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

niwrap_mrtrix/mrtrix/tck2fixel.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TCK2FIXEL_METADATA = Metadata(
-    id="7fb114318f85708b8964636c42efd5059fa77887.boutiques",
+    id="90f8734af004cf66512561b61fbe57f5bc2f690a.boutiques",
     name="tck2fixel",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,35 @@ TCK2FIXEL_METADATA = Metadata(
 
 
 Tck2fixelConfigParameters = typing.TypedDict('Tck2fixelConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Tck2fixelConfigParametersTagged = typing.TypedDict('Tck2fixelConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Tck2fixelParameters = typing.TypedDict('Tck2fixelParameters', {
-    "__STYXTYPE__": typing.Literal["tck2fixel"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/tck2fixel"]],
+    "angle": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Tck2fixelConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "tracks": InputPathType,
+    "fixel_folder_in": InputPathType,
+    "fixel_folder_out": str,
+    "fixel_data_out": str,
+})
+Tck2fixelParametersTagged = typing.TypedDict('Tck2fixelParametersTagged', {
+    "@type": typing.Literal["mrtrix/tck2fixel"],
     "angle": typing.NotRequired[float | None],
     "info": bool,
     "quiet": bool,
@@ -36,44 +57,12 @@ Tck2fixelParameters = typing.TypedDict('Tck2fixelParameters', {
     "fixel_folder_out": str,
     "fixel_data_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 {
-        "tck2fixel": tck2fixel_cargs,
-        "config": tck2fixel_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 tck2fixel_config_params(
     key: str,
     value: str,
-) -> Tck2fixelConfigParameters:
+) -> Tck2fixelConfigParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +73,7 @@ def tck2fixel_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -106,14 +95,14 @@ def tck2fixel_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 Tck2fixelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `tck2fixel(...)`.
+    Output object returned when calling `Tck2fixelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -133,7 +122,7 @@ def tck2fixel_params(
     config: list[Tck2fixelConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Tck2fixelParameters:
+) -> Tck2fixelParametersTagged:
     """
     Build parameters.
     
@@ -162,7 +151,7 @@ def tck2fixel_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tck2fixel",
+        "@type": "mrtrix/tck2fixel",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -198,34 +187,34 @@ def tck2fixel_cargs(
     """
     cargs = []
     cargs.append("tck2fixel")
-    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 [tck2fixel_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("tracks")))
-    cargs.append(execution.input_file(params.get("fixel_folder_in")))
-    cargs.append(params.get("fixel_folder_out"))
-    cargs.append(params.get("fixel_data_out"))
+    cargs.append(execution.input_file(params.get("tracks", None)))
+    cargs.append(execution.input_file(params.get("fixel_folder_in", None)))
+    cargs.append(params.get("fixel_folder_out", None))
+    cargs.append(params.get("fixel_data_out", None))
     return cargs
 
 
@@ -250,9 +239,11 @@ def tck2fixel_outputs(
 
 def tck2fixel_execute(
     params: Tck2fixelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Tck2fixelOutputs:
     """
+    tck2fixel
+    
     Compute a fixel TDI map from a tractogram.
     
     
@@ -267,10 +258,12 @@ def tck2fixel_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Tck2fixelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TCK2FIXEL_METADATA)
     params = execution.params(params)
     cargs = tck2fixel_cargs(params, execution)
     ret = tck2fixel_outputs(params, execution)
@@ -295,6 +288,8 @@ def tck2fixel(
     runner: Runner | None = None,
 ) -> Tck2fixelOutputs:
     """
+    tck2fixel
+    
     Compute a fixel TDI map from a tractogram.
     
