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

niwrap_freesurfer/freesurfer/mri_fwhm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_FWHM_METADATA = Metadata(
-    id="45b5bc003ed2b047c475c3acaeebef825cbc7118.boutiques",
+    id="a87036336f44e8e9e6b59e0eae6ffd84f3110fbb.boutiques",
     name="mri_fwhm",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,45 @@ MRI_FWHM_METADATA = Metadata(
 
 
 MriFwhmParameters = typing.TypedDict('MriFwhmParameters', {
-    "__STYXTYPE__": typing.Literal["mri_fwhm"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_fwhm"]],
+    "inputvol": InputPathType,
+    "outputvol": str,
+    "save_detrended": bool,
+    "save_unmasked": bool,
+    "smooth_only": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "mask_thresh": typing.NotRequired[float | None],
+    "auto_mask": typing.NotRequired[float | None],
+    "nerode": typing.NotRequired[float | None],
+    "mask_inv": bool,
+    "out_mask": typing.NotRequired[str | None],
+    "detrend_matrix": typing.NotRequired[InputPathType | None],
+    "detrend_order": typing.NotRequired[float | None],
+    "square_input": bool,
+    "smooth_by_fwhm": typing.NotRequired[float | None],
+    "smooth_by_gstd": typing.NotRequired[float | None],
+    "median_filter": typing.NotRequired[float | None],
+    "smooth_to_fwhm": typing.NotRequired[float | None],
+    "to_fwhm_tol": typing.NotRequired[float | None],
+    "to_fwhm_nmax": typing.NotRequired[float | None],
+    "to_fwhm_file": typing.NotRequired[str | None],
+    "summary_file": typing.NotRequired[str | None],
+    "dat_file": typing.NotRequired[str | None],
+    "fwhm_dat_file": typing.NotRequired[str | None],
+    "fwhm_vol_mean_file": typing.NotRequired[str | None],
+    "fwhm_vol": typing.NotRequired[str | None],
+    "synth": bool,
+    "synth_frames": typing.NotRequired[float | None],
+    "nframes_min": typing.NotRequired[float | None],
+    "ispm": bool,
+    "nspm_zero_padding": typing.NotRequired[float | None],
+    "threads": typing.NotRequired[float | None],
+    "debug": bool,
+    "checkopts": bool,
+    "version": bool,
+})
+MriFwhmParametersTagged = typing.TypedDict('MriFwhmParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_fwhm"],
     "inputvol": InputPathType,
     "outputvol": str,
     "save_detrended": bool,
@@ -51,43 +89,11 @@ MriFwhmParameters = typing.TypedDict('MriFwhmParameters', {
     "checkopts": bool,
     "version": 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_fwhm": mri_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 {
-        "mri_fwhm": mri_fwhm_outputs,
-    }.get(t)
 
 
 class MriFwhmOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_fwhm(...)`.
+    Output object returned when calling `MriFwhmParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -143,7 +149,7 @@ def mri_fwhm_params(
     debug: bool = False,
     checkopts: bool = False,
     version: bool = False,
-) -> MriFwhmParameters:
+) -> MriFwhmParametersTagged:
     """
     Build parameters.
     
