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

niwrap_freesurfer/freesurfer/fsr_import.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FSR_IMPORT_METADATA = Metadata(
-    id="b30a1cfc4e13a11d981b6cbab57fcadbba24f4a3.boutiques",
+    id="05df7cff2812d596480af946c600372f2d6a73fb.boutiques",
     name="fsr-import",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ FSR_IMPORT_METADATA = Metadata(
 
 
 FsrImportParameters = typing.TypedDict('FsrImportParameters', {
-    "__STYXTYPE__": typing.Literal["fsr-import"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fsr-import"]],
+    "outdir": str,
+    "t1w_input": typing.NotRequired[list[InputPathType] | None],
+    "t2w_input": typing.NotRequired[list[InputPathType] | None],
+    "flair_input": typing.NotRequired[list[InputPathType] | None],
+    "custom_mode_input": typing.NotRequired[list[str] | None],
+    "force_update": bool,
+    "no_conform": bool,
+    "hires": bool,
+})
+FsrImportParametersTagged = typing.TypedDict('FsrImportParametersTagged', {
+    "@type": typing.Literal["freesurfer/fsr-import"],
     "outdir": str,
     "t1w_input": typing.NotRequired[list[InputPathType] | None],
     "t2w_input": typing.NotRequired[list[InputPathType] | None],
@@ -24,43 +35,11 @@ FsrImportParameters = typing.TypedDict('FsrImportParameters', {
     "no_conform": bool,
     "hires": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fsr-import": fsr_import_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 {
-        "fsr-import": fsr_import_outputs,
-    }.get(t)
 
 
 class FsrImportOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fsr_import(...)`.
+    Output object returned when calling `FsrImportParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,8 +49,6 @@ class FsrImportOutputs(typing.NamedTuple):
     """Output directory for T2-weighted images"""
     out_flair: OutputPathType
     """Output directory for FLAIR images"""
-    out_custom_modes: OutputPathType
-    """Output directory for custom modality images based on mode"""
 
 
 def fsr_import_params(
@@ -83,7 +60,7 @@ def fsr_import_params(
     force_update: bool = False,
     no_conform: bool = False,
     hires: bool = False,
-) -> FsrImportParameters:
+) -> FsrImportParametersTagged:
     """
     Build parameters.
     
@@ -101,7 +78,7 @@ def fsr_import_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fsr-import",
+        "@type": "freesurfer/fsr-import",
         "outdir": outdir,
         "force_update": force_update,
         "no_conform": no_conform,
@@ -135,33 +112,33 @@ def fsr_import_cargs(
     cargs.append("fsr-import")
     cargs.extend([
         "--o",
-        params.get("outdir")
+        params.get("outdir", None)
     ])
-    if params.get("t1w_input") is not None:
+    if params.get("t1w_input", None) is not None:
         cargs.extend([
             "--t1w",
-            *[execution.input_file(f) for f in params.get("t1w_input")]
+            *[execution.input_file(f) for f in params.get("t1w_input", None)]
         ])
-    if params.get("t2w_input") is not None:
+    if params.get("t2w_input", None) is not None:
         cargs.extend([
             "--t2w",
-            *[execution.input_file(f) for f in params.get("t2w_input")]
+            *[execution.input_file(f) for f in params.get("t2w_input", None)]
         ])
-    if params.get("flair_input") is not None:
+    if params.get("flair_input", None) is not None:
         cargs.extend([
             "--flair",
-            *[execution.input_file(f) for f in params.get("flair_input")]
+            *[execution.input_file(f) for f in params.get("flair_input", None)]
         ])
-    if params.get("custom_mode_input") is not None:
+    if params.get("custom_mode_input", None) is not None:
         cargs.extend([
             "--mode",
-            *params.get("custom_mode_input")
+            *params.get("custom_mode_input", None)
         ])
-    if params.get("force_update"):
+    if params.get("force_update", False):
         cargs.append("--force-update")
-    if params.get("no_conform"):
+    if params.get("no_conform", False):
         cargs.append("--no-conform")
-    if params.get("hires"):
+    if params.get("hires", False):
         cargs.append("--hires")
     return cargs
 
@@ -181,19 +158,20 @@ def fsr_import_outputs(
     """
     ret = FsrImportOutputs(
         root=execution.output_file("."),
-        out_t1w=execution.output_file(params.get("outdir") + "/t1w/*.mgz"),
-        out_t2w=execution.output_file(params.get("outdir") + "/t2w/*.mgz"),
-        out_flair=execution.output_file(params.get("outdir") + "/flair/*.mgz"),
-        out_custom_modes=execution.output_file(params.get("outdir") + "/*/*.mgz"),
+        out_t1w=execution.output_file(params.get("outdir", None) + "/t1w"),
+        out_t2w=execution.output_file(params.get("outdir", None) + "/t2w"),
+        out_flair=execution.output_file(params.get("outdir", None) + "/flair_input"),
     )
     return ret
 
 
 def fsr_import_execute(
     params: FsrImportParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FsrImportOutputs:
     """
+    fsr-import
+    
     Copies/converts data into a directory structure for samseg-expected format.
     
