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

niwrap_afni/afni/fat_proc_connec_vis.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FAT_PROC_CONNEC_VIS_METADATA = Metadata(
-    id="c7edba572e19b781cc1e3adc9d9172250d96c76f.boutiques",
+    id="a58923b78acab8becd209cc6970f62f6b79c8032.boutiques",
     name="fat_proc_connec_vis",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,21 @@ FAT_PROC_CONNEC_VIS_METADATA = Metadata(
 
 
 FatProcConnecVisParameters = typing.TypedDict('FatProcConnecVisParameters', {
-    "__STYXTYPE__": typing.Literal["fat_proc_connec_vis"],
+    "@type": typing.NotRequired[typing.Literal["afni/fat_proc_connec_vis"]],
+    "in_rois": str,
+    "prefix": str,
+    "prefix_file": typing.NotRequired[str | None],
+    "tsmoo_kpb": typing.NotRequired[float | None],
+    "tsmoo_niter": typing.NotRequired[float | None],
+    "iso_opt": typing.NotRequired[str | None],
+    "trackid_no_or": bool,
+    "output_tcat": bool,
+    "output_tstat": bool,
+    "wdir": typing.NotRequired[str | None],
+    "no_clean": bool,
+})
+FatProcConnecVisParametersTagged = typing.TypedDict('FatProcConnecVisParametersTagged', {
+    "@type": typing.Literal["afni/fat_proc_connec_vis"],
     "in_rois": str,
     "prefix": str,
     "prefix_file": typing.NotRequired[str | None],
@@ -27,43 +41,11 @@ FatProcConnecVisParameters = typing.TypedDict('FatProcConnecVisParameters', {
     "wdir": typing.NotRequired[str | None],
     "no_clean": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fat_proc_connec_vis": fat_proc_connec_vis_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 {
-        "fat_proc_connec_vis": fat_proc_connec_vis_outputs,
-    }.get(t)
 
 
 class FatProcConnecVisOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fat_proc_connec_vis(...)`.
+    Output object returned when calling `FatProcConnecVisParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -88,7 +70,7 @@ def fat_proc_connec_vis_params(
     output_tstat: bool = False,
     wdir: str | None = None,
     no_clean: bool = False,
-) -> FatProcConnecVisParameters:
+) -> FatProcConnecVisParametersTagged:
     """
     Build parameters.
     
@@ -132,7 +114,7 @@ def fat_proc_connec_vis_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fat_proc_connec_vis",
+        "@type": "afni/fat_proc_connec_vis",
         "in_rois": in_rois,
         "prefix": prefix,
         "trackid_no_or": trackid_no_or,
@@ -168,40 +150,40 @@ def fat_proc_connec_vis_cargs(
     """
     cargs = []
     cargs.append("fat_proc_connec_vis")
-    cargs.append(params.get("in_rois"))
-    cargs.append(params.get("prefix"))
-    if params.get("prefix_file") is not None:
+    cargs.append(params.get("in_rois", None))
+    cargs.append(params.get("prefix", None))
+    if params.get("prefix_file", None) is not None:
         cargs.extend([
             "-prefix_file",
-            params.get("prefix_file")
+            params.get("prefix_file", None)
         ])
-    if params.get("tsmoo_kpb") is not None:
+    if params.get("tsmoo_kpb", None) is not None:
         cargs.extend([
             "-tsmoo_kpb",
-            str(params.get("tsmoo_kpb"))
+            str(params.get("tsmoo_kpb", None))
         ])
-    if params.get("tsmoo_niter") is not None:
+    if params.get("tsmoo_niter", None) is not None:
         cargs.extend([
             "-tsmoo_niter",
-            str(params.get("tsmoo_niter"))
+            str(params.get("tsmoo_niter", None))
         ])
-    if params.get("iso_opt") is not None:
+    if params.get("iso_opt", None) is not None:
         cargs.extend([
             "-iso_opt",
-            params.get("iso_opt")
+            params.get("iso_opt", None)
         ])
-    if params.get("trackid_no_or"):
+    if params.get("trackid_no_or", False):
         cargs.append("-trackid_no_or")
-    if params.get("output_tcat"):
+    if params.get("output_tcat", False):
         cargs.append("-output_tcat")
-    if params.get("output_tstat"):
+    if params.get("output_tstat", False):
         cargs.append("-output_tstat")
-    if params.get("wdir") is not None:
+    if params.get("wdir", None) is not None:
         cargs.extend([
             "-wdir",
-            params.get("wdir")
+            params.get("wdir", None)
         ])
-    if params.get("no_clean"):
+    if params.get("no_clean", False):
         cargs.append("-no_clean")
     return cargs
 
