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

niwrap_freesurfer/freesurfer/mris_label2annot.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_LABEL2ANNOT_METADATA = Metadata(
-    id="d70e8a79afda30a0877ba03bbf9cf7ee2db78bd3.boutiques",
+    id="b98075a318f3e4669715c4b2ae9c4f49493080c4.boutiques",
     name="mris_label2annot",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,24 @@ MRIS_LABEL2ANNOT_METADATA = Metadata(
 
 
 MrisLabel2annotParameters = typing.TypedDict('MrisLabel2annotParameters', {
-    "__STYXTYPE__": typing.Literal["mris_label2annot"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_label2annot"]],
+    "subject": str,
+    "hemi": str,
+    "ctabfile": InputPathType,
+    "annotname": str,
+    "index_offset": typing.NotRequired[float | None],
+    "label_files": typing.NotRequired[list[InputPathType] | None],
+    "annot_path": typing.NotRequired[str | None],
+    "labeldir": typing.NotRequired[str | None],
+    "ldir_default": bool,
+    "no_unknown": bool,
+    "thresh": typing.NotRequired[float | None],
+    "maxstatwinner": bool,
+    "surf": typing.NotRequired[str | None],
+    "subjects_dir": typing.NotRequired[str | None],
+})
+MrisLabel2annotParametersTagged = typing.TypedDict('MrisLabel2annotParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_label2annot"],
     "subject": str,
     "hemi": str,
     "ctabfile": InputPathType,
@@ -30,43 +47,11 @@ MrisLabel2annotParameters = typing.TypedDict('MrisLabel2annotParameters', {
     "surf": typing.NotRequired[str | None],
     "subjects_dir": 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 {
-        "mris_label2annot": mris_label2annot_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 {
-        "mris_label2annot": mris_label2annot_outputs,
-    }.get(t)
 
 
 class MrisLabel2annotOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_label2annot(...)`.
+    Output object returned when calling `MrisLabel2annotParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -89,7 +74,7 @@ def mris_label2annot_params(
     maxstatwinner: bool = False,
     surf: str | None = None,
     subjects_dir: str | None = None,
-) -> MrisLabel2annotParameters:
+) -> MrisLabel2annotParametersTagged:
     """
     Build parameters.
     
@@ -112,7 +97,7 @@ def mris_label2annot_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_label2annot",
+        "@type": "freesurfer/mris_label2annot",
         "subject": subject,
         "hemi": hemi,
         "ctabfile": ctabfile,
@@ -155,60 +140,60 @@ def mris_label2annot_cargs(
     cargs.append("mris_label2annot")
     cargs.extend([
         "-s",
-        params.get("subject")
+        params.get("subject", None)
     ])
     cargs.extend([
         "-h",
-        params.get("hemi")
+        params.get("hemi", None)
     ])
     cargs.extend([
         "-ctab",
-        execution.input_file(params.get("ctabfile"))
+        execution.input_file(params.get("ctabfile", None))
     ])
     cargs.extend([
         "-a",
-        params.get("annotname")
+        params.get("annotname", None)
     ])
-    if params.get("index_offset") is not None:
+    if params.get("index_offset", None) is not None:
         cargs.extend([
             "--offset",
-            str(params.get("index_offset"))
+            str(params.get("index_offset", None))
         ])
-    if params.get("label_files") is not None:
+    if params.get("label_files", None) is not None:
         cargs.extend([
             "--l",
-            *[execution.input_file(f) for f in params.get("label_files")]
+            *[execution.input_file(f) for f in params.get("label_files", None)]
         ])
-    if params.get("annot_path") is not None:
+    if params.get("annot_path", None) is not None:
         cargs.extend([
             "--annot-path",
-            params.get("annot_path")
+            params.get("annot_path", None)
         ])
-    if params.get("labeldir") is not None:
+    if params.get("labeldir", None) is not None:
         cargs.extend([
             "--ldir",
-            params.get("labeldir")
+            params.get("labeldir", None)
         ])
-    if params.get("ldir_default"):
+    if params.get("ldir_default", False):
         cargs.append("--ldir-default")
-    if params.get("no_unknown"):
+    if params.get("no_unknown", False):
         cargs.append("--no-unknown")
-    if params.get("thresh") is not None:
+    if params.get("thresh", None) is not None:
         cargs.extend([
             "--thresh",
-            str(params.get("thresh"))
+            str(params.get("thresh", None))
         ])
-    if params.get("maxstatwinner"):
+    if params.get("maxstatwinner", False):
         cargs.append("--maxstatwinner")
-    if params.get("surf") is not None:
+    if params.get("surf", None) is not None:
         cargs.extend([
             "--surf",
-            params.get("surf")
+            params.get("surf", None)
         ])
-    if params.get("subjects_dir") is not None:
+    if params.get("subjects_dir", None) is not None:
         cargs.extend([
             "--sd",
-            params.get("subjects_dir")
+            params.get("subjects_dir", None)
         ])
     return cargs
 
