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

niwrap_freesurfer/freesurfer/mri_paint.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_PAINT_METADATA = Metadata(
-    id="6516a3cbf50c0b983fd6dd6fca7b67e4566c67bc.boutiques",
+    id="dec6a4dce4882cf1b15d956692f1b6e908fbc2be.boutiques",
     name="mri_paint",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRI_PAINT_METADATA = Metadata(
 
 
 MriPaintParameters = typing.TypedDict('MriPaintParameters', {
-    "__STYXTYPE__": typing.Literal["mri_paint"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_paint"]],
+    "input_volume": InputPathType,
+    "input_surface": InputPathType,
+    "registration_file": InputPathType,
+    "output_float_file": str,
+    "image_offset": typing.NotRequired[float | None],
+    "paint_surf_coords": bool,
+})
+MriPaintParametersTagged = typing.TypedDict('MriPaintParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_paint"],
     "input_volume": InputPathType,
     "input_surface": InputPathType,
     "registration_file": InputPathType,
@@ -22,43 +31,11 @@ MriPaintParameters = typing.TypedDict('MriPaintParameters', {
     "image_offset": typing.NotRequired[float | None],
     "paint_surf_coords": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_paint": mri_paint_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 {
-        "mri_paint": mri_paint_outputs,
-    }.get(t)
 
 
 class MriPaintOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_paint(...)`.
+    Output object returned when calling `MriPaintParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def mri_paint_params(
     output_float_file: str,
     image_offset: float | None = None,
     paint_surf_coords: bool = False,
-) -> MriPaintParameters:
+) -> MriPaintParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +65,7 @@ def mri_paint_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_paint",
+        "@type": "freesurfer/mri_paint",
         "input_volume": input_volume,
         "input_surface": input_surface,
         "registration_file": registration_file,
@@ -115,16 +92,16 @@ def mri_paint_cargs(
     """
     cargs = []
     cargs.append("mri_paint")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(execution.input_file(params.get("registration_file")))
-    cargs.append(params.get("output_float_file"))
-    if params.get("image_offset") is not None:
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(execution.input_file(params.get("registration_file", None)))
+    cargs.append(params.get("output_float_file", None))
+    if params.get("image_offset", None) is not None:
         cargs.extend([
             "-imageoffset",
-            str(params.get("image_offset"))
+            str(params.get("image_offset", None))
         ])
-    if params.get("paint_surf_coords"):
+    if params.get("paint_surf_coords", False):
         cargs.append("-S")
     return cargs
 
@@ -144,16 +121,18 @@ def mri_paint_outputs(
     """
     ret = MriPaintOutputs(
         root=execution.output_file("."),
-        output_float=execution.output_file(params.get("output_float_file")),
+        output_float=execution.output_file(params.get("output_float_file", None)),
     )
     return ret
 
 
 def mri_paint_execute(
     params: MriPaintParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriPaintOutputs:
     """
+    mri_paint
+    
     This program will paint average Talairach stats onto a surface.
     
     Author: FreeSurfer Developers
@@ -162,10 +141,12 @@ def mri_paint_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriPaintOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_PAINT_METADATA)
     params = execution.params(params)
     cargs = mri_paint_cargs(params, execution)
     ret = mri_paint_outputs(params, execution)
@@ -183,6 +164,8 @@ def mri_paint(
     runner: Runner | None = None,
 ) -> MriPaintOutputs:
     """
+    mri_paint
+    
     This program will paint average Talairach stats onto a surface.
     
     Author: FreeSurfer Developers
@@ -200,8 +183,6 @@ def mri_paint(
     Returns:
         NamedTuple of outputs (described in `MriPaintOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_PAINT_METADATA)
     params = mri_paint_params(
         input_volume=input_volume,
         input_surface=input_surface,
@@ -210,13 +191,13 @@ def mri_paint(
         image_offset=image_offset,
         paint_surf_coords=paint_surf_coords,
     )
-    return mri_paint_execute(params, execution)
+    return mri_paint_execute(params, runner)
 
 
 __all__ = [
     "MRI_PAINT_METADATA",
     "MriPaintOutputs",
-    "MriPaintParameters",
     "mri_paint",
+    "mri_paint_execute",
     "mri_paint_params",
 ]

niwrap_freesurfer/freesurfer/mri_parse_sdcmdir.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_PARSE_SDCMDIR_METADATA = Metadata(
-    id="da51e5d5af342cf720bb1d988d04c5f9f98e067a.boutiques",
+    id="b8bf5c0b6d4658befffadf65022ae055d1766b9c.boutiques",
     name="mri_parse_sdcmdir",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,26 @@ MRI_PARSE_SDCMDIR_METADATA = Metadata(
 
