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

niwrap_freesurfer/freesurfer/fix_subject_rh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIX_SUBJECT_RH_METADATA = Metadata(
-    id="d6f9654d878ef28530ea8f9531c3a06325244e6b.boutiques",
+    id="7b0c00f96ed707e5becf1e78fffdf851eb61fdf4.boutiques",
     name="fix_subject-rh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ FIX_SUBJECT_RH_METADATA = Metadata(
 
 
 FixSubjectRhParameters = typing.TypedDict('FixSubjectRhParameters', {
-    "__STYXTYPE__": typing.Literal["fix_subject-rh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fix_subject-rh"]],
+    "input_directory": str,
+    "help_flag": bool,
+})
+FixSubjectRhParametersTagged = typing.TypedDict('FixSubjectRhParametersTagged', {
+    "@type": typing.Literal["freesurfer/fix_subject-rh"],
     "input_directory": str,
     "help_flag": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fix_subject-rh": fix_subject_rh_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 FixSubjectRhOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fix_subject_rh(...)`.
+    Output object returned when calling `FixSubjectRhParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class FixSubjectRhOutputs(typing.NamedTuple):
 def fix_subject_rh_params(
     input_directory: str,
     help_flag: bool = False,
-) -> FixSubjectRhParameters:
+) -> FixSubjectRhParametersTagged:
     """
     Build parameters.
     
@@ -74,7 +48,7 @@ def fix_subject_rh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fix_subject-rh",
+        "@type": "freesurfer/fix_subject-rh",
         "input_directory": input_directory,
         "help_flag": help_flag,
     }
@@ -98,9 +72,9 @@ def fix_subject_rh_cargs(
     cargs.append("fix_subject-rh")
     cargs.extend([
         "-rh",
-        params.get("input_directory")
+        params.get("input_directory", None)
     ])
-    if params.get("help_flag"):
+    if params.get("help_flag", False):
         cargs.append("--help")
     return cargs
 
@@ -126,9 +100,11 @@ def fix_subject_rh_outputs(
 
 def fix_subject_rh_execute(
     params: FixSubjectRhParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FixSubjectRhOutputs:
     """
+    fix_subject-rh
+    
     A tool from FreeSurfer that performs operations on the right hemisphere data
     within a specified directory.
     
@@ -138,10 +114,12 @@ def fix_subject_rh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FixSubjectRhOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIX_SUBJECT_RH_METADATA)
     params = execution.params(params)
     cargs = fix_subject_rh_cargs(params, execution)
     ret = fix_subject_rh_outputs(params, execution)
@@ -155,6 +133,8 @@ def fix_subject_rh(
     runner: Runner | None = None,
 ) -> FixSubjectRhOutputs:
     """
+    fix_subject-rh
+    
     A tool from FreeSurfer that performs operations on the right hemisphere data
     within a specified directory.
     
@@ -170,19 +150,17 @@ def fix_subject_rh(
     Returns:
         NamedTuple of outputs (described in `FixSubjectRhOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FIX_SUBJECT_RH_METADATA)
     params = fix_subject_rh_params(
         input_directory=input_directory,
         help_flag=help_flag,
     )
-    return fix_subject_rh_execute(params, execution)
+    return fix_subject_rh_execute(params, runner)
 
 
 __all__ = [
     "FIX_SUBJECT_RH_METADATA",
     "FixSubjectRhOutputs",
-    "FixSubjectRhParameters",
     "fix_subject_rh",
+    "fix_subject_rh_execute",
     "fix_subject_rh_params",
 ]

niwrap_freesurfer/freesurfer/fixup_mni_paths.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIXUP_MNI_PATHS_METADATA = Metadata(
-    id="c3f882d4801a38a0ebe1d369afcdd5e436615473.boutiques",
+    id="2c7dba42b378fddcebc95bd3b583793305a381ee.boutiques",
     name="fixup_mni_paths",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,18 @@ FIXUP_MNI_PATHS_METADATA = Metadata(
 
