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

niwrap_freesurfer/freesurfer/mri_normalize_tp2.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_NORMALIZE_TP2_METADATA = Metadata(
-    id="90f7ef1c696e6598cec236ade9c15ef365878182.boutiques",
+    id="7ccaab32bd525f6ee42b1cbbfcf682b23bc371c8.boutiques",
     name="mri_normalize_tp2",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,21 @@ MRI_NORMALIZE_TP2_METADATA = Metadata(
 
 
 MriNormalizeTp2Parameters = typing.TypedDict('MriNormalizeTp2Parameters', {
-    "__STYXTYPE__": typing.Literal["mri_normalize_tp2"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_normalize_tp2"]],
+    "input_vol": InputPathType,
+    "normalized_vol": str,
+    "t1_volume": typing.NotRequired[InputPathType | None],
+    "mask1": typing.NotRequired[InputPathType | None],
+    "mask2": typing.NotRequired[InputPathType | None],
+    "threshold": typing.NotRequired[float | None],
+    "ctrl": typing.NotRequired[InputPathType | None],
+    "xform": typing.NotRequired[InputPathType | None],
+    "invert_flag": bool,
+    "lta_src": typing.NotRequired[InputPathType | None],
+    "lta_dst": typing.NotRequired[InputPathType | None],
+})
+MriNormalizeTp2ParametersTagged = typing.TypedDict('MriNormalizeTp2ParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_normalize_tp2"],
     "input_vol": InputPathType,
     "normalized_vol": str,
     "t1_volume": typing.NotRequired[InputPathType | None],
@@ -27,43 +41,11 @@ MriNormalizeTp2Parameters = typing.TypedDict('MriNormalizeTp2Parameters', {
     "lta_src": typing.NotRequired[InputPathType | None],
     "lta_dst": typing.NotRequired[InputPathType | 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_normalize_tp2": mri_normalize_tp2_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_normalize_tp2": mri_normalize_tp2_outputs,
-    }.get(t)
 
 
 class MriNormalizeTp2Outputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_normalize_tp2(...)`.
+    Output object returned when calling `MriNormalizeTp2Parameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -83,7 +65,7 @@ def mri_normalize_tp2_params(
     invert_flag: bool = False,
     lta_src: InputPathType | None = None,
     lta_dst: InputPathType | None = None,
-) -> MriNormalizeTp2Parameters:
+) -> MriNormalizeTp2ParametersTagged:
     """
     Build parameters.
     
@@ -103,7 +85,7 @@ def mri_normalize_tp2_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_normalize_tp2",
+        "@type": "freesurfer/mri_normalize_tp2",
         "input_vol": input_vol,
         "normalized_vol": normalized_vol,
         "invert_flag": invert_flag,
@@ -142,49 +124,49 @@ def mri_normalize_tp2_cargs(
     """
     cargs = []
     cargs.append("mri_normalize_tp2")
-    cargs.append(execution.input_file(params.get("input_vol")))
-    cargs.append(params.get("normalized_vol"))
-    if params.get("t1_volume") is not None:
+    cargs.append(execution.input_file(params.get("input_vol", None)))
+    cargs.append(params.get("normalized_vol", None))
+    if params.get("t1_volume", None) is not None:
         cargs.extend([
             "-T1",
-            execution.input_file(params.get("t1_volume"))
+            execution.input_file(params.get("t1_volume", None))
         ])
-    if params.get("mask1") is not None:
+    if params.get("mask1", None) is not None:
         cargs.extend([
             "-mask1",
-            execution.input_file(params.get("mask1"))
+            execution.input_file(params.get("mask1", None))
         ])
-    if params.get("mask2") is not None:
+    if params.get("mask2", None) is not None:
         cargs.extend([
             "-mask2",
-            execution.input_file(params.get("mask2"))
+            execution.input_file(params.get("mask2", None))
         ])
-    if params.get("threshold") is not None:
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "-threshold",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    if params.get("ctrl") is not None:
+    if params.get("ctrl", None) is not None:
         cargs.extend([
             "-ctrl",
-            execution.input_file(params.get("ctrl"))
+            execution.input_file(params.get("ctrl", None))
         ])
-    if params.get("xform") is not None:
+    if params.get("xform", None) is not None:
         cargs.extend([
             "-xform",
-            execution.input_file(params.get("xform"))
+            execution.input_file(params.get("xform", None))
         ])
-    if params.get("invert_flag"):
+    if params.get("invert_flag", False):
         cargs.append("-invert")
-    if params.get("lta_src") is not None:
+    if params.get("lta_src", None) is not None:
         cargs.extend([
             "-lta_src",
-            execution.input_file(params.get("lta_src"))
+            execution.input_file(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",
-            execution.input_file(params.get("lta_dst"))
+            execution.input_file(params.get("lta_dst", None))
         ])
     return cargs
 