 
 MriParseSdcmdirParameters = typing.TypedDict('MriParseSdcmdirParameters', {
-    "__STYXTYPE__": typing.Literal["mri_parse_sdcmdir"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_parse_sdcmdir"]],
+    "sdicomdir": str,
+    "outfile": typing.NotRequired[str | None],
+    "sortbyrun": bool,
+    "summarize": bool,
+    "dwi": bool,
+})
+MriParseSdcmdirParametersTagged = typing.TypedDict('MriParseSdcmdirParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_parse_sdcmdir"],
     "sdicomdir": str,
     "outfile": typing.NotRequired[str | None],
     "sortbyrun": bool,
     "summarize": bool,
     "dwi": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_parse_sdcmdir": mri_parse_sdcmdir_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 MriParseSdcmdirOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_parse_sdcmdir(...)`.
+    Output object returned when calling `MriParseSdcmdirParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -68,7 +45,7 @@ def mri_parse_sdcmdir_params(
     sortbyrun: bool = False,
     summarize: bool = False,
     dwi: bool = False,
-) -> MriParseSdcmdirParameters:
+) -> MriParseSdcmdirParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +60,7 @@ def mri_parse_sdcmdir_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_parse_sdcmdir",
+        "@type": "freesurfer/mri_parse_sdcmdir",
         "sdicomdir": sdicomdir,
         "sortbyrun": sortbyrun,
         "summarize": summarize,
@@ -111,18 +88,18 @@ def mri_parse_sdcmdir_cargs(
     cargs.append("mri_parse_sdcmdir")
     cargs.extend([
         "--d",
-        params.get("sdicomdir")
+        params.get("sdicomdir", None)
     ])
-    if params.get("outfile") is not None:
+    if params.get("outfile", None) is not None:
         cargs.extend([
             "--o",
-            params.get("outfile")
+            params.get("outfile", None)
         ])
-    if params.get("sortbyrun"):
+    if params.get("sortbyrun", False):
         cargs.append("--sortbyrun")
-    if params.get("summarize"):
+    if params.get("summarize", False):
         cargs.append("--summarize")
-    if params.get("dwi"):
+    if params.get("dwi", False):
         cargs.append("--dwi")
     return cargs
 
@@ -148,11 +125,13 @@ def mri_parse_sdcmdir_outputs(
 
 def mri_parse_sdcmdir_execute(
     params: MriParseSdcmdirParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriParseSdcmdirOutputs:
     """
-    This program parses the Siemens DICOM files in a given directory and prints out
-    information about each file.
+    mri_parse_sdcmdir
+    
+    This program parses the Siemens DICOM files in a given directory and prints
+    out information about each file.
     
     Author: FreeSurfer Developers
     
@@ -160,10 +139,12 @@ def mri_parse_sdcmdir_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriParseSdcmdirOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_PARSE_SDCMDIR_METADATA)
     params = execution.params(params)
     cargs = mri_parse_sdcmdir_cargs(params, execution)
     ret = mri_parse_sdcmdir_outputs(params, execution)
@@ -180,8 +161,10 @@ def mri_parse_sdcmdir(
     runner: Runner | None = None,
 ) -> MriParseSdcmdirOutputs:
     """
-    This program parses the Siemens DICOM files in a given directory and prints out
-    information about each file.
+    mri_parse_sdcmdir
+    
+    This program parses the Siemens DICOM files in a given directory and prints
+    out information about each file.
     
     Author: FreeSurfer Developers
     
@@ -198,8 +181,6 @@ def mri_parse_sdcmdir(
     Returns:
         NamedTuple of outputs (described in `MriParseSdcmdirOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_PARSE_SDCMDIR_METADATA)
     params = mri_parse_sdcmdir_params(
         sdicomdir=sdicomdir,
         outfile=outfile,
@@ -207,13 +188,13 @@ def mri_parse_sdcmdir(
         summarize=summarize,
         dwi=dwi,
     )
-    return mri_parse_sdcmdir_execute(params, execution)
+    return mri_parse_sdcmdir_execute(params, runner)
 
 
 __all__ = [
     "MRI_PARSE_SDCMDIR_METADATA",
     "MriParseSdcmdirOutputs",
-    "MriParseSdcmdirParameters",
     "mri_parse_sdcmdir",
+    "mri_parse_sdcmdir_execute",
     "mri_parse_sdcmdir_params",
 ]

niwrap_freesurfer/freesurfer/mri_path2label.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_PATH2LABEL_METADATA = Metadata(
-    id="12d0b2997587b36a9d69c2e0647f2619028fb232.boutiques",
+    id="f6aabaa35d15694a3404575387789931acf2e412.boutiques",
     name="mri_path2label",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,21 @@ MRI_PATH2LABEL_METADATA = Metadata(
 
