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

niwrap_mrtrix/mrtrix/voxel2mesh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 VOXEL2MESH_METADATA = Metadata(
-    id="f74c43ba4b3142a027e629205b8aad59f7f8a496.boutiques",
+    id="85ff2c9f04efcbe2d5484d2e2ccd18c1577521ed.boutiques",
     name="voxel2mesh",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,34 @@ VOXEL2MESH_METADATA = Metadata(
 
 
 Voxel2meshConfigParameters = typing.TypedDict('Voxel2meshConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Voxel2meshConfigParametersTagged = typing.TypedDict('Voxel2meshConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Voxel2meshParameters = typing.TypedDict('Voxel2meshParameters', {
-    "__STYXTYPE__": typing.Literal["voxel2mesh"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/voxel2mesh"]],
+    "blocky": bool,
+    "threshold": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Voxel2meshConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+Voxel2meshParametersTagged = typing.TypedDict('Voxel2meshParametersTagged', {
+    "@type": typing.Literal["mrtrix/voxel2mesh"],
     "blocky": bool,
     "threshold": typing.NotRequired[float | None],
     "info": bool,
@@ -35,45 +55,12 @@ Voxel2meshParameters = typing.TypedDict('Voxel2meshParameters', {
     "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 {
-        "voxel2mesh": voxel2mesh_cargs,
-        "config": voxel2mesh_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 {
-        "voxel2mesh": voxel2mesh_outputs,
-    }.get(t)
 
 
 def voxel2mesh_config_params(
     key: str,
     value: str,
-) -> Voxel2meshConfigParameters:
+) -> Voxel2meshConfigParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +71,7 @@ def voxel2mesh_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -106,14 +93,14 @@ def voxel2mesh_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 Voxel2meshOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `voxel2mesh(...)`.
+    Output object returned when calling `Voxel2meshParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -134,7 +121,7 @@ def voxel2mesh_params(
     config: list[Voxel2meshConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Voxel2meshParameters:
+) -> Voxel2meshParametersTagged:
     """
     Build parameters.
     
@@ -161,7 +148,7 @@ def voxel2mesh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "voxel2mesh",
+        "@type": "mrtrix/voxel2mesh",
         "blocky": blocky,
         "info": info,
         "quiet": quiet,
@@ -196,34 +183,34 @@ def voxel2mesh_cargs(
     """
     cargs = []
     cargs.append("voxel2mesh")
-    if params.get("blocky"):
+    if params.get("blocky", False):
         cargs.append("-blocky")
-    if params.get("threshold") is not None:
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "-threshold",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    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 [voxel2mesh_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
 
 
@@ -242,16 +229,18 @@ def voxel2mesh_outputs(
     """
     ret = Voxel2meshOutputs(
         root=execution.output_file("."),
-        output=execution.output_file(params.get("output")),
+        output=execution.output_file(params.get("output", None)),
     )
     return ret
 
 
 def voxel2mesh_execute(
     params: Voxel2meshParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Voxel2meshOutputs:
     """
+    voxel2mesh
+    
     Generate a surface mesh representation from a voxel image.
     
     This command utilises the Marching Cubes algorithm to generate a polygonal
@@ -275,10 +264,12 @@ def voxel2mesh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Voxel2meshOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(VOXEL2MESH_METADATA)
     params = execution.params(params)
     cargs = voxel2mesh_cargs(params, execution)
     ret = voxel2mesh_outputs(params, execution)
@@ -302,6 +293,8 @@ def voxel2mesh(
     runner: Runner | None = None,
 ) -> Voxel2meshOutputs:
     """
+    voxel2mesh
+    
     Generate a surface mesh representation from a voxel image.
     