@@ -221,22 +203,24 @@ def fat_proc_connec_vis_outputs(
     """
     ret = FatProcConnecVisOutputs(
         root=execution.output_file("."),
-        cmd_txt=execution.output_file(params.get("prefix") + "_cmd.txt"),
-        tcat_file=execution.output_file(params.get("prefix") + "_tcat.nii.gz"),
-        tstat_file=execution.output_file(params.get("prefix") + "_tstat.nii.gz"),
+        cmd_txt=execution.output_file(params.get("prefix", None) + "_cmd.txt"),
+        tcat_file=execution.output_file(params.get("prefix", None) + "_tcat.nii.gz"),
+        tstat_file=execution.output_file(params.get("prefix", None) + "_tstat.nii.gz"),
     )
     return ret
 
 
 def fat_proc_connec_vis_execute(
     params: FatProcConnecVisParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FatProcConnecVisOutputs:
     """
-    This program is for visualizing the volumetric output of tracking, mainly for
-    the '-dump_rois ...' from 3dTrackID. It creates surface-ized views of the
-    separate white matter connection maps (WMCs) which can be viewed simultaneously
-    in 3D with SUMA.
+    fat_proc_connec_vis
+    
+    This program is for visualizing the volumetric output of tracking, mainly
+    for the '-dump_rois ...' from 3dTrackID. It creates surface-ized views of
+    the separate white matter connection maps (WMCs) which can be viewed
+    simultaneously in 3D with SUMA.
     
     Author: AFNI Developers
     
@@ -244,10 +228,12 @@ def fat_proc_connec_vis_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FatProcConnecVisOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_PROC_CONNEC_VIS_METADATA)
     params = execution.params(params)
     cargs = fat_proc_connec_vis_cargs(params, execution)
     ret = fat_proc_connec_vis_outputs(params, execution)
@@ -270,10 +256,12 @@ def fat_proc_connec_vis(
     runner: Runner | None = None,
 ) -> FatProcConnecVisOutputs:
     """
-    This program is for visualizing the volumetric output of tracking, mainly for
-    the '-dump_rois ...' from 3dTrackID. It creates surface-ized views of the
-    separate white matter connection maps (WMCs) which can be viewed simultaneously
-    in 3D with SUMA.
+    fat_proc_connec_vis
+    
+    This program is for visualizing the volumetric output of tracking, mainly
+    for the '-dump_rois ...' from 3dTrackID. It creates surface-ized views of
+    the separate white matter connection maps (WMCs) which can be viewed
+    simultaneously in 3D with SUMA.
     
     Author: AFNI Developers
     
@@ -319,8 +307,6 @@ def fat_proc_connec_vis(
     Returns:
         NamedTuple of outputs (described in `FatProcConnecVisOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FAT_PROC_CONNEC_VIS_METADATA)
     params = fat_proc_connec_vis_params(
         in_rois=in_rois,
         prefix=prefix,
@@ -334,13 +320,13 @@ def fat_proc_connec_vis(
         wdir=wdir,
         no_clean=no_clean,
     )
-    return fat_proc_connec_vis_execute(params, execution)
+    return fat_proc_connec_vis_execute(params, runner)
 
 
 __all__ = [
     "FAT_PROC_CONNEC_VIS_METADATA",
     "FatProcConnecVisOutputs",
-    "FatProcConnecVisParameters",
     "fat_proc_connec_vis",
+    "fat_proc_connec_vis_execute",
     "fat_proc_connec_vis_params",
 ]

niwrap_afni/afni/fat_proc_convert_dcm_anat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FAT_PROC_CONVERT_DCM_ANAT_METADATA = Metadata(
-    id="a80923cdd78e0662fd7a0129b4fa64d202e36c9c.boutiques",
+    id="00ccb72c63c849ac69cc34eadc7fc75e88bc1ced.boutiques",
     name="fat_proc_convert_dcm_anat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,20 @@ FAT_PROC_CONVERT_DCM_ANAT_METADATA = Metadata(
 
 
 FatProcConvertDcmAnatParameters = typing.TypedDict('FatProcConvertDcmAnatParameters', {
-    "__STYXTYPE__": typing.Literal["fat_proc_convert_dcm_anat"],
+    "@type": typing.NotRequired[typing.Literal["afni/fat_proc_convert_dcm_anat"]],
+    "dicom_directory": typing.NotRequired[str | None],
+    "nifti_input": typing.NotRequired[InputPathType | None],
+    "prefix": str,
+    "workdir": typing.NotRequired[str | None],
+    "orient": typing.NotRequired[str | None],
+    "no_clean": bool,
+    "reorig_reorient_off": bool,
+    "qc_prefix": typing.NotRequired[str | None],
+    "no_cmd_out": bool,
+    "no_qc_view": bool,
+})
+FatProcConvertDcmAnatParametersTagged = typing.TypedDict('FatProcConvertDcmAnatParametersTagged', {
+    "@type": typing.Literal["afni/fat_proc_convert_dcm_anat"],
     "dicom_directory": typing.NotRequired[str | None],
     "nifti_input": typing.NotRequired[InputPathType | None],
     "prefix": str,
@@ -26,43 +39,11 @@ FatProcConvertDcmAnatParameters = typing.TypedDict('FatProcConvertDcmAnatParamet
     "no_cmd_out": bool,
     "no_qc_view": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fat_proc_convert_dcm_anat": fat_proc_convert_dcm_anat_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 {
-        "fat_proc_convert_dcm_anat": fat_proc_convert_dcm_anat_outputs,
-    }.get(t)
 
 
 class FatProcConvertDcmAnatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fat_proc_convert_dcm_anat(...)`.
+    Output object returned when calling `FatProcConvertDcmAnatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +62,7 @@ def fat_proc_convert_dcm_anat_params(
     qc_prefix: str | None = None,
     no_cmd_out: bool = False,
     no_qc_view: bool = False,
-) -> FatProcConvertDcmAnatParameters:
+) -> FatProcConvertDcmAnatParametersTagged:
     """
     Build parameters.
     
