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

niwrap_freesurfer/freesurfer/mri_make_uchar.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_MAKE_UCHAR_METADATA = Metadata(
-    id="125a7b8010e7a6e47c1c93bba9839070d4e12157.boutiques",
+    id="3fb5e642570f4b2a846337e6be47633d5e4e61e0.boutiques",
     name="mri_make_uchar",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ MRI_MAKE_UCHAR_METADATA = Metadata(
 
 
 MriMakeUcharParameters = typing.TypedDict('MriMakeUcharParameters', {
-    "__STYXTYPE__": typing.Literal["mri_make_uchar"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_make_uchar"]],
+    "input_volume": InputPathType,
+    "talairach_xform": InputPathType,
+    "output_volume": str,
+    "first_percentile": typing.NotRequired[float | None],
+    "wm_percentile": typing.NotRequired[float | None],
+    "max_radius": typing.NotRequired[float | None],
+    "cumulative_histo": typing.NotRequired[str | None],
+    "vradvol": typing.NotRequired[str | None],
+})
+MriMakeUcharParametersTagged = typing.TypedDict('MriMakeUcharParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_make_uchar"],
     "input_volume": InputPathType,
     "talairach_xform": InputPathType,
     "output_volume": str,
@@ -24,43 +35,11 @@ MriMakeUcharParameters = typing.TypedDict('MriMakeUcharParameters', {
     "cumulative_histo": typing.NotRequired[str | None],
     "vradvol": 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 {
-        "mri_make_uchar": mri_make_uchar_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_make_uchar": mri_make_uchar_outputs,
-    }.get(t)
 
 
 class MriMakeUcharOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_make_uchar(...)`.
+    Output object returned when calling `MriMakeUcharParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,12 +51,12 @@ def mri_make_uchar_params(
     input_volume: InputPathType,
     talairach_xform: InputPathType,
     output_volume: str,
-    first_percentile: float | None = 0.01,
-    wm_percentile: float | None = 0.9,
-    max_radius: float | None = 50,
+    first_percentile: float | None = None,
+    wm_percentile: float | None = None,
+    max_radius: float | None = None,
     cumulative_histo: str | None = None,
     vradvol: str | None = None,
-) -> MriMakeUcharParameters:
+) -> MriMakeUcharParametersTagged:
     """
     Build parameters.
     
@@ -96,7 +75,7 @@ def mri_make_uchar_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_make_uchar",
+        "@type": "freesurfer/mri_make_uchar",
         "input_volume": input_volume,
         "talairach_xform": talairach_xform,
         "output_volume": output_volume,
@@ -129,33 +108,33 @@ def mri_make_uchar_cargs(
     """
     cargs = []
     cargs.append("mri_make_uchar")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(execution.input_file(params.get("talairach_xform")))
-    cargs.append(params.get("output_volume"))
-    if params.get("first_percentile") is not None:
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(execution.input_file(params.get("talairach_xform", None)))
+    cargs.append(params.get("output_volume", None))
+    if params.get("first_percentile", None) is not None:
         cargs.extend([
             "-f",
-            str(params.get("first_percentile"))
+            str(params.get("first_percentile", None))
         ])
-    if params.get("wm_percentile") is not None:
+    if params.get("wm_percentile", None) is not None:
         cargs.extend([
             "-w",
-            str(params.get("wm_percentile"))
+            str(params.get("wm_percentile", None))
         ])
-    if params.get("max_radius") is not None:
+    if params.get("max_radius", None) is not None:
         cargs.extend([
             "-r",
-            str(params.get("max_radius"))
+            str(params.get("max_radius", None))
         ])
-    if params.get("cumulative_histo") is not None:
+    if params.get("cumulative_histo", None) is not None:
         cargs.extend([
             "-h",
-            params.get("cumulative_histo")
+            params.get("cumulative_histo", None)
         ])
-    if params.get("vradvol") is not None:
+    if params.get("vradvol", None) is not None:
         cargs.extend([
             "-v",
-            params.get("vradvol")
+            params.get("vradvol", None)
         ])
     return cargs
 
@@ -175,17 +154,20 @@ def mri_make_uchar_outputs(
     """
     ret = MriMakeUcharOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_volume")),
+        output_file=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def mri_make_uchar_execute(
     params: MriMakeUcharParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriMakeUcharOutputs:
     """
-    Tool to adjust intensity of brain MRI images using a Talairach transformation.
+    mri_make_uchar
+    
+    Tool to adjust intensity of brain MRI images using a Talairach
+    transformation.
     
