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

niwrap_freesurfer/freesurfer/make_average_volume.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MAKE_AVERAGE_VOLUME_METADATA = Metadata(
-    id="d5918126931a1262771808902f81e13cdc611a10.boutiques",
+    id="6f40ff65943cb8e7db2c3bba2a4245dae06bf55e.boutiques",
     name="make_average_volume",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,25 @@ MAKE_AVERAGE_VOLUME_METADATA = Metadata(
 
 
 MakeAverageVolumeParameters = typing.TypedDict('MakeAverageVolumeParameters', {
-    "__STYXTYPE__": typing.Literal["make_average_volume"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/make_average_volume"]],
+    "subjects": list[str],
+    "fsgd": typing.NotRequired[InputPathType | None],
+    "out": typing.NotRequired[str | None],
+    "topdir": typing.NotRequired[str | None],
+    "xform": typing.NotRequired[str | None],
+    "sdir": typing.NotRequired[str | None],
+    "sd_flag": bool,
+    "force_flag": bool,
+    "keep_all_orig_flag": bool,
+    "no_aseg_flag": bool,
+    "ctab": typing.NotRequired[str | None],
+    "ctab_default_flag": bool,
+    "echo_flag": bool,
+    "debug_flag": bool,
+    "nocleanup_flag": bool,
+})
+MakeAverageVolumeParametersTagged = typing.TypedDict('MakeAverageVolumeParametersTagged', {
+    "@type": typing.Literal["freesurfer/make_average_volume"],
     "subjects": list[str],
     "fsgd": typing.NotRequired[InputPathType | None],
     "out": typing.NotRequired[str | None],
@@ -31,42 +49,11 @@ MakeAverageVolumeParameters = typing.TypedDict('MakeAverageVolumeParameters', {
     "debug_flag": bool,
     "nocleanup_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 {
-        "make_average_volume": make_average_volume_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 MakeAverageVolumeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `make_average_volume(...)`.
+    Output object returned when calling `MakeAverageVolumeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -88,7 +75,7 @@ def make_average_volume_params(
     echo_flag: bool = False,
     debug_flag: bool = False,
     nocleanup_flag: bool = False,
-) -> MakeAverageVolumeParameters:
+) -> MakeAverageVolumeParametersTagged:
     """
     Build parameters.
     
@@ -113,7 +100,7 @@ def make_average_volume_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "make_average_volume",
+        "@type": "freesurfer/make_average_volume",
         "subjects": subjects,
         "sd_flag": sd_flag,
         "force_flag": force_flag,
@@ -156,53 +143,53 @@ def make_average_volume_cargs(
     cargs.append("make_average_volume")
     cargs.extend([
         "--subjects",
-        *params.get("subjects")
+        *params.get("subjects", None)
     ])
-    if params.get("fsgd") is not None:
+    if params.get("fsgd", None) is not None:
         cargs.extend([
             "--fsgd",
-            execution.input_file(params.get("fsgd"))
+            execution.input_file(params.get("fsgd", None))
         ])
-    if params.get("out") is not None:
+    if params.get("out", None) is not None:
         cargs.extend([
             "--out",
-            params.get("out")
+            params.get("out", None)
         ])
-    if params.get("topdir") is not None:
+    if params.get("topdir", None) is not None:
         cargs.extend([
             "--topdir",
-            params.get("topdir")
+            params.get("topdir", None)
         ])
-    if params.get("xform") is not None:
+    if params.get("xform", None) is not None:
         cargs.extend([
             "--xform",
-            params.get("xform")
+            params.get("xform", None)
         ])
-    if params.get("sdir") is not None:
+    if params.get("sdir", None) is not None:
         cargs.extend([
             "--sdir",
-            params.get("sdir")
+            params.get("sdir", None)
         ])
-    if params.get("sd_flag"):
+    if params.get("sd_flag", False):
         cargs.append("--sd")
-    if params.get("force_flag"):
+    if params.get("force_flag", False):
         cargs.append("--force")
-    if params.get("keep_all_orig_flag"):
+    if params.get("keep_all_orig_flag", False):
         cargs.append("--keep-all-orig")
-    if params.get("no_aseg_flag"):
+    if params.get("no_aseg_flag", False):
         cargs.append("--no-aseg")
-    if params.get("ctab") is not None:
+    if params.get("ctab", None) is not None:
         cargs.extend([
             "--ctab",
-            params.get("ctab")
+            params.get("ctab", None)
         ])
-    if params.get("ctab_default_flag"):
+    if params.get("ctab_default_flag", False):
         cargs.append("--ctab-default")
-    if params.get("echo_flag"):
+    if params.get("echo_flag", False):
         cargs.append("--echo")
-    if params.get("debug_flag"):
+    if params.get("debug_flag", False):
         cargs.append("--debug")
-    if params.get("nocleanup_flag"):
+    if params.get("nocleanup_flag", False):
         cargs.append("--nocleanup")
     return cargs
 
