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

niwrap_freesurfer/freesurfer/isnifti.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ISNIFTI_METADATA = Metadata(
-    id="0ec07279947545d1155748f4d9a448ee304204a0.boutiques",
+    id="99a950590917d27a496537b3dec8ccbeb6bac9a0.boutiques",
     name="isnifti",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ ISNIFTI_METADATA = Metadata(
 
 
 IsniftiParameters = typing.TypedDict('IsniftiParameters', {
-    "__STYXTYPE__": typing.Literal["isnifti"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/isnifti"]],
+    "infile": InputPathType,
+})
+IsniftiParametersTagged = typing.TypedDict('IsniftiParametersTagged', {
+    "@type": typing.Literal["freesurfer/isnifti"],
     "infile": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "isnifti": isnifti_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 IsniftiOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `isnifti(...)`.
+    Output object returned when calling `IsniftiParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class IsniftiOutputs(typing.NamedTuple):
 
 def isnifti_params(
     infile: InputPathType,
-) -> IsniftiParameters:
+) -> IsniftiParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def isnifti_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "isnifti",
+        "@type": "freesurfer/isnifti",
         "infile": infile,
     }
     return params
@@ -91,7 +64,7 @@ def isnifti_cargs(
     """
     cargs = []
     cargs.append("isnifti")
-    cargs.append(execution.input_file(params.get("infile")))
+    cargs.append(execution.input_file(params.get("infile", None)))
     return cargs
 
 
@@ -116,9 +89,11 @@ def isnifti_outputs(
 
 def isnifti_execute(
     params: IsniftiParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> IsniftiOutputs:
     """
+    isnifti
+    
     A simple tool to check if a file is a NIfTI image.
     
     Author: FreeSurfer Developers
@@ -127,10 +102,12 @@ def isnifti_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `IsniftiOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ISNIFTI_METADATA)
     params = execution.params(params)
     cargs = isnifti_cargs(params, execution)
     ret = isnifti_outputs(params, execution)
@@ -143,6 +120,8 @@ def isnifti(
     runner: Runner | None = None,
 ) -> IsniftiOutputs:
     """
+    isnifti
+    
     A simple tool to check if a file is a NIfTI image.
     
     Author: FreeSurfer Developers
@@ -155,18 +134,16 @@ def isnifti(
     Returns:
         NamedTuple of outputs (described in `IsniftiOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ISNIFTI_METADATA)
     params = isnifti_params(
         infile=infile,
     )
-    return isnifti_execute(params, execution)
+    return isnifti_execute(params, runner)
 
 
 __all__ = [
     "ISNIFTI_METADATA",
     "IsniftiOutputs",
-    "IsniftiParameters",
     "isnifti",
+    "isnifti_execute",
     "isnifti_params",
 ]

niwrap_freesurfer/freesurfer/isolate_labels_csh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ISOLATE_LABELS_CSH_METADATA = Metadata(
-    id="3b540edf6cbbc409752b8941b289e046f63fe950.boutiques",
+    id="e20006c5ec4b137448d99abb3104cf26b17519ce.boutiques",
     name="isolate_labels.csh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ ISOLATE_LABELS_CSH_METADATA = Metadata(
 
 
 IsolateLabelsCshParameters = typing.TypedDict('IsolateLabelsCshParameters', {
-    "__STYXTYPE__": typing.Literal["isolate_labels.csh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/isolate_labels.csh"]],
+    "label_volume": InputPathType,
+    "output_prefix": str,
+    "label_option": typing.NotRequired[str | None],
+    "lowercase_label_option": typing.NotRequired[str | None],
+    "version": bool,
+    "keepval": bool,
+    "help": bool,
+})
+IsolateLabelsCshParametersTagged = typing.TypedDict('IsolateLabelsCshParametersTagged', {
+    "@type": typing.Literal["freesurfer/isolate_labels.csh"],
     "label_volume": InputPathType,
     "output_prefix": str,
     "label_option": typing.NotRequired[str | None],
@@ -23,42 +33,11 @@ IsolateLabelsCshParameters = typing.TypedDict('IsolateLabelsCshParameters', {
     "keepval": bool,
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "isolate_labels.csh": isolate_labels_csh_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 IsolateLabelsCshOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `isolate_labels_csh(...)`.
+    Output object returned when calling `IsolateLabelsCshParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,7 +51,7 @@ def isolate_labels_csh_params(
     version: bool = False,
     keepval: bool = False,
     help_: bool = False,
-) -> IsolateLabelsCshParameters:
+) -> IsolateLabelsCshParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +69,7 @@ def isolate_labels_csh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "isolate_labels.csh",
+        "@type": "freesurfer/isolate_labels.csh",
         "label_volume": label_volume,
         "output_prefix": output_prefix,
         "version": version,
@@ -121,27 +100,27 @@ def isolate_labels_csh_cargs(
     cargs.append("isolate_labels.csh")
     cargs.extend([
         "--vol",
-        execution.input_file(params.get("label_volume"))
+        execution.input_file(params.get("label_volume", None))
     ])
     cargs.extend([
         "--outprefix",
-        params.get("output_prefix")
+        params.get("output_prefix", None)
     ])
-    if params.get("label_option") is not None:
+    if params.get("label_option", None) is not None:
         cargs.extend([
             "--L",
-            params.get("label_option")
+            params.get("label_option", None)
         ])
-    if params.get("lowercase_label_option") is not None:
+    if params.get("lowercase_label_option", None) is not None:
         cargs.extend([
             "--l",
-            params.get("lowercase_label_option")
+            params.get("lowercase_label_option", None)
         ])
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
-    if params.get("keepval"):
+    if params.get("keepval", False):
         cargs.append("--keepval")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
     return cargs
 
