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

niwrap_mrtrix/mrtrix/warpconvert.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 WARPCONVERT_METADATA = Metadata(
-    id="32e6c5d3c78c56a0fcca0c5a864eb34e71feeb43.boutiques",
+    id="7468f4768b6e008e092ad5508a8d2b4875bab30a.boutiques",
     name="warpconvert",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,36 @@ WARPCONVERT_METADATA = Metadata(
 
 
 WarpconvertConfigParameters = typing.TypedDict('WarpconvertConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+WarpconvertConfigParametersTagged = typing.TypedDict('WarpconvertConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 WarpconvertParameters = typing.TypedDict('WarpconvertParameters', {
-    "__STYXTYPE__": typing.Literal["warpconvert"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/warpconvert"]],
+    "template": typing.NotRequired[InputPathType | None],
+    "midway_space": bool,
+    "from": typing.NotRequired[int | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[WarpconvertConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "in": InputPathType,
+    "type": str,
+    "out": str,
+})
+WarpconvertParametersTagged = typing.TypedDict('WarpconvertParametersTagged', {
+    "@type": typing.Literal["mrtrix/warpconvert"],
     "template": typing.NotRequired[InputPathType | None],
     "midway_space": bool,
     "from": typing.NotRequired[int | None],
@@ -37,45 +59,12 @@ WarpconvertParameters = typing.TypedDict('WarpconvertParameters', {
     "type": str,
     "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 {
-        "warpconvert": warpconvert_cargs,
-        "config": warpconvert_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 {
-        "warpconvert": warpconvert_outputs,
-    }.get(t)
 
 
 def warpconvert_config_params(
     key: str,
     value: str,
-) -> WarpconvertConfigParameters:
+) -> WarpconvertConfigParametersTagged:
     """
     Build parameters.
     
@@ -86,7 +75,7 @@ def warpconvert_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -108,14 +97,14 @@ def warpconvert_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 WarpconvertOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `warpconvert(...)`.
+    Output object returned when calling `WarpconvertParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -138,7 +127,7 @@ def warpconvert_params(
     config: list[WarpconvertConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> WarpconvertParameters:
+) -> WarpconvertParametersTagged:
     """
     Build parameters.
     
@@ -178,7 +167,7 @@ def warpconvert_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "warpconvert",
+        "@type": "mrtrix/warpconvert",
         "midway_space": midway_space,
         "info": info,
         "quiet": quiet,
@@ -216,40 +205,40 @@ def warpconvert_cargs(
     """
     cargs = []
     cargs.append("warpconvert")
-    if params.get("template") is not None:
+    if params.get("template", None) is not None:
         cargs.extend([
             "-template",
-            execution.input_file(params.get("template"))
+            execution.input_file(params.get("template", None))
         ])
-    if params.get("midway_space"):
+    if params.get("midway_space", False):
         cargs.append("-midway_space")
-    if params.get("from") is not None:
+    if params.get("from", None) is not None:
         cargs.extend([
             "-from",
-            str(params.get("from"))
+            str(params.get("from", 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 [warpconvert_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("type"))
-    cargs.append(params.get("out"))
+    cargs.append(execution.input_file(params.get("in", None)))
+    cargs.append(params.get("type", None))
+    cargs.append(params.get("out", None))
     return cargs
 
 
@@ -268,16 +257,18 @@ def warpconvert_outputs(
     """
     ret = WarpconvertOutputs(
         root=execution.output_file("."),
-        out=execution.output_file(params.get("out")),
+        out=execution.output_file(params.get("out", None)),
     )
     return ret
 
 
 def warpconvert_execute(
     params: WarpconvertParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> WarpconvertOutputs:
     """
+    warpconvert
+    
     Convert between different representations of a non-linear warp.
     
     A deformation field is defined as an image where each voxel defines the
@@ -297,10 +288,12 @@ def warpconvert_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `WarpconvertOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(WARPCONVERT_METADATA)
     params = execution.params(params)
     cargs = warpconvert_cargs(params, execution)
     ret = warpconvert_outputs(params, execution)
@@ -326,6 +319,8 @@ def warpconvert(
     runner: Runner | None = None,
 ) -> WarpconvertOutputs:
     """
+    warpconvert
+    
     Convert between different representations of a non-linear warp.
     
     A deformation field is defined as an image where each voxel defines the
@@ -379,8 +374,6 @@ def warpconvert(
     Returns:
         NamedTuple of outputs (described in `WarpconvertOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(WARPCONVERT_METADATA)
     params = warpconvert_params(
         template=template,
         midway_space=midway_space,
@@ -397,15 +390,14 @@ def warpconvert(
         type_=type_,
         out=out,
     )
-    return warpconvert_execute(params, execution)
+    return warpconvert_execute(params, runner)
 
