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

niwrap_freesurfer/freesurfer/gdcmconv_fs.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 GDCMCONV_FS_METADATA = Metadata(
-    id="33b8dc164d4657e5b24c4c1c814e2af7b9be58de.boutiques",
+    id="4c87edca5ec76949a0836b632419b5e22128e9fd.boutiques",
     name="gdcmconv.fs",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,50 @@ GDCMCONV_FS_METADATA = Metadata(
 
 
 GdcmconvFsParameters = typing.TypedDict('GdcmconvFsParameters', {
-    "__STYXTYPE__": typing.Literal["gdcmconv.fs"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/gdcmconv.fs"]],
+    "input_file": InputPathType,
+    "output_file": str,
+    "explicit_flag": bool,
+    "implicit_flag": bool,
+    "use_dict_flag": bool,
+    "with_private_dict_flag": bool,
+    "check_meta_flag": bool,
+    "root_uid": typing.NotRequired[str | None],
+    "remove_gl_flag": bool,
+    "remove_private_tags_flag": bool,
+    "remove_retired_flag": bool,
+    "apply_lut_flag": bool,
+    "photometric_interpretation": typing.NotRequired[str | None],
+    "raw_flag": bool,
+    "deflated_flag": bool,
+    "jpeg_flag": bool,
+    "j2k_flag": bool,
+    "jpegls_flag": bool,
+    "rle_flag": bool,
+    "force_flag": bool,
+    "generate_icon_flag": bool,
+    "icon_minmax": typing.NotRequired[list[float] | None],
+    "icon_auto_minmax_flag": bool,
+    "compress_icon_flag": bool,
+    "planar_configuration": typing.NotRequired[str | None],
+    "lossy_flag": bool,
+    "split": typing.NotRequired[float | None],
+    "verbose_flag": bool,
+    "warning_flag": bool,
+    "debug_flag": bool,
+    "error_flag": bool,
+    "quiet_flag": bool,
+    "jpeg_quality": typing.NotRequired[float | None],
+    "lossy_error": typing.NotRequired[int | None],
+    "rate": typing.NotRequired[float | None],
+    "j2k_quality": typing.NotRequired[float | None],
+    "tile": typing.NotRequired[list[float] | None],
+    "number_resolution": typing.NotRequired[float | None],
+    "irreversible_flag": bool,
+    "ignore_errors_flag": bool,
+})
+GdcmconvFsParametersTagged = typing.TypedDict('GdcmconvFsParametersTagged', {
+    "@type": typing.Literal["freesurfer/gdcmconv.fs"],
     "input_file": InputPathType,
     "output_file": str,
     "explicit_flag": bool,
@@ -56,42 +99,11 @@ GdcmconvFsParameters = typing.TypedDict('GdcmconvFsParameters', {
     "irreversible_flag": bool,
     "ignore_errors_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 {
-        "gdcmconv.fs": gdcmconv_fs_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 GdcmconvFsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `gdcmconv_fs(...)`.
+    Output object returned when calling `GdcmconvFsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -138,7 +150,7 @@ def gdcmconv_fs_params(
     number_resolution: float | None = None,
     irreversible_flag: bool = False,
     ignore_errors_flag: bool = False,
-) -> GdcmconvFsParameters:
+) -> GdcmconvFsParametersTagged:
     """
     Build parameters.
     
