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

niwrap_mrtrix/mrtrix/tckglobal.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TCKGLOBAL_METADATA = Metadata(
-    id="cae2ccc88f0085f525ed9602a03dca47884d2293.boutiques",
+    id="31e24266a6d4374cd9c0a8ed5d9d697b1c511208.boutiques",
     name="tckglobal",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,20 +14,64 @@ TCKGLOBAL_METADATA = Metadata(
 
 
 TckglobalRisoParameters = typing.TypedDict('TckglobalRisoParameters', {
-    "__STYXTYPE__": typing.Literal["riso"],
+    "@type": typing.NotRequired[typing.Literal["riso"]],
+    "response": InputPathType,
+})
+TckglobalRisoParametersTagged = typing.TypedDict('TckglobalRisoParametersTagged', {
+    "@type": typing.Literal["riso"],
     "response": InputPathType,
 })
 
 
 TckglobalConfigParameters = typing.TypedDict('TckglobalConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+TckglobalConfigParametersTagged = typing.TypedDict('TckglobalConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 TckglobalParameters = typing.TypedDict('TckglobalParameters', {
-    "__STYXTYPE__": typing.Literal["tckglobal"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/tckglobal"]],
+    "grad": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "riso": typing.NotRequired[list[TckglobalRisoParameters] | None],
+    "lmax": typing.NotRequired[int | None],
+    "length": typing.NotRequired[float | None],
+    "weight": typing.NotRequired[float | None],
+    "ppot": typing.NotRequired[float | None],
+    "cpot": typing.NotRequired[float | None],
+    "t0": typing.NotRequired[float | None],
+    "t1": typing.NotRequired[float | None],
+    "niter": typing.NotRequired[int | None],
+    "fod": typing.NotRequired[str | None],
+    "noapo": bool,
+    "fiso": typing.NotRequired[str | None],
+    "eext": typing.NotRequired[str | None],
+    "etrend": typing.NotRequired[str | None],
+    "balance": typing.NotRequired[float | None],
+    "density": typing.NotRequired[float | None],
+    "prob": typing.NotRequired[list[float] | None],
+    "beta": typing.NotRequired[float | None],
+    "lambda": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TckglobalConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "source": InputPathType,
+    "response": InputPathType,
+    "tracks": str,
+})
+TckglobalParametersTagged = typing.TypedDict('TckglobalParametersTagged', {
+    "@type": typing.Literal["mrtrix/tckglobal"],
     "grad": typing.NotRequired[InputPathType | None],
     "mask": typing.NotRequired[InputPathType | None],
     "riso": typing.NotRequired[list[TckglobalRisoParameters] | None],
@@ -61,45 +105,11 @@ TckglobalParameters = typing.TypedDict('TckglobalParameters', {
     "response": InputPathType,
     "tracks": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "tckglobal": tckglobal_cargs,
-        "riso": tckglobal_riso_cargs,
-        "config": tckglobal_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 {
-        "tckglobal": tckglobal_outputs,
-    }.get(t)
 
 
 def tckglobal_riso_params(
     response: InputPathType,
-) -> TckglobalRisoParameters:
+) -> TckglobalRisoParametersTagged:
     """
     Build parameters.
     
@@ -110,7 +120,7 @@ def tckglobal_riso_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "riso",
+        "@type": "riso",
         "response": response,
     }
     return params
@@ -131,14 +141,14 @@ def tckglobal_riso_cargs(
     """
     cargs = []
     cargs.append("-riso")
-    cargs.append(execution.input_file(params.get("response")))
+    cargs.append(execution.input_file(params.get("response", None)))
     return cargs
 
 
 def tckglobal_config_params(
     key: str,
     value: str,
-) -> TckglobalConfigParameters:
+) -> TckglobalConfigParametersTagged:
     """
     Build parameters.
     
@@ -149,7 +159,7 @@ def tckglobal_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -171,14 +181,14 @@ def tckglobal_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 TckglobalOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `tckglobal(...)`.
+    Output object returned when calling `TckglobalParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -234,7 +244,7 @@ def tckglobal_params(
     config: list[TckglobalConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> TckglobalParameters:
+) -> TckglobalParametersTagged:
     """
     Build parameters.
     