@@ -228,16 +213,18 @@ def mris_label2annot_outputs(
     """
     ret = MrisLabel2annotOutputs(
         root=execution.output_file("."),
-        annot_file=execution.output_file(params.get("hemi") + "." + params.get("annotname") + ".annot"),
+        annot_file=execution.output_file(params.get("hemi", None) + "." + params.get("annotname", None) + ".annot"),
     )
     return ret
 
 
 def mris_label2annot_execute(
     params: MrisLabel2annotParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisLabel2annotOutputs:
     """
+    mris_label2annot
+    
     Converts a set of surface labels to an annotation file.
     
     Author: FreeSurfer Developers
@@ -246,10 +233,12 @@ def mris_label2annot_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisLabel2annotOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_LABEL2ANNOT_METADATA)
     params = execution.params(params)
     cargs = mris_label2annot_cargs(params, execution)
     ret = mris_label2annot_outputs(params, execution)
@@ -275,6 +264,8 @@ def mris_label2annot(
     runner: Runner | None = None,
 ) -> MrisLabel2annotOutputs:
     """
+    mris_label2annot
+    
     Converts a set of surface labels to an annotation file.
     
     Author: FreeSurfer Developers
@@ -300,8 +291,6 @@ def mris_label2annot(
     Returns:
         NamedTuple of outputs (described in `MrisLabel2annotOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_LABEL2ANNOT_METADATA)
     params = mris_label2annot_params(
         subject=subject,
         hemi=hemi,
@@ -318,13 +307,13 @@ def mris_label2annot(
         surf=surf,
         subjects_dir=subjects_dir,
     )
-    return mris_label2annot_execute(params, execution)
+    return mris_label2annot_execute(params, runner)
 
 
 __all__ = [
     "MRIS_LABEL2ANNOT_METADATA",
     "MrisLabel2annotOutputs",
-    "MrisLabel2annotParameters",
     "mris_label2annot",
+    "mris_label2annot_execute",
     "mris_label2annot_params",
 ]

niwrap_freesurfer/freesurfer/mris_label_area.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_LABEL_AREA_METADATA = Metadata(
-    id="b4e5745ec8a606dfe0c21b7eb2d0b3bdcb9605f3.boutiques",
+    id="df2a4a379b8bd5c6514abb40377a6f76b7d17955.boutiques",
     name="mris_label_area",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ MRIS_LABEL_AREA_METADATA = Metadata(
 