     This command utilises the Marching Cubes algorithm to generate a polygonal
@@ -346,8 +339,6 @@ def voxel2mesh(
     Returns:
         NamedTuple of outputs (described in `Voxel2meshOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(VOXEL2MESH_METADATA)
     params = voxel2mesh_params(
         blocky=blocky,
         threshold=threshold,
@@ -362,15 +353,14 @@ def voxel2mesh(
         input_=input_,
         output=output,
     )
-    return voxel2mesh_execute(params, execution)
+    return voxel2mesh_execute(params, runner)
 
 
 __all__ = [
     "VOXEL2MESH_METADATA",
-    "Voxel2meshConfigParameters",
     "Voxel2meshOutputs",
-    "Voxel2meshParameters",
     "voxel2mesh",
     "voxel2mesh_config_params",
+    "voxel2mesh_execute",
     "voxel2mesh_params",
 ]

niwrap_mrtrix/mrtrix/warp2metric.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 WARP2METRIC_METADATA = Metadata(
-    id="eefc64bdbf00cdc4394ee65fe8d05cf1a06e7ae9.boutiques",
+    id="6239916d39fe990e43c4b408dab7798207712e0c.boutiques",
     name="warp2metric",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,7 +14,13 @@ WARP2METRIC_METADATA = Metadata(
 
 
 Warp2metricFcParameters = typing.TypedDict('Warp2metricFcParameters', {
-    "__STYXTYPE__": typing.Literal["fc"],
+    "@type": typing.NotRequired[typing.Literal["fc"]],
+    "template_fixel_directory": InputPathType,
+    "output_fixel_directory": str,
+    "output_fixel_data": str,
+})
+Warp2metricFcParametersTagged = typing.TypedDict('Warp2metricFcParametersTagged', {
+    "@type": typing.Literal["fc"],
     "template_fixel_directory": InputPathType,
     "output_fixel_directory": str,
     "output_fixel_data": str,
@@ -22,14 +28,34 @@ Warp2metricFcParameters = typing.TypedDict('Warp2metricFcParameters', {
 
 
 Warp2metricConfigParameters = typing.TypedDict('Warp2metricConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Warp2metricConfigParametersTagged = typing.TypedDict('Warp2metricConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Warp2metricParameters = typing.TypedDict('Warp2metricParameters', {
-    "__STYXTYPE__": typing.Literal["warp2metric"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/warp2metric"]],
+    "fc": typing.NotRequired[Warp2metricFcParameters | None],
+    "jmat": typing.NotRequired[str | None],
+    "jdet": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Warp2metricConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "in": InputPathType,
+})
+Warp2metricParametersTagged = typing.TypedDict('Warp2metricParametersTagged', {
+    "@type": typing.Literal["mrtrix/warp2metric"],
     "fc": typing.NotRequired[Warp2metricFcParameters | None],
     "jmat": typing.NotRequired[str | None],
     "jdet": typing.NotRequired[str | None],
@@ -43,47 +69,13 @@ Warp2metricParameters = typing.TypedDict('Warp2metricParameters', {
     "version": bool,
     "in": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "warp2metric": warp2metric_cargs,
-        "fc": warp2metric_fc_cargs,
-        "config": warp2metric_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 {
-        "warp2metric": warp2metric_outputs,
-    }.get(t)
 
 
 def warp2metric_fc_params(
     template_fixel_directory: InputPathType,
     output_fixel_directory: str,
     output_fixel_data: str,
-) -> Warp2metricFcParameters:
+) -> Warp2metricFcParametersTagged:
     """
     Build parameters.
     
@@ -107,7 +99,7 @@ def warp2metric_fc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fc",
+        "@type": "fc",
         "template_fixel_directory": template_fixel_directory,
         "output_fixel_directory": output_fixel_directory,
         "output_fixel_data": output_fixel_data,
@@ -130,16 +122,16 @@ def warp2metric_fc_cargs(
     """
     cargs = []
     cargs.append("-fc")
-    cargs.append(execution.input_file(params.get("template_fixel_directory")))
-    cargs.append(params.get("output_fixel_directory"))
-    cargs.append(params.get("output_fixel_data"))
+    cargs.append(execution.input_file(params.get("template_fixel_directory", None)))
+    cargs.append(params.get("output_fixel_directory", None))
+    cargs.append(params.get("output_fixel_data", None))
     return cargs
 
 
 def warp2metric_config_params(
     key: str,
     value: str,
-) -> Warp2metricConfigParameters:
+) -> Warp2metricConfigParametersTagged:
     """
     Build parameters.
     