 
 FixupMniPathsParameters = typing.TypedDict('FixupMniPathsParameters', {
-    "__STYXTYPE__": typing.Literal["fixup_mni_paths"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fixup_mni_paths"]],
+    "verbose": bool,
+})
+FixupMniPathsParametersTagged = typing.TypedDict('FixupMniPathsParametersTagged', {
+    "@type": typing.Literal["freesurfer/fixup_mni_paths"],
     "verbose": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fixup_mni_paths": fixup_mni_paths_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 {
-        "fixup_mni_paths": fixup_mni_paths_outputs,
-    }.get(t)
 
 
 class FixupMniPathsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fixup_mni_paths(...)`.
+    Output object returned when calling `FixupMniPathsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -87,7 +59,7 @@ class FixupMniPathsOutputs(typing.NamedTuple):
 
 def fixup_mni_paths_params(
     verbose: bool = False,
-) -> FixupMniPathsParameters:
+) -> FixupMniPathsParametersTagged:
     """
     Build parameters.
     
@@ -97,7 +69,7 @@ def fixup_mni_paths_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fixup_mni_paths",
+        "@type": "freesurfer/fixup_mni_paths",
         "verbose": verbose,
     }
     return params
@@ -118,7 +90,7 @@ def fixup_mni_paths_cargs(
     """
     cargs = []
     cargs.append("fixup_mni_paths")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-v")
     return cargs
 
@@ -157,9 +129,11 @@ def fixup_mni_paths_outputs(
 
 def fixup_mni_paths_execute(
     params: FixupMniPathsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FixupMniPathsOutputs:
     """
+    fixup_mni_paths
+    
     A utility for patching MNI tools to ensure correct paths are used.
     
     Author: FreeSurfer Developers
@@ -168,10 +142,12 @@ def fixup_mni_paths_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FixupMniPathsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXUP_MNI_PATHS_METADATA)
     params = execution.params(params)
     cargs = fixup_mni_paths_cargs(params, execution)
     ret = fixup_mni_paths_outputs(params, execution)
@@ -184,6 +160,8 @@ def fixup_mni_paths(
     runner: Runner | None = None,
 ) -> FixupMniPathsOutputs:
     """
+    fixup_mni_paths
+    
     A utility for patching MNI tools to ensure correct paths are used.
     
     Author: FreeSurfer Developers
@@ -196,18 +174,16 @@ def fixup_mni_paths(
     Returns:
         NamedTuple of outputs (described in `FixupMniPathsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FIXUP_MNI_PATHS_METADATA)
     params = fixup_mni_paths_params(
         verbose=verbose,
     )
-    return fixup_mni_paths_execute(params, execution)
+    return fixup_mni_paths_execute(params, runner)
 
 
 __all__ = [
     "FIXUP_MNI_PATHS_METADATA",
     "FixupMniPathsOutputs",
-    "FixupMniPathsParameters",
     "fixup_mni_paths",
+    "fixup_mni_paths_execute",
     "fixup_mni_paths_params",
 ]

niwrap_freesurfer/freesurfer/flip_4dfp.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FLIP_4DFP_METADATA = Metadata(
-    id="8ea4c9ced73015848191893b7f55466d9dc889a2.boutiques",
+    id="72aeaef961cef1989aa2360038200c45341617ae.boutiques",
     name="flip_4dfp",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ FLIP_4DFP_METADATA = Metadata(
 
 
 Flip4dfpParameters = typing.TypedDict('Flip4dfpParameters', {
-    "__STYXTYPE__": typing.Literal["flip_4dfp"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/flip_4dfp"]],
+    "input_image": InputPathType,
+    "output_image": typing.NotRequired[str | None],
+    "flip_x": bool,
+    "flip_y": bool,
+    "flip_z": bool,
+    "endianness": typing.NotRequired[typing.Literal["b", "l"] | None],
+})
+Flip4dfpParametersTagged = typing.TypedDict('Flip4dfpParametersTagged', {
+    "@type": typing.Literal["freesurfer/flip_4dfp"],
     "input_image": InputPathType,
     "output_image": typing.NotRequired[str | None],
     "flip_x": bool,
@@ -22,43 +31,11 @@ Flip4dfpParameters = typing.TypedDict('Flip4dfpParameters', {
     "flip_z": bool,
     "endianness": typing.NotRequired[typing.Literal["b", "l"] | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "flip_4dfp": flip_4dfp_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 {
-        "flip_4dfp": flip_4dfp_outputs,
-    }.get(t)
 
