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

niwrap_freesurfer/freesurfer/mri_mark_temporal_lobe.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_MARK_TEMPORAL_LOBE_METADATA = Metadata(
-    id="75e6e60a85ce6a2bfb0234747d1412e2709192d8.boutiques",
+    id="cdc706940df41145e69814f5506bef3ea15ae487.boutiques",
     name="mri_mark_temporal_lobe",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRI_MARK_TEMPORAL_LOBE_METADATA = Metadata(
 
 
 MriMarkTemporalLobeParameters = typing.TypedDict('MriMarkTemporalLobeParameters', {
-    "__STYXTYPE__": typing.Literal["mri_mark_temporal_lobe"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_mark_temporal_lobe"]],
+    "spacing": typing.NotRequired[str | None],
+    "use_gradient": bool,
+    "subjects": list[InputPathType],
+    "output_file": str,
+})
+MriMarkTemporalLobeParametersTagged = typing.TypedDict('MriMarkTemporalLobeParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_mark_temporal_lobe"],
     "spacing": typing.NotRequired[str | None],
     "use_gradient": bool,
     "subjects": list[InputPathType],
     "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 {
-        "mri_mark_temporal_lobe": mri_mark_temporal_lobe_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_mark_temporal_lobe": mri_mark_temporal_lobe_outputs,
-    }.get(t)
 
 
 class MriMarkTemporalLobeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_mark_temporal_lobe(...)`.
+    Output object returned when calling `MriMarkTemporalLobeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mri_mark_temporal_lobe_params(
     output_file: str,
     spacing: str | None = None,
     use_gradient: bool = False,
-) -> MriMarkTemporalLobeParameters:
+) -> MriMarkTemporalLobeParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def mri_mark_temporal_lobe_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_mark_temporal_lobe",
+        "@type": "freesurfer/mri_mark_temporal_lobe",
         "use_gradient": use_gradient,
         "subjects": subjects,
         "output_file": output_file,
@@ -107,13 +82,13 @@ def mri_mark_temporal_lobe_cargs(
     """
     cargs = []
     cargs.append("mri_mark_temporal_lobe")
-    if params.get("spacing") is not None:
+    if params.get("spacing", None) is not None:
         cargs.extend([
             "-spacing",
-            params.get("spacing")
+            params.get("spacing", None)
         ])
-    if params.get("use_gradient"):
-        cargs.append("-gradient" + "".join([execution.input_file(f) for f in params.get("subjects")]) + params.get("output_file"))
+    if params.get("use_gradient", False):
+        cargs.append("-gradient" + "".join([execution.input_file(f) for f in params.get("subjects", None)]) + params.get("output_file", None))
     return cargs
 
 
@@ -132,16 +107,18 @@ def mri_mark_temporal_lobe_outputs(
     """
     ret = MriMarkTemporalLobeOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_file")),
+        output_file=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def mri_mark_temporal_lobe_execute(
     params: MriMarkTemporalLobeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriMarkTemporalLobeOutputs:
     """
+    mri_mark_temporal_lobe
+    
     A tool for marking the temporal lobe in MRI images.
     
     Author: FreeSurfer Developers
@@ -150,10 +127,12 @@ def mri_mark_temporal_lobe_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriMarkTemporalLobeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_MARK_TEMPORAL_LOBE_METADATA)
     params = execution.params(params)
     cargs = mri_mark_temporal_lobe_cargs(params, execution)
     ret = mri_mark_temporal_lobe_outputs(params, execution)
@@ -169,6 +148,8 @@ def mri_mark_temporal_lobe(
     runner: Runner | None = None,
 ) -> MriMarkTemporalLobeOutputs:
     """
+    mri_mark_temporal_lobe
+    
     A tool for marking the temporal lobe in MRI images.
     
     Author: FreeSurfer Developers
@@ -184,21 +165,19 @@ def mri_mark_temporal_lobe(
     Returns:
         NamedTuple of outputs (described in `MriMarkTemporalLobeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_MARK_TEMPORAL_LOBE_METADATA)
     params = mri_mark_temporal_lobe_params(
         spacing=spacing,
         use_gradient=use_gradient,
         subjects=subjects,
         output_file=output_file,
     )
-    return mri_mark_temporal_lobe_execute(params, execution)
+    return mri_mark_temporal_lobe_execute(params, runner)
 
