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

niwrap_freesurfer/freesurfer/trac_preproc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TRAC_PREPROC_METADATA = Metadata(
-    id="42b88183bcd352135a6f2621284dcf3f4430c692.boutiques",
+    id="21913fdc47128e05a924c3bd9320265aa78c9220.boutiques",
     name="trac-preproc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,22 @@ TRAC_PREPROC_METADATA = Metadata(
 
 
 TracPreprocParameters = typing.TypedDict('TracPreprocParameters', {
-    "__STYXTYPE__": typing.Literal["trac-preproc"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/trac-preproc"]],
+    "dmrirc_file": InputPathType,
+    "log_file": typing.NotRequired[str | None],
+    "nolog": bool,
+    "cmd_file": typing.NotRequired[str | None],
+    "nocmd": bool,
+    "no_isrunning": bool,
+    "umask": typing.NotRequired[str | None],
+    "group_id": typing.NotRequired[str | None],
+    "allow_core_dump": bool,
+    "debug": bool,
+    "dontrun": bool,
+    "version": bool,
+})
+TracPreprocParametersTagged = typing.TypedDict('TracPreprocParametersTagged', {
+    "@type": typing.Literal["freesurfer/trac-preproc"],
     "dmrirc_file": InputPathType,
     "log_file": typing.NotRequired[str | None],
     "nolog": bool,
@@ -28,42 +43,11 @@ TracPreprocParameters = typing.TypedDict('TracPreprocParameters', {
     "dontrun": bool,
     "version": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "trac-preproc": trac_preproc_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 TracPreprocOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `trac_preproc(...)`.
+    Output object returned when calling `TracPreprocParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -82,7 +66,7 @@ def trac_preproc_params(
     debug: bool = False,
     dontrun: bool = False,
     version: bool = False,
-) -> TracPreprocParameters:
+) -> TracPreprocParametersTagged:
     """
     Build parameters.
     
@@ -104,7 +88,7 @@ def trac_preproc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "trac-preproc",
+        "@type": "freesurfer/trac-preproc",
         "dmrirc_file": dmrirc_file,
         "nolog": nolog,
         "nocmd": nocmd,
@@ -142,41 +126,41 @@ def trac_preproc_cargs(
     cargs.append("trac-preproc")
     cargs.extend([
         "-c",
-        execution.input_file(params.get("dmrirc_file"))
+        execution.input_file(params.get("dmrirc_file", None))
     ])
-    if params.get("log_file") is not None:
+    if params.get("log_file", None) is not None:
         cargs.extend([
             "-log",
-            params.get("log_file")
+            params.get("log_file", None)
         ])
-    if params.get("nolog"):
+    if params.get("nolog", False):
         cargs.append("-nolog")
-    if params.get("cmd_file") is not None:
+    if params.get("cmd_file", None) is not None:
         cargs.extend([
             "-cmd",
-            params.get("cmd_file")
+            params.get("cmd_file", None)
         ])
-    if params.get("nocmd"):
+    if params.get("nocmd", False):
         cargs.append("-nocmd")
-    if params.get("no_isrunning"):
+    if params.get("no_isrunning", False):
         cargs.append("-no-isrunning")
-    if params.get("umask") is not None:
+    if params.get("umask", None) is not None:
         cargs.extend([
             "-umask",
-            params.get("umask")
+            params.get("umask", None)
         ])
-    if params.get("group_id") is not None:
+    if params.get("group_id", None) is not None:
         cargs.extend([
             "-grp",
-            params.get("group_id")
+            params.get("group_id", None)
         ])
-    if params.get("allow_core_dump"):
+    if params.get("allow_core_dump", False):
         cargs.append("-allowcoredump")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-debug")
-    if params.get("dontrun"):
+    if params.get("dontrun", False):
         cargs.append("-dontrun")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-version")
     return cargs
 
@@ -202,9 +186,11 @@ def trac_preproc_outputs(
 
 def trac_preproc_execute(
     params: TracPreprocParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TracPreprocOutputs:
     """
+    trac-preproc
+    
     Tractography pre-processing for a single subject.
     
