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

niwrap_mrtrix/mrtrix/sh2response.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SH2RESPONSE_METADATA = Metadata(
-    id="4c236ffa31670f857674394a6afbe6341c337edb.boutiques",
+    id="b0158f6418a85b394a1f360188b67bbde8c8da29.boutiques",
     name="sh2response",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,36 @@ SH2RESPONSE_METADATA = Metadata(
 
 
 Sh2responseConfigParameters = typing.TypedDict('Sh2responseConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Sh2responseConfigParametersTagged = typing.TypedDict('Sh2responseConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Sh2responseParameters = typing.TypedDict('Sh2responseParameters', {
-    "__STYXTYPE__": typing.Literal["sh2response"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/sh2response"]],
+    "lmax": typing.NotRequired[int | None],
+    "dump": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Sh2responseConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "SH": InputPathType,
+    "mask": InputPathType,
+    "directions": InputPathType,
+    "response": str,
+})
+Sh2responseParametersTagged = typing.TypedDict('Sh2responseParametersTagged', {
+    "@type": typing.Literal["mrtrix/sh2response"],
     "lmax": typing.NotRequired[int | None],
     "dump": typing.NotRequired[str | None],
     "info": bool,
@@ -37,45 +59,12 @@ Sh2responseParameters = typing.TypedDict('Sh2responseParameters', {
     "directions": InputPathType,
     "response": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "sh2response": sh2response_cargs,
-        "config": sh2response_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 {
-        "sh2response": sh2response_outputs,
-    }.get(t)
 
 
 def sh2response_config_params(
     key: str,
     value: str,
-) -> Sh2responseConfigParameters:
+) -> Sh2responseConfigParametersTagged:
     """
     Build parameters.
     
@@ -86,7 +75,7 @@ def sh2response_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -108,14 +97,14 @@ def sh2response_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 Sh2responseOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `sh2response(...)`.
+    Output object returned when calling `Sh2responseParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -141,7 +130,7 @@ def sh2response_params(
     config: list[Sh2responseConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Sh2responseParameters:
+) -> Sh2responseParametersTagged:
     """
     Build parameters.
     
@@ -173,7 +162,7 @@ def sh2response_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "sh2response",
+        "@type": "mrtrix/sh2response",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -211,39 +200,39 @@ def sh2response_cargs(
     """
     cargs = []
     cargs.append("sh2response")
-    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("dump") is not None:
+    if params.get("dump", None) is not None:
         cargs.extend([
             "-dump",
-            params.get("dump")
+            params.get("dump", 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 [sh2response_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("SH")))
-    cargs.append(execution.input_file(params.get("mask")))
-    cargs.append(execution.input_file(params.get("directions")))
-    cargs.append(params.get("response"))
+    cargs.append(execution.input_file(params.get("SH", None)))
+    cargs.append(execution.input_file(params.get("mask", None)))
+    cargs.append(execution.input_file(params.get("directions", None)))
+    cargs.append(params.get("response", None))
     return cargs
 
 
@@ -262,17 +251,19 @@ def sh2response_outputs(
     """
     ret = Sh2responseOutputs(
         root=execution.output_file("."),
-        response=execution.output_file(params.get("response")),
-        dump=execution.output_file(params.get("dump")) if (params.get("dump") is not None) else None,
+        response=execution.output_file(params.get("response", None)),
+        dump=execution.output_file(params.get("dump", None)) if (params.get("dump") is not None) else None,
     )
     return ret
 
 
 def sh2response_execute(
     params: Sh2responseParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Sh2responseOutputs:
     """
+    sh2response
+    
     Generate an appropriate response function from the image data for spherical
     deconvolution.
     
@@ -290,10 +281,12 @@ def sh2response_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Sh2responseOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SH2RESPONSE_METADATA)
     params = execution.params(params)
     cargs = sh2response_cargs(params, execution)
     ret = sh2response_outputs(params, execution)
@@ -319,6 +312,8 @@ def sh2response(
     runner: Runner | None = None,
 ) -> Sh2responseOutputs:
     """
+    sh2response
+    
     Generate an appropriate response function from the image data for spherical
     deconvolution.
     
