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

niwrap_afni/afni/v_3d_track_id.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TRACK_ID_METADATA = Metadata(
-    id="3f64f0f6b5dc6322ed516320e5dec4b5ffc35c45.boutiques",
+    id="271a6d06fcdd1a0c38a4653204095709b49743ea.boutiques",
     name="3dTrackID",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,54 @@ V_3D_TRACK_ID_METADATA = Metadata(
 
 
 V3dTrackIdParameters = typing.TypedDict('V3dTrackIdParameters', {
-    "__STYXTYPE__": typing.Literal["3dTrackID"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dTrackID"]],
+    "mode": typing.Literal["DET", "MINIP", "PROB"],
+    "netrois": InputPathType,
+    "prefix": str,
+    "dti_in": typing.NotRequired[str | None],
+    "dti_list": typing.NotRequired[InputPathType | None],
+    "dti_extra": typing.NotRequired[str | None],
+    "dti_search_no": bool,
+    "hardi_gfa": typing.NotRequired[InputPathType | None],
+    "hardi_dirs": typing.NotRequired[InputPathType | None],
+    "hardi_pars": typing.NotRequired[str | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "thru_mask": typing.NotRequired[InputPathType | None],
+    "targ_surf_stop": bool,
+    "targ_surf_twixt": bool,
+    "logic": typing.Literal["OR", "AND"],
+    "mini_num": typing.NotRequired[float | None],
+    "uncert": typing.NotRequired[InputPathType | None],
+    "unc_min_fa": typing.NotRequired[float | None],
+    "unc_min_v": typing.NotRequired[float | None],
+    "algopt": typing.NotRequired[InputPathType | None],
+    "alg_thresh_fa": typing.NotRequired[float | None],
+    "alg_thresh_ang": typing.NotRequired[float | None],
+    "alg_thresh_len": typing.NotRequired[float | None],
+    "alg_nseed_x": typing.NotRequired[float | None],
+    "alg_nseed_y": typing.NotRequired[float | None],
+    "alg_nseed_z": typing.NotRequired[float | None],
+    "alg_thresh_frac": typing.NotRequired[float | None],
+    "alg_nseed_vox": typing.NotRequired[float | None],
+    "alg_nmonte": typing.NotRequired[float | None],
+    "extra_tr_par": bool,
+    "uncut_at_rois": bool,
+    "dump_rois": typing.NotRequired[typing.Literal["DUMP", "AFNI", "BOTH", "AFNI_MAP"] | None],
+    "dump_no_labtab": bool,
+    "dump_lab_consec": bool,
+    "posteriori": bool,
+    "rec_orig": bool,
+    "do_trk_out": bool,
+    "trk_opp_orient": bool,
+    "nifti": bool,
+    "no_indipair_out": bool,
+    "write_rois": bool,
+    "write_opts": bool,
+    "pair_out_power": bool,
+    "verb": typing.NotRequired[float | None],
+})
+V3dTrackIdParametersTagged = typing.TypedDict('V3dTrackIdParametersTagged', {
+    "@type": typing.Literal["afni/3dTrackID"],
     "mode": typing.Literal["DET", "MINIP", "PROB"],
     "netrois": InputPathType,
     "prefix": str,
@@ -60,43 +107,11 @@ V3dTrackIdParameters = typing.TypedDict('V3dTrackIdParameters', {
     "pair_out_power": bool,
     "verb": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dTrackID": v_3d_track_id_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 {
-        "3dTrackID": v_3d_track_id_outputs,
-    }.get(t)
 
 
 class V3dTrackIdOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_track_id(...)`.
+    Output object returned when calling `V3dTrackIdParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -165,7 +180,7 @@ def v_3d_track_id_params(
     write_opts: bool = False,
     pair_out_power: bool = False,
     verb: float | None = None,
-) -> V3dTrackIdParameters:
+) -> V3dTrackIdParametersTagged:
     """
     Build parameters.
     
