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

niwrap_freesurfer/freesurfer/fs_tutorial_data.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FS_TUTORIAL_DATA_METADATA = Metadata(
-    id="bd2bd293ebd9f33142807aa996b1099448b46897.boutiques",
+    id="57fbe6fd6f6adb6dc73c2b2a53ea70fb27a95b17.boutiques",
     name="fs_tutorial_data",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,18 @@ FS_TUTORIAL_DATA_METADATA = Metadata(
 
 
 FsTutorialDataParameters = typing.TypedDict('FsTutorialDataParameters', {
-    "__STYXTYPE__": typing.Literal["fs_tutorial_data"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fs_tutorial_data"]],
+    "rsync_options": typing.NotRequired[list[str] | None],
+})
+FsTutorialDataParametersTagged = typing.TypedDict('FsTutorialDataParametersTagged', {
+    "@type": typing.Literal["freesurfer/fs_tutorial_data"],
     "rsync_options": typing.NotRequired[list[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 {
-        "fs_tutorial_data": fs_tutorial_data_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 {
-        "fs_tutorial_data": fs_tutorial_data_outputs,
-    }.get(t)
 
 
 class FsTutorialDataOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fs_tutorial_data(...)`.
+    Output object returned when calling `FsTutorialDataParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -63,7 +35,7 @@ class FsTutorialDataOutputs(typing.NamedTuple):
 
 def fs_tutorial_data_params(
     rsync_options: list[str] | None = None,
-) -> FsTutorialDataParameters:
+) -> FsTutorialDataParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +45,7 @@ def fs_tutorial_data_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fs_tutorial_data",
+        "@type": "freesurfer/fs_tutorial_data",
     }
     if rsync_options is not None:
         params["rsync_options"] = rsync_options
@@ -95,8 +67,8 @@ def fs_tutorial_data_cargs(
     """
     cargs = []
     cargs.append("fs_tutorial_data")
-    if params.get("rsync_options") is not None:
-        cargs.extend(params.get("rsync_options"))
+    if params.get("rsync_options", None) is not None:
+        cargs.extend(params.get("rsync_options", None))
     return cargs
 
 
@@ -122,9 +94,11 @@ def fs_tutorial_data_outputs(
 
 def fs_tutorial_data_execute(
     params: FsTutorialDataParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FsTutorialDataOutputs:
     """
+    fs_tutorial_data
+    
     Tool to download and install FreeSurfer tutorial data.
     
     Author: FreeSurfer Developers
@@ -133,10 +107,12 @@ def fs_tutorial_data_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsTutorialDataOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FS_TUTORIAL_DATA_METADATA)
     params = execution.params(params)
     cargs = fs_tutorial_data_cargs(params, execution)
     ret = fs_tutorial_data_outputs(params, execution)
@@ -149,6 +125,8 @@ def fs_tutorial_data(
     runner: Runner | None = None,
 ) -> FsTutorialDataOutputs:
     """
+    fs_tutorial_data
+    
     Tool to download and install FreeSurfer tutorial data.
     
     Author: FreeSurfer Developers
@@ -161,18 +139,16 @@ def fs_tutorial_data(
     Returns:
         NamedTuple of outputs (described in `FsTutorialDataOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FS_TUTORIAL_DATA_METADATA)
     params = fs_tutorial_data_params(
         rsync_options=rsync_options,
     )
-    return fs_tutorial_data_execute(params, execution)
+    return fs_tutorial_data_execute(params, runner)
 
 
 __all__ = [
     "FS_TUTORIAL_DATA_METADATA",
     "FsTutorialDataOutputs",
-    "FsTutorialDataParameters",
     "fs_tutorial_data",
+    "fs_tutorial_data_execute",
     "fs_tutorial_data_params",
 ]

niwrap_freesurfer/freesurfer/fs_update.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FS_UPDATE_METADATA = Metadata(
-    id="7559054caea5811a27d56eadbc3ee13035050ade.boutiques",
+    id="292e488f1c73fb2b7f19675d398ffc2bdba4ec20.boutiques",
     name="fs_update",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,24 @@ FS_UPDATE_METADATA = Metadata(
 
