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

niwrap_freesurfer/freesurfer/dmri_forrest.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_FORREST_METADATA = Metadata(
-    id="783d39ff3f4d8b9efc1b1df20b2f6005684a7a50.boutiques",
+    id="ebecca227e9034cc6a0760500386f32431828b49.boutiques",
     name="dmri_forrest",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,19 @@ DMRI_FORREST_METADATA = Metadata(
 
 
 DmriForrestParameters = typing.TypedDict('DmriForrestParameters', {
-    "__STYXTYPE__": typing.Literal["dmri_forrest"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dmri_forrest"]],
+    "test_dir": str,
+    "train_file": InputPathType,
+    "mask_file": InputPathType,
+    "tract_files": list[InputPathType],
+    "seg_file": typing.NotRequired[InputPathType | None],
+    "diff_file": typing.NotRequired[InputPathType | None],
+    "debug": bool,
+    "checkopts": bool,
+    "help": bool,
+})
+DmriForrestParametersTagged = typing.TypedDict('DmriForrestParametersTagged', {
+    "@type": typing.Literal["freesurfer/dmri_forrest"],
     "test_dir": str,
     "train_file": InputPathType,
     "mask_file": InputPathType,
@@ -25,42 +37,11 @@ DmriForrestParameters = typing.TypedDict('DmriForrestParameters', {
     "checkopts": bool,
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "dmri_forrest": dmri_forrest_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)
 
 
 class DmriForrestOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dmri_forrest(...)`.
+    Output object returned when calling `DmriForrestParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -76,7 +57,7 @@ def dmri_forrest_params(
     debug: bool = False,
     checkopts: bool = False,
     help_: bool = False,
-) -> DmriForrestParameters:
+) -> DmriForrestParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +76,7 @@ def dmri_forrest_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dmri_forrest",
+        "@type": "freesurfer/dmri_forrest",
         "test_dir": test_dir,
         "train_file": train_file,
         "mask_file": mask_file,
@@ -128,35 +109,35 @@ def dmri_forrest_cargs(
     cargs.append("dmri_forrest")
     cargs.extend([
         "--test",
-        params.get("test_dir")
+        params.get("test_dir", None)
     ])
     cargs.extend([
         "--train",
-        execution.input_file(params.get("train_file"))
+        execution.input_file(params.get("train_file", None))
     ])
     cargs.extend([
         "--mask",
-        execution.input_file(params.get("mask_file"))
+        execution.input_file(params.get("mask_file", None))
     ])
     cargs.extend([
         "--tract",
-        *[execution.input_file(f) for f in params.get("tract_files")]
+        *[execution.input_file(f) for f in params.get("tract_files", None)]
     ])
-    if params.get("seg_file") is not None:
+    if params.get("seg_file", None) is not None:
         cargs.extend([
             "--seg",
-            execution.input_file(params.get("seg_file"))
+            execution.input_file(params.get("seg_file", None))
         ])
-    if params.get("diff_file") is not None:
+    if params.get("diff_file", None) is not None:
         cargs.extend([
             "--diff",
-            execution.input_file(params.get("diff_file"))
+            execution.input_file(params.get("diff_file", None))
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("checkopts"):
+    if params.get("checkopts", False):
         cargs.append("--checkopts")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
     return cargs
 
@@ -182,9 +163,11 @@ def dmri_forrest_outputs(
 
 def dmri_forrest_execute(
     params: DmriForrestParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DmriForrestOutputs:
     """
+    dmri_forrest
+    
     dmri_forrest is a tool for processing diffusion MRI data using a random
     forest-based method.
     
@@ -194,10 +177,12 @@ def dmri_forrest_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DmriForrestOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DMRI_FORREST_METADATA)
     params = execution.params(params)
     cargs = dmri_forrest_cargs(params, execution)
     ret = dmri_forrest_outputs(params, execution)
@@ -218,6 +203,8 @@ def dmri_forrest(
     runner: Runner | None = None,
 ) -> DmriForrestOutputs:
     """
+    dmri_forrest
+    
     dmri_forrest is a tool for processing diffusion MRI data using a random
     forest-based method.
     