     Author: FreeSurfer Developers
@@ -213,10 +199,12 @@ def trac_preproc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TracPreprocOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TRAC_PREPROC_METADATA)
     params = execution.params(params)
     cargs = trac_preproc_cargs(params, execution)
     ret = trac_preproc_outputs(params, execution)
@@ -240,6 +228,8 @@ def trac_preproc(
     runner: Runner | None = None,
 ) -> TracPreprocOutputs:
     """
+    trac-preproc
+    
     Tractography pre-processing for a single subject.
     
     Author: FreeSurfer Developers
@@ -264,8 +254,6 @@ def trac_preproc(
     Returns:
         NamedTuple of outputs (described in `TracPreprocOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TRAC_PREPROC_METADATA)
     params = trac_preproc_params(
         dmrirc_file=dmrirc_file,
         log_file=log_file,
@@ -280,13 +268,13 @@ def trac_preproc(
         dontrun=dontrun,
         version=version,
     )
-    return trac_preproc_execute(params, execution)
+    return trac_preproc_execute(params, runner)
 
 
 __all__ = [
     "TRAC_PREPROC_METADATA",
     "TracPreprocOutputs",
-    "TracPreprocParameters",
     "trac_preproc",
+    "trac_preproc_execute",
     "trac_preproc_params",
 ]

niwrap_freesurfer/freesurfer/tractstats2table.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TRACTSTATS2TABLE_METADATA = Metadata(
-    id="deb2a42839930436dbac59d0fe2517f06e878809.boutiques",
+    id="e6daf3e869f229283190a4ed57894649a7cde47b.boutiques",
     name="tractstats2table",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,19 @@ TRACTSTATS2TABLE_METADATA = Metadata(
 
 
 Tractstats2tableParameters = typing.TypedDict('Tractstats2tableParameters', {
-    "__STYXTYPE__": typing.Literal["tractstats2table"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/tractstats2table"]],
+    "inputs": typing.NotRequired[list[str] | None],
+    "load_pathstats_from_file": typing.NotRequired[InputPathType | None],
+    "overall": bool,
+    "byvoxel": bool,
+    "byvoxel_measure": typing.NotRequired[typing.Literal["AD", "RD", "MD", "FA"] | None],
+    "tablefile": InputPathType,
+    "delimiter": typing.NotRequired[typing.Literal["tab", "comma", "space", "semicolon"] | None],
+    "transpose": bool,
+    "debug": bool,
+})
+Tractstats2tableParametersTagged = typing.TypedDict('Tractstats2tableParametersTagged', {
+    "@type": typing.Literal["freesurfer/tractstats2table"],
     "inputs": typing.NotRequired[list[str] | None],
     "load_pathstats_from_file": typing.NotRequired[InputPathType | None],
     "overall": bool,
@@ -25,43 +37,11 @@ Tractstats2tableParameters = typing.TypedDict('Tractstats2tableParameters', {
     "transpose": bool,
     "debug": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "tractstats2table": tractstats2table_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 {
-        "tractstats2table": tractstats2table_outputs,
-    }.get(t)
 
 
 class Tractstats2tableOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `tractstats2table(...)`.
+    Output object returned when calling `Tractstats2tableParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -76,10 +56,10 @@ def tractstats2table_params(
     overall: bool = False,
     byvoxel: bool = False,
     byvoxel_measure: typing.Literal["AD", "RD", "MD", "FA"] | None = None,
-    delimiter: typing.Literal["tab", "comma", "space", "semicolon"] | None = "tab",
+    delimiter: typing.Literal["tab", "comma", "space", "semicolon"] | None = None,
     transpose: bool = False,
     debug: bool = False,
-) -> Tractstats2tableParameters:
+) -> Tractstats2tableParametersTagged:
     """
     Build parameters.
     
