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

niwrap_freesurfer/freesurfer/mri_synthsr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_SYNTHSR_METADATA = Metadata(
-    id="c3a59ed15b3a93af72a3a56ab7153b2f5388b6e1.boutiques",
+    id="7f3f0cfbdf98e5e3ff73c3ba6cd3464d5c2398ab.boutiques",
     name="mri_synthsr",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,20 @@ MRI_SYNTHSR_METADATA = Metadata(
 
 
 MriSynthsrParameters = typing.TypedDict('MriSynthsrParameters', {
-    "__STYXTYPE__": typing.Literal["mri_synthsr"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_synthsr"]],
+    "input": str,
+    "output": str,
+    "ct": bool,
+    "disable_sharpening": bool,
+    "disable_flipping": bool,
+    "lowfield": bool,
+    "v1": bool,
+    "threads": typing.NotRequired[float | None],
+    "cpu": bool,
+    "model": typing.NotRequired[str | None],
+})
+MriSynthsrParametersTagged = typing.TypedDict('MriSynthsrParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_synthsr"],
     "input": str,
     "output": str,
     "ct": bool,
@@ -26,42 +39,11 @@ MriSynthsrParameters = typing.TypedDict('MriSynthsrParameters', {
     "cpu": bool,
     "model": 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 {
-        "mri_synthsr": mri_synthsr_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 MriSynthsrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_synthsr(...)`.
+    Output object returned when calling `MriSynthsrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -78,7 +60,7 @@ def mri_synthsr_params(
     threads: float | None = None,
     cpu: bool = False,
     model: str | None = None,
-) -> MriSynthsrParameters:
+) -> MriSynthsrParametersTagged:
     """
     Build parameters.
     
@@ -102,7 +84,7 @@ def mri_synthsr_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_synthsr",
+        "@type": "freesurfer/mri_synthsr",
         "input": input_,
         "output": output,
         "ct": ct,
@@ -134,29 +116,29 @@ def mri_synthsr_cargs(
     """
     cargs = []
     cargs.append("mri_synthsr")
-    cargs.append(params.get("input"))
-    cargs.append(params.get("output"))
-    if params.get("ct"):
+    cargs.append(params.get("input", None))
+    cargs.append(params.get("output", None))
+    if params.get("ct", False):
         cargs.append("--ct")
-    if params.get("disable_sharpening"):
+    if params.get("disable_sharpening", False):
         cargs.append("--disable_sharpening")
-    if params.get("disable_flipping"):
+    if params.get("disable_flipping", False):
         cargs.append("--disable_flipping")
-    if params.get("lowfield"):
+    if params.get("lowfield", False):
         cargs.append("--lowfield")
-    if params.get("v1"):
+    if params.get("v1", False):
         cargs.append("--v1")
-    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("cpu"):
+    if params.get("cpu", False):
         cargs.append("--cpu")
-    if params.get("model") is not None:
+    if params.get("model", None) is not None:
         cargs.extend([
             "--model",
-            params.get("model")
+            params.get("model", None)
         ])
     return cargs
 
@@ -182,11 +164,13 @@ def mri_synthsr_outputs(
 
 def mri_synthsr_execute(
     params: MriSynthsrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriSynthsrOutputs:
     """
-    Implementation of SynthSR that generates a synthetic 1mm MP-RAGE from a scan of
-    any contrast and resolution.
+    mri_synthsr
+    
+    Implementation of SynthSR that generates a synthetic 1mm MP-RAGE from a scan
+    of any contrast and resolution.
     
     Author: FreeSurfer Developers
     
@@ -194,10 +178,12 @@ def mri_synthsr_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriSynthsrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_SYNTHSR_METADATA)
     params = execution.params(params)
     cargs = mri_synthsr_cargs(params, execution)
     ret = mri_synthsr_outputs(params, execution)
@@ -219,8 +205,10 @@ def mri_synthsr(
     runner: Runner | None = None,
 ) -> MriSynthsrOutputs:
     """
-    Implementation of SynthSR that generates a synthetic 1mm MP-RAGE from a scan of
-    any contrast and resolution.
+    mri_synthsr
+    
+    Implementation of SynthSR that generates a synthetic 1mm MP-RAGE from a scan
+    of any contrast and resolution.
     
