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

niwrap_freesurfer/freesurfer/aparc_stats_aseg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 APARC_STATS_ASEG_METADATA = Metadata(
-    id="360c0f479d9ecf69674e8fbf165f4e1174d824c3.boutiques",
+    id="a79f87035b2ff30425eabbe5a44088217b2d1ee1.boutiques",
     name="aparc_stats_aseg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,32 @@ APARC_STATS_ASEG_METADATA = Metadata(
 
 
 AparcStatsAsegParameters = typing.TypedDict('AparcStatsAsegParameters', {
-    "__STYXTYPE__": typing.Literal["aparc_stats_aseg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/aparc_stats_aseg"]],
+    "subject_name": str,
+    "gcs_name": str,
+    "subject_dir": typing.NotRequired[str | None],
+    "gcs_dir": typing.NotRequired[str | None],
+    "parc_name": typing.NotRequired[str | None],
+    "output_dir": typing.NotRequired[str | None],
+    "log_file": typing.NotRequired[str | None],
+    "lh_flag": bool,
+    "rh_flag": bool,
+    "a2009s_flag": bool,
+    "no_aseg_flag": bool,
+    "no_cortparc_flag": bool,
+    "no_parcstats_flag": bool,
+    "no_aparc2aseg_flag": bool,
+    "random_seed": typing.NotRequired[float | None],
+    "th3_flag": bool,
+    "no_th3_flag": bool,
+    "longitudinal": typing.NotRequired[list[str] | None],
+    "expert_file": typing.NotRequired[str | None],
+    "expert_use_flag": bool,
+    "expert_clean_flag": bool,
+    "expert_overwrite_flag": bool,
+})
+AparcStatsAsegParametersTagged = typing.TypedDict('AparcStatsAsegParametersTagged', {
+    "@type": typing.Literal["freesurfer/aparc_stats_aseg"],
     "subject_name": str,
     "gcs_name": str,
     "subject_dir": typing.NotRequired[str | None],
@@ -38,42 +63,11 @@ AparcStatsAsegParameters = typing.TypedDict('AparcStatsAsegParameters', {
     "expert_clean_flag": bool,
     "expert_overwrite_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 {
-        "aparc_stats_aseg": aparc_stats_aseg_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 AparcStatsAsegOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `aparc_stats_aseg(...)`.
+    Output object returned when calling `AparcStatsAsegParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -102,7 +96,7 @@ def aparc_stats_aseg_params(
     expert_use_flag: bool = False,
     expert_clean_flag: bool = False,
     expert_overwrite_flag: bool = False,
-) -> AparcStatsAsegParameters:
+) -> AparcStatsAsegParametersTagged:
     """
     Build parameters.
     