@@ -189,7 +195,7 @@ def mri_fwhm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_fwhm",
+        "@type": "freesurfer/mri_fwhm",
         "inputvol": inputvol,
         "outputvol": outputvol,
         "save_detrended": save_detrended,
@@ -269,146 +275,146 @@ def mri_fwhm_cargs(
     cargs.append("mri_fwhm")
     cargs.extend([
         "--i",
-        execution.input_file(params.get("inputvol"))
+        execution.input_file(params.get("inputvol", None))
     ])
     cargs.extend([
         "--o",
-        params.get("outputvol")
+        params.get("outputvol", None)
     ])
-    if params.get("save_detrended"):
+    if params.get("save_detrended", False):
         cargs.append("--save-detrended")
-    if params.get("save_unmasked"):
+    if params.get("save_unmasked", False):
         cargs.append("--save-unmasked")
-    if params.get("smooth_only"):
+    if params.get("smooth_only", False):
         cargs.append("--smooth-only")
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "--mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
-    if params.get("mask_thresh") is not None:
+    if params.get("mask_thresh", None) is not None:
         cargs.extend([
             "--mask-thresh",
-            str(params.get("mask_thresh"))
+            str(params.get("mask_thresh", None))
         ])
-    if params.get("auto_mask") is not None:
+    if params.get("auto_mask", None) is not None:
         cargs.extend([
             "--auto-mask",
-            str(params.get("auto_mask"))
+            str(params.get("auto_mask", None))
         ])
-    if params.get("nerode") is not None:
+    if params.get("nerode", None) is not None:
         cargs.extend([
             "--nerode",
-            str(params.get("nerode"))
+            str(params.get("nerode", None))
         ])
-    if params.get("mask_inv"):
+    if params.get("mask_inv", False):
         cargs.append("--mask-inv")
-    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("detrend_matrix") is not None:
+    if params.get("detrend_matrix", None) is not None:
         cargs.extend([
             "--X",
-            execution.input_file(params.get("detrend_matrix"))
+            execution.input_file(params.get("detrend_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("square_input"):
+    if params.get("square_input", False):
         cargs.append("--sqr")
-    if params.get("smooth_by_fwhm") is not None:
+    if params.get("smooth_by_fwhm", None) is not None:
         cargs.extend([
             "--fwhm",
-            str(params.get("smooth_by_fwhm"))
+            str(params.get("smooth_by_fwhm", None))
         ])
-    if params.get("smooth_by_gstd") is not None:
+    if params.get("smooth_by_gstd", None) is not None:
         cargs.extend([
             "--gstd",
-            str(params.get("smooth_by_gstd"))
+            str(params.get("smooth_by_gstd", None))
         ])
-    if params.get("median_filter") is not None:
+    if params.get("median_filter", None) is not None:
         cargs.extend([
             "--median",
-            str(params.get("median_filter"))
+            str(params.get("median_filter", None))
         ])
-    if params.get("smooth_to_fwhm") is not None:
+    if params.get("smooth_to_fwhm", None) is not None:
         cargs.extend([
             "--to-fwhm",
-            str(params.get("smooth_to_fwhm"))
+            str(params.get("smooth_to_fwhm", None))
         ])
-    if params.get("to_fwhm_tol") is not None:
+    if params.get("to_fwhm_tol", None) is not None:
         cargs.extend([
             "--to-fwhm-tol",
-            str(params.get("to_fwhm_tol"))
+            str(params.get("to_fwhm_tol", None))
         ])
-    if params.get("to_fwhm_nmax") is not None:
+    if params.get("to_fwhm_nmax", None) is not None:
         cargs.extend([
             "--to-fwhm-nmax",
-            str(params.get("to_fwhm_nmax"))
+            str(params.get("to_fwhm_nmax", None))
         ])
-    if params.get("to_fwhm_file") is not None:
+    if params.get("to_fwhm_file", None) is not None:
         cargs.extend([
             "--to-fwhm-file",
-            params.get("to_fwhm_file")
+            params.get("to_fwhm_file", None)
         ])
-    if params.get("summary_file") is not None:
+    if params.get("summary_file", None) is not None:
         cargs.extend([
             "--sum",
-            params.get("summary_file")
+            params.get("summary_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("fwhm_dat_file") is not None:
+    if params.get("fwhm_dat_file", None) is not None:
         cargs.extend([
             "--fwhmdat",
-            params.get("fwhm_dat_file")
+            params.get("fwhm_dat_file", None)
         ])
-    if params.get("fwhm_vol_mean_file") is not None:
+    if params.get("fwhm_vol_mean_file", None) is not None:
         cargs.extend([
             "--fwhmvolmn",
-            params.get("fwhm_vol_mean_file")
+            params.get("fwhm_vol_mean_file", None)
         ])
-    if params.get("fwhm_vol") is not None:
+    if params.get("fwhm_vol", None) is not None:
         cargs.extend([
             "--fwhmvol",
-            params.get("fwhm_vol")
+            params.get("fwhm_vol", None)
         ])
-    if params.get("synth"):
+    if params.get("synth", 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("nframes_min") is not None:
+    if params.get("nframes_min", None) is not None:
         cargs.extend([
             "--nframesmin",
-            str(params.get("nframes_min"))
+            str(params.get("nframes_min", None))
         ])
-    if params.get("ispm"):
+    if params.get("ispm", False):
         cargs.append("--ispm")
-    if params.get("nspm_zero_padding") is not None:
+    if params.get("nspm_zero_padding", None) is not None:
         cargs.extend([
             "--in_nspmzeropad",
-            str(params.get("nspm_zero_padding"))
+            str(params.get("nspm_zero_padding", None))
         ])
-    if params.get("threads") is not None:
+    if params.get("threads", None) is not None:
         cargs.extend([
             "--nthreads",
-            str(params.get("threads"))
+            str(params.get("threads", 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")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
     return cargs
 