 
 MrisLabelAreaParameters = typing.TypedDict('MrisLabelAreaParameters', {
-    "__STYXTYPE__": typing.Literal["mris_label_area"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_label_area"]],
+    "pct_flag": bool,
+    "log_file": typing.NotRequired[str | None],
+    "brain_vol": typing.NotRequired[str | None],
+    "subject_name": str,
+    "hemi": str,
+    "surf_name": str,
+    "annot_name": str,
+    "labels": list[str],
+})
+MrisLabelAreaParametersTagged = typing.TypedDict('MrisLabelAreaParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_label_area"],
     "pct_flag": bool,
     "log_file": typing.NotRequired[str | None],
     "brain_vol": typing.NotRequired[str | None],
@@ -24,42 +35,11 @@ MrisLabelAreaParameters = typing.TypedDict('MrisLabelAreaParameters', {
     "annot_name": str,
     "labels": list[str],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_label_area": mris_label_area_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 MrisLabelAreaOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_label_area(...)`.
+    Output object returned when calling `MrisLabelAreaParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,7 +54,7 @@ def mris_label_area_params(
     pct_flag: bool = False,
     log_file: str | None = None,
     brain_vol: str | None = None,
-) -> MrisLabelAreaParameters:
+) -> MrisLabelAreaParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +71,7 @@ def mris_label_area_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_label_area",
+        "@type": "freesurfer/mris_label_area",
         "pct_flag": pct_flag,
         "subject_name": subject_name,
         "hemi": hemi,
@@ -121,23 +101,23 @@ def mris_label_area_cargs(
     """
     cargs = []
     cargs.append("mris_label_area")
-    if params.get("pct_flag"):
+    if params.get("pct_flag", False):
         cargs.append("-p")
-    if params.get("log_file") is not None:
+    if params.get("log_file", None) is not None:
         cargs.extend([
             "-l",
-            params.get("log_file")
+            params.get("log_file", None)
         ])
-    if params.get("brain_vol") is not None:
+    if params.get("brain_vol", None) is not None:
         cargs.extend([
             "-b",
-            params.get("brain_vol")
+            params.get("brain_vol", None)
         ])
-    cargs.append(params.get("subject_name"))
-    cargs.append(params.get("hemi"))
-    cargs.append(params.get("surf_name"))
-    cargs.append(params.get("annot_name"))
-    cargs.extend(params.get("labels"))
+    cargs.append(params.get("subject_name", None))
+    cargs.append(params.get("hemi", None))
+    cargs.append(params.get("surf_name", None))
+    cargs.append(params.get("annot_name", None))
+    cargs.extend(params.get("labels", None))
     return cargs
 
 
@@ -162,9 +142,11 @@ def mris_label_area_outputs(
 
 def mris_label_area_execute(
     params: MrisLabelAreaParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisLabelAreaOutputs:
     """
+    mris_label_area
+    
     Compute the area of specific labels on a surface of a brain hemisphere in
     FreeSurfer.
     
@@ -174,10 +156,12 @@ def mris_label_area_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisLabelAreaOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_LABEL_AREA_METADATA)
     params = execution.params(params)
     cargs = mris_label_area_cargs(params, execution)
     ret = mris_label_area_outputs(params, execution)
@@ -197,6 +181,8 @@ def mris_label_area(
     runner: Runner | None = None,
 ) -> MrisLabelAreaOutputs:
     """
+    mris_label_area
+    
     Compute the area of specific labels on a surface of a brain hemisphere in
     FreeSurfer.
     
@@ -217,8 +203,6 @@ def mris_label_area(
     Returns:
         NamedTuple of outputs (described in `MrisLabelAreaOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_LABEL_AREA_METADATA)
     params = mris_label_area_params(
         pct_flag=pct_flag,
         log_file=log_file,
@@ -229,13 +213,13 @@ def mris_label_area(
         annot_name=annot_name,
         labels=labels,
     )
-    return mris_label_area_execute(params, execution)
+    return mris_label_area_execute(params, runner)
 
 
 __all__ = [
     "MRIS_LABEL_AREA_METADATA",
     "MrisLabelAreaOutputs",
-    "MrisLabelAreaParameters",
     "mris_label_area",
+    "mris_label_area_execute",
     "mris_label_area_params",
 ]

niwrap_freesurfer/freesurfer/mris_label_calc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_LABEL_CALC_METADATA = Metadata(
-    id="d93d02a327398015e84d46734009d6fa6287d4ae.boutiques",
+    id="fc4b584ed4e81ed34a6bdc6abd5ac19ba43c90f5.boutiques",
     name="mris_label_calc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ MRIS_LABEL_CALC_METADATA = Metadata(
 
