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

niwrap_freesurfer/freesurfer/mris_anatomical_stats.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_ANATOMICAL_STATS_METADATA = Metadata(
-    id="117a911cbb95d3ef62e62e40a756554d2c622c20.boutiques",
+    id="cbbc3cda6939c89c43dd0fcdc637d5dda69ea2e4.boutiques",
     name="mris_anatomical_stats",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,24 @@ MRIS_ANATOMICAL_STATS_METADATA = Metadata(
 
 
 MrisAnatomicalStatsParameters = typing.TypedDict('MrisAnatomicalStatsParameters', {
-    "__STYXTYPE__": typing.Literal["mris_anatomical_stats"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_anatomical_stats"]],
+    "subjectname": str,
+    "hemisphere": str,
+    "surfacename": typing.NotRequired[str | None],
+    "thickness_range": typing.NotRequired[list[float] | None],
+    "label_file": typing.NotRequired[InputPathType | None],
+    "thickness_file": typing.NotRequired[InputPathType | None],
+    "annotation_file": typing.NotRequired[InputPathType | None],
+    "tabular_output": bool,
+    "tablefile": typing.NotRequired[str | None],
+    "logfile": typing.NotRequired[str | None],
+    "nsmooth": typing.NotRequired[float | None],
+    "color_table": typing.NotRequired[str | None],
+    "noglobal": bool,
+    "th3_computation": bool,
+})
+MrisAnatomicalStatsParametersTagged = typing.TypedDict('MrisAnatomicalStatsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_anatomical_stats"],
     "subjectname": str,
     "hemisphere": str,
     "surfacename": typing.NotRequired[str | None],
@@ -30,43 +47,11 @@ MrisAnatomicalStatsParameters = typing.TypedDict('MrisAnatomicalStatsParameters'
     "noglobal": bool,
     "th3_computation": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_anatomical_stats": mris_anatomical_stats_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_anatomical_stats": mris_anatomical_stats_outputs,
-    }.get(t)
 
 
 class MrisAnatomicalStatsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_anatomical_stats(...)`.
+    Output object returned when calling `MrisAnatomicalStatsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -93,7 +78,7 @@ def mris_anatomical_stats_params(
     color_table: str | None = None,
     noglobal: bool = False,
     th3_computation: bool = False,
-) -> MrisAnatomicalStatsParameters:
+) -> MrisAnatomicalStatsParametersTagged:
     """
     Build parameters.
     
@@ -119,7 +104,7 @@ def mris_anatomical_stats_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_anatomical_stats",
+        "@type": "freesurfer/mris_anatomical_stats",
         "subjectname": subjectname,
         "hemisphere": hemisphere,
         "tabular_output": tabular_output,
@@ -162,55 +147,55 @@ def mris_anatomical_stats_cargs(
     """
     cargs = []
     cargs.append("mris_anatomical_stats")
-    cargs.append(params.get("subjectname"))
-    cargs.append(params.get("hemisphere"))
-    if params.get("surfacename") is not None:
-        cargs.append(params.get("surfacename"))
-    if params.get("thickness_range") is not None:
+    cargs.append(params.get("subjectname", None))
+    cargs.append(params.get("hemisphere", None))
+    if params.get("surfacename", None) is not None:
+        cargs.append(params.get("surfacename", None))
+    if params.get("thickness_range", None) is not None:
         cargs.extend([
             "-i",
-            *map(str, params.get("thickness_range"))
+            *map(str, params.get("thickness_range", None))
         ])
-    if params.get("label_file") is not None:
+    if params.get("label_file", None) is not None:
         cargs.extend([
             "-l",
-            execution.input_file(params.get("label_file"))
+            execution.input_file(params.get("label_file", None))
         ])
-    if params.get("thickness_file") is not None:
+    if params.get("thickness_file", None) is not None:
         cargs.extend([
             "-t",
-            execution.input_file(params.get("thickness_file"))
+            execution.input_file(params.get("thickness_file", None))
         ])
-    if params.get("annotation_file") is not None:
+    if params.get("annotation_file", None) is not None:
         cargs.extend([
             "-a",
-            execution.input_file(params.get("annotation_file"))
+            execution.input_file(params.get("annotation_file", None))
         ])
-    if params.get("tabular_output"):
+    if params.get("tabular_output", False):
         cargs.append("-b")
-    if params.get("tablefile") is not None:
+    if params.get("tablefile", None) is not None:
         cargs.extend([
             "-f",
-            params.get("tablefile")
+            params.get("tablefile", None)
         ])
-    if params.get("logfile") is not None:
+    if params.get("logfile", None) is not None:
         cargs.extend([
             "-log",
-            params.get("logfile")
+            params.get("logfile", None)
         ])
-    if params.get("nsmooth") is not None:
+    if params.get("nsmooth", None) is not None:
         cargs.extend([
             "-nsmooth",
-            str(params.get("nsmooth"))
+            str(params.get("nsmooth", None))
         ])
-    if params.get("color_table") is not None:
+    if params.get("color_table", None) is not None:
         cargs.extend([
             "-c",
-            params.get("color_table")
+            params.get("color_table", None)
         ])
-    if params.get("noglobal"):
+    if params.get("noglobal", False):
         cargs.append("-noglobal")
-    if params.get("th3_computation"):
+    if params.get("th3_computation", False):
         cargs.append("-th3")
     return cargs
 
