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

niwrap_mrtrix/mrtrix/mrdegibbs.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRDEGIBBS_METADATA = Metadata(
-    id="1e8895a9bf3df6beb54e386b789aaa61dbdf2143.boutiques",
+    id="832d935b5fa8fdff97b78ecd355cb0d26be8033a.boutiques",
     name="mrdegibbs",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,37 @@ MRDEGIBBS_METADATA = Metadata(
 
 
 MrdegibbsConfigParameters = typing.TypedDict('MrdegibbsConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+MrdegibbsConfigParametersTagged = typing.TypedDict('MrdegibbsConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 MrdegibbsParameters = typing.TypedDict('MrdegibbsParameters', {
-    "__STYXTYPE__": typing.Literal["mrdegibbs"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/mrdegibbs"]],
+    "axes": typing.NotRequired[list[int] | None],
+    "nshifts": typing.NotRequired[int | None],
+    "minW": typing.NotRequired[int | None],
+    "maxW": typing.NotRequired[int | None],
+    "datatype": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrdegibbsConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "in": InputPathType,
+    "out": str,
+})
+MrdegibbsParametersTagged = typing.TypedDict('MrdegibbsParametersTagged', {
+    "@type": typing.Literal["mrtrix/mrdegibbs"],
     "axes": typing.NotRequired[list[int] | None],
     "nshifts": typing.NotRequired[int | None],
     "minW": typing.NotRequired[int | None],
@@ -38,45 +61,12 @@ MrdegibbsParameters = typing.TypedDict('MrdegibbsParameters', {
     "in": InputPathType,
     "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 {
-        "mrdegibbs": mrdegibbs_cargs,
-        "config": mrdegibbs_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 {
-        "mrdegibbs": mrdegibbs_outputs,
-    }.get(t)
 
 
 def mrdegibbs_config_params(
     key: str,
     value: str,
-) -> MrdegibbsConfigParameters:
+) -> MrdegibbsConfigParametersTagged:
     """
     Build parameters.
     
@@ -87,7 +77,7 @@ def mrdegibbs_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -109,14 +99,14 @@ def mrdegibbs_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 MrdegibbsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mrdegibbs(...)`.
+    Output object returned when calling `MrdegibbsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -140,7 +130,7 @@ def mrdegibbs_params(
     config: list[MrdegibbsConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> MrdegibbsParameters:
+) -> MrdegibbsParametersTagged:
     """
     Build parameters.
     
@@ -173,7 +163,7 @@ def mrdegibbs_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mrdegibbs",
+        "@type": "mrtrix/mrdegibbs",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -215,52 +205,52 @@ def mrdegibbs_cargs(
     """
     cargs = []
     cargs.append("mrdegibbs")
-    if params.get("axes") is not None:
+    if params.get("axes", None) is not None:
         cargs.extend([
             "-axes",
-            *map(str, params.get("axes"))
+            *map(str, params.get("axes", None))
         ])
-    if params.get("nshifts") is not None:
+    if params.get("nshifts", None) is not None:
         cargs.extend([
             "-nshifts",
-            str(params.get("nshifts"))
+            str(params.get("nshifts", None))
         ])
-    if params.get("minW") is not None:
+    if params.get("minW", None) is not None:
         cargs.extend([
             "-minW",
-            str(params.get("minW"))
+            str(params.get("minW", None))
         ])
-    if params.get("maxW") is not None:
+    if params.get("maxW", None) is not None:
         cargs.extend([
             "-maxW",
-            str(params.get("maxW"))
+            str(params.get("maxW", None))
         ])
-    if params.get("datatype") is not None:
+    if params.get("datatype", None) is not None:
         cargs.extend([
             "-datatype",
-            params.get("datatype")
+            params.get("datatype", 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 [mrdegibbs_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("in")))
-    cargs.append(params.get("out"))
+    cargs.append(execution.input_file(params.get("in", None)))
+    cargs.append(params.get("out", None))
     return cargs
 
 
@@ -279,16 +269,18 @@ def mrdegibbs_outputs(
     """
     ret = MrdegibbsOutputs(
         root=execution.output_file("."),
-        out=execution.output_file(params.get("out")),
+        out=execution.output_file(params.get("out", None)),
     )
     return ret
 
 
 def mrdegibbs_execute(
     params: MrdegibbsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrdegibbsOutputs:
     """
+    mrdegibbs
+    
     Remove Gibbs Ringing Artifacts.
     
     This application attempts to remove Gibbs ringing artefacts from MRI images
@@ -321,10 +313,12 @@ def mrdegibbs_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrdegibbsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRDEGIBBS_METADATA)
     params = execution.params(params)
     cargs = mrdegibbs_cargs(params, execution)
     ret = mrdegibbs_outputs(params, execution)
@@ -351,6 +345,8 @@ def mrdegibbs(
     runner: Runner | None = None,
 ) -> MrdegibbsOutputs:
     """
+    mrdegibbs
+    
     Remove Gibbs Ringing Artifacts.
     