 
 MriPath2labelParameters = typing.TypedDict('MriPath2labelParameters', {
-    "__STYXTYPE__": typing.Literal["mri_path2label"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_path2label"]],
+    "input_file": str,
+    "output_file": str,
+    "single": bool,
+    "path_to_label": bool,
+    "label_to_path": bool,
+    "connect": typing.NotRequired[list[str] | None],
+    "fill": typing.NotRequired[list[str] | None],
+    "confillx": typing.NotRequired[list[str] | None],
+    "confill": typing.NotRequired[list[str] | None],
+    "source_file": typing.NotRequired[str | None],
+    "dest_file": typing.NotRequired[str | None],
+})
+MriPath2labelParametersTagged = typing.TypedDict('MriPath2labelParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_path2label"],
     "input_file": str,
     "output_file": str,
     "single": bool,
@@ -27,42 +41,11 @@ MriPath2labelParameters = typing.TypedDict('MriPath2labelParameters', {
     "source_file": typing.NotRequired[str | None],
     "dest_file": 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 {
-        "mri_path2label": mri_path2label_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 MriPath2labelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_path2label(...)`.
+    Output object returned when calling `MriPath2labelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -80,7 +63,7 @@ def mri_path2label_params(
     confill: list[str] | None = None,
     source_file: str | None = None,
     dest_file: str | None = None,
-) -> MriPath2labelParameters:
+) -> MriPath2labelParametersTagged:
     """
     Build parameters.
     
@@ -104,7 +87,7 @@ def mri_path2label_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_path2label",
+        "@type": "freesurfer/mri_path2label",
         "input_file": input_file,
         "output_file": output_file,
         "single": single,
@@ -141,43 +124,43 @@ def mri_path2label_cargs(
     """
     cargs = []
     cargs.append("mri_path2label")
-    cargs.append(params.get("input_file"))
-    cargs.append(params.get("output_file"))
-    if params.get("single"):
+    cargs.append(params.get("input_file", None))
+    cargs.append(params.get("output_file", None))
+    if params.get("single", False):
         cargs.append("--single")
-    if params.get("path_to_label"):
+    if params.get("path_to_label", False):
         cargs.append("--path2label")
-    if params.get("label_to_path"):
+    if params.get("label_to_path", False):
         cargs.append("--label2path")
-    if params.get("connect") is not None:
+    if params.get("connect", None) is not None:
         cargs.extend([
             "--connect",
-            *params.get("connect")
+            *params.get("connect", None)
         ])
-    if params.get("fill") is not None:
+    if params.get("fill", None) is not None:
         cargs.extend([
             "--fill",
-            *params.get("fill")
+            *params.get("fill", None)
         ])
-    if params.get("confillx") is not None:
+    if params.get("confillx", None) is not None:
         cargs.extend([
             "--confillx",
-            *params.get("confillx")
+            *params.get("confillx", None)
         ])
-    if params.get("confill") is not None:
+    if params.get("confill", None) is not None:
         cargs.extend([
             "--confill",
-            *params.get("confill")
+            *params.get("confill", None)
         ])
-    if params.get("source_file") is not None:
+    if params.get("source_file", None) is not None:
         cargs.extend([
             "--i",
-            params.get("source_file")
+            params.get("source_file", None)
         ])
-    if params.get("dest_file") is not None:
+    if params.get("dest_file", None) is not None:
         cargs.extend([
             "--o",
-            params.get("dest_file")
+            params.get("dest_file", None)
         ])
     return cargs
 
@@ -203,9 +186,11 @@ def mri_path2label_outputs(
 
 def mri_path2label_execute(
     params: MriPath2labelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriPath2labelOutputs:
     """
+    mri_path2label
+    
     Converts a path file to a label or a label file to a path file.
     
     Author: FreeSurfer Developers
@@ -214,10 +199,12 @@ def mri_path2label_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriPath2labelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_PATH2LABEL_METADATA)
     params = execution.params(params)
     cargs = mri_path2label_cargs(params, execution)
     ret = mri_path2label_outputs(params, execution)
@@ -240,6 +227,8 @@ def mri_path2label(
     runner: Runner | None = None,
 ) -> MriPath2labelOutputs:
     """
+    mri_path2label
+    
     Converts a path file to a label or a label file to a path file.
     
     Author: FreeSurfer Developers
@@ -266,8 +255,6 @@ def mri_path2label(
     Returns:
         NamedTuple of outputs (described in `MriPath2labelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_PATH2LABEL_METADATA)
     params = mri_path2label_params(
         input_file=input_file,
         output_file=output_file,
@@ -281,13 +268,13 @@ def mri_path2label(
         source_file=source_file,
         dest_file=dest_file,
     )
-    return mri_path2label_execute(params, execution)
+    return mri_path2label_execute(params, runner)
 
 
 __all__ = [
     "MRI_PATH2LABEL_METADATA",
     "MriPath2labelOutputs",
-    "MriPath2labelParameters",
     "mri_path2label",
+    "mri_path2label_execute",
     "mri_path2label_params",
 ]