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

niwrap_mrtrix/mrtrix/mrmath.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRMATH_METADATA = Metadata(
-    id="db96b07f1077adff39e302c1a364e5fdc77ddbc2.boutiques",
+    id="53ebb217f19a2e0a5175c77890d64115b390d7bd.boutiques",
     name="mrmath",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,36 @@ MRMATH_METADATA = Metadata(
 
 
 MrmathConfigParameters = typing.TypedDict('MrmathConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+MrmathConfigParametersTagged = typing.TypedDict('MrmathConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 MrmathParameters = typing.TypedDict('MrmathParameters', {
-    "__STYXTYPE__": typing.Literal["mrmath"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/mrmath"]],
+    "axis": typing.NotRequired[int | None],
+    "keep_unary_axes": bool,
+    "datatype": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrmathConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": list[InputPathType],
+    "operation": str,
+    "output": str,
+})
+MrmathParametersTagged = typing.TypedDict('MrmathParametersTagged', {
+    "@type": typing.Literal["mrtrix/mrmath"],
     "axis": typing.NotRequired[int | None],
     "keep_unary_axes": bool,
     "datatype": typing.NotRequired[str | None],
@@ -37,45 +59,12 @@ MrmathParameters = typing.TypedDict('MrmathParameters', {
     "operation": str,
     "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 {
-        "mrmath": mrmath_cargs,
-        "config": mrmath_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 {
-        "mrmath": mrmath_outputs,
-    }.get(t)
 
 
 def mrmath_config_params(
     key: str,
     value: str,
-) -> MrmathConfigParameters:
+) -> MrmathConfigParametersTagged:
     """
     Build parameters.
     
@@ -86,7 +75,7 @@ def mrmath_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -108,14 +97,14 @@ def mrmath_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 MrmathOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mrmath(...)`.
+    Output object returned when calling `MrmathParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -138,7 +127,7 @@ def mrmath_params(
     config: list[MrmathConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> MrmathParameters:
+) -> MrmathParametersTagged:
     """
     Build parameters.
     
@@ -172,7 +161,7 @@ def mrmath_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mrmath",
+        "@type": "mrtrix/mrmath",
         "keep_unary_axes": keep_unary_axes,
         "info": info,
         "quiet": quiet,
@@ -210,40 +199,40 @@ def mrmath_cargs(
     """
     cargs = []
     cargs.append("mrmath")
-    if params.get("axis") is not None:
+    if params.get("axis", None) is not None:
         cargs.extend([
             "-axis",
-            str(params.get("axis"))
+            str(params.get("axis", None))
         ])
-    if params.get("keep_unary_axes"):
+    if params.get("keep_unary_axes", False):
         cargs.append("-keep_unary_axes")
-    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 [mrmath_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("input")])
-    cargs.append(params.get("operation"))
-    cargs.append(params.get("output"))
+    cargs.extend([execution.input_file(f) for f in params.get("input", None)])
+    cargs.append(params.get("operation", None))
+    cargs.append(params.get("output", None))
     return cargs
 
 
@@ -262,18 +251,20 @@ def mrmath_outputs(
     """
     ret = MrmathOutputs(
         root=execution.output_file("."),
-        output=execution.output_file(params.get("output")),
+        output=execution.output_file(params.get("output", None)),
     )
     return ret
 
 
 def mrmath_execute(
     params: MrmathParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrmathOutputs:
     """
-    Compute summary statistic on image intensities either across images, or along a
-    specified axis of a single image.
+    mrmath
+    
+    Compute summary statistic on image intensities either across images, or
+    along a specified axis of a single image.
     
     Supported operations are:
     
@@ -298,10 +289,12 @@ def mrmath_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrmathOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRMATH_METADATA)
     params = execution.params(params)
     cargs = mrmath_cargs(params, execution)
     ret = mrmath_outputs(params, execution)
@@ -327,8 +320,10 @@ def mrmath(
     runner: Runner | None = None,
 ) -> MrmathOutputs:
     """
-    Compute summary statistic on image intensities either across images, or along a
-    specified axis of a single image.
+    mrmath
+    
+    Compute summary statistic on image intensities either across images, or
+    along a specified axis of a single image.
     
     Supported operations are:
     
@@ -381,8 +376,6 @@ def mrmath(
     Returns:
         NamedTuple of outputs (described in `MrmathOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRMATH_METADATA)
     params = mrmath_params(
         axis=axis,
         keep_unary_axes=keep_unary_axes,
@@ -399,15 +392,14 @@ def mrmath(
         operation=operation,
         output=output,
     )
-    return mrmath_execute(params, execution)
+    return mrmath_execute(params, runner)
 
 
 __all__ = [
     "MRMATH_METADATA",
-    "MrmathConfigParameters",
     "MrmathOutputs",
-    "MrmathParameters",
     "mrmath",
     "mrmath_config_params",
+    "mrmath_execute",
     "mrmath_params",
 ]

niwrap_mrtrix/mrtrix/mrmetric.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRMETRIC_METADATA = Metadata(
-    id="3a782263384acdebc8f7c321f87ddf5d013231ae.boutiques",
+    id="900f502c877db64aba337cc23f205ccc871706a3.boutiques",
     name="mrmetric",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,39 @@ MRMETRIC_METADATA = Metadata(
 
