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

niwrap_freesurfer/freesurfer/bbregister.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BBREGISTER_METADATA = Metadata(
-    id="5afef238c6734753905291f538bd2eab731681c0.boutiques",
+    id="7463c20db1e37dac761678dd13e5d83f67e9b51f.boutiques",
     name="bbregister",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,26 @@ BBREGISTER_METADATA = Metadata(
 
 
 BbregisterParameters = typing.TypedDict('BbregisterParameters', {
-    "__STYXTYPE__": typing.Literal["bbregister"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/bbregister"]],
+    "subject": str,
+    "moveable_volume": InputPathType,
+    "reg_file": str,
+    "contrast_type_t1": bool,
+    "contrast_type_t2": bool,
+    "vsm": typing.NotRequired[InputPathType | None],
+    "init_coreg": bool,
+    "no_coreg_ref_mask": bool,
+    "init_header": bool,
+    "init_reg": typing.NotRequired[InputPathType | None],
+    "intvol": typing.NotRequired[InputPathType | None],
+    "mid_frame": bool,
+    "frame_no": typing.NotRequired[float | None],
+    "template_out": typing.NotRequired[str | None],
+    "o_outvol": typing.NotRequired[str | None],
+    "s_from_reg": bool,
+})
+BbregisterParametersTagged = typing.TypedDict('BbregisterParametersTagged', {
+    "@type": typing.Literal["freesurfer/bbregister"],
     "subject": str,
     "moveable_volume": InputPathType,
     "reg_file": str,
@@ -32,43 +51,11 @@ BbregisterParameters = typing.TypedDict('BbregisterParameters', {
     "o_outvol": typing.NotRequired[str | None],
     "s_from_reg": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "bbregister": bbregister_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 {
-        "bbregister": bbregister_outputs,
-    }.get(t)
 
 
 class BbregisterOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `bbregister(...)`.
+    Output object returned when calling `BbregisterParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -95,7 +82,7 @@ def bbregister_params(
     template_out: str | None = None,
     o_outvol: str | None = None,
     s_from_reg: bool = False,
-) -> BbregisterParameters:
+) -> BbregisterParametersTagged:
     """
     Build parameters.
     
@@ -127,7 +114,7 @@ def bbregister_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "bbregister",
+        "@type": "freesurfer/bbregister",
         "subject": subject,
         "moveable_volume": moveable_volume,
         "reg_file": reg_file,
@@ -171,59 +158,59 @@ def bbregister_cargs(
     cargs.append("bbregister")
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
     cargs.extend([
         "--mov",
-        execution.input_file(params.get("moveable_volume"))
+        execution.input_file(params.get("moveable_volume", None))
     ])
     cargs.extend([
         "--reg",
-        params.get("reg_file")
+        params.get("reg_file", None)
     ])
-    if params.get("contrast_type_t1"):
+    if params.get("contrast_type_t1", False):
         cargs.append("--t1")
-    if params.get("contrast_type_t2"):
+    if params.get("contrast_type_t2", False):
         cargs.append("--t2")
-    if params.get("vsm") is not None:
+    if params.get("vsm", None) is not None:
         cargs.extend([
             "--vsm",
-            execution.input_file(params.get("vsm"))
+            execution.input_file(params.get("vsm", None))
         ])
-    if params.get("init_coreg"):
+    if params.get("init_coreg", False):
         cargs.append("--init-coreg")
-    if params.get("no_coreg_ref_mask"):
+    if params.get("no_coreg_ref_mask", False):
         cargs.append("--no-coreg-ref-mask")
-    if params.get("init_header"):
+    if params.get("init_header", False):
         cargs.append("--init-header")
-    if params.get("init_reg") is not None:
+    if params.get("init_reg", None) is not None:
         cargs.extend([
             "--init-reg",
-            execution.input_file(params.get("init_reg"))
+            execution.input_file(params.get("init_reg", None))
         ])
-    if params.get("intvol") is not None:
+    if params.get("intvol", None) is not None:
         cargs.extend([
             "--int",
-            execution.input_file(params.get("intvol"))
+            execution.input_file(params.get("intvol", None))
         ])
-    if params.get("mid_frame"):
+    if params.get("mid_frame", False):
         cargs.append("--mid-frame")
-    if params.get("frame_no") is not None:
+    if params.get("frame_no", None) is not None:
         cargs.extend([
             "--frame",
-            str(params.get("frame_no"))
+            str(params.get("frame_no", None))
         ])
-    if params.get("template_out") is not None:
+    if params.get("template_out", None) is not None:
         cargs.extend([
             "--template-out",
-            params.get("template_out")
+            params.get("template_out", None)
         ])
-    if params.get("o_outvol") is not None:
+    if params.get("o_outvol", None) is not None:
         cargs.extend([
             "--o",
-            params.get("o_outvol")
+            params.get("o_outvol", None)
         ])
-    if params.get("s_from_reg"):
+    if params.get("s_from_reg", False):
         cargs.append("--s-from-reg")
     return cargs
 
