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

niwrap_mrtrix/mrtrix/shconv.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SHCONV_METADATA = Metadata(
-    id="fd5362bc6d2af00ffe1866d4f370ae826df3dd4d.boutiques",
+    id="b17c6209ec80f04a818c3feb05bf3e7580772b75.boutiques",
     name="shconv",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,28 +14,56 @@ SHCONV_METADATA = Metadata(
 
 
 ShconvVariousStringParameters = typing.TypedDict('ShconvVariousStringParameters', {
-    "__STYXTYPE__": typing.Literal["VariousString"],
+    "@type": typing.NotRequired[typing.Literal["VariousString"]],
+    "obj": str,
+})
+ShconvVariousStringParametersTagged = typing.TypedDict('ShconvVariousStringParametersTagged', {
+    "@type": typing.Literal["VariousString"],
     "obj": str,
 })
 
 
 ShconvVariousFileParameters = typing.TypedDict('ShconvVariousFileParameters', {
-    "__STYXTYPE__": typing.Literal["VariousFile"],
+    "@type": typing.NotRequired[typing.Literal["VariousFile"]],
+    "obj": InputPathType,
+})
+ShconvVariousFileParametersTagged = typing.TypedDict('ShconvVariousFileParametersTagged', {
+    "@type": typing.Literal["VariousFile"],
     "obj": InputPathType,
 })
 
 
 ShconvConfigParameters = typing.TypedDict('ShconvConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+ShconvConfigParametersTagged = typing.TypedDict('ShconvConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 ShconvParameters = typing.TypedDict('ShconvParameters', {
-    "__STYXTYPE__": typing.Literal["shconv"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/shconv"]],
+    "datatype": typing.NotRequired[str | None],
+    "strides": typing.NotRequired[typing.Union[ShconvVariousStringParametersTagged, ShconvVariousFileParametersTagged] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[ShconvConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "odf_response": list[str],
+    "SH_out": str,
+})
+ShconvParametersTagged = typing.TypedDict('ShconvParametersTagged', {
+    "@type": typing.Literal["mrtrix/shconv"],
     "datatype": typing.NotRequired[str | None],
-    "strides": typing.NotRequired[typing.Union[ShconvVariousStringParameters, ShconvVariousFileParameters] | None],
+    "strides": typing.NotRequired[typing.Union[ShconvVariousStringParametersTagged, ShconvVariousFileParametersTagged] | None],
     "info": bool,
     "quiet": bool,
     "debug": bool,
@@ -49,7 +77,7 @@ ShconvParameters = typing.TypedDict('ShconvParameters', {
 })
 
 
-def dyn_cargs(
+def shconv_strides_cargs_dyn_fn(
     t: str,
 ) -> typing.Any:
     """
@@ -61,14 +89,12 @@ def dyn_cargs(
         Build cargs function.
     """
     return {
-        "shconv": shconv_cargs,
         "VariousString": shconv_various_string_cargs,
         "VariousFile": shconv_various_file_cargs,
-        "config": shconv_config_cargs,
     }.get(t)
 
 
-def dyn_outputs(
+def shconv_strides_outputs_dyn_fn(
     t: str,
 ) -> typing.Any:
     """
@@ -80,13 +106,12 @@ def dyn_outputs(
         Build outputs function.
     """
     return {
-        "shconv": shconv_outputs,
     }.get(t)
 
 
 def shconv_various_string_params(
     obj: str,
-) -> ShconvVariousStringParameters:
+) -> ShconvVariousStringParametersTagged:
     """
     Build parameters.
     
@@ -96,7 +121,7 @@ def shconv_various_string_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "VariousString",
+        "@type": "VariousString",
         "obj": obj,
     }
     return params
@@ -116,13 +141,13 @@ def shconv_various_string_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append(params.get("obj"))
+    cargs.append(params.get("obj", None))
     return cargs
 
 
 def shconv_various_file_params(
     obj: InputPathType,
-) -> ShconvVariousFileParameters:
+) -> ShconvVariousFileParametersTagged:
     """
     Build parameters.
     
