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

niwrap_freesurfer/freesurfer/mri_label2vol.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_LABEL2VOL_METADATA = Metadata(
-    id="cd26e42611cf3dfd2ed0aa17d46d76686633fdae.boutiques",
+    id="f8778b7510a9fb33a51b0fb6e712b2755808320c.boutiques",
     name="mri_label2vol",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,28 @@ MRI_LABEL2VOL_METADATA = Metadata(
 
 
 MriLabel2volParameters = typing.TypedDict('MriLabel2volParameters', {
-    "__STYXTYPE__": typing.Literal["mri_label2vol"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_label2vol"]],
+    "labels": typing.NotRequired[list[str] | None],
+    "annotation": typing.NotRequired[InputPathType | None],
+    "segmentation": typing.NotRequired[InputPathType | None],
+    "template": InputPathType,
+    "registration": typing.NotRequired[InputPathType | None],
+    "identity_flag": bool,
+    "fill_threshold": typing.NotRequired[float | None],
+    "label_vox_vol": typing.NotRequired[float | None],
+    "projection": typing.NotRequired[str | None],
+    "subject": typing.NotRequired[str | None],
+    "hemisphere": typing.NotRequired[str | None],
+    "output_volume": str,
+    "hits_volume": typing.NotRequired[str | None],
+    "label_stat_volume": typing.NotRequired[str | None],
+    "stat_threshold": typing.NotRequired[float | None],
+    "offset": typing.NotRequired[float | None],
+    "defects": typing.NotRequired[str | None],
+    "native_vox2ras_flag": bool,
+})
+MriLabel2volParametersTagged = typing.TypedDict('MriLabel2volParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_label2vol"],
     "labels": typing.NotRequired[list[str] | None],
     "annotation": typing.NotRequired[InputPathType | None],
     "segmentation": typing.NotRequired[InputPathType | None],
@@ -34,43 +55,11 @@ MriLabel2volParameters = typing.TypedDict('MriLabel2volParameters', {
     "defects": typing.NotRequired[str | None],
     "native_vox2ras_flag": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_label2vol": mri_label2vol_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 {
-        "mri_label2vol": mri_label2vol_outputs,
-    }.get(t)
 
 
 class MriLabel2volOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_label2vol(...)`.
+    Output object returned when calling `MriLabel2volParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -101,7 +90,7 @@ def mri_label2vol_params(
     offset: float | None = None,
     defects: str | None = None,
     native_vox2ras_flag: bool = False,
-) -> MriLabel2volParameters:
+) -> MriLabel2volParametersTagged:
     """
     Build parameters.
     
