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

niwrap_mrtrix/mrtrix/mrstats.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRSTATS_METADATA = Metadata(
-    id="a0e8ad6624129b47028cef6351f07fe776fbe211.boutiques",
+    id="28fb063299fa07970bfa62d606e13e87fd3bc94e.boutiques",
     name="mrstats",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,20 +14,45 @@ MRSTATS_METADATA = Metadata(
 
 
 MrstatsOutputParameters = typing.TypedDict('MrstatsOutputParameters', {
-    "__STYXTYPE__": typing.Literal["output"],
+    "@type": typing.NotRequired[typing.Literal["output"]],
+    "field": str,
+})
+MrstatsOutputParametersTagged = typing.TypedDict('MrstatsOutputParametersTagged', {
+    "@type": typing.Literal["output"],
     "field": str,
 })
 
 
 MrstatsConfigParameters = typing.TypedDict('MrstatsConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+MrstatsConfigParametersTagged = typing.TypedDict('MrstatsConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 MrstatsParameters = typing.TypedDict('MrstatsParameters', {
-    "__STYXTYPE__": typing.Literal["mrstats"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/mrstats"]],
+    "output": typing.NotRequired[list[MrstatsOutputParameters] | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "ignorezero": bool,
+    "allvolumes": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrstatsConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "image": InputPathType,
+})
+MrstatsParametersTagged = typing.TypedDict('MrstatsParametersTagged', {
+    "@type": typing.Literal["mrtrix/mrstats"],
     "output": typing.NotRequired[list[MrstatsOutputParameters] | None],
     "mask": typing.NotRequired[InputPathType | None],
     "ignorezero": bool,
@@ -42,44 +67,11 @@ MrstatsParameters = typing.TypedDict('MrstatsParameters', {
     "version": bool,
     "image": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mrstats": mrstats_cargs,
-        "output": mrstats_output_cargs,
-        "config": mrstats_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 mrstats_output_params(
     field: str,
-) -> MrstatsOutputParameters:
+) -> MrstatsOutputParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +87,7 @@ def mrstats_output_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "output",
+        "@type": "output",
         "field": field,
     }
     return params
@@ -116,14 +108,14 @@ def mrstats_output_cargs(
     """
     cargs = []
     cargs.append("-output")
-    cargs.append(params.get("field"))
+    cargs.append(params.get("field", None))
     return cargs
 
 
 def mrstats_config_params(
     key: str,
     value: str,
-) -> MrstatsConfigParameters:
+) -> MrstatsConfigParametersTagged:
     """
     Build parameters.
     
@@ -134,7 +126,7 @@ def mrstats_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -156,14 +148,14 @@ def mrstats_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 MrstatsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mrstats(...)`.
+    Output object returned when calling `MrstatsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -183,7 +175,7 @@ def mrstats_params(
     config: list[MrstatsConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> MrstatsParameters:
+) -> MrstatsParametersTagged:
     """
     Build parameters.
     
@@ -216,7 +208,7 @@ def mrstats_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mrstats",
+        "@type": "mrtrix/mrstats",
         "ignorezero": ignorezero,
         "allvolumes": allvolumes,
         "info": info,
@@ -253,37 +245,37 @@ def mrstats_cargs(
     """
     cargs = []
     cargs.append("mrstats")
-    if params.get("output") is not None:
-        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("output")] for a in c])
-    if params.get("mask") is not None:
+    if params.get("output", None) is not None:
+        cargs.extend([a for c in [mrstats_output_cargs(s, execution) for s in params.get("output", None)] for a in c])
+    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("ignorezero"):
+    if params.get("ignorezero", False):
         cargs.append("-ignorezero")
-    if params.get("allvolumes"):
+    if params.get("allvolumes", False):
         cargs.append("-allvolumes")
-    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 [mrstats_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("image")))
+    cargs.append(execution.input_file(params.get("image", None)))
     return cargs
 
 
@@ -308,9 +300,11 @@ def mrstats_outputs(
 
 def mrstats_execute(
     params: MrstatsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrstatsOutputs:
     """
+    mrstats
+    
     Compute images statistics.
     