@@ -228,9 +215,11 @@ def make_average_volume_outputs(
 
 def make_average_volume_execute(
     params: MakeAverageVolumeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MakeAverageVolumeOutputs:
     """
+    make_average_volume
+    
     Creates average volumes from a set of subjects.
     
     Author: FreeSurfer Developers
@@ -239,10 +228,12 @@ def make_average_volume_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MakeAverageVolumeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_AVERAGE_VOLUME_METADATA)
     params = execution.params(params)
     cargs = make_average_volume_cargs(params, execution)
     ret = make_average_volume_outputs(params, execution)
@@ -269,6 +260,8 @@ def make_average_volume(
     runner: Runner | None = None,
 ) -> MakeAverageVolumeOutputs:
     """
+    make_average_volume
+    
     Creates average volumes from a set of subjects.
     
     Author: FreeSurfer Developers
@@ -296,8 +289,6 @@ def make_average_volume(
     Returns:
         NamedTuple of outputs (described in `MakeAverageVolumeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MAKE_AVERAGE_VOLUME_METADATA)
     params = make_average_volume_params(
         subjects=subjects,
         fsgd=fsgd,
@@ -315,13 +306,13 @@ def make_average_volume(
         debug_flag=debug_flag,
         nocleanup_flag=nocleanup_flag,
     )
-    return make_average_volume_execute(params, execution)
+    return make_average_volume_execute(params, runner)
 
 
 __all__ = [
     "MAKE_AVERAGE_VOLUME_METADATA",
     "MakeAverageVolumeOutputs",
-    "MakeAverageVolumeParameters",
     "make_average_volume",
+    "make_average_volume_execute",
     "make_average_volume_params",
 ]

niwrap_freesurfer/freesurfer/make_cortex_label.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MAKE_CORTEX_LABEL_METADATA = Metadata(
-    id="2211504b8e9709cb80a7eb6e4d9b734d783a055e.boutiques",
+    id="a04fe7b449fb0eb369323600f79464f44befce9b.boutiques",
     name="make_cortex_label",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,62 +14,39 @@ MAKE_CORTEX_LABEL_METADATA = Metadata(
 
 
 MakeCortexLabelParameters = typing.TypedDict('MakeCortexLabelParameters', {
-    "__STYXTYPE__": typing.Literal["make_cortex_label"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/make_cortex_label"]],
+    "subject": str,
+    "hemi": typing.NotRequired[str | None],
+    "use_a2009s": bool,
+    "output_name": typing.NotRequired[str | None],
+})
+MakeCortexLabelParametersTagged = typing.TypedDict('MakeCortexLabelParametersTagged', {
+    "@type": typing.Literal["freesurfer/make_cortex_label"],
     "subject": str,
     "hemi": typing.NotRequired[str | None],
     "use_a2009s": bool,
     "output_name": typing.NotRequired[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 {
-        "make_cortex_label": make_cortex_label_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 {
-        "make_cortex_label": make_cortex_label_outputs,
-    }.get(t)
 
 
 class MakeCortexLabelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `make_cortex_label(...)`.
+    Output object returned when calling `MakeCortexLabelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    output_label_file: OutputPathType | None
-    """The output cortex label file."""
+    lh_output_label_file: OutputPathType | None
+    """The left hemisphere output cortex label file."""
+    rh_output_label_file: OutputPathType | None
+    """The right hemisphere output cortex label file."""
 
