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

niwrap_freesurfer/freesurfer/mri_fill.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_FILL_METADATA = Metadata(
-    id="2a100d8e479ae058f7c3c1d4ee987f6a69d4ae3f.boutiques",
+    id="232e544bc8412279feacfc13d95f26c79eac673a.boutiques",
     name="mri_fill",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,27 @@ MRI_FILL_METADATA = Metadata(
 
 
 MriFillParameters = typing.TypedDict('MriFillParameters', {
-    "__STYXTYPE__": typing.Literal["mri_fill"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_fill"]],
+    "input_mr_dir": str,
+    "output_mr_dir": str,
+    "threshold": typing.NotRequired[float | None],
+    "xform_name": typing.NotRequired[str | None],
+    "segmentation_file": typing.NotRequired[InputPathType | None],
+    "atlas_file": typing.NotRequired[InputPathType | None],
+    "fill_ven": bool,
+    "seed_cc_tal": typing.NotRequired[list[float] | None],
+    "seed_pons_tal": typing.NotRequired[list[float] | None],
+    "seed_lh_tal": typing.NotRequired[list[float] | None],
+    "seed_rh_tal": typing.NotRequired[list[float] | None],
+    "seed_cc_vox": typing.NotRequired[list[float] | None],
+    "seed_pons_vox": typing.NotRequired[list[float] | None],
+    "auto_man_files": typing.NotRequired[list[str] | None],
+    "no_auto_man": bool,
+    "pointset_args": typing.NotRequired[list[str] | None],
+    "ctab_file": typing.NotRequired[InputPathType | None],
+})
+MriFillParametersTagged = typing.TypedDict('MriFillParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_fill"],
     "input_mr_dir": str,
     "output_mr_dir": str,
     "threshold": typing.NotRequired[float | None],
@@ -33,43 +53,11 @@ MriFillParameters = typing.TypedDict('MriFillParameters', {
     "pointset_args": typing.NotRequired[list[str] | None],
     "ctab_file": 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_fill": mri_fill_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_fill": mri_fill_outputs,
-    }.get(t)
 
 
 class MriFillOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_fill(...)`.
+    Output object returned when calling `MriFillParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -96,7 +84,7 @@ def mri_fill_params(
     no_auto_man: bool = False,
     pointset_args: list[str] | None = None,
     ctab_file: InputPathType | None = None,
-) -> MriFillParameters:
+) -> MriFillParametersTagged:
     """
     Build parameters.
     
@@ -131,7 +119,7 @@ def mri_fill_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_fill",
+        "@type": "freesurfer/mri_fill",
         "input_mr_dir": input_mr_dir,
         "output_mr_dir": output_mr_dir,
         "fill_ven": fill_ven,
@@ -181,76 +169,76 @@ def mri_fill_cargs(
     """
     cargs = []
     cargs.append("mri_fill")
-    cargs.append(params.get("input_mr_dir"))
-    cargs.append(params.get("output_mr_dir"))
-    if params.get("threshold") is not None:
+    cargs.append(params.get("input_mr_dir", None))
+    cargs.append(params.get("output_mr_dir", None))
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "-T",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    if params.get("xform_name") is not None:
+    if params.get("xform_name", None) is not None:
         cargs.extend([
             "-xform",
-            params.get("xform_name")
+            params.get("xform_name", None)
         ])
-    if params.get("segmentation_file") is not None:
+    if params.get("segmentation_file", None) is not None:
         cargs.extend([
             "-segmentation",
-            execution.input_file(params.get("segmentation_file"))
+            execution.input_file(params.get("segmentation_file", None))
         ])
-    if params.get("atlas_file") is not None:
+    if params.get("atlas_file", None) is not None:
         cargs.extend([
             "-atlas",
-            execution.input_file(params.get("atlas_file"))
+            execution.input_file(params.get("atlas_file", None))
         ])
-    if params.get("fill_ven"):
+    if params.get("fill_ven", False):
         cargs.append("-fillven")
-    if params.get("seed_cc_tal") is not None:
+    if params.get("seed_cc_tal", None) is not None:
         cargs.extend([
             "-C",
-            *map(str, params.get("seed_cc_tal"))
+            *map(str, params.get("seed_cc_tal", None))
         ])
-    if params.get("seed_pons_tal") is not None:
+    if params.get("seed_pons_tal", None) is not None:
         cargs.extend([
             "-P",
-            *map(str, params.get("seed_pons_tal"))
+            *map(str, params.get("seed_pons_tal", None))
         ])
-    if params.get("seed_lh_tal") is not None:
+    if params.get("seed_lh_tal", None) is not None:
         cargs.extend([
             "-lh",
-            *map(str, params.get("seed_lh_tal"))
+            *map(str, params.get("seed_lh_tal", None))
         ])
-    if params.get("seed_rh_tal") is not None:
+    if params.get("seed_rh_tal", None) is not None:
         cargs.extend([
             "-rh",
-            *map(str, params.get("seed_rh_tal"))
+            *map(str, params.get("seed_rh_tal", None))
         ])
-    if params.get("seed_cc_vox") is not None:
+    if params.get("seed_cc_vox", None) is not None:
         cargs.extend([
             "-CV",
-            *map(str, params.get("seed_cc_vox"))
+            *map(str, params.get("seed_cc_vox", None))
         ])
-    if params.get("seed_pons_vox") is not None:
+    if params.get("seed_pons_vox", None) is not None:
         cargs.extend([
             "-PV",
-            *map(str, params.get("seed_pons_vox"))
+            *map(str, params.get("seed_pons_vox", None))
         ])
-    if params.get("auto_man_files") is not None:
+    if params.get("auto_man_files", None) is not None:
         cargs.extend([
             "-auto-man",
-            *params.get("auto_man_files")
+            *params.get("auto_man_files", None)
         ])
-    if params.get("no_auto_man"):
+    if params.get("no_auto_man", False):
         cargs.append("-no-auto-man")
-    if params.get("pointset_args") is not None:
+    if params.get("pointset_args", None) is not None:
         cargs.extend([
             "-pointset",
-            *params.get("pointset_args")
+            *params.get("pointset_args", None)
         ])
-    if params.get("ctab_file") is not None:
+    if params.get("ctab_file", None) is not None:
         cargs.extend([
             "-ctab",
-            execution.input_file(params.get("ctab_file"))
+            execution.input_file(params.get("ctab_file", None))
         ])
     return cargs
 
