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

niwrap_mrtrix/mrtrix/fixelreorient.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIXELREORIENT_METADATA = Metadata(
-    id="1d1bbfeda8f81b813fcbd9b8dd41dc9022366bdd.boutiques",
+    id="c2bf37ec8d7ea2da68c628776a8974d1b5351f66.boutiques",
     name="fixelreorient",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,33 @@ FIXELREORIENT_METADATA = Metadata(
 
 
 FixelreorientConfigParameters = typing.TypedDict('FixelreorientConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+FixelreorientConfigParametersTagged = typing.TypedDict('FixelreorientConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 FixelreorientParameters = typing.TypedDict('FixelreorientParameters', {
-    "__STYXTYPE__": typing.Literal["fixelreorient"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/fixelreorient"]],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[FixelreorientConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "fixel_in": InputPathType,
+    "warp": InputPathType,
+    "fixel_out": str,
+})
+FixelreorientParametersTagged = typing.TypedDict('FixelreorientParametersTagged', {
+    "@type": typing.Literal["mrtrix/fixelreorient"],
     "info": bool,
     "quiet": bool,
     "debug": bool,
@@ -34,45 +53,12 @@ FixelreorientParameters = typing.TypedDict('FixelreorientParameters', {
     "warp": InputPathType,
     "fixel_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 {
-        "fixelreorient": fixelreorient_cargs,
-        "config": fixelreorient_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 {
-        "fixelreorient": fixelreorient_outputs,
-    }.get(t)
 
 
 def fixelreorient_config_params(
     key: str,
     value: str,
-) -> FixelreorientConfigParameters:
+) -> FixelreorientConfigParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +69,7 @@ def fixelreorient_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -105,14 +91,14 @@ def fixelreorient_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 FixelreorientOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fixelreorient(...)`.
+    Output object returned when calling `FixelreorientParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -135,7 +121,7 @@ def fixelreorient_params(
     config: list[FixelreorientConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> FixelreorientParameters:
+) -> FixelreorientParametersTagged:
     """
     Build parameters.
     
@@ -166,7 +152,7 @@ def fixelreorient_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fixelreorient",
+        "@type": "mrtrix/fixelreorient",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -199,28 +185,28 @@ def fixelreorient_cargs(
     """
     cargs = []
     cargs.append("fixelreorient")
-    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 [fixelreorient_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("warp")))
-    cargs.append(params.get("fixel_out"))
+    cargs.append(execution.input_file(params.get("fixel_in", None)))
+    cargs.append(execution.input_file(params.get("warp", None)))
+    cargs.append(params.get("fixel_out", None))
     return cargs
 
 
@@ -239,16 +225,18 @@ def fixelreorient_outputs(
     """
     ret = FixelreorientOutputs(
         root=execution.output_file("."),
-        fixel_out=execution.output_file(params.get("fixel_out")),
+        fixel_out=execution.output_file(params.get("fixel_out", None)),
     )
     return ret
 
 
 def fixelreorient_execute(
     params: FixelreorientParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FixelreorientOutputs:
     """
+    fixelreorient
+    
     Reorient fixel directions.
     
     Reorientation is performed by transforming the vector representing the fixel
@@ -265,10 +253,12 @@ def fixelreorient_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FixelreorientOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXELREORIENT_METADATA)
     params = execution.params(params)
     cargs = fixelreorient_cargs(params, execution)
     ret = fixelreorient_outputs(params, execution)
@@ -291,6 +281,8 @@ def fixelreorient(
     runner: Runner | None = None,
 ) -> FixelreorientOutputs:
     """
+    fixelreorient
+    
     Reorient fixel directions.
     
     Reorientation is performed by transforming the vector representing the fixel
@@ -332,8 +324,6 @@ def fixelreorient(
     Returns:
         NamedTuple of outputs (described in `FixelreorientOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FIXELREORIENT_METADATA)
     params = fixelreorient_params(
         info=info,
         quiet=quiet,
@@ -347,15 +337,14 @@ def fixelreorient(
         warp=warp,
         fixel_out=fixel_out,
     )
-    return fixelreorient_execute(params, execution)
+    return fixelreorient_execute(params, runner)
 
 
 __all__ = [
     "FIXELREORIENT_METADATA",
-    "FixelreorientConfigParameters",
     "FixelreorientOutputs",
-    "FixelreorientParameters",
     "fixelreorient",
     "fixelreorient_config_params",
+    "fixelreorient_execute",
     "fixelreorient_params",
 ]

niwrap_mrtrix/mrtrix/fod2dec.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FOD2DEC_METADATA = Metadata(
-    id="91adc9acb5fba88b24df9894f64378c570f25a44.boutiques",
+    id="56fd41eb31bb1240fd6341ac5abf21815b0e9dac.boutiques",
     name="fod2dec",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,39 @@ FOD2DEC_METADATA = Metadata(
 
