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

niwrap_mrtrix/mrtrix/fixel2peaks.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIXEL2PEAKS_METADATA = Metadata(
-    id="5e3b8600a7924403d728fedc4abecdb6bc9848fe.boutiques",
+    id="0d92be2b2e1ceff15fcfee87e64154e86fddb5a8.boutiques",
     name="fixel2peaks",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,26 +14,54 @@ FIXEL2PEAKS_METADATA = Metadata(
 
 
 Fixel2peaksConfigParameters = typing.TypedDict('Fixel2peaksConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Fixel2peaksConfigParametersTagged = typing.TypedDict('Fixel2peaksConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Fixel2peaksVariousStringParameters = typing.TypedDict('Fixel2peaksVariousStringParameters', {
-    "__STYXTYPE__": typing.Literal["VariousString"],
+    "@type": typing.NotRequired[typing.Literal["VariousString"]],
+    "obj": str,
+})
+Fixel2peaksVariousStringParametersTagged = typing.TypedDict('Fixel2peaksVariousStringParametersTagged', {
+    "@type": typing.Literal["VariousString"],
     "obj": str,
 })
 
 
 Fixel2peaksVariousFileParameters = typing.TypedDict('Fixel2peaksVariousFileParameters', {
-    "__STYXTYPE__": typing.Literal["VariousFile"],
+    "@type": typing.NotRequired[typing.Literal["VariousFile"]],
+    "obj": InputPathType,
+})
+Fixel2peaksVariousFileParametersTagged = typing.TypedDict('Fixel2peaksVariousFileParametersTagged', {
+    "@type": typing.Literal["VariousFile"],
     "obj": InputPathType,
 })
 
 
 Fixel2peaksParameters = typing.TypedDict('Fixel2peaksParameters', {
-    "__STYXTYPE__": typing.Literal["fixel2peaks"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/fixel2peaks"]],
+    "number": typing.NotRequired[int | None],
+    "nan": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Fixel2peaksConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "in": typing.Union[Fixel2peaksVariousStringParametersTagged, Fixel2peaksVariousFileParametersTagged],
+    "out": str,
+})
+Fixel2peaksParametersTagged = typing.TypedDict('Fixel2peaksParametersTagged', {
+    "@type": typing.Literal["mrtrix/fixel2peaks"],
     "number": typing.NotRequired[int | None],
     "nan": bool,
     "info": bool,
@@ -44,12 +72,12 @@ Fixel2peaksParameters = typing.TypedDict('Fixel2peaksParameters', {
     "config": typing.NotRequired[list[Fixel2peaksConfigParameters] | None],
     "help": bool,
     "version": bool,
-    "in": typing.Union[Fixel2peaksVariousStringParameters, Fixel2peaksVariousFileParameters],
+    "in": typing.Union[Fixel2peaksVariousStringParametersTagged, Fixel2peaksVariousFileParametersTagged],
     "out": str,
 })
 
 
-def dyn_cargs(
+def fixel2peaks_in_cargs_dyn_fn(
     t: str,
 ) -> typing.Any:
     """
@@ -61,14 +89,12 @@ def dyn_cargs(
         Build cargs function.
     """
     return {
-        "fixel2peaks": fixel2peaks_cargs,
-        "config": fixel2peaks_config_cargs,
         "VariousString": fixel2peaks_various_string_cargs,
         "VariousFile": fixel2peaks_various_file_cargs,
     }.get(t)
 
 
-def dyn_outputs(
+def fixel2peaks_in_outputs_dyn_fn(
     t: str,
 ) -> typing.Any:
     """
@@ -80,14 +106,13 @@ def dyn_outputs(
         Build outputs function.
     """
     return {
-        "fixel2peaks": fixel2peaks_outputs,
     }.get(t)
 
 
 def fixel2peaks_config_params(
     key: str,
     value: str,
-) -> Fixel2peaksConfigParameters:
+) -> Fixel2peaksConfigParametersTagged:
     """
     Build parameters.
     
@@ -98,7 +123,7 @@ def fixel2peaks_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -120,14 +145,14 @@ def fixel2peaks_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 fixel2peaks_various_string_params(
     obj: str,
-) -> Fixel2peaksVariousStringParameters:
+) -> Fixel2peaksVariousStringParametersTagged:
     """
     Build parameters.
     
@@ -137,7 +162,7 @@ def fixel2peaks_various_string_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "VariousString",
+        "@type": "VariousString",
         "obj": obj,
     }
     return params
@@ -157,13 +182,13 @@ def fixel2peaks_various_string_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append(params.get("obj"))
+    cargs.append(params.get("obj", None))
     return cargs
 
 
 def fixel2peaks_various_file_params(
     obj: InputPathType,
-) -> Fixel2peaksVariousFileParameters:
+) -> Fixel2peaksVariousFileParametersTagged:
     """
     Build parameters.
     