@@ -228,7 +243,7 @@ def v_3d_track_id_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dTrackID",
+        "@type": "afni/3dTrackID",
         "mode": mode,
         "netrois": netrois,
         "prefix": prefix,
@@ -316,90 +331,90 @@ def v_3d_track_id_cargs(
     """
     cargs = []
     cargs.append("3dTrackID")
-    cargs.append(params.get("mode"))
-    cargs.append(execution.input_file(params.get("netrois")))
-    cargs.append(params.get("prefix"))
-    if params.get("dti_in") is not None:
-        cargs.append(params.get("dti_in"))
-    if params.get("dti_list") is not None:
-        cargs.append(execution.input_file(params.get("dti_list")))
-    if params.get("dti_extra") is not None:
-        cargs.append(params.get("dti_extra"))
-    if params.get("dti_search_no"):
+    cargs.append(params.get("mode", None))
+    cargs.append(execution.input_file(params.get("netrois", None)))
+    cargs.append(params.get("prefix", None))
+    if params.get("dti_in", None) is not None:
+        cargs.append(params.get("dti_in", None))
+    if params.get("dti_list", None) is not None:
+        cargs.append(execution.input_file(params.get("dti_list", None)))
+    if params.get("dti_extra", None) is not None:
+        cargs.append(params.get("dti_extra", None))
+    if params.get("dti_search_no", False):
         cargs.append("-dti_search_NO")
-    if params.get("hardi_gfa") is not None:
-        cargs.append(execution.input_file(params.get("hardi_gfa")))
-    if params.get("hardi_dirs") is not None:
-        cargs.append(execution.input_file(params.get("hardi_dirs")))
-    if params.get("hardi_pars") is not None:
-        cargs.append(params.get("hardi_pars"))
-    if params.get("mask") is not None:
-        cargs.append(execution.input_file(params.get("mask")))
-    if params.get("thru_mask") is not None:
-        cargs.append(execution.input_file(params.get("thru_mask")))
-    if params.get("targ_surf_stop"):
+    if params.get("hardi_gfa", None) is not None:
+        cargs.append(execution.input_file(params.get("hardi_gfa", None)))
+    if params.get("hardi_dirs", None) is not None:
+        cargs.append(execution.input_file(params.get("hardi_dirs", None)))
+    if params.get("hardi_pars", None) is not None:
+        cargs.append(params.get("hardi_pars", None))
+    if params.get("mask", None) is not None:
+        cargs.append(execution.input_file(params.get("mask", None)))
+    if params.get("thru_mask", None) is not None:
+        cargs.append(execution.input_file(params.get("thru_mask", None)))
+    if params.get("targ_surf_stop", False):
         cargs.append("-targ_surf_stop")
-    if params.get("targ_surf_twixt"):
+    if params.get("targ_surf_twixt", False):
         cargs.append("-targ_surf_twixt")
-    cargs.append(params.get("logic"))
-    if params.get("mini_num") is not None:
-        cargs.append(str(params.get("mini_num")))
-    if params.get("uncert") is not None:
-        cargs.append(execution.input_file(params.get("uncert")))
-    if params.get("unc_min_fa") is not None:
-        cargs.append(str(params.get("unc_min_fa")))
-    if params.get("unc_min_v") is not None:
-        cargs.append(str(params.get("unc_min_v")))
-    if params.get("algopt") is not None:
-        cargs.append(execution.input_file(params.get("algopt")))
-    if params.get("alg_thresh_fa") is not None:
-        cargs.append(str(params.get("alg_thresh_fa")))
-    if params.get("alg_thresh_ang") is not None:
-        cargs.append(str(params.get("alg_thresh_ang")))
-    if params.get("alg_thresh_len") is not None:
-        cargs.append(str(params.get("alg_thresh_len")))
-    if params.get("alg_nseed_x") is not None:
-        cargs.append(str(params.get("alg_nseed_x")))
-    if params.get("alg_nseed_y") is not None:
-        cargs.append(str(params.get("alg_nseed_y")))
-    if params.get("alg_nseed_z") is not None:
-        cargs.append(str(params.get("alg_nseed_z")))
-    if params.get("alg_thresh_frac") is not None:
-        cargs.append(str(params.get("alg_thresh_frac")))
-    if params.get("alg_nseed_vox") is not None:
-        cargs.append(str(params.get("alg_nseed_vox")))
-    if params.get("alg_nmonte") is not None:
-        cargs.append(str(params.get("alg_nmonte")))
-    if params.get("extra_tr_par"):
+    cargs.append(params.get("logic", None))
+    if params.get("mini_num", None) is not None:
+        cargs.append(str(params.get("mini_num", None)))
+    if params.get("uncert", None) is not None:
+        cargs.append(execution.input_file(params.get("uncert", None)))
+    if params.get("unc_min_fa", None) is not None:
+        cargs.append(str(params.get("unc_min_fa", None)))
+    if params.get("unc_min_v", None) is not None:
+        cargs.append(str(params.get("unc_min_v", None)))
+    if params.get("algopt", None) is not None:
+        cargs.append(execution.input_file(params.get("algopt", None)))
+    if params.get("alg_thresh_fa", None) is not None:
+        cargs.append(str(params.get("alg_thresh_fa", None)))
+    if params.get("alg_thresh_ang", None) is not None:
+        cargs.append(str(params.get("alg_thresh_ang", None)))
+    if params.get("alg_thresh_len", None) is not None:
+        cargs.append(str(params.get("alg_thresh_len", None)))
+    if params.get("alg_nseed_x", None) is not None:
+        cargs.append(str(params.get("alg_nseed_x", None)))
+    if params.get("alg_nseed_y", None) is not None:
+        cargs.append(str(params.get("alg_nseed_y", None)))
+    if params.get("alg_nseed_z", None) is not None:
+        cargs.append(str(params.get("alg_nseed_z", None)))
+    if params.get("alg_thresh_frac", None) is not None:
+        cargs.append(str(params.get("alg_thresh_frac", None)))
+    if params.get("alg_nseed_vox", None) is not None:
+        cargs.append(str(params.get("alg_nseed_vox", None)))
+    if params.get("alg_nmonte", None) is not None:
+        cargs.append(str(params.get("alg_nmonte", None)))
+    if params.get("extra_tr_par", False):
         cargs.append("-extra_tr_par")
-    if params.get("uncut_at_rois"):
+    if params.get("uncut_at_rois", False):
         cargs.append("-uncut_at_rois")
-    if params.get("dump_rois") is not None:
-        cargs.append(params.get("dump_rois"))
-    if params.get("dump_no_labtab"):
+    if params.get("dump_rois", None) is not None:
+        cargs.append(params.get("dump_rois", None))
+    if params.get("dump_no_labtab", False):
         cargs.append("-dump_no_labtab")
-    if params.get("dump_lab_consec"):
+    if params.get("dump_lab_consec", False):
         cargs.append("-dump_lab_consec")
-    if params.get("posteriori"):
+    if params.get("posteriori", False):
         cargs.append("-posteriori")
-    if params.get("rec_orig"):
+    if params.get("rec_orig", False):
         cargs.append("-rec_orig")
-    if params.get("do_trk_out"):
+    if params.get("do_trk_out", False):
         cargs.append("-do_trk_out")
-    if params.get("trk_opp_orient"):
+    if params.get("trk_opp_orient", False):
         cargs.append("-trk_opp_orient")
-    if params.get("nifti"):
+    if params.get("nifti", False):
         cargs.append("-nifti")
-    if params.get("no_indipair_out"):
+    if params.get("no_indipair_out", False):
         cargs.append("-no_indipair_out")
-    if params.get("write_rois"):
+    if params.get("write_rois", False):
         cargs.append("-write_rois")
-    if params.get("write_opts"):
+    if params.get("write_opts", False):
         cargs.append("-write_opts")
-    if params.get("pair_out_power"):
+    if params.get("pair_out_power", False):
         cargs.append("-pair_out_power")
-    if params.get("verb") is not None:
-        cargs.append(str(params.get("verb")))
+    if params.get("verb", None) is not None:
+        cargs.append(str(params.get("verb", None)))
     return cargs
 
