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

niwrap_mrtrix/mrtrix/mrcheckerboardmask.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRCHECKERBOARDMASK_METADATA = Metadata(
-    id="a3b0ea1bbc979f69d0d7f7f9d44b33ccf51605d8.boutiques",
+    id="f1aa53a7b6030f421a6e8c4455b70ae4ec643303.boutiques",
     name="mrcheckerboardmask",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,35 @@ MRCHECKERBOARDMASK_METADATA = Metadata(
 
 
 MrcheckerboardmaskConfigParameters = typing.TypedDict('MrcheckerboardmaskConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+MrcheckerboardmaskConfigParametersTagged = typing.TypedDict('MrcheckerboardmaskConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 MrcheckerboardmaskParameters = typing.TypedDict('MrcheckerboardmaskParameters', {
-    "__STYXTYPE__": typing.Literal["mrcheckerboardmask"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/mrcheckerboardmask"]],
+    "tiles": typing.NotRequired[int | None],
+    "invert": bool,
+    "nan": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrcheckerboardmaskConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+MrcheckerboardmaskParametersTagged = typing.TypedDict('MrcheckerboardmaskParametersTagged', {
+    "@type": typing.Literal["mrtrix/mrcheckerboardmask"],
     "tiles": typing.NotRequired[int | None],
     "invert": bool,
     "nan": bool,
@@ -36,45 +57,12 @@ MrcheckerboardmaskParameters = typing.TypedDict('MrcheckerboardmaskParameters',
     "input": InputPathType,
     "output": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mrcheckerboardmask": mrcheckerboardmask_cargs,
-        "config": mrcheckerboardmask_config_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 {
-        "mrcheckerboardmask": mrcheckerboardmask_outputs,
-    }.get(t)
 
 
 def mrcheckerboardmask_config_params(
     key: str,
     value: str,
-) -> MrcheckerboardmaskConfigParameters:
+) -> MrcheckerboardmaskConfigParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +73,7 @@ def mrcheckerboardmask_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -107,14 +95,14 @@ def mrcheckerboardmask_config_cargs(
     """
     cargs = []
     cargs.append("-config")
-    cargs.append(params.get("key"))
-    cargs.append(params.get("value"))
+    cargs.append(params.get("key", None))
+    cargs.append(params.get("value", None))
     return cargs
 
 
 class MrcheckerboardmaskOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mrcheckerboardmask(...)`.
+    Output object returned when calling `MrcheckerboardmaskParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -136,7 +124,7 @@ def mrcheckerboardmask_params(
     config: list[MrcheckerboardmaskConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> MrcheckerboardmaskParameters:
+) -> MrcheckerboardmaskParametersTagged:
     """
     Build parameters.
     
@@ -162,7 +150,7 @@ def mrcheckerboardmask_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mrcheckerboardmask",
+        "@type": "mrtrix/mrcheckerboardmask",
         "invert": invert,
         "nan": nan,
         "info": info,
@@ -198,36 +186,36 @@ def mrcheckerboardmask_cargs(
     """
     cargs = []
     cargs.append("mrcheckerboardmask")
-    if params.get("tiles") is not None:
+    if params.get("tiles", None) is not None:
         cargs.extend([
             "-tiles",
-            str(params.get("tiles"))
+            str(params.get("tiles", None))
         ])
-    if params.get("invert"):
+    if params.get("invert", False):
         cargs.append("-invert")
-    if params.get("nan"):
+    if params.get("nan", False):
         cargs.append("-nan")
-    if params.get("info"):
+    if params.get("info", False):
         cargs.append("-info")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-debug")
-    if params.get("force"):
+    if params.get("force", False):
         cargs.append("-force")
-    if params.get("nthreads") is not None:
+    if params.get("nthreads", None) is not None:
         cargs.extend([
             "-nthreads",
-            str(params.get("nthreads"))
+            str(params.get("nthreads", None))
         ])
-    if params.get("config") is not None:
-        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("config")] for a in c])
-    if params.get("help"):
+    if params.get("config", None) is not None:
+        cargs.extend([a for c in [mrcheckerboardmask_config_cargs(s, execution) for s in params.get("config", None)] for a in c])
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-version")
-    cargs.append(execution.input_file(params.get("input")))
-    cargs.append(params.get("output"))
+    cargs.append(execution.input_file(params.get("input", None)))
+    cargs.append(params.get("output", None))
     return cargs
 
 
@@ -246,16 +234,18 @@ def mrcheckerboardmask_outputs(
     """
     ret = MrcheckerboardmaskOutputs(
         root=execution.output_file("."),
-        output=execution.output_file(params.get("output")),
+        output=execution.output_file(params.get("output", None)),
     )
     return ret
 
 
 def mrcheckerboardmask_execute(
     params: MrcheckerboardmaskParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrcheckerboardmaskOutputs:
     """
+    mrcheckerboardmask
+    
     Create bitwise checkerboard image.
     