@@ -240,8 +227,6 @@ def dmri_forrest(
     Returns:
         NamedTuple of outputs (described in `DmriForrestOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DMRI_FORREST_METADATA)
     params = dmri_forrest_params(
         test_dir=test_dir,
         train_file=train_file,
@@ -253,13 +238,13 @@ def dmri_forrest(
         checkopts=checkopts,
         help_=help_,
     )
-    return dmri_forrest_execute(params, execution)
+    return dmri_forrest_execute(params, runner)
 
 
 __all__ = [
     "DMRI_FORREST_METADATA",
     "DmriForrestOutputs",
-    "DmriForrestParameters",
     "dmri_forrest",
+    "dmri_forrest_execute",
     "dmri_forrest_params",
 ]

niwrap_freesurfer/freesurfer/dmri_group.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_GROUP_METADATA = Metadata(
-    id="93e524a844ab2f832a6731597f76dcfcfbb61112.boutiques",
+    id="bbcba71ee223998296e5cb23fe97ac0a430c9718.boutiques",
     name="dmri_group",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ DMRI_GROUP_METADATA = Metadata(
 
 
 DmriGroupParameters = typing.TypedDict('DmriGroupParameters', {
-    "__STYXTYPE__": typing.Literal["dmri_group"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dmri_group"]],
+    "input_list": InputPathType,
+    "reference_volume": InputPathType,
+    "output_base": str,
+    "no_interpolation": bool,
+    "sections_num": typing.NotRequired[float | None],
+    "debug_mode": bool,
+    "check_options": bool,
+})
+DmriGroupParametersTagged = typing.TypedDict('DmriGroupParametersTagged', {
+    "@type": typing.Literal["freesurfer/dmri_group"],
     "input_list": InputPathType,
     "reference_volume": InputPathType,
     "output_base": str,
@@ -23,42 +33,11 @@ DmriGroupParameters = typing.TypedDict('DmriGroupParameters', {
     "debug_mode": bool,
     "check_options": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "dmri_group": dmri_group_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)
 
 
 class DmriGroupOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dmri_group(...)`.
+    Output object returned when calling `DmriGroupParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,7 +51,7 @@ def dmri_group_params(
     sections_num: float | None = None,
     debug_mode: bool = False,
     check_options: bool = False,
-) -> DmriGroupParameters:
+) -> DmriGroupParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +69,7 @@ def dmri_group_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dmri_group",
+        "@type": "freesurfer/dmri_group",
         "input_list": input_list,
         "reference_volume": reference_volume,
         "output_base": output_base,
@@ -120,26 +99,26 @@ def dmri_group_cargs(
     cargs.append("dmri_group")
     cargs.extend([
         "--list",
-        execution.input_file(params.get("input_list"))
+        execution.input_file(params.get("input_list", None))
     ])
     cargs.extend([
         "--ref",
-        execution.input_file(params.get("reference_volume"))
+        execution.input_file(params.get("reference_volume", None))
     ])
     cargs.extend([
         "--out",
-        params.get("output_base")
+        params.get("output_base", None)
     ])
-    if params.get("no_interpolation"):
+    if params.get("no_interpolation", False):
         cargs.append("--nointerp")
-    if params.get("sections_num") is not None:
+    if params.get("sections_num", None) is not None:
         cargs.extend([
             "--sec",
-            str(params.get("sections_num"))
+            str(params.get("sections_num", None))
         ])
-    if params.get("debug_mode"):
+    if params.get("debug_mode", False):
         cargs.append("--debug")
-    if params.get("check_options"):
+    if params.get("check_options", False):
         cargs.append("--checkopts")
     return cargs
 
@@ -165,9 +144,11 @@ def dmri_group_outputs(
 
 def dmri_group_execute(
     params: DmriGroupParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DmriGroupOutputs:
     """
+    dmri_group
+    
     A tool to process and analyze diffusion MRI group data.
     
     Author: FreeSurfer Developers
@@ -176,10 +157,12 @@ def dmri_group_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DmriGroupOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DMRI_GROUP_METADATA)
     params = execution.params(params)
     cargs = dmri_group_cargs(params, execution)
     ret = dmri_group_outputs(params, execution)
@@ -198,6 +181,8 @@ def dmri_group(
     runner: Runner | None = None,
 ) -> DmriGroupOutputs:
     """
+    dmri_group
+    
     A tool to process and analyze diffusion MRI group data.
     