 
 def make_cortex_label_params(
     subject: str,
     hemi: str | None = None,
     use_a2009s: bool = False,
-    output_name: str | None = "cortex",
-) -> MakeCortexLabelParameters:
+    output_name: str | None = None,
+) -> MakeCortexLabelParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +61,7 @@ def make_cortex_label_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "make_cortex_label",
+        "@type": "freesurfer/make_cortex_label",
         "subject": subject,
         "use_a2009s": use_a2009s,
     }
@@ -112,19 +89,19 @@ def make_cortex_label_cargs(
     cargs.append("make_cortex_label")
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("hemi") is not None:
+    if params.get("hemi", None) is not None:
         cargs.extend([
             "--h",
-            params.get("hemi")
+            params.get("hemi", None)
         ])
-    if params.get("use_a2009s"):
+    if params.get("use_a2009s", False):
         cargs.append("--a2009s")
-    if params.get("output_name") is not None:
+    if params.get("output_name", None) is not None:
         cargs.extend([
             "--o",
-            params.get("output_name")
+            params.get("output_name", None)
         ])
     return cargs
 
@@ -144,16 +121,19 @@ def make_cortex_label_outputs(
     """
     ret = MakeCortexLabelOutputs(
         root=execution.output_file("."),
-        output_label_file=execution.output_file("?h." + params.get("output_name") + ".label") if (params.get("output_name") is not None) else None,
+        lh_output_label_file=execution.output_file("lh." + params.get("output_name", None) + ".label") if (params.get("output_name") is not None) else None,
+        rh_output_label_file=execution.output_file("rh." + params.get("output_name", None) + ".label") if (params.get("output_name") is not None) else None,
     )
     return ret
 
 
 def make_cortex_label_execute(
     params: MakeCortexLabelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MakeCortexLabelOutputs:
     """
+    make_cortex_label
+    
     A tool to create cortical labels.
     
     Author: FreeSurfer Developers
@@ -162,10 +142,12 @@ def make_cortex_label_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MakeCortexLabelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_CORTEX_LABEL_METADATA)
     params = execution.params(params)
     cargs = make_cortex_label_cargs(params, execution)
     ret = make_cortex_label_outputs(params, execution)
@@ -177,10 +159,12 @@ def make_cortex_label(
     subject: str,
     hemi: str | None = None,
     use_a2009s: bool = False,
-    output_name: str | None = "cortex",
+    output_name: str | None = None,
     runner: Runner | None = None,
 ) -> MakeCortexLabelOutputs:
     """
+    make_cortex_label
+    
     A tool to create cortical labels.
     
     Author: FreeSurfer Developers
@@ -198,21 +182,19 @@ def make_cortex_label(
     Returns:
         NamedTuple of outputs (described in `MakeCortexLabelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MAKE_CORTEX_LABEL_METADATA)
     params = make_cortex_label_params(
         subject=subject,
         hemi=hemi,
         use_a2009s=use_a2009s,
         output_name=output_name,
     )
-    return make_cortex_label_execute(params, execution)
+    return make_cortex_label_execute(params, runner)
 
 
 __all__ = [
     "MAKE_CORTEX_LABEL_METADATA",
     "MakeCortexLabelOutputs",
-    "MakeCortexLabelParameters",
     "make_cortex_label",
+    "make_cortex_label_execute",
     "make_cortex_label_params",
 ]

niwrap_freesurfer/freesurfer/make_exvivo_filled.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MAKE_EXVIVO_FILLED_METADATA = Metadata(
-    id="ea9e6e6bb03c9eb7e7861ad8386b4df6348f9898.boutiques",
+    id="7ee5fe2318131f79440c68789b7f04a126f5b450.boutiques",
     name="make_exvivo_filled",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,24 @@ MAKE_EXVIVO_FILLED_METADATA = Metadata(
 
