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

niwrap_mrtrix/mrtrix/fixel2tsf.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIXEL2TSF_METADATA = Metadata(
-    id="e93f2c3f230efc9c99322e33cb8144f25fec561e.boutiques",
+    id="633221e2ad511634bae92b1740122dc5ec9d02cb.boutiques",
     name="fixel2tsf",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,34 @@ FIXEL2TSF_METADATA = Metadata(
 
 
 Fixel2tsfConfigParameters = typing.TypedDict('Fixel2tsfConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Fixel2tsfConfigParametersTagged = typing.TypedDict('Fixel2tsfConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Fixel2tsfParameters = typing.TypedDict('Fixel2tsfParameters', {
-    "__STYXTYPE__": typing.Literal["fixel2tsf"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/fixel2tsf"]],
+    "angle": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Fixel2tsfConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "fixel_in": InputPathType,
+    "tracks": InputPathType,
+    "tsf": str,
+})
+Fixel2tsfParametersTagged = typing.TypedDict('Fixel2tsfParametersTagged', {
+    "@type": typing.Literal["mrtrix/fixel2tsf"],
     "angle": typing.NotRequired[float | None],
     "info": bool,
     "quiet": bool,
@@ -35,45 +55,12 @@ Fixel2tsfParameters = typing.TypedDict('Fixel2tsfParameters', {
     "tracks": InputPathType,
     "tsf": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fixel2tsf": fixel2tsf_cargs,
-        "config": fixel2tsf_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 {
-        "fixel2tsf": fixel2tsf_outputs,
-    }.get(t)
 
 
 def fixel2tsf_config_params(
     key: str,
     value: str,
-) -> Fixel2tsfConfigParameters:
+) -> Fixel2tsfConfigParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +71,7 @@ def fixel2tsf_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -106,14 +93,14 @@ def fixel2tsf_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 Fixel2tsfOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fixel2tsf(...)`.
+    Output object returned when calling `Fixel2tsfParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -134,7 +121,7 @@ def fixel2tsf_params(
     config: list[Fixel2tsfConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Fixel2tsfParameters:
+) -> Fixel2tsfParametersTagged:
     """
     Build parameters.
     
@@ -160,7 +147,7 @@ def fixel2tsf_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fixel2tsf",
+        "@type": "mrtrix/fixel2tsf",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -195,33 +182,33 @@ def fixel2tsf_cargs(
     """
     cargs = []
     cargs.append("fixel2tsf")
-    if params.get("angle") is not None:
+    if params.get("angle", None) is not None:
         cargs.extend([
             "-angle",
-            str(params.get("angle"))
+            str(params.get("angle", 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 [fixel2tsf_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("fixel_in")))
-    cargs.append(execution.input_file(params.get("tracks")))
-    cargs.append(params.get("tsf"))
+    cargs.append(execution.input_file(params.get("fixel_in", None)))
+    cargs.append(execution.input_file(params.get("tracks", None)))
+    cargs.append(params.get("tsf", None))
     return cargs
 
 
@@ -240,16 +227,18 @@ def fixel2tsf_outputs(
     """
     ret = Fixel2tsfOutputs(
         root=execution.output_file("."),
-        tsf=execution.output_file(params.get("tsf")),
+        tsf=execution.output_file(params.get("tsf", None)),
     )
     return ret
 
 
 def fixel2tsf_execute(
     params: Fixel2tsfParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Fixel2tsfOutputs:
     """
+    fixel2tsf
+    
     Map fixel values to a track scalar file based on an input tractogram.
     
     This command is useful for visualising all brain fixels (e.g. the output
@@ -265,10 +254,12 @@ def fixel2tsf_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Fixel2tsfOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXEL2TSF_METADATA)
     params = execution.params(params)
     cargs = fixel2tsf_cargs(params, execution)
     ret = fixel2tsf_outputs(params, execution)
@@ -292,6 +283,8 @@ def fixel2tsf(
     runner: Runner | None = None,
 ) -> Fixel2tsfOutputs:
     """
+    fixel2tsf
+    
     Map fixel values to a track scalar file based on an input tractogram.
     
     This command is useful for visualising all brain fixels (e.g. the output
@@ -327,8 +320,6 @@ def fixel2tsf(
     Returns:
         NamedTuple of outputs (described in `Fixel2tsfOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FIXEL2TSF_METADATA)
     params = fixel2tsf_params(
         angle=angle,
         info=info,
@@ -343,15 +334,14 @@ def fixel2tsf(
         tracks=tracks,
         tsf=tsf,
     )
-    return fixel2tsf_execute(params, execution)
+    return fixel2tsf_execute(params, runner)
 
 
 __all__ = [
     "FIXEL2TSF_METADATA",
-    "Fixel2tsfConfigParameters",
     "Fixel2tsfOutputs",
-    "Fixel2tsfParameters",
     "fixel2tsf",
     "fixel2tsf_config_params",
+    "fixel2tsf_execute",
     "fixel2tsf_params",
 ]

niwrap_mrtrix/mrtrix/fixel2voxel.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIXEL2VOXEL_METADATA = Metadata(
-    id="0afc45451f7f27c8cd742d2496ae81b774ab9243.boutiques",
+    id="0e517d0eb23dea1741bca5bac37fc1918bda4919.boutiques",
     name="fixel2voxel",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,36 @@ FIXEL2VOXEL_METADATA = Metadata(
 