     
@@ -270,10 +260,12 @@ def mrcheckerboardmask_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrcheckerboardmaskOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRCHECKERBOARDMASK_METADATA)
     params = execution.params(params)
     cargs = mrcheckerboardmask_cargs(params, execution)
     ret = mrcheckerboardmask_outputs(params, execution)
@@ -298,6 +290,8 @@ def mrcheckerboardmask(
     runner: Runner | None = None,
 ) -> MrcheckerboardmaskOutputs:
     """
+    mrcheckerboardmask
+    
     Create bitwise checkerboard image.
     
     
@@ -332,8 +326,6 @@ def mrcheckerboardmask(
     Returns:
         NamedTuple of outputs (described in `MrcheckerboardmaskOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRCHECKERBOARDMASK_METADATA)
     params = mrcheckerboardmask_params(
         tiles=tiles,
         invert=invert,
@@ -349,15 +341,14 @@ def mrcheckerboardmask(
         input_=input_,
         output=output,
     )
-    return mrcheckerboardmask_execute(params, execution)
+    return mrcheckerboardmask_execute(params, runner)
 
 
 __all__ = [
     "MRCHECKERBOARDMASK_METADATA",
-    "MrcheckerboardmaskConfigParameters",
     "MrcheckerboardmaskOutputs",
-    "MrcheckerboardmaskParameters",
     "mrcheckerboardmask",
     "mrcheckerboardmask_config_params",
+    "mrcheckerboardmask_execute",
     "mrcheckerboardmask_params",
 ]

niwrap_mrtrix/mrtrix/mrclusterstats.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRCLUSTERSTATS_METADATA = Metadata(
-    id="c57e5e73fb4141a5486cb8917fc726340ee4455f.boutiques",
+    id="3cccb6a587fcc1d359cee16156cb510a9fec0521.boutiques",
     name="mrclusterstats",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,20 +14,65 @@ MRCLUSTERSTATS_METADATA = Metadata(
 
 
 MrclusterstatsColumnParameters = typing.TypedDict('MrclusterstatsColumnParameters', {
-    "__STYXTYPE__": typing.Literal["column"],
+    "@type": typing.NotRequired[typing.Literal["column"]],
+    "path": InputPathType,
+})
+MrclusterstatsColumnParametersTagged = typing.TypedDict('MrclusterstatsColumnParametersTagged', {
+    "@type": typing.Literal["column"],
     "path": InputPathType,
 })
 
 
 MrclusterstatsConfigParameters = typing.TypedDict('MrclusterstatsConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+MrclusterstatsConfigParametersTagged = typing.TypedDict('MrclusterstatsConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 MrclusterstatsParameters = typing.TypedDict('MrclusterstatsParameters', {
-    "__STYXTYPE__": typing.Literal["mrclusterstats"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/mrclusterstats"]],
+    "notest": bool,
+    "errors": typing.NotRequired[str | None],
+    "exchange_within": typing.NotRequired[InputPathType | None],
+    "exchange_whole": typing.NotRequired[InputPathType | None],
+    "strong": bool,
+    "nshuffles": typing.NotRequired[int | None],
+    "permutations": typing.NotRequired[InputPathType | None],
+    "nonstationarity": bool,
+    "skew_nonstationarity": typing.NotRequired[float | None],
+    "nshuffles_nonstationarity": typing.NotRequired[int | None],
+    "permutations_nonstationarity": typing.NotRequired[InputPathType | None],
+    "tfce_dh": typing.NotRequired[float | None],
+    "tfce_e": typing.NotRequired[float | None],
+    "tfce_h": typing.NotRequired[float | None],
+    "variance": typing.NotRequired[InputPathType | None],
+    "ftests": typing.NotRequired[InputPathType | None],
+    "fonly": bool,
+    "column": typing.NotRequired[list[MrclusterstatsColumnParameters] | None],
+    "threshold": typing.NotRequired[float | None],
+    "connectivity": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrclusterstatsConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "design": InputPathType,
+    "contrast": InputPathType,
+    "mask": InputPathType,
+    "output": str,
+})
+MrclusterstatsParametersTagged = typing.TypedDict('MrclusterstatsParametersTagged', {
+    "@type": typing.Literal["mrtrix/mrclusterstats"],
     "notest": bool,
     "errors": typing.NotRequired[str | None],
     "exchange_within": typing.NotRequired[InputPathType | None],
@@ -62,44 +107,11 @@ MrclusterstatsParameters = typing.TypedDict('MrclusterstatsParameters', {
     "mask": InputPathType,
     "output": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mrclusterstats": mrclusterstats_cargs,
-        "column": mrclusterstats_column_cargs,
-        "config": mrclusterstats_config_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)
 
 
 def mrclusterstats_column_params(
     path: InputPathType,
-) -> MrclusterstatsColumnParameters:
+) -> MrclusterstatsColumnParametersTagged:
     """
     Build parameters.
     
