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

niwrap_freesurfer/freesurfer/mris_entropy.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_ENTROPY_METADATA = Metadata(
-    id="d0ec05255b1b8c8b390b137853362c1447b2a789.boutiques",
+    id="fc6eb2f6c959a184199ac74e25c7e74b0f12a7f6.boutiques",
     name="mris_entropy",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRIS_ENTROPY_METADATA = Metadata(
 
 
 MrisEntropyParameters = typing.TypedDict('MrisEntropyParameters', {
-    "__STYXTYPE__": typing.Literal["mris_entropy"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_entropy"]],
+    "subject": str,
+    "hemi": str,
+    "wfile": InputPathType,
+    "curvfile": InputPathType,
+    "average_iterations": typing.NotRequired[float | None],
+    "normalize": bool,
+})
+MrisEntropyParametersTagged = typing.TypedDict('MrisEntropyParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_entropy"],
     "subject": str,
     "hemi": str,
     "wfile": InputPathType,
@@ -22,43 +31,11 @@ MrisEntropyParameters = typing.TypedDict('MrisEntropyParameters', {
     "average_iterations": typing.NotRequired[float | None],
     "normalize": 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_entropy": mris_entropy_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_entropy": mris_entropy_outputs,
-    }.get(t)
 
 
 class MrisEntropyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_entropy(...)`.
+    Output object returned when calling `MrisEntropyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,9 +48,9 @@ def mris_entropy_params(
     hemi: str,
     wfile: InputPathType,
     curvfile: InputPathType,
-    average_iterations: float | None = 0,
+    average_iterations: float | None = None,
     normalize: bool = False,
-) -> MrisEntropyParameters:
+) -> MrisEntropyParametersTagged:
     """
     Build parameters.
     
@@ -89,7 +66,7 @@ def mris_entropy_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_entropy",
+        "@type": "freesurfer/mris_entropy",
         "subject": subject,
         "hemi": hemi,
         "wfile": wfile,
@@ -116,16 +93,16 @@ def mris_entropy_cargs(
     """
     cargs = []
     cargs.append("mris_entropy")
-    cargs.append(params.get("subject"))
-    cargs.append(params.get("hemi"))
-    cargs.append(execution.input_file(params.get("wfile")))
-    cargs.append(execution.input_file(params.get("curvfile")))
-    if params.get("average_iterations") is not None:
+    cargs.append(params.get("subject", None))
+    cargs.append(params.get("hemi", None))
+    cargs.append(execution.input_file(params.get("wfile", None)))
+    cargs.append(execution.input_file(params.get("curvfile", None)))
+    if params.get("average_iterations", None) is not None:
         cargs.extend([
             "-a",
-            str(params.get("average_iterations"))
+            str(params.get("average_iterations", None))
         ])
-    if params.get("normalize"):
+    if params.get("normalize", False):
         cargs.append("-n")
     return cargs
 
@@ -145,16 +122,18 @@ def mris_entropy_outputs(
     """
     ret = MrisEntropyOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("subject") + "_" + params.get("hemi") + "_output.txt"),
+        output_file=execution.output_file(params.get("subject", None) + "_" + params.get("hemi", None) + "_output.txt"),
     )
     return ret
 
 
 def mris_entropy_execute(
     params: MrisEntropyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisEntropyOutputs:
     """
+    mris_entropy
+    
     Computes the entropy of a surface activation pattern for FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -163,10 +142,12 @@ def mris_entropy_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisEntropyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_ENTROPY_METADATA)
     params = execution.params(params)
     cargs = mris_entropy_cargs(params, execution)
     ret = mris_entropy_outputs(params, execution)
@@ -179,11 +160,13 @@ def mris_entropy(
     hemi: str,
     wfile: InputPathType,
     curvfile: InputPathType,
-    average_iterations: float | None = 0,
+    average_iterations: float | None = None,
     normalize: bool = False,
     runner: Runner | None = None,
 ) -> MrisEntropyOutputs:
     """
+    mris_entropy
+    
     Computes the entropy of a surface activation pattern for FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -202,8 +185,6 @@ def mris_entropy(
     Returns:
         NamedTuple of outputs (described in `MrisEntropyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_ENTROPY_METADATA)
     params = mris_entropy_params(
         subject=subject,
         hemi=hemi,
@@ -212,13 +193,13 @@ def mris_entropy(
         average_iterations=average_iterations,
         normalize=normalize,
     )
-    return mris_entropy_execute(params, execution)
+    return mris_entropy_execute(params, runner)
 