@@ -362,8 +357,6 @@ def sh2response(
     Returns:
         NamedTuple of outputs (described in `Sh2responseOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SH2RESPONSE_METADATA)
     params = sh2response_params(
         lmax=lmax,
         dump=dump,
@@ -380,15 +373,14 @@ def sh2response(
         directions=directions,
         response=response,
     )
-    return sh2response_execute(params, execution)
+    return sh2response_execute(params, runner)
 
 
 __all__ = [
     "SH2RESPONSE_METADATA",
-    "Sh2responseConfigParameters",
     "Sh2responseOutputs",
-    "Sh2responseParameters",
     "sh2response",
     "sh2response_config_params",
+    "sh2response_execute",
     "sh2response_params",
 ]

niwrap_mrtrix/mrtrix/shbasis.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SHBASIS_METADATA = Metadata(
-    id="342d9aaa228ccec745a5fbb2776b3c0c98248b3c.boutiques",
+    id="8d1c3a9e142d8ac3b0cfbca9e0fcd6b3d41e317e.boutiques",
     name="shbasis",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,32 @@ SHBASIS_METADATA = Metadata(
 
 
 ShbasisConfigParameters = typing.TypedDict('ShbasisConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+ShbasisConfigParametersTagged = typing.TypedDict('ShbasisConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 ShbasisParameters = typing.TypedDict('ShbasisParameters', {
-    "__STYXTYPE__": typing.Literal["shbasis"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/shbasis"]],
+    "convert": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[ShbasisConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "SH": list[InputPathType],
+})
+ShbasisParametersTagged = typing.TypedDict('ShbasisParametersTagged', {
+    "@type": typing.Literal["mrtrix/shbasis"],
     "convert": typing.NotRequired[str | None],
     "info": bool,
     "quiet": bool,
@@ -33,44 +51,12 @@ ShbasisParameters = typing.TypedDict('ShbasisParameters', {
     "version": bool,
     "SH": list[InputPathType],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "shbasis": shbasis_cargs,
-        "config": shbasis_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 shbasis_config_params(
     key: str,
     value: str,
-) -> ShbasisConfigParameters:
+) -> ShbasisConfigParametersTagged:
     """
     Build parameters.
     
@@ -81,7 +67,7 @@ def shbasis_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -103,14 +89,14 @@ def shbasis_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 ShbasisOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `shbasis(...)`.
+    Output object returned when calling `ShbasisParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -127,7 +113,7 @@ def shbasis_params(
     config: list[ShbasisConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> ShbasisParameters:
+) -> ShbasisParametersTagged:
     """
     Build parameters.
     
@@ -151,7 +137,7 @@ def shbasis_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "shbasis",
+        "@type": "mrtrix/shbasis",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -184,31 +170,31 @@ def shbasis_cargs(
     """
     cargs = []
     cargs.append("shbasis")
-    if params.get("convert") is not None:
+    if params.get("convert", None) is not None:
         cargs.extend([
             "-convert",
-            params.get("convert")
+            params.get("convert", 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 [shbasis_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([execution.input_file(f) for f in params.get("SH")])
+    cargs.extend([execution.input_file(f) for f in params.get("SH", None)])
     return cargs
 
 
@@ -233,9 +219,11 @@ def shbasis_outputs(
 
 def shbasis_execute(
     params: ShbasisParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ShbasisOutputs:
     """
+    shbasis
+    
     Examine the values in spherical harmonic images to estimate (and optionally
     change) the SH basis used.
     
@@ -269,10 +257,12 @@ def shbasis_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ShbasisOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SHBASIS_METADATA)
     params = execution.params(params)
     cargs = shbasis_cargs(params, execution)
     ret = shbasis_outputs(params, execution)
@@ -294,6 +284,8 @@ def shbasis(
     runner: Runner | None = None,
 ) -> ShbasisOutputs:
     """
+    shbasis
+    
     Examine the values in spherical harmonic images to estimate (and optionally
     change) the SH basis used.
     
@@ -345,8 +337,6 @@ def shbasis(
     Returns:
         NamedTuple of outputs (described in `ShbasisOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SHBASIS_METADATA)
     params = shbasis_params(
         convert=convert,
         info=info,
@@ -359,15 +349,14 @@ def shbasis(
         version=version,
         sh=sh,
     )
-    return shbasis_execute(params, execution)
+    return shbasis_execute(params, runner)
 
 
 __all__ = [
     "SHBASIS_METADATA",
-    "ShbasisConfigParameters",
     "ShbasisOutputs",
-    "ShbasisParameters",
     "shbasis",
     "shbasis_config_params",
+    "shbasis_execute",
     "shbasis_params",
 ]