@@ -101,7 +81,7 @@ def tractstats2table_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tractstats2table",
+        "@type": "freesurfer/tractstats2table",
         "overall": overall,
         "byvoxel": byvoxel,
         "tablefile": tablefile,
@@ -134,37 +114,37 @@ def tractstats2table_cargs(
     """
     cargs = []
     cargs.append("tractstats2table")
-    if params.get("inputs") is not None:
+    if params.get("inputs", None) is not None:
         cargs.extend([
             "--inputs",
-            *params.get("inputs")
+            *params.get("inputs", None)
         ])
-    if params.get("load_pathstats_from_file") is not None:
+    if params.get("load_pathstats_from_file", None) is not None:
         cargs.extend([
             "--load-pathstats-from-file",
-            execution.input_file(params.get("load_pathstats_from_file"))
+            execution.input_file(params.get("load_pathstats_from_file", None))
         ])
-    if params.get("overall"):
+    if params.get("overall", False):
         cargs.append("-o")
-    if params.get("byvoxel"):
+    if params.get("byvoxel", False):
         cargs.append("-b")
-    if params.get("byvoxel_measure") is not None:
+    if params.get("byvoxel_measure", None) is not None:
         cargs.extend([
             "--byvoxel-measure",
-            params.get("byvoxel_measure")
+            params.get("byvoxel_measure", None)
         ])
     cargs.extend([
         "-t",
-        execution.input_file(params.get("tablefile"))
+        execution.input_file(params.get("tablefile", None))
     ])
-    if params.get("delimiter") is not None:
+    if params.get("delimiter", None) is not None:
         cargs.extend([
             "-d",
-            params.get("delimiter")
+            params.get("delimiter", None)
         ])
-    if params.get("transpose"):
+    if params.get("transpose", False):
         cargs.append("--transpose")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-v")
     return cargs
 
@@ -184,16 +164,18 @@ def tractstats2table_outputs(
     """
     ret = Tractstats2tableOutputs(
         root=execution.output_file("."),
-        output_tablefile=execution.output_file(pathlib.Path(params.get("tablefile")).name),
+        output_tablefile=execution.output_file(pathlib.Path(params.get("tablefile", None)).name),
     )
     return ret
 
 
 def tractstats2table_execute(
     params: Tractstats2tableParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Tractstats2tableOutputs:
     """
+    tractstats2table
+    
     Converts a track overall stats file created by tracula into a table used for
     group statistics.
     
@@ -203,10 +185,12 @@ def tractstats2table_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Tractstats2tableOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TRACTSTATS2TABLE_METADATA)
     params = execution.params(params)
     cargs = tractstats2table_cargs(params, execution)
     ret = tractstats2table_outputs(params, execution)
@@ -221,12 +205,14 @@ def tractstats2table(
     overall: bool = False,
     byvoxel: bool = False,
     byvoxel_measure: typing.Literal["AD", "RD", "MD", "FA"] | None = None,
-    delimiter: typing.Literal["tab", "comma", "space", "semicolon"] | None = "tab",
+    delimiter: typing.Literal["tab", "comma", "space", "semicolon"] | None = None,
     transpose: bool = False,
     debug: bool = False,
     runner: Runner | None = None,
 ) -> Tractstats2tableOutputs:
     """
+    tractstats2table
+    
     Converts a track overall stats file created by tracula into a table used for
     group statistics.
     