 
 __all__ = [
     "MRIS_ENTROPY_METADATA",
     "MrisEntropyOutputs",
-    "MrisEntropyParameters",
     "mris_entropy",
+    "mris_entropy_execute",
     "mris_entropy_params",
 ]

niwrap_freesurfer/freesurfer/mris_errors.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_ERRORS_METADATA = Metadata(
-    id="84c4666dcea46df17569c6e5d435ebf2cb451d60.boutiques",
+    id="9d478a5004349307c376e9fd6df896b2d77765f1.boutiques",
     name="mris_errors",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ MRIS_ERRORS_METADATA = Metadata(
 
 
 MrisErrorsParameters = typing.TypedDict('MrisErrorsParameters', {
-    "__STYXTYPE__": typing.Literal["mris_errors"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_errors"]],
+    "input_image_file": InputPathType,
+})
+MrisErrorsParametersTagged = typing.TypedDict('MrisErrorsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_errors"],
     "input_image_file": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_errors": mris_errors_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 MrisErrorsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_errors(...)`.
+    Output object returned when calling `MrisErrorsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class MrisErrorsOutputs(typing.NamedTuple):
 
 def mris_errors_params(
     input_image_file: InputPathType,
-) -> MrisErrorsParameters:
+) -> MrisErrorsParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def mris_errors_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_errors",
+        "@type": "freesurfer/mris_errors",
         "input_image_file": input_image_file,
     }
     return params
@@ -91,7 +64,7 @@ def mris_errors_cargs(
     """
     cargs = []
     cargs.append("mris_errors")
-    cargs.append(execution.input_file(params.get("input_image_file")))
+    cargs.append(execution.input_file(params.get("input_image_file", None)))
     return cargs
 
 
@@ -116,9 +89,11 @@ def mris_errors_outputs(
 
 def mris_errors_execute(
     params: MrisErrorsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisErrorsOutputs:
     """
+    mris_errors
+    
     This program will unfold an MRI on the surface of an ellipsoid.
     
     Author: FreeSurfer Developers
@@ -127,10 +102,12 @@ def mris_errors_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisErrorsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_ERRORS_METADATA)
     params = execution.params(params)
     cargs = mris_errors_cargs(params, execution)
     ret = mris_errors_outputs(params, execution)
@@ -143,6 +120,8 @@ def mris_errors(
     runner: Runner | None = None,
 ) -> MrisErrorsOutputs:
     """
+    mris_errors
+    
     This program will unfold an MRI on the surface of an ellipsoid.
     
     Author: FreeSurfer Developers
@@ -155,18 +134,16 @@ def mris_errors(
     Returns:
         NamedTuple of outputs (described in `MrisErrorsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_ERRORS_METADATA)
     params = mris_errors_params(
         input_image_file=input_image_file,
     )
-    return mris_errors_execute(params, execution)
+    return mris_errors_execute(params, runner)
 
 
 __all__ = [
     "MRIS_ERRORS_METADATA",
     "MrisErrorsOutputs",
-    "MrisErrorsParameters",
     "mris_errors",
+    "mris_errors_execute",
     "mris_errors_params",
 ]

niwrap_freesurfer/freesurfer/mris_estimate_wm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_ESTIMATE_WM_METADATA = Metadata(
-    id="11a5a3a14f4d64a3dc467b2437ed45bcb49d300b.boutiques",
+    id="a6424f146242a7603bdb2652648f72e0fc5f3a7d.boutiques",
     name="mris_estimate_wm",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,19 @@ MRIS_ESTIMATE_WM_METADATA = Metadata(
 