     
@@ -332,8 +327,6 @@ def tck2fixel(
     Returns:
         NamedTuple of outputs (described in `Tck2fixelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TCK2FIXEL_METADATA)
     params = tck2fixel_params(
         angle=angle,
         info=info,
@@ -349,15 +342,14 @@ def tck2fixel(
         fixel_folder_out=fixel_folder_out,
         fixel_data_out=fixel_data_out,
     )
-    return tck2fixel_execute(params, execution)
+    return tck2fixel_execute(params, runner)
 
 
 __all__ = [
     "TCK2FIXEL_METADATA",
-    "Tck2fixelConfigParameters",
     "Tck2fixelOutputs",
-    "Tck2fixelParameters",
     "tck2fixel",
     "tck2fixel_config_params",
+    "tck2fixel_execute",
     "tck2fixel_params",
 ]

niwrap_mrtrix/mrtrix/tckconvert.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TCKCONVERT_METADATA = Metadata(
-    id="6f2654c4a12a998f581d8c09fe91e9d32503db7a.boutiques",
+    id="55a4f5691d675bdf7129499cb50a199b880d7c7a.boutiques",
     name="tckconvert",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,26 +14,62 @@ TCKCONVERT_METADATA = Metadata(
 
 
 TckconvertConfigParameters = typing.TypedDict('TckconvertConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+TckconvertConfigParametersTagged = typing.TypedDict('TckconvertConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 TckconvertVariousStringParameters = typing.TypedDict('TckconvertVariousStringParameters', {
-    "__STYXTYPE__": typing.Literal["VariousString"],
+    "@type": typing.NotRequired[typing.Literal["VariousString"]],
+    "obj": str,
+})
+TckconvertVariousStringParametersTagged = typing.TypedDict('TckconvertVariousStringParametersTagged', {
+    "@type": typing.Literal["VariousString"],
     "obj": str,
 })
 
 
 TckconvertVariousFileParameters = typing.TypedDict('TckconvertVariousFileParameters', {
-    "__STYXTYPE__": typing.Literal["VariousFile"],
+    "@type": typing.NotRequired[typing.Literal["VariousFile"]],
+    "obj": InputPathType,
+})
+TckconvertVariousFileParametersTagged = typing.TypedDict('TckconvertVariousFileParametersTagged', {
+    "@type": typing.Literal["VariousFile"],
     "obj": InputPathType,
 })
 
 
 TckconvertParameters = typing.TypedDict('TckconvertParameters', {
-    "__STYXTYPE__": typing.Literal["tckconvert"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/tckconvert"]],
+    "scanner2voxel": typing.NotRequired[InputPathType | None],
+    "scanner2image": typing.NotRequired[InputPathType | None],
+    "voxel2scanner": typing.NotRequired[InputPathType | None],
+    "image2scanner": typing.NotRequired[InputPathType | None],
+    "sides": typing.NotRequired[int | None],
+    "increment": typing.NotRequired[int | None],
+    "dec": bool,
+    "radius": typing.NotRequired[float | None],
+    "ascii": bool,
+    "binary": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TckconvertConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": typing.Union[TckconvertVariousStringParametersTagged, TckconvertVariousFileParametersTagged],
+    "output": str,
+})
+TckconvertParametersTagged = typing.TypedDict('TckconvertParametersTagged', {
+    "@type": typing.Literal["mrtrix/tckconvert"],
     "scanner2voxel": typing.NotRequired[InputPathType | None],
     "scanner2image": typing.NotRequired[InputPathType | None],
     "voxel2scanner": typing.NotRequired[InputPathType | None],
@@ -52,12 +88,12 @@ TckconvertParameters = typing.TypedDict('TckconvertParameters', {
     "config": typing.NotRequired[list[TckconvertConfigParameters] | None],
     "help": bool,
     "version": bool,
-    "input": typing.Union[TckconvertVariousStringParameters, TckconvertVariousFileParameters],
+    "input": typing.Union[TckconvertVariousStringParametersTagged, TckconvertVariousFileParametersTagged],
     "output": str,
 })
 
