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

niwrap_freesurfer/freesurfer/mris_calc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_CALC_METADATA = Metadata(
-    id="8fa829f5f800088c450bcf7fa7d7097fee3c8f04.boutiques",
+    id="8b8a28709e24748f1c6f6156bf3e2e9f1ffe0a0f.boutiques",
     name="mris_calc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRIS_CALC_METADATA = Metadata(
 
 
 MrisCalcParameters = typing.TypedDict('MrisCalcParameters', {
-    "__STYXTYPE__": typing.Literal["mris_calc"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_calc"]],
+    "input_file1": InputPathType,
+    "action": str,
+    "input_file2_or_float": typing.NotRequired[InputPathType | None],
+    "output_file": typing.NotRequired[str | None],
+    "label_file": typing.NotRequired[InputPathType | None],
+    "verbosity": typing.NotRequired[str | None],
+})
+MrisCalcParametersTagged = typing.TypedDict('MrisCalcParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_calc"],
     "input_file1": InputPathType,
     "action": str,
     "input_file2_or_float": typing.NotRequired[InputPathType | None],
@@ -22,43 +31,11 @@ MrisCalcParameters = typing.TypedDict('MrisCalcParameters', {
     "label_file": typing.NotRequired[InputPathType | None],
     "verbosity": 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 {
-        "mris_calc": mris_calc_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 {
-        "mris_calc": mris_calc_outputs,
-    }.get(t)
 
 
 class MrisCalcOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_calc(...)`.
+    Output object returned when calling `MrisCalcParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def mris_calc_params(
     output_file: str | None = None,
     label_file: InputPathType | None = None,
     verbosity: str | None = None,
-) -> MrisCalcParameters:
+) -> MrisCalcParametersTagged:
     """
     Build parameters.
     
@@ -93,7 +70,7 @@ def mris_calc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_calc",
+        "@type": "freesurfer/mris_calc",
         "input_file1": input_file1,
         "action": action,
     }
@@ -123,24 +100,24 @@ def mris_calc_cargs(
     """
     cargs = []
     cargs.append("mris_calc")
-    cargs.append(execution.input_file(params.get("input_file1")))
-    cargs.append(params.get("action"))
-    if params.get("input_file2_or_float") is not None:
-        cargs.append(execution.input_file(params.get("input_file2_or_float")))
-    if params.get("output_file") is not None:
+    cargs.append(execution.input_file(params.get("input_file1", None)))
+    cargs.append(params.get("action", None))
+    if params.get("input_file2_or_float", None) is not None:
+        cargs.append(execution.input_file(params.get("input_file2_or_float", None)))
+    if params.get("output_file", None) is not None:
         cargs.extend([
             "--output",
-            params.get("output_file")
+            params.get("output_file", None)
         ])
-    if params.get("label_file") is not None:
+    if params.get("label_file", None) is not None:
         cargs.extend([
             "--label",
-            execution.input_file(params.get("label_file"))
+            execution.input_file(params.get("label_file", None))
         ])
-    if params.get("verbosity") is not None:
+    if params.get("verbosity", None) is not None:
         cargs.extend([
             "--verbosity",
-            params.get("verbosity")
+            params.get("verbosity", None)
         ])
     return cargs
 
@@ -160,16 +137,18 @@ def mris_calc_outputs(
     """
     ret = MrisCalcOutputs(
         root=execution.output_file("."),
-        output_curv_file=execution.output_file(params.get("output_file")) if (params.get("output_file") is not None) else None,
+        output_curv_file=execution.output_file(params.get("output_file", None)) if (params.get("output_file") is not None) else None,
     )
     return ret
 
 
 def mris_calc_execute(
     params: MrisCalcParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisCalcOutputs:
     """
+    mris_calc
+    
     Simple calculator that operates on FreeSurfer curvatures and volumes.
     
     Author: FreeSurfer Developers
@@ -178,10 +157,12 @@ def mris_calc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisCalcOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_CALC_METADATA)
     params = execution.params(params)
     cargs = mris_calc_cargs(params, execution)
     ret = mris_calc_outputs(params, execution)
@@ -199,6 +180,8 @@ def mris_calc(
     runner: Runner | None = None,
 ) -> MrisCalcOutputs:
     """
+    mris_calc
+    
     Simple calculator that operates on FreeSurfer curvatures and volumes.
     