@@ -173,7 +198,7 @@ def fixel2peaks_various_file_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "VariousFile",
+        "@type": "VariousFile",
         "obj": obj,
     }
     return params
@@ -193,13 +218,13 @@ def fixel2peaks_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 Fixel2peaksOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fixel2peaks(...)`.
+    Output object returned when calling `Fixel2peaksParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -208,7 +233,7 @@ class Fixel2peaksOutputs(typing.NamedTuple):
 
 
 def fixel2peaks_params(
-    in_: typing.Union[Fixel2peaksVariousStringParameters, Fixel2peaksVariousFileParameters],
+    in_: typing.Union[Fixel2peaksVariousStringParametersTagged, Fixel2peaksVariousFileParametersTagged],
     out: str,
     number: int | None = None,
     nan: bool = False,
@@ -220,7 +245,7 @@ def fixel2peaks_params(
     config: list[Fixel2peaksConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Fixel2peaksParameters:
+) -> Fixel2peaksParametersTagged:
     """
     Build parameters.
     
@@ -246,7 +271,7 @@ def fixel2peaks_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fixel2peaks",
+        "@type": "mrtrix/fixel2peaks",
         "nan": nan,
         "info": info,
         "quiet": quiet,
@@ -281,34 +306,34 @@ def fixel2peaks_cargs(
     """
     cargs = []
     cargs.append("fixel2peaks")
-    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("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 [fixel2peaks_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("in")["__STYXTYPE__"])(params.get("in"), execution))
-    cargs.append(params.get("out"))
+    cargs.extend(fixel2peaks_in_cargs_dyn_fn(params.get("in", None)["@type"])(params.get("in", None), execution))
+    cargs.append(params.get("out", None))
     return cargs
 
 
@@ -327,16 +352,18 @@ def fixel2peaks_outputs(
     """
     ret = Fixel2peaksOutputs(
         root=execution.output_file("."),
-        out=execution.output_file(params.get("out")),
+        out=execution.output_file(params.get("out", None)),
     )
     return ret
 
 
 def fixel2peaks_execute(
     params: Fixel2peaksParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Fixel2peaksOutputs:
     """
+    fixel2peaks
+    
     Convert data in the fixel directory format into a 4D image of 3-vectors.
     
     If a fixel data file is provided as input, then the 3-vectors in the output
@@ -354,10 +381,12 @@ def fixel2peaks_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Fixel2peaksOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXEL2PEAKS_METADATA)
     params = execution.params(params)
     cargs = fixel2peaks_cargs(params, execution)
     ret = fixel2peaks_outputs(params, execution)
@@ -366,7 +395,7 @@ def fixel2peaks_execute(
 
 
 def fixel2peaks(
-    in_: typing.Union[Fixel2peaksVariousStringParameters, Fixel2peaksVariousFileParameters],
+    in_: typing.Union[Fixel2peaksVariousStringParametersTagged, Fixel2peaksVariousFileParametersTagged],
     out: str,
     number: int | None = None,
     nan: bool = False,
@@ -381,6 +410,8 @@ def fixel2peaks(
     runner: Runner | None = None,
 ) -> Fixel2peaksOutputs:
     """
+    fixel2peaks
+    
     Convert data in the fixel directory format into a 4D image of 3-vectors.
     
     If a fixel data file is provided as input, then the 3-vectors in the output
@@ -418,8 +449,6 @@ def fixel2peaks(
     Returns:
         NamedTuple of outputs (described in `Fixel2peaksOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FIXEL2PEAKS_METADATA)
     params = fixel2peaks_params(
         number=number,
         nan=nan,
@@ -434,18 +463,15 @@ def fixel2peaks(
         in_=in_,
         out=out,
     )
-    return fixel2peaks_execute(params, execution)
+    return fixel2peaks_execute(params, runner)
 
 
 __all__ = [
     "FIXEL2PEAKS_METADATA",
-    "Fixel2peaksConfigParameters",
     "Fixel2peaksOutputs",
-    "Fixel2peaksParameters",
-    "Fixel2peaksVariousFileParameters",
-    "Fixel2peaksVariousStringParameters",
     "fixel2peaks",
     "fixel2peaks_config_params",
+    "fixel2peaks_execute",
     "fixel2peaks_params",
     "fixel2peaks_various_file_params",
     "fixel2peaks_various_string_params",

niwrap_mrtrix/mrtrix/fixel2sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIXEL2SH_METADATA = Metadata(
-    id="456492282209c486d341a6ea246caa0ca9702172.boutiques",
+    id="8c1f4206ebf1611310a84b3b1b1527e0a6b154c6.boutiques",
     name="fixel2sh",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,33 @@ FIXEL2SH_METADATA = Metadata(
 