@@ -204,17 +186,20 @@ def mri_normalize_tp2_outputs(
     """
     ret = MriNormalizeTp2Outputs(
         root=execution.output_file("."),
-        output_normalized_vol=execution.output_file(params.get("normalized_vol")),
+        output_normalized_vol=execution.output_file(params.get("normalized_vol", None)),
     )
     return ret
 
 
 def mri_normalize_tp2_execute(
     params: MriNormalizeTp2Parameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriNormalizeTp2Outputs:
     """
-    Normalize the input volume using control points of tp1 to help normalize tp2.
+    mri_normalize_tp2
+    
+    Normalize the input volume using control points of tp1 to help normalize
+    tp2.
     
     Author: FreeSurfer Developers
     
@@ -222,10 +207,12 @@ def mri_normalize_tp2_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriNormalizeTp2Outputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_NORMALIZE_TP2_METADATA)
     params = execution.params(params)
     cargs = mri_normalize_tp2_cargs(params, execution)
     ret = mri_normalize_tp2_outputs(params, execution)
@@ -248,7 +235,10 @@ def mri_normalize_tp2(
     runner: Runner | None = None,
 ) -> MriNormalizeTp2Outputs:
     """
-    Normalize the input volume using control points of tp1 to help normalize tp2.
+    mri_normalize_tp2
+    
+    Normalize the input volume using control points of tp1 to help normalize
+    tp2.
     
     Author: FreeSurfer Developers
     
@@ -270,8 +260,6 @@ def mri_normalize_tp2(
     Returns:
         NamedTuple of outputs (described in `MriNormalizeTp2Outputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_NORMALIZE_TP2_METADATA)
     params = mri_normalize_tp2_params(
         input_vol=input_vol,
         normalized_vol=normalized_vol,
@@ -285,13 +273,13 @@ def mri_normalize_tp2(
         lta_src=lta_src,
         lta_dst=lta_dst,
     )
-    return mri_normalize_tp2_execute(params, execution)
+    return mri_normalize_tp2_execute(params, runner)
 
 
 __all__ = [
     "MRI_NORMALIZE_TP2_METADATA",
     "MriNormalizeTp2Outputs",
-    "MriNormalizeTp2Parameters",
     "mri_normalize_tp2",
+    "mri_normalize_tp2_execute",
     "mri_normalize_tp2_params",
 ]

niwrap_freesurfer/freesurfer/mri_nu_correct_mni.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_NU_CORRECT_MNI_METADATA = Metadata(
-    id="6a55a380e55be6662d699e0b6bc9d3854bb183c1.boutiques",
+    id="e97bbbb4bc37047d82235aa8b33fd61f71d4a9a0.boutiques",
     name="mri_nu_correct.mni",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,23 @@ MRI_NU_CORRECT_MNI_METADATA = Metadata(
 
 
 MriNuCorrectMniParameters = typing.TypedDict('MriNuCorrectMniParameters', {
-    "__STYXTYPE__": typing.Literal["mri_nu_correct.mni"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_nu_correct.mni"]],
+    "input_volume": InputPathType,
+    "output_volume": str,
+    "iterations": float,
+    "proto_iterations": typing.NotRequired[float | None],
+    "mask_volume": typing.NotRequired[InputPathType | None],
+    "stop_threshold": typing.NotRequired[float | None],
+    "uchar_transform": typing.NotRequired[InputPathType | None],
+    "ants_n3": bool,
+    "ants_n4": bool,
+    "no_uchar": bool,
+    "ants_n4_replace_zeros": bool,
+    "cm_flag": bool,
+    "debug_flag": bool,
+})
+MriNuCorrectMniParametersTagged = typing.TypedDict('MriNuCorrectMniParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_nu_correct.mni"],
     "input_volume": InputPathType,
     "output_volume": str,
     "iterations": float,
@@ -29,43 +45,11 @@ MriNuCorrectMniParameters = typing.TypedDict('MriNuCorrectMniParameters', {
     "cm_flag": bool,
     "debug_flag": 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_nu_correct.mni": mri_nu_correct_mni_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_nu_correct.mni": mri_nu_correct_mni_outputs,
-    }.get(t)
 