@@ -135,7 +129,7 @@ def aparc_stats_aseg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "aparc_stats_aseg",
+        "@type": "freesurfer/aparc_stats_aseg",
         "subject_name": subject_name,
         "gcs_name": gcs_name,
         "lh_flag": lh_flag,
@@ -187,75 +181,75 @@ def aparc_stats_aseg_cargs(
     cargs.append("aparc_stats_aseg")
     cargs.extend([
         "-s",
-        params.get("subject_name")
+        params.get("subject_name", None)
     ])
     cargs.extend([
         "-gcs",
-        params.get("gcs_name")
+        params.get("gcs_name", None)
     ])
-    if params.get("subject_dir") is not None:
+    if params.get("subject_dir", None) is not None:
         cargs.extend([
             "-sd",
-            params.get("subject_dir")
+            params.get("subject_dir", None)
         ])
-    if params.get("gcs_dir") is not None:
+    if params.get("gcs_dir", None) is not None:
         cargs.extend([
             "-gcsd",
-            params.get("gcs_dir")
+            params.get("gcs_dir", None)
         ])
-    if params.get("parc_name") is not None:
+    if params.get("parc_name", None) is not None:
         cargs.extend([
             "-name",
-            params.get("parc_name")
+            params.get("parc_name", None)
         ])
-    if params.get("output_dir") is not None:
+    if params.get("output_dir", None) is not None:
         cargs.extend([
             "-o",
-            params.get("output_dir")
+            params.get("output_dir", 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("lh_flag"):
+    if params.get("lh_flag", False):
         cargs.append("-lh")
-    if params.get("rh_flag"):
+    if params.get("rh_flag", False):
         cargs.append("-rh")
-    if params.get("a2009s_flag"):
+    if params.get("a2009s_flag", False):
         cargs.append("-a2009s")
-    if params.get("no_aseg_flag"):
+    if params.get("no_aseg_flag", False):
         cargs.append("-noaseg")
-    if params.get("no_cortparc_flag"):
+    if params.get("no_cortparc_flag", False):
         cargs.append("-nocortparc")
-    if params.get("no_parcstats_flag"):
+    if params.get("no_parcstats_flag", False):
         cargs.append("-noparcstats")
-    if params.get("no_aparc2aseg_flag"):
+    if params.get("no_aparc2aseg_flag", False):
         cargs.append("-noaparc2aseg")
-    if params.get("random_seed") is not None:
+    if params.get("random_seed", None) is not None:
         cargs.extend([
             "-seed",
-            str(params.get("random_seed"))
+            str(params.get("random_seed", None))
         ])
-    if params.get("th3_flag"):
+    if params.get("th3_flag", False):
         cargs.append("-th3")
-    if params.get("no_th3_flag"):
+    if params.get("no_th3_flag", False):
         cargs.append("-no-th3")
-    if params.get("longitudinal") is not None:
+    if params.get("longitudinal", None) is not None:
         cargs.extend([
             "-long",
-            *params.get("longitudinal")
+            *params.get("longitudinal", None)
         ])
-    if params.get("expert_file") is not None:
+    if params.get("expert_file", None) is not None:
         cargs.extend([
             "-expert",
-            params.get("expert_file")
+            params.get("expert_file", None)
         ])
-    if params.get("expert_use_flag"):
+    if params.get("expert_use_flag", False):
         cargs.append("-xopts-use")
-    if params.get("expert_clean_flag"):
+    if params.get("expert_clean_flag", False):
         cargs.append("-xopts-clean")
-    if params.get("expert_overwrite_flag"):
+    if params.get("expert_overwrite_flag", False):
         cargs.append("-xopts-overwrite")
     return cargs
 
@@ -281,9 +275,11 @@ def aparc_stats_aseg_outputs(
 
 def aparc_stats_aseg_execute(
     params: AparcStatsAsegParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AparcStatsAsegOutputs:
     """
+    aparc_stats_aseg
+    
     This program runs mris_ca_label, mris_anatomical_stats and mri_aparc2aseg.
     
     Author: FreeSurfer Developers
@@ -292,10 +288,12 @@ def aparc_stats_aseg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AparcStatsAsegOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(APARC_STATS_ASEG_METADATA)
     params = execution.params(params)
     cargs = aparc_stats_aseg_cargs(params, execution)
     ret = aparc_stats_aseg_outputs(params, execution)
@@ -329,6 +327,8 @@ def aparc_stats_aseg(
     runner: Runner | None = None,
 ) -> AparcStatsAsegOutputs:
     """
+    aparc_stats_aseg
+    
     This program runs mris_ca_label, mris_anatomical_stats and mri_aparc2aseg.
     
     Author: FreeSurfer Developers
@@ -364,8 +364,6 @@ def aparc_stats_aseg(
     Returns:
         NamedTuple of outputs (described in `AparcStatsAsegOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(APARC_STATS_ASEG_METADATA)
     params = aparc_stats_aseg_params(
         subject_name=subject_name,
         gcs_name=gcs_name,
@@ -390,13 +388,13 @@ def aparc_stats_aseg(
         expert_clean_flag=expert_clean_flag,
         expert_overwrite_flag=expert_overwrite_flag,
     )
-    return aparc_stats_aseg_execute(params, execution)
+    return aparc_stats_aseg_execute(params, runner)
 
 
 __all__ = [
     "APARC_STATS_ASEG_METADATA",
     "AparcStatsAsegOutputs",
-    "AparcStatsAsegParameters",
     "aparc_stats_aseg",
+    "aparc_stats_aseg_execute",
     "aparc_stats_aseg_params",
 ]

niwrap_freesurfer/freesurfer/aparcstats2table.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 APARCSTATS2TABLE_METADATA = Metadata(
-    id="1521fea28c99f52d4d63d7ca1b13780658752d3a.boutiques",
+    id="2dfe86d8f3cbaf4479df19a82085ad457536316c.boutiques",
     name="aparcstats2table",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,28 @@ APARCSTATS2TABLE_METADATA = Metadata(
 