@@ -230,18 +215,20 @@ def mris_anatomical_stats_outputs(
     """
     ret = MrisAnatomicalStatsOutputs(
         root=execution.output_file("."),
-        output_log_file=execution.output_file(params.get("logfile") + ".txt") if (params.get("logfile") is not None) else None,
-        output_table_file=execution.output_file(params.get("tablefile") + ".txt") if (params.get("tablefile") is not None) else None,
-        output_ctab_file=execution.output_file(params.get("color_table") + ".txt") if (params.get("color_table") is not None) else None,
+        output_log_file=execution.output_file(params.get("logfile", None) + ".txt") if (params.get("logfile") is not None) else None,
+        output_table_file=execution.output_file(params.get("tablefile", None) + ".txt") if (params.get("tablefile") is not None) else None,
+        output_ctab_file=execution.output_file(params.get("color_table", None) + ".txt") if (params.get("color_table") is not None) else None,
     )
     return ret
 
 
 def mris_anatomical_stats_execute(
     params: MrisAnatomicalStatsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisAnatomicalStatsOutputs:
     """
+    mris_anatomical_stats
+    
     This program computes a number of anatomical properties.
     
     Author: FreeSurfer Developers
@@ -250,10 +237,12 @@ def mris_anatomical_stats_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisAnatomicalStatsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_ANATOMICAL_STATS_METADATA)
     params = execution.params(params)
     cargs = mris_anatomical_stats_cargs(params, execution)
     ret = mris_anatomical_stats_outputs(params, execution)
@@ -279,6 +268,8 @@ def mris_anatomical_stats(
     runner: Runner | None = None,
 ) -> MrisAnatomicalStatsOutputs:
     """
+    mris_anatomical_stats
+    
     This program computes a number of anatomical properties.
     
     Author: FreeSurfer Developers
@@ -307,8 +298,6 @@ def mris_anatomical_stats(
     Returns:
         NamedTuple of outputs (described in `MrisAnatomicalStatsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_ANATOMICAL_STATS_METADATA)
     params = mris_anatomical_stats_params(
         subjectname=subjectname,
         hemisphere=hemisphere,
@@ -325,13 +314,13 @@ def mris_anatomical_stats(
         noglobal=noglobal,
         th3_computation=th3_computation,
     )
-    return mris_anatomical_stats_execute(params, execution)
+    return mris_anatomical_stats_execute(params, runner)
 
 
 __all__ = [
     "MRIS_ANATOMICAL_STATS_METADATA",
     "MrisAnatomicalStatsOutputs",
-    "MrisAnatomicalStatsParameters",
     "mris_anatomical_stats",
+    "mris_anatomical_stats_execute",
     "mris_anatomical_stats_params",
 ]

niwrap_freesurfer/freesurfer/mris_annot_diff.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_ANNOT_DIFF_METADATA = Metadata(
-    id="e43af53d28c80f63eea91ad71688942a768343a5.boutiques",
+    id="c90f8e1815276c38fcf1be63fbfc82687972330c.boutiques",
     name="mris_annot_diff",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,24 @@ MRIS_ANNOT_DIFF_METADATA = Metadata(
 