@@ -191,7 +203,7 @@ def gdcmconv_fs_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "gdcmconv.fs",
+        "@type": "freesurfer/gdcmconv.fs",
         "input_file": input_file,
         "output_file": output_file,
         "explicit_flag": explicit_flag,
@@ -262,116 +274,116 @@ def gdcmconv_fs_cargs(
     """
     cargs = []
     cargs.append("gdcmconv.fs")
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(params.get("output_file"))
-    if params.get("explicit_flag"):
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    cargs.append(params.get("output_file", None))
+    if params.get("explicit_flag", False):
         cargs.append("-X")
-    if params.get("implicit_flag"):
+    if params.get("implicit_flag", False):
         cargs.append("-M")
-    if params.get("use_dict_flag"):
+    if params.get("use_dict_flag", False):
         cargs.append("-U")
-    if params.get("with_private_dict_flag"):
+    if params.get("with_private_dict_flag", False):
         cargs.append("--with-private-dict")
-    if params.get("check_meta_flag"):
+    if params.get("check_meta_flag", False):
         cargs.append("-C")
-    if params.get("root_uid") is not None:
+    if params.get("root_uid", None) is not None:
         cargs.extend([
             "--root-uid",
-            params.get("root_uid")
+            params.get("root_uid", None)
         ])
-    if params.get("remove_gl_flag"):
+    if params.get("remove_gl_flag", False):
         cargs.append("--remove-gl")
-    if params.get("remove_private_tags_flag"):
+    if params.get("remove_private_tags_flag", False):
         cargs.append("--remove-private-tags")
-    if params.get("remove_retired_flag"):
+    if params.get("remove_retired_flag", False):
         cargs.append("--remove-retired")
-    if params.get("apply_lut_flag"):
+    if params.get("apply_lut_flag", False):
         cargs.append("-l")
-    if params.get("photometric_interpretation") is not None:
+    if params.get("photometric_interpretation", None) is not None:
         cargs.extend([
             "-P",
-            params.get("photometric_interpretation")
+            params.get("photometric_interpretation", None)
         ])
-    if params.get("raw_flag"):
+    if params.get("raw_flag", False):
         cargs.append("-w")
-    if params.get("deflated_flag"):
+    if params.get("deflated_flag", False):
         cargs.append("-d")
-    if params.get("jpeg_flag"):
+    if params.get("jpeg_flag", False):
         cargs.append("-J")
-    if params.get("j2k_flag"):
+    if params.get("j2k_flag", False):
         cargs.append("-K")
-    if params.get("jpegls_flag"):
+    if params.get("jpegls_flag", False):
         cargs.append("-L")
-    if params.get("rle_flag"):
+    if params.get("rle_flag", False):
         cargs.append("-R")
-    if params.get("force_flag"):
+    if params.get("force_flag", False):
         cargs.append("-F")
-    if params.get("generate_icon_flag"):
+    if params.get("generate_icon_flag", False):
         cargs.append("--generate-icon")
-    if params.get("icon_minmax") is not None:
+    if params.get("icon_minmax", None) is not None:
         cargs.extend([
             "--icon-minmax",
-            *map(str, params.get("icon_minmax"))
+            *map(str, params.get("icon_minmax", None))
         ])
-    if params.get("icon_auto_minmax_flag"):
+    if params.get("icon_auto_minmax_flag", False):
         cargs.append("--icon-auto-minmax")
-    if params.get("compress_icon_flag"):
+    if params.get("compress_icon_flag", False):
         cargs.append("--compress-icon")
-    if params.get("planar_configuration") is not None:
+    if params.get("planar_configuration", None) is not None:
         cargs.extend([
             "--planar-configuration",
-            params.get("planar_configuration")
+            params.get("planar_configuration", None)
         ])
-    if params.get("lossy_flag"):
+    if params.get("lossy_flag", False):
         cargs.append("-Y")
-    if params.get("split") is not None:
+    if params.get("split", None) is not None:
         cargs.extend([
             "-S",
-            str(params.get("split"))
+            str(params.get("split", None))
         ])
-    if params.get("verbose_flag"):
+    if params.get("verbose_flag", False):
         cargs.append("-V")
-    if params.get("warning_flag"):
+    if params.get("warning_flag", False):
         cargs.append("-W")
-    if params.get("debug_flag"):
+    if params.get("debug_flag", False):
         cargs.append("-D")
-    if params.get("error_flag"):
+    if params.get("error_flag", False):
         cargs.append("-E")
-    if params.get("quiet_flag"):
+    if params.get("quiet_flag", False):
         cargs.append("--quiet")
-    if params.get("jpeg_quality") is not None:
+    if params.get("jpeg_quality", None) is not None:
         cargs.extend([
             "-q",
-            str(params.get("jpeg_quality"))
+            str(params.get("jpeg_quality", None))
         ])
-    if params.get("lossy_error") is not None:
+    if params.get("lossy_error", None) is not None:
         cargs.extend([
             "-e",
-            str(params.get("lossy_error"))
+            str(params.get("lossy_error", None))
         ])
-    if params.get("rate") is not None:
+    if params.get("rate", None) is not None:
         cargs.extend([
             "-r",
-            str(params.get("rate"))
+            str(params.get("rate", None))
         ])
-    if params.get("j2k_quality") is not None:
+    if params.get("j2k_quality", None) is not None:
         cargs.extend([
             "-q",
-            str(params.get("j2k_quality"))
+            str(params.get("j2k_quality", None))
         ])
-    if params.get("tile") is not None:
+    if params.get("tile", None) is not None:
         cargs.extend([
             "-t",
-            *map(str, params.get("tile"))
+            *map(str, params.get("tile", None))
         ])
-    if params.get("number_resolution") is not None:
+    if params.get("number_resolution", None) is not None:
         cargs.extend([
             "-n",
-            str(params.get("number_resolution"))
+            str(params.get("number_resolution", None))
         ])
-    if params.get("irreversible_flag"):
+    if params.get("irreversible_flag", False):
         cargs.append("--irreversible")
-    if params.get("ignore_errors_flag"):
+    if params.get("ignore_errors_flag", False):
         cargs.append("-I")
     return cargs
 
@@ -397,9 +409,11 @@ def gdcmconv_fs_outputs(
 
 def gdcmconv_fs_execute(
     params: GdcmconvFsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> GdcmconvFsOutputs:
     """
+    gdcmconv.fs
+    
     Convert a DICOM file into another DICOM file.
     