@@ -137,7 +126,7 @@ def mri_label2vol_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_label2vol",
+        "@type": "freesurfer/mri_label2vol",
         "template": template,
         "identity_flag": identity_flag,
         "output_volume": output_volume,
@@ -189,87 +178,87 @@ def mri_label2vol_cargs(
     """
     cargs = []
     cargs.append("mri_label2vol")
-    if params.get("labels") is not None:
+    if params.get("labels", None) is not None:
         cargs.extend([
             "--label",
-            *params.get("labels")
+            *params.get("labels", None)
         ])
-    if params.get("annotation") is not None:
+    if params.get("annotation", None) is not None:
         cargs.extend([
             "--annot",
-            execution.input_file(params.get("annotation"))
+            execution.input_file(params.get("annotation", None))
         ])
-    if params.get("segmentation") is not None:
+    if params.get("segmentation", None) is not None:
         cargs.extend([
             "--seg",
-            execution.input_file(params.get("segmentation"))
+            execution.input_file(params.get("segmentation", None))
         ])
     cargs.extend([
         "--temp",
-        execution.input_file(params.get("template"))
+        execution.input_file(params.get("template", None))
     ])
-    if params.get("registration") is not None:
+    if params.get("registration", None) is not None:
         cargs.extend([
             "--reg",
-            execution.input_file(params.get("registration"))
+            execution.input_file(params.get("registration", None))
         ])
-    if params.get("identity_flag"):
+    if params.get("identity_flag", False):
         cargs.append("--identity")
-    if params.get("fill_threshold") is not None:
+    if params.get("fill_threshold", None) is not None:
         cargs.extend([
             "--fillthresh",
-            str(params.get("fill_threshold"))
+            str(params.get("fill_threshold", None))
         ])
-    if params.get("label_vox_vol") is not None:
+    if params.get("label_vox_vol", None) is not None:
         cargs.extend([
             "--labvoxvol",
-            str(params.get("label_vox_vol"))
+            str(params.get("label_vox_vol", None))
         ])
-    if params.get("projection") is not None:
+    if params.get("projection", None) is not None:
         cargs.extend([
             "--proj",
-            params.get("projection")
+            params.get("projection", None)
         ])
-    if params.get("subject") is not None:
+    if params.get("subject", None) is not None:
         cargs.extend([
             "--subject",
-            params.get("subject")
+            params.get("subject", None)
         ])
-    if params.get("hemisphere") is not None:
+    if params.get("hemisphere", None) is not None:
         cargs.extend([
             "--hemi",
-            params.get("hemisphere")
+            params.get("hemisphere", None)
         ])
     cargs.extend([
         "--o",
-        params.get("output_volume")
+        params.get("output_volume", None)
     ])
-    if params.get("hits_volume") is not None:
+    if params.get("hits_volume", None) is not None:
         cargs.extend([
             "--hits",
-            params.get("hits_volume")
+            params.get("hits_volume", None)
         ])
-    if params.get("label_stat_volume") is not None:
+    if params.get("label_stat_volume", None) is not None:
         cargs.extend([
             "--label-stat",
-            params.get("label_stat_volume")
+            params.get("label_stat_volume", None)
         ])
-    if params.get("stat_threshold") is not None:
+    if params.get("stat_threshold", None) is not None:
         cargs.extend([
             "--stat-thresh",
-            str(params.get("stat_threshold"))
+            str(params.get("stat_threshold", None))
         ])
-    if params.get("offset") is not None:
+    if params.get("offset", None) is not None:
         cargs.extend([
             "--offset",
-            str(params.get("offset"))
+            str(params.get("offset", None))
         ])
-    if params.get("defects") is not None:
+    if params.get("defects", None) is not None:
         cargs.extend([
             "--defects",
-            params.get("defects")
+            params.get("defects", None)
         ])
-    if params.get("native_vox2ras_flag"):
+    if params.get("native_vox2ras_flag", False):
         cargs.append("--native-vox2ras")
     return cargs
 
@@ -289,18 +278,20 @@ def mri_label2vol_outputs(
     """
     ret = MriLabel2volOutputs(
         root=execution.output_file("."),
-        output_vol=execution.output_file(params.get("output_volume")),
-        hits_vol=execution.output_file(params.get("hits_volume")) if (params.get("hits_volume") is not None) else None,
-        label_stat_vol=execution.output_file(params.get("label_stat_volume")) if (params.get("label_stat_volume") is not None) else None,
+        output_vol=execution.output_file(params.get("output_volume", None)),
+        hits_vol=execution.output_file(params.get("hits_volume", None)) if (params.get("hits_volume") is not None) else None,
+        label_stat_vol=execution.output_file(params.get("label_stat_volume", None)) if (params.get("label_stat_volume") is not None) else None,
     )
     return ret
 
 
 def mri_label2vol_execute(
     params: MriLabel2volParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriLabel2volOutputs:
     """
+    mri_label2vol
+    
     Converts a label or a set of labels into a volume.
     
     Author: FreeSurfer Developers
@@ -309,10 +300,12 @@ def mri_label2vol_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriLabel2volOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_LABEL2VOL_METADATA)
     params = execution.params(params)
     cargs = mri_label2vol_cargs(params, execution)
     ret = mri_label2vol_outputs(params, execution)
@@ -342,6 +335,8 @@ def mri_label2vol(
     runner: Runner | None = None,
 ) -> MriLabel2volOutputs:
     """
+    mri_label2vol
+    
     Converts a label or a set of labels into a volume.
     
