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

niwrap_mrtrix/mrtrix/tckstats.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TCKSTATS_METADATA = Metadata(
-    id="5978fa2db061f719e30d3e2617f6bb60e013d444.boutiques",
+    id="1c376e03915b6fa825105cf6a3a1f00bd7cafd03.boutiques",
     name="tckstats",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,20 +14,46 @@ TCKSTATS_METADATA = Metadata(
 
 
 TckstatsOutputParameters = typing.TypedDict('TckstatsOutputParameters', {
-    "__STYXTYPE__": typing.Literal["output"],
+    "@type": typing.NotRequired[typing.Literal["output"]],
+    "field": str,
+})
+TckstatsOutputParametersTagged = typing.TypedDict('TckstatsOutputParametersTagged', {
+    "@type": typing.Literal["output"],
     "field": str,
 })
 
 
 TckstatsConfigParameters = typing.TypedDict('TckstatsConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+TckstatsConfigParametersTagged = typing.TypedDict('TckstatsConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 TckstatsParameters = typing.TypedDict('TckstatsParameters', {
-    "__STYXTYPE__": typing.Literal["tckstats"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/tckstats"]],
+    "output": typing.NotRequired[list[TckstatsOutputParameters] | None],
+    "histogram": typing.NotRequired[str | None],
+    "dump": typing.NotRequired[str | None],
+    "ignorezero": bool,
+    "tck_weights_in": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TckstatsConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "tracks_in": InputPathType,
+})
+TckstatsParametersTagged = typing.TypedDict('TckstatsParametersTagged', {
+    "@type": typing.Literal["mrtrix/tckstats"],
     "output": typing.NotRequired[list[TckstatsOutputParameters] | None],
     "histogram": typing.NotRequired[str | None],
     "dump": typing.NotRequired[str | None],
@@ -43,45 +69,11 @@ TckstatsParameters = typing.TypedDict('TckstatsParameters', {
     "version": bool,
     "tracks_in": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "tckstats": tckstats_cargs,
-        "output": tckstats_output_cargs,
-        "config": tckstats_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 {
-        "tckstats": tckstats_outputs,
-    }.get(t)
 
 
 def tckstats_output_params(
     field: str,
-) -> TckstatsOutputParameters:
+) -> TckstatsOutputParametersTagged:
     """
     Build parameters.
     
@@ -93,7 +85,7 @@ def tckstats_output_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "output",
+        "@type": "output",
         "field": field,
     }
     return params
@@ -114,14 +106,14 @@ def tckstats_output_cargs(
     """
     cargs = []
     cargs.append("-output")
-    cargs.append(params.get("field"))
+    cargs.append(params.get("field", None))
     return cargs
 
 
 def tckstats_config_params(
     key: str,
     value: str,
-) -> TckstatsConfigParameters:
+) -> TckstatsConfigParametersTagged:
     """
     Build parameters.
     
@@ -132,7 +124,7 @@ def tckstats_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -154,14 +146,14 @@ def tckstats_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 TckstatsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `tckstats(...)`.
+    Output object returned when calling `TckstatsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -186,7 +178,7 @@ def tckstats_params(
     config: list[TckstatsConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> TckstatsParameters:
+) -> TckstatsParametersTagged:
     """
     Build parameters.
     
@@ -217,7 +209,7 @@ def tckstats_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tckstats",
+        "@type": "mrtrix/tckstats",
         "ignorezero": ignorezero,
         "info": info,
         "quiet": quiet,
@@ -257,45 +249,45 @@ def tckstats_cargs(
     """
     cargs = []
     cargs.append("tckstats")
-    if params.get("output") is not None:
-        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("output")] for a in c])
-    if params.get("histogram") is not None:
+    if params.get("output", None) is not None:
+        cargs.extend([a for c in [tckstats_output_cargs(s, execution) for s in params.get("output", None)] for a in c])
+    if params.get("histogram", None) is not None:
         cargs.extend([
             "-histogram",
-            params.get("histogram")
+            params.get("histogram", 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("ignorezero"):
+    if params.get("ignorezero", False):
         cargs.append("-ignorezero")
-    if params.get("tck_weights_in") is not None:
+    if params.get("tck_weights_in", None) is not None:
         cargs.extend([
             "-tck_weights_in",
-            execution.input_file(params.get("tck_weights_in"))
+            execution.input_file(params.get("tck_weights_in", 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 [tckstats_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("tracks_in")))
+    cargs.append(execution.input_file(params.get("tracks_in", None)))
     return cargs
 
 
@@ -314,17 +306,19 @@ def tckstats_outputs(
     """
     ret = TckstatsOutputs(
         root=execution.output_file("."),
-        histogram=execution.output_file(params.get("histogram")) if (params.get("histogram") is not None) else None,
-        dump=execution.output_file(params.get("dump")) if (params.get("dump") is not None) else None,
+        histogram=execution.output_file(params.get("histogram", None)) if (params.get("histogram") is not None) else None,
+        dump=execution.output_file(params.get("dump", None)) if (params.get("dump") is not None) else None,
     )
     return ret
 
 
 def tckstats_execute(
     params: TckstatsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TckstatsOutputs:
     """
+    tckstats
+    
     Calculate statistics on streamlines lengths.
     
