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

niwrap_mrtrix/mrtrix/amp2sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 AMP2SH_METADATA = Metadata(
-    id="3ffc8e2dc7b2cc939f7521568d9e286d5b4007ad.boutiques",
+    id="b1deae186542fe482c4a2e51622f124fe000c4fc.boutiques",
     name="amp2sh",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,33 +14,51 @@ AMP2SH_METADATA = Metadata(
 
 
 Amp2shFslgradParameters = typing.TypedDict('Amp2shFslgradParameters', {
-    "__STYXTYPE__": typing.Literal["fslgrad"],
+    "@type": typing.NotRequired[typing.Literal["fslgrad"]],
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+Amp2shFslgradParametersTagged = typing.TypedDict('Amp2shFslgradParametersTagged', {
+    "@type": typing.Literal["fslgrad"],
     "bvecs": InputPathType,
     "bvals": InputPathType,
 })
 
 
 Amp2shVariousStringParameters = typing.TypedDict('Amp2shVariousStringParameters', {
-    "__STYXTYPE__": typing.Literal["VariousString"],
+    "@type": typing.NotRequired[typing.Literal["VariousString"]],
+    "obj": str,
+})
+Amp2shVariousStringParametersTagged = typing.TypedDict('Amp2shVariousStringParametersTagged', {
+    "@type": typing.Literal["VariousString"],
     "obj": str,
 })
 
 
 Amp2shVariousFileParameters = typing.TypedDict('Amp2shVariousFileParameters', {
-    "__STYXTYPE__": typing.Literal["VariousFile"],
+    "@type": typing.NotRequired[typing.Literal["VariousFile"]],
+    "obj": InputPathType,
+})
+Amp2shVariousFileParametersTagged = typing.TypedDict('Amp2shVariousFileParametersTagged', {
+    "@type": typing.Literal["VariousFile"],
     "obj": InputPathType,
 })
 
 
 Amp2shConfigParameters = typing.TypedDict('Amp2shConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Amp2shConfigParametersTagged = typing.TypedDict('Amp2shConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Amp2shParameters = typing.TypedDict('Amp2shParameters', {
-    "__STYXTYPE__": typing.Literal["amp2sh"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/amp2sh"]],
     "lmax": typing.NotRequired[int | None],
     "normalise": bool,
     "directions": typing.NotRequired[InputPathType | None],
@@ -48,7 +66,28 @@ Amp2shParameters = typing.TypedDict('Amp2shParameters', {
     "grad": typing.NotRequired[InputPathType | None],
     "fslgrad": typing.NotRequired[Amp2shFslgradParameters | None],
     "shells": typing.NotRequired[list[float] | None],
-    "strides": typing.NotRequired[typing.Union[Amp2shVariousStringParameters, Amp2shVariousFileParameters] | None],
+    "strides": typing.NotRequired[typing.Union[Amp2shVariousStringParametersTagged, Amp2shVariousFileParametersTagged] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Amp2shConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "amp": InputPathType,
+    "SH": str,
+})
+Amp2shParametersTagged = typing.TypedDict('Amp2shParametersTagged', {
+    "@type": typing.Literal["mrtrix/amp2sh"],
+    "lmax": typing.NotRequired[int | None],
+    "normalise": bool,
+    "directions": typing.NotRequired[InputPathType | None],
+    "rician": typing.NotRequired[InputPathType | None],
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[Amp2shFslgradParameters | None],
+    "shells": typing.NotRequired[list[float] | None],
+    "strides": typing.NotRequired[typing.Union[Amp2shVariousStringParametersTagged, Amp2shVariousFileParametersTagged] | None],
     "info": bool,
     "quiet": bool,
     "debug": bool,
@@ -62,7 +101,7 @@ Amp2shParameters = typing.TypedDict('Amp2shParameters', {
 })
 
 
-def dyn_cargs(
+def amp2sh_strides_cargs_dyn_fn(
     t: str,
 ) -> typing.Any:
     """
@@ -74,15 +113,12 @@ def dyn_cargs(
         Build cargs function.
     """
     return {
-        "amp2sh": amp2sh_cargs,
-        "fslgrad": amp2sh_fslgrad_cargs,
         "VariousString": amp2sh_various_string_cargs,
         "VariousFile": amp2sh_various_file_cargs,
-        "config": amp2sh_config_cargs,
     }.get(t)
 
