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

niwrap_freesurfer/freesurfer/mris_fwhm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_FWHM_METADATA = Metadata(
-    id="38f19d2c0adc1d4c124b77ae43af464be6971c32.boutiques",
+    id="a1a32f8d7f7e5d30241888e0d9b40c74ddb0107e.boutiques",
     name="mris_fwhm",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,41 @@ MRIS_FWHM_METADATA = Metadata(
 
 
 MrisFwhmParameters = typing.TypedDict('MrisFwhmParameters', {
-    "__STYXTYPE__": typing.Literal["mris_fwhm"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_fwhm"]],
+    "input_file": InputPathType,
+    "subject": str,
+    "hemi": str,
+    "surf": typing.NotRequired[str | None],
+    "label_file": typing.NotRequired[InputPathType | None],
+    "cortex_flag": bool,
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "x_matrix": typing.NotRequired[InputPathType | None],
+    "detrend_order": typing.NotRequired[float | None],
+    "smooth_only_flag": bool,
+    "no_detrend_flag": bool,
+    "sqr_flag": bool,
+    "sum_file": typing.NotRequired[str | None],
+    "dat_file": typing.NotRequired[str | None],
+    "ar1dat_file": typing.NotRequired[str | None],
+    "ar1vol": typing.NotRequired[str | None],
+    "fwhmmap": typing.NotRequired[str | None],
+    "prune_flag": bool,
+    "no_prune_flag": bool,
+    "out_mask": typing.NotRequired[str | None],
+    "varnorm_flag": bool,
+    "fwhm": typing.NotRequired[float | None],
+    "niters_only": typing.NotRequired[str | None],
+    "output_file": str,
+    "sd": typing.NotRequired[str | None],
+    "synth_flag": bool,
+    "synth_frames": typing.NotRequired[float | None],
+    "threads": typing.NotRequired[float | None],
+    "debug_flag": bool,
+    "checkopts_flag": bool,
+    "version_flag": bool,
+})
+MrisFwhmParametersTagged = typing.TypedDict('MrisFwhmParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_fwhm"],
     "input_file": InputPathType,
     "subject": str,
     "hemi": str,
@@ -47,42 +81,11 @@ MrisFwhmParameters = typing.TypedDict('MrisFwhmParameters', {
     "checkopts_flag": bool,
     "version_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 {
-        "mris_fwhm": mris_fwhm_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 MrisFwhmOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_fwhm(...)`.
+    Output object returned when calling `MrisFwhmParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -120,7 +123,7 @@ def mris_fwhm_params(
     debug_flag: bool = False,
     checkopts_flag: bool = False,
     version_flag: bool = False,
-) -> MrisFwhmParameters:
+) -> MrisFwhmParametersTagged:
     """
     Build parameters.
     