 
 Aparcstats2tableParameters = typing.TypedDict('Aparcstats2tableParameters', {
-    "__STYXTYPE__": typing.Literal["aparcstats2table"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/aparcstats2table"]],
+    "subjects": typing.NotRequired[list[str] | None],
+    "subjectsfile": typing.NotRequired[InputPathType | None],
+    "qdec": typing.NotRequired[InputPathType | None],
+    "qdec_long": typing.NotRequired[InputPathType | None],
+    "hemi": str,
+    "tablefile": InputPathType,
+    "parcellation": typing.NotRequired[str | None],
+    "measure": typing.NotRequired[str | None],
+    "delimiter": typing.NotRequired[str | None],
+    "skip_missing": bool,
+    "parcid_only": bool,
+    "common_parcs": bool,
+    "parcs_file": typing.NotRequired[InputPathType | None],
+    "report_rois": bool,
+    "transpose": bool,
+    "debug": bool,
+    "etiv": bool,
+    "scale": typing.NotRequired[float | None],
+})
+Aparcstats2tableParametersTagged = typing.TypedDict('Aparcstats2tableParametersTagged', {
+    "@type": typing.Literal["freesurfer/aparcstats2table"],
     "subjects": typing.NotRequired[list[str] | None],
     "subjectsfile": typing.NotRequired[InputPathType | None],
     "qdec": typing.NotRequired[InputPathType | None],
@@ -34,43 +55,11 @@ Aparcstats2tableParameters = typing.TypedDict('Aparcstats2tableParameters', {
     "etiv": bool,
     "scale": 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 {
-        "aparcstats2table": aparcstats2table_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 {
-        "aparcstats2table": aparcstats2table_outputs,
-    }.get(t)
 
 
 class Aparcstats2tableOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `aparcstats2table(...)`.
+    Output object returned when calling `Aparcstats2tableParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -85,9 +74,9 @@ def aparcstats2table_params(
     subjectsfile: InputPathType | None = None,
     qdec: InputPathType | None = None,
     qdec_long: InputPathType | None = None,
-    parcellation: str | None = "aparc",
-    measure: str | None = "area",
-    delimiter: str | None = "tab",
+    parcellation: str | None = None,
+    measure: str | None = None,
+    delimiter: str | None = None,
     skip_missing: bool = False,
     parcid_only: bool = False,
     common_parcs: bool = False,
@@ -96,8 +85,8 @@ def aparcstats2table_params(
     transpose: bool = False,
     debug: bool = False,
     etiv: bool = False,
-    scale: float | None = 1,
-) -> Aparcstats2tableParameters:
+    scale: float | None = None,
+) -> Aparcstats2tableParametersTagged:
     """
     Build parameters.
     
