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

niwrap_freesurfer/freesurfer/long_stats_combine.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LONG_STATS_COMBINE_METADATA = Metadata(
-    id="bc07fa2d21f0070237805d7567bf0841a65a42f5.boutiques",
+    id="55027fbac1d768ae04a1fd31571b55d66733a83b.boutiques",
     name="long_stats_combine",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ LONG_STATS_COMBINE_METADATA = Metadata(
 
 
 LongStatsCombineParameters = typing.TypedDict('LongStatsCombineParameters', {
-    "__STYXTYPE__": typing.Literal["long_stats_combine"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/long_stats_combine"]],
+    "qdec": InputPathType,
+    "stats": str,
+    "measure": str,
+    "subject_dir": str,
+    "output_qdec": str,
+    "output_stats": typing.NotRequired[str | None],
+    "input_stats": typing.NotRequired[InputPathType | None],
+    "cross_sectional": bool,
+})
+LongStatsCombineParametersTagged = typing.TypedDict('LongStatsCombineParametersTagged', {
+    "@type": typing.Literal["freesurfer/long_stats_combine"],
     "qdec": InputPathType,
     "stats": str,
     "measure": str,
@@ -24,43 +35,11 @@ LongStatsCombineParameters = typing.TypedDict('LongStatsCombineParameters', {
     "input_stats": typing.NotRequired[InputPathType | None],
     "cross_sectional": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "long_stats_combine": long_stats_combine_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 {
-        "long_stats_combine": long_stats_combine_outputs,
-    }.get(t)
 
 
 class LongStatsCombineOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `long_stats_combine(...)`.
+    Output object returned when calling `LongStatsCombineParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +58,7 @@ def long_stats_combine_params(
     output_stats: str | None = None,
     input_stats: InputPathType | None = None,
     cross_sectional: bool = False,
-) -> LongStatsCombineParameters:
+) -> LongStatsCombineParametersTagged:
     """
     Build parameters.
     
@@ -99,7 +78,7 @@ def long_stats_combine_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "long_stats_combine",
+        "@type": "freesurfer/long_stats_combine",
         "qdec": qdec,
         "stats": stats,
         "measure": measure,
@@ -131,35 +110,35 @@ def long_stats_combine_cargs(
     cargs.append("long_stats_combine")
     cargs.extend([
         "--qdec",
-        execution.input_file(params.get("qdec"))
+        execution.input_file(params.get("qdec", None))
     ])
     cargs.extend([
         "--stats",
-        params.get("stats")
+        params.get("stats", None)
     ])
     cargs.extend([
         "--meas",
-        params.get("measure")
+        params.get("measure", None)
     ])
     cargs.extend([
         "--sd",
-        params.get("subject_dir")
+        params.get("subject_dir", None)
     ])
     cargs.extend([
         "--outqdec",
-        params.get("output_qdec")
+        params.get("output_qdec", None)
     ])
-    if params.get("output_stats") is not None:
+    if params.get("output_stats", None) is not None:
         cargs.extend([
             "--outstats",
-            params.get("output_stats")
+            params.get("output_stats", None)
         ])
-    if params.get("input_stats") is not None:
+    if params.get("input_stats", None) is not None:
         cargs.extend([
             "--instats",
-            execution.input_file(params.get("input_stats"))
+            execution.input_file(params.get("input_stats", None))
         ])
-    if params.get("cross_sectional"):
+    if params.get("cross_sectional", False):
         cargs.append("--cross")
     return cargs
 
@@ -179,17 +158,19 @@ def long_stats_combine_outputs(
     """
     ret = LongStatsCombineOutputs(
         root=execution.output_file("."),
-        output_qdec_file=execution.output_file(params.get("output_qdec")),
-        output_stacked_stats_file=execution.output_file(params.get("output_stats")) if (params.get("output_stats") is not None) else None,
+        output_qdec_file=execution.output_file(params.get("output_qdec", None)),
+        output_stacked_stats_file=execution.output_file(params.get("output_stats", None)) if (params.get("output_stats") is not None) else None,
     )
     return ret
 
 
 def long_stats_combine_execute(
     params: LongStatsCombineParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> LongStatsCombineOutputs:
     """
+    long_stats_combine
+    
     Adds columns from stats into longitudinal qdec table, using longitudinally
     processed results.
     