     Author: FreeSurfer Developers
     
@@ -193,10 +175,12 @@ def mri_make_uchar_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriMakeUcharOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_MAKE_UCHAR_METADATA)
     params = execution.params(params)
     cargs = mri_make_uchar_cargs(params, execution)
     ret = mri_make_uchar_outputs(params, execution)
@@ -208,15 +192,18 @@ def mri_make_uchar(
     input_volume: InputPathType,
     talairach_xform: InputPathType,
     output_volume: str,
-    first_percentile: float | None = 0.01,
-    wm_percentile: float | None = 0.9,
-    max_radius: float | None = 50,
+    first_percentile: float | None = None,
+    wm_percentile: float | None = None,
+    max_radius: float | None = None,
     cumulative_histo: str | None = None,
     vradvol: str | None = None,
     runner: Runner | None = None,
 ) -> MriMakeUcharOutputs:
     """
-    Tool to adjust intensity of brain MRI images using a Talairach transformation.
+    mri_make_uchar
+    
+    Tool to adjust intensity of brain MRI images using a Talairach
+    transformation.
     
     Author: FreeSurfer Developers
     
@@ -237,8 +224,6 @@ def mri_make_uchar(
     Returns:
         NamedTuple of outputs (described in `MriMakeUcharOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_MAKE_UCHAR_METADATA)
     params = mri_make_uchar_params(
         input_volume=input_volume,
         talairach_xform=talairach_xform,
@@ -249,13 +234,13 @@ def mri_make_uchar(
         cumulative_histo=cumulative_histo,
         vradvol=vradvol,
     )
-    return mri_make_uchar_execute(params, execution)
+    return mri_make_uchar_execute(params, runner)
 
 
 __all__ = [
     "MRI_MAKE_UCHAR_METADATA",
     "MriMakeUcharOutputs",
-    "MriMakeUcharParameters",
     "mri_make_uchar",
+    "mri_make_uchar_execute",
     "mri_make_uchar_params",
 ]

niwrap_freesurfer/freesurfer/mri_map_cpdat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_MAP_CPDAT_METADATA = Metadata(
-    id="3145524ba5c9130823389616d1a5740a150f0c94.boutiques",
+    id="e068d6939bcd3d49ba62b977d41106025ca19c99.boutiques",
     name="mri_map_cpdat",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRI_MAP_CPDAT_METADATA = Metadata(
 
 
 MriMapCpdatParameters = typing.TypedDict('MriMapCpdatParameters', {
-    "__STYXTYPE__": typing.Literal["mri_map_cpdat"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_map_cpdat"]],
+    "input_file": InputPathType,
+    "output_file": str,
+    "lta_file": typing.NotRequired[InputPathType | None],
+    "to_mni305": typing.NotRequired[str | None],
+    "from_mni305": typing.NotRequired[str | None],
+    "subject_list_file": typing.NotRequired[InputPathType | None],
+})
+MriMapCpdatParametersTagged = typing.TypedDict('MriMapCpdatParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_map_cpdat"],
     "input_file": InputPathType,
     "output_file": str,
     "lta_file": typing.NotRequired[InputPathType | None],
@@ -22,43 +31,11 @@ MriMapCpdatParameters = typing.TypedDict('MriMapCpdatParameters', {
     "from_mni305": typing.NotRequired[str | None],
     "subject_list_file": typing.NotRequired[InputPathType | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_map_cpdat": mri_map_cpdat_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_map_cpdat": mri_map_cpdat_outputs,
-    }.get(t)
 
 
 class MriMapCpdatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_map_cpdat(...)`.
+    Output object returned when calling `MriMapCpdatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def mri_map_cpdat_params(
     to_mni305: str | None = None,
     from_mni305: str | None = None,
     subject_list_file: InputPathType | None = None,
-) -> MriMapCpdatParameters:
+) -> MriMapCpdatParametersTagged:
     """
     Build parameters.
     