     This application attempts to remove Gibbs ringing artefacts from MRI images
@@ -410,8 +406,6 @@ def mrdegibbs(
     Returns:
         NamedTuple of outputs (described in `MrdegibbsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRDEGIBBS_METADATA)
     params = mrdegibbs_params(
         axes=axes,
         nshifts=nshifts,
@@ -429,15 +423,14 @@ def mrdegibbs(
         in_=in_,
         out=out,
     )
-    return mrdegibbs_execute(params, execution)
+    return mrdegibbs_execute(params, runner)
 
 
 __all__ = [
     "MRDEGIBBS_METADATA",
-    "MrdegibbsConfigParameters",
     "MrdegibbsOutputs",
-    "MrdegibbsParameters",
     "mrdegibbs",
     "mrdegibbs_config_params",
+    "mrdegibbs_execute",
     "mrdegibbs_params",
 ]

niwrap_mrtrix/mrtrix/mrdump.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRDUMP_METADATA = Metadata(
-    id="4245b09acbe36314b090cb352200374f5d140a3c.boutiques",
+    id="606c9d0900d68319d10a0372597796b0e18d5074.boutiques",
     name="mrdump",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,33 @@ MRDUMP_METADATA = Metadata(
 
 
 MrdumpConfigParameters = typing.TypedDict('MrdumpConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+MrdumpConfigParametersTagged = typing.TypedDict('MrdumpConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 MrdumpParameters = typing.TypedDict('MrdumpParameters', {
-    "__STYXTYPE__": typing.Literal["mrdump"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/mrdump"]],
+    "mask": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrdumpConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": typing.NotRequired[str | None],
+})
+MrdumpParametersTagged = typing.TypedDict('MrdumpParametersTagged', {
+    "@type": typing.Literal["mrtrix/mrdump"],
     "mask": typing.NotRequired[InputPathType | None],
     "info": bool,
     "quiet": bool,
@@ -34,45 +53,12 @@ MrdumpParameters = typing.TypedDict('MrdumpParameters', {
     "input": InputPathType,
     "output": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mrdump": mrdump_cargs,
-        "config": mrdump_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 {
-        "mrdump": mrdump_outputs,
-    }.get(t)
 
 
 def mrdump_config_params(
     key: str,
     value: str,
-) -> MrdumpConfigParameters:
+) -> MrdumpConfigParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +69,7 @@ def mrdump_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -105,14 +91,14 @@ def mrdump_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 MrdumpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mrdump(...)`.
+    Output object returned when calling `MrdumpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -132,7 +118,7 @@ def mrdump_params(
     help_: bool = False,
     version: bool = False,
     output: str | None = None,
-) -> MrdumpParameters:
+) -> MrdumpParametersTagged:
     """
     Build parameters.
     
@@ -157,7 +143,7 @@ def mrdump_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mrdump",
+        "@type": "mrtrix/mrdump",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -192,33 +178,33 @@ def mrdump_cargs(
     """
     cargs = []
     cargs.append("mrdump")
-    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("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 [mrdump_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")))
-    if params.get("output") is not None:
-        cargs.append(params.get("output"))
+    cargs.append(execution.input_file(params.get("input", None)))
+    if params.get("output", None) is not None:
+        cargs.append(params.get("output", None))
     return cargs
 
 
@@ -237,16 +223,18 @@ def mrdump_outputs(
     """
     ret = MrdumpOutputs(
         root=execution.output_file("."),
-        output=execution.output_file(params.get("output")) if (params.get("output") is not None) else None,
+        output=execution.output_file(params.get("output", None)) if (params.get("output") is not None) else None,
     )
     return ret
 
 
 def mrdump_execute(
     params: MrdumpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrdumpOutputs:
     """
+    mrdump
+    
     Print out the values within an image.
     
     If no destination file is specified, the voxel locations will be printed to
@@ -262,10 +250,12 @@ def mrdump_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrdumpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRDUMP_METADATA)
     params = execution.params(params)
     cargs = mrdump_cargs(params, execution)
     ret = mrdump_outputs(params, execution)
@@ -288,6 +278,8 @@ def mrdump(
     runner: Runner | None = None,
 ) -> MrdumpOutputs:
     """
+    mrdump
+    
     Print out the values within an image.
     
     If no destination file is specified, the voxel locations will be printed to
@@ -322,8 +314,6 @@ def mrdump(
     Returns:
         NamedTuple of outputs (described in `MrdumpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRDUMP_METADATA)
     params = mrdump_params(
         mask=mask,
         info=info,
@@ -337,15 +327,14 @@ def mrdump(
         input_=input_,
         output=output,
     )
-    return mrdump_execute(params, execution)
+    return mrdump_execute(params, runner)
 
 
 __all__ = [
     "MRDUMP_METADATA",
-    "MrdumpConfigParameters",
     "MrdumpOutputs",
-    "MrdumpParameters",
     "mrdump",
     "mrdump_config_params",
+    "mrdump_execute",
     "mrdump_params",
 ]