@@ -199,10 +180,12 @@ def long_stats_combine_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `LongStatsCombineOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LONG_STATS_COMBINE_METADATA)
     params = execution.params(params)
     cargs = long_stats_combine_cargs(params, execution)
     ret = long_stats_combine_outputs(params, execution)
@@ -222,6 +205,8 @@ def long_stats_combine(
     runner: Runner | None = None,
 ) -> LongStatsCombineOutputs:
     """
+    long_stats_combine
+    
     Adds columns from stats into longitudinal qdec table, using longitudinally
     processed results.
     
@@ -245,8 +230,6 @@ def long_stats_combine(
     Returns:
         NamedTuple of outputs (described in `LongStatsCombineOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LONG_STATS_COMBINE_METADATA)
     params = long_stats_combine_params(
         qdec=qdec,
         stats=stats,
@@ -257,13 +240,13 @@ def long_stats_combine(
         input_stats=input_stats,
         cross_sectional=cross_sectional,
     )
-    return long_stats_combine_execute(params, execution)
+    return long_stats_combine_execute(params, runner)
 
 
 __all__ = [
     "LONG_STATS_COMBINE_METADATA",
     "LongStatsCombineOutputs",
-    "LongStatsCombineParameters",
     "long_stats_combine",
+    "long_stats_combine_execute",
     "long_stats_combine_params",
 ]

niwrap_freesurfer/freesurfer/long_stats_slopes.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LONG_STATS_SLOPES_METADATA = Metadata(
-    id="de2de4aa13f59ce6306d8614149cac899e10b6b1.boutiques",
+    id="d64386d393c03eaef387719a9babd66fe150124b.boutiques",
     name="long_stats_slopes",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,37 @@ LONG_STATS_SLOPES_METADATA = Metadata(
 
 
 LongStatsSlopesParameters = typing.TypedDict('LongStatsSlopesParameters', {
-    "__STYXTYPE__": typing.Literal["long_stats_slopes"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/long_stats_slopes"]],
+    "qdec_table": InputPathType,
+    "stats_file": InputPathType,
+    "measure": str,
+    "subjects_dir": str,
+    "do_avg": bool,
+    "do_rate": bool,
+    "do_pc1fit": bool,
+    "do_pc1": bool,
+    "do_spc": bool,
+    "do_stack": bool,
+    "resid": typing.NotRequired[float | None],
+    "time_var": typing.NotRequired[str | None],
+    "generic_time": bool,
+    "cross_sectional": bool,
+    "out_avg": typing.NotRequired[str | None],
+    "out_rate": typing.NotRequired[str | None],
+    "out_pc1fit": typing.NotRequired[str | None],
+    "out_pc1": typing.NotRequired[str | None],
+    "out_spc": typing.NotRequired[str | None],
+    "out_resid": typing.NotRequired[str | None],
+    "out_stack": typing.NotRequired[str | None],
+    "stack_avg": typing.NotRequired[str | None],
+    "stack_rate": typing.NotRequired[str | None],
+    "stack_pc1fit": typing.NotRequired[str | None],
+    "stack_pc1": typing.NotRequired[str | None],
+    "stack_spc": typing.NotRequired[str | None],
+    "stack_resid": typing.NotRequired[str | None],
+})
+LongStatsSlopesParametersTagged = typing.TypedDict('LongStatsSlopesParametersTagged', {
+    "@type": typing.Literal["freesurfer/long_stats_slopes"],
     "qdec_table": InputPathType,
     "stats_file": InputPathType,
     "measure": str,
@@ -43,42 +73,11 @@ LongStatsSlopesParameters = typing.TypedDict('LongStatsSlopesParameters', {
     "stack_spc": typing.NotRequired[str | None],
     "stack_resid": 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 {
-        "long_stats_slopes": long_stats_slopes_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 LongStatsSlopesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `long_stats_slopes(...)`.
+    Output object returned when calling `LongStatsSlopesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -112,7 +111,7 @@ def long_stats_slopes_params(
     stack_pc1: str | None = None,
     stack_spc: str | None = None,
     stack_resid: str | None = None,
-) -> LongStatsSlopesParameters:
+) -> LongStatsSlopesParametersTagged:
     """
     Build parameters.
     