     Author: FreeSurfer Developers
     
@@ -246,8 +234,6 @@ def mri_synthsr(
     Returns:
         NamedTuple of outputs (described in `MriSynthsrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_SYNTHSR_METADATA)
     params = mri_synthsr_params(
         input_=input_,
         output=output,
@@ -260,13 +246,13 @@ def mri_synthsr(
         cpu=cpu,
         model=model,
     )
-    return mri_synthsr_execute(params, execution)
+    return mri_synthsr_execute(params, runner)
 
 
 __all__ = [
     "MRI_SYNTHSR_METADATA",
     "MriSynthsrOutputs",
-    "MriSynthsrParameters",
     "mri_synthsr",
+    "mri_synthsr_execute",
     "mri_synthsr_params",
 ]

niwrap_freesurfer/freesurfer/mri_synthsr_hyperfine.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_SYNTHSR_HYPERFINE_METADATA = Metadata(
-    id="4e58102f9b885e826be8d96a7d9856f922b77bc5.boutiques",
+    id="57ebf5df91e40f506a0d1c025ac3cea3737635c1.boutiques",
     name="mri_synthsr_hyperfine",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ MRI_SYNTHSR_HYPERFINE_METADATA = Metadata(
 
 
 MriSynthsrHyperfineParameters = typing.TypedDict('MriSynthsrHyperfineParameters', {
-    "__STYXTYPE__": typing.Literal["mri_synthsr_hyperfine"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_synthsr_hyperfine"]],
+    "t1_image": InputPathType,
+    "t2_image": InputPathType,
+    "output": str,
+    "threads": typing.NotRequired[float | None],
+    "cpu": bool,
+})
+MriSynthsrHyperfineParametersTagged = typing.TypedDict('MriSynthsrHyperfineParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_synthsr_hyperfine"],
     "t1_image": InputPathType,
     "t2_image": InputPathType,
     "output": str,
     "threads": typing.NotRequired[float | None],
     "cpu": 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_synthsr_hyperfine": mri_synthsr_hyperfine_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_synthsr_hyperfine": mri_synthsr_hyperfine_outputs,
-    }.get(t)
 
 
 class MriSynthsrHyperfineOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_synthsr_hyperfine(...)`.
+    Output object returned when calling `MriSynthsrHyperfineParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,9 +45,9 @@ def mri_synthsr_hyperfine_params(
     t1_image: InputPathType,
     t2_image: InputPathType,
     output: str,
-    threads: float | None = 1,
+    threads: float | None = None,
     cpu: bool = False,
-) -> MriSynthsrHyperfineParameters:
+) -> MriSynthsrHyperfineParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +66,7 @@ def mri_synthsr_hyperfine_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_synthsr_hyperfine",
+        "@type": "freesurfer/mri_synthsr_hyperfine",
         "t1_image": t1_image,
         "t2_image": t2_image,
         "output": output,
@@ -118,22 +94,22 @@ def mri_synthsr_hyperfine_cargs(
     cargs.append("mri_synthsr_hyperfine")
     cargs.extend([
         "--t1",
-        execution.input_file(params.get("t1_image"))
+        execution.input_file(params.get("t1_image", None))
     ])
     cargs.extend([
         "--t2",
-        execution.input_file(params.get("t2_image"))
+        execution.input_file(params.get("t2_image", None))
     ])
     cargs.extend([
         "--o",
-        params.get("output")
+        params.get("output", 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("cpu"):
+    if params.get("cpu", False):
         cargs.append("--cpu")
     return cargs
 
@@ -153,18 +129,20 @@ def mri_synthsr_hyperfine_outputs(
     """
     ret = MriSynthsrHyperfineOutputs(
         root=execution.output_file("."),
-        synthetic_mprage=execution.output_file(params.get("output")),
+        synthetic_mprage=execution.output_file(params.get("output", None)),
     )
     return ret
 
 
 def mri_synthsr_hyperfine_execute(
     params: MriSynthsrHyperfineParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriSynthsrHyperfineOutputs:
     """
-    Implementation of SynthSR that generates a synthetic 1mm MP-RAGE from a pair of
-    T1-T2 standard Hyperfine scans (1.5x1.5x5mm axial).
+    mri_synthsr_hyperfine
+    
+    Implementation of SynthSR that generates a synthetic 1mm MP-RAGE from a pair
+    of T1-T2 standard Hyperfine scans (1.5x1.5x5mm axial).
     