@@ -163,7 +166,7 @@ def mris_fwhm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_fwhm",
+        "@type": "freesurfer/mris_fwhm",
         "input_file": input_file,
         "subject": subject,
         "hemi": hemi,
@@ -232,121 +235,121 @@ def mris_fwhm_cargs(
     cargs.append("mris_fwhm")
     cargs.extend([
         "--i",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "--subject",
-        params.get("subject")
+        params.get("subject", None)
     ])
     cargs.extend([
         "--hemi",
-        params.get("hemi")
+        params.get("hemi", None)
     ])
-    if params.get("surf") is not None:
+    if params.get("surf", None) is not None:
         cargs.extend([
             "--surf",
-            params.get("surf")
+            params.get("surf", 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("cortex_flag"):
+    if params.get("cortex_flag", False):
         cargs.append("--cortex")
-    if params.get("mask_file") is not None:
+    if params.get("mask_file", None) is not None:
         cargs.extend([
             "--mask",
-            execution.input_file(params.get("mask_file"))
+            execution.input_file(params.get("mask_file", None))
         ])
-    if params.get("x_matrix") is not None:
+    if params.get("x_matrix", None) is not None:
         cargs.extend([
             "--X",
-            execution.input_file(params.get("x_matrix"))
+            execution.input_file(params.get("x_matrix", None))
         ])
-    if params.get("detrend_order") is not None:
+    if params.get("detrend_order", None) is not None:
         cargs.extend([
             "--detrend",
-            str(params.get("detrend_order"))
+            str(params.get("detrend_order", None))
         ])
-    if params.get("smooth_only_flag"):
+    if params.get("smooth_only_flag", False):
         cargs.append("--smooth-only")
-    if params.get("no_detrend_flag"):
+    if params.get("no_detrend_flag", False):
         cargs.append("--no-detrend")
-    if params.get("sqr_flag"):
+    if params.get("sqr_flag", False):
         cargs.append("--sqr")
-    if params.get("sum_file") is not None:
+    if params.get("sum_file", None) is not None:
         cargs.extend([
             "--sum",
-            params.get("sum_file")
+            params.get("sum_file", None)
         ])
-    if params.get("dat_file") is not None:
+    if params.get("dat_file", None) is not None:
         cargs.extend([
             "--dat",
-            params.get("dat_file")
+            params.get("dat_file", None)
         ])
-    if params.get("ar1dat_file") is not None:
+    if params.get("ar1dat_file", None) is not None:
         cargs.extend([
             "--ar1dat",
-            params.get("ar1dat_file")
+            params.get("ar1dat_file", None)
         ])
-    if params.get("ar1vol") is not None:
+    if params.get("ar1vol", None) is not None:
         cargs.extend([
             "--ar1",
-            params.get("ar1vol")
+            params.get("ar1vol", None)
         ])
-    if params.get("fwhmmap") is not None:
+    if params.get("fwhmmap", None) is not None:
         cargs.extend([
             "--fwhm-map",
-            params.get("fwhmmap")
+            params.get("fwhmmap", None)
         ])
-    if params.get("prune_flag"):
+    if params.get("prune_flag", False):
         cargs.append("--prune")
-    if params.get("no_prune_flag"):
+    if params.get("no_prune_flag", False):
         cargs.append("--no-prune")
-    if params.get("out_mask") is not None:
+    if params.get("out_mask", None) is not None:
         cargs.extend([
             "--out-mask",
-            params.get("out_mask")
+            params.get("out_mask", None)
         ])
-    if params.get("varnorm_flag"):
+    if params.get("varnorm_flag", False):
         cargs.append("--varnorm")
-    if params.get("fwhm") is not None:
+    if params.get("fwhm", None) is not None:
         cargs.extend([
             "--fwhm",
-            str(params.get("fwhm"))
+            str(params.get("fwhm", None))
         ])
-    if params.get("niters_only") is not None:
+    if params.get("niters_only", None) is not None:
         cargs.extend([
             "--niters-only",
-            params.get("niters_only")
+            params.get("niters_only", None)
         ])
     cargs.extend([
         "--o",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
-    if params.get("sd") is not None:
+    if params.get("sd", None) is not None:
         cargs.extend([
             "--sd",
-            params.get("sd")
+            params.get("sd", None)
         ])
-    if params.get("synth_flag"):
+    if params.get("synth_flag", False):
         cargs.append("--synth")
-    if params.get("synth_frames") is not None:
+    if params.get("synth_frames", None) is not None:
         cargs.extend([
             "--synth-frames",
-            str(params.get("synth_frames"))
+            str(params.get("synth_frames", None))
         ])
-    if params.get("threads") is not None:
+    if params.get("threads", None) is not None:
         cargs.extend([
             "--threads",
-            str(params.get("threads"))
+            str(params.get("threads", None))
         ])
-    if params.get("debug_flag"):
+    if params.get("debug_flag", False):
         cargs.append("--debug")
-    if params.get("checkopts_flag"):
+    if params.get("checkopts_flag", False):
         cargs.append("--checkopts")
-    if params.get("version_flag"):
+    if params.get("version_flag", False):
         cargs.append("--version")
     return cargs
 
@@ -372,9 +375,11 @@ def mris_fwhm_outputs(
 
 def mris_fwhm_execute(
     params: MrisFwhmParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisFwhmOutputs:
     """
+    mris_fwhm
+    
     Smooths surface data and/or estimates FWHM.
     
     Author: FreeSurfer Developers
@@ -383,10 +388,12 @@ def mris_fwhm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisFwhmOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_FWHM_METADATA)
     params = execution.params(params)
     cargs = mris_fwhm_cargs(params, execution)
     ret = mris_fwhm_outputs(params, execution)
@@ -429,6 +436,8 @@ def mris_fwhm(
     runner: Runner | None = None,
 ) -> MrisFwhmOutputs:
     """
+    mris_fwhm
+    
     Smooths surface data and/or estimates FWHM.
     