 
 MrmetricConfigParameters = typing.TypedDict('MrmetricConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+MrmetricConfigParametersTagged = typing.TypedDict('MrmetricConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 MrmetricParameters = typing.TypedDict('MrmetricParameters', {
-    "__STYXTYPE__": typing.Literal["mrmetric"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/mrmetric"]],
+    "space": typing.NotRequired[str | None],
+    "interp": typing.NotRequired[str | None],
+    "metric": typing.NotRequired[str | None],
+    "mask1": typing.NotRequired[InputPathType | None],
+    "mask2": typing.NotRequired[InputPathType | None],
+    "nonormalisation": bool,
+    "overlap": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrmetricConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "image1": InputPathType,
+    "image2": InputPathType,
+})
+MrmetricParametersTagged = typing.TypedDict('MrmetricParametersTagged', {
+    "@type": typing.Literal["mrtrix/mrmetric"],
     "space": typing.NotRequired[str | None],
     "interp": typing.NotRequired[str | None],
     "metric": typing.NotRequired[str | None],
@@ -40,44 +65,12 @@ MrmetricParameters = typing.TypedDict('MrmetricParameters', {
     "image1": InputPathType,
     "image2": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mrmetric": mrmetric_cargs,
-        "config": mrmetric_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 mrmetric_config_params(
     key: str,
     value: str,
-) -> MrmetricConfigParameters:
+) -> MrmetricConfigParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +81,7 @@ def mrmetric_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -110,14 +103,14 @@ def mrmetric_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 MrmetricOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mrmetric(...)`.
+    Output object returned when calling `MrmetricParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -141,7 +134,7 @@ def mrmetric_params(
     config: list[MrmetricConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> MrmetricParameters:
+) -> MrmetricParametersTagged:
     """
     Build parameters.
     
@@ -178,7 +171,7 @@ def mrmetric_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mrmetric",
+        "@type": "mrtrix/mrmetric",
         "nonormalisation": nonormalisation,
         "overlap": overlap,
         "info": info,
@@ -222,56 +215,56 @@ def mrmetric_cargs(
     """
     cargs = []
     cargs.append("mrmetric")
-    if params.get("space") is not None:
+    if params.get("space", None) is not None:
         cargs.extend([
             "-space",
-            params.get("space")
+            params.get("space", None)
         ])
-    if params.get("interp") is not None:
+    if params.get("interp", None) is not None:
         cargs.extend([
             "-interp",
-            params.get("interp")
+            params.get("interp", None)
         ])
-    if params.get("metric") is not None:
+    if params.get("metric", None) is not None:
         cargs.extend([
             "-metric",
-            params.get("metric")
+            params.get("metric", None)
         ])
-    if params.get("mask1") is not None:
+    if params.get("mask1", None) is not None:
         cargs.extend([
             "-mask1",
-            execution.input_file(params.get("mask1"))
+            execution.input_file(params.get("mask1", None))
         ])
-    if params.get("mask2") is not None:
+    if params.get("mask2", None) is not None:
         cargs.extend([
             "-mask2",
-            execution.input_file(params.get("mask2"))
+            execution.input_file(params.get("mask2", None))
         ])
-    if params.get("nonormalisation"):
+    if params.get("nonormalisation", False):
         cargs.append("-nonormalisation")
-    if params.get("overlap"):
+    if params.get("overlap", False):
         cargs.append("-overlap")
-    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 [mrmetric_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("image1")))
-    cargs.append(execution.input_file(params.get("image2")))
+    cargs.append(execution.input_file(params.get("image1", None)))
+    cargs.append(execution.input_file(params.get("image2", None)))
     return cargs
 
 
@@ -296,9 +289,11 @@ def mrmetric_outputs(
 
 def mrmetric_execute(
     params: MrmetricParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrmetricOutputs:
     """
+    mrmetric
+    
     Computes a dissimilarity metric between two images.
     
     Currently only the mean squared difference is fully implemented.
@@ -313,10 +308,12 @@ def mrmetric_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrmetricOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRMETRIC_METADATA)
     params = execution.params(params)
     cargs = mrmetric_cargs(params, execution)
     ret = mrmetric_outputs(params, execution)
@@ -345,6 +342,8 @@ def mrmetric(
     runner: Runner | None = None,
 ) -> MrmetricOutputs:
     """
+    mrmetric
+    
     Computes a dissimilarity metric between two images.
     
     Currently only the mean squared difference is fully implemented.
@@ -390,8 +389,6 @@ def mrmetric(
     Returns:
         NamedTuple of outputs (described in `MrmetricOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRMETRIC_METADATA)
     params = mrmetric_params(
         space=space,
         interp=interp,
@@ -411,15 +408,14 @@ def mrmetric(
         image1=image1,
         image2=image2,
     )
-    return mrmetric_execute(params, execution)
+    return mrmetric_execute(params, runner)
 
 
 __all__ = [
     "MRMETRIC_METADATA",
-    "MrmetricConfigParameters",
     "MrmetricOutputs",
-    "MrmetricParameters",
     "mrmetric",
     "mrmetric_config_params",
+    "mrmetric_execute",
     "mrmetric_params",
 ]