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

niwrap_mrtrix/mrtrix/vectorstats.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 VECTORSTATS_METADATA = Metadata(
-    id="24ba2da446c51868e04d07323b5e99fb4f2ccaad.boutiques",
+    id="bb3edd72079d87de8242594d71273892006e9def.boutiques",
     name="vectorstats",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,20 +14,55 @@ VECTORSTATS_METADATA = Metadata(
 
 
 VectorstatsColumnParameters = typing.TypedDict('VectorstatsColumnParameters', {
-    "__STYXTYPE__": typing.Literal["column"],
+    "@type": typing.NotRequired[typing.Literal["column"]],
+    "path": InputPathType,
+})
+VectorstatsColumnParametersTagged = typing.TypedDict('VectorstatsColumnParametersTagged', {
+    "@type": typing.Literal["column"],
     "path": InputPathType,
 })
 
 
 VectorstatsConfigParameters = typing.TypedDict('VectorstatsConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+VectorstatsConfigParametersTagged = typing.TypedDict('VectorstatsConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 VectorstatsParameters = typing.TypedDict('VectorstatsParameters', {
-    "__STYXTYPE__": typing.Literal["vectorstats"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/vectorstats"]],
+    "notest": bool,
+    "errors": typing.NotRequired[str | None],
+    "exchange_within": typing.NotRequired[InputPathType | None],
+    "exchange_whole": typing.NotRequired[InputPathType | None],
+    "strong": bool,
+    "nshuffles": typing.NotRequired[int | None],
+    "permutations": typing.NotRequired[InputPathType | None],
+    "variance": typing.NotRequired[InputPathType | None],
+    "ftests": typing.NotRequired[InputPathType | None],
+    "fonly": bool,
+    "column": typing.NotRequired[list[VectorstatsColumnParameters] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[VectorstatsConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "design": InputPathType,
+    "contrast": InputPathType,
+    "output": str,
+})
+VectorstatsParametersTagged = typing.TypedDict('VectorstatsParametersTagged', {
+    "@type": typing.Literal["mrtrix/vectorstats"],
     "notest": bool,
     "errors": typing.NotRequired[str | None],
     "exchange_within": typing.NotRequired[InputPathType | None],
@@ -52,44 +87,11 @@ VectorstatsParameters = typing.TypedDict('VectorstatsParameters', {
     "contrast": 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 {
-        "vectorstats": vectorstats_cargs,
-        "column": vectorstats_column_cargs,
-        "config": vectorstats_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 vectorstats_column_params(
     path: InputPathType,
-) -> VectorstatsColumnParameters:
+) -> VectorstatsColumnParametersTagged:
     """
     Build parameters.
     
@@ -102,7 +104,7 @@ def vectorstats_column_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "column",
+        "@type": "column",
         "path": path,
     }
     return params
@@ -123,14 +125,14 @@ def vectorstats_column_cargs(
     """
     cargs = []
     cargs.append("-column")
-    cargs.append(execution.input_file(params.get("path")))
+    cargs.append(execution.input_file(params.get("path", None)))
     return cargs
 
 
 def vectorstats_config_params(
     key: str,
     value: str,
-) -> VectorstatsConfigParameters:
+) -> VectorstatsConfigParametersTagged:
     """
     Build parameters.
     
@@ -141,7 +143,7 @@ def vectorstats_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -163,14 +165,14 @@ def vectorstats_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 VectorstatsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `vectorstats(...)`.
+    Output object returned when calling `VectorstatsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -200,7 +202,7 @@ def vectorstats_params(
     config: list[VectorstatsConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> VectorstatsParameters:
+) -> VectorstatsParametersTagged:
     """
     Build parameters.
     