 
 MakeExvivoFilledParameters = typing.TypedDict('MakeExvivoFilledParameters', {
-    "__STYXTYPE__": typing.Literal["make_exvivo_filled"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/make_exvivo_filled"]],
+    "subject_name": str,
+    "input_samseg": InputPathType,
+    "input_intensity_vol": InputPathType,
+    "hemi_both": str,
+})
+MakeExvivoFilledParametersTagged = typing.TypedDict('MakeExvivoFilledParametersTagged', {
+    "@type": typing.Literal["freesurfer/make_exvivo_filled"],
     "subject_name": str,
     "input_samseg": InputPathType,
     "input_intensity_vol": InputPathType,
     "hemi_both": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "make_exvivo_filled": make_exvivo_filled_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 MakeExvivoFilledOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `make_exvivo_filled(...)`.
+    Output object returned when calling `MakeExvivoFilledParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def make_exvivo_filled_params(
     input_samseg: InputPathType,
     input_intensity_vol: InputPathType,
     hemi_both: str,
-) -> MakeExvivoFilledParameters:
+) -> MakeExvivoFilledParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +55,7 @@ def make_exvivo_filled_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "make_exvivo_filled",
+        "@type": "freesurfer/make_exvivo_filled",
         "subject_name": subject_name,
         "input_samseg": input_samseg,
         "input_intensity_vol": input_intensity_vol,
@@ -103,10 +79,10 @@ def make_exvivo_filled_cargs(
     """
     cargs = []
     cargs.append("make_exvivo_filled")
-    cargs.append(params.get("subject_name"))
-    cargs.append(execution.input_file(params.get("input_samseg")))
-    cargs.append(execution.input_file(params.get("input_intensity_vol")))
-    cargs.append(params.get("hemi_both"))
+    cargs.append(params.get("subject_name", None))
+    cargs.append(execution.input_file(params.get("input_samseg", None)))
+    cargs.append(execution.input_file(params.get("input_intensity_vol", None)))
+    cargs.append(params.get("hemi_both", None))
     return cargs
 
 
@@ -131,9 +107,11 @@ def make_exvivo_filled_outputs(
 
 def make_exvivo_filled_execute(
     params: MakeExvivoFilledParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MakeExvivoFilledOutputs:
     """
+    make_exvivo_filled
+    
     A command-line tool for generating filled ex vivo brain images.
     
     Author: FreeSurfer Developers
@@ -142,10 +120,12 @@ def make_exvivo_filled_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MakeExvivoFilledOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_EXVIVO_FILLED_METADATA)
     params = execution.params(params)
     cargs = make_exvivo_filled_cargs(params, execution)
     ret = make_exvivo_filled_outputs(params, execution)
@@ -161,6 +141,8 @@ def make_exvivo_filled(
     runner: Runner | None = None,
 ) -> MakeExvivoFilledOutputs:
     """
+    make_exvivo_filled
+    
     A command-line tool for generating filled ex vivo brain images.
     
     Author: FreeSurfer Developers
@@ -176,21 +158,19 @@ def make_exvivo_filled(
     Returns:
         NamedTuple of outputs (described in `MakeExvivoFilledOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MAKE_EXVIVO_FILLED_METADATA)
     params = make_exvivo_filled_params(
         subject_name=subject_name,
         input_samseg=input_samseg,
         input_intensity_vol=input_intensity_vol,
         hemi_both=hemi_both,
     )
-    return make_exvivo_filled_execute(params, execution)
+    return make_exvivo_filled_execute(params, runner)
 
 
 __all__ = [
     "MAKE_EXVIVO_FILLED_METADATA",
     "MakeExvivoFilledOutputs",
-    "MakeExvivoFilledParameters",
     "make_exvivo_filled",
+    "make_exvivo_filled_execute",
     "make_exvivo_filled_params",
 ]