@@ -159,7 +158,7 @@ def long_stats_slopes_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "long_stats_slopes",
+        "@type": "freesurfer/long_stats_slopes",
         "qdec_table": qdec_table,
         "stats_file": stats_file,
         "measure": measure,
@@ -223,110 +222,110 @@ def long_stats_slopes_cargs(
     cargs.append("long_stats_slopes")
     cargs.extend([
         "--qdec",
-        execution.input_file(params.get("qdec_table"))
+        execution.input_file(params.get("qdec_table", None))
     ])
     cargs.extend([
         "--stats",
-        execution.input_file(params.get("stats_file"))
+        execution.input_file(params.get("stats_file", None))
     ])
     cargs.extend([
         "--meas",
-        params.get("measure")
+        params.get("measure", None)
     ])
     cargs.extend([
         "--sd",
-        params.get("subjects_dir")
+        params.get("subjects_dir", None)
     ])
-    if params.get("do_avg"):
+    if params.get("do_avg", False):
         cargs.append("--do-avg")
-    if params.get("do_rate"):
+    if params.get("do_rate", False):
         cargs.append("--do-rate")
-    if params.get("do_pc1fit"):
+    if params.get("do_pc1fit", False):
         cargs.append("--do-pc1fit")
-    if params.get("do_pc1"):
+    if params.get("do_pc1", False):
         cargs.append("--do-pc1")
-    if params.get("do_spc"):
+    if params.get("do_spc", False):
         cargs.append("--do-spc")
-    if params.get("do_stack"):
+    if params.get("do_stack", False):
         cargs.append("--do-stack")
-    if params.get("resid") is not None:
+    if params.get("resid", None) is not None:
         cargs.extend([
             "--resid",
-            str(params.get("resid"))
+            str(params.get("resid", None))
         ])
-    if params.get("time_var") is not None:
+    if params.get("time_var", None) is not None:
         cargs.extend([
             "--time",
-            params.get("time_var")
+            params.get("time_var", None)
         ])
-    if params.get("generic_time"):
+    if params.get("generic_time", False):
         cargs.append("--generic-time")
-    if params.get("cross_sectional"):
+    if params.get("cross_sectional", False):
         cargs.append("--cross")
-    if params.get("out_avg") is not None:
+    if params.get("out_avg", None) is not None:
         cargs.extend([
             "--out-avg",
-            params.get("out_avg")
+            params.get("out_avg", None)
         ])
-    if params.get("out_rate") is not None:
+    if params.get("out_rate", None) is not None:
         cargs.extend([
             "--out-rate",
-            params.get("out_rate")
+            params.get("out_rate", None)
         ])
-    if params.get("out_pc1fit") is not None:
+    if params.get("out_pc1fit", None) is not None:
         cargs.extend([
             "--out-pc1fit",
-            params.get("out_pc1fit")
+            params.get("out_pc1fit", None)
         ])
-    if params.get("out_pc1") is not None:
+    if params.get("out_pc1", None) is not None:
         cargs.extend([
             "--out-pc1",
-            params.get("out_pc1")
+            params.get("out_pc1", None)
         ])
-    if params.get("out_spc") is not None:
+    if params.get("out_spc", None) is not None:
         cargs.extend([
             "--out-spc",
-            params.get("out_spc")
+            params.get("out_spc", None)
         ])
-    if params.get("out_resid") is not None:
+    if params.get("out_resid", None) is not None:
         cargs.extend([
             "--out-resid",
-            params.get("out_resid")
+            params.get("out_resid", None)
         ])
-    if params.get("out_stack") is not None:
+    if params.get("out_stack", None) is not None:
         cargs.extend([
             "--out-stack",
-            params.get("out_stack")
+            params.get("out_stack", None)
         ])
-    if params.get("stack_avg") is not None:
+    if params.get("stack_avg", None) is not None:
         cargs.extend([
             "--stack-avg",
-            params.get("stack_avg")
+            params.get("stack_avg", None)
         ])
-    if params.get("stack_rate") is not None:
+    if params.get("stack_rate", None) is not None:
         cargs.extend([
             "--stack-rate",
-            params.get("stack_rate")
+            params.get("stack_rate", None)
         ])
-    if params.get("stack_pc1fit") is not None:
+    if params.get("stack_pc1fit", None) is not None:
         cargs.extend([
             "--stack-pc1fit",
-            params.get("stack_pc1fit")
+            params.get("stack_pc1fit", None)
         ])
-    if params.get("stack_pc1") is not None:
+    if params.get("stack_pc1", None) is not None:
         cargs.extend([
             "--stack-pc1",
-            params.get("stack_pc1")
+            params.get("stack_pc1", None)
         ])
-    if params.get("stack_spc") is not None:
+    if params.get("stack_spc", None) is not None:
         cargs.extend([
             "--stack-spc",
-            params.get("stack_spc")
+            params.get("stack_spc", None)
         ])
-    if params.get("stack_resid") is not None:
+    if params.get("stack_resid", None) is not None:
         cargs.extend([
             "--stack-resid",
-            params.get("stack_resid")
+            params.get("stack_resid", None)
         ])
     return cargs
 