 
 FsUpdateParameters = typing.TypedDict('FsUpdateParameters', {
-    "__STYXTYPE__": typing.Literal["fs_update"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fs_update"]],
+    "update_path": typing.NotRequired[str | None],
+    "help_short": bool,
+    "help_medium": bool,
+    "help_long": bool,
+})
+FsUpdateParametersTagged = typing.TypedDict('FsUpdateParametersTagged', {
+    "@type": typing.Literal["freesurfer/fs_update"],
     "update_path": typing.NotRequired[str | None],
     "help_short": bool,
     "help_medium": bool,
     "help_long": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fs_update": fs_update_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 FsUpdateOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fs_update(...)`.
+    Output object returned when calling `FsUpdateParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def fs_update_params(
     help_short: bool = False,
     help_medium: bool = False,
     help_long: bool = False,
-) -> FsUpdateParameters:
+) -> FsUpdateParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +56,7 @@ def fs_update_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fs_update",
+        "@type": "freesurfer/fs_update",
         "help_short": help_short,
         "help_medium": help_medium,
         "help_long": help_long,
@@ -105,13 +81,13 @@ def fs_update_cargs(
     """
     cargs = []
     cargs.append("fs_update")
-    if params.get("update_path") is not None:
-        cargs.append(params.get("update_path"))
-    if params.get("help_short"):
+    if params.get("update_path", None) is not None:
+        cargs.append(params.get("update_path", None))
+    if params.get("help_short", False):
         cargs.append("-h")
-    if params.get("help_medium"):
+    if params.get("help_medium", False):
         cargs.append("-help")
-    if params.get("help_long"):
+    if params.get("help_long", False):
         cargs.append("--help")
     return cargs
 
@@ -137,9 +113,11 @@ def fs_update_outputs(
 
 def fs_update_execute(
     params: FsUpdateParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FsUpdateOutputs:
     """
+    fs_update
+    
     Utility to update the FreeSurfer installation.
     
     Author: FreeSurfer Developers
@@ -148,10 +126,12 @@ def fs_update_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsUpdateOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FS_UPDATE_METADATA)
     params = execution.params(params)
     cargs = fs_update_cargs(params, execution)
     ret = fs_update_outputs(params, execution)
@@ -167,6 +147,8 @@ def fs_update(
     runner: Runner | None = None,
 ) -> FsUpdateOutputs:
     """
+    fs_update
+    
     Utility to update the FreeSurfer installation.
     
     Author: FreeSurfer Developers
@@ -183,21 +165,19 @@ def fs_update(
     Returns:
         NamedTuple of outputs (described in `FsUpdateOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FS_UPDATE_METADATA)
     params = fs_update_params(
         update_path=update_path,
         help_short=help_short,
         help_medium=help_medium,
         help_long=help_long,
     )
-    return fs_update_execute(params, execution)
+    return fs_update_execute(params, runner)
 
 
 __all__ = [
     "FS_UPDATE_METADATA",
     "FsUpdateOutputs",
-    "FsUpdateParameters",
     "fs_update",
+    "fs_update_execute",
     "fs_update_params",
 ]

niwrap_freesurfer/freesurfer/fscalc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FSCALC_METADATA = Metadata(
-    id="ea4a3f00afbc065f06ad7bec64190787fc5e16a4.boutiques",
+    id="ae4a7625eb43dd733c4d61d54bfadf65d95eb4e4.boutiques",
     name="fscalc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,19 @@ FSCALC_METADATA = Metadata(
 
 
 FscalcParameters = typing.TypedDict('FscalcParameters', {
-    "__STYXTYPE__": typing.Literal["fscalc"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fscalc"]],
+    "input1": str,
+    "operation": str,
+    "input2": typing.NotRequired[str | None],
+    "output_file": str,
+    "output_data_type": typing.NotRequired[str | None],
+    "debug": bool,
+    "tmpdir": typing.NotRequired[str | None],
+    "nocleanup": bool,
+    "log_file": typing.NotRequired[str | None],
+})
+FscalcParametersTagged = typing.TypedDict('FscalcParametersTagged', {
+    "@type": typing.Literal["freesurfer/fscalc"],
     "input1": str,
     "operation": str,
     "input2": typing.NotRequired[str | None],
@@ -25,43 +37,11 @@ FscalcParameters = typing.TypedDict('FscalcParameters', {
     "nocleanup": bool,
     "log_file": 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 {
-        "fscalc": fscalc_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 {
-        "fscalc": fscalc_outputs,
-    }.get(t)
 
 
 class FscalcOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fscalc(...)`.
+    Output object returned when calling `FscalcParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +59,7 @@ def fscalc_params(
     tmpdir: str | None = None,
     nocleanup: bool = False,
     log_file: str | None = None,
-) -> FscalcParameters:
+) -> FscalcParametersTagged:
     """
     Build parameters.
     