@@ -252,8 +238,6 @@ def tractstats2table(
     Returns:
         NamedTuple of outputs (described in `Tractstats2tableOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TRACTSTATS2TABLE_METADATA)
     params = tractstats2table_params(
         inputs=inputs,
         load_pathstats_from_file=load_pathstats_from_file,
@@ -265,13 +249,13 @@ def tractstats2table(
         transpose=transpose,
         debug=debug,
     )
-    return tractstats2table_execute(params, execution)
+    return tractstats2table_execute(params, runner)
 
 
 __all__ = [
     "TRACTSTATS2TABLE_METADATA",
     "Tractstats2tableOutputs",
-    "Tractstats2tableParameters",
     "tractstats2table",
+    "tractstats2table_execute",
     "tractstats2table_params",
 ]

niwrap_freesurfer/freesurfer/train_gcs_atlas.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TRAIN_GCS_ATLAS_METADATA = Metadata(
-    id="b6cf07c4cdf258fcf1766d6d9378e42cf9ae6cdc.boutiques",
+    id="a1af0dade42962e79b309666f7e6a29a25239ed2.boutiques",
     name="train-gcs-atlas",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,22 @@ TRAIN_GCS_ATLAS_METADATA = Metadata(
 
 
 TrainGcsAtlasParameters = typing.TypedDict('TrainGcsAtlasParameters', {
-    "__STYXTYPE__": typing.Literal["train-gcs-atlas"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/train-gcs-atlas"]],
+    "manual_parcellation": typing.NotRequired[str | None],
+    "subjlist_file": typing.NotRequired[InputPathType | None],
+    "left_hemi": bool,
+    "right_hemi": bool,
+    "hemi_spec": typing.NotRequired[str | None],
+    "output_gcs": str,
+    "surf_reg": typing.NotRequired[InputPathType | None],
+    "color_table": typing.NotRequired[InputPathType | None],
+    "exclude_subject": typing.NotRequired[str | None],
+    "jackknife_flag": bool,
+    "aseg_filename": typing.NotRequired[str | None],
+    "threads": typing.NotRequired[float | None],
+})
+TrainGcsAtlasParametersTagged = typing.TypedDict('TrainGcsAtlasParametersTagged', {
+    "@type": typing.Literal["freesurfer/train-gcs-atlas"],
     "manual_parcellation": typing.NotRequired[str | None],
     "subjlist_file": typing.NotRequired[InputPathType | None],
     "left_hemi": bool,
@@ -28,43 +43,11 @@ TrainGcsAtlasParameters = typing.TypedDict('TrainGcsAtlasParameters', {
     "aseg_filename": typing.NotRequired[str | None],
     "threads": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "train-gcs-atlas": train_gcs_atlas_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 {
-        "train-gcs-atlas": train_gcs_atlas_outputs,
-    }.get(t)
 
 
 class TrainGcsAtlasOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `train_gcs_atlas(...)`.
+    Output object returned when calling `TrainGcsAtlasParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -85,7 +68,7 @@ def train_gcs_atlas_params(
     jackknife_flag: bool = False,
     aseg_filename: str | None = None,
     threads: float | None = None,
-) -> TrainGcsAtlasParameters:
+) -> TrainGcsAtlasParametersTagged:
     """
     Build parameters.
     