@@ -112,7 +124,7 @@ def mrclusterstats_column_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "column",
+        "@type": "column",
         "path": path,
     }
     return params
@@ -133,14 +145,14 @@ def mrclusterstats_column_cargs(
     """
     cargs = []
     cargs.append("-column")
-    cargs.append(execution.input_file(params.get("path")))
+    cargs.append(execution.input_file(params.get("path", None)))
     return cargs
 
 
 def mrclusterstats_config_params(
     key: str,
     value: str,
-) -> MrclusterstatsConfigParameters:
+) -> MrclusterstatsConfigParametersTagged:
     """
     Build parameters.
     
@@ -151,7 +163,7 @@ def mrclusterstats_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -173,14 +185,14 @@ def mrclusterstats_config_cargs(
     """
     cargs = []
     cargs.append("-config")
-    cargs.append(params.get("key"))
-    cargs.append(params.get("value"))
+    cargs.append(params.get("key", None))
+    cargs.append(params.get("value", None))
     return cargs
 
 
 class MrclusterstatsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mrclusterstats(...)`.
+    Output object returned when calling `MrclusterstatsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -220,7 +232,7 @@ def mrclusterstats_params(
     config: list[MrclusterstatsConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> MrclusterstatsParameters:
+) -> MrclusterstatsParametersTagged:
     """
     Build parameters.
     