@@ -132,7 +157,7 @@ def shconv_various_file_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "VariousFile",
+        "@type": "VariousFile",
         "obj": obj,
     }
     return params
@@ -152,14 +177,14 @@ def shconv_various_file_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append(execution.input_file(params.get("obj")))
+    cargs.append(execution.input_file(params.get("obj", None)))
     return cargs
 
 
 def shconv_config_params(
     key: str,
     value: str,
-) -> ShconvConfigParameters:
+) -> ShconvConfigParametersTagged:
     """
     Build parameters.
     
@@ -170,7 +195,7 @@ def shconv_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -192,14 +217,14 @@ def shconv_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 ShconvOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `shconv(...)`.
+    Output object returned when calling `ShconvParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -211,7 +236,7 @@ def shconv_params(
     odf_response: list[str],
     sh_out: str,
     datatype: str | None = None,
-    strides: typing.Union[ShconvVariousStringParameters, ShconvVariousFileParameters] | None = None,
+    strides: typing.Union[ShconvVariousStringParametersTagged, ShconvVariousFileParametersTagged] | None = None,
     info: bool = False,
     quiet: bool = False,
     debug: bool = False,
@@ -220,7 +245,7 @@ def shconv_params(
     config: list[ShconvConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> ShconvParameters:
+) -> ShconvParametersTagged:
     """
     Build parameters.
     
@@ -253,7 +278,7 @@ def shconv_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "shconv",
+        "@type": "mrtrix/shconv",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -289,37 +314,37 @@ def shconv_cargs(
     """
     cargs = []
     cargs.append("shconv")
-    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("strides") is not None:
+    if params.get("strides", None) is not None:
         cargs.extend([
             "-strides",
-            *dyn_cargs(params.get("strides")["__STYXTYPE__"])(params.get("strides"), execution)
+            *shconv_strides_cargs_dyn_fn(params.get("strides", None)["@type"])(params.get("strides", None), execution)
         ])
-    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 [shconv_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(params.get("odf_response"))
-    cargs.append(params.get("SH_out"))
+    cargs.extend(params.get("odf_response", None))
+    cargs.append(params.get("SH_out", None))
     return cargs
 
 
@@ -338,16 +363,18 @@ def shconv_outputs(
     """
     ret = ShconvOutputs(
         root=execution.output_file("."),
-        sh_out=execution.output_file(params.get("SH_out")),
+        sh_out=execution.output_file(params.get("SH_out", None)),
     )
     return ret
 
 
 def shconv_execute(
     params: ShconvParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ShconvOutputs:
     """
+    shconv
+    
     Perform spherical convolution.
     
     Provided with matching pairs of response function and ODF images (containing
@@ -379,10 +406,12 @@ def shconv_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ShconvOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SHCONV_METADATA)
     params = execution.params(params)
     cargs = shconv_cargs(params, execution)
     ret = shconv_outputs(params, execution)
@@ -394,7 +423,7 @@ def shconv(
     odf_response: list[str],
     sh_out: str,
     datatype: str | None = None,
-    strides: typing.Union[ShconvVariousStringParameters, ShconvVariousFileParameters] | None = None,
+    strides: typing.Union[ShconvVariousStringParametersTagged, ShconvVariousFileParametersTagged] | None = None,
     info: bool = False,
     quiet: bool = False,
     debug: bool = False,
@@ -406,6 +435,8 @@ def shconv(
     runner: Runner | None = None,
 ) -> ShconvOutputs:
     """
+    shconv
+    
     Perform spherical convolution.
     
     Provided with matching pairs of response function and ODF images (containing
@@ -464,8 +495,6 @@ def shconv(
     Returns:
         NamedTuple of outputs (described in `ShconvOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SHCONV_METADATA)
     params = shconv_params(
         datatype=datatype,
         strides=strides,
@@ -480,18 +509,15 @@ def shconv(
         odf_response=odf_response,
         sh_out=sh_out,
     )
-    return shconv_execute(params, execution)
+    return shconv_execute(params, runner)
 
 
 __all__ = [
     "SHCONV_METADATA",
-    "ShconvConfigParameters",
     "ShconvOutputs",
-    "ShconvParameters",
-    "ShconvVariousFileParameters",
-    "ShconvVariousStringParameters",
     "shconv",
     "shconv_config_params",
+    "shconv_execute",
     "shconv_params",
     "shconv_various_file_params",
     "shconv_various_string_params",

niwrap_mrtrix/mrtrix/tck2connectome.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TCK2CONNECTOME_METADATA = Metadata(
-    id="738d3835f7defdf440eba97b62da7245751874db.boutiques",
+    id="a66d5312bce1284177c4cf9ad60b3718c4a1a2b0.boutiques",
     name="tck2connectome",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,49 @@ TCK2CONNECTOME_METADATA = Metadata(
 