     Author: FreeSurfer Developers
@@ -408,10 +422,12 @@ def gdcmconv_fs_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `GdcmconvFsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(GDCMCONV_FS_METADATA)
     params = execution.params(params)
     cargs = gdcmconv_fs_cargs(params, execution)
     ret = gdcmconv_fs_outputs(params, execution)
@@ -463,6 +479,8 @@ def gdcmconv_fs(
     runner: Runner | None = None,
 ) -> GdcmconvFsOutputs:
     """
+    gdcmconv.fs
+    
     Convert a DICOM file into another DICOM file.
     
     Author: FreeSurfer Developers
@@ -518,8 +536,6 @@ def gdcmconv_fs(
     Returns:
         NamedTuple of outputs (described in `GdcmconvFsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(GDCMCONV_FS_METADATA)
     params = gdcmconv_fs_params(
         input_file=input_file,
         output_file=output_file,
@@ -562,13 +578,13 @@ def gdcmconv_fs(
         irreversible_flag=irreversible_flag,
         ignore_errors_flag=ignore_errors_flag,
     )
-    return gdcmconv_fs_execute(params, execution)
+    return gdcmconv_fs_execute(params, runner)
 
 
 __all__ = [
     "GDCMCONV_FS_METADATA",
     "GdcmconvFsOutputs",
-    "GdcmconvFsParameters",
     "gdcmconv_fs",
+    "gdcmconv_fs_execute",
     "gdcmconv_fs_params",
 ]

niwrap_freesurfer/freesurfer/gems_compute_atlas_probs.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 GEMS_COMPUTE_ATLAS_PROBS_METADATA = Metadata(
-    id="bb2ad12b36b45df1472550e075ee393432a9c45e.boutiques",
+    id="515f7d1aaa2b2e2bd3ac13b072dede9d860ff7a0.boutiques",
     name="gems_compute_atlas_probs",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,26 @@ GEMS_COMPUTE_ATLAS_PROBS_METADATA = Metadata(
 
 
 GemsComputeAtlasProbsParameters = typing.TypedDict('GemsComputeAtlasProbsParameters', {
-    "__STYXTYPE__": typing.Literal["gems_compute_atlas_probs"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/gems_compute_atlas_probs"]],
+    "subjects_dir": str,
+    "mesh_collections": list[str],
+    "out_dir": str,
+    "segmentations_dir": typing.NotRequired[str | None],
+    "gt_from_fs": bool,
+    "segmentation_name": typing.NotRequired[str | None],
+    "multi_structure": bool,
+    "labels": typing.NotRequired[list[str] | None],
+    "from_samseg": bool,
+    "em_iterations": typing.NotRequired[float | None],
+    "show_figs": bool,
+    "save_figs": bool,
+    "save_average_figs": bool,
+    "subjects_file": typing.NotRequired[str | None],
+    "labels_file": typing.NotRequired[str | None],
+    "samseg_subdir": typing.NotRequired[str | None],
+})
+GemsComputeAtlasProbsParametersTagged = typing.TypedDict('GemsComputeAtlasProbsParametersTagged', {
+    "@type": typing.Literal["freesurfer/gems_compute_atlas_probs"],
     "subjects_dir": str,
     "mesh_collections": list[str],
     "out_dir": str,
@@ -32,42 +51,11 @@ GemsComputeAtlasProbsParameters = typing.TypedDict('GemsComputeAtlasProbsParamet
     "labels_file": typing.NotRequired[str | None],
     "samseg_subdir": 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 {
-        "gems_compute_atlas_probs": gems_compute_atlas_probs_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 GemsComputeAtlasProbsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `gems_compute_atlas_probs(...)`.
+    Output object returned when calling `GemsComputeAtlasProbsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -90,7 +78,7 @@ def gems_compute_atlas_probs_params(
     subjects_file: str | None = None,
     labels_file: str | None = None,
     samseg_subdir: str | None = None,
-) -> GemsComputeAtlasProbsParameters:
+) -> GemsComputeAtlasProbsParametersTagged:
     """
     Build parameters.
     