@@ -106,7 +89,7 @@ def train_gcs_atlas_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "train-gcs-atlas",
+        "@type": "freesurfer/train-gcs-atlas",
         "left_hemi": left_hemi,
         "right_hemi": right_hemi,
         "output_gcs": output_gcs,
@@ -146,55 +129,55 @@ def train_gcs_atlas_cargs(
     """
     cargs = []
     cargs.append("train-gcs-atlas")
-    if params.get("manual_parcellation") is not None:
+    if params.get("manual_parcellation", None) is not None:
         cargs.extend([
             "--man",
-            params.get("manual_parcellation")
+            params.get("manual_parcellation", None)
         ])
-    if params.get("subjlist_file") is not None:
+    if params.get("subjlist_file", None) is not None:
         cargs.extend([
             "--f",
-            execution.input_file(params.get("subjlist_file"))
+            execution.input_file(params.get("subjlist_file", None))
         ])
-    if params.get("left_hemi"):
+    if params.get("left_hemi", False):
         cargs.append("--lh")
-    if params.get("right_hemi"):
+    if params.get("right_hemi", False):
         cargs.append("--rh")
-    if params.get("hemi_spec") is not None:
+    if params.get("hemi_spec", None) is not None:
         cargs.extend([
             "--hemi",
-            params.get("hemi_spec")
+            params.get("hemi_spec", None)
         ])
     cargs.extend([
         "--o",
-        params.get("output_gcs")
+        params.get("output_gcs", None)
     ])
-    if params.get("surf_reg") is not None:
+    if params.get("surf_reg", None) is not None:
         cargs.extend([
             "--reg",
-            execution.input_file(params.get("surf_reg"))
+            execution.input_file(params.get("surf_reg", None))
         ])
-    if params.get("color_table") is not None:
+    if params.get("color_table", None) is not None:
         cargs.extend([
             "--ctab",
-            execution.input_file(params.get("color_table"))
+            execution.input_file(params.get("color_table", None))
         ])
-    if params.get("exclude_subject") is not None:
+    if params.get("exclude_subject", None) is not None:
         cargs.extend([
             "--x",
-            params.get("exclude_subject")
+            params.get("exclude_subject", None)
         ])
-    if params.get("jackknife_flag"):
+    if params.get("jackknife_flag", False):
         cargs.append("--jackknife")
-    if params.get("aseg_filename") is not None:
+    if params.get("aseg_filename", None) is not None:
         cargs.extend([
             "--aseg",
-            params.get("aseg_filename")
+            params.get("aseg_filename", None)
         ])
-    if params.get("threads") is not None:
+    if params.get("threads", None) is not None:
         cargs.extend([
             "--threads",
-            str(params.get("threads"))
+            str(params.get("threads", None))
         ])
     return cargs
 
@@ -214,16 +197,18 @@ def train_gcs_atlas_outputs(
     """
     ret = TrainGcsAtlasOutputs(
         root=execution.output_file("."),
-        output_gcs_file=execution.output_file(params.get("output_gcs")),
+        output_gcs_file=execution.output_file(params.get("output_gcs", None)),
     )
     return ret
 
 
 def train_gcs_atlas_execute(
     params: TrainGcsAtlasParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TrainGcsAtlasOutputs:
     """
+    train-gcs-atlas
+    
     Script to train a surface-based gaussian classifier for cortical surface
     parcellation.
     
@@ -233,10 +218,12 @@ def train_gcs_atlas_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TrainGcsAtlasOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TRAIN_GCS_ATLAS_METADATA)
     params = execution.params(params)
     cargs = train_gcs_atlas_cargs(params, execution)
     ret = train_gcs_atlas_outputs(params, execution)
@@ -260,6 +247,8 @@ def train_gcs_atlas(
     runner: Runner | None = None,
 ) -> TrainGcsAtlasOutputs:
     """
+    train-gcs-atlas
+    
     Script to train a surface-based gaussian classifier for cortical surface
     parcellation.
     
@@ -284,8 +273,6 @@ def train_gcs_atlas(
     Returns:
         NamedTuple of outputs (described in `TrainGcsAtlasOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TRAIN_GCS_ATLAS_METADATA)
     params = train_gcs_atlas_params(
         manual_parcellation=manual_parcellation,
         subjlist_file=subjlist_file,
@@ -300,13 +287,13 @@ def train_gcs_atlas(
         aseg_filename=aseg_filename,
         threads=threads,
     )
-    return train_gcs_atlas_execute(params, execution)
+    return train_gcs_atlas_execute(params, runner)
 
 
 __all__ = [
     "TRAIN_GCS_ATLAS_METADATA",
     "TrainGcsAtlasOutputs",
-    "TrainGcsAtlasParameters",
     "train_gcs_atlas",
+    "train_gcs_atlas_execute",
     "train_gcs_atlas_params",
 ]