 
 class Flip4dfpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `flip_4dfp(...)`.
+    Output object returned when calling `Flip4dfpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def flip_4dfp_params(
     flip_y: bool = False,
     flip_z: bool = False,
     endianness: typing.Literal["b", "l"] | None = None,
-) -> Flip4dfpParameters:
+) -> Flip4dfpParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +67,7 @@ def flip_4dfp_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "flip_4dfp",
+        "@type": "freesurfer/flip_4dfp",
         "input_image": input_image,
         "flip_x": flip_x,
         "flip_y": flip_y,
@@ -118,19 +95,19 @@ def flip_4dfp_cargs(
     """
     cargs = []
     cargs.append("flip_4dfp")
-    cargs.append(execution.input_file(params.get("input_image")))
-    if params.get("output_image") is not None:
-        cargs.append(params.get("output_image"))
-    if params.get("flip_x"):
+    cargs.append(execution.input_file(params.get("input_image", None)))
+    if params.get("output_image", None) is not None:
+        cargs.append(params.get("output_image", None))
+    if params.get("flip_x", False):
         cargs.append("-x")
-    if params.get("flip_y"):
+    if params.get("flip_y", False):
         cargs.append("-y")
-    if params.get("flip_z"):
+    if params.get("flip_z", False):
         cargs.append("-z")
-    if params.get("endianness") is not None:
+    if params.get("endianness", None) is not None:
         cargs.extend([
             "-@",
-            params.get("endianness")
+            params.get("endianness", None)
         ])
     return cargs
 
@@ -150,16 +127,18 @@ def flip_4dfp_outputs(
     """
     ret = Flip4dfpOutputs(
         root=execution.output_file("."),
-        flipped_image=execution.output_file(params.get("output_image") + ".4dfp.img") if (params.get("output_image") is not None) else None,
+        flipped_image=execution.output_file(params.get("output_image", None) + ".4dfp.img") if (params.get("output_image") is not None) else None,
     )
     return ret
 
 
 def flip_4dfp_execute(
     params: Flip4dfpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Flip4dfpOutputs:
     """
+    flip_4dfp
+    
     A tool to flip 4dfp images along specified axes.
     
     Author: FreeSurfer Developers
@@ -168,10 +147,12 @@ def flip_4dfp_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Flip4dfpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FLIP_4DFP_METADATA)
     params = execution.params(params)
     cargs = flip_4dfp_cargs(params, execution)
     ret = flip_4dfp_outputs(params, execution)
@@ -189,6 +170,8 @@ def flip_4dfp(
     runner: Runner | None = None,
 ) -> Flip4dfpOutputs:
     """
+    flip_4dfp
+    
     A tool to flip 4dfp images along specified axes.
     
     Author: FreeSurfer Developers
@@ -208,8 +191,6 @@ def flip_4dfp(
     Returns:
         NamedTuple of outputs (described in `Flip4dfpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FLIP_4DFP_METADATA)
     params = flip_4dfp_params(
         input_image=input_image,
         output_image=output_image,
@@ -218,13 +199,13 @@ def flip_4dfp(
         flip_z=flip_z,
         endianness=endianness,
     )
-    return flip_4dfp_execute(params, execution)
+    return flip_4dfp_execute(params, runner)
 
 
 __all__ = [
     "FLIP_4DFP_METADATA",
     "Flip4dfpOutputs",
-    "Flip4dfpParameters",
     "flip_4dfp",
+    "flip_4dfp_execute",
     "flip_4dfp_params",
 ]

niwrap_freesurfer/freesurfer/flirt_newdefault_20080811_sch.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FLIRT_NEWDEFAULT_20080811_SCH_METADATA = Metadata(
-    id="feb43e2c92a18f6dadfa470638890ab96bd75d9d.boutiques",
+    id="a098601132318cbfe2ff266fbec4a2a5cae16d22.boutiques",
     name="flirt.newdefault.20080811.sch",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,22 @@ FLIRT_NEWDEFAULT_20080811_SCH_METADATA = Metadata(
 