 
-def dyn_outputs(
+def amp2sh_strides_outputs_dyn_fn(
     t: str,
 ) -> typing.Any:
     """
@@ -94,14 +130,13 @@ def dyn_outputs(
         Build outputs function.
     """
     return {
-        "amp2sh": amp2sh_outputs,
     }.get(t)
 
 
 def amp2sh_fslgrad_params(
     bvecs: InputPathType,
     bvals: InputPathType,
-) -> Amp2shFslgradParameters:
+) -> Amp2shFslgradParametersTagged:
     """
     Build parameters.
     
@@ -118,7 +153,7 @@ def amp2sh_fslgrad_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fslgrad",
+        "@type": "fslgrad",
         "bvecs": bvecs,
         "bvals": bvals,
     }
@@ -140,14 +175,14 @@ def amp2sh_fslgrad_cargs(
     """
     cargs = []
     cargs.append("-fslgrad")
-    cargs.append(execution.input_file(params.get("bvecs")))
-    cargs.append(execution.input_file(params.get("bvals")))
+    cargs.append(execution.input_file(params.get("bvecs", None)))
+    cargs.append(execution.input_file(params.get("bvals", None)))
     return cargs
 
 
 def amp2sh_various_string_params(
     obj: str,
-) -> Amp2shVariousStringParameters:
+) -> Amp2shVariousStringParametersTagged:
     """
     Build parameters.
     
@@ -157,7 +192,7 @@ def amp2sh_various_string_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "VariousString",
+        "@type": "VariousString",
         "obj": obj,
     }
     return params
@@ -177,13 +212,13 @@ def amp2sh_various_string_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append(params.get("obj"))
+    cargs.append(params.get("obj", None))
     return cargs
 
 
 def amp2sh_various_file_params(
     obj: InputPathType,
-) -> Amp2shVariousFileParameters:
+) -> Amp2shVariousFileParametersTagged:
     """
     Build parameters.
     
@@ -193,7 +228,7 @@ def amp2sh_various_file_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "VariousFile",
+        "@type": "VariousFile",
         "obj": obj,
     }
     return params
@@ -213,14 +248,14 @@ def amp2sh_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
 
 
 def amp2sh_config_params(
     key: str,
     value: str,
-) -> Amp2shConfigParameters:
+) -> Amp2shConfigParametersTagged:
     """
     Build parameters.
     
@@ -231,7 +266,7 @@ def amp2sh_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -253,14 +288,14 @@ def amp2sh_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 Amp2shOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `amp2sh(...)`.
+    Output object returned when calling `Amp2shParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -278,7 +313,7 @@ def amp2sh_params(
     grad: InputPathType | None = None,
     fslgrad: Amp2shFslgradParameters | None = None,
     shells: list[float] | None = None,
-    strides: typing.Union[Amp2shVariousStringParameters, Amp2shVariousFileParameters] | None = None,
+    strides: typing.Union[Amp2shVariousStringParametersTagged, Amp2shVariousFileParametersTagged] | None = None,
     info: bool = False,
     quiet: bool = False,
     debug: bool = False,
@@ -287,7 +322,7 @@ def amp2sh_params(
     config: list[Amp2shConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Amp2shParameters:
+) -> Amp2shParametersTagged:
     """
     Build parameters.
     