     
@@ -325,10 +319,12 @@ def mrstats_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrstatsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRSTATS_METADATA)
     params = execution.params(params)
     cargs = mrstats_cargs(params, execution)
     ret = mrstats_outputs(params, execution)
@@ -353,6 +349,8 @@ def mrstats(
     runner: Runner | None = None,
 ) -> MrstatsOutputs:
     """
+    mrstats
+    
     Compute images statistics.
     
     
@@ -394,8 +392,6 @@ def mrstats(
     Returns:
         NamedTuple of outputs (described in `MrstatsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRSTATS_METADATA)
     params = mrstats_params(
         output=output,
         mask=mask,
@@ -411,17 +407,15 @@ def mrstats(
         version=version,
         image=image,
     )
-    return mrstats_execute(params, execution)
+    return mrstats_execute(params, runner)
 
 
 __all__ = [
     "MRSTATS_METADATA",
-    "MrstatsConfigParameters",
-    "MrstatsOutputParameters",
     "MrstatsOutputs",
-    "MrstatsParameters",
     "mrstats",
     "mrstats_config_params",
+    "mrstats_execute",
     "mrstats_output_params",
     "mrstats_params",
 ]

niwrap_mrtrix/mrtrix/mrthreshold.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRTHRESHOLD_METADATA = Metadata(
-    id="63955d6506c219775e9ca4df901c67a97355416d.boutiques",
+    id="c55432e6110a1d139e985a99eec2382bb7a91c6e.boutiques",
     name="mrthreshold",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,43 @@ MRTHRESHOLD_METADATA = Metadata(
 
 
 MrthresholdConfigParameters = typing.TypedDict('MrthresholdConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+MrthresholdConfigParametersTagged = typing.TypedDict('MrthresholdConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 MrthresholdParameters = typing.TypedDict('MrthresholdParameters', {
-    "__STYXTYPE__": typing.Literal["mrthreshold"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/mrthreshold"]],
+    "abs": typing.NotRequired[float | None],
+    "percentile": typing.NotRequired[float | None],
+    "top": typing.NotRequired[int | None],
+    "bottom": typing.NotRequired[int | None],
+    "allvolumes": bool,
+    "ignorezero": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "comparison": typing.NotRequired[str | None],
+    "invert": bool,
+    "out_masked": bool,
+    "nan": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrthresholdConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": typing.NotRequired[str | None],
+})
+MrthresholdParametersTagged = typing.TypedDict('MrthresholdParametersTagged', {
+    "@type": typing.Literal["mrtrix/mrthreshold"],
     "abs": typing.NotRequired[float | None],
     "percentile": typing.NotRequired[float | None],
     "top": typing.NotRequired[int | None],
@@ -44,45 +73,12 @@ MrthresholdParameters = typing.TypedDict('MrthresholdParameters', {
     "input": InputPathType,
     "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 {
-        "mrthreshold": mrthreshold_cargs,
-        "config": mrthreshold_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 {
-        "mrthreshold": mrthreshold_outputs,
-    }.get(t)
 
 
 def mrthreshold_config_params(
     key: str,
     value: str,
-) -> MrthresholdConfigParameters:
+) -> MrthresholdConfigParametersTagged:
     """
     Build parameters.
     
@@ -93,7 +89,7 @@ def mrthreshold_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -115,14 +111,14 @@ def mrthreshold_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 MrthresholdOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mrthreshold(...)`.
+    Output object returned when calling `MrthresholdParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -152,7 +148,7 @@ def mrthreshold_params(
     help_: bool = False,
     version: bool = False,
     output: str | None = None,
-) -> MrthresholdParameters:
+) -> MrthresholdParametersTagged:
     """
     Build parameters.
     