@@ -306,7 +316,7 @@ def tckglobal_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tckglobal",
+        "@type": "mrtrix/tckglobal",
         "noapo": noapo,
         "info": info,
         "quiet": quiet,
@@ -380,127 +390,127 @@ def tckglobal_cargs(
     """
     cargs = []
     cargs.append("tckglobal")
-    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("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("riso") is not None:
-        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("riso")] for a in c])
-    if params.get("lmax") is not None:
+    if params.get("riso", None) is not None:
+        cargs.extend([a for c in [tckglobal_riso_cargs(s, execution) for s in params.get("riso", None)] for a in c])
+    if params.get("lmax", None) is not None:
         cargs.extend([
             "-lmax",
-            str(params.get("lmax"))
+            str(params.get("lmax", None))
         ])
-    if params.get("length") is not None:
+    if params.get("length", None) is not None:
         cargs.extend([
             "-length",
-            str(params.get("length"))
+            str(params.get("length", None))
         ])
-    if params.get("weight") is not None:
+    if params.get("weight", None) is not None:
         cargs.extend([
             "-weight",
-            str(params.get("weight"))
+            str(params.get("weight", None))
         ])
-    if params.get("ppot") is not None:
+    if params.get("ppot", None) is not None:
         cargs.extend([
             "-ppot",
-            str(params.get("ppot"))
+            str(params.get("ppot", None))
         ])
-    if params.get("cpot") is not None:
+    if params.get("cpot", None) is not None:
         cargs.extend([
             "-cpot",
-            str(params.get("cpot"))
+            str(params.get("cpot", None))
         ])
-    if params.get("t0") is not None:
+    if params.get("t0", None) is not None:
         cargs.extend([
             "-t0",
-            str(params.get("t0"))
+            str(params.get("t0", None))
         ])
-    if params.get("t1") is not None:
+    if params.get("t1", None) is not None:
         cargs.extend([
             "-t1",
-            str(params.get("t1"))
+            str(params.get("t1", None))
         ])
-    if params.get("niter") is not None:
+    if params.get("niter", None) is not None:
         cargs.extend([
             "-niter",
-            str(params.get("niter"))
+            str(params.get("niter", None))
         ])
-    if params.get("fod") is not None:
+    if params.get("fod", None) is not None:
         cargs.extend([
             "-fod",
-            params.get("fod")
+            params.get("fod", None)
         ])
-    if params.get("noapo"):
+    if params.get("noapo", False):
         cargs.append("-noapo")
-    if params.get("fiso") is not None:
+    if params.get("fiso", None) is not None:
         cargs.extend([
             "-fiso",
-            params.get("fiso")
+            params.get("fiso", None)
         ])
-    if params.get("eext") is not None:
+    if params.get("eext", None) is not None:
         cargs.extend([
             "-eext",
-            params.get("eext")
+            params.get("eext", None)
         ])
-    if params.get("etrend") is not None:
+    if params.get("etrend", None) is not None:
         cargs.extend([
             "-etrend",
-            params.get("etrend")
+            params.get("etrend", None)
         ])
-    if params.get("balance") is not None:
+    if params.get("balance", None) is not None:
         cargs.extend([
             "-balance",
-            str(params.get("balance"))
+            str(params.get("balance", None))
         ])
-    if params.get("density") is not None:
+    if params.get("density", None) is not None:
         cargs.extend([
             "-density",
-            str(params.get("density"))
+            str(params.get("density", None))
         ])
-    if params.get("prob") is not None:
+    if params.get("prob", None) is not None:
         cargs.extend([
             "-prob",
-            *map(str, params.get("prob"))
+            *map(str, params.get("prob", None))
         ])
-    if params.get("beta") is not None:
+    if params.get("beta", None) is not None:
         cargs.extend([
             "-beta",
-            str(params.get("beta"))
+            str(params.get("beta", None))
         ])
-    if params.get("lambda") is not None:
+    if params.get("lambda", None) is not None:
         cargs.extend([
             "-lambda",
-            str(params.get("lambda"))
+            str(params.get("lambda", 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 [tckglobal_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("source")))
-    cargs.append(execution.input_file(params.get("response")))
-    cargs.append(params.get("tracks"))
+    cargs.append(execution.input_file(params.get("source", None)))
+    cargs.append(execution.input_file(params.get("response", None)))
+    cargs.append(params.get("tracks", None))
     return cargs
 
 
@@ -519,20 +529,22 @@ def tckglobal_outputs(
     """
     ret = TckglobalOutputs(
         root=execution.output_file("."),
-        tracks=execution.output_file(params.get("tracks")),
-        fod=execution.output_file(params.get("fod")) if (params.get("fod") is not None) else None,
-        fiso=execution.output_file(params.get("fiso")) if (params.get("fiso") is not None) else None,
-        eext=execution.output_file(params.get("eext")) if (params.get("eext") is not None) else None,
-        etrend=execution.output_file(params.get("etrend")) if (params.get("etrend") is not None) else None,
+        tracks=execution.output_file(params.get("tracks", None)),
+        fod=execution.output_file(params.get("fod", None)) if (params.get("fod") is not None) else None,
+        fiso=execution.output_file(params.get("fiso", None)) if (params.get("fiso") is not None) else None,
+        eext=execution.output_file(params.get("eext", None)) if (params.get("eext") is not None) else None,
+        etrend=execution.output_file(params.get("etrend", None)) if (params.get("etrend") is not None) else None,
     )
     return ret
 
 
 def tckglobal_execute(
     params: TckglobalParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TckglobalOutputs:
     """
+    tckglobal
+    
     Multi-Shell Multi-Tissue Global Tractography.
     