@@ -352,11 +351,14 @@ def long_stats_slopes_outputs(
 
 def long_stats_slopes_execute(
     params: LongStatsSlopesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> LongStatsSlopesOutputs:
     """
+    long_stats_slopes
+    
     Computes slopes of statistics in a longitudinal study for each subject from
-    processed results, outputting to designated directories for further analysis.
+    processed results, outputting to designated directories for further
+    analysis.
     
     Author: FreeSurfer Developers
     
@@ -364,10 +366,12 @@ def long_stats_slopes_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `LongStatsSlopesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LONG_STATS_SLOPES_METADATA)
     params = execution.params(params)
     cargs = long_stats_slopes_cargs(params, execution)
     ret = long_stats_slopes_outputs(params, execution)
@@ -406,8 +410,11 @@ def long_stats_slopes(
     runner: Runner | None = None,
 ) -> LongStatsSlopesOutputs:
     """
+    long_stats_slopes
+    
     Computes slopes of statistics in a longitudinal study for each subject from
-    processed results, outputting to designated directories for further analysis.
+    processed results, outputting to designated directories for further
+    analysis.
     
     Author: FreeSurfer Developers
     
@@ -456,8 +463,6 @@ def long_stats_slopes(
     Returns:
         NamedTuple of outputs (described in `LongStatsSlopesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LONG_STATS_SLOPES_METADATA)
     params = long_stats_slopes_params(
         qdec_table=qdec_table,
         stats_file=stats_file,
@@ -487,13 +492,13 @@ def long_stats_slopes(
         stack_spc=stack_spc,
         stack_resid=stack_resid,
     )
-    return long_stats_slopes_execute(params, execution)
+    return long_stats_slopes_execute(params, runner)
 
 
 __all__ = [
     "LONG_STATS_SLOPES_METADATA",
     "LongStatsSlopesOutputs",
-    "LongStatsSlopesParameters",
     "long_stats_slopes",
+    "long_stats_slopes_execute",
     "long_stats_slopes_params",
 ]