@@ -167,11 +146,13 @@ def isolate_labels_csh_outputs(
 
 def isolate_labels_csh_execute(
     params: IsolateLabelsCshParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> IsolateLabelsCshOutputs:
     """
-    Tool to separate out a particular or all labels into individual binary files for
-    subsequent shape analysis.
+    isolate_labels.csh
+    
+    Tool to separate out a particular or all labels into individual binary files
+    for subsequent shape analysis.
     
     Author: FreeSurfer Developers
     
@@ -179,10 +160,12 @@ def isolate_labels_csh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `IsolateLabelsCshOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ISOLATE_LABELS_CSH_METADATA)
     params = execution.params(params)
     cargs = isolate_labels_csh_cargs(params, execution)
     ret = isolate_labels_csh_outputs(params, execution)
@@ -201,8 +184,10 @@ def isolate_labels_csh(
     runner: Runner | None = None,
 ) -> IsolateLabelsCshOutputs:
     """
-    Tool to separate out a particular or all labels into individual binary files for
-    subsequent shape analysis.
+    isolate_labels.csh
+    
+    Tool to separate out a particular or all labels into individual binary files
+    for subsequent shape analysis.
     
     Author: FreeSurfer Developers
     
@@ -222,8 +207,6 @@ def isolate_labels_csh(
     Returns:
         NamedTuple of outputs (described in `IsolateLabelsCshOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ISOLATE_LABELS_CSH_METADATA)
     params = isolate_labels_csh_params(
         label_volume=label_volume,
         output_prefix=output_prefix,
@@ -233,13 +216,13 @@ def isolate_labels_csh(
         keepval=keepval,
         help_=help_,
     )
-    return isolate_labels_csh_execute(params, execution)
+    return isolate_labels_csh_execute(params, runner)
 
 
 __all__ = [
     "ISOLATE_LABELS_CSH_METADATA",
     "IsolateLabelsCshOutputs",
-    "IsolateLabelsCshParameters",
     "isolate_labels_csh",
+    "isolate_labels_csh_execute",
     "isolate_labels_csh_params",
 ]

niwrap_freesurfer/freesurfer/isolate_labels_keeporigval_csh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ISOLATE_LABELS_KEEPORIGVAL_CSH_METADATA = Metadata(
-    id="a6c0e69eb1ba1ff02a31f0459157a99e801ba645.boutiques",
+    id="1326bd6d6c5da13df656f1de4b71d08c81e0847b.boutiques",
     name="isolate_labels_keeporigval.csh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,55 +14,29 @@ ISOLATE_LABELS_KEEPORIGVAL_CSH_METADATA = Metadata(
 
 
 IsolateLabelsKeeporigvalCshParameters = typing.TypedDict('IsolateLabelsKeeporigvalCshParameters', {
-    "__STYXTYPE__": typing.Literal["isolate_labels_keeporigval.csh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/isolate_labels_keeporigval.csh"]],
+    "vol": InputPathType,
+    "outprefix": str,
+    "label": typing.NotRequired[str | None],
+    "version": bool,
+    "help": bool,
+})
+IsolateLabelsKeeporigvalCshParametersTagged = typing.TypedDict('IsolateLabelsKeeporigvalCshParametersTagged', {
+    "@type": typing.Literal["freesurfer/isolate_labels_keeporigval.csh"],
     "vol": InputPathType,
     "outprefix": str,
     "label": typing.NotRequired[str | None],
     "version": bool,
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "isolate_labels_keeporigval.csh": isolate_labels_keeporigval_csh_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 {
-        "isolate_labels_keeporigval.csh": isolate_labels_keeporigval_csh_outputs,
-    }.get(t)
 
