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

niwrap_freesurfer/freesurfer/quantify_brainstem_structures_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 QUANTIFY_BRAINSTEM_STRUCTURES_SH_METADATA = Metadata(
-    id="458a2cce6618958955b2061c46dc04c83d13a6a3.boutiques",
+    id="f0f7a48a99ba41002908868fa64cb52bf46fc52f.boutiques",
     name="quantifyBrainstemStructures.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ QUANTIFY_BRAINSTEM_STRUCTURES_SH_METADATA = Metadata(
 
 
 QuantifyBrainstemStructuresShParameters = typing.TypedDict('QuantifyBrainstemStructuresShParameters', {
-    "__STYXTYPE__": typing.Literal["quantifyBrainstemStructures.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/quantifyBrainstemStructures.sh"]],
+    "output_file": str,
+    "subjects_directory": typing.NotRequired[str | None],
+})
+QuantifyBrainstemStructuresShParametersTagged = typing.TypedDict('QuantifyBrainstemStructuresShParametersTagged', {
+    "@type": typing.Literal["freesurfer/quantifyBrainstemStructures.sh"],
     "output_file": str,
     "subjects_directory": 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 {
-        "quantifyBrainstemStructures.sh": quantify_brainstem_structures_sh_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 {
-        "quantifyBrainstemStructures.sh": quantify_brainstem_structures_sh_outputs,
-    }.get(t)
 
 
 class QuantifyBrainstemStructuresShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `quantify_brainstem_structures_sh(...)`.
+    Output object returned when calling `QuantifyBrainstemStructuresShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,8 +37,8 @@ class QuantifyBrainstemStructuresShOutputs(typing.NamedTuple):
 
 def quantify_brainstem_structures_sh_params(
     output_file: str,
-    subjects_directory: str | None = "/usr/local/freesurfer/subjects",
-) -> QuantifyBrainstemStructuresShParameters:
+    subjects_directory: str | None = None,
+) -> QuantifyBrainstemStructuresShParametersTagged:
     """
     Build parameters.
     
@@ -78,7 +51,7 @@ def quantify_brainstem_structures_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "quantifyBrainstemStructures.sh",
+        "@type": "freesurfer/quantifyBrainstemStructures.sh",
         "output_file": output_file,
     }
     if subjects_directory is not None:
@@ -101,9 +74,9 @@ def quantify_brainstem_structures_sh_cargs(
     """
     cargs = []
     cargs.append("quantifyBrainstemStructures.sh")
-    cargs.append(params.get("output_file"))
-    if params.get("subjects_directory") is not None:
-        cargs.append(params.get("subjects_directory"))
+    cargs.append(params.get("output_file", None))
+    if params.get("subjects_directory", None) is not None:
+        cargs.append(params.get("subjects_directory", None))
     return cargs
 
 
@@ -122,18 +95,20 @@ def quantify_brainstem_structures_sh_outputs(
     """
     ret = QuantifyBrainstemStructuresShOutputs(
         root=execution.output_file("."),
-        results_file=execution.output_file(params.get("output_file")),
+        results_file=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def quantify_brainstem_structures_sh_execute(
     params: QuantifyBrainstemStructuresShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> QuantifyBrainstemStructuresShOutputs:
     """
-    A script to gather results from FreeSurfer brainstem processing and write them
-    to an output file.
+    quantifyBrainstemStructures.sh
+    
+    A script to gather results from FreeSurfer brainstem processing and write
+    them to an output file.
     
     Author: FreeSurfer Developers
     
@@ -141,10 +116,12 @@ def quantify_brainstem_structures_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `QuantifyBrainstemStructuresShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(QUANTIFY_BRAINSTEM_STRUCTURES_SH_METADATA)
     params = execution.params(params)
     cargs = quantify_brainstem_structures_sh_cargs(params, execution)
     ret = quantify_brainstem_structures_sh_outputs(params, execution)
@@ -154,12 +131,14 @@ def quantify_brainstem_structures_sh_execute(
 
 def quantify_brainstem_structures_sh(
     output_file: str,
-    subjects_directory: str | None = "/usr/local/freesurfer/subjects",
+    subjects_directory: str | None = None,
     runner: Runner | None = None,
 ) -> QuantifyBrainstemStructuresShOutputs:
     """
-    A script to gather results from FreeSurfer brainstem processing and write them
-    to an output file.
+    quantifyBrainstemStructures.sh
+    
+    A script to gather results from FreeSurfer brainstem processing and write
+    them to an output file.
     