     Author: FreeSurfer Developers
@@ -474,8 +483,6 @@ def mris_fwhm(
     Returns:
         NamedTuple of outputs (described in `MrisFwhmOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_FWHM_METADATA)
     params = mris_fwhm_params(
         input_file=input_file,
         subject=subject,
@@ -509,13 +516,13 @@ def mris_fwhm(
         checkopts_flag=checkopts_flag,
         version_flag=version_flag,
     )
-    return mris_fwhm_execute(params, execution)
+    return mris_fwhm_execute(params, runner)
 
 
 __all__ = [
     "MRIS_FWHM_METADATA",
     "MrisFwhmOutputs",
-    "MrisFwhmParameters",
     "mris_fwhm",
+    "mris_fwhm_execute",
     "mris_fwhm_params",
 ]

niwrap_freesurfer/freesurfer/mris_gradient.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_GRADIENT_METADATA = Metadata(
-    id="6a9aec026f78bb086a8f7293da907aa14fad157f.boutiques",
+    id="f6760899fb661a954861cf6ca458010aedcf71b9.boutiques",
     name="mris_gradient",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRIS_GRADIENT_METADATA = Metadata(
 
 
 MrisGradientParameters = typing.TypedDict('MrisGradientParameters', {
-    "__STYXTYPE__": typing.Literal["mris_gradient"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_gradient"]],
+    "input_surface": InputPathType,
+    "input_vector_field": InputPathType,
+    "output_gradient_file": str,
+})
+MrisGradientParametersTagged = typing.TypedDict('MrisGradientParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_gradient"],
     "input_surface": InputPathType,
     "input_vector_field": InputPathType,
     "output_gradient_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 {
-        "mris_gradient": mris_gradient_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_gradient": mris_gradient_outputs,
-    }.get(t)
 
 
 class MrisGradientOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_gradient(...)`.
+    Output object returned when calling `MrisGradientParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def mris_gradient_params(
     input_surface: InputPathType,
     input_vector_field: InputPathType,
     output_gradient_file: str,
-) -> MrisGradientParameters:
+) -> MrisGradientParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +54,7 @@ def mris_gradient_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_gradient",
+        "@type": "freesurfer/mris_gradient",
         "input_surface": input_surface,
         "input_vector_field": input_vector_field,
         "output_gradient_file": output_gradient_file,
@@ -103,9 +77,9 @@ def mris_gradient_cargs(
     """
     cargs = []
     cargs.append("mris_gradient")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(execution.input_file(params.get("input_vector_field")))
-    cargs.append(params.get("output_gradient_file"))
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(execution.input_file(params.get("input_vector_field", None)))
+    cargs.append(params.get("output_gradient_file", None))
     return cargs
 
 
@@ -124,16 +98,18 @@ def mris_gradient_outputs(
     """
     ret = MrisGradientOutputs(
         root=execution.output_file("."),
-        output_gradient=execution.output_file(params.get("output_gradient_file")),
+        output_gradient=execution.output_file(params.get("output_gradient_file", None)),
     )
     return ret
 
 
 def mris_gradient_execute(
     params: MrisGradientParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisGradientOutputs:
     """
+    mris_gradient
+    
     This program computes the gradient of an intensity profile of the cortical
     ribbon and writes the resulting measurement into a .mgz file.
     
@@ -143,10 +119,12 @@ def mris_gradient_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisGradientOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_GRADIENT_METADATA)
     params = execution.params(params)
     cargs = mris_gradient_cargs(params, execution)
     ret = mris_gradient_outputs(params, execution)
@@ -161,6 +139,8 @@ def mris_gradient(
     runner: Runner | None = None,
 ) -> MrisGradientOutputs:
     """
+    mris_gradient
+    
     This program computes the gradient of an intensity profile of the cortical
     ribbon and writes the resulting measurement into a .mgz file.
     
@@ -177,20 +157,18 @@ def mris_gradient(
     Returns:
         NamedTuple of outputs (described in `MrisGradientOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_GRADIENT_METADATA)
     params = mris_gradient_params(
         input_surface=input_surface,
         input_vector_field=input_vector_field,
         output_gradient_file=output_gradient_file,
     )
-    return mris_gradient_execute(params, execution)
+    return mris_gradient_execute(params, runner)
 