 
 __all__ = [
     "MRI_MARK_TEMPORAL_LOBE_METADATA",
     "MriMarkTemporalLobeOutputs",
-    "MriMarkTemporalLobeParameters",
     "mri_mark_temporal_lobe",
+    "mri_mark_temporal_lobe_execute",
     "mri_mark_temporal_lobe_params",
 ]

niwrap_freesurfer/freesurfer/mri_mask.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_MASK_METADATA = Metadata(
-    id="641315fad16dad855c4213cb6224cc3d0beb7e63.boutiques",
+    id="bfd4609988cf9405815a95f6e9d94025535e22d1.boutiques",
     name="mri_mask",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,31 @@ MRI_MASK_METADATA = Metadata(
 
 
 MriMaskParameters = typing.TypedDict('MriMaskParameters', {
-    "__STYXTYPE__": typing.Literal["mri_mask"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_mask"]],
+    "input_volume": InputPathType,
+    "mask_volume": InputPathType,
+    "output_volume": str,
+    "xform": typing.NotRequired[str | None],
+    "lta_src": typing.NotRequired[str | None],
+    "lta_dst": typing.NotRequired[str | None],
+    "threshold": typing.NotRequired[float | None],
+    "npad": typing.NotRequired[float | None],
+    "npad_vector": typing.NotRequired[list[float] | None],
+    "npad_multi_vector": typing.NotRequired[list[float] | None],
+    "abs": bool,
+    "invert": bool,
+    "no_invert": bool,
+    "rh_labels": bool,
+    "lh_labels": bool,
+    "dilate": typing.NotRequired[float | None],
+    "no_cerebellum": bool,
+    "oval_value": typing.NotRequired[float | None],
+    "transfer_value": typing.NotRequired[float | None],
+    "keep_mask_deletion_edits": bool,
+    "samseg": bool,
+})
+MriMaskParametersTagged = typing.TypedDict('MriMaskParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_mask"],
     "input_volume": InputPathType,
     "mask_volume": InputPathType,
     "output_volume": str,
@@ -37,43 +61,11 @@ MriMaskParameters = typing.TypedDict('MriMaskParameters', {
     "keep_mask_deletion_edits": bool,
     "samseg": 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_mask": mri_mask_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_mask": mri_mask_outputs,
-    }.get(t)
 
 
 class MriMaskOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_mask(...)`.
+    Output object returned when calling `MriMaskParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -103,7 +95,7 @@ def mri_mask_params(
     transfer_value: float | None = None,
     keep_mask_deletion_edits: bool = False,
     samseg: bool = False,
-) -> MriMaskParameters:
+) -> MriMaskParametersTagged:
     """
     Build parameters.
     
@@ -146,7 +138,7 @@ def mri_mask_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_mask",
+        "@type": "freesurfer/mri_mask",
         "input_volume": input_volume,
         "mask_volume": mask_volume,
         "output_volume": output_volume,
@@ -197,74 +189,74 @@ def mri_mask_cargs(
     """
     cargs = []
     cargs.append("mri_mask")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(execution.input_file(params.get("mask_volume")))
-    cargs.append(params.get("output_volume"))
-    if params.get("xform") is not None:
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(execution.input_file(params.get("mask_volume", None)))
+    cargs.append(params.get("output_volume", None))
+    if params.get("xform", None) is not None:
         cargs.extend([
             "-xform",
-            params.get("xform")
+            params.get("xform", None)
         ])
-    if params.get("lta_src") is not None:
+    if params.get("lta_src", None) is not None:
         cargs.extend([
             "-lta_src",
-            params.get("lta_src")
+            params.get("lta_src", None)
         ])
-    if params.get("lta_dst") is not None:
+    if params.get("lta_dst", None) is not None:
         cargs.extend([
             "-lta_dst",
-            params.get("lta_dst")
+            params.get("lta_dst", None)
         ])
-    if params.get("threshold") is not None:
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "-T",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    if params.get("npad") is not None:
+    if params.get("npad", None) is not None:
         cargs.extend([
             "-bb",
-            str(params.get("npad"))
+            str(params.get("npad", None))
         ])
-    if params.get("npad_vector") is not None:
+    if params.get("npad_vector", None) is not None:
         cargs.extend([
             "-bbm",
-            *map(str, params.get("npad_vector"))
+            *map(str, params.get("npad_vector", None))
         ])
-    if params.get("npad_multi_vector") is not None:
+    if params.get("npad_multi_vector", None) is not None:
         cargs.extend([
             "-bbmm",
-            *map(str, params.get("npad_multi_vector"))
+            *map(str, params.get("npad_multi_vector", None))
         ])
-    if params.get("abs"):
+    if params.get("abs", False):
         cargs.append("-abs")
-    if params.get("invert"):
+    if params.get("invert", False):
         cargs.append("-invert")
-    if params.get("no_invert"):
+    if params.get("no_invert", False):
         cargs.append("-no-invert")
-    if params.get("rh_labels"):
+    if params.get("rh_labels", False):
         cargs.append("-rh")
-    if params.get("lh_labels"):
+    if params.get("lh_labels", False):
         cargs.append("-lh")
-    if params.get("dilate") is not None:
+    if params.get("dilate", None) is not None:
         cargs.extend([
             "-dilate",
-            str(params.get("dilate"))
+            str(params.get("dilate", None))
         ])
-    if params.get("no_cerebellum"):
+    if params.get("no_cerebellum", False):
         cargs.append("-no_cerebellum")
-    if params.get("oval_value") is not None:
+    if params.get("oval_value", None) is not None:
         cargs.extend([
             "-oval",
-            str(params.get("oval_value"))
+            str(params.get("oval_value", None))
         ])
-    if params.get("transfer_value") is not None:
+    if params.get("transfer_value", None) is not None:
         cargs.extend([
             "-transfer",
-            str(params.get("transfer_value"))
+            str(params.get("transfer_value", None))
         ])
-    if params.get("keep_mask_deletion_edits"):
+    if params.get("keep_mask_deletion_edits", False):
         cargs.append("-keep_mask_deletion_edits")
-    if params.get("samseg"):
+    if params.get("samseg", False):
         cargs.append("-samseg")
     return cargs
 