 
-def dyn_cargs(
+def tckconvert_input_cargs_dyn_fn(
     t: str,
 ) -> typing.Any:
     """
@@ -69,14 +105,12 @@ def dyn_cargs(
         Build cargs function.
     """
     return {
-        "tckconvert": tckconvert_cargs,
-        "config": tckconvert_config_cargs,
         "VariousString": tckconvert_various_string_cargs,
         "VariousFile": tckconvert_various_file_cargs,
     }.get(t)
 
 
-def dyn_outputs(
+def tckconvert_input_outputs_dyn_fn(
     t: str,
 ) -> typing.Any:
     """
@@ -88,14 +122,13 @@ def dyn_outputs(
         Build outputs function.
     """
     return {
-        "tckconvert": tckconvert_outputs,
     }.get(t)
 
 
 def tckconvert_config_params(
     key: str,
     value: str,
-) -> TckconvertConfigParameters:
+) -> TckconvertConfigParametersTagged:
     """
     Build parameters.
     
@@ -106,7 +139,7 @@ def tckconvert_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -128,14 +161,14 @@ def tckconvert_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
 
 
 def tckconvert_various_string_params(
     obj: str,
-) -> TckconvertVariousStringParameters:
+) -> TckconvertVariousStringParametersTagged:
     """
     Build parameters.
     
@@ -145,7 +178,7 @@ def tckconvert_various_string_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "VariousString",
+        "@type": "VariousString",
         "obj": obj,
     }
     return params
@@ -165,13 +198,13 @@ def tckconvert_various_string_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append(params.get("obj"))
+    cargs.append(params.get("obj", None))
     return cargs
 
 
 def tckconvert_various_file_params(
     obj: InputPathType,
-) -> TckconvertVariousFileParameters:
+) -> TckconvertVariousFileParametersTagged:
     """
     Build parameters.
     
@@ -181,7 +214,7 @@ def tckconvert_various_file_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "VariousFile",
+        "@type": "VariousFile",
         "obj": obj,
     }
     return params
@@ -201,13 +234,13 @@ def tckconvert_various_file_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append(execution.input_file(params.get("obj")))
+    cargs.append(execution.input_file(params.get("obj", None)))
     return cargs
 
 
 class TckconvertOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `tckconvert(...)`.
+    Output object returned when calling `TckconvertParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -216,7 +249,7 @@ class TckconvertOutputs(typing.NamedTuple):
 
 
 def tckconvert_params(
-    input_: typing.Union[TckconvertVariousStringParameters, TckconvertVariousFileParameters],
+    input_: typing.Union[TckconvertVariousStringParametersTagged, TckconvertVariousFileParametersTagged],
     output: str,
     scanner2voxel: InputPathType | None = None,
     scanner2image: InputPathType | None = None,
@@ -236,7 +269,7 @@ def tckconvert_params(
     config: list[TckconvertConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> TckconvertParameters:
+) -> TckconvertParametersTagged:
     """
     Build parameters.
     