@@ -270,16 +258,18 @@ def mri_fill_outputs(
     """
     ret = MriFillOutputs(
         root=execution.output_file("."),
-        filled_volume=execution.output_file(params.get("output_mr_dir") + "/filled"),
+        filled_volume=execution.output_file(params.get("output_mr_dir", None) + "/filled"),
     )
     return ret
 
 
 def mri_fill_execute(
     params: MriFillParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriFillOutputs:
     """
+    mri_fill
+    
     Tool for creating hemispheric cutting planes and filling white matter for
     surface tessellation.
     
@@ -289,10 +279,12 @@ def mri_fill_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriFillOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_FILL_METADATA)
     params = execution.params(params)
     cargs = mri_fill_cargs(params, execution)
     ret = mri_fill_outputs(params, execution)
@@ -321,6 +313,8 @@ def mri_fill(
     runner: Runner | None = None,
 ) -> MriFillOutputs:
     """
+    mri_fill
+    
     Tool for creating hemispheric cutting planes and filling white matter for
     surface tessellation.
     
@@ -359,8 +353,6 @@ def mri_fill(
     Returns:
         NamedTuple of outputs (described in `MriFillOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_FILL_METADATA)
     params = mri_fill_params(
         input_mr_dir=input_mr_dir,
         output_mr_dir=output_mr_dir,
@@ -380,13 +372,13 @@ def mri_fill(
         pointset_args=pointset_args,
         ctab_file=ctab_file,
     )
-    return mri_fill_execute(params, execution)
+    return mri_fill_execute(params, runner)
 
 
 __all__ = [
     "MRI_FILL_METADATA",
     "MriFillOutputs",
-    "MriFillParameters",
     "mri_fill",
+    "mri_fill_execute",
     "mri_fill_params",
 ]

niwrap_freesurfer/freesurfer/mri_fit_bias.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_FIT_BIAS_METADATA = Metadata(
-    id="1eacfe3c45c52ee2621a3e01000cfc1b2f3a0ed6.boutiques",
+    id="e95edea1c7cb7312ebeb7fcbe1c320472f69a481.boutiques",
     name="mri_fit_bias",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,22 @@ MRI_FIT_BIAS_METADATA = Metadata(
 
 
 MriFitBiasParameters = typing.TypedDict('MriFitBiasParameters', {
-    "__STYXTYPE__": typing.Literal["mri_fit_bias"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_fit_bias"]],
+    "inputvol": InputPathType,
+    "lpf_cutoff": typing.NotRequired[float | None],
+    "segvol": InputPathType,
+    "maskvol": InputPathType,
+    "outvol": str,
+    "biasfield": str,
+    "dctvol": typing.NotRequired[str | None],
+    "threshold": typing.NotRequired[float | None],
+    "nerode": typing.NotRequired[float | None],
+    "nthreads": typing.NotRequired[float | None],
+    "debug": bool,
+    "checkopts": bool,
+})
+MriFitBiasParametersTagged = typing.TypedDict('MriFitBiasParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_fit_bias"],
     "inputvol": InputPathType,
     "lpf_cutoff": typing.NotRequired[float | None],
     "segvol": InputPathType,
@@ -28,43 +43,11 @@ MriFitBiasParameters = typing.TypedDict('MriFitBiasParameters', {
     "debug": bool,
     "checkopts": 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_fit_bias": mri_fit_bias_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_fit_bias": mri_fit_bias_outputs,
-    }.get(t)
 
 
 class MriFitBiasOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_fit_bias(...)`.
+    Output object returned when calling `MriFitBiasParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -80,14 +63,14 @@ def mri_fit_bias_params(
     maskvol: InputPathType,
     outvol: str,
     biasfield: str,
-    lpf_cutoff: float | None = 23.0,
+    lpf_cutoff: float | None = None,
     dctvol: str | None = None,
     threshold: float | None = None,
-    nerode: float | None = 1,
+    nerode: float | None = None,
     nthreads: float | None = None,
     debug: bool = False,
     checkopts: bool = False,
-) -> MriFitBiasParameters:
+) -> MriFitBiasParametersTagged:
     """
     Build parameters.
     