@@ -284,16 +276,18 @@ def mri_mask_outputs(
     """
     ret = MriMaskOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_volume")),
+        output_file=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def mri_mask_execute(
     params: MriMaskParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriMaskOutputs:
     """
+    mri_mask
+    
     Applies a mask volume (typically skull stripped).
     
     Author: FreeSurfer Developers
@@ -302,10 +296,12 @@ def mri_mask_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriMaskOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_MASK_METADATA)
     params = execution.params(params)
     cargs = mri_mask_cargs(params, execution)
     ret = mri_mask_outputs(params, execution)
@@ -338,6 +334,8 @@ def mri_mask(
     runner: Runner | None = None,
 ) -> MriMaskOutputs:
     """
+    mri_mask
+    
     Applies a mask volume (typically skull stripped).
     
     Author: FreeSurfer Developers
@@ -383,8 +381,6 @@ def mri_mask(
     Returns:
         NamedTuple of outputs (described in `MriMaskOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_MASK_METADATA)
     params = mri_mask_params(
         input_volume=input_volume,
         mask_volume=mask_volume,
@@ -408,13 +404,13 @@ def mri_mask(
         keep_mask_deletion_edits=keep_mask_deletion_edits,
         samseg=samseg,
     )
-    return mri_mask_execute(params, execution)
+    return mri_mask_execute(params, runner)
 
 
 __all__ = [
     "MRI_MASK_METADATA",
     "MriMaskOutputs",
-    "MriMaskParameters",
     "mri_mask",
+    "mri_mask_execute",
     "mri_mask_params",
 ]

niwrap_freesurfer/freesurfer/mri_matrix_multiply.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_MATRIX_MULTIPLY_METADATA = Metadata(
-    id="83fe54c8f9d006084c7a0544c59692e087c8825f.boutiques",
+    id="dcd8df7a1c911a2a155552a7959ee170bb02f794.boutiques",
     name="mri_matrix_multiply",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ MRI_MATRIX_MULTIPLY_METADATA = Metadata(
 
 
 MriMatrixMultiplyParameters = typing.TypedDict('MriMatrixMultiplyParameters', {
-    "__STYXTYPE__": typing.Literal["mri_matrix_multiply"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_matrix_multiply"]],
+    "input_matrices": list[InputPathType],
+    "inverted_input_matrices": typing.NotRequired[list[InputPathType] | None],
+    "output_matrix": str,
+    "verbose": bool,
+    "fsl": bool,
+    "binarize": bool,
+    "subject_name": typing.NotRequired[str | None],
+})
+MriMatrixMultiplyParametersTagged = typing.TypedDict('MriMatrixMultiplyParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_matrix_multiply"],
     "input_matrices": list[InputPathType],
     "inverted_input_matrices": typing.NotRequired[list[InputPathType] | None],
     "output_matrix": str,
@@ -23,43 +33,11 @@ MriMatrixMultiplyParameters = typing.TypedDict('MriMatrixMultiplyParameters', {
     "binarize": bool,
     "subject_name": 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_matrix_multiply": mri_matrix_multiply_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_matrix_multiply": mri_matrix_multiply_outputs,
-    }.get(t)
 
 
 class MriMatrixMultiplyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_matrix_multiply(...)`.
+    Output object returned when calling `MriMatrixMultiplyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def mri_matrix_multiply_params(
     fsl: bool = False,
     binarize: bool = False,
     subject_name: str | None = None,
-) -> MriMatrixMultiplyParameters:
+) -> MriMatrixMultiplyParametersTagged:
     """
     Build parameters.
     