@@ -277,7 +310,7 @@ def tckconvert_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tckconvert",
+        "@type": "mrtrix/tckconvert",
         "dec": dec,
         "ascii": ascii_,
         "binary": binary,
@@ -326,68 +359,68 @@ def tckconvert_cargs(
     """
     cargs = []
     cargs.append("tckconvert")
-    if params.get("scanner2voxel") is not None:
+    if params.get("scanner2voxel", None) is not None:
         cargs.extend([
             "-scanner2voxel",
-            execution.input_file(params.get("scanner2voxel"))
+            execution.input_file(params.get("scanner2voxel", None))
         ])
-    if params.get("scanner2image") is not None:
+    if params.get("scanner2image", None) is not None:
         cargs.extend([
             "-scanner2image",
-            execution.input_file(params.get("scanner2image"))
+            execution.input_file(params.get("scanner2image", None))
         ])
-    if params.get("voxel2scanner") is not None:
+    if params.get("voxel2scanner", None) is not None:
         cargs.extend([
             "-voxel2scanner",
-            execution.input_file(params.get("voxel2scanner"))
+            execution.input_file(params.get("voxel2scanner", None))
         ])
-    if params.get("image2scanner") is not None:
+    if params.get("image2scanner", None) is not None:
         cargs.extend([
             "-image2scanner",
-            execution.input_file(params.get("image2scanner"))
+            execution.input_file(params.get("image2scanner", None))
         ])
-    if params.get("sides") is not None:
+    if params.get("sides", None) is not None:
         cargs.extend([
             "-sides",
-            str(params.get("sides"))
+            str(params.get("sides", None))
         ])
-    if params.get("increment") is not None:
+    if params.get("increment", None) is not None:
         cargs.extend([
             "-increment",
-            str(params.get("increment"))
+            str(params.get("increment", None))
         ])
-    if params.get("dec"):
+    if params.get("dec", False):
         cargs.append("-dec")
-    if params.get("radius") is not None:
+    if params.get("radius", None) is not None:
         cargs.extend([
             "-radius",
-            str(params.get("radius"))
+            str(params.get("radius", None))
         ])
-    if params.get("ascii"):
+    if params.get("ascii", False):
         cargs.append("-ascii")
-    if params.get("binary"):
+    if params.get("binary", False):
         cargs.append("-binary")
-    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 [tckconvert_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.extend(dyn_cargs(params.get("input")["__STYXTYPE__"])(params.get("input"), execution))
-    cargs.append(params.get("output"))
+    cargs.extend(tckconvert_input_cargs_dyn_fn(params.get("input", None)["@type"])(params.get("input", None), execution))
+    cargs.append(params.get("output", None))
     return cargs
 
 
@@ -406,16 +439,18 @@ def tckconvert_outputs(
     """
     ret = TckconvertOutputs(
         root=execution.output_file("."),
-        output=execution.output_file(params.get("output")),
+        output=execution.output_file(params.get("output", None)),
     )
     return ret
 
 
 def tckconvert_execute(
     params: TckconvertParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TckconvertOutputs:
     """
+    tckconvert
+    
     Convert between different track file formats.
     
     The program currently supports MRtrix .tck files (input/output), ascii text
@@ -442,10 +477,12 @@ def tckconvert_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TckconvertOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TCKCONVERT_METADATA)
     params = execution.params(params)
     cargs = tckconvert_cargs(params, execution)
     ret = tckconvert_outputs(params, execution)
@@ -454,7 +491,7 @@ def tckconvert_execute(
 
 
 def tckconvert(
-    input_: typing.Union[TckconvertVariousStringParameters, TckconvertVariousFileParameters],
+    input_: typing.Union[TckconvertVariousStringParametersTagged, TckconvertVariousFileParametersTagged],
     output: str,
     scanner2voxel: InputPathType | None = None,
     scanner2image: InputPathType | None = None,
@@ -477,6 +514,8 @@ def tckconvert(
     runner: Runner | None = None,
 ) -> TckconvertOutputs:
     """
+    tckconvert
+    
     Convert between different track file formats.
     
     The program currently supports MRtrix .tck files (input/output), ascii text
@@ -538,8 +577,6 @@ def tckconvert(
     Returns:
         NamedTuple of outputs (described in `TckconvertOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TCKCONVERT_METADATA)
     params = tckconvert_params(
         scanner2voxel=scanner2voxel,
         scanner2image=scanner2image,
@@ -562,18 +599,15 @@ def tckconvert(
         input_=input_,
         output=output,
     )
-    return tckconvert_execute(params, execution)
+    return tckconvert_execute(params, runner)
 
 
 __all__ = [
     "TCKCONVERT_METADATA",
-    "TckconvertConfigParameters",
     "TckconvertOutputs",
-    "TckconvertParameters",
-    "TckconvertVariousFileParameters",
-    "TckconvertVariousStringParameters",
     "tckconvert",
     "tckconvert_config_params",
+    "tckconvert_execute",
     "tckconvert_params",
     "tckconvert_various_file_params",
     "tckconvert_various_string_params",