     Author: FreeSurfer Developers
     
@@ -172,10 +150,12 @@ def mri_synthsr_hyperfine_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriSynthsrHyperfineOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_SYNTHSR_HYPERFINE_METADATA)
     params = execution.params(params)
     cargs = mri_synthsr_hyperfine_cargs(params, execution)
     ret = mri_synthsr_hyperfine_outputs(params, execution)
@@ -187,13 +167,15 @@ def mri_synthsr_hyperfine(
     t1_image: InputPathType,
     t2_image: InputPathType,
     output: str,
-    threads: float | None = 1,
+    threads: float | None = None,
     cpu: bool = False,
     runner: Runner | None = None,
 ) -> MriSynthsrHyperfineOutputs:
     """
-    Implementation of SynthSR that generates a synthetic 1mm MP-RAGE from a pair of
-    T1-T2 standard Hyperfine scans (1.5x1.5x5mm axial).
+    mri_synthsr_hyperfine
+    
+    Implementation of SynthSR that generates a synthetic 1mm MP-RAGE from a pair
+    of T1-T2 standard Hyperfine scans (1.5x1.5x5mm axial).
     
     Author: FreeSurfer Developers
     
@@ -214,8 +196,6 @@ def mri_synthsr_hyperfine(
     Returns:
         NamedTuple of outputs (described in `MriSynthsrHyperfineOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_SYNTHSR_HYPERFINE_METADATA)
     params = mri_synthsr_hyperfine_params(
         t1_image=t1_image,
         t2_image=t2_image,
@@ -223,13 +203,13 @@ def mri_synthsr_hyperfine(
         threads=threads,
         cpu=cpu,
     )
-    return mri_synthsr_hyperfine_execute(params, execution)
+    return mri_synthsr_hyperfine_execute(params, runner)
 
 
 __all__ = [
     "MRI_SYNTHSR_HYPERFINE_METADATA",
     "MriSynthsrHyperfineOutputs",
-    "MriSynthsrHyperfineParameters",
     "mri_synthsr_hyperfine",
+    "mri_synthsr_hyperfine_execute",
     "mri_synthsr_hyperfine_params",
 ]

niwrap_freesurfer/freesurfer/mri_synthstrip.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_SYNTHSTRIP_METADATA = Metadata(
-    id="1bad1037e1505334c7abff4075ad10604d8b54f6.boutiques",
+    id="1c24c2e7370835b696180eabd118abecf2ed7c3f.boutiques",
     name="mri_synthstrip",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ MRI_SYNTHSTRIP_METADATA = Metadata(
 
 
 MriSynthstripParameters = typing.TypedDict('MriSynthstripParameters', {
-    "__STYXTYPE__": typing.Literal["mri_synthstrip"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_synthstrip"]],
+    "image": InputPathType,
+    "output_image": typing.NotRequired[str | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "gpu": bool,
+    "border": typing.NotRequired[float | None],
+    "exclude_csf": bool,
+    "model_weights": typing.NotRequired[InputPathType | None],
+})
+MriSynthstripParametersTagged = typing.TypedDict('MriSynthstripParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_synthstrip"],
     "image": InputPathType,
     "output_image": typing.NotRequired[str | None],
     "mask": typing.NotRequired[InputPathType | None],
@@ -23,43 +33,11 @@ MriSynthstripParameters = typing.TypedDict('MriSynthstripParameters', {
     "exclude_csf": bool,
     "model_weights": 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_synthstrip": mri_synthstrip_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_synthstrip": mri_synthstrip_outputs,
-    }.get(t)
 
 
 class MriSynthstripOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_synthstrip(...)`.
+    Output object returned when calling `MriSynthstripParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,10 +52,10 @@ def mri_synthstrip_params(
     output_image: str | None = None,
     mask: InputPathType | None = None,
     gpu: bool = False,
-    border: float | None = 1,
+    border: float | None = None,
     exclude_csf: bool = False,
     model_weights: InputPathType | None = None,
-) -> MriSynthstripParameters:
+) -> MriSynthstripParametersTagged:
     """
     Build parameters.
     
