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

niwrap_freesurfer/freesurfer/long_stats_tps.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LONG_STATS_TPS_METADATA = Metadata(
-    id="6c6ba4b0e888d88fa279b18e6e58656975356f16.boutiques",
+    id="3f40c800d9afacf20579a53c52fdd58307c8abdb.boutiques",
     name="long_stats_tps",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ LONG_STATS_TPS_METADATA = Metadata(
 
 
 LongStatsTpsParameters = typing.TypedDict('LongStatsTpsParameters', {
-    "__STYXTYPE__": typing.Literal["long_stats_tps"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/long_stats_tps"]],
+    "qdec_table": InputPathType,
+    "stats_file": str,
+    "measure": str,
+    "subjects_dir": str,
+    "time_point": float,
+    "output_file": str,
+    "qcolumn": typing.NotRequired[str | None],
+    "cross_sectional": bool,
+})
+LongStatsTpsParametersTagged = typing.TypedDict('LongStatsTpsParametersTagged', {
+    "@type": typing.Literal["freesurfer/long_stats_tps"],
     "qdec_table": InputPathType,
     "stats_file": str,
     "measure": str,
@@ -24,43 +35,11 @@ LongStatsTpsParameters = typing.TypedDict('LongStatsTpsParameters', {
     "qcolumn": typing.NotRequired[str | 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_tps": long_stats_tps_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_tps": long_stats_tps_outputs,
-    }.get(t)
 
 
 class LongStatsTpsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `long_stats_tps(...)`.
+    Output object returned when calling `LongStatsTpsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def long_stats_tps_params(
     output_file: str,
     qcolumn: str | None = None,
     cross_sectional: bool = False,
-) -> LongStatsTpsParameters:
+) -> LongStatsTpsParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +74,7 @@ def long_stats_tps_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "long_stats_tps",
+        "@type": "freesurfer/long_stats_tps",
         "qdec_table": qdec_table,
         "stats_file": stats_file,
         "measure": measure,
@@ -126,34 +105,34 @@ def long_stats_tps_cargs(
     cargs.append("long_stats_tps")
     cargs.extend([
         "--qdec",
-        execution.input_file(params.get("qdec_table"))
+        execution.input_file(params.get("qdec_table", None))
     ])
     cargs.extend([
         "--stats",
-        params.get("stats_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)
     ])
     cargs.extend([
         "--tp",
-        str(params.get("time_point"))
+        str(params.get("time_point", None))
     ])
     cargs.extend([
         "--out",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
-    if params.get("qcolumn") is not None:
+    if params.get("qcolumn", None) is not None:
         cargs.extend([
             "--qcol",
-            params.get("qcolumn")
+            params.get("qcolumn", None)
         ])
-    if params.get("cross_sectional"):
+    if params.get("cross_sectional", False):
         cargs.append("--cross")
     return cargs
 
@@ -173,16 +152,18 @@ def long_stats_tps_outputs(
     """
     ret = LongStatsTpsOutputs(
         root=execution.output_file("."),
-        stacked_results=execution.output_file(params.get("output_file")),
+        stacked_results=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def long_stats_tps_execute(
     params: LongStatsTpsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> LongStatsTpsOutputs:
     """
+    long_stats_tps
+    
     Stack results for individual time points based on longitudinal qdec table.
     
     Author: FreeSurfer Developers
@@ -191,10 +172,12 @@ def long_stats_tps_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `LongStatsTpsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LONG_STATS_TPS_METADATA)
     params = execution.params(params)
     cargs = long_stats_tps_cargs(params, execution)
     ret = long_stats_tps_outputs(params, execution)
@@ -214,6 +197,8 @@ def long_stats_tps(
     runner: Runner | None = None,
 ) -> LongStatsTpsOutputs:
     """
+    long_stats_tps
+    
     Stack results for individual time points based on longitudinal qdec table.
     
     Author: FreeSurfer Developers
@@ -234,8 +219,6 @@ def long_stats_tps(
     Returns:
         NamedTuple of outputs (described in `LongStatsTpsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LONG_STATS_TPS_METADATA)
     params = long_stats_tps_params(
         qdec_table=qdec_table,
         stats_file=stats_file,
@@ -246,13 +229,13 @@ def long_stats_tps(
         qcolumn=qcolumn,
         cross_sectional=cross_sectional,
     )
-    return long_stats_tps_execute(params, execution)
+    return long_stats_tps_execute(params, runner)
 