@@ -108,7 +89,7 @@ def fat_proc_convert_dcm_anat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fat_proc_convert_dcm_anat",
+        "@type": "afni/fat_proc_convert_dcm_anat",
         "prefix": prefix,
         "no_clean": no_clean,
         "reorig_reorient_off": reorig_reorient_off,
@@ -143,42 +124,42 @@ def fat_proc_convert_dcm_anat_cargs(
     """
     cargs = []
     cargs.append("fat_proc_convert_dcm_anat")
-    if params.get("dicom_directory") is not None:
+    if params.get("dicom_directory", None) is not None:
         cargs.extend([
             "-indir",
-            params.get("dicom_directory")
+            params.get("dicom_directory", None)
         ])
-    if params.get("nifti_input") is not None:
+    if params.get("nifti_input", None) is not None:
         cargs.extend([
             "-innii",
-            execution.input_file(params.get("nifti_input"))
+            execution.input_file(params.get("nifti_input", None))
         ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("workdir") is not None:
+    if params.get("workdir", None) is not None:
         cargs.extend([
             "-workdir",
-            params.get("workdir")
+            params.get("workdir", None)
         ])
-    if params.get("orient") is not None:
+    if params.get("orient", None) is not None:
         cargs.extend([
             "-orient",
-            params.get("orient")
+            params.get("orient", None)
         ])
-    if params.get("no_clean"):
+    if params.get("no_clean", False):
         cargs.append("-no_clean")
-    if params.get("reorig_reorient_off"):
+    if params.get("reorig_reorient_off", False):
         cargs.append("-reorig_reorient_off")
-    if params.get("qc_prefix") is not None:
+    if params.get("qc_prefix", None) is not None:
         cargs.extend([
             "-qc_prefix",
-            params.get("qc_prefix")
+            params.get("qc_prefix", None)
         ])
-    if params.get("no_cmd_out"):
+    if params.get("no_cmd_out", False):
         cargs.append("-no_cmd_out")
-    if params.get("no_qc_view"):
+    if params.get("no_qc_view", False):
         cargs.append("-no_qc_view")
     return cargs
 
@@ -198,16 +179,18 @@ def fat_proc_convert_dcm_anat_outputs(
     """
     ret = FatProcConvertDcmAnatOutputs(
         root=execution.output_file("."),
-        output_volume=execution.output_file(params.get("prefix") + ".nii.gz"),
+        output_volume=execution.output_file(params.get("prefix", None) + ".nii.gz"),
     )
     return ret
 
 
 def fat_proc_convert_dcm_anat_execute(
     params: FatProcConvertDcmAnatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FatProcConvertDcmAnatOutputs:
     """
+    fat_proc_convert_dcm_anat
+    
     Converts an anatomical dataset from DICOM files into a volume, specifically
     designed to fit in line with other processing such as DTI analysis.
     
@@ -217,10 +200,12 @@ def fat_proc_convert_dcm_anat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FatProcConvertDcmAnatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_PROC_CONVERT_DCM_ANAT_METADATA)
     params = execution.params(params)
     cargs = fat_proc_convert_dcm_anat_cargs(params, execution)
     ret = fat_proc_convert_dcm_anat_outputs(params, execution)
@@ -242,6 +227,8 @@ def fat_proc_convert_dcm_anat(
     runner: Runner | None = None,
 ) -> FatProcConvertDcmAnatOutputs:
     """
+    fat_proc_convert_dcm_anat
+    
     Converts an anatomical dataset from DICOM files into a volume, specifically
     designed to fit in line with other processing such as DTI analysis.
     
@@ -272,8 +259,6 @@ def fat_proc_convert_dcm_anat(
     Returns:
         NamedTuple of outputs (described in `FatProcConvertDcmAnatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FAT_PROC_CONVERT_DCM_ANAT_METADATA)
     params = fat_proc_convert_dcm_anat_params(
         dicom_directory=dicom_directory,
         nifti_input=nifti_input,
@@ -286,13 +271,13 @@ def fat_proc_convert_dcm_anat(
         no_cmd_out=no_cmd_out,
         no_qc_view=no_qc_view,
     )
-    return fat_proc_convert_dcm_anat_execute(params, execution)
+    return fat_proc_convert_dcm_anat_execute(params, runner)
 
 
 __all__ = [
     "FAT_PROC_CONVERT_DCM_ANAT_METADATA",
     "FatProcConvertDcmAnatOutputs",
-    "FatProcConvertDcmAnatParameters",
     "fat_proc_convert_dcm_anat",
+    "fat_proc_convert_dcm_anat_execute",
     "fat_proc_convert_dcm_anat_params",
 ]