 
 Fixel2voxelConfigParameters = typing.TypedDict('Fixel2voxelConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Fixel2voxelConfigParametersTagged = typing.TypedDict('Fixel2voxelConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Fixel2voxelParameters = typing.TypedDict('Fixel2voxelParameters', {
-    "__STYXTYPE__": typing.Literal["fixel2voxel"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/fixel2voxel"]],
+    "number": typing.NotRequired[int | None],
+    "fill": typing.NotRequired[float | None],
+    "weighted": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Fixel2voxelConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "fixel_in": InputPathType,
+    "operation": str,
+    "image_out": str,
+})
+Fixel2voxelParametersTagged = typing.TypedDict('Fixel2voxelParametersTagged', {
+    "@type": typing.Literal["mrtrix/fixel2voxel"],
     "number": typing.NotRequired[int | None],
     "fill": typing.NotRequired[float | None],
     "weighted": typing.NotRequired[InputPathType | None],
@@ -37,45 +59,12 @@ Fixel2voxelParameters = typing.TypedDict('Fixel2voxelParameters', {
     "operation": str,
     "image_out": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fixel2voxel": fixel2voxel_cargs,
-        "config": fixel2voxel_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 {
-        "fixel2voxel": fixel2voxel_outputs,
-    }.get(t)
 
 
 def fixel2voxel_config_params(
     key: str,
     value: str,
-) -> Fixel2voxelConfigParameters:
+) -> Fixel2voxelConfigParametersTagged:
     """
     Build parameters.
     
@@ -86,7 +75,7 @@ def fixel2voxel_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -108,14 +97,14 @@ def fixel2voxel_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 Fixel2voxelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fixel2voxel(...)`.
+    Output object returned when calling `Fixel2voxelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -138,7 +127,7 @@ def fixel2voxel_params(
     config: list[Fixel2voxelConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Fixel2voxelParameters:
+) -> Fixel2voxelParametersTagged:
     """
     Build parameters.
     
@@ -170,7 +159,7 @@ def fixel2voxel_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fixel2voxel",
+        "@type": "mrtrix/fixel2voxel",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -209,43 +198,43 @@ def fixel2voxel_cargs(
     """
     cargs = []
     cargs.append("fixel2voxel")
-    if params.get("number") is not None:
+    if params.get("number", None) is not None:
         cargs.extend([
             "-number",
-            str(params.get("number"))
+            str(params.get("number", None))
         ])
-    if params.get("fill") is not None:
+    if params.get("fill", None) is not None:
         cargs.extend([
             "-fill",
-            str(params.get("fill"))
+            str(params.get("fill", None))
         ])
-    if params.get("weighted") is not None:
+    if params.get("weighted", None) is not None:
         cargs.extend([
             "-weighted",
-            execution.input_file(params.get("weighted"))
+            execution.input_file(params.get("weighted", 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 [fixel2voxel_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("fixel_in")))
-    cargs.append(params.get("operation"))
-    cargs.append(params.get("image_out"))
+    cargs.append(execution.input_file(params.get("fixel_in", None)))
+    cargs.append(params.get("operation", None))
+    cargs.append(params.get("image_out", None))
     return cargs
 
 
@@ -264,16 +253,18 @@ def fixel2voxel_outputs(
     """
     ret = Fixel2voxelOutputs(
         root=execution.output_file("."),
-        image_out=execution.output_file(params.get("image_out")),
+        image_out=execution.output_file(params.get("image_out", None)),
     )
     return ret
 
 
 def fixel2voxel_execute(
     params: Fixel2voxelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Fixel2voxelOutputs:
     """
+    fixel2voxel
+    
     Convert a fixel-based sparse-data image into some form of scalar image.
     
     Fixel data can be reduced to voxel data in a number of ways:
@@ -312,10 +303,12 @@ def fixel2voxel_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Fixel2voxelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXEL2VOXEL_METADATA)
     params = execution.params(params)
     cargs = fixel2voxel_cargs(params, execution)
     ret = fixel2voxel_outputs(params, execution)
@@ -341,6 +334,8 @@ def fixel2voxel(
     runner: Runner | None = None,
 ) -> Fixel2voxelOutputs:
     """
+    fixel2voxel
+    
     Convert a fixel-based sparse-data image into some form of scalar image.
     
     Fixel data can be reduced to voxel data in a number of ways:
@@ -405,8 +400,6 @@ def fixel2voxel(
     Returns:
         NamedTuple of outputs (described in `Fixel2voxelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FIXEL2VOXEL_METADATA)
     params = fixel2voxel_params(
         number=number,
         fill=fill,
@@ -423,15 +416,14 @@ def fixel2voxel(
         operation=operation,
         image_out=image_out,
     )
-    return fixel2voxel_execute(params, execution)
+    return fixel2voxel_execute(params, runner)
 
 
 __all__ = [
     "FIXEL2VOXEL_METADATA",
-    "Fixel2voxelConfigParameters",
     "Fixel2voxelOutputs",
-    "Fixel2voxelParameters",
     "fixel2voxel",
     "fixel2voxel_config_params",
+    "fixel2voxel_execute",
     "fixel2voxel_params",
 ]