     Author: FreeSurfer Developers
@@ -221,8 +204,6 @@ def mris_calc(
     Returns:
         NamedTuple of outputs (described in `MrisCalcOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_CALC_METADATA)
     params = mris_calc_params(
         input_file1=input_file1,
         action=action,
@@ -231,13 +212,13 @@ def mris_calc(
         label_file=label_file,
         verbosity=verbosity,
     )
-    return mris_calc_execute(params, execution)
+    return mris_calc_execute(params, runner)
 
 
 __all__ = [
     "MRIS_CALC_METADATA",
     "MrisCalcOutputs",
-    "MrisCalcParameters",
     "mris_calc",
+    "mris_calc_execute",
     "mris_calc_params",
 ]

niwrap_freesurfer/freesurfer/mris_compute_acorr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_COMPUTE_ACORR_METADATA = Metadata(
-    id="c87ef9e1a360bff02be52c7cd358fb4259d79971.boutiques",
+    id="0e07071f4f37f6918a11761e3deabc99cac8c12d.boutiques",
     name="mris_compute_acorr",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRIS_COMPUTE_ACORR_METADATA = Metadata(
 
 
 MrisComputeAcorrParameters = typing.TypedDict('MrisComputeAcorrParameters', {
-    "__STYXTYPE__": typing.Literal["mris_compute_acorr"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_compute_acorr"]],
+    "output_subject": str,
+    "hemi": str,
+    "surf": InputPathType,
+    "curv": InputPathType,
+    "c1_subjects": list[str],
+    "c2_subjects": list[str],
+})
+MrisComputeAcorrParametersTagged = typing.TypedDict('MrisComputeAcorrParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_compute_acorr"],
     "output_subject": str,
     "hemi": str,
     "surf": InputPathType,
@@ -22,42 +31,11 @@ MrisComputeAcorrParameters = typing.TypedDict('MrisComputeAcorrParameters', {
     "c1_subjects": list[str],
     "c2_subjects": list[str],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_compute_acorr": mris_compute_acorr_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 MrisComputeAcorrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_compute_acorr(...)`.
+    Output object returned when calling `MrisComputeAcorrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def mris_compute_acorr_params(
     curv: InputPathType,
     c1_subjects: list[str],
     c2_subjects: list[str],
-) -> MrisComputeAcorrParameters:
+) -> MrisComputeAcorrParametersTagged:
     """
     Build parameters.
     
@@ -86,7 +64,7 @@ def mris_compute_acorr_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_compute_acorr",
+        "@type": "freesurfer/mris_compute_acorr",
         "output_subject": output_subject,
         "hemi": hemi,
         "surf": surf,
@@ -114,13 +92,13 @@ def mris_compute_acorr_cargs(
     cargs.append("mris_compute_acorr")
     cargs.extend([
         "-o",
-        params.get("output_subject")
+        params.get("output_subject", None)
     ])
-    cargs.append(params.get("hemi"))
-    cargs.append(execution.input_file(params.get("surf")))
-    cargs.append(execution.input_file(params.get("curv")))
-    cargs.extend(params.get("c1_subjects"))
-    cargs.extend(params.get("c2_subjects"))
+    cargs.append(params.get("hemi", None))
+    cargs.append(execution.input_file(params.get("surf", None)))
+    cargs.append(execution.input_file(params.get("curv", None)))
+    cargs.extend(params.get("c1_subjects", None))
+    cargs.extend(params.get("c2_subjects", None))
     return cargs
 
 
@@ -145,10 +123,13 @@ def mris_compute_acorr_outputs(
 
 def mris_compute_acorr_execute(
     params: MrisComputeAcorrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisComputeAcorrOutputs:
     """
-    Compute the autocorrelation function of a curvature file on a spherical surface.
+    mris_compute_acorr
+    
+    Compute the autocorrelation function of a curvature file on a spherical
+    surface.
     
     Author: FreeSurfer Developers
     
@@ -156,10 +137,12 @@ def mris_compute_acorr_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisComputeAcorrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_COMPUTE_ACORR_METADATA)
     params = execution.params(params)
     cargs = mris_compute_acorr_cargs(params, execution)
     ret = mris_compute_acorr_outputs(params, execution)
@@ -177,7 +160,10 @@ def mris_compute_acorr(
     runner: Runner | None = None,
 ) -> MrisComputeAcorrOutputs:
     """
-    Compute the autocorrelation function of a curvature file on a spherical surface.
+    mris_compute_acorr
+    
+    Compute the autocorrelation function of a curvature file on a spherical
+    surface.
     
     Author: FreeSurfer Developers
     
@@ -195,8 +181,6 @@ def mris_compute_acorr(
     Returns:
         NamedTuple of outputs (described in `MrisComputeAcorrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_COMPUTE_ACORR_METADATA)
     params = mris_compute_acorr_params(
         output_subject=output_subject,
         hemi=hemi,
@@ -205,13 +189,13 @@ def mris_compute_acorr(
         c1_subjects=c1_subjects,
         c2_subjects=c2_subjects,
     )
-    return mris_compute_acorr_execute(params, execution)
+    return mris_compute_acorr_execute(params, runner)
 
 
 __all__ = [
     "MRIS_COMPUTE_ACORR_METADATA",
     "MrisComputeAcorrOutputs",
-    "MrisComputeAcorrParameters",
     "mris_compute_acorr",
+    "mris_compute_acorr_execute",
     "mris_compute_acorr_params",
 ]

niwrap_freesurfer/freesurfer/mris_compute_layer_intensities.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_COMPUTE_LAYER_INTENSITIES_METADATA = Metadata(
-    id="f24960e9a74b3ae18e3affaefde83e7e04cb8a2b.boutiques",
+    id="2a0eb3ef93dc3fd21876edfb530230812af2e366.boutiques",
     name="mris_compute_layer_intensities",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRIS_COMPUTE_LAYER_INTENSITIES_METADATA = Metadata(
 