 
 MrisLabelCalcParameters = typing.TypedDict('MrisLabelCalcParameters', {
-    "__STYXTYPE__": typing.Literal["mris_label_calc"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_label_calc"]],
+    "command": typing.Literal["union", "intersect", "invert", "erode", "dilate"],
+    "input1": InputPathType,
+    "input2": InputPathType,
+    "output": str,
+    "iterations": typing.NotRequired[int | None],
+})
+MrisLabelCalcParametersTagged = typing.TypedDict('MrisLabelCalcParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_label_calc"],
     "command": typing.Literal["union", "intersect", "invert", "erode", "dilate"],
     "input1": InputPathType,
     "input2": InputPathType,
     "output": str,
     "iterations": typing.NotRequired[int | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_label_calc": mris_label_calc_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 {
-        "mris_label_calc": mris_label_calc_outputs,
-    }.get(t)
 
 
 class MrisLabelCalcOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_label_calc(...)`.
+    Output object returned when calling `MrisLabelCalcParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def mris_label_calc_params(
     input2: InputPathType,
     output: str,
     iterations: int | None = None,
-) -> MrisLabelCalcParameters:
+) -> MrisLabelCalcParametersTagged:
     """
     Build parameters.
     
@@ -86,7 +62,7 @@ def mris_label_calc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_label_calc",
+        "@type": "freesurfer/mris_label_calc",
         "command": command,
         "input1": input1,
         "input2": input2,
@@ -112,14 +88,14 @@ def mris_label_calc_cargs(
     """
     cargs = []
     cargs.append("mris_label_calc")
-    cargs.append(params.get("command"))
-    cargs.append(execution.input_file(params.get("input1")))
-    cargs.append(execution.input_file(params.get("input2")))
-    cargs.append(params.get("output"))
-    if params.get("iterations") is not None:
+    cargs.append(params.get("command", None))
+    cargs.append(execution.input_file(params.get("input1", None)))
+    cargs.append(execution.input_file(params.get("input2", None)))
+    cargs.append(params.get("output", None))
+    if params.get("iterations", None) is not None:
         cargs.extend([
             "<n>",
-            str(params.get("iterations"))
+            str(params.get("iterations", None))
         ])
     return cargs
 
@@ -139,16 +115,18 @@ def mris_label_calc_outputs(
     """
     ret = MrisLabelCalcOutputs(
         root=execution.output_file("."),
-        output_label=execution.output_file(params.get("output") + ".label"),
+        output_label=execution.output_file(params.get("output", None) + ".label"),
     )
     return ret
 
 
 def mris_label_calc_execute(
     params: MrisLabelCalcParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisLabelCalcOutputs:
     """
+    mris_label_calc
+    
     Tool for surface label calculations.
     
     Author: FreeSurfer Developers
@@ -157,10 +135,12 @@ def mris_label_calc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisLabelCalcOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_LABEL_CALC_METADATA)
     params = execution.params(params)
     cargs = mris_label_calc_cargs(params, execution)
     ret = mris_label_calc_outputs(params, execution)
@@ -177,6 +157,8 @@ def mris_label_calc(
     runner: Runner | None = None,
 ) -> MrisLabelCalcOutputs:
     """
+    mris_label_calc
+    
     Tool for surface label calculations.
     
     Author: FreeSurfer Developers
@@ -194,8 +176,6 @@ def mris_label_calc(
     Returns:
         NamedTuple of outputs (described in `MrisLabelCalcOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_LABEL_CALC_METADATA)
     params = mris_label_calc_params(
         command=command,
         input1=input1,
@@ -203,13 +183,13 @@ def mris_label_calc(
         output=output,
         iterations=iterations,
     )
-    return mris_label_calc_execute(params, execution)
+    return mris_label_calc_execute(params, runner)
 
 
 __all__ = [
     "MRIS_LABEL_CALC_METADATA",
     "MrisLabelCalcOutputs",
-    "MrisLabelCalcParameters",
     "mris_label_calc",
+    "mris_label_calc_execute",
     "mris_label_calc_params",
 ]