 
 FlirtNewdefault20080811SchParameters = typing.TypedDict('FlirtNewdefault20080811SchParameters', {
-    "__STYXTYPE__": typing.Literal["flirt.newdefault.20080811.sch"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/flirt.newdefault.20080811.sch"]],
+    "term_option": typing.NotRequired[str | None],
+    "curses_flag": bool,
+    "scrollback_flag": bool,
+})
+FlirtNewdefault20080811SchParametersTagged = typing.TypedDict('FlirtNewdefault20080811SchParametersTagged', {
+    "@type": typing.Literal["freesurfer/flirt.newdefault.20080811.sch"],
     "term_option": typing.NotRequired[str | None],
     "curses_flag": bool,
     "scrollback_flag": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "flirt.newdefault.20080811.sch": flirt_newdefault_20080811_sch_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 FlirtNewdefault20080811SchOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `flirt_newdefault_20080811_sch(...)`.
+    Output object returned when calling `FlirtNewdefault20080811SchParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +39,7 @@ def flirt_newdefault_20080811_sch_params(
     term_option: str | None = None,
     curses_flag: bool = False,
     scrollback_flag: bool = False,
-) -> FlirtNewdefault20080811SchParameters:
+) -> FlirtNewdefault20080811SchParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +51,7 @@ def flirt_newdefault_20080811_sch_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "flirt.newdefault.20080811.sch",
+        "@type": "freesurfer/flirt.newdefault.20080811.sch",
         "curses_flag": curses_flag,
         "scrollback_flag": scrollback_flag,
     }
@@ -100,14 +75,14 @@ def flirt_newdefault_20080811_sch_cargs(
     """
     cargs = []
     cargs.append("flirt.newdefault.20080811.sch")
-    if params.get("term_option") is not None:
+    if params.get("term_option", None) is not None:
         cargs.extend([
             "-T",
-            params.get("term_option")
+            params.get("term_option", None)
         ])
-    if params.get("curses_flag"):
+    if params.get("curses_flag", False):
         cargs.append("-V")
-    if params.get("scrollback_flag"):
+    if params.get("scrollback_flag", False):
         cargs.append("-x")
     return cargs
 
@@ -133,10 +108,13 @@ def flirt_newdefault_20080811_sch_outputs(
 
 def flirt_newdefault_20080811_sch_execute(
     params: FlirtNewdefault20080811SchParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FlirtNewdefault20080811SchOutputs:
     """
-    FLIRT (FMRIB's Linear Image Registration Tool) new default configuration script.
+    flirt.newdefault.20080811.sch
+    
+    FLIRT (FMRIB's Linear Image Registration Tool) new default configuration
+    script.
     
     Author: FreeSurfer Developers
     
@@ -144,10 +122,12 @@ def flirt_newdefault_20080811_sch_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FlirtNewdefault20080811SchOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FLIRT_NEWDEFAULT_20080811_SCH_METADATA)
     params = execution.params(params)
     cargs = flirt_newdefault_20080811_sch_cargs(params, execution)
     ret = flirt_newdefault_20080811_sch_outputs(params, execution)
@@ -162,7 +142,10 @@ def flirt_newdefault_20080811_sch(
     runner: Runner | None = None,
 ) -> FlirtNewdefault20080811SchOutputs:
     """
-    FLIRT (FMRIB's Linear Image Registration Tool) new default configuration script.
+    flirt.newdefault.20080811.sch
+    
+    FLIRT (FMRIB's Linear Image Registration Tool) new default configuration
+    script.
     
     Author: FreeSurfer Developers
     
@@ -176,20 +159,18 @@ def flirt_newdefault_20080811_sch(
     Returns:
         NamedTuple of outputs (described in `FlirtNewdefault20080811SchOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FLIRT_NEWDEFAULT_20080811_SCH_METADATA)
     params = flirt_newdefault_20080811_sch_params(
         term_option=term_option,
         curses_flag=curses_flag,
         scrollback_flag=scrollback_flag,
     )
-    return flirt_newdefault_20080811_sch_execute(params, execution)
+    return flirt_newdefault_20080811_sch_execute(params, runner)
 
 
 __all__ = [
     "FLIRT_NEWDEFAULT_20080811_SCH_METADATA",
     "FlirtNewdefault20080811SchOutputs",
-    "FlirtNewdefault20080811SchParameters",
     "flirt_newdefault_20080811_sch",
+    "flirt_newdefault_20080811_sch_execute",
     "flirt_newdefault_20080811_sch_params",
 ]