 
 class MriNuCorrectMniOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_nu_correct_mni(...)`.
+    Output object returned when calling `MriNuCorrectMniParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -87,7 +71,7 @@ def mri_nu_correct_mni_params(
     ants_n4_replace_zeros: bool = False,
     cm_flag: bool = False,
     debug_flag: bool = False,
-) -> MriNuCorrectMniParameters:
+) -> MriNuCorrectMniParametersTagged:
     """
     Build parameters.
     
@@ -114,7 +98,7 @@ def mri_nu_correct_mni_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_nu_correct.mni",
+        "@type": "freesurfer/mri_nu_correct.mni",
         "input_volume": input_volume,
         "output_volume": output_volume,
         "iterations": iterations,
@@ -153,47 +137,47 @@ def mri_nu_correct_mni_cargs(
     cargs.append("mri_nu_correct.mni")
     cargs.extend([
         "--i",
-        execution.input_file(params.get("input_volume"))
+        execution.input_file(params.get("input_volume", None))
     ])
     cargs.extend([
         "--o",
-        params.get("output_volume")
+        params.get("output_volume", None)
     ])
     cargs.extend([
         "--n",
-        str(params.get("iterations"))
+        str(params.get("iterations", None))
     ])
-    if params.get("proto_iterations") is not None:
+    if params.get("proto_iterations", None) is not None:
         cargs.extend([
             "--proto-iters",
-            str(params.get("proto_iterations"))
+            str(params.get("proto_iterations", None))
         ])
-    if params.get("mask_volume") is not None:
+    if params.get("mask_volume", None) is not None:
         cargs.extend([
             "--mask",
-            execution.input_file(params.get("mask_volume"))
+            execution.input_file(params.get("mask_volume", None))
         ])
-    if params.get("stop_threshold") is not None:
+    if params.get("stop_threshold", None) is not None:
         cargs.extend([
             "--stop",
-            str(params.get("stop_threshold"))
+            str(params.get("stop_threshold", None))
         ])
-    if params.get("uchar_transform") is not None:
+    if params.get("uchar_transform", None) is not None:
         cargs.extend([
             "--uchar",
-            execution.input_file(params.get("uchar_transform"))
+            execution.input_file(params.get("uchar_transform", None))
         ])
-    if params.get("ants_n3"):
+    if params.get("ants_n3", False):
         cargs.append("--ants-n3")
-    if params.get("ants_n4"):
+    if params.get("ants_n4", False):
         cargs.append("--ants-n4")
-    if params.get("no_uchar"):
+    if params.get("no_uchar", False):
         cargs.append("--no-uchar")
-    if params.get("ants_n4_replace_zeros"):
+    if params.get("ants_n4_replace_zeros", False):
         cargs.append("--ants-n4-replace-zeros")
-    if params.get("cm_flag"):
+    if params.get("cm_flag", False):
         cargs.append("--cm")
-    if params.get("debug_flag"):
+    if params.get("debug_flag", False):
         cargs.append("--debug")
     return cargs
 
@@ -213,16 +197,18 @@ def mri_nu_correct_mni_outputs(
     """
     ret = MriNuCorrectMniOutputs(
         root=execution.output_file("."),
-        corrected_output=execution.output_file(params.get("output_volume")),
+        corrected_output=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def mri_nu_correct_mni_execute(
     params: MriNuCorrectMniParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriNuCorrectMniOutputs:
     """
+    mri_nu_correct.mni
+    
     Wrapper for nu_correct, used for correcting intensity non-uniformity (bias
     fields).
     