@@ -254,7 +256,7 @@ def vectorstats_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "vectorstats",
+        "@type": "mrtrix/vectorstats",
         "notest": notest,
         "strong": strong,
         "fonly": fonly,
@@ -307,72 +309,72 @@ def vectorstats_cargs(
     """
     cargs = []
     cargs.append("vectorstats")
-    if params.get("notest"):
+    if params.get("notest", False):
         cargs.append("-notest")
-    if params.get("errors") is not None:
+    if params.get("errors", None) is not None:
         cargs.extend([
             "-errors",
-            params.get("errors")
+            params.get("errors", None)
         ])
-    if params.get("exchange_within") is not None:
+    if params.get("exchange_within", None) is not None:
         cargs.extend([
             "-exchange_within",
-            execution.input_file(params.get("exchange_within"))
+            execution.input_file(params.get("exchange_within", None))
         ])
-    if params.get("exchange_whole") is not None:
+    if params.get("exchange_whole", None) is not None:
         cargs.extend([
             "-exchange_whole",
-            execution.input_file(params.get("exchange_whole"))
+            execution.input_file(params.get("exchange_whole", None))
         ])
-    if params.get("strong"):
+    if params.get("strong", False):
         cargs.append("-strong")
-    if params.get("nshuffles") is not None:
+    if params.get("nshuffles", None) is not None:
         cargs.extend([
             "-nshuffles",
-            str(params.get("nshuffles"))
+            str(params.get("nshuffles", None))
         ])
-    if params.get("permutations") is not None:
+    if params.get("permutations", None) is not None:
         cargs.extend([
             "-permutations",
-            execution.input_file(params.get("permutations"))
+            execution.input_file(params.get("permutations", None))
         ])
-    if params.get("variance") is not None:
+    if params.get("variance", None) is not None:
         cargs.extend([
             "-variance",
-            execution.input_file(params.get("variance"))
+            execution.input_file(params.get("variance", None))
         ])
-    if params.get("ftests") is not None:
+    if params.get("ftests", None) is not None:
         cargs.extend([
             "-ftests",
-            execution.input_file(params.get("ftests"))
+            execution.input_file(params.get("ftests", None))
         ])
-    if params.get("fonly"):
+    if params.get("fonly", False):
         cargs.append("-fonly")
-    if params.get("column") is not None:
-        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("column")] for a in c])
-    if params.get("info"):
+    if params.get("column", None) is not None:
+        cargs.extend([a for c in [vectorstats_column_cargs(s, execution) for s in params.get("column", None)] for a in c])
+    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 [vectorstats_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")))
-    cargs.append(execution.input_file(params.get("design")))
-    cargs.append(execution.input_file(params.get("contrast")))
-    cargs.append(params.get("output"))
+    cargs.append(execution.input_file(params.get("input", None)))
+    cargs.append(execution.input_file(params.get("design", None)))
+    cargs.append(execution.input_file(params.get("contrast", None)))
+    cargs.append(params.get("output", None))
     return cargs
 
 
@@ -397,9 +399,11 @@ def vectorstats_outputs(
 
 def vectorstats_execute(
     params: VectorstatsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VectorstatsOutputs:
     """
+    vectorstats
+    
     Statistical testing of vector data using non-parametric permutation testing.
     
     This command can be used to perform permutation testing of any form of data.
@@ -428,10 +432,12 @@ def vectorstats_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VectorstatsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(VECTORSTATS_METADATA)
     params = execution.params(params)
     cargs = vectorstats_cargs(params, execution)
     ret = vectorstats_outputs(params, execution)
@@ -466,6 +472,8 @@ def vectorstats(
     runner: Runner | None = None,
 ) -> VectorstatsOutputs:
     """
+    vectorstats
+    
     Statistical testing of vector data using non-parametric permutation testing.
     
     This command can be used to perform permutation testing of any form of data.
@@ -542,8 +550,6 @@ def vectorstats(
     Returns:
         NamedTuple of outputs (described in `VectorstatsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(VECTORSTATS_METADATA)
     params = vectorstats_params(
         notest=notest,
         errors=errors,
@@ -569,17 +575,15 @@ def vectorstats(
         contrast=contrast,
         output=output,
     )
-    return vectorstats_execute(params, execution)
+    return vectorstats_execute(params, runner)
 
 
 __all__ = [
     "VECTORSTATS_METADATA",
-    "VectorstatsColumnParameters",
-    "VectorstatsConfigParameters",
     "VectorstatsOutputs",
-    "VectorstatsParameters",
     "vectorstats",
     "vectorstats_column_params",
     "vectorstats_config_params",
+    "vectorstats_execute",
     "vectorstats_params",
 ]

niwrap_mrtrix/mrtrix/voxel2fixel.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 VOXEL2FIXEL_METADATA = Metadata(
-    id="408593a6668880f0604aa841e52091056f3631b3.boutiques",
+    id="d594503cf463c1f9580f4bafd342dc5f91a012f8.boutiques",
     name="voxel2fixel",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,34 @@ VOXEL2FIXEL_METADATA = Metadata(
 