 
 __all__ = [
     "LONG_STATS_TPS_METADATA",
     "LongStatsTpsOutputs",
-    "LongStatsTpsParameters",
     "long_stats_tps",
+    "long_stats_tps_execute",
     "long_stats_tps_params",
 ]

niwrap_freesurfer/freesurfer/long_submit_jobs.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LONG_SUBMIT_JOBS_METADATA = Metadata(
-    id="086cfad901401d521e1ad829af326fc9c4c50c61.boutiques",
+    id="18251cf341386f051a3990122d1513452f6f5cbd.boutiques",
     name="long_submit_jobs",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,35 @@ LONG_SUBMIT_JOBS_METADATA = Metadata(
 
 
 LongSubmitJobsParameters = typing.TypedDict('LongSubmitJobsParameters', {
-    "__STYXTYPE__": typing.Literal["long_submit_jobs"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/long_submit_jobs"]],
+    "qdec": InputPathType,
+    "cdir": str,
+    "bdir": typing.NotRequired[str | None],
+    "ldir": typing.NotRequired[str | None],
+    "scriptsdir": typing.NotRequired[str | None],
+    "cross": bool,
+    "base": bool,
+    "long": bool,
+    "cflags": typing.NotRequired[str | None],
+    "bflags": typing.NotRequired[str | None],
+    "lflags": typing.NotRequired[str | None],
+    "affine": bool,
+    "force": bool,
+    "simulate": bool,
+    "simfiles": bool,
+    "check": bool,
+    "pause": typing.NotRequired[float | None],
+    "max": typing.NotRequired[float | None],
+    "queue": typing.NotRequired[str | None],
+    "cmem": typing.NotRequired[float | None],
+    "bmem": typing.NotRequired[float | None],
+    "lmem": typing.NotRequired[float | None],
+    "cnodes": typing.NotRequired[float | None],
+    "bnodes": typing.NotRequired[float | None],
+    "lnodes": typing.NotRequired[float | None],
+})
+LongSubmitJobsParametersTagged = typing.TypedDict('LongSubmitJobsParametersTagged', {
+    "@type": typing.Literal["freesurfer/long_submit_jobs"],
     "qdec": InputPathType,
     "cdir": str,
     "bdir": typing.NotRequired[str | None],
@@ -41,42 +69,11 @@ LongSubmitJobsParameters = typing.TypedDict('LongSubmitJobsParameters', {
     "bnodes": typing.NotRequired[float | None],
     "lnodes": 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 {
-        "long_submit_jobs": long_submit_jobs_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 LongSubmitJobsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `long_submit_jobs(...)`.
+    Output object returned when calling `LongSubmitJobsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -108,7 +105,7 @@ def long_submit_jobs_params(
     cnodes: float | None = None,
     bnodes: float | None = None,
     lnodes: float | None = None,
-) -> LongSubmitJobsParameters:
+) -> LongSubmitJobsParametersTagged:
     """
     Build parameters.
     