@@ -428,24 +434,26 @@ def mri_fwhm_outputs(
     """
     ret = MriFwhmOutputs(
         root=execution.output_file("."),
-        output_volume_file=execution.output_file(params.get("outputvol")),
-        final_mask_output_file=execution.output_file(params.get("out_mask")) if (params.get("out_mask") is not None) else None,
-        summary_log_file=execution.output_file(params.get("summary_file")) if (params.get("summary_file") is not None) else None,
-        final_fwhm_estimate_file=execution.output_file(params.get("dat_file")) if (params.get("dat_file") is not None) else None,
-        fwhm_of_each_dimension_file=execution.output_file(params.get("fwhm_dat_file")) if (params.get("fwhm_dat_file") is not None) else None,
-        mean_fwhm_volume_file=execution.output_file(params.get("fwhm_vol_mean_file")) if (params.get("fwhm_vol_mean_file") is not None) else None,
-        fwhm_volume_file=execution.output_file(params.get("fwhm_vol")) if (params.get("fwhm_vol") is not None) else None,
+        output_volume_file=execution.output_file(params.get("outputvol", None)),
+        final_mask_output_file=execution.output_file(params.get("out_mask", None)) if (params.get("out_mask") is not None) else None,
+        summary_log_file=execution.output_file(params.get("summary_file", None)) if (params.get("summary_file") is not None) else None,
+        final_fwhm_estimate_file=execution.output_file(params.get("dat_file", None)) if (params.get("dat_file") is not None) else None,
+        fwhm_of_each_dimension_file=execution.output_file(params.get("fwhm_dat_file", None)) if (params.get("fwhm_dat_file") is not None) else None,
+        mean_fwhm_volume_file=execution.output_file(params.get("fwhm_vol_mean_file", None)) if (params.get("fwhm_vol_mean_file") is not None) else None,
+        fwhm_volume_file=execution.output_file(params.get("fwhm_vol", None)) if (params.get("fwhm_vol") is not None) else None,
     )
     return ret
 
 
 def mri_fwhm_execute(
     params: MriFwhmParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriFwhmOutputs:
     """
-    FreeSurfer program to estimate the global Gaussian smoothness of a multi-frame,
-    volume-based data set.
+    mri_fwhm
+    
+    FreeSurfer program to estimate the global Gaussian smoothness of a
+    multi-frame, volume-based data set.
     
     Author: FreeSurfer Developers
     
@@ -453,10 +461,12 @@ def mri_fwhm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriFwhmOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_FWHM_METADATA)
     params = execution.params(params)
     cargs = mri_fwhm_cargs(params, execution)
     ret = mri_fwhm_outputs(params, execution)
@@ -503,8 +513,10 @@ def mri_fwhm(
     runner: Runner | None = None,
 ) -> MriFwhmOutputs:
     """
-    FreeSurfer program to estimate the global Gaussian smoothness of a multi-frame,
-    volume-based data set.
+    mri_fwhm
+    
+    FreeSurfer program to estimate the global Gaussian smoothness of a
+    multi-frame, volume-based data set.
     
     Author: FreeSurfer Developers
     
@@ -552,8 +564,6 @@ def mri_fwhm(
     Returns:
         NamedTuple of outputs (described in `MriFwhmOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_FWHM_METADATA)
     params = mri_fwhm_params(
         inputvol=inputvol,
         outputvol=outputvol,
@@ -591,13 +601,13 @@ def mri_fwhm(
         checkopts=checkopts,
         version=version,
     )
-    return mri_fwhm_execute(params, execution)
+    return mri_fwhm_execute(params, runner)
 