     Author: FreeSurfer Developers
@@ -202,10 +180,12 @@ def fsr_import_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsrImportOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FSR_IMPORT_METADATA)
     params = execution.params(params)
     cargs = fsr_import_cargs(params, execution)
     ret = fsr_import_outputs(params, execution)
@@ -225,6 +205,8 @@ def fsr_import(
     runner: Runner | None = None,
 ) -> FsrImportOutputs:
     """
+    fsr-import
+    
     Copies/converts data into a directory structure for samseg-expected format.
     
     Author: FreeSurfer Developers
@@ -245,8 +227,6 @@ def fsr_import(
     Returns:
         NamedTuple of outputs (described in `FsrImportOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSR_IMPORT_METADATA)
     params = fsr_import_params(
         outdir=outdir,
         t1w_input=t1w_input,
@@ -257,13 +237,13 @@ def fsr_import(
         no_conform=no_conform,
         hires=hires,
     )
-    return fsr_import_execute(params, execution)
+    return fsr_import_execute(params, runner)
 
 
 __all__ = [
     "FSR_IMPORT_METADATA",
     "FsrImportOutputs",
-    "FsrImportParameters",
     "fsr_import",
+    "fsr_import_execute",
     "fsr_import_params",
 ]

niwrap_freesurfer/freesurfer/fsrealpath.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FSREALPATH_METADATA = Metadata(
-    id="72d52c391bbfeb21a2f969aa0469ec4c8267957d.boutiques",
+    id="8239db172af5555995f2868bbea7ad04857bacdb.boutiques",
     name="fsrealpath",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ FSREALPATH_METADATA = Metadata(
 
 
 FsrealpathParameters = typing.TypedDict('FsrealpathParameters', {
-    "__STYXTYPE__": typing.Literal["fsrealpath"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fsrealpath"]],
+    "path": str,
+    "help": bool,
+})
+FsrealpathParametersTagged = typing.TypedDict('FsrealpathParametersTagged', {
+    "@type": typing.Literal["freesurfer/fsrealpath"],
     "path": str,
     "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 {
-        "fsrealpath": fsrealpath_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 FsrealpathOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fsrealpath(...)`.
+    Output object returned when calling `FsrealpathParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class FsrealpathOutputs(typing.NamedTuple):
 def fsrealpath_params(
     path: str,
     help_: bool = False,
-) -> FsrealpathParameters:
+) -> FsrealpathParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def fsrealpath_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fsrealpath",
+        "@type": "freesurfer/fsrealpath",
         "path": path,
         "help": help_,
     }
@@ -95,8 +69,8 @@ def fsrealpath_cargs(
     """
     cargs = []
     cargs.append("fsrealpath")
-    cargs.append(params.get("path"))
-    if params.get("help"):
+    cargs.append(params.get("path", None))
+    if params.get("help", False):
         cargs.append("-h")
     return cargs
 
@@ -122,9 +96,11 @@ def fsrealpath_outputs(
 
 def fsrealpath_execute(
     params: FsrealpathParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FsrealpathOutputs:
     """
+    fsrealpath
+    
     Resolve symbolic links in a path.
     
     Author: FreeSurfer Developers
@@ -133,10 +109,12 @@ def fsrealpath_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsrealpathOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FSREALPATH_METADATA)
     params = execution.params(params)
     cargs = fsrealpath_cargs(params, execution)
     ret = fsrealpath_outputs(params, execution)
@@ -150,6 +128,8 @@ def fsrealpath(
     runner: Runner | None = None,
 ) -> FsrealpathOutputs:
     """
+    fsrealpath
+    
     Resolve symbolic links in a path.
     