 
 Voxel2fixelConfigParameters = typing.TypedDict('Voxel2fixelConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Voxel2fixelConfigParametersTagged = typing.TypedDict('Voxel2fixelConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Voxel2fixelParameters = typing.TypedDict('Voxel2fixelParameters', {
-    "__STYXTYPE__": typing.Literal["voxel2fixel"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/voxel2fixel"]],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Voxel2fixelConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "image_in": InputPathType,
+    "fixel_directory_in": InputPathType,
+    "fixel_directory_out": str,
+    "fixel_data_out": str,
+})
+Voxel2fixelParametersTagged = typing.TypedDict('Voxel2fixelParametersTagged', {
+    "@type": typing.Literal["mrtrix/voxel2fixel"],
     "info": bool,
     "quiet": bool,
     "debug": bool,
@@ -35,44 +55,12 @@ Voxel2fixelParameters = typing.TypedDict('Voxel2fixelParameters', {
     "fixel_directory_out": str,
     "fixel_data_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 {
-        "voxel2fixel": voxel2fixel_cargs,
-        "config": voxel2fixel_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 voxel2fixel_config_params(
     key: str,
     value: str,
-) -> Voxel2fixelConfigParameters:
+) -> Voxel2fixelConfigParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +71,7 @@ def voxel2fixel_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -105,14 +93,14 @@ def voxel2fixel_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 Voxel2fixelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `voxel2fixel(...)`.
+    Output object returned when calling `Voxel2fixelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -131,7 +119,7 @@ def voxel2fixel_params(
     config: list[Voxel2fixelConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Voxel2fixelParameters:
+) -> Voxel2fixelParametersTagged:
     """
     Build parameters.
     
@@ -158,7 +146,7 @@ def voxel2fixel_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "voxel2fixel",
+        "@type": "mrtrix/voxel2fixel",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -192,29 +180,29 @@ def voxel2fixel_cargs(
     """
     cargs = []
     cargs.append("voxel2fixel")
-    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 [voxel2fixel_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("image_in")))
-    cargs.append(execution.input_file(params.get("fixel_directory_in")))
-    cargs.append(params.get("fixel_directory_out"))
-    cargs.append(params.get("fixel_data_out"))
+    cargs.append(execution.input_file(params.get("image_in", None)))
+    cargs.append(execution.input_file(params.get("fixel_directory_in", None)))
+    cargs.append(params.get("fixel_directory_out", None))
+    cargs.append(params.get("fixel_data_out", None))
     return cargs
 
 
@@ -239,9 +227,11 @@ def voxel2fixel_outputs(
 
 def voxel2fixel_execute(
     params: Voxel2fixelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Voxel2fixelOutputs:
     """
+    voxel2fixel
+    
     Map the scalar value in each voxel to all fixels within that voxel.
     
     This command is designed to enable CFE-based statistical analysis to be
@@ -257,10 +247,12 @@ def voxel2fixel_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Voxel2fixelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(VOXEL2FIXEL_METADATA)
     params = execution.params(params)
     cargs = voxel2fixel_cargs(params, execution)
     ret = voxel2fixel_outputs(params, execution)
@@ -284,6 +276,8 @@ def voxel2fixel(
     runner: Runner | None = None,
 ) -> Voxel2fixelOutputs:
     """
+    voxel2fixel
+    
     Map the scalar value in each voxel to all fixels within that voxel.
     
     This command is designed to enable CFE-based statistical analysis to be
@@ -320,8 +314,6 @@ def voxel2fixel(
     Returns:
         NamedTuple of outputs (described in `Voxel2fixelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(VOXEL2FIXEL_METADATA)
     params = voxel2fixel_params(
         info=info,
         quiet=quiet,
@@ -336,15 +328,14 @@ def voxel2fixel(
         fixel_directory_out=fixel_directory_out,
         fixel_data_out=fixel_data_out,
     )
-    return voxel2fixel_execute(params, execution)
+    return voxel2fixel_execute(params, runner)
 
 
 __all__ = [
     "VOXEL2FIXEL_METADATA",
-    "Voxel2fixelConfigParameters",
     "Voxel2fixelOutputs",
-    "Voxel2fixelParameters",
     "voxel2fixel",
     "voxel2fixel_config_params",
+    "voxel2fixel_execute",
     "voxel2fixel_params",
 ]