@@ -150,7 +142,7 @@ def warp2metric_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -172,14 +164,14 @@ def warp2metric_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 Warp2metricOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `warp2metric(...)`.
+    Output object returned when calling `Warp2metricParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -204,7 +196,7 @@ def warp2metric_params(
     config: list[Warp2metricConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Warp2metricParameters:
+) -> Warp2metricParametersTagged:
     """
     Build parameters.
     
@@ -234,7 +226,7 @@ def warp2metric_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "warp2metric",
+        "@type": "mrtrix/warp2metric",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -271,38 +263,38 @@ def warp2metric_cargs(
     """
     cargs = []
     cargs.append("warp2metric")
-    if params.get("fc") is not None:
-        cargs.extend(dyn_cargs(params.get("fc")["__STYXTYPE__"])(params.get("fc"), execution))
-    if params.get("jmat") is not None:
+    if params.get("fc", None) is not None:
+        cargs.extend(warp2metric_fc_cargs(params.get("fc", None), execution))
+    if params.get("jmat", None) is not None:
         cargs.extend([
             "-jmat",
-            params.get("jmat")
+            params.get("jmat", None)
         ])
-    if params.get("jdet") is not None:
+    if params.get("jdet", None) is not None:
         cargs.extend([
             "-jdet",
-            params.get("jdet")
+            params.get("jdet", None)
         ])
-    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 [warp2metric_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("in")))
+    cargs.append(execution.input_file(params.get("in", None)))
     return cargs
 
 
@@ -321,17 +313,19 @@ def warp2metric_outputs(
     """
     ret = Warp2metricOutputs(
         root=execution.output_file("."),
-        jmat=execution.output_file(params.get("jmat")) if (params.get("jmat") is not None) else None,
-        jdet=execution.output_file(params.get("jdet")) if (params.get("jdet") is not None) else None,
+        jmat=execution.output_file(params.get("jmat", None)) if (params.get("jmat") is not None) else None,
+        jdet=execution.output_file(params.get("jdet", None)) if (params.get("jdet") is not None) else None,
     )
     return ret
 
 
 def warp2metric_execute(
     params: Warp2metricParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Warp2metricOutputs:
     """
+    warp2metric
+    
     Compute fixel-wise or voxel-wise metrics from a 4D deformation field.
     
     
@@ -349,10 +343,12 @@ def warp2metric_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Warp2metricOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(WARP2METRIC_METADATA)
     params = execution.params(params)
     cargs = warp2metric_cargs(params, execution)
     ret = warp2metric_outputs(params, execution)
@@ -376,6 +372,8 @@ def warp2metric(
     runner: Runner | None = None,
 ) -> Warp2metricOutputs:
     """
+    warp2metric
+    
     Compute fixel-wise or voxel-wise metrics from a 4D deformation field.
     
     
@@ -417,8 +415,6 @@ def warp2metric(
     Returns:
         NamedTuple of outputs (described in `Warp2metricOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(WARP2METRIC_METADATA)
     params = warp2metric_params(
         fc=fc,
         jmat=jmat,
@@ -433,17 +429,15 @@ def warp2metric(
         version=version,
         in_=in_,
     )
-    return warp2metric_execute(params, execution)
+    return warp2metric_execute(params, runner)
 
 
 __all__ = [
     "WARP2METRIC_METADATA",
-    "Warp2metricConfigParameters",
-    "Warp2metricFcParameters",
     "Warp2metricOutputs",
-    "Warp2metricParameters",
     "warp2metric",
     "warp2metric_config_params",
+    "warp2metric_execute",
     "warp2metric_fc_params",
     "warp2metric_params",
 ]