@@ -89,7 +66,7 @@ def mri_map_cpdat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_map_cpdat",
+        "@type": "freesurfer/mri_map_cpdat",
         "input_file": input_file,
         "output_file": output_file,
     }
@@ -121,31 +98,31 @@ def mri_map_cpdat_cargs(
     cargs.append("mri_map_cpdat")
     cargs.extend([
         "-in",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "-out",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
-    if params.get("lta_file") is not None:
+    if params.get("lta_file", None) is not None:
         cargs.extend([
             "-lta",
-            execution.input_file(params.get("lta_file"))
+            execution.input_file(params.get("lta_file", None))
         ])
-    if params.get("to_mni305") is not None:
+    if params.get("to_mni305", None) is not None:
         cargs.extend([
             "-tomni305",
-            params.get("to_mni305")
+            params.get("to_mni305", None)
         ])
-    if params.get("from_mni305") is not None:
+    if params.get("from_mni305", None) is not None:
         cargs.extend([
             "-frommni305",
-            params.get("from_mni305")
+            params.get("from_mni305", None)
         ])
-    if params.get("subject_list_file") is not None:
+    if params.get("subject_list_file", None) is not None:
         cargs.extend([
             "-slf",
-            execution.input_file(params.get("subject_list_file"))
+            execution.input_file(params.get("subject_list_file", None))
         ])
     return cargs
 
@@ -165,16 +142,18 @@ def mri_map_cpdat_outputs(
     """
     ret = MriMapCpdatOutputs(
         root=execution.output_file("."),
-        output_ctrl_file=execution.output_file(params.get("output_file")),
+        output_ctrl_file=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def mri_map_cpdat_execute(
     params: MriMapCpdatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriMapCpdatOutputs:
     """
+    mri_map_cpdat
+    
     Maps a control.dat file to a different space using an LTA.
     
     Author: FreeSurfer Developers
@@ -183,10 +162,12 @@ def mri_map_cpdat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriMapCpdatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_MAP_CPDAT_METADATA)
     params = execution.params(params)
     cargs = mri_map_cpdat_cargs(params, execution)
     ret = mri_map_cpdat_outputs(params, execution)
@@ -204,6 +185,8 @@ def mri_map_cpdat(
     runner: Runner | None = None,
 ) -> MriMapCpdatOutputs:
     """
+    mri_map_cpdat
+    
     Maps a control.dat file to a different space using an LTA.
     
     Author: FreeSurfer Developers
@@ -222,8 +205,6 @@ def mri_map_cpdat(
     Returns:
         NamedTuple of outputs (described in `MriMapCpdatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_MAP_CPDAT_METADATA)
     params = mri_map_cpdat_params(
         input_file=input_file,
         output_file=output_file,
@@ -232,13 +213,13 @@ def mri_map_cpdat(
         from_mni305=from_mni305,
         subject_list_file=subject_list_file,
     )
-    return mri_map_cpdat_execute(params, execution)
+    return mri_map_cpdat_execute(params, runner)
 
 
 __all__ = [
     "MRI_MAP_CPDAT_METADATA",
     "MriMapCpdatOutputs",
-    "MriMapCpdatParameters",
     "mri_map_cpdat",
+    "mri_map_cpdat_execute",
     "mri_map_cpdat_params",
 ]

niwrap_freesurfer/freesurfer/mri_maps2csd.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_MAPS2CSD_METADATA = Metadata(
-    id="d328ee0b019757e28944558a983176ab01acb919.boutiques",
+    id="46584c91fd775e671e63254b9776d74742ff4a73.boutiques",
     name="mri_maps2csd",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,21 @@ MRI_MAPS2CSD_METADATA = Metadata(
 
 
 MriMaps2csdParameters = typing.TypedDict('MriMaps2csdParameters', {
-    "__STYXTYPE__": typing.Literal["mri_maps2csd"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_maps2csd"]],
+    "input_files": list[str],
+    "csd_file": typing.NotRequired[str | None],
+    "pdf_file": typing.NotRequired[str | None],
+    "subject_hemi_surf": typing.NotRequired[str | None],
+    "thresh": typing.NotRequired[float | None],
+    "sign": typing.NotRequired[str | None],
+    "csd_apply_file": typing.NotRequired[str | None],
+    "apply_out": typing.NotRequired[str | None],
+    "subjects_dir": typing.NotRequired[str | None],
+    "debug": bool,
+    "checkopts": bool,
+})
+MriMaps2csdParametersTagged = typing.TypedDict('MriMaps2csdParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_maps2csd"],
     "input_files": list[str],
     "csd_file": typing.NotRequired[str | None],
     "pdf_file": typing.NotRequired[str | None],
@@ -27,42 +41,11 @@ MriMaps2csdParameters = typing.TypedDict('MriMaps2csdParameters', {
     "debug": bool,
     "checkopts": 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_maps2csd": mri_maps2csd_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 MriMaps2csdOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_maps2csd(...)`.
+    Output object returned when calling `MriMaps2csdParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -80,7 +63,7 @@ def mri_maps2csd_params(
     subjects_dir: str | None = None,
     debug: bool = False,
     checkopts: bool = False,
-) -> MriMaps2csdParameters:
+) -> MriMaps2csdParametersTagged:
     """
     Build parameters.
     