     Author: FreeSurfer Developers
@@ -380,8 +375,6 @@ def mri_label2vol(
     Returns:
         NamedTuple of outputs (described in `MriLabel2volOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_LABEL2VOL_METADATA)
     params = mri_label2vol_params(
         labels=labels,
         annotation=annotation,
@@ -402,13 +395,13 @@ def mri_label2vol(
         defects=defects,
         native_vox2ras_flag=native_vox2ras_flag,
     )
-    return mri_label2vol_execute(params, execution)
+    return mri_label2vol_execute(params, runner)
 
 
 __all__ = [
     "MRI_LABEL2VOL_METADATA",
     "MriLabel2volOutputs",
-    "MriLabel2volParameters",
     "mri_label2vol",
+    "mri_label2vol_execute",
     "mri_label2vol_params",
 ]

niwrap_freesurfer/freesurfer/mri_label_histo.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_LABEL_HISTO_METADATA = Metadata(
-    id="7d795cae67b9944e82e8ebe14bb1a696c471f786.boutiques",
+    id="643c58f8665ec46cd1322bb1c0c35f74ac658dc2.boutiques",
     name="mri_label_histo",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRI_LABEL_HISTO_METADATA = Metadata(
 
 
 MriLabelHistoParameters = typing.TypedDict('MriLabelHistoParameters', {
-    "__STYXTYPE__": typing.Literal["mri_label_histo"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_label_histo"]],
+    "t1_volume": InputPathType,
+    "labeled_volume": InputPathType,
+    "label": float,
+    "output": str,
+})
+MriLabelHistoParametersTagged = typing.TypedDict('MriLabelHistoParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_label_histo"],
     "t1_volume": InputPathType,
     "labeled_volume": InputPathType,
     "label": float,
     "output": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_label_histo": mri_label_histo_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 {
-        "mri_label_histo": mri_label_histo_outputs,
-    }.get(t)
 
 
 class MriLabelHistoOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_label_histo(...)`.
+    Output object returned when calling `MriLabelHistoParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mri_label_histo_params(
     labeled_volume: InputPathType,
     label: float,
     output: str,
-) -> MriLabelHistoParameters:
+) -> MriLabelHistoParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def mri_label_histo_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_label_histo",
+        "@type": "freesurfer/mri_label_histo",
         "t1_volume": t1_volume,
         "labeled_volume": labeled_volume,
         "label": label,
@@ -106,10 +81,10 @@ def mri_label_histo_cargs(
     """
     cargs = []
     cargs.append("mri_label_histo")
-    cargs.append(execution.input_file(params.get("t1_volume")))
-    cargs.append(execution.input_file(params.get("labeled_volume")))
-    cargs.append(str(params.get("label")))
-    cargs.append(params.get("output"))
+    cargs.append(execution.input_file(params.get("t1_volume", None)))
+    cargs.append(execution.input_file(params.get("labeled_volume", None)))
+    cargs.append(str(params.get("label", None)))
+    cargs.append(params.get("output", None))
     return cargs
 
 
@@ -128,16 +103,18 @@ def mri_label_histo_outputs(
     """
     ret = MriLabelHistoOutputs(
         root=execution.output_file("."),
-        histogram_output=execution.output_file(params.get("output")),
+        histogram_output=execution.output_file(params.get("output", None)),
     )
     return ret
 
 
 def mri_label_histo_execute(
     params: MriLabelHistoParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriLabelHistoOutputs:
     """
+    mri_label_histo
+    
     Tool for creating a histogram of voxel values within a specified label.
     
     Author: FreeSurfer Developers
@@ -146,10 +123,12 @@ def mri_label_histo_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriLabelHistoOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_LABEL_HISTO_METADATA)
     params = execution.params(params)
     cargs = mri_label_histo_cargs(params, execution)
     ret = mri_label_histo_outputs(params, execution)
@@ -165,6 +144,8 @@ def mri_label_histo(
     runner: Runner | None = None,
 ) -> MriLabelHistoOutputs:
     """
+    mri_label_histo
+    
     Tool for creating a histogram of voxel values within a specified label.
     