@@ -98,7 +78,7 @@ def fscalc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fscalc",
+        "@type": "freesurfer/fscalc",
         "input1": input1,
         "operation": operation,
         "output_file": output_file,
@@ -131,32 +111,32 @@ def fscalc_cargs(
     """
     cargs = []
     cargs.append("fscalc")
-    cargs.append(params.get("input1"))
-    cargs.append(params.get("operation"))
-    if params.get("input2") is not None:
-        cargs.append(params.get("input2"))
+    cargs.append(params.get("input1", None))
+    cargs.append(params.get("operation", None))
+    if params.get("input2", None) is not None:
+        cargs.append(params.get("input2", None))
     cargs.extend([
         "--o",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
-    if params.get("output_data_type") is not None:
+    if params.get("output_data_type", None) is not None:
         cargs.extend([
             "--odt",
-            params.get("output_data_type")
+            params.get("output_data_type", None)
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("tmpdir") is not None:
+    if params.get("tmpdir", None) is not None:
         cargs.extend([
             "--tmpdir",
-            params.get("tmpdir")
+            params.get("tmpdir", None)
         ])
-    if params.get("nocleanup"):
+    if params.get("nocleanup", False):
         cargs.append("--nocleanup")
-    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)
         ])
     return cargs
 
@@ -176,18 +156,20 @@ def fscalc_outputs(
     """
     ret = FscalcOutputs(
         root=execution.output_file("."),
-        result_vol=execution.output_file(params.get("output_file")),
+        result_vol=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def fscalc_execute(
     params: FscalcParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FscalcOutputs:
     """
-    A frontend tool to perform mathematical operations on volumes/surfaces of data
-    using mris_calc.
+    fscalc
+    
+    A frontend tool to perform mathematical operations on volumes/surfaces of
+    data using mris_calc.
     
     Author: FreeSurfer Developers
     
@@ -195,10 +177,12 @@ def fscalc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FscalcOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FSCALC_METADATA)
     params = execution.params(params)
     cargs = fscalc_cargs(params, execution)
     ret = fscalc_outputs(params, execution)
@@ -219,8 +203,10 @@ def fscalc(
     runner: Runner | None = None,
 ) -> FscalcOutputs:
     """
-    A frontend tool to perform mathematical operations on volumes/surfaces of data
-    using mris_calc.
+    fscalc
+    
+    A frontend tool to perform mathematical operations on volumes/surfaces of
+    data using mris_calc.
     
     Author: FreeSurfer Developers
     
@@ -241,8 +227,6 @@ def fscalc(
     Returns:
         NamedTuple of outputs (described in `FscalcOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSCALC_METADATA)
     params = fscalc_params(
         input1=input1,
         operation=operation,
@@ -254,13 +238,13 @@ def fscalc(
         nocleanup=nocleanup,
         log_file=log_file,
     )
-    return fscalc_execute(params, execution)
+    return fscalc_execute(params, runner)
 
 
 __all__ = [
     "FSCALC_METADATA",
     "FscalcOutputs",
-    "FscalcParameters",
     "fscalc",
+    "fscalc_execute",
     "fscalc_params",
 ]

niwrap_freesurfer/freesurfer/fsdcmdecompress.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FSDCMDECOMPRESS_METADATA = Metadata(
-    id="30d6a93931c489cde2efd8a6696b27e23a3c1869.boutiques",
+    id="67cffa7eac1e8233815a6f4a9ab769accda8f46c.boutiques",
     name="fsdcmdecompress",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ FSDCMDECOMPRESS_METADATA = Metadata(
 