@@ -110,7 +93,7 @@ def mri_fit_bias_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_fit_bias",
+        "@type": "freesurfer/mri_fit_bias",
         "inputvol": inputvol,
         "segvol": segvol,
         "maskvol": maskvol,
@@ -149,52 +132,52 @@ def mri_fit_bias_cargs(
     cargs.append("mri_fit_bias")
     cargs.extend([
         "--i",
-        execution.input_file(params.get("inputvol"))
+        execution.input_file(params.get("inputvol", None))
     ])
-    if params.get("lpf_cutoff") is not None:
+    if params.get("lpf_cutoff", None) is not None:
         cargs.extend([
             "--cutoff",
-            str(params.get("lpf_cutoff"))
+            str(params.get("lpf_cutoff", None))
         ])
     cargs.extend([
         "--seg",
-        execution.input_file(params.get("segvol"))
+        execution.input_file(params.get("segvol", None))
     ])
     cargs.extend([
         "--mask",
-        execution.input_file(params.get("maskvol"))
+        execution.input_file(params.get("maskvol", None))
     ])
     cargs.extend([
         "--o",
-        params.get("outvol")
+        params.get("outvol", None)
     ])
     cargs.extend([
         "--bias",
-        params.get("biasfield")
+        params.get("biasfield", None)
     ])
-    if params.get("dctvol") is not None:
+    if params.get("dctvol", None) is not None:
         cargs.extend([
             "--dct",
-            params.get("dctvol")
+            params.get("dctvol", None)
         ])
-    if params.get("threshold") is not None:
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "--thresh",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    if params.get("nerode") is not None:
+    if params.get("nerode", None) is not None:
         cargs.extend([
             "--erode",
-            str(params.get("nerode"))
+            str(params.get("nerode", None))
         ])
-    if params.get("nthreads") is not None:
+    if params.get("nthreads", None) is not None:
         cargs.extend([
             "--threads",
-            str(params.get("nthreads"))
+            str(params.get("nthreads", None))
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("checkopts"):
+    if params.get("checkopts", False):
         cargs.append("--checkopts")
     return cargs
 
@@ -214,17 +197,19 @@ def mri_fit_bias_outputs(
     """
     ret = MriFitBiasOutputs(
         root=execution.output_file("."),
-        corrected_output=execution.output_file(params.get("outvol")),
-        generated_bias_field=execution.output_file(params.get("biasfield")),
+        corrected_output=execution.output_file(params.get("outvol", None)),
+        generated_bias_field=execution.output_file(params.get("biasfield", None)),
     )
     return ret
 
 
 def mri_fit_bias_execute(
     params: MriFitBiasParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriFitBiasOutputs:
     """
+    mri_fit_bias
+    
     A tool for intensity normalization and bias correction in MRI images.
     
     Author: FreeSurfer Developers
@@ -233,10 +218,12 @@ def mri_fit_bias_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriFitBiasOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_FIT_BIAS_METADATA)
     params = execution.params(params)
     cargs = mri_fit_bias_cargs(params, execution)
     ret = mri_fit_bias_outputs(params, execution)
@@ -250,16 +237,18 @@ def mri_fit_bias(
     maskvol: InputPathType,
     outvol: str,
     biasfield: str,
-    lpf_cutoff: float | None = 23.0,
+    lpf_cutoff: float | None = None,
     dctvol: str | None = None,
     threshold: float | None = None,
-    nerode: float | None = 1,
+    nerode: float | None = None,
     nthreads: float | None = None,
     debug: bool = False,
     checkopts: bool = False,
     runner: Runner | None = None,
 ) -> MriFitBiasOutputs:
     """
+    mri_fit_bias
+    
     A tool for intensity normalization and bias correction in MRI images.
     
     Author: FreeSurfer Developers
@@ -285,8 +274,6 @@ def mri_fit_bias(
     Returns:
         NamedTuple of outputs (described in `MriFitBiasOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_FIT_BIAS_METADATA)
     params = mri_fit_bias_params(
         inputvol=inputvol,
         lpf_cutoff=lpf_cutoff,
@@ -301,13 +288,13 @@ def mri_fit_bias(
         debug=debug,
         checkopts=checkopts,
     )
-    return mri_fit_bias_execute(params, execution)
+    return mri_fit_bias_execute(params, runner)
 
 
 __all__ = [
     "MRI_FIT_BIAS_METADATA",
     "MriFitBiasOutputs",
-    "MriFitBiasParameters",
     "mri_fit_bias",
+    "mri_fit_bias_execute",
     "mri_fit_bias_params",
 ]