 
 __all__ = [
     "MRI_FWHM_METADATA",
     "MriFwhmOutputs",
-    "MriFwhmParameters",
     "mri_fwhm",
+    "mri_fwhm_execute",
     "mri_fwhm_params",
 ]

niwrap_freesurfer/freesurfer/mri_gca_ambiguous.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_GCA_AMBIGUOUS_METADATA = Metadata(
-    id="63a7b920414008d2c45c3b5d6f41aa0558942e6d.boutiques",
+    id="c1f7a9f8341d18317f7c5d914e50447802fcb29f.boutiques",
     name="mri_gca_ambiguous",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ MRI_GCA_AMBIGUOUS_METADATA = Metadata(
 
 
 MriGcaAmbiguousParameters = typing.TypedDict('MriGcaAmbiguousParameters', {
-    "__STYXTYPE__": typing.Literal["mri_gca_ambiguous"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_gca_ambiguous"]],
+    "gca_file": InputPathType,
+    "output_volume": str,
+})
+MriGcaAmbiguousParametersTagged = typing.TypedDict('MriGcaAmbiguousParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_gca_ambiguous"],
     "gca_file": InputPathType,
     "output_volume": 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_gca_ambiguous": mri_gca_ambiguous_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_gca_ambiguous": mri_gca_ambiguous_outputs,
-    }.get(t)
 
 
 class MriGcaAmbiguousOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_gca_ambiguous(...)`.
+    Output object returned when calling `MriGcaAmbiguousParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class MriGcaAmbiguousOutputs(typing.NamedTuple):
 def mri_gca_ambiguous_params(
     gca_file: InputPathType,
     output_volume: str,
-) -> MriGcaAmbiguousParameters:
+) -> MriGcaAmbiguousParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def mri_gca_ambiguous_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_gca_ambiguous",
+        "@type": "freesurfer/mri_gca_ambiguous",
         "gca_file": gca_file,
         "output_volume": output_volume,
     }
@@ -98,8 +71,8 @@ def mri_gca_ambiguous_cargs(
     """
     cargs = []
     cargs.append("mri_gca_ambiguous")
-    cargs.append(execution.input_file(params.get("gca_file")))
-    cargs.append(params.get("output_volume"))
+    cargs.append(execution.input_file(params.get("gca_file", None)))
+    cargs.append(params.get("output_volume", None))
     return cargs
 
 
@@ -118,18 +91,20 @@ def mri_gca_ambiguous_outputs(
     """
     ret = MriGcaAmbiguousOutputs(
         root=execution.output_file("."),
-        output_image=execution.output_file(params.get("output_volume")),
+        output_image=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def mri_gca_ambiguous_execute(
     params: MriGcaAmbiguousParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriGcaAmbiguousOutputs:
     """
-    This program computes an ambiguity measure across a GCA and outputs an MR image
-    of it.
+    mri_gca_ambiguous
+    
+    This program computes an ambiguity measure across a GCA and outputs an MR
+    image of it.
     
     Author: FreeSurfer Developers
     
@@ -137,10 +112,12 @@ def mri_gca_ambiguous_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriGcaAmbiguousOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_GCA_AMBIGUOUS_METADATA)
     params = execution.params(params)
     cargs = mri_gca_ambiguous_cargs(params, execution)
     ret = mri_gca_ambiguous_outputs(params, execution)
@@ -154,8 +131,10 @@ def mri_gca_ambiguous(
     runner: Runner | None = None,
 ) -> MriGcaAmbiguousOutputs:
     """
-    This program computes an ambiguity measure across a GCA and outputs an MR image
-    of it.
+    mri_gca_ambiguous
+    
+    This program computes an ambiguity measure across a GCA and outputs an MR
+    image of it.
     
     Author: FreeSurfer Developers
     
@@ -168,19 +147,17 @@ def mri_gca_ambiguous(
     Returns:
         NamedTuple of outputs (described in `MriGcaAmbiguousOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_GCA_AMBIGUOUS_METADATA)
     params = mri_gca_ambiguous_params(
         gca_file=gca_file,
         output_volume=output_volume,
     )
-    return mri_gca_ambiguous_execute(params, execution)
+    return mri_gca_ambiguous_execute(params, runner)
 
 
 __all__ = [
     "MRI_GCA_AMBIGUOUS_METADATA",
     "MriGcaAmbiguousOutputs",
-    "MriGcaAmbiguousParameters",
     "mri_gca_ambiguous",
+    "mri_gca_ambiguous_execute",
     "mri_gca_ambiguous_params",
 ]