@@ -344,7 +379,7 @@ def amp2sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "amp2sh",
+        "@type": "mrtrix/amp2sh",
         "normalise": normalise,
         "info": info,
         "quiet": quiet,
@@ -391,61 +426,61 @@ def amp2sh_cargs(
     """
     cargs = []
     cargs.append("amp2sh")
-    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("normalise"):
+    if params.get("normalise", False):
         cargs.append("-normalise")
-    if params.get("directions") is not None:
+    if params.get("directions", None) is not None:
         cargs.extend([
             "-directions",
-            execution.input_file(params.get("directions"))
+            execution.input_file(params.get("directions", None))
         ])
-    if params.get("rician") is not None:
+    if params.get("rician", None) is not None:
         cargs.extend([
             "-rician",
-            execution.input_file(params.get("rician"))
+            execution.input_file(params.get("rician", None))
         ])
-    if params.get("grad") is not None:
+    if params.get("grad", None) is not None:
         cargs.extend([
             "-grad",
-            execution.input_file(params.get("grad"))
+            execution.input_file(params.get("grad", None))
         ])
-    if params.get("fslgrad") is not None:
-        cargs.extend(dyn_cargs(params.get("fslgrad")["__STYXTYPE__"])(params.get("fslgrad"), execution))
-    if params.get("shells") is not None:
+    if params.get("fslgrad", None) is not None:
+        cargs.extend(amp2sh_fslgrad_cargs(params.get("fslgrad", None), execution))
+    if params.get("shells", None) is not None:
         cargs.extend([
             "-shells",
-            ",".join(map(str, params.get("shells")))
+            ",".join(map(str, params.get("shells", None)))
         ])
-    if params.get("strides") is not None:
+    if params.get("strides", None) is not None:
         cargs.extend([
             "-strides",
-            *dyn_cargs(params.get("strides")["__STYXTYPE__"])(params.get("strides"), execution)
+            *amp2sh_strides_cargs_dyn_fn(params.get("strides", None)["@type"])(params.get("strides", None), execution)
         ])
-    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 [amp2sh_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("amp")))
-    cargs.append(params.get("SH"))
+    cargs.append(execution.input_file(params.get("amp", None)))
+    cargs.append(params.get("SH", None))
     return cargs
 
 
@@ -464,18 +499,20 @@ def amp2sh_outputs(
     """
     ret = Amp2shOutputs(
         root=execution.output_file("."),
-        sh=execution.output_file(params.get("SH")),
+        sh=execution.output_file(params.get("SH", None)),
     )
     return ret
 
 
 def amp2sh_execute(
     params: Amp2shParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Amp2shOutputs:
     """
-    Convert a set of amplitudes (defined along a set of corresponding directions) to
-    their spherical harmonic representation.
+    amp2sh
+    
+    Convert a set of amplitudes (defined along a set of corresponding
+    directions) to their spherical harmonic representation.
     
     The spherical harmonic decomposition is calculated by least-squares linear
     fitting to the amplitude data.
@@ -502,10 +539,12 @@ def amp2sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Amp2shOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AMP2SH_METADATA)
     params = execution.params(params)
     cargs = amp2sh_cargs(params, execution)
     ret = amp2sh_outputs(params, execution)
@@ -523,7 +562,7 @@ def amp2sh(
     grad: InputPathType | None = None,
     fslgrad: Amp2shFslgradParameters | None = None,
     shells: list[float] | None = None,
-    strides: typing.Union[Amp2shVariousStringParameters, Amp2shVariousFileParameters] | None = None,
+    strides: typing.Union[Amp2shVariousStringParametersTagged, Amp2shVariousFileParametersTagged] | None = None,
     info: bool = False,
     quiet: bool = False,
     debug: bool = False,
@@ -535,8 +574,10 @@ def amp2sh(
     runner: Runner | None = None,
 ) -> Amp2shOutputs:
     """
-    Convert a set of amplitudes (defined along a set of corresponding directions) to
-    their spherical harmonic representation.
+    amp2sh
+    
+    Convert a set of amplitudes (defined along a set of corresponding
+    directions) to their spherical harmonic representation.
     
     The spherical harmonic decomposition is calculated by least-squares linear
     fitting to the amplitude data.
@@ -614,8 +655,6 @@ def amp2sh(
     Returns:
         NamedTuple of outputs (described in `Amp2shOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(AMP2SH_METADATA)
     params = amp2sh_params(
         lmax=lmax,
         normalise=normalise,
@@ -636,19 +675,15 @@ def amp2sh(
         amp=amp,
         sh=sh,
     )
-    return amp2sh_execute(params, execution)
+    return amp2sh_execute(params, runner)
 
 
 __all__ = [
     "AMP2SH_METADATA",
-    "Amp2shConfigParameters",
-    "Amp2shFslgradParameters",
     "Amp2shOutputs",
-    "Amp2shParameters",
-    "Amp2shVariousFileParameters",
-    "Amp2shVariousStringParameters",
     "amp2sh",
     "amp2sh_config_params",
+    "amp2sh_execute",
     "amp2sh_fslgrad_params",
     "amp2sh_params",
     "amp2sh_various_file_params",