 
 Tck2connectomeConfigParameters = typing.TypedDict('Tck2connectomeConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Tck2connectomeConfigParametersTagged = typing.TypedDict('Tck2connectomeConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Tck2connectomeParameters = typing.TypedDict('Tck2connectomeParameters', {
-    "__STYXTYPE__": typing.Literal["tck2connectome"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/tck2connectome"]],
+    "assignment_end_voxels": bool,
+    "assignment_radial_search": typing.NotRequired[float | None],
+    "assignment_reverse_search": typing.NotRequired[float | None],
+    "assignment_forward_search": typing.NotRequired[float | None],
+    "assignment_all_voxels": bool,
+    "scale_length": bool,
+    "scale_invlength": bool,
+    "scale_invnodevol": bool,
+    "scale_file": typing.NotRequired[InputPathType | None],
+    "symmetric": bool,
+    "zero_diagonal": bool,
+    "stat_edge": typing.NotRequired[str | None],
+    "tck_weights_in": typing.NotRequired[InputPathType | None],
+    "keep_unassigned": bool,
+    "out_assignments": typing.NotRequired[str | None],
+    "vector": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Tck2connectomeConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "tracks_in": InputPathType,
+    "nodes_in": InputPathType,
+    "connectome_out": str,
+})
+Tck2connectomeParametersTagged = typing.TypedDict('Tck2connectomeParametersTagged', {
+    "@type": typing.Literal["mrtrix/tck2connectome"],
     "assignment_end_voxels": bool,
     "assignment_radial_search": typing.NotRequired[float | None],
     "assignment_reverse_search": typing.NotRequired[float | None],
@@ -50,45 +85,12 @@ Tck2connectomeParameters = typing.TypedDict('Tck2connectomeParameters', {
     "nodes_in": InputPathType,
     "connectome_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 {
-        "tck2connectome": tck2connectome_cargs,
-        "config": tck2connectome_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 {
-        "tck2connectome": tck2connectome_outputs,
-    }.get(t)
 
 
 def tck2connectome_config_params(
     key: str,
     value: str,
-) -> Tck2connectomeConfigParameters:
+) -> Tck2connectomeConfigParametersTagged:
     """
     Build parameters.
     
@@ -99,7 +101,7 @@ def tck2connectome_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -121,14 +123,14 @@ def tck2connectome_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 Tck2connectomeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `tck2connectome(...)`.
+    Output object returned when calling `Tck2connectomeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -167,7 +169,7 @@ def tck2connectome_params(
     config: list[Tck2connectomeConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Tck2connectomeParameters:
+) -> Tck2connectomeParametersTagged:
     """
     Build parameters.
     