     Author: FreeSurfer Developers
     
@@ -174,19 +153,17 @@ def quantify_brainstem_structures_sh(
     Returns:
         NamedTuple of outputs (described in `QuantifyBrainstemStructuresShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(QUANTIFY_BRAINSTEM_STRUCTURES_SH_METADATA)
     params = quantify_brainstem_structures_sh_params(
         output_file=output_file,
         subjects_directory=subjects_directory,
     )
-    return quantify_brainstem_structures_sh_execute(params, execution)
+    return quantify_brainstem_structures_sh_execute(params, runner)
 
 
 __all__ = [
     "QUANTIFY_BRAINSTEM_STRUCTURES_SH_METADATA",
     "QuantifyBrainstemStructuresShOutputs",
-    "QuantifyBrainstemStructuresShParameters",
     "quantify_brainstem_structures_sh",
+    "quantify_brainstem_structures_sh_execute",
     "quantify_brainstem_structures_sh_params",
 ]

niwrap_freesurfer/freesurfer/quantify_hasubregions_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 QUANTIFY_HASUBREGIONS_SH_METADATA = Metadata(
-    id="2c2579fdfb34fa03272c566e729ceed9f991aef2.boutiques",
+    id="528c73385a4d95e317b02403967b6af61a7b7bfc.boutiques",
     name="quantifyHAsubregions.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ QUANTIFY_HASUBREGIONS_SH_METADATA = Metadata(
 
 
 QuantifyHasubregionsShParameters = typing.TypedDict('QuantifyHasubregionsShParameters', {
-    "__STYXTYPE__": typing.Literal["quantifyHAsubregions.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/quantifyHAsubregions.sh"]],
+    "prefix": str,
+    "suffix": str,
+    "output_file": str,
+    "subjects_directory": typing.NotRequired[str | None],
+})
+QuantifyHasubregionsShParametersTagged = typing.TypedDict('QuantifyHasubregionsShParametersTagged', {
+    "@type": typing.Literal["freesurfer/quantifyHAsubregions.sh"],
     "prefix": str,
     "suffix": str,
     "output_file": str,
     "subjects_directory": 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 {
-        "quantifyHAsubregions.sh": quantify_hasubregions_sh_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 {
-        "quantifyHAsubregions.sh": quantify_hasubregions_sh_outputs,
-    }.get(t)
 
 
 class QuantifyHasubregionsShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `quantify_hasubregions_sh(...)`.
+    Output object returned when calling `QuantifyHasubregionsShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def quantify_hasubregions_sh_params(
     suffix: str,
     output_file: str,
     subjects_directory: str | None = None,
-) -> QuantifyHasubregionsShParameters:
+) -> QuantifyHasubregionsShParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +58,7 @@ def quantify_hasubregions_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "quantifyHAsubregions.sh",
+        "@type": "freesurfer/quantifyHAsubregions.sh",
         "prefix": prefix,
         "suffix": suffix,
         "output_file": output_file,
@@ -108,11 +83,11 @@ def quantify_hasubregions_sh_cargs(
     """
     cargs = []
     cargs.append("quantifyHAsubregions.sh")
-    cargs.append(params.get("prefix"))
-    cargs.append(params.get("suffix"))
-    cargs.append(params.get("output_file"))
-    if params.get("subjects_directory") is not None:
-        cargs.append(params.get("subjects_directory"))
+    cargs.append(params.get("prefix", None))
+    cargs.append(params.get("suffix", None))
+    cargs.append(params.get("output_file", None))
+    if params.get("subjects_directory", None) is not None:
+        cargs.append(params.get("subjects_directory", None))
     return cargs
 
 
@@ -131,16 +106,18 @@ def quantify_hasubregions_sh_outputs(
     """
     ret = QuantifyHasubregionsShOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_file")),
+        output_file=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def quantify_hasubregions_sh_execute(
     params: QuantifyHasubregionsShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> QuantifyHasubregionsShOutputs:
     """
+    quantifyHAsubregions.sh
+    
     Tool to quantify hippocampal subregions using FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -149,10 +126,12 @@ def quantify_hasubregions_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `QuantifyHasubregionsShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(QUANTIFY_HASUBREGIONS_SH_METADATA)
     params = execution.params(params)
     cargs = quantify_hasubregions_sh_cargs(params, execution)
     ret = quantify_hasubregions_sh_outputs(params, execution)
@@ -168,6 +147,8 @@ def quantify_hasubregions_sh(
     runner: Runner | None = None,
 ) -> QuantifyHasubregionsShOutputs:
     """
+    quantifyHAsubregions.sh
+    
     Tool to quantify hippocampal subregions using FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -184,21 +165,19 @@ def quantify_hasubregions_sh(
     Returns:
         NamedTuple of outputs (described in `QuantifyHasubregionsShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(QUANTIFY_HASUBREGIONS_SH_METADATA)
     params = quantify_hasubregions_sh_params(
         prefix=prefix,
         suffix=suffix,
         output_file=output_file,
         subjects_directory=subjects_directory,
     )
-    return quantify_hasubregions_sh_execute(params, execution)
+    return quantify_hasubregions_sh_execute(params, runner)
 