 
 class IsolateLabelsKeeporigvalCshOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `isolate_labels_keeporigval_csh(...)`.
+    Output object returned when calling `IsolateLabelsKeeporigvalCshParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    output_label_files: OutputPathType
-    """Output binary label file(s)"""
 
 
 def isolate_labels_keeporigval_csh_params(
@@ -71,7 +45,7 @@ def isolate_labels_keeporigval_csh_params(
     label: str | None = None,
     version: bool = False,
     help_: bool = False,
-) -> IsolateLabelsKeeporigvalCshParameters:
+) -> IsolateLabelsKeeporigvalCshParametersTagged:
     """
     Build parameters.
     
@@ -86,7 +60,7 @@ def isolate_labels_keeporigval_csh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "isolate_labels_keeporigval.csh",
+        "@type": "freesurfer/isolate_labels_keeporigval.csh",
         "vol": vol,
         "outprefix": outprefix,
         "version": version,
@@ -114,20 +88,20 @@ def isolate_labels_keeporigval_csh_cargs(
     cargs.append("isolate_labels_keeporigval.csh")
     cargs.extend([
         "--vol",
-        execution.input_file(params.get("vol"))
+        execution.input_file(params.get("vol", None))
     ])
     cargs.extend([
         "--outprefix",
-        params.get("outprefix")
+        params.get("outprefix", None)
     ])
-    if params.get("label") is not None:
+    if params.get("label", None) is not None:
         cargs.extend([
             "--l",
-            params.get("label")
+            params.get("label", None)
         ])
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
     return cargs
 
@@ -147,18 +121,19 @@ def isolate_labels_keeporigval_csh_outputs(
     """
     ret = IsolateLabelsKeeporigvalCshOutputs(
         root=execution.output_file("."),
-        output_label_files=execution.output_file(params.get("outprefix") + "_label*.nii.gz"),
     )
     return ret
 
 
 def isolate_labels_keeporigval_csh_execute(
     params: IsolateLabelsKeeporigvalCshParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> IsolateLabelsKeeporigvalCshOutputs:
     """
-    Separates out a particular or all labels into individual binary files keeping
-    the original label values for subsequent shape analysis.
+    isolate_labels_keeporigval.csh
+    
+    Separates out a particular or all labels into individual binary files
+    keeping the original label values for subsequent shape analysis.
     
     Author: FreeSurfer Developers
     
@@ -166,10 +141,12 @@ def isolate_labels_keeporigval_csh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `IsolateLabelsKeeporigvalCshOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ISOLATE_LABELS_KEEPORIGVAL_CSH_METADATA)
     params = execution.params(params)
     cargs = isolate_labels_keeporigval_csh_cargs(params, execution)
     ret = isolate_labels_keeporigval_csh_outputs(params, execution)
@@ -186,8 +163,10 @@ def isolate_labels_keeporigval_csh(
     runner: Runner | None = None,
 ) -> IsolateLabelsKeeporigvalCshOutputs:
     """
-    Separates out a particular or all labels into individual binary files keeping
-    the original label values for subsequent shape analysis.
+    isolate_labels_keeporigval.csh
+    
+    Separates out a particular or all labels into individual binary files
+    keeping the original label values for subsequent shape analysis.
     
     Author: FreeSurfer Developers
     
@@ -204,8 +183,6 @@ def isolate_labels_keeporigval_csh(
     Returns:
         NamedTuple of outputs (described in `IsolateLabelsKeeporigvalCshOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ISOLATE_LABELS_KEEPORIGVAL_CSH_METADATA)
     params = isolate_labels_keeporigval_csh_params(
         vol=vol,
         outprefix=outprefix,
@@ -213,13 +190,13 @@ def isolate_labels_keeporigval_csh(
         version=version,
         help_=help_,
     )
-    return isolate_labels_keeporigval_csh_execute(params, execution)
+    return isolate_labels_keeporigval_csh_execute(params, runner)
 
 
 __all__ = [
     "ISOLATE_LABELS_KEEPORIGVAL_CSH_METADATA",
     "IsolateLabelsKeeporigvalCshOutputs",
-    "IsolateLabelsKeeporigvalCshParameters",
     "isolate_labels_keeporigval_csh",
+    "isolate_labels_keeporigval_csh_execute",
     "isolate_labels_keeporigval_csh_params",
 ]