@@ -232,10 +218,12 @@ def mri_nu_correct_mni_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriNuCorrectMniOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_NU_CORRECT_MNI_METADATA)
     params = execution.params(params)
     cargs = mri_nu_correct_mni_cargs(params, execution)
     ret = mri_nu_correct_mni_outputs(params, execution)
@@ -260,6 +248,8 @@ def mri_nu_correct_mni(
     runner: Runner | None = None,
 ) -> MriNuCorrectMniOutputs:
     """
+    mri_nu_correct.mni
+    
     Wrapper for nu_correct, used for correcting intensity non-uniformity (bias
     fields).
     
@@ -290,8 +280,6 @@ def mri_nu_correct_mni(
     Returns:
         NamedTuple of outputs (described in `MriNuCorrectMniOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_NU_CORRECT_MNI_METADATA)
     params = mri_nu_correct_mni_params(
         input_volume=input_volume,
         output_volume=output_volume,
@@ -307,13 +295,13 @@ def mri_nu_correct_mni(
         cm_flag=cm_flag,
         debug_flag=debug_flag,
     )
-    return mri_nu_correct_mni_execute(params, execution)
+    return mri_nu_correct_mni_execute(params, runner)
 
 
 __all__ = [
     "MRI_NU_CORRECT_MNI_METADATA",
     "MriNuCorrectMniOutputs",
-    "MriNuCorrectMniParameters",
     "mri_nu_correct_mni",
+    "mri_nu_correct_mni_execute",
     "mri_nu_correct_mni_params",
 ]

niwrap_freesurfer/freesurfer/mri_or.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_OR_METADATA = Metadata(
-    id="950324820d0db5f38e35e56b2de3aab6e8c67c1e.boutiques",
+    id="dffeb3efda59bfcbcb950926fbb576c58009fdf3.boutiques",
     name="mri_or",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ MRI_OR_METADATA = Metadata(
 
 
 MriOrParameters = typing.TypedDict('MriOrParameters', {
-    "__STYXTYPE__": typing.Literal["mri_or"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_or"]],
+    "original_labels": bool,
+    "input_files": list[InputPathType],
+})
+MriOrParametersTagged = typing.TypedDict('MriOrParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_or"],
     "original_labels": bool,
     "input_files": list[InputPathType],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_or": mri_or_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 MriOrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_or(...)`.
+    Output object returned when calling `MriOrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class MriOrOutputs(typing.NamedTuple):
 def mri_or_params(
     input_files: list[InputPathType],
     original_labels: bool = False,
-) -> MriOrParameters:
+) -> MriOrParametersTagged:
     """
     Build parameters.
     
@@ -75,7 +49,7 @@ def mri_or_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_or",
+        "@type": "freesurfer/mri_or",
         "original_labels": original_labels,
         "input_files": input_files,
     }
@@ -97,9 +71,9 @@ def mri_or_cargs(
     """
     cargs = []
     cargs.append("mri_or")
-    if params.get("original_labels"):
+    if params.get("original_labels", False):
         cargs.append("-o")
-    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    cargs.extend([execution.input_file(f) for f in params.get("input_files", None)])
     return cargs
 
 
@@ -124,9 +98,11 @@ def mri_or_outputs(
 
 def mri_or_execute(
     params: MriOrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriOrOutputs:
     """
+    mri_or
+    
     Performs a logical voxel-wise OR on a series of volumes.
     
     Author: FreeSurfer Developers
@@ -135,10 +111,12 @@ def mri_or_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriOrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_OR_METADATA)
     params = execution.params(params)
     cargs = mri_or_cargs(params, execution)
     ret = mri_or_outputs(params, execution)
@@ -152,6 +130,8 @@ def mri_or(
     runner: Runner | None = None,
 ) -> MriOrOutputs:
     """
+    mri_or
+    
     Performs a logical voxel-wise OR on a series of volumes.
     
     Author: FreeSurfer Developers
@@ -167,19 +147,17 @@ def mri_or(
     Returns:
         NamedTuple of outputs (described in `MriOrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_OR_METADATA)
     params = mri_or_params(
         original_labels=original_labels,
         input_files=input_files,
     )
-    return mri_or_execute(params, execution)
+    return mri_or_execute(params, runner)
 
 
 __all__ = [
     "MRI_OR_METADATA",
     "MriOrOutputs",
-    "MriOrParameters",
     "mri_or",
+    "mri_or_execute",
     "mri_or_params",
 ]