 
 MrisEstimateWmParameters = typing.TypedDict('MrisEstimateWmParameters', {
-    "__STYXTYPE__": typing.Literal["mris_estimate_wm"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_estimate_wm"]],
+    "subjs": list[str],
+    "hemi": str,
+    "sdir": typing.NotRequired[str | None],
+    "model": typing.NotRequired[str | None],
+    "suffix": typing.NotRequired[str | None],
+    "gpu": bool,
+    "rsi": bool,
+    "single_iter": bool,
+    "vol": typing.NotRequired[str | None],
+})
+MrisEstimateWmParametersTagged = typing.TypedDict('MrisEstimateWmParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_estimate_wm"],
     "subjs": list[str],
     "hemi": str,
     "sdir": typing.NotRequired[str | None],
@@ -25,42 +37,11 @@ MrisEstimateWmParameters = typing.TypedDict('MrisEstimateWmParameters', {
     "single_iter": bool,
     "vol": 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_estimate_wm": mris_estimate_wm_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 MrisEstimateWmOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_estimate_wm(...)`.
+    Output object returned when calling `MrisEstimateWmParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -76,7 +57,7 @@ def mris_estimate_wm_params(
     rsi: bool = False,
     single_iter: bool = False,
     vol: str | None = None,
-) -> MrisEstimateWmParameters:
+) -> MrisEstimateWmParametersTagged:
     """
     Build parameters.
     
@@ -94,7 +75,7 @@ def mris_estimate_wm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_estimate_wm",
+        "@type": "freesurfer/mris_estimate_wm",
         "subjs": subjs,
         "hemi": hemi,
         "gpu": gpu,
@@ -129,37 +110,37 @@ def mris_estimate_wm_cargs(
     cargs.append("mris_estimate_wm")
     cargs.extend([
         "-s",
-        *params.get("subjs")
+        *params.get("subjs", None)
     ])
     cargs.extend([
         "--hemi",
-        params.get("hemi")
+        params.get("hemi", None)
     ])
-    if params.get("sdir") is not None:
+    if params.get("sdir", None) is not None:
         cargs.extend([
             "-d",
-            params.get("sdir")
+            params.get("sdir", None)
         ])
-    if params.get("model") is not None:
+    if params.get("model", None) is not None:
         cargs.extend([
             "-m",
-            params.get("model")
+            params.get("model", None)
         ])
-    if params.get("suffix") is not None:
+    if params.get("suffix", None) is not None:
         cargs.extend([
             "-x",
-            params.get("suffix")
+            params.get("suffix", None)
         ])
-    if params.get("gpu"):
+    if params.get("gpu", False):
         cargs.append("-g")
-    if params.get("rsi"):
+    if params.get("rsi", False):
         cargs.append("--rsi")
-    if params.get("single_iter"):
+    if params.get("single_iter", False):
         cargs.append("--single-iter")
-    if params.get("vol") is not None:
+    if params.get("vol", None) is not None:
         cargs.extend([
             "--vol",
-            params.get("vol")
+            params.get("vol", None)
         ])
     return cargs
 
@@ -185,9 +166,11 @@ def mris_estimate_wm_outputs(
 
 def mris_estimate_wm_execute(
     params: MrisEstimateWmParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisEstimateWmOutputs:
     """
+    mris_estimate_wm
+    
     Tool to estimate white matter surfaces using MRI data.
     
     Author: FreeSurfer Developers
@@ -196,10 +179,12 @@ def mris_estimate_wm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisEstimateWmOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_ESTIMATE_WM_METADATA)
     params = execution.params(params)
     cargs = mris_estimate_wm_cargs(params, execution)
     ret = mris_estimate_wm_outputs(params, execution)
@@ -220,6 +205,8 @@ def mris_estimate_wm(
     runner: Runner | None = None,
 ) -> MrisEstimateWmOutputs:
     """
+    mris_estimate_wm
+    
     Tool to estimate white matter surfaces using MRI data.
     