 
 __all__ = [
     "QUANTIFY_HASUBREGIONS_SH_METADATA",
     "QuantifyHasubregionsShOutputs",
-    "QuantifyHasubregionsShParameters",
     "quantify_hasubregions_sh",
+    "quantify_hasubregions_sh_execute",
     "quantify_hasubregions_sh_params",
 ]

niwrap_freesurfer/freesurfer/quantify_thalamic_nuclei_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 QUANTIFY_THALAMIC_NUCLEI_SH_METADATA = Metadata(
-    id="c597d875efd70402af0d29eccadf64e0e07bc431.boutiques",
+    id="becd71f526ddb334a82ac57838edfe920def004a.boutiques",
     name="quantifyThalamicNuclei.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ QUANTIFY_THALAMIC_NUCLEI_SH_METADATA = Metadata(
 
 
 QuantifyThalamicNucleiShParameters = typing.TypedDict('QuantifyThalamicNucleiShParameters', {
-    "__STYXTYPE__": typing.Literal["quantifyThalamicNuclei.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/quantifyThalamicNuclei.sh"]],
+    "output_file": str,
+    "analysis_id": str,
+    "subjects_directory": typing.NotRequired[str | None],
+})
+QuantifyThalamicNucleiShParametersTagged = typing.TypedDict('QuantifyThalamicNucleiShParametersTagged', {
+    "@type": typing.Literal["freesurfer/quantifyThalamicNuclei.sh"],
     "output_file": str,
     "analysis_id": str,
     "subjects_directory": 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 {
-        "quantifyThalamicNuclei.sh": quantify_thalamic_nuclei_sh_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 {
-        "quantifyThalamicNuclei.sh": quantify_thalamic_nuclei_sh_outputs,
-    }.get(t)
 
 
 class QuantifyThalamicNucleiShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `quantify_thalamic_nuclei_sh(...)`.
+    Output object returned when calling `QuantifyThalamicNucleiShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def quantify_thalamic_nuclei_sh_params(
     output_file: str,
     analysis_id: str,
     subjects_directory: str | None = None,
-) -> QuantifyThalamicNucleiShParameters:
+) -> QuantifyThalamicNucleiShParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def quantify_thalamic_nuclei_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "quantifyThalamicNuclei.sh",
+        "@type": "freesurfer/quantifyThalamicNuclei.sh",
         "output_file": output_file,
         "analysis_id": analysis_id,
     }
@@ -103,10 +77,10 @@ def quantify_thalamic_nuclei_sh_cargs(
     """
     cargs = []
     cargs.append("quantifyThalamicNuclei.sh")
-    cargs.append(params.get("output_file"))
-    cargs.append(params.get("analysis_id"))
-    if params.get("subjects_directory") is not None:
-        cargs.append(params.get("subjects_directory"))
+    cargs.append(params.get("output_file", None))
+    cargs.append(params.get("analysis_id", None))
+    if params.get("subjects_directory", None) is not None:
+        cargs.append(params.get("subjects_directory", None))
     return cargs
 
 
@@ -125,16 +99,18 @@ def quantify_thalamic_nuclei_sh_outputs(
     """
     ret = QuantifyThalamicNucleiShOutputs(
         root=execution.output_file("."),
-        results_file=execution.output_file(params.get("output_file")),
+        results_file=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def quantify_thalamic_nuclei_sh_execute(
     params: QuantifyThalamicNucleiShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> QuantifyThalamicNucleiShOutputs:
     """
+    quantifyThalamicNuclei.sh
+    
     Command-line tool to quantify thalamic nuclei using FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -143,10 +119,12 @@ def quantify_thalamic_nuclei_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `QuantifyThalamicNucleiShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(QUANTIFY_THALAMIC_NUCLEI_SH_METADATA)
     params = execution.params(params)
     cargs = quantify_thalamic_nuclei_sh_cargs(params, execution)
     ret = quantify_thalamic_nuclei_sh_outputs(params, execution)
@@ -161,6 +139,8 @@ def quantify_thalamic_nuclei_sh(
     runner: Runner | None = None,
 ) -> QuantifyThalamicNucleiShOutputs:
     """
+    quantifyThalamicNuclei.sh
+    
     Command-line tool to quantify thalamic nuclei using FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -175,20 +155,18 @@ def quantify_thalamic_nuclei_sh(
     Returns:
         NamedTuple of outputs (described in `QuantifyThalamicNucleiShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(QUANTIFY_THALAMIC_NUCLEI_SH_METADATA)
     params = quantify_thalamic_nuclei_sh_params(
         output_file=output_file,
         analysis_id=analysis_id,
         subjects_directory=subjects_directory,
     )
-    return quantify_thalamic_nuclei_sh_execute(params, execution)
+    return quantify_thalamic_nuclei_sh_execute(params, runner)
 
 
 __all__ = [
     "QUANTIFY_THALAMIC_NUCLEI_SH_METADATA",
     "QuantifyThalamicNucleiShOutputs",
-    "QuantifyThalamicNucleiShParameters",
     "quantify_thalamic_nuclei_sh",
+    "quantify_thalamic_nuclei_sh_execute",
     "quantify_thalamic_nuclei_sh_params",
 ]