     This command will reconstruct the global white matter fibre tractogram that
@@ -563,10 +575,12 @@ def tckglobal_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TckglobalOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TCKGLOBAL_METADATA)
     params = execution.params(params)
     cargs = tckglobal_cargs(params, execution)
     ret = tckglobal_outputs(params, execution)
@@ -610,6 +624,8 @@ def tckglobal(
     runner: Runner | None = None,
 ) -> TckglobalOutputs:
     """
+    tckglobal
+    
     Multi-Shell Multi-Tissue Global Tractography.
     
     This command will reconstruct the global white matter fibre tractogram that
@@ -706,8 +722,6 @@ def tckglobal(
     Returns:
         NamedTuple of outputs (described in `TckglobalOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TCKGLOBAL_METADATA)
     params = tckglobal_params(
         grad=grad,
         mask=mask,
@@ -742,17 +756,15 @@ def tckglobal(
         response=response,
         tracks=tracks,
     )
-    return tckglobal_execute(params, execution)
+    return tckglobal_execute(params, runner)
 
 
 __all__ = [
     "TCKGLOBAL_METADATA",
-    "TckglobalConfigParameters",
     "TckglobalOutputs",
-    "TckglobalParameters",
-    "TckglobalRisoParameters",
     "tckglobal",
     "tckglobal_config_params",
+    "tckglobal_execute",
     "tckglobal_params",
     "tckglobal_riso_params",
 ]

niwrap_mrtrix/mrtrix/tckinfo.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TCKINFO_METADATA = Metadata(
-    id="d14e5332a781430b64c1d2c8df942fabc0642b0b.boutiques",
+    id="0d096f25f496f4f8a788a3cdb85dd77497b69433.boutiques",
     name="tckinfo",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,32 @@ TCKINFO_METADATA = Metadata(
 
 
 TckinfoConfigParameters = typing.TypedDict('TckinfoConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+TckinfoConfigParametersTagged = typing.TypedDict('TckinfoConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 TckinfoParameters = typing.TypedDict('TckinfoParameters', {
-    "__STYXTYPE__": typing.Literal["tckinfo"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/tckinfo"]],
+    "count": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TckinfoConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "tracks": list[InputPathType],
+})
+TckinfoParametersTagged = typing.TypedDict('TckinfoParametersTagged', {
+    "@type": typing.Literal["mrtrix/tckinfo"],
     "count": bool,
     "info": bool,
     "quiet": bool,
@@ -33,44 +51,12 @@ TckinfoParameters = typing.TypedDict('TckinfoParameters', {
     "version": bool,
     "tracks": 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 {
-        "tckinfo": tckinfo_cargs,
-        "config": tckinfo_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 tckinfo_config_params(
     key: str,
     value: str,
-) -> TckinfoConfigParameters:
+) -> TckinfoConfigParametersTagged:
     """
     Build parameters.
     
@@ -81,7 +67,7 @@ def tckinfo_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -103,14 +89,14 @@ def tckinfo_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 TckinfoOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `tckinfo(...)`.
+    Output object returned when calling `TckinfoParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -127,7 +113,7 @@ def tckinfo_params(
     config: list[TckinfoConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> TckinfoParameters:
+) -> TckinfoParametersTagged:
     """
     Build parameters.
     
@@ -150,7 +136,7 @@ def tckinfo_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tckinfo",
+        "@type": "mrtrix/tckinfo",
         "count": count,
         "info": info,
         "quiet": quiet,
@@ -182,28 +168,28 @@ def tckinfo_cargs(
     """
     cargs = []
     cargs.append("tckinfo")
-    if params.get("count"):
+    if params.get("count", False):
         cargs.append("-count")
-    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 [tckinfo_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("tracks")])
+    cargs.extend([execution.input_file(f) for f in params.get("tracks", None)])
     return cargs
 
 
@@ -228,9 +214,11 @@ def tckinfo_outputs(
 
 def tckinfo_execute(
     params: TckinfoParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TckinfoOutputs:
     """
+    tckinfo
+    
     Print out information about a track file.
     
     
@@ -245,10 +233,12 @@ def tckinfo_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TckinfoOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TCKINFO_METADATA)
     params = execution.params(params)
     cargs = tckinfo_cargs(params, execution)
     ret = tckinfo_outputs(params, execution)
@@ -270,6 +260,8 @@ def tckinfo(
     runner: Runner | None = None,
 ) -> TckinfoOutputs:
     """
+    tckinfo
+    
     Print out information about a track file.
     
     
@@ -301,8 +293,6 @@ def tckinfo(
     Returns:
         NamedTuple of outputs (described in `TckinfoOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TCKINFO_METADATA)
     params = tckinfo_params(
         count=count,
         info=info,
@@ -315,15 +305,14 @@ def tckinfo(
         version=version,
         tracks=tracks,
     )
-    return tckinfo_execute(params, execution)
+    return tckinfo_execute(params, runner)
 
 
 __all__ = [
     "TCKINFO_METADATA",
-    "TckinfoConfigParameters",
     "TckinfoOutputs",
-    "TckinfoParameters",
     "tckinfo",
     "tckinfo_config_params",
+    "tckinfo_execute",
     "tckinfo_params",
 ]