@@ -117,7 +105,7 @@ def gems_compute_atlas_probs_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "gems_compute_atlas_probs",
+        "@type": "freesurfer/gems_compute_atlas_probs",
         "subjects_dir": subjects_dir,
         "mesh_collections": mesh_collections,
         "out_dir": out_dir,
@@ -162,62 +150,62 @@ def gems_compute_atlas_probs_cargs(
     cargs.append("gems_compute_atlas_probs")
     cargs.extend([
         "--subjects-dir",
-        params.get("subjects_dir")
+        params.get("subjects_dir", None)
     ])
     cargs.extend([
         "--mesh-collections",
-        *params.get("mesh_collections")
+        *params.get("mesh_collections", None)
     ])
     cargs.extend([
         "--out-dir",
-        params.get("out_dir")
+        params.get("out_dir", None)
     ])
-    if params.get("segmentations_dir") is not None:
+    if params.get("segmentations_dir", None) is not None:
         cargs.extend([
             "--segmentations-dir",
-            params.get("segmentations_dir")
+            params.get("segmentations_dir", None)
         ])
-    if params.get("gt_from_fs"):
+    if params.get("gt_from_fs", False):
         cargs.append("--gt-from-FS")
-    if params.get("segmentation_name") is not None:
+    if params.get("segmentation_name", None) is not None:
         cargs.extend([
             "--segmentation-name",
-            params.get("segmentation_name")
+            params.get("segmentation_name", None)
         ])
-    if params.get("multi_structure"):
+    if params.get("multi_structure", False):
         cargs.append("--multi-structure")
-    if params.get("labels") is not None:
+    if params.get("labels", None) is not None:
         cargs.extend([
             "--labels",
-            *params.get("labels")
+            *params.get("labels", None)
         ])
-    if params.get("from_samseg"):
+    if params.get("from_samseg", False):
         cargs.append("--from-samseg")
-    if params.get("em_iterations") is not None:
+    if params.get("em_iterations", None) is not None:
         cargs.extend([
             "--EM-iterations",
-            str(params.get("em_iterations"))
+            str(params.get("em_iterations", None))
         ])
-    if params.get("show_figs"):
+    if params.get("show_figs", False):
         cargs.append("--show-figs")
-    if params.get("save_figs"):
+    if params.get("save_figs", False):
         cargs.append("--save-figs")
-    if params.get("save_average_figs"):
+    if params.get("save_average_figs", False):
         cargs.append("--save-average-figs")
-    if params.get("subjects_file") is not None:
+    if params.get("subjects_file", None) is not None:
         cargs.extend([
             "--subjects_file",
-            params.get("subjects_file")
+            params.get("subjects_file", None)
         ])
-    if params.get("labels_file") is not None:
+    if params.get("labels_file", None) is not None:
         cargs.extend([
             "--labels_file",
-            params.get("labels_file")
+            params.get("labels_file", None)
         ])
-    if params.get("samseg_subdir") is not None:
+    if params.get("samseg_subdir", None) is not None:
         cargs.extend([
             "--samseg-subdir",
-            params.get("samseg_subdir")
+            params.get("samseg_subdir", None)
         ])
     return cargs
 
@@ -243,9 +231,11 @@ def gems_compute_atlas_probs_outputs(
 
 def gems_compute_atlas_probs_execute(
     params: GemsComputeAtlasProbsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> GemsComputeAtlasProbsOutputs:
     """
+    gems_compute_atlas_probs
+    
     Tool to compute atlas probabilities using SAMSEG results.
     
     Author: FreeSurfer Developers
@@ -254,10 +244,12 @@ def gems_compute_atlas_probs_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `GemsComputeAtlasProbsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(GEMS_COMPUTE_ATLAS_PROBS_METADATA)
     params = execution.params(params)
     cargs = gems_compute_atlas_probs_cargs(params, execution)
     ret = gems_compute_atlas_probs_outputs(params, execution)
@@ -285,6 +277,8 @@ def gems_compute_atlas_probs(
     runner: Runner | None = None,
 ) -> GemsComputeAtlasProbsOutputs:
     """
+    gems_compute_atlas_probs
+    
     Tool to compute atlas probabilities using SAMSEG results.
     
     Author: FreeSurfer Developers
@@ -314,8 +308,6 @@ def gems_compute_atlas_probs(
     Returns:
         NamedTuple of outputs (described in `GemsComputeAtlasProbsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(GEMS_COMPUTE_ATLAS_PROBS_METADATA)
     params = gems_compute_atlas_probs_params(
         subjects_dir=subjects_dir,
         mesh_collections=mesh_collections,
@@ -334,13 +326,13 @@ def gems_compute_atlas_probs(
         labels_file=labels_file,
         samseg_subdir=samseg_subdir,
     )
-    return gems_compute_atlas_probs_execute(params, execution)
+    return gems_compute_atlas_probs_execute(params, runner)
 
 
 __all__ = [
     "GEMS_COMPUTE_ATLAS_PROBS_METADATA",
     "GemsComputeAtlasProbsOutputs",
-    "GemsComputeAtlasProbsParameters",
     "gems_compute_atlas_probs",
+    "gems_compute_atlas_probs_execute",
     "gems_compute_atlas_probs_params",
 ]