@@ -124,7 +113,7 @@ def aparcstats2table_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "aparcstats2table",
+        "@type": "freesurfer/aparcstats2table",
         "hemi": hemi,
         "tablefile": tablefile,
         "skip_missing": skip_missing,
@@ -171,72 +160,72 @@ def aparcstats2table_cargs(
     """
     cargs = []
     cargs.append("aparcstats2table")
-    if params.get("subjects") is not None:
+    if params.get("subjects", None) is not None:
         cargs.extend([
             "--subjects",
-            *params.get("subjects")
+            *params.get("subjects", None)
         ])
-    if params.get("subjectsfile") is not None:
+    if params.get("subjectsfile", None) is not None:
         cargs.extend([
             "--subjectsfile",
-            execution.input_file(params.get("subjectsfile"))
+            execution.input_file(params.get("subjectsfile", None))
         ])
-    if params.get("qdec") is not None:
+    if params.get("qdec", None) is not None:
         cargs.extend([
             "--qdec",
-            execution.input_file(params.get("qdec"))
+            execution.input_file(params.get("qdec", None))
         ])
-    if params.get("qdec_long") is not None:
+    if params.get("qdec_long", None) is not None:
         cargs.extend([
             "--qdec-long",
-            execution.input_file(params.get("qdec_long"))
+            execution.input_file(params.get("qdec_long", None))
         ])
     cargs.extend([
         "--hemi",
-        params.get("hemi")
+        params.get("hemi", None)
     ])
     cargs.extend([
         "-t",
-        execution.input_file(params.get("tablefile"))
+        execution.input_file(params.get("tablefile", None))
     ])
-    if params.get("parcellation") is not None:
+    if params.get("parcellation", None) is not None:
         cargs.extend([
             "--parc",
-            params.get("parcellation")
+            params.get("parcellation", None)
         ])
-    if params.get("measure") is not None:
+    if params.get("measure", None) is not None:
         cargs.extend([
             "-m",
-            params.get("measure")
+            params.get("measure", 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("skip_missing"):
+    if params.get("skip_missing", False):
         cargs.append("--skip")
-    if params.get("parcid_only"):
+    if params.get("parcid_only", False):
         cargs.append("--parcid-only")
-    if params.get("common_parcs"):
+    if params.get("common_parcs", False):
         cargs.append("--common-parcs")
-    if params.get("parcs_file") is not None:
+    if params.get("parcs_file", None) is not None:
         cargs.extend([
             "--parcs-from-file",
-            execution.input_file(params.get("parcs_file"))
+            execution.input_file(params.get("parcs_file", None))
         ])
-    if params.get("report_rois"):
+    if params.get("report_rois", False):
         cargs.append("--report-rois")
-    if params.get("transpose"):
+    if params.get("transpose", False):
         cargs.append("--transpose")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-v")
-    if params.get("etiv"):
+    if params.get("etiv", False):
         cargs.append("--etiv")
-    if params.get("scale") is not None:
+    if params.get("scale", None) is not None:
         cargs.extend([
             "--scale",
-            str(params.get("scale"))
+            str(params.get("scale", None))
         ])
     return cargs
 
@@ -256,16 +245,18 @@ def aparcstats2table_outputs(
     """
     ret = Aparcstats2tableOutputs(
         root=execution.output_file("."),
-        output_table=execution.output_file(pathlib.Path(params.get("tablefile")).name),
+        output_table=execution.output_file(pathlib.Path(params.get("tablefile", None)).name),
     )
     return ret
 
 
 def aparcstats2table_execute(
     params: Aparcstats2tableParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Aparcstats2tableOutputs:
     """
+    aparcstats2table
+    
     Converts a cortical stats file into a table format with subjects as rows and
     parcellations as columns.
     
@@ -275,10 +266,12 @@ def aparcstats2table_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Aparcstats2tableOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(APARCSTATS2TABLE_METADATA)
     params = execution.params(params)
     cargs = aparcstats2table_cargs(params, execution)
     ret = aparcstats2table_outputs(params, execution)
@@ -293,9 +286,9 @@ def aparcstats2table(
     subjectsfile: InputPathType | None = None,
     qdec: InputPathType | None = None,
     qdec_long: InputPathType | None = None,
-    parcellation: str | None = "aparc",
-    measure: str | None = "area",
-    delimiter: str | None = "tab",
+    parcellation: str | None = None,
+    measure: str | None = None,
+    delimiter: str | None = None,
     skip_missing: bool = False,
     parcid_only: bool = False,
     common_parcs: bool = False,
@@ -304,10 +297,12 @@ def aparcstats2table(
     transpose: bool = False,
     debug: bool = False,
     etiv: bool = False,
-    scale: float | None = 1,
+    scale: float | None = None,
     runner: Runner | None = None,
 ) -> Aparcstats2tableOutputs:
     """
+    aparcstats2table
+    
     Converts a cortical stats file into a table format with subjects as rows and
     parcellations as columns.
     
@@ -338,8 +333,6 @@ def aparcstats2table(
     Returns:
         NamedTuple of outputs (described in `Aparcstats2tableOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(APARCSTATS2TABLE_METADATA)
     params = aparcstats2table_params(
         subjects=subjects,
         subjectsfile=subjectsfile,
@@ -360,13 +353,13 @@ def aparcstats2table(
         etiv=etiv,
         scale=scale,
     )
-    return aparcstats2table_execute(params, execution)
+    return aparcstats2table_execute(params, runner)
 
 
 __all__ = [
     "APARCSTATS2TABLE_METADATA",
     "Aparcstats2tableOutputs",
-    "Aparcstats2tableParameters",
     "aparcstats2table",
+    "aparcstats2table_execute",
     "aparcstats2table_params",
 ]