     Author: FreeSurfer Developers
@@ -180,21 +161,19 @@ def mri_label_histo(
     Returns:
         NamedTuple of outputs (described in `MriLabelHistoOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_LABEL_HISTO_METADATA)
     params = mri_label_histo_params(
         t1_volume=t1_volume,
         labeled_volume=labeled_volume,
         label=label,
         output=output,
     )
-    return mri_label_histo_execute(params, execution)
+    return mri_label_histo_execute(params, runner)
 
 
 __all__ = [
     "MRI_LABEL_HISTO_METADATA",
     "MriLabelHistoOutputs",
-    "MriLabelHistoParameters",
     "mri_label_histo",
+    "mri_label_histo_execute",
     "mri_label_histo_params",
 ]

niwrap_freesurfer/freesurfer/mri_label_vals.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_LABEL_VALS_METADATA = Metadata(
-    id="470e3234390d2b43d7acd775c577640281aecf54.boutiques",
+    id="15ff606d2887e79e2bfb5436245a0c3edde29022.boutiques",
     name="mri_label_vals",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,24 @@ MRI_LABEL_VALS_METADATA = Metadata(
 
 
 MriLabelValsParameters = typing.TypedDict('MriLabelValsParameters', {
-    "__STYXTYPE__": typing.Literal["mri_label_vals"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_label_vals"]],
+    "volume": InputPathType,
+    "label_file": InputPathType,
+    "cras_flag": bool,
+    "help_flag": bool,
+})
+MriLabelValsParametersTagged = typing.TypedDict('MriLabelValsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_label_vals"],
     "volume": InputPathType,
     "label_file": InputPathType,
     "cras_flag": bool,
     "help_flag": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_label_vals": mri_label_vals_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 MriLabelValsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_label_vals(...)`.
+    Output object returned when calling `MriLabelValsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def mri_label_vals_params(
     label_file: InputPathType,
     cras_flag: bool = False,
     help_flag: bool = False,
-) -> MriLabelValsParameters:
+) -> MriLabelValsParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +56,7 @@ def mri_label_vals_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_label_vals",
+        "@type": "freesurfer/mri_label_vals",
         "volume": volume,
         "label_file": label_file,
         "cras_flag": cras_flag,
@@ -104,11 +80,11 @@ def mri_label_vals_cargs(
     """
     cargs = []
     cargs.append("mri_label_vals")
-    cargs.append(execution.input_file(params.get("volume")))
-    cargs.append(execution.input_file(params.get("label_file")))
-    if params.get("cras_flag"):
+    cargs.append(execution.input_file(params.get("volume", None)))
+    cargs.append(execution.input_file(params.get("label_file", None)))
+    if params.get("cras_flag", False):
         cargs.append("-cras")
-    if params.get("help_flag"):
+    if params.get("help_flag", False):
         cargs.append("-u")
     return cargs
 
@@ -134,9 +110,11 @@ def mri_label_vals_outputs(
 
 def mri_label_vals_execute(
     params: MriLabelValsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriLabelValsOutputs:
     """
+    mri_label_vals
+    
     Extract values at label coordinates from a volume.
     
     Author: FreeSurfer Developers
@@ -145,10 +123,12 @@ def mri_label_vals_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriLabelValsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_LABEL_VALS_METADATA)
     params = execution.params(params)
     cargs = mri_label_vals_cargs(params, execution)
     ret = mri_label_vals_outputs(params, execution)
@@ -164,6 +144,8 @@ def mri_label_vals(
     runner: Runner | None = None,
 ) -> MriLabelValsOutputs:
     """
+    mri_label_vals
+    
     Extract values at label coordinates from a volume.
     
     Author: FreeSurfer Developers
@@ -180,21 +162,19 @@ def mri_label_vals(
     Returns:
         NamedTuple of outputs (described in `MriLabelValsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_LABEL_VALS_METADATA)
     params = mri_label_vals_params(
         volume=volume,
         label_file=label_file,
         cras_flag=cras_flag,
         help_flag=help_flag,
     )
-    return mri_label_vals_execute(params, execution)
+    return mri_label_vals_execute(params, runner)
 
 
 __all__ = [
     "MRI_LABEL_VALS_METADATA",
     "MriLabelValsOutputs",
-    "MriLabelValsParameters",
     "mri_label_vals",
+    "mri_label_vals_execute",
     "mri_label_vals_params",
 ]