@@ -92,7 +70,7 @@ def mri_matrix_multiply_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_matrix_multiply",
+        "@type": "freesurfer/mri_matrix_multiply",
         "input_matrices": input_matrices,
         "output_matrix": output_matrix,
         "verbose": verbose,
@@ -123,27 +101,27 @@ def mri_matrix_multiply_cargs(
     cargs.append("mri_matrix_multiply")
     cargs.extend([
         "-im",
-        *[execution.input_file(f) for f in params.get("input_matrices")]
+        *[execution.input_file(f) for f in params.get("input_matrices", None)]
     ])
-    if params.get("inverted_input_matrices") is not None:
+    if params.get("inverted_input_matrices", None) is not None:
         cargs.extend([
             "-iim",
-            *[execution.input_file(f) for f in params.get("inverted_input_matrices")]
+            *[execution.input_file(f) for f in params.get("inverted_input_matrices", None)]
         ])
     cargs.extend([
         "-om",
-        params.get("output_matrix")
+        params.get("output_matrix", None)
     ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-v")
-    if params.get("fsl"):
+    if params.get("fsl", False):
         cargs.append("-fsl")
-    if params.get("binarize"):
+    if params.get("binarize", False):
         cargs.append("-bin")
-    if params.get("subject_name") is not None:
+    if params.get("subject_name", None) is not None:
         cargs.extend([
             "-s",
-            params.get("subject_name")
+            params.get("subject_name", None)
         ])
     return cargs
 
@@ -163,17 +141,20 @@ def mri_matrix_multiply_outputs(
     """
     ret = MriMatrixMultiplyOutputs(
         root=execution.output_file("."),
-        output_matrix_file=execution.output_file(params.get("output_matrix")),
+        output_matrix_file=execution.output_file(params.get("output_matrix", None)),
     )
     return ret
 
 
 def mri_matrix_multiply_execute(
     params: MriMatrixMultiplyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriMatrixMultiplyOutputs:
     """
-    Command-line tool for multiplying and manipulating MRI transformation matrices.
+    mri_matrix_multiply
+    
+    Command-line tool for multiplying and manipulating MRI transformation
+    matrices.
     
     Author: FreeSurfer Developers
     
@@ -181,10 +162,12 @@ def mri_matrix_multiply_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriMatrixMultiplyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_MATRIX_MULTIPLY_METADATA)
     params = execution.params(params)
     cargs = mri_matrix_multiply_cargs(params, execution)
     ret = mri_matrix_multiply_outputs(params, execution)
@@ -203,7 +186,10 @@ def mri_matrix_multiply(
     runner: Runner | None = None,
 ) -> MriMatrixMultiplyOutputs:
     """
-    Command-line tool for multiplying and manipulating MRI transformation matrices.
+    mri_matrix_multiply
+    
+    Command-line tool for multiplying and manipulating MRI transformation
+    matrices.
     
     Author: FreeSurfer Developers
     
@@ -222,8 +208,6 @@ def mri_matrix_multiply(
     Returns:
         NamedTuple of outputs (described in `MriMatrixMultiplyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_MATRIX_MULTIPLY_METADATA)
     params = mri_matrix_multiply_params(
         input_matrices=input_matrices,
         inverted_input_matrices=inverted_input_matrices,
@@ -233,13 +217,13 @@ def mri_matrix_multiply(
         binarize=binarize,
         subject_name=subject_name,
     )
-    return mri_matrix_multiply_execute(params, execution)
+    return mri_matrix_multiply_execute(params, runner)
 
 
 __all__ = [
     "MRI_MATRIX_MULTIPLY_METADATA",
     "MriMatrixMultiplyOutputs",
-    "MriMatrixMultiplyParameters",
     "mri_matrix_multiply",
+    "mri_matrix_multiply_execute",
     "mri_matrix_multiply_params",
 ]