@@ -243,19 +230,21 @@ def bbregister_outputs(
     """
     ret = BbregisterOutputs(
         root=execution.output_file("."),
-        reg_output=execution.output_file(params.get("reg_file")),
-        out_volume=execution.output_file(params.get("o_outvol")) if (params.get("o_outvol") is not None) else None,
+        reg_output=execution.output_file(params.get("reg_file", None)),
+        out_volume=execution.output_file(params.get("o_outvol", None)) if (params.get("o_outvol") is not None) else None,
     )
     return ret
 
 
 def bbregister_execute(
     params: BbregisterParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> BbregisterOutputs:
     """
-    Performs within-subject, cross-modal registration using a boundary-based cost
-    function.
+    bbregister
+    
+    Performs within-subject, cross-modal registration using a boundary-based
+    cost function.
     
     Author: FreeSurfer Developers
     
@@ -263,10 +252,12 @@ def bbregister_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `BbregisterOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(BBREGISTER_METADATA)
     params = execution.params(params)
     cargs = bbregister_cargs(params, execution)
     ret = bbregister_outputs(params, execution)
@@ -294,8 +285,10 @@ def bbregister(
     runner: Runner | None = None,
 ) -> BbregisterOutputs:
     """
-    Performs within-subject, cross-modal registration using a boundary-based cost
-    function.
+    bbregister
+    
+    Performs within-subject, cross-modal registration using a boundary-based
+    cost function.
     
     Author: FreeSurfer Developers
     
@@ -329,8 +322,6 @@ def bbregister(
     Returns:
         NamedTuple of outputs (described in `BbregisterOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(BBREGISTER_METADATA)
     params = bbregister_params(
         subject=subject,
         moveable_volume=moveable_volume,
@@ -349,13 +340,13 @@ def bbregister(
         o_outvol=o_outvol,
         s_from_reg=s_from_reg,
     )
-    return bbregister_execute(params, execution)
+    return bbregister_execute(params, runner)
 
 
 __all__ = [
     "BBREGISTER_METADATA",
     "BbregisterOutputs",
-    "BbregisterParameters",
     "bbregister",
+    "bbregister_execute",
     "bbregister_params",
 ]

niwrap_freesurfer/freesurfer/bedpostx_mgh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BEDPOSTX_MGH_METADATA = Metadata(
-    id="3ed864ec81d1c034c4ff17b4f55cad7b918d2d91.boutiques",
+    id="30878138f06e8d8b5b7cb02eea3673a7add660b9.boutiques",
     name="bedpostx_mgh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ BEDPOSTX_MGH_METADATA = Metadata(
 
 
 BedpostxMghParameters = typing.TypedDict('BedpostxMghParameters', {
-    "__STYXTYPE__": typing.Literal["bedpostx_mgh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/bedpostx_mgh"]],
+    "subject_directory": str,
+    "fibres": typing.NotRequired[float | None],
+    "ard_weight": typing.NotRequired[float | None],
+    "burnin": typing.NotRequired[float | None],
+    "jumps": typing.NotRequired[float | None],
+    "sample_every": typing.NotRequired[float | None],
+    "deconv_model": typing.NotRequired[float | None],
+    "gradient_nonlin": bool,
+})
+BedpostxMghParametersTagged = typing.TypedDict('BedpostxMghParametersTagged', {
+    "@type": typing.Literal["freesurfer/bedpostx_mgh"],
     "subject_directory": str,
     "fibres": typing.NotRequired[float | None],
     "ard_weight": typing.NotRequired[float | None],
@@ -24,42 +35,11 @@ BedpostxMghParameters = typing.TypedDict('BedpostxMghParameters', {
     "deconv_model": typing.NotRequired[float | None],
     "gradient_nonlin": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "bedpostx_mgh": bedpostx_mgh_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 BedpostxMghOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `bedpostx_mgh(...)`.
+    Output object returned when calling `BedpostxMghParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,7 +54,7 @@ def bedpostx_mgh_params(
     sample_every: float | None = None,
     deconv_model: float | None = None,
     gradient_nonlin: bool = False,
-) -> BedpostxMghParameters:
+) -> BedpostxMghParametersTagged:
     """
     Build parameters.
     