@@ -298,7 +310,7 @@ def mrclusterstats_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mrclusterstats",
+        "@type": "mrtrix/mrclusterstats",
         "notest": notest,
         "strong": strong,
         "nonstationarity": nonstationarity,
@@ -368,112 +380,112 @@ def mrclusterstats_cargs(
     """
     cargs = []
     cargs.append("mrclusterstats")
-    if params.get("notest"):
+    if params.get("notest", False):
         cargs.append("-notest")
-    if params.get("errors") is not None:
+    if params.get("errors", None) is not None:
         cargs.extend([
             "-errors",
-            params.get("errors")
+            params.get("errors", None)
         ])
-    if params.get("exchange_within") is not None:
+    if params.get("exchange_within", None) is not None:
         cargs.extend([
             "-exchange_within",
-            execution.input_file(params.get("exchange_within"))
+            execution.input_file(params.get("exchange_within", None))
         ])
-    if params.get("exchange_whole") is not None:
+    if params.get("exchange_whole", None) is not None:
         cargs.extend([
             "-exchange_whole",
-            execution.input_file(params.get("exchange_whole"))
+            execution.input_file(params.get("exchange_whole", None))
         ])
-    if params.get("strong"):
+    if params.get("strong", False):
         cargs.append("-strong")
-    if params.get("nshuffles") is not None:
+    if params.get("nshuffles", None) is not None:
         cargs.extend([
             "-nshuffles",
-            str(params.get("nshuffles"))
+            str(params.get("nshuffles", None))
         ])
-    if params.get("permutations") is not None:
+    if params.get("permutations", None) is not None:
         cargs.extend([
             "-permutations",
-            execution.input_file(params.get("permutations"))
+            execution.input_file(params.get("permutations", None))
         ])
-    if params.get("nonstationarity"):
+    if params.get("nonstationarity", False):
         cargs.append("-nonstationarity")
-    if params.get("skew_nonstationarity") is not None:
+    if params.get("skew_nonstationarity", None) is not None:
         cargs.extend([
             "-skew_nonstationarity",
-            str(params.get("skew_nonstationarity"))
+            str(params.get("skew_nonstationarity", None))
         ])
-    if params.get("nshuffles_nonstationarity") is not None:
+    if params.get("nshuffles_nonstationarity", None) is not None:
         cargs.extend([
             "-nshuffles_nonstationarity",
-            str(params.get("nshuffles_nonstationarity"))
+            str(params.get("nshuffles_nonstationarity", None))
         ])
-    if params.get("permutations_nonstationarity") is not None:
+    if params.get("permutations_nonstationarity", None) is not None:
         cargs.extend([
             "-permutations_nonstationarity",
-            execution.input_file(params.get("permutations_nonstationarity"))
+            execution.input_file(params.get("permutations_nonstationarity", None))
         ])
-    if params.get("tfce_dh") is not None:
+    if params.get("tfce_dh", None) is not None:
         cargs.extend([
             "-tfce_dh",
-            str(params.get("tfce_dh"))
+            str(params.get("tfce_dh", None))
         ])
-    if params.get("tfce_e") is not None:
+    if params.get("tfce_e", None) is not None:
         cargs.extend([
             "-tfce_e",
-            str(params.get("tfce_e"))
+            str(params.get("tfce_e", None))
         ])
-    if params.get("tfce_h") is not None:
+    if params.get("tfce_h", None) is not None:
         cargs.extend([
             "-tfce_h",
-            str(params.get("tfce_h"))
+            str(params.get("tfce_h", None))
         ])
-    if params.get("variance") is not None:
+    if params.get("variance", None) is not None:
         cargs.extend([
             "-variance",
-            execution.input_file(params.get("variance"))
+            execution.input_file(params.get("variance", None))
         ])
-    if params.get("ftests") is not None:
+    if params.get("ftests", None) is not None:
         cargs.extend([
             "-ftests",
-            execution.input_file(params.get("ftests"))
+            execution.input_file(params.get("ftests", None))
         ])
-    if params.get("fonly"):
+    if params.get("fonly", False):
         cargs.append("-fonly")
-    if params.get("column") is not None:
-        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("column")] for a in c])
-    if params.get("threshold") is not None:
+    if params.get("column", None) is not None:
+        cargs.extend([a for c in [mrclusterstats_column_cargs(s, execution) for s in params.get("column", None)] for a in c])
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "-threshold",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    if params.get("connectivity"):
+    if params.get("connectivity", False):
         cargs.append("-connectivity")
-    if params.get("info"):
+    if params.get("info", False):
         cargs.append("-info")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-debug")
-    if params.get("force"):
+    if params.get("force", False):
         cargs.append("-force")
-    if params.get("nthreads") is not None:
+    if params.get("nthreads", None) is not None:
         cargs.extend([
             "-nthreads",
-            str(params.get("nthreads"))
+            str(params.get("nthreads", None))
         ])
-    if params.get("config") is not None:
-        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("config")] for a in c])
-    if params.get("help"):
+    if params.get("config", None) is not None:
+        cargs.extend([a for c in [mrclusterstats_config_cargs(s, execution) for s in params.get("config", None)] for a in c])
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-version")
-    cargs.append(execution.input_file(params.get("input")))
-    cargs.append(execution.input_file(params.get("design")))
-    cargs.append(execution.input_file(params.get("contrast")))
-    cargs.append(execution.input_file(params.get("mask")))
-    cargs.append(params.get("output"))
+    cargs.append(execution.input_file(params.get("input", None)))
+    cargs.append(execution.input_file(params.get("design", None)))
+    cargs.append(execution.input_file(params.get("contrast", None)))
+    cargs.append(execution.input_file(params.get("mask", None)))
+    cargs.append(params.get("output", None))
     return cargs
 
 
@@ -498,9 +510,11 @@ def mrclusterstats_outputs(
 
 def mrclusterstats_execute(
     params: MrclusterstatsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrclusterstatsOutputs:
     """
+    mrclusterstats
+    
     Voxel-based analysis using permutation testing and threshold-free cluster
     enhancement.
     
@@ -532,10 +546,12 @@ def mrclusterstats_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrclusterstatsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRCLUSTERSTATS_METADATA)
     params = execution.params(params)
     cargs = mrclusterstats_cargs(params, execution)
     ret = mrclusterstats_outputs(params, execution)
@@ -580,6 +596,8 @@ def mrclusterstats(
     runner: Runner | None = None,
 ) -> MrclusterstatsOutputs:
     """
+    mrclusterstats
+    
     Voxel-based analysis using permutation testing and threshold-free cluster
     enhancement.
     
@@ -683,8 +701,6 @@ def mrclusterstats(
     Returns:
         NamedTuple of outputs (described in `MrclusterstatsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRCLUSTERSTATS_METADATA)
     params = mrclusterstats_params(
         notest=notest,
         errors=errors,
@@ -720,17 +736,15 @@ def mrclusterstats(
         mask=mask,
         output=output,
     )
-    return mrclusterstats_execute(params, execution)
+    return mrclusterstats_execute(params, runner)
 
 
 __all__ = [
     "MRCLUSTERSTATS_METADATA",
-    "MrclusterstatsColumnParameters",
-    "MrclusterstatsConfigParameters",
     "MrclusterstatsOutputs",
-    "MrclusterstatsParameters",
     "mrclusterstats",
     "mrclusterstats_column_params",
     "mrclusterstats_config_params",
+    "mrclusterstats_execute",
     "mrclusterstats_params",
 ]