@@ -101,7 +84,7 @@ def mri_maps2csd_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_maps2csd",
+        "@type": "freesurfer/mri_maps2csd",
         "input_files": input_files,
         "debug": debug,
         "checkopts": checkopts,
@@ -142,48 +125,48 @@ def mri_maps2csd_cargs(
     cargs.append("mri_maps2csd")
     cargs.extend([
         "--i",
-        *params.get("input_files")
+        *params.get("input_files", None)
     ])
-    if params.get("csd_file") is not None:
+    if params.get("csd_file", None) is not None:
         cargs.extend([
             "--csd",
-            params.get("csd_file")
+            params.get("csd_file", None)
         ])
-    if params.get("pdf_file") is not None:
+    if params.get("pdf_file", None) is not None:
         cargs.extend([
             "--pdf",
-            params.get("pdf_file")
+            params.get("pdf_file", None)
         ])
-    if params.get("subject_hemi_surf") is not None:
+    if params.get("subject_hemi_surf", None) is not None:
         cargs.extend([
             "--s",
-            params.get("subject_hemi_surf")
+            params.get("subject_hemi_surf", None)
         ])
-    if params.get("thresh") is not None:
+    if params.get("thresh", None) is not None:
         cargs.extend([
             "--thresh",
-            str(params.get("thresh"))
+            str(params.get("thresh", None))
         ])
-    if params.get("sign") is not None:
+    if params.get("sign", None) is not None:
         cargs.extend([
             "--sign",
-            params.get("sign")
+            params.get("sign", None)
         ])
-    if params.get("csd_apply_file") is not None:
+    if params.get("csd_apply_file", None) is not None:
         cargs.extend([
             "--csd-apply",
-            params.get("csd_apply_file")
+            params.get("csd_apply_file", None)
         ])
-    if params.get("apply_out") is not None:
-        cargs.append(params.get("apply_out"))
-    if params.get("subjects_dir") is not None:
+    if params.get("apply_out", None) is not None:
+        cargs.append(params.get("apply_out", None))
+    if params.get("subjects_dir", None) is not None:
         cargs.extend([
             "--sd",
-            params.get("subjects_dir")
+            params.get("subjects_dir", None)
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("checkopts"):
+    if params.get("checkopts", False):
         cargs.append("--checkopts")
     return cargs
 
@@ -209,9 +192,11 @@ def mri_maps2csd_outputs(
 
 def mri_maps2csd_execute(
     params: MriMaps2csdParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriMaps2csdOutputs:
     """
+    mri_maps2csd
+    
     Tool to create CSD files and PDFs from input maps and apply them.
     
     Author: FreeSurfer Developers
@@ -220,10 +205,12 @@ def mri_maps2csd_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriMaps2csdOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_MAPS2CSD_METADATA)
     params = execution.params(params)
     cargs = mri_maps2csd_cargs(params, execution)
     ret = mri_maps2csd_outputs(params, execution)
@@ -246,6 +233,8 @@ def mri_maps2csd(
     runner: Runner | None = None,
 ) -> MriMaps2csdOutputs:
     """
+    mri_maps2csd
+    
     Tool to create CSD files and PDFs from input maps and apply them.
     
     Author: FreeSurfer Developers
@@ -269,8 +258,6 @@ def mri_maps2csd(
     Returns:
         NamedTuple of outputs (described in `MriMaps2csdOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_MAPS2CSD_METADATA)
     params = mri_maps2csd_params(
         input_files=input_files,
         csd_file=csd_file,
@@ -284,13 +271,13 @@ def mri_maps2csd(
         debug=debug,
         checkopts=checkopts,
     )
-    return mri_maps2csd_execute(params, execution)
+    return mri_maps2csd_execute(params, runner)
 
 
 __all__ = [
     "MRI_MAPS2CSD_METADATA",
     "MriMaps2csdOutputs",
-    "MriMaps2csdParameters",
     "mri_maps2csd",
+    "mri_maps2csd_execute",
     "mri_maps2csd_params",
 ]