     Author: FreeSurfer Developers
@@ -218,8 +203,6 @@ def dmri_group(
     Returns:
         NamedTuple of outputs (described in `DmriGroupOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DMRI_GROUP_METADATA)
     params = dmri_group_params(
         input_list=input_list,
         reference_volume=reference_volume,
@@ -229,13 +212,13 @@ def dmri_group(
         debug_mode=debug_mode,
         check_options=check_options,
     )
-    return dmri_group_execute(params, execution)
+    return dmri_group_execute(params, runner)
 
 
 __all__ = [
     "DMRI_GROUP_METADATA",
     "DmriGroupOutputs",
-    "DmriGroupParameters",
     "dmri_group",
+    "dmri_group_execute",
     "dmri_group_params",
 ]

niwrap_freesurfer/freesurfer/dmri_group_by_endpoints.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_GROUP_BY_ENDPOINTS_METADATA = Metadata(
-    id="87310592b138bba2f86c81c258d64cefe1c90e23.boutiques",
+    id="4ef63d1408c6a62e2a9cb214c784c2c56fa402f9.boutiques",
     name="dmri_groupByEndpoints",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,22 @@ DMRI_GROUP_BY_ENDPOINTS_METADATA = Metadata(
 
 
 DmriGroupByEndpointsParameters = typing.TypedDict('DmriGroupByEndpointsParameters', {
-    "__STYXTYPE__": typing.Literal["dmri_groupByEndpoints"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dmri_groupByEndpoints"]],
+    "streamline_file": InputPathType,
+    "image_file": InputPathType,
+    "output_directory": str,
+})
+DmriGroupByEndpointsParametersTagged = typing.TypedDict('DmriGroupByEndpointsParametersTagged', {
+    "@type": typing.Literal["freesurfer/dmri_groupByEndpoints"],
     "streamline_file": InputPathType,
     "image_file": InputPathType,
     "output_directory": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "dmri_groupByEndpoints": dmri_group_by_endpoints_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)
 
 
 class DmriGroupByEndpointsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dmri_group_by_endpoints(...)`.
+    Output object returned when calling `DmriGroupByEndpointsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +39,7 @@ def dmri_group_by_endpoints_params(
     streamline_file: InputPathType,
     image_file: InputPathType,
     output_directory: str,
-) -> DmriGroupByEndpointsParameters:
+) -> DmriGroupByEndpointsParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +51,7 @@ def dmri_group_by_endpoints_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dmri_groupByEndpoints",
+        "@type": "freesurfer/dmri_groupByEndpoints",
         "streamline_file": streamline_file,
         "image_file": image_file,
         "output_directory": output_directory,
@@ -101,15 +76,15 @@ def dmri_group_by_endpoints_cargs(
     cargs.append("dmri_groupByEndpoints")
     cargs.extend([
         "-s",
-        execution.input_file(params.get("streamline_file"))
+        execution.input_file(params.get("streamline_file", None))
     ])
     cargs.extend([
         "-i",
-        execution.input_file(params.get("image_file"))
+        execution.input_file(params.get("image_file", None))
     ])
     cargs.extend([
         "-d",
-        params.get("output_directory")
+        params.get("output_directory", None)
     ])
     return cargs
 
@@ -135,9 +110,11 @@ def dmri_group_by_endpoints_outputs(
 
 def dmri_group_by_endpoints_execute(
     params: DmriGroupByEndpointsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DmriGroupByEndpointsOutputs:
     """
+    dmri_groupByEndpoints
+    
     A tool to group streamlines by their endpoints using diffusion MRI data.
     
     Author: FreeSurfer Developers
@@ -146,10 +123,12 @@ def dmri_group_by_endpoints_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DmriGroupByEndpointsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DMRI_GROUP_BY_ENDPOINTS_METADATA)
     params = execution.params(params)
     cargs = dmri_group_by_endpoints_cargs(params, execution)
     ret = dmri_group_by_endpoints_outputs(params, execution)
@@ -164,6 +143,8 @@ def dmri_group_by_endpoints(
     runner: Runner | None = None,
 ) -> DmriGroupByEndpointsOutputs:
     """
+    dmri_groupByEndpoints
+    
     A tool to group streamlines by their endpoints using diffusion MRI data.
     
     Author: FreeSurfer Developers
@@ -178,20 +159,18 @@ def dmri_group_by_endpoints(
     Returns:
         NamedTuple of outputs (described in `DmriGroupByEndpointsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DMRI_GROUP_BY_ENDPOINTS_METADATA)
     params = dmri_group_by_endpoints_params(
         streamline_file=streamline_file,
         image_file=image_file,
         output_directory=output_directory,
     )
-    return dmri_group_by_endpoints_execute(params, execution)
+    return dmri_group_by_endpoints_execute(params, runner)
 
 
 __all__ = [
     "DMRI_GROUP_BY_ENDPOINTS_METADATA",
     "DmriGroupByEndpointsOutputs",
-    "DmriGroupByEndpointsParameters",
     "dmri_group_by_endpoints",
+    "dmri_group_by_endpoints_execute",
     "dmri_group_by_endpoints_params",
 ]