@@ -94,7 +74,7 @@ def bedpostx_mgh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "bedpostx_mgh",
+        "@type": "freesurfer/bedpostx_mgh",
         "subject_directory": subject_directory,
         "gradient_nonlin": gradient_nonlin,
     }
@@ -128,38 +108,38 @@ def bedpostx_mgh_cargs(
     """
     cargs = []
     cargs.append("bedpostx_mgh")
-    cargs.append(params.get("subject_directory"))
-    if params.get("fibres") is not None:
+    cargs.append(params.get("subject_directory", None))
+    if params.get("fibres", None) is not None:
         cargs.extend([
             "-n",
-            str(params.get("fibres"))
+            str(params.get("fibres", None))
         ])
-    if params.get("ard_weight") is not None:
+    if params.get("ard_weight", None) is not None:
         cargs.extend([
             "-w",
-            str(params.get("ard_weight"))
+            str(params.get("ard_weight", None))
         ])
-    if params.get("burnin") is not None:
+    if params.get("burnin", None) is not None:
         cargs.extend([
             "-b",
-            str(params.get("burnin"))
+            str(params.get("burnin", None))
         ])
-    if params.get("jumps") is not None:
+    if params.get("jumps", None) is not None:
         cargs.extend([
             "-j",
-            str(params.get("jumps"))
+            str(params.get("jumps", None))
         ])
-    if params.get("sample_every") is not None:
+    if params.get("sample_every", None) is not None:
         cargs.extend([
             "-s",
-            str(params.get("sample_every"))
+            str(params.get("sample_every", None))
         ])
-    if params.get("deconv_model") is not None:
+    if params.get("deconv_model", None) is not None:
         cargs.extend([
             "-model",
-            str(params.get("deconv_model"))
+            str(params.get("deconv_model", None))
         ])
-    if params.get("gradient_nonlin"):
+    if params.get("gradient_nonlin", False):
         cargs.append("-g")
     return cargs
 
@@ -185,9 +165,11 @@ def bedpostx_mgh_outputs(
 
 def bedpostx_mgh_execute(
     params: BedpostxMghParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> BedpostxMghOutputs:
     """
+    bedpostx_mgh
+    
     A modified version of FSL's bedpostx compatible with PBS queueing system for
     parallel computation.
     
@@ -197,10 +179,12 @@ def bedpostx_mgh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `BedpostxMghOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(BEDPOSTX_MGH_METADATA)
     params = execution.params(params)
     cargs = bedpostx_mgh_cargs(params, execution)
     ret = bedpostx_mgh_outputs(params, execution)
@@ -220,6 +204,8 @@ def bedpostx_mgh(
     runner: Runner | None = None,
 ) -> BedpostxMghOutputs:
     """
+    bedpostx_mgh
+    
     A modified version of FSL's bedpostx compatible with PBS queueing system for
     parallel computation.
     
@@ -243,8 +229,6 @@ def bedpostx_mgh(
     Returns:
         NamedTuple of outputs (described in `BedpostxMghOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(BEDPOSTX_MGH_METADATA)
     params = bedpostx_mgh_params(
         subject_directory=subject_directory,
         fibres=fibres,
@@ -255,13 +239,13 @@ def bedpostx_mgh(
         deconv_model=deconv_model,
         gradient_nonlin=gradient_nonlin,
     )
-    return bedpostx_mgh_execute(params, execution)
+    return bedpostx_mgh_execute(params, runner)
 
 
 __all__ = [
     "BEDPOSTX_MGH_METADATA",
     "BedpostxMghOutputs",
-    "BedpostxMghParameters",
     "bedpostx_mgh",
+    "bedpostx_mgh_execute",
     "bedpostx_mgh_params",
 ]

niwrap_freesurfer/freesurfer/beta2sxa.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BETA2SXA_METADATA = Metadata(
-    id="f0f822c3fdfc6946f2efbf9d1eba0fc23f0154a3.boutiques",
+    id="0cf345ab66dc4b1164643c5f220562d8ef37bfa7.boutiques",
     name="beta2sxa",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ BETA2SXA_METADATA = Metadata(
 