 
 __all__ = [
     "MRIS_GRADIENT_METADATA",
     "MrisGradientOutputs",
-    "MrisGradientParameters",
     "mris_gradient",
+    "mris_gradient_execute",
     "mris_gradient_params",
 ]

niwrap_freesurfer/freesurfer/mris_hausdorff_dist.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_HAUSDORFF_DIST_METADATA = Metadata(
-    id="2307a7fed7f332800240bbbcff45ea710d29bdf9.boutiques",
+    id="64eba6961187895801a4abe68f10630f78635fe9.boutiques",
     name="mris_hausdorff_dist",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRIS_HAUSDORFF_DIST_METADATA = Metadata(
 
 
 MrisHausdorffDistParameters = typing.TypedDict('MrisHausdorffDistParameters', {
-    "__STYXTYPE__": typing.Literal["mris_hausdorff_dist"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_hausdorff_dist"]],
+    "surface": InputPathType,
+    "label1": InputPathType,
+    "label2": InputPathType,
+    "annot_name": typing.NotRequired[str | None],
+})
+MrisHausdorffDistParametersTagged = typing.TypedDict('MrisHausdorffDistParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_hausdorff_dist"],
     "surface": InputPathType,
     "label1": InputPathType,
     "label2": InputPathType,
     "annot_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 {
-        "mris_hausdorff_dist": mris_hausdorff_dist_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_hausdorff_dist": mris_hausdorff_dist_outputs,
-    }.get(t)
 
 
 class MrisHausdorffDistOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_hausdorff_dist(...)`.
+    Output object returned when calling `MrisHausdorffDistParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mris_hausdorff_dist_params(
     label1: InputPathType,
     label2: InputPathType,
     annot_name: str | None = None,
-) -> MrisHausdorffDistParameters:
+) -> MrisHausdorffDistParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +58,7 @@ def mris_hausdorff_dist_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_hausdorff_dist",
+        "@type": "freesurfer/mris_hausdorff_dist",
         "surface": surface,
         "label1": label1,
         "label2": label2,
@@ -108,13 +83,13 @@ def mris_hausdorff_dist_cargs(
     """
     cargs = []
     cargs.append("mris_hausdorff_dist")
-    cargs.append(execution.input_file(params.get("surface")))
-    cargs.append(execution.input_file(params.get("label1")))
-    cargs.append(execution.input_file(params.get("label2")))
-    if params.get("annot_name") is not None:
+    cargs.append(execution.input_file(params.get("surface", None)))
+    cargs.append(execution.input_file(params.get("label1", None)))
+    cargs.append(execution.input_file(params.get("label2", None)))
+    if params.get("annot_name", None) is not None:
         cargs.extend([
             "-a",
-            params.get("annot_name")
+            params.get("annot_name", None)
         ])
     return cargs
 
@@ -141,10 +116,13 @@ def mris_hausdorff_dist_outputs(
 
 def mris_hausdorff_dist_execute(
     params: MrisHausdorffDistParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisHausdorffDistOutputs:
     """
-    This program computes the Hausdorff distance between two labels on a surface.
+    mris_hausdorff_dist
+    
+    This program computes the Hausdorff distance between two labels on a
+    surface.
     
     Author: FreeSurfer Developers
     
@@ -152,10 +130,12 @@ def mris_hausdorff_dist_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisHausdorffDistOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_HAUSDORFF_DIST_METADATA)
     params = execution.params(params)
     cargs = mris_hausdorff_dist_cargs(params, execution)
     ret = mris_hausdorff_dist_outputs(params, execution)
@@ -171,7 +151,10 @@ def mris_hausdorff_dist(
     runner: Runner | None = None,
 ) -> MrisHausdorffDistOutputs:
     """
-    This program computes the Hausdorff distance between two labels on a surface.
+    mris_hausdorff_dist
+    
+    This program computes the Hausdorff distance between two labels on a
+    surface.
     
     Author: FreeSurfer Developers
     
@@ -187,21 +170,19 @@ def mris_hausdorff_dist(
     Returns:
         NamedTuple of outputs (described in `MrisHausdorffDistOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_HAUSDORFF_DIST_METADATA)
     params = mris_hausdorff_dist_params(
         surface=surface,
         label1=label1,
         label2=label2,
         annot_name=annot_name,
     )
-    return mris_hausdorff_dist_execute(params, execution)
+    return mris_hausdorff_dist_execute(params, runner)
 
 
 __all__ = [
     "MRIS_HAUSDORFF_DIST_METADATA",
     "MrisHausdorffDistOutputs",
-    "MrisHausdorffDistParameters",
     "mris_hausdorff_dist",
+    "mris_hausdorff_dist_execute",
     "mris_hausdorff_dist_params",
 ]