 
 __all__ = [
     "WARPCONVERT_METADATA",
-    "WarpconvertConfigParameters",
     "WarpconvertOutputs",
-    "WarpconvertParameters",
     "warpconvert",
     "warpconvert_config_params",
+    "warpconvert_execute",
     "warpconvert_params",
 ]

niwrap_mrtrix/mrtrix/warpcorrect.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 WARPCORRECT_METADATA = Metadata(
-    id="0f830221bdd17e83588ad92fc905ee407c4292f6.boutiques",
+    id="d93e432b2c126575958a3ff19d36f91ad4461c2e.boutiques",
     name="warpcorrect",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,34 @@ WARPCORRECT_METADATA = Metadata(
 
 
 WarpcorrectConfigParameters = typing.TypedDict('WarpcorrectConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+WarpcorrectConfigParametersTagged = typing.TypedDict('WarpcorrectConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 WarpcorrectParameters = typing.TypedDict('WarpcorrectParameters', {
-    "__STYXTYPE__": typing.Literal["warpcorrect"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/warpcorrect"]],
+    "marker": typing.NotRequired[list[float] | None],
+    "tolerance": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[WarpcorrectConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "in": InputPathType,
+    "out": str,
+})
+WarpcorrectParametersTagged = typing.TypedDict('WarpcorrectParametersTagged', {
+    "@type": typing.Literal["mrtrix/warpcorrect"],
     "marker": typing.NotRequired[list[float] | None],
     "tolerance": typing.NotRequired[float | None],
     "info": bool,
@@ -35,45 +55,12 @@ WarpcorrectParameters = typing.TypedDict('WarpcorrectParameters', {
     "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 {
-        "warpcorrect": warpcorrect_cargs,
-        "config": warpcorrect_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 {
-        "warpcorrect": warpcorrect_outputs,
-    }.get(t)
 
 
 def warpcorrect_config_params(
     key: str,
     value: str,
-) -> WarpcorrectConfigParameters:
+) -> WarpcorrectConfigParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +71,7 @@ def warpcorrect_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -106,14 +93,14 @@ def warpcorrect_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 WarpcorrectOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `warpcorrect(...)`.
+    Output object returned when calling `WarpcorrectParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -134,7 +121,7 @@ def warpcorrect_params(
     config: list[WarpcorrectConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> WarpcorrectParameters:
+) -> WarpcorrectParametersTagged:
     """
     Build parameters.
     
@@ -161,7 +148,7 @@ def warpcorrect_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "warpcorrect",
+        "@type": "mrtrix/warpcorrect",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -197,37 +184,37 @@ def warpcorrect_cargs(
     """
     cargs = []
     cargs.append("warpcorrect")
-    if params.get("marker") is not None:
+    if params.get("marker", None) is not None:
         cargs.extend([
             "-marker",
-            *map(str, params.get("marker"))
+            *map(str, params.get("marker", None))
         ])
-    if params.get("tolerance") is not None:
+    if params.get("tolerance", None) is not None:
         cargs.extend([
             "-tolerance",
-            str(params.get("tolerance"))
+            str(params.get("tolerance", 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 [warpcorrect_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
 
 
@@ -246,18 +233,20 @@ def warpcorrect_outputs(
     """
     ret = WarpcorrectOutputs(
         root=execution.output_file("."),
-        out=execution.output_file(params.get("out")),
+        out=execution.output_file(params.get("out", None)),
     )
     return ret
 
 
 def warpcorrect_execute(
     params: WarpcorrectParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> WarpcorrectOutputs:
     """
-    Replaces voxels in a deformation field that point to a specific out of bounds
-    location with nan,nan,nan.
+    warpcorrect
+    
+    Replaces voxels in a deformation field that point to a specific out of
+    bounds location with nan,nan,nan.
     
     This can be used in conjunction with the warpinit command to compute a
     MRtrix compatible deformation field from non-linear transformations
@@ -273,10 +262,12 @@ def warpcorrect_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `WarpcorrectOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(WARPCORRECT_METADATA)
     params = execution.params(params)
     cargs = warpcorrect_cargs(params, execution)
     ret = warpcorrect_outputs(params, execution)
@@ -300,8 +291,10 @@ def warpcorrect(
     runner: Runner | None = None,
 ) -> WarpcorrectOutputs:
     """
-    Replaces voxels in a deformation field that point to a specific out of bounds
-    location with nan,nan,nan.
+    warpcorrect
+    
+    Replaces voxels in a deformation field that point to a specific out of
+    bounds location with nan,nan,nan.
     
     This can be used in conjunction with the warpinit command to compute a
     MRtrix compatible deformation field from non-linear transformations
@@ -338,8 +331,6 @@ def warpcorrect(
     Returns:
         NamedTuple of outputs (described in `WarpcorrectOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(WARPCORRECT_METADATA)
     params = warpcorrect_params(
         marker=marker,
         tolerance=tolerance,
@@ -354,15 +345,14 @@ def warpcorrect(
         in_=in_,
         out=out,
     )
-    return warpcorrect_execute(params, execution)
+    return warpcorrect_execute(params, runner)
 
 
 __all__ = [
     "WARPCORRECT_METADATA",
-    "WarpcorrectConfigParameters",
     "WarpcorrectOutputs",
-    "WarpcorrectParameters",
     "warpcorrect",
     "warpcorrect_config_params",
+    "warpcorrect_execute",
     "warpcorrect_params",
 ]