 
 Beta2sxaParameters = typing.TypedDict('Beta2sxaParameters', {
-    "__STYXTYPE__": typing.Literal["beta2sxa"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/beta2sxa"]],
+    "beta_files": list[InputPathType],
+    "number_of_conditions": float,
+    "number_of_per_subjects": float,
+    "sxa_output": typing.NotRequired[str | None],
+})
+Beta2sxaParametersTagged = typing.TypedDict('Beta2sxaParametersTagged', {
+    "@type": typing.Literal["freesurfer/beta2sxa"],
     "beta_files": list[InputPathType],
     "number_of_conditions": float,
     "number_of_per_subjects": float,
     "sxa_output": 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 {
-        "beta2sxa": beta2sxa_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 {
-        "beta2sxa": beta2sxa_outputs,
-    }.get(t)
 
 
 class Beta2sxaOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `beta2sxa(...)`.
+    Output object returned when calling `Beta2sxaParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -68,8 +43,8 @@ def beta2sxa_params(
     beta_files: list[InputPathType],
     number_of_conditions: float,
     number_of_per_subjects: float,
-    sxa_output: str | None = "h.beta",
-) -> Beta2sxaParameters:
+    sxa_output: str | None = None,
+) -> Beta2sxaParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def beta2sxa_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "beta2sxa",
+        "@type": "freesurfer/beta2sxa",
         "beta_files": beta_files,
         "number_of_conditions": number_of_conditions,
         "number_of_per_subjects": number_of_per_subjects,
@@ -109,20 +84,20 @@ def beta2sxa_cargs(
     cargs.append("beta2sxa")
     cargs.extend([
         "--b",
-        *[execution.input_file(f) for f in params.get("beta_files")]
+        *[execution.input_file(f) for f in params.get("beta_files", None)]
     ])
     cargs.extend([
         "--nc",
-        str(params.get("number_of_conditions"))
+        str(params.get("number_of_conditions", None))
     ])
     cargs.extend([
         "--nper",
-        str(params.get("number_of_per_subjects"))
+        str(params.get("number_of_per_subjects", None))
     ])
-    if params.get("sxa_output") is not None:
+    if params.get("sxa_output", None) is not None:
         cargs.extend([
             "--o",
-            params.get("sxa_output")
+            params.get("sxa_output", None)
         ])
     return cargs
 
@@ -149,11 +124,13 @@ def beta2sxa_outputs(
 
 def beta2sxa_execute(
     params: Beta2sxaParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Beta2sxaOutputs:
     """
-    A script to create files for plotting in tkmedit or tksurfer based on tabular
-    data.
+    beta2sxa
+    
+    A script to create files for plotting in tkmedit or tksurfer based on
+    tabular data.
     
     Author: FreeSurfer Developers
     
@@ -161,10 +138,12 @@ def beta2sxa_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Beta2sxaOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(BETA2SXA_METADATA)
     params = execution.params(params)
     cargs = beta2sxa_cargs(params, execution)
     ret = beta2sxa_outputs(params, execution)
@@ -176,12 +155,14 @@ def beta2sxa(
     beta_files: list[InputPathType],
     number_of_conditions: float,
     number_of_per_subjects: float,
-    sxa_output: str | None = "h.beta",
+    sxa_output: str | None = None,
     runner: Runner | None = None,
 ) -> Beta2sxaOutputs:
     """
-    A script to create files for plotting in tkmedit or tksurfer based on tabular
-    data.
+    beta2sxa
+    
+    A script to create files for plotting in tkmedit or tksurfer based on
+    tabular data.
     
     Author: FreeSurfer Developers
     
@@ -196,21 +177,19 @@ def beta2sxa(
     Returns:
         NamedTuple of outputs (described in `Beta2sxaOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(BETA2SXA_METADATA)
     params = beta2sxa_params(
         beta_files=beta_files,
         number_of_conditions=number_of_conditions,
         number_of_per_subjects=number_of_per_subjects,
         sxa_output=sxa_output,
     )
-    return beta2sxa_execute(params, execution)
+    return beta2sxa_execute(params, runner)
 
 
 __all__ = [
     "BETA2SXA_METADATA",
     "Beta2sxaOutputs",
-    "Beta2sxaParameters",
     "beta2sxa",
+    "beta2sxa_execute",
     "beta2sxa_params",
 ]