 
 Fixel2shConfigParameters = typing.TypedDict('Fixel2shConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Fixel2shConfigParametersTagged = typing.TypedDict('Fixel2shConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Fixel2shParameters = typing.TypedDict('Fixel2shParameters', {
-    "__STYXTYPE__": typing.Literal["fixel2sh"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/fixel2sh"]],
+    "lmax": typing.NotRequired[int | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Fixel2shConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "fixel_in": InputPathType,
+    "sh_out": str,
+})
+Fixel2shParametersTagged = typing.TypedDict('Fixel2shParametersTagged', {
+    "@type": typing.Literal["mrtrix/fixel2sh"],
     "lmax": typing.NotRequired[int | None],
     "info": bool,
     "quiet": bool,
@@ -34,45 +53,12 @@ Fixel2shParameters = typing.TypedDict('Fixel2shParameters', {
     "fixel_in": InputPathType,
     "sh_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 {
-        "fixel2sh": fixel2sh_cargs,
-        "config": fixel2sh_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 {
-        "fixel2sh": fixel2sh_outputs,
-    }.get(t)
 
 
 def fixel2sh_config_params(
     key: str,
     value: str,
-) -> Fixel2shConfigParameters:
+) -> Fixel2shConfigParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +69,7 @@ def fixel2sh_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -105,14 +91,14 @@ def fixel2sh_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 Fixel2shOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fixel2sh(...)`.
+    Output object returned when calling `Fixel2shParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -132,7 +118,7 @@ def fixel2sh_params(
     config: list[Fixel2shConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Fixel2shParameters:
+) -> Fixel2shParametersTagged:
     """
     Build parameters.
     
@@ -156,7 +142,7 @@ def fixel2sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fixel2sh",
+        "@type": "mrtrix/fixel2sh",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -190,32 +176,32 @@ def fixel2sh_cargs(
     """
     cargs = []
     cargs.append("fixel2sh")
-    if params.get("lmax") is not None:
+    if params.get("lmax", None) is not None:
         cargs.extend([
             "-lmax",
-            str(params.get("lmax"))
+            str(params.get("lmax", 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 [fixel2sh_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("sh_out"))
+    cargs.append(execution.input_file(params.get("fixel_in", None)))
+    cargs.append(params.get("sh_out", None))
     return cargs
 
 
@@ -234,16 +220,18 @@ def fixel2sh_outputs(
     """
     ret = Fixel2shOutputs(
         root=execution.output_file("."),
-        sh_out=execution.output_file(params.get("sh_out")),
+        sh_out=execution.output_file(params.get("sh_out", None)),
     )
     return ret
 
 
 def fixel2sh_execute(
     params: Fixel2shParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Fixel2shOutputs:
     """
+    fixel2sh
+    
     Convert a fixel-based sparse-data image into an spherical harmonic image.
     
     This command generates spherical harmonic data from fixels that can be
@@ -264,10 +252,12 @@ def fixel2sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Fixel2shOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXEL2SH_METADATA)
     params = execution.params(params)
     cargs = fixel2sh_cargs(params, execution)
     ret = fixel2sh_outputs(params, execution)
@@ -290,6 +280,8 @@ def fixel2sh(
     runner: Runner | None = None,
 ) -> Fixel2shOutputs:
     """
+    fixel2sh
+    
     Convert a fixel-based sparse-data image into an spherical harmonic image.
     
     This command generates spherical harmonic data from fixels that can be
@@ -328,8 +320,6 @@ def fixel2sh(
     Returns:
         NamedTuple of outputs (described in `Fixel2shOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FIXEL2SH_METADATA)
     params = fixel2sh_params(
         lmax=lmax,
         info=info,
@@ -343,15 +333,14 @@ def fixel2sh(
         fixel_in=fixel_in,
         sh_out=sh_out,
     )
-    return fixel2sh_execute(params, execution)
+    return fixel2sh_execute(params, runner)
 
 
 __all__ = [
     "FIXEL2SH_METADATA",
-    "Fixel2shConfigParameters",
     "Fixel2shOutputs",
-    "Fixel2shParameters",
     "fixel2sh",
     "fixel2sh_config_params",
+    "fixel2sh_execute",
     "fixel2sh_params",
 ]