@@ -230,7 +232,7 @@ def tck2connectome_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tck2connectome",
+        "@type": "mrtrix/tck2connectome",
         "assignment_end_voxels": assignment_end_voxels,
         "assignment_all_voxels": assignment_all_voxels,
         "scale_length": scale_length,
@@ -286,81 +288,81 @@ def tck2connectome_cargs(
     """
     cargs = []
     cargs.append("tck2connectome")
-    if params.get("assignment_end_voxels"):
+    if params.get("assignment_end_voxels", False):
         cargs.append("-assignment_end_voxels")
-    if params.get("assignment_radial_search") is not None:
+    if params.get("assignment_radial_search", None) is not None:
         cargs.extend([
             "-assignment_radial_search",
-            str(params.get("assignment_radial_search"))
+            str(params.get("assignment_radial_search", None))
         ])
-    if params.get("assignment_reverse_search") is not None:
+    if params.get("assignment_reverse_search", None) is not None:
         cargs.extend([
             "-assignment_reverse_search",
-            str(params.get("assignment_reverse_search"))
+            str(params.get("assignment_reverse_search", None))
         ])
-    if params.get("assignment_forward_search") is not None:
+    if params.get("assignment_forward_search", None) is not None:
         cargs.extend([
             "-assignment_forward_search",
-            str(params.get("assignment_forward_search"))
+            str(params.get("assignment_forward_search", None))
         ])
-    if params.get("assignment_all_voxels"):
+    if params.get("assignment_all_voxels", False):
         cargs.append("-assignment_all_voxels")
-    if params.get("scale_length"):
+    if params.get("scale_length", False):
         cargs.append("-scale_length")
-    if params.get("scale_invlength"):
+    if params.get("scale_invlength", False):
         cargs.append("-scale_invlength")
-    if params.get("scale_invnodevol"):
+    if params.get("scale_invnodevol", False):
         cargs.append("-scale_invnodevol")
-    if params.get("scale_file") is not None:
+    if params.get("scale_file", None) is not None:
         cargs.extend([
             "-scale_file",
-            execution.input_file(params.get("scale_file"))
+            execution.input_file(params.get("scale_file", None))
         ])
-    if params.get("symmetric"):
+    if params.get("symmetric", False):
         cargs.append("-symmetric")
-    if params.get("zero_diagonal"):
+    if params.get("zero_diagonal", False):
         cargs.append("-zero_diagonal")
-    if params.get("stat_edge") is not None:
+    if params.get("stat_edge", None) is not None:
         cargs.extend([
             "-stat_edge",
-            params.get("stat_edge")
+            params.get("stat_edge", None)
         ])
-    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("keep_unassigned"):
+    if params.get("keep_unassigned", False):
         cargs.append("-keep_unassigned")
-    if params.get("out_assignments") is not None:
+    if params.get("out_assignments", None) is not None:
         cargs.extend([
             "-out_assignments",
-            params.get("out_assignments")
+            params.get("out_assignments", None)
         ])
-    if params.get("vector"):
+    if params.get("vector", False):
         cargs.append("-vector")
-    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 [tck2connectome_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("nodes_in")))
-    cargs.append(params.get("connectome_out"))
+    cargs.append(execution.input_file(params.get("tracks_in", None)))
+    cargs.append(execution.input_file(params.get("nodes_in", None)))
+    cargs.append(params.get("connectome_out", None))
     return cargs
 
 
@@ -379,17 +381,19 @@ def tck2connectome_outputs(
     """
     ret = Tck2connectomeOutputs(
         root=execution.output_file("."),
-        connectome_out=execution.output_file(params.get("connectome_out")),
-        out_assignments=execution.output_file(params.get("out_assignments")) if (params.get("out_assignments") is not None) else None,
+        connectome_out=execution.output_file(params.get("connectome_out", None)),
+        out_assignments=execution.output_file(params.get("out_assignments", None)) if (params.get("out_assignments") is not None) else None,
     )
     return ret
 
 
 def tck2connectome_execute(
     params: Tck2connectomeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Tck2connectomeOutputs:
     """
+    tck2connectome
+    
     Generate a connectome matrix from a streamlines file and a node parcellation
     image.
     
@@ -413,10 +417,12 @@ def tck2connectome_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Tck2connectomeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TCK2CONNECTOME_METADATA)
     params = execution.params(params)
     cargs = tck2connectome_cargs(params, execution)
     ret = tck2connectome_outputs(params, execution)
@@ -455,6 +461,8 @@ def tck2connectome(
     runner: Runner | None = None,
 ) -> Tck2connectomeOutputs:
     """
+    tck2connectome
+    
     Generate a connectome matrix from a streamlines file and a node parcellation
     image.
     
@@ -535,8 +543,6 @@ def tck2connectome(
     Returns:
         NamedTuple of outputs (described in `Tck2connectomeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TCK2CONNECTOME_METADATA)
     params = tck2connectome_params(
         assignment_end_voxels=assignment_end_voxels,
         assignment_radial_search=assignment_radial_search,
@@ -566,15 +572,14 @@ def tck2connectome(
         nodes_in=nodes_in,
         connectome_out=connectome_out,
     )
-    return tck2connectome_execute(params, execution)
+    return tck2connectome_execute(params, runner)
 
 
 __all__ = [
     "TCK2CONNECTOME_METADATA",
-    "Tck2connectomeConfigParameters",
     "Tck2connectomeOutputs",
-    "Tck2connectomeParameters",
     "tck2connectome",
     "tck2connectome_config_params",
+    "tck2connectome_execute",
     "tck2connectome_params",
 ]