 
 MrisAnnotDiffParameters = typing.TypedDict('MrisAnnotDiffParameters', {
-    "__STYXTYPE__": typing.Literal["mris_annot_diff"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_annot_diff"]],
+    "annot1": InputPathType,
+    "annot2": InputPathType,
+    "diff_ctab": bool,
+    "verbose": bool,
+})
+MrisAnnotDiffParametersTagged = typing.TypedDict('MrisAnnotDiffParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_annot_diff"],
     "annot1": InputPathType,
     "annot2": InputPathType,
     "diff_ctab": bool,
     "verbose": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_annot_diff": mris_annot_diff_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 MrisAnnotDiffOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_annot_diff(...)`.
+    Output object returned when calling `MrisAnnotDiffParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def mris_annot_diff_params(
     annot2: InputPathType,
     diff_ctab: bool = False,
     verbose: bool = False,
-) -> MrisAnnotDiffParameters:
+) -> MrisAnnotDiffParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +55,7 @@ def mris_annot_diff_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_annot_diff",
+        "@type": "freesurfer/mris_annot_diff",
         "annot1": annot1,
         "annot2": annot2,
         "diff_ctab": diff_ctab,
@@ -103,11 +79,11 @@ def mris_annot_diff_cargs(
     """
     cargs = []
     cargs.append("mris_annot_diff")
-    cargs.append(execution.input_file(params.get("annot1")))
-    cargs.append(execution.input_file(params.get("annot2")))
-    if params.get("diff_ctab"):
+    cargs.append(execution.input_file(params.get("annot1", None)))
+    cargs.append(execution.input_file(params.get("annot2", None)))
+    if params.get("diff_ctab", False):
         cargs.append("--diff-ctab")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("--verbose")
     return cargs
 
@@ -133,9 +109,11 @@ def mris_annot_diff_outputs(
 
 def mris_annot_diff_execute(
     params: MrisAnnotDiffParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisAnnotDiffOutputs:
     """
+    mris_annot_diff
+    
     Compare two surface annotation files. The program works with .annot only.
     
     Author: FreeSurfer Developers
@@ -144,10 +122,12 @@ def mris_annot_diff_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisAnnotDiffOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_ANNOT_DIFF_METADATA)
     params = execution.params(params)
     cargs = mris_annot_diff_cargs(params, execution)
     ret = mris_annot_diff_outputs(params, execution)
@@ -163,6 +143,8 @@ def mris_annot_diff(
     runner: Runner | None = None,
 ) -> MrisAnnotDiffOutputs:
     """
+    mris_annot_diff
+    
     Compare two surface annotation files. The program works with .annot only.
     
     Author: FreeSurfer Developers
@@ -178,21 +160,19 @@ def mris_annot_diff(
     Returns:
         NamedTuple of outputs (described in `MrisAnnotDiffOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_ANNOT_DIFF_METADATA)
     params = mris_annot_diff_params(
         annot1=annot1,
         annot2=annot2,
         diff_ctab=diff_ctab,
         verbose=verbose,
     )
-    return mris_annot_diff_execute(params, execution)
+    return mris_annot_diff_execute(params, runner)
 
 
 __all__ = [
     "MRIS_ANNOT_DIFF_METADATA",
     "MrisAnnotDiffOutputs",
-    "MrisAnnotDiffParameters",
     "mris_annot_diff",
+    "mris_annot_diff_execute",
     "mris_annot_diff_params",
 ]

niwrap_freesurfer/freesurfer/mris_annot_to_segmentation.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_ANNOT_TO_SEGMENTATION_METADATA = Metadata(
-    id="f2187529fdf57449595cf8d2c0a0b2fc7b737908.boutiques",
+    id="173263ceaaa6a90b36517642e4ba601fc62578ed.boutiques",
     name="mris_annot_to_segmentation",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRIS_ANNOT_TO_SEGMENTATION_METADATA = Metadata(
 