 
 FsdcmdecompressParameters = typing.TypedDict('FsdcmdecompressParameters', {
-    "__STYXTYPE__": typing.Literal["fsdcmdecompress"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fsdcmdecompress"]],
+    "indcmfile": InputPathType,
+    "outdcmfile": str,
+    "dcmtk": bool,
+    "jpeg": bool,
+    "rle": bool,
+    "gdcm": bool,
+})
+FsdcmdecompressParametersTagged = typing.TypedDict('FsdcmdecompressParametersTagged', {
+    "@type": typing.Literal["freesurfer/fsdcmdecompress"],
     "indcmfile": InputPathType,
     "outdcmfile": str,
     "dcmtk": bool,
@@ -22,43 +31,11 @@ FsdcmdecompressParameters = typing.TypedDict('FsdcmdecompressParameters', {
     "rle": bool,
     "gdcm": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fsdcmdecompress": fsdcmdecompress_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 {
-        "fsdcmdecompress": fsdcmdecompress_outputs,
-    }.get(t)
 
 
 class FsdcmdecompressOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fsdcmdecompress(...)`.
+    Output object returned when calling `FsdcmdecompressParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def fsdcmdecompress_params(
     jpeg: bool = False,
     rle: bool = False,
     gdcm: bool = False,
-) -> FsdcmdecompressParameters:
+) -> FsdcmdecompressParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +65,7 @@ def fsdcmdecompress_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fsdcmdecompress",
+        "@type": "freesurfer/fsdcmdecompress",
         "indcmfile": indcmfile,
         "outdcmfile": outdcmfile,
         "dcmtk": dcmtk,
@@ -116,19 +93,19 @@ def fsdcmdecompress_cargs(
     cargs.append("fsdcmdecompress")
     cargs.extend([
         "--i",
-        execution.input_file(params.get("indcmfile"))
+        execution.input_file(params.get("indcmfile", None))
     ])
     cargs.extend([
         "--o",
-        params.get("outdcmfile")
+        params.get("outdcmfile", None)
     ])
-    if params.get("dcmtk"):
+    if params.get("dcmtk", False):
         cargs.append("--dcmtk")
-    if params.get("jpeg"):
+    if params.get("jpeg", False):
         cargs.append("--jpeg")
-    if params.get("rle"):
+    if params.get("rle", False):
         cargs.append("--rle")
-    if params.get("gdcm"):
+    if params.get("gdcm", False):
         cargs.append("--gdcm")
     return cargs
 
@@ -148,16 +125,18 @@ def fsdcmdecompress_outputs(
     """
     ret = FsdcmdecompressOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(params.get("outdcmfile")),
+        out_file=execution.output_file(params.get("outdcmfile", None)),
     )
     return ret
 
 
 def fsdcmdecompress_execute(
     params: FsdcmdecompressParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FsdcmdecompressOutputs:
     """
+    fsdcmdecompress
+    
     A tool for decompressing DICOM files using GDCM or DCMTK.
     
     Author: FreeSurfer Developers
@@ -166,10 +145,12 @@ def fsdcmdecompress_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsdcmdecompressOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FSDCMDECOMPRESS_METADATA)
     params = execution.params(params)
     cargs = fsdcmdecompress_cargs(params, execution)
     ret = fsdcmdecompress_outputs(params, execution)
@@ -187,6 +168,8 @@ def fsdcmdecompress(
     runner: Runner | None = None,
 ) -> FsdcmdecompressOutputs:
     """
+    fsdcmdecompress
+    
     A tool for decompressing DICOM files using GDCM or DCMTK.
     
     Author: FreeSurfer Developers
@@ -204,8 +187,6 @@ def fsdcmdecompress(
     Returns:
         NamedTuple of outputs (described in `FsdcmdecompressOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSDCMDECOMPRESS_METADATA)
     params = fsdcmdecompress_params(
         indcmfile=indcmfile,
         outdcmfile=outdcmfile,
@@ -214,13 +195,13 @@ def fsdcmdecompress(
         rle=rle,
         gdcm=gdcm,
     )
-    return fsdcmdecompress_execute(params, execution)
+    return fsdcmdecompress_execute(params, runner)
 
 
 __all__ = [
     "FSDCMDECOMPRESS_METADATA",
     "FsdcmdecompressOutputs",
-    "FsdcmdecompressParameters",
     "fsdcmdecompress",
+    "fsdcmdecompress_execute",
     "fsdcmdecompress_params",
 ]