@@ -93,7 +71,7 @@ def mri_synthstrip_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_synthstrip",
+        "@type": "freesurfer/mri_synthstrip",
         "image": image,
         "gpu": gpu,
         "exclude_csf": exclude_csf,
@@ -126,31 +104,31 @@ def mri_synthstrip_cargs(
     cargs.append("mri_synthstrip")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("image"))
+        execution.input_file(params.get("image", None))
     ])
-    if params.get("output_image") is not None:
+    if params.get("output_image", None) is not None:
         cargs.extend([
             "-o",
-            "[" + params.get("output_image") + "]"
+            "[" + params.get("output_image", None) + "]"
         ])
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-m",
-            "[" + execution.input_file(params.get("mask")) + "]"
+            "[" + execution.input_file(params.get("mask", None)) + "]"
         ])
-    if params.get("gpu"):
+    if params.get("gpu", False):
         cargs.append("[" + "-g" + "]")
-    if params.get("border") is not None:
+    if params.get("border", None) is not None:
         cargs.extend([
             "-b",
-            "[" + str(params.get("border")) + "]"
+            "[" + str(params.get("border", None)) + "]"
         ])
-    if params.get("exclude_csf"):
+    if params.get("exclude_csf", False):
         cargs.append("[" + "--no-csf" + "]")
-    if params.get("model_weights") is not None:
+    if params.get("model_weights", None) is not None:
         cargs.extend([
             "--model",
-            "[" + execution.input_file(params.get("model_weights")) + "]"
+            "[" + execution.input_file(params.get("model_weights", None)) + "]"
         ])
     return cargs
 
@@ -170,17 +148,19 @@ def mri_synthstrip_outputs(
     """
     ret = MriSynthstripOutputs(
         root=execution.output_file("."),
-        output_image_file=execution.output_file(params.get("output_image")) if (params.get("output_image") is not None) else None,
-        output_mask_file=execution.output_file(pathlib.Path(params.get("mask")).name) if (params.get("mask") is not None) else None,
+        output_image_file=execution.output_file(params.get("output_image", None)) if (params.get("output_image") is not None) else None,
+        output_mask_file=execution.output_file(pathlib.Path(params.get("mask", None)).name) if (params.get("mask") is not None) else None,
     )
     return ret
 
 
 def mri_synthstrip_execute(
     params: MriSynthstripParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriSynthstripOutputs:
     """
+    mri_synthstrip
+    
     Robust, universal skull-stripping for brain images of any type.
     
     Author: FreeSurfer Developers
@@ -189,10 +169,12 @@ def mri_synthstrip_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriSynthstripOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_SYNTHSTRIP_METADATA)
     params = execution.params(params)
     cargs = mri_synthstrip_cargs(params, execution)
     ret = mri_synthstrip_outputs(params, execution)
@@ -205,12 +187,14 @@ def mri_synthstrip(
     output_image: str | None = None,
     mask: InputPathType | None = None,
     gpu: bool = False,
-    border: float | None = 1,
+    border: float | None = None,
     exclude_csf: bool = False,
     model_weights: InputPathType | None = None,
     runner: Runner | None = None,
 ) -> MriSynthstripOutputs:
     """
+    mri_synthstrip
+    
     Robust, universal skull-stripping for brain images of any type.
     
     Author: FreeSurfer Developers
@@ -229,8 +213,6 @@ def mri_synthstrip(
     Returns:
         NamedTuple of outputs (described in `MriSynthstripOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_SYNTHSTRIP_METADATA)
     params = mri_synthstrip_params(
         image=image,
         output_image=output_image,
@@ -240,13 +222,13 @@ def mri_synthstrip(
         exclude_csf=exclude_csf,
         model_weights=model_weights,
     )
-    return mri_synthstrip_execute(params, execution)
+    return mri_synthstrip_execute(params, runner)
 
 
 __all__ = [
     "MRI_SYNTHSTRIP_METADATA",
     "MriSynthstripOutputs",
-    "MriSynthstripParameters",
     "mri_synthstrip",
+    "mri_synthstrip_execute",
     "mri_synthstrip_params",
 ]