 
 MrisAnnotToSegmentationParameters = typing.TypedDict('MrisAnnotToSegmentationParameters', {
-    "__STYXTYPE__": typing.Literal["mris_annot_to_segmentation"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_annot_to_segmentation"]],
+    "subject_name": str,
+    "hemi": str,
+    "surface": str,
+    "annot_file": InputPathType,
+    "color_table": InputPathType,
+    "output_volume": str,
+})
+MrisAnnotToSegmentationParametersTagged = typing.TypedDict('MrisAnnotToSegmentationParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_annot_to_segmentation"],
     "subject_name": str,
     "hemi": str,
     "surface": str,
@@ -22,43 +31,11 @@ MrisAnnotToSegmentationParameters = typing.TypedDict('MrisAnnotToSegmentationPar
     "color_table": InputPathType,
     "output_volume": 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_annot_to_segmentation": mris_annot_to_segmentation_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_annot_to_segmentation": mris_annot_to_segmentation_outputs,
-    }.get(t)
 
 
 class MrisAnnotToSegmentationOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_annot_to_segmentation(...)`.
+    Output object returned when calling `MrisAnnotToSegmentationParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def mris_annot_to_segmentation_params(
     annot_file: InputPathType,
     color_table: InputPathType,
     output_volume: str,
-) -> MrisAnnotToSegmentationParameters:
+) -> MrisAnnotToSegmentationParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +65,7 @@ def mris_annot_to_segmentation_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_annot_to_segmentation",
+        "@type": "freesurfer/mris_annot_to_segmentation",
         "subject_name": subject_name,
         "hemi": hemi,
         "surface": surface,
@@ -114,12 +91,12 @@ def mris_annot_to_segmentation_cargs(
     """
     cargs = []
     cargs.append("mris_annot_to_segmentation")
-    cargs.append(params.get("subject_name"))
-    cargs.append(params.get("hemi"))
-    cargs.append(params.get("surface"))
-    cargs.append(execution.input_file(params.get("annot_file")))
-    cargs.append(execution.input_file(params.get("color_table")))
-    cargs.append(params.get("output_volume"))
+    cargs.append(params.get("subject_name", None))
+    cargs.append(params.get("hemi", None))
+    cargs.append(params.get("surface", None))
+    cargs.append(execution.input_file(params.get("annot_file", None)))
+    cargs.append(execution.input_file(params.get("color_table", None)))
+    cargs.append(params.get("output_volume", None))
     return cargs
 
 
@@ -138,16 +115,18 @@ def mris_annot_to_segmentation_outputs(
     """
     ret = MrisAnnotToSegmentationOutputs(
         root=execution.output_file("."),
-        output_volume_file=execution.output_file(params.get("output_volume")),
+        output_volume_file=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def mris_annot_to_segmentation_execute(
     params: MrisAnnotToSegmentationParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisAnnotToSegmentationOutputs:
     """
+    mris_annot_to_segmentation
+    
     Converts annotation files to segmentation volumes in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -156,10 +135,12 @@ def mris_annot_to_segmentation_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisAnnotToSegmentationOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_ANNOT_TO_SEGMENTATION_METADATA)
     params = execution.params(params)
     cargs = mris_annot_to_segmentation_cargs(params, execution)
     ret = mris_annot_to_segmentation_outputs(params, execution)
@@ -177,6 +158,8 @@ def mris_annot_to_segmentation(
     runner: Runner | None = None,
 ) -> MrisAnnotToSegmentationOutputs:
     """
+    mris_annot_to_segmentation
+    
     Converts annotation files to segmentation volumes in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -194,8 +177,6 @@ def mris_annot_to_segmentation(
     Returns:
         NamedTuple of outputs (described in `MrisAnnotToSegmentationOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_ANNOT_TO_SEGMENTATION_METADATA)
     params = mris_annot_to_segmentation_params(
         subject_name=subject_name,
         hemi=hemi,
@@ -204,13 +185,13 @@ def mris_annot_to_segmentation(
         color_table=color_table,
         output_volume=output_volume,
     )
-    return mris_annot_to_segmentation_execute(params, execution)
+    return mris_annot_to_segmentation_execute(params, runner)
 
 
 __all__ = [
     "MRIS_ANNOT_TO_SEGMENTATION_METADATA",
     "MrisAnnotToSegmentationOutputs",
-    "MrisAnnotToSegmentationParameters",
     "mris_annot_to_segmentation",
+    "mris_annot_to_segmentation_execute",
     "mris_annot_to_segmentation_params",
 ]