     Author: FreeSurfer Developers
@@ -240,8 +227,6 @@ def mris_estimate_wm(
     Returns:
         NamedTuple of outputs (described in `MrisEstimateWmOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_ESTIMATE_WM_METADATA)
     params = mris_estimate_wm_params(
         subjs=subjs,
         hemi=hemi,
@@ -253,13 +238,13 @@ def mris_estimate_wm(
         single_iter=single_iter,
         vol=vol,
     )
-    return mris_estimate_wm_execute(params, execution)
+    return mris_estimate_wm_execute(params, runner)
 
 
 __all__ = [
     "MRIS_ESTIMATE_WM_METADATA",
     "MrisEstimateWmOutputs",
-    "MrisEstimateWmParameters",
     "mris_estimate_wm",
+    "mris_estimate_wm_execute",
     "mris_estimate_wm_params",
 ]

niwrap_freesurfer/freesurfer/mris_euler_number.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_EULER_NUMBER_METADATA = Metadata(
-    id="ff5edf807126bfa9fa22edba44beeccaa0e44710.boutiques",
+    id="72b1fab042aa7159acf7f9f958b916daac555d65.boutiques",
     name="mris_euler_number",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ MRIS_EULER_NUMBER_METADATA = Metadata(
 
 
 MrisEulerNumberParameters = typing.TypedDict('MrisEulerNumberParameters', {
-    "__STYXTYPE__": typing.Literal["mris_euler_number"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_euler_number"]],
+    "input_surface": InputPathType,
+    "output_file": typing.NotRequired[str | None],
+})
+MrisEulerNumberParametersTagged = typing.TypedDict('MrisEulerNumberParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_euler_number"],
     "input_surface": InputPathType,
     "output_file": 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_euler_number": mris_euler_number_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_euler_number": mris_euler_number_outputs,
-    }.get(t)
 
 
 class MrisEulerNumberOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_euler_number(...)`.
+    Output object returned when calling `MrisEulerNumberParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class MrisEulerNumberOutputs(typing.NamedTuple):
 def mris_euler_number_params(
     input_surface: InputPathType,
     output_file: str | None = None,
-) -> MrisEulerNumberParameters:
+) -> MrisEulerNumberParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def mris_euler_number_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_euler_number",
+        "@type": "freesurfer/mris_euler_number",
         "input_surface": input_surface,
     }
     if output_file is not None:
@@ -99,11 +72,11 @@ def mris_euler_number_cargs(
     """
     cargs = []
     cargs.append("mris_euler_number")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    if params.get("output_file") is not None:
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    if params.get("output_file", None) is not None:
         cargs.extend([
             "-o",
-            params.get("output_file")
+            params.get("output_file", None)
         ])
     return cargs
 
@@ -123,16 +96,18 @@ def mris_euler_number_outputs(
     """
     ret = MrisEulerNumberOutputs(
         root=execution.output_file("."),
-        outfile=execution.output_file(params.get("output_file")) if (params.get("output_file") is not None) else None,
+        outfile=execution.output_file(params.get("output_file", None)) if (params.get("output_file") is not None) else None,
     )
     return ret
 
 
 def mris_euler_number_execute(
     params: MrisEulerNumberParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisEulerNumberOutputs:
     """
+    mris_euler_number
+    
     This program computes EulerNumber for a cortical surface.
     
     Author: FreeSurfer Developers
@@ -141,10 +116,12 @@ def mris_euler_number_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisEulerNumberOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_EULER_NUMBER_METADATA)
     params = execution.params(params)
     cargs = mris_euler_number_cargs(params, execution)
     ret = mris_euler_number_outputs(params, execution)
@@ -158,6 +135,8 @@ def mris_euler_number(
     runner: Runner | None = None,
 ) -> MrisEulerNumberOutputs:
     """
+    mris_euler_number
+    
     This program computes EulerNumber for a cortical surface.
     
     Author: FreeSurfer Developers
@@ -171,19 +150,17 @@ def mris_euler_number(
     Returns:
         NamedTuple of outputs (described in `MrisEulerNumberOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_EULER_NUMBER_METADATA)
     params = mris_euler_number_params(
         input_surface=input_surface,
         output_file=output_file,
     )
-    return mris_euler_number_execute(params, execution)
+    return mris_euler_number_execute(params, runner)
 
 
 __all__ = [
     "MRIS_EULER_NUMBER_METADATA",
     "MrisEulerNumberOutputs",
-    "MrisEulerNumberParameters",
     "mris_euler_number",
+    "mris_euler_number_execute",
     "mris_euler_number_params",
 ]