@@ -144,7 +141,7 @@ def long_submit_jobs_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "long_submit_jobs",
+        "@type": "freesurfer/long_submit_jobs",
         "qdec": qdec,
         "cdir": cdir,
         "cross": cross,
@@ -206,102 +203,102 @@ def long_submit_jobs_cargs(
     cargs.append("long_submit_jobs")
     cargs.extend([
         "--qdec",
-        execution.input_file(params.get("qdec"))
+        execution.input_file(params.get("qdec", None))
     ])
     cargs.extend([
         "--cdir",
-        params.get("cdir")
+        params.get("cdir", None)
     ])
-    if params.get("bdir") is not None:
+    if params.get("bdir", None) is not None:
         cargs.extend([
             "--bdir",
-            params.get("bdir")
+            params.get("bdir", None)
         ])
-    if params.get("ldir") is not None:
+    if params.get("ldir", None) is not None:
         cargs.extend([
             "--ldir",
-            params.get("ldir")
+            params.get("ldir", None)
         ])
-    if params.get("scriptsdir") is not None:
+    if params.get("scriptsdir", None) is not None:
         cargs.extend([
             "--scriptsdir",
-            params.get("scriptsdir")
+            params.get("scriptsdir", None)
         ])
-    if params.get("cross"):
+    if params.get("cross", False):
         cargs.append("--cross")
-    if params.get("base"):
+    if params.get("base", False):
         cargs.append("--base")
-    if params.get("long"):
+    if params.get("long", False):
         cargs.append("--long")
-    if params.get("cflags") is not None:
+    if params.get("cflags", None) is not None:
         cargs.extend([
             "--cflags",
-            params.get("cflags")
+            params.get("cflags", None)
         ])
-    if params.get("bflags") is not None:
+    if params.get("bflags", None) is not None:
         cargs.extend([
             "--bflags",
-            params.get("bflags")
+            params.get("bflags", None)
         ])
-    if params.get("lflags") is not None:
+    if params.get("lflags", None) is not None:
         cargs.extend([
             "--lflags",
-            params.get("lflags")
+            params.get("lflags", None)
         ])
-    if params.get("affine"):
+    if params.get("affine", False):
         cargs.append("--affine")
-    if params.get("force"):
+    if params.get("force", False):
         cargs.append("--force")
-    if params.get("simulate"):
+    if params.get("simulate", False):
         cargs.append("--simulate")
-    if params.get("simfiles"):
+    if params.get("simfiles", False):
         cargs.append("--simfiles")
-    if params.get("check"):
+    if params.get("check", False):
         cargs.append("--check")
-    if params.get("pause") is not None:
+    if params.get("pause", None) is not None:
         cargs.extend([
             "--pause",
-            str(params.get("pause"))
+            str(params.get("pause", None))
         ])
-    if params.get("max") is not None:
+    if params.get("max", None) is not None:
         cargs.extend([
             "--max",
-            str(params.get("max"))
+            str(params.get("max", None))
         ])
-    if params.get("queue") is not None:
+    if params.get("queue", None) is not None:
         cargs.extend([
             "--queue",
-            params.get("queue")
+            params.get("queue", None)
         ])
-    if params.get("cmem") is not None:
+    if params.get("cmem", None) is not None:
         cargs.extend([
             "--cmem",
-            str(params.get("cmem"))
+            str(params.get("cmem", None))
         ])
-    if params.get("bmem") is not None:
+    if params.get("bmem", None) is not None:
         cargs.extend([
             "--bmem",
-            str(params.get("bmem"))
+            str(params.get("bmem", None))
         ])
-    if params.get("lmem") is not None:
+    if params.get("lmem", None) is not None:
         cargs.extend([
             "--lmem",
-            str(params.get("lmem"))
+            str(params.get("lmem", None))
         ])
-    if params.get("cnodes") is not None:
+    if params.get("cnodes", None) is not None:
         cargs.extend([
             "--cnodes",
-            str(params.get("cnodes"))
+            str(params.get("cnodes", None))
         ])
-    if params.get("bnodes") is not None:
+    if params.get("bnodes", None) is not None:
         cargs.extend([
             "--bnodes",
-            str(params.get("bnodes"))
+            str(params.get("bnodes", None))
         ])
-    if params.get("lnodes") is not None:
+    if params.get("lnodes", None) is not None:
         cargs.extend([
             "--lnodes",
-            str(params.get("lnodes"))
+            str(params.get("lnodes", None))
         ])
     return cargs
 
@@ -327,9 +324,11 @@ def long_submit_jobs_outputs(
 
 def long_submit_jobs_execute(
     params: LongSubmitJobsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> LongSubmitJobsOutputs:
     """
+    long_submit_jobs
+    
     Submits longitudinal processing jobs to the NMR cluster (seychelles or
     launchpad).
     
@@ -339,10 +338,12 @@ def long_submit_jobs_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `LongSubmitJobsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LONG_SUBMIT_JOBS_METADATA)
     params = execution.params(params)
     cargs = long_submit_jobs_cargs(params, execution)
     ret = long_submit_jobs_outputs(params, execution)
@@ -379,6 +380,8 @@ def long_submit_jobs(
     runner: Runner | None = None,
 ) -> LongSubmitJobsOutputs:
     """
+    long_submit_jobs
+    
     Submits longitudinal processing jobs to the NMR cluster (seychelles or
     launchpad).
     
@@ -418,8 +421,6 @@ def long_submit_jobs(
     Returns:
         NamedTuple of outputs (described in `LongSubmitJobsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LONG_SUBMIT_JOBS_METADATA)
     params = long_submit_jobs_params(
         qdec=qdec,
         cdir=cdir,
@@ -447,13 +448,13 @@ def long_submit_jobs(
         bnodes=bnodes,
         lnodes=lnodes,
     )
-    return long_submit_jobs_execute(params, execution)
+    return long_submit_jobs_execute(params, runner)
 
 
 __all__ = [
     "LONG_SUBMIT_JOBS_METADATA",
     "LongSubmitJobsOutputs",
-    "LongSubmitJobsParameters",
     "long_submit_jobs",
+    "long_submit_jobs_execute",
     "long_submit_jobs_params",
 ]