 
 Fod2decConfigParameters = typing.TypedDict('Fod2decConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Fod2decConfigParametersTagged = typing.TypedDict('Fod2decConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Fod2decParameters = typing.TypedDict('Fod2decParameters', {
-    "__STYXTYPE__": typing.Literal["fod2dec"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/fod2dec"]],
+    "mask": typing.NotRequired[InputPathType | None],
+    "contrast": typing.NotRequired[InputPathType | None],
+    "lum": bool,
+    "lum_coefs": typing.NotRequired[list[float] | None],
+    "lum_gamma": typing.NotRequired[float | None],
+    "threshold": typing.NotRequired[float | None],
+    "no_weight": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Fod2decConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+Fod2decParametersTagged = typing.TypedDict('Fod2decParametersTagged', {
+    "@type": typing.Literal["mrtrix/fod2dec"],
     "mask": typing.NotRequired[InputPathType | None],
     "contrast": typing.NotRequired[InputPathType | None],
     "lum": bool,
@@ -40,45 +65,12 @@ Fod2decParameters = typing.TypedDict('Fod2decParameters', {
     "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 {
-        "fod2dec": fod2dec_cargs,
-        "config": fod2dec_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 {
-        "fod2dec": fod2dec_outputs,
-    }.get(t)
 
 
 def fod2dec_config_params(
     key: str,
     value: str,
-) -> Fod2decConfigParameters:
+) -> Fod2decConfigParametersTagged:
     """
     Build parameters.
     
@@ -89,7 +81,7 @@ def fod2dec_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -111,14 +103,14 @@ def fod2dec_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 Fod2decOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fod2dec(...)`.
+    Output object returned when calling `Fod2decParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -144,7 +136,7 @@ def fod2dec_params(
     config: list[Fod2decConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Fod2decParameters:
+) -> Fod2decParametersTagged:
     """
     Build parameters.
     
@@ -191,7 +183,7 @@ def fod2dec_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fod2dec",
+        "@type": "mrtrix/fod2dec",
         "lum": lum,
         "no_weight": no_weight,
         "info": info,
@@ -235,56 +227,56 @@ def fod2dec_cargs(
     """
     cargs = []
     cargs.append("fod2dec")
-    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("contrast") is not None:
+    if params.get("contrast", None) is not None:
         cargs.extend([
             "-contrast",
-            execution.input_file(params.get("contrast"))
+            execution.input_file(params.get("contrast", None))
         ])
-    if params.get("lum"):
+    if params.get("lum", False):
         cargs.append("-lum")
-    if params.get("lum_coefs") is not None:
+    if params.get("lum_coefs", None) is not None:
         cargs.extend([
             "-lum_coefs",
-            *map(str, params.get("lum_coefs"))
+            *map(str, params.get("lum_coefs", None))
         ])
-    if params.get("lum_gamma") is not None:
+    if params.get("lum_gamma", None) is not None:
         cargs.extend([
             "-lum_gamma",
-            str(params.get("lum_gamma"))
+            str(params.get("lum_gamma", None))
         ])
-    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("no_weight"):
+    if params.get("no_weight", False):
         cargs.append("-no_weight")
-    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 [fod2dec_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
 
 
@@ -303,16 +295,18 @@ def fod2dec_outputs(
     """
     ret = Fod2decOutputs(
         root=execution.output_file("."),
-        output=execution.output_file(params.get("output")),
+        output=execution.output_file(params.get("output", None)),
     )
     return ret
 
 
 def fod2dec_execute(
     params: Fod2decParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Fod2decOutputs:
     """
+    fod2dec
+    
     Generate FOD-based DEC maps, with optional panchromatic sharpening and/or
     luminance/perception correction.
     
@@ -337,10 +331,12 @@ def fod2dec_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Fod2decOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FOD2DEC_METADATA)
     params = execution.params(params)
     cargs = fod2dec_cargs(params, execution)
     ret = fod2dec_outputs(params, execution)
@@ -369,6 +365,8 @@ def fod2dec(
     runner: Runner | None = None,
 ) -> Fod2decOutputs:
     """
+    fod2dec
+    
     Generate FOD-based DEC maps, with optional panchromatic sharpening and/or
     luminance/perception correction.
     
@@ -434,8 +432,6 @@ def fod2dec(
     Returns:
         NamedTuple of outputs (described in `Fod2decOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FOD2DEC_METADATA)
     params = fod2dec_params(
         mask=mask,
         contrast=contrast,
@@ -455,15 +451,14 @@ def fod2dec(
         input_=input_,
         output=output,
     )
-    return fod2dec_execute(params, execution)
+    return fod2dec_execute(params, runner)
 
 
 __all__ = [
     "FOD2DEC_METADATA",
-    "Fod2decConfigParameters",
     "Fod2decOutputs",
-    "Fod2decParameters",
     "fod2dec",
     "fod2dec_config_params",
+    "fod2dec_execute",
     "fod2dec_params",
 ]