 
 MrisComputeLayerIntensitiesParameters = typing.TypedDict('MrisComputeLayerIntensitiesParameters', {
-    "__STYXTYPE__": typing.Literal["mris_compute_layer_intensities"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_compute_layer_intensities"]],
+    "input_intensity_volume": InputPathType,
+    "layer_volume_fractions_file": InputPathType,
+    "input_surface": InputPathType,
+    "output_overlay": str,
+})
+MrisComputeLayerIntensitiesParametersTagged = typing.TypedDict('MrisComputeLayerIntensitiesParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_compute_layer_intensities"],
     "input_intensity_volume": InputPathType,
     "layer_volume_fractions_file": InputPathType,
     "input_surface": InputPathType,
     "output_overlay": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_compute_layer_intensities": mris_compute_layer_intensities_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 {
-        "mris_compute_layer_intensities": mris_compute_layer_intensities_outputs,
-    }.get(t)
 
 
 class MrisComputeLayerIntensitiesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_compute_layer_intensities(...)`.
+    Output object returned when calling `MrisComputeLayerIntensitiesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mris_compute_layer_intensities_params(
     layer_volume_fractions_file: InputPathType,
     input_surface: InputPathType,
     output_overlay: str,
-) -> MrisComputeLayerIntensitiesParameters:
+) -> MrisComputeLayerIntensitiesParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def mris_compute_layer_intensities_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_compute_layer_intensities",
+        "@type": "freesurfer/mris_compute_layer_intensities",
         "input_intensity_volume": input_intensity_volume,
         "layer_volume_fractions_file": layer_volume_fractions_file,
         "input_surface": input_surface,
@@ -106,10 +81,10 @@ def mris_compute_layer_intensities_cargs(
     """
     cargs = []
     cargs.append("mris_compute_layer_intensities")
-    cargs.append(execution.input_file(params.get("input_intensity_volume")))
-    cargs.append(execution.input_file(params.get("layer_volume_fractions_file")))
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(params.get("output_overlay"))
+    cargs.append(execution.input_file(params.get("input_intensity_volume", None)))
+    cargs.append(execution.input_file(params.get("layer_volume_fractions_file", None)))
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(params.get("output_overlay", None))
     return cargs
 
 
@@ -128,18 +103,20 @@ def mris_compute_layer_intensities_outputs(
     """
     ret = MrisComputeLayerIntensitiesOutputs(
         root=execution.output_file("."),
-        output_overlay_file=execution.output_file(params.get("output_overlay")),
+        output_overlay_file=execution.output_file(params.get("output_overlay", None)),
     )
     return ret
 
 
 def mris_compute_layer_intensities_execute(
     params: MrisComputeLayerIntensitiesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisComputeLayerIntensitiesOutputs:
     """
-    Computes intensity overlays for specified cortical layers based on input volumes
-    and surfaces.
+    mris_compute_layer_intensities
+    
+    Computes intensity overlays for specified cortical layers based on input
+    volumes and surfaces.
     
     Author: FreeSurfer Developers
     
@@ -147,10 +124,12 @@ def mris_compute_layer_intensities_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisComputeLayerIntensitiesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_COMPUTE_LAYER_INTENSITIES_METADATA)
     params = execution.params(params)
     cargs = mris_compute_layer_intensities_cargs(params, execution)
     ret = mris_compute_layer_intensities_outputs(params, execution)
@@ -166,8 +145,10 @@ def mris_compute_layer_intensities(
     runner: Runner | None = None,
 ) -> MrisComputeLayerIntensitiesOutputs:
     """
-    Computes intensity overlays for specified cortical layers based on input volumes
-    and surfaces.
+    mris_compute_layer_intensities
+    
+    Computes intensity overlays for specified cortical layers based on input
+    volumes and surfaces.
     
     Author: FreeSurfer Developers
     
@@ -182,21 +163,19 @@ def mris_compute_layer_intensities(
     Returns:
         NamedTuple of outputs (described in `MrisComputeLayerIntensitiesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_COMPUTE_LAYER_INTENSITIES_METADATA)
     params = mris_compute_layer_intensities_params(
         input_intensity_volume=input_intensity_volume,
         layer_volume_fractions_file=layer_volume_fractions_file,
         input_surface=input_surface,
         output_overlay=output_overlay,
     )
-    return mris_compute_layer_intensities_execute(params, execution)
+    return mris_compute_layer_intensities_execute(params, runner)
 
 
 __all__ = [
     "MRIS_COMPUTE_LAYER_INTENSITIES_METADATA",
     "MrisComputeLayerIntensitiesOutputs",
-    "MrisComputeLayerIntensitiesParameters",
     "mris_compute_layer_intensities",
+    "mris_compute_layer_intensities_execute",
     "mris_compute_layer_intensities_params",
 ]