     Author: FreeSurfer Developers
@@ -163,19 +143,17 @@ def fsrealpath(
     Returns:
         NamedTuple of outputs (described in `FsrealpathOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSREALPATH_METADATA)
     params = fsrealpath_params(
         path=path,
         help_=help_,
     )
-    return fsrealpath_execute(params, execution)
+    return fsrealpath_execute(params, runner)
 
 
 __all__ = [
     "FSREALPATH_METADATA",
     "FsrealpathOutputs",
-    "FsrealpathParameters",
     "fsrealpath",
+    "fsrealpath_execute",
     "fsrealpath_params",
 ]

niwrap_freesurfer/freesurfer/fsvglrun.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FSVGLRUN_METADATA = Metadata(
-    id="ad655adf03c2f7e801ecfdc1e82750b8a5a683b5.boutiques",
+    id="b9aa8b75c4e91fb4790a0905f2c4ba9fcb2f9645.boutiques",
     name="fsvglrun",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,26 @@ FSVGLRUN_METADATA = Metadata(
 
 
 FsvglrunParameters = typing.TypedDict('FsvglrunParameters', {
-    "__STYXTYPE__": typing.Literal["fsvglrun"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fsvglrun"]],
+    "zeroth_arg_name": typing.NotRequired[str | None],
+    "empty_env": bool,
+    "dashed_arg": bool,
+    "command": str,
+    "command_args": typing.NotRequired[list[str] | None],
+})
+FsvglrunParametersTagged = typing.TypedDict('FsvglrunParametersTagged', {
+    "@type": typing.Literal["freesurfer/fsvglrun"],
     "zeroth_arg_name": typing.NotRequired[str | None],
     "empty_env": bool,
     "dashed_arg": bool,
     "command": str,
     "command_args": typing.NotRequired[list[str] | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fsvglrun": fsvglrun_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 FsvglrunOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fsvglrun(...)`.
+    Output object returned when calling `FsvglrunParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -68,7 +45,7 @@ def fsvglrun_params(
     empty_env: bool = False,
     dashed_arg: bool = False,
     command_args: list[str] | None = None,
-) -> FsvglrunParameters:
+) -> FsvglrunParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +60,7 @@ def fsvglrun_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fsvglrun",
+        "@type": "freesurfer/fsvglrun",
         "empty_env": empty_env,
         "dashed_arg": dashed_arg,
         "command": command,
@@ -110,18 +87,18 @@ def fsvglrun_cargs(
     """
     cargs = []
     cargs.append("fsvglrun")
-    if params.get("zeroth_arg_name") is not None:
+    if params.get("zeroth_arg_name", None) is not None:
         cargs.extend([
             "-a",
-            params.get("zeroth_arg_name")
+            params.get("zeroth_arg_name", None)
         ])
-    if params.get("empty_env"):
+    if params.get("empty_env", False):
         cargs.append("-c")
-    if params.get("dashed_arg"):
+    if params.get("dashed_arg", False):
         cargs.append("-l")
-    cargs.append(params.get("command"))
-    if params.get("command_args") is not None:
-        cargs.extend(params.get("command_args"))
+    cargs.append(params.get("command", None))
+    if params.get("command_args", None) is not None:
+        cargs.extend(params.get("command_args", None))
     return cargs
 
 
@@ -146,9 +123,11 @@ def fsvglrun_outputs(
 
 def fsvglrun_execute(
     params: FsvglrunParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FsvglrunOutputs:
     """
+    fsvglrun
+    
     A tool to execute a command, replacing the shell with the specified program,
     typically used within FreeSurfer environment.
     
@@ -158,10 +137,12 @@ def fsvglrun_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsvglrunOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FSVGLRUN_METADATA)
     params = execution.params(params)
     cargs = fsvglrun_cargs(params, execution)
     ret = fsvglrun_outputs(params, execution)
@@ -178,6 +159,8 @@ def fsvglrun(
     runner: Runner | None = None,
 ) -> FsvglrunOutputs:
     """
+    fsvglrun
+    
     A tool to execute a command, replacing the shell with the specified program,
     typically used within FreeSurfer environment.
     
@@ -196,8 +179,6 @@ def fsvglrun(
     Returns:
         NamedTuple of outputs (described in `FsvglrunOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSVGLRUN_METADATA)
     params = fsvglrun_params(
         zeroth_arg_name=zeroth_arg_name,
         empty_env=empty_env,
@@ -205,13 +186,13 @@ def fsvglrun(
         command=command,
         command_args=command_args,
     )
-    return fsvglrun_execute(params, execution)
+    return fsvglrun_execute(params, runner)
 
 
 __all__ = [
     "FSVGLRUN_METADATA",
     "FsvglrunOutputs",
-    "FsvglrunParameters",
     "fsvglrun",
+    "fsvglrun_execute",
     "fsvglrun_params",
 ]