@@ -197,7 +193,7 @@ def mrthreshold_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mrthreshold",
+        "@type": "mrtrix/mrthreshold",
         "allvolumes": allvolumes,
         "ignorezero": ignorezero,
         "invert": invert,
@@ -247,68 +243,68 @@ def mrthreshold_cargs(
     """
     cargs = []
     cargs.append("mrthreshold")
-    if params.get("abs") is not None:
+    if params.get("abs", None) is not None:
         cargs.extend([
             "-abs",
-            str(params.get("abs"))
+            str(params.get("abs", None))
         ])
-    if params.get("percentile") is not None:
+    if params.get("percentile", None) is not None:
         cargs.extend([
             "-percentile",
-            str(params.get("percentile"))
+            str(params.get("percentile", None))
         ])
-    if params.get("top") is not None:
+    if params.get("top", None) is not None:
         cargs.extend([
             "-top",
-            str(params.get("top"))
+            str(params.get("top", None))
         ])
-    if params.get("bottom") is not None:
+    if params.get("bottom", None) is not None:
         cargs.extend([
             "-bottom",
-            str(params.get("bottom"))
+            str(params.get("bottom", None))
         ])
-    if params.get("allvolumes"):
+    if params.get("allvolumes", False):
         cargs.append("-allvolumes")
-    if params.get("ignorezero"):
+    if params.get("ignorezero", False):
         cargs.append("-ignorezero")
-    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("comparison") is not None:
+    if params.get("comparison", None) is not None:
         cargs.extend([
             "-comparison",
-            params.get("comparison")
+            params.get("comparison", None)
         ])
-    if params.get("invert"):
+    if params.get("invert", False):
         cargs.append("-invert")
-    if params.get("out_masked"):
+    if params.get("out_masked", False):
         cargs.append("-out_masked")
-    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 [mrthreshold_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")))
-    if params.get("output") is not None:
-        cargs.append(params.get("output"))
+    cargs.append(execution.input_file(params.get("input", None)))
+    if params.get("output", None) is not None:
+        cargs.append(params.get("output", None))
     return cargs
 
 
@@ -327,16 +323,18 @@ def mrthreshold_outputs(
     """
     ret = MrthresholdOutputs(
         root=execution.output_file("."),
-        output=execution.output_file(params.get("output")) if (params.get("output") is not None) else None,
+        output=execution.output_file(params.get("output", None)) if (params.get("output") is not None) else None,
     )
     return ret
 
 
 def mrthreshold_execute(
     params: MrthresholdParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrthresholdOutputs:
     """
+    mrthreshold
+    
     Create bitwise image by thresholding image intensity.
     
     The threshold value to be applied can be determined in one of a number of
@@ -386,10 +384,12 @@ def mrthreshold_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrthresholdOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRTHRESHOLD_METADATA)
     params = execution.params(params)
     cargs = mrthreshold_cargs(params, execution)
     ret = mrthreshold_outputs(params, execution)
@@ -422,6 +422,8 @@ def mrthreshold(
     runner: Runner | None = None,
 ) -> MrthresholdOutputs:
     """
+    mrthreshold
+    
     Create bitwise image by thresholding image intensity.
     
     The threshold value to be applied can be determined in one of a number of
@@ -510,8 +512,6 @@ def mrthreshold(
     Returns:
         NamedTuple of outputs (described in `MrthresholdOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRTHRESHOLD_METADATA)
     params = mrthreshold_params(
         abs_=abs_,
         percentile=percentile,
@@ -535,15 +535,14 @@ def mrthreshold(
         input_=input_,
         output=output,
     )
-    return mrthreshold_execute(params, execution)
+    return mrthreshold_execute(params, runner)
 
 
 __all__ = [
     "MRTHRESHOLD_METADATA",
-    "MrthresholdConfigParameters",
     "MrthresholdOutputs",
-    "MrthresholdParameters",
     "mrthreshold",
     "mrthreshold_config_params",
+    "mrthreshold_execute",
     "mrthreshold_params",
 ]