri_linear_align")
-    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
 
 
@@ -126,9 +101,11 @@ def mri_linear_align_outputs(
 
 def mri_linear_align_execute(
     params: MriLinearAlignParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriLinearAlignOutputs:
     """
+    mri_linear_align
+    
     MRI Linear Alignment Tool for Freesurfer.
     
     Author: FreeSurfer Developers
@@ -137,10 +114,12 @@ def mri_linear_align_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriLinearAlignOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_LINEAR_ALIGN_METADATA)
     params = execution.params(params)
     cargs = mri_linear_align_cargs(params, execution)
     ret = mri_linear_align_outputs(params, execution)
@@ -155,6 +134,8 @@ def mri_linear_align(
     runner: Runner | None = None,
 ) -> MriLinearAlignOutputs:
     """
+    mri_linear_align
+    
     MRI Linear Alignment Tool for Freesurfer.
     
     Author: FreeSurfer Developers
@@ -169,20 +150,18 @@ def mri_linear_align(
     Returns:
         NamedTuple of outputs (described in `MriLinearAlignOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_LINEAR_ALIGN_METADATA)
     params = mri_linear_align_params(
         source=source,
         target=target,
         output_xform=output_xform,
     )
-    return mri_linear_align_execute(params, execution)
+    return mri_linear_align_execute(params, runner)
 
 
 __all__ = [
     "MRI_LINEAR_ALIGN_METADATA",
     "MriLinearAlignOutputs",
-    "MriLinearAlignParameters",
     "mri_linear_align",
+    "mri_linear_align_execute",
     "mri_linear_align_params",
 ]

niwrap_freesurfer/freesurfer/mri_linear_align_binary.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_LINEAR_ALIGN_BINARY_METADATA = Metadata(
-    id="242145fa282d137e4b7de6e359d41edf76dd7839.boutiques",
+    id="04b5557cd3d195da179f41a7dfa80e26c9101d03.boutiques",
     name="mri_linear_align_binary",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRI_LINEAR_ALIGN_BINARY_METADATA = Metadata(
 
 
 MriLinearAlignBinaryParameters = typing.TypedDict('MriLinearAlignBinaryParameters', {
-    "__STYXTYPE__": typing.Literal["mri_linear_align_binary"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_linear_align_binary"]],
+    "source": InputPathType,
+    "target": InputPathType,
+    "output_xform": str,
+    "target_label": typing.NotRequired[str | None],
+})
+MriLinearAlignBinaryParametersTagged = typing.TypedDict('MriLinearAlignBinaryParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_linear_align_binary"],
     "source": InputPathType,
     "target": InputPathType,
     "output_xform": str,
     "target_label": 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_linear_align_binary": mri_linear_align_binary_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_linear_align_binary": mri_linear_align_binary_outputs,
-    }.get(t)
 
 
 class MriLinearAlignBinaryOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_linear_align_binary(...)`.
+    Output object returned when calling `MriLinearAlignBinaryParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mri_linear_align_binary_params(
     target: InputPathType,
     output_xform: str,
     target_label: str | None = None,
-) -> MriLinearAlignBinaryParameters:
+) -> MriLinearAlignBinaryParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +58,7 @@ def mri_linear_align_binary_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_linear_align_binary",
+        "@type": "freesurfer/mri_linear_align_binary",
         "source": source,
         "target": target,
         "output_xform": output_xform,
@@ -108,13 +83,13 @@ def mri_linear_align_binary_cargs(
     """
     cargs = []
     cargs.append("mri_linear_align_binary")
-    cargs.append(execution.input_file(params.get("source")))
-    cargs.append(execution.input_file(params.get("target")))
-    cargs.append(params.get("output_xform"))
-    if params.get("target_label") is not None:
+    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))
+    if params.get("target_label", None) is not None:
         cargs.extend([
             "-h",
-            params.get("target_label")
+            params.get("target_label", None)
         ])
     return cargs
 
@@ -134,16 +109,18 @@ def mri_linear_align_binary_outputs(
     """
     ret = MriLinearAlignBinaryOutputs(
         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_linear_align_binary_execute(
     params: MriLinearAlignBinaryParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriLinearAlignBinaryOutputs:
     """
+    mri_linear_align_binary
+    
     A tool for linear alignment of MRI images.
     
     Author: FreeSurfer Developers
@@ -152,10 +129,12 @@ def mri_linear_align_binary_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriLinearAlignBinaryOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_LINEAR_ALIGN_BINARY_METADATA)
     params = execution.params(params)
     cargs = mri_linear_align_binary_cargs(params, execution)
     ret = mri_linear_align_binary_outputs(params, execution)
@@ -171,6 +150,8 @@ def mri_linear_align_binary(
     runner: Runner | None = None,
 ) -> MriLinearAlignBinaryOutputs:
     """
+    mri_linear_align_binary
+    
     A tool for linear alignment of MRI images.
     
     Author: FreeSurfer Developers
@@ -187,21 +168,19 @@ def mri_linear_align_binary(
     Returns:
         NamedTuple of outputs (described in `MriLinearAlignBinaryOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_LINEAR_ALIGN_BINARY_METADATA)
     params = mri_linear_align_binary_params(
         source=source,
         target=target,
         output_xform=output_xform,
         target_label=target_label,
     )
-    return mri_linear_align_binary_execute(params, execution)
+    return mri_linear_align_binary_execute(params, runner)
 
 
 __all__ = [
     "MRI_LINEAR_ALIGN_BINARY_METADATA",
     "MriLinearAlignBinaryOutputs",
-    "MriLinearAlignBinaryParameters",
     "mri_linear_align_binary",
+    "mri_linear_align_binary_execute",
     "mri_linear_align_binary_params",
 ]