     
@@ -339,10 +333,12 @@ def tckstats_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TckstatsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TCKSTATS_METADATA)
     params = execution.params(params)
     cargs = tckstats_cargs(params, execution)
     ret = tckstats_outputs(params, execution)
@@ -368,6 +364,8 @@ def tckstats(
     runner: Runner | None = None,
 ) -> TckstatsOutputs:
     """
+    tckstats
+    
     Calculate statistics on streamlines lengths.
     
     
@@ -407,8 +405,6 @@ def tckstats(
     Returns:
         NamedTuple of outputs (described in `TckstatsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TCKSTATS_METADATA)
     params = tckstats_params(
         output=output,
         histogram=histogram,
@@ -425,17 +421,15 @@ def tckstats(
         version=version,
         tracks_in=tracks_in,
     )
-    return tckstats_execute(params, execution)
+    return tckstats_execute(params, runner)
 
 
 __all__ = [
     "TCKSTATS_METADATA",
-    "TckstatsConfigParameters",
-    "TckstatsOutputParameters",
     "TckstatsOutputs",
-    "TckstatsParameters",
     "tckstats",
     "tckstats_config_params",
+    "tckstats_execute",
     "tckstats_output_params",
     "tckstats_params",
 ]

niwrap_mrtrix/mrtrix/tcktransform.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TCKTRANSFORM_METADATA = Metadata(
-    id="39d807cb4f7b1be3ec75416e1baa8cd35d636522.boutiques",
+    id="e269e831330358a696661d691299c44a7c3630bb.boutiques",
     name="tcktransform",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,33 @@ TCKTRANSFORM_METADATA = Metadata(
 
 
 TcktransformConfigParameters = typing.TypedDict('TcktransformConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+TcktransformConfigParametersTagged = typing.TypedDict('TcktransformConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 TcktransformParameters = typing.TypedDict('TcktransformParameters', {
-    "__STYXTYPE__": typing.Literal["tcktransform"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/tcktransform"]],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TcktransformConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "tracks": InputPathType,
+    "transform": InputPathType,
+    "output": str,
+})
+TcktransformParametersTagged = typing.TypedDict('TcktransformParametersTagged', {
+    "@type": typing.Literal["mrtrix/tcktransform"],
     "info": bool,
     "quiet": bool,
     "debug": bool,
@@ -34,45 +53,12 @@ TcktransformParameters = typing.TypedDict('TcktransformParameters', {
     "transform": 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 {
-        "tcktransform": tcktransform_cargs,
-        "config": tcktransform_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 {
-        "tcktransform": tcktransform_outputs,
-    }.get(t)
 
 
 def tcktransform_config_params(
     key: str,
     value: str,
-) -> TcktransformConfigParameters:
+) -> TcktransformConfigParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +69,7 @@ def tcktransform_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -105,14 +91,14 @@ def tcktransform_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 TcktransformOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `tcktransform(...)`.
+    Output object returned when calling `TcktransformParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -132,7 +118,7 @@ def tcktransform_params(
     config: list[TcktransformConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> TcktransformParameters:
+) -> TcktransformParametersTagged:
     """
     Build parameters.
     
@@ -156,7 +142,7 @@ def tcktransform_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tcktransform",
+        "@type": "mrtrix/tcktransform",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -189,28 +175,28 @@ def tcktransform_cargs(
     """
     cargs = []
     cargs.append("tcktransform")
-    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 [tcktransform_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("tracks")))
-    cargs.append(execution.input_file(params.get("transform")))
-    cargs.append(params.get("output"))
+    cargs.append(execution.input_file(params.get("tracks", None)))
+    cargs.append(execution.input_file(params.get("transform", None)))
+    cargs.append(params.get("output", None))
     return cargs
 
 
@@ -229,16 +215,18 @@ def tcktransform_outputs(
     """
     ret = TcktransformOutputs(
         root=execution.output_file("."),
-        output=execution.output_file(params.get("output")),
+        output=execution.output_file(params.get("output", None)),
     )
     return ret
 
 
 def tcktransform_execute(
     params: TcktransformParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TcktransformOutputs:
     """
+    tcktransform
+    
     Apply a spatial transformation to a tracks file.
     
     
@@ -253,10 +241,12 @@ def tcktransform_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TcktransformOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TCKTRANSFORM_METADATA)
     params = execution.params(params)
     cargs = tcktransform_cargs(params, execution)
     ret = tcktransform_outputs(params, execution)
@@ -279,6 +269,8 @@ def tcktransform(
     runner: Runner | None = None,
 ) -> TcktransformOutputs:
     """
+    tcktransform
+    
     Apply a spatial transformation to a tracks file.
     
     
@@ -311,8 +303,6 @@ def tcktransform(
     Returns:
         NamedTuple of outputs (described in `TcktransformOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TCKTRANSFORM_METADATA)
     params = tcktransform_params(
         info=info,
         quiet=quiet,
@@ -326,15 +316,14 @@ def tcktransform(
         transform=transform,
         output=output,
     )
-    return tcktransform_execute(params, execution)
+    return tcktransform_execute(params, runner)
 
 
 __all__ = [
     "TCKTRANSFORM_METADATA",
-    "TcktransformConfigParameters",
     "TcktransformOutputs",
-    "TcktransformParameters",
     "tcktransform",
     "tcktransform_config_params",
+    "tcktransform_execute",
     "tcktransform_params",
 ]