 
@@ -418,24 +433,26 @@ def v_3d_track_id_outputs(
     """
     ret = V3dTrackIdOutputs(
         root=execution.output_file("."),
-        indimap=execution.output_file(params.get("prefix") + "_INDIMAP.nii.gz"),
-        pairmap=execution.output_file(params.get("prefix") + "_PAIRMAP.nii.gz"),
-        grid=execution.output_file(params.get("prefix") + ".grid"),
-        niml_tract=execution.output_file(params.get("prefix") + ".niml.tract"),
-        niml_dset=execution.output_file(params.get("prefix") + ".niml.dset"),
-        trk=execution.output_file(params.get("prefix") + ".trk"),
-        pairmap_labeltable=execution.output_file(params.get("prefix") + "_PAIRS.niml.lt"),
-        roi_labels=execution.output_file(params.get("prefix") + "_roi.labs"),
-        option_values=execution.output_file(params.get("prefix") + ".niml.opts"),
+        indimap=execution.output_file(params.get("prefix", None) + "_INDIMAP.nii.gz"),
+        pairmap=execution.output_file(params.get("prefix", None) + "_PAIRMAP.nii.gz"),
+        grid=execution.output_file(params.get("prefix", None) + ".grid"),
+        niml_tract=execution.output_file(params.get("prefix", None) + ".niml.tract"),
+        niml_dset=execution.output_file(params.get("prefix", None) + ".niml.dset"),
+        trk=execution.output_file(params.get("prefix", None) + ".trk"),
+        pairmap_labeltable=execution.output_file(params.get("prefix", None) + "_PAIRS.niml.lt"),
+        roi_labels=execution.output_file(params.get("prefix", None) + "_roi.labs"),
+        option_values=execution.output_file(params.get("prefix", None) + ".niml.opts"),
     )
     return ret
 
 
 def v_3d_track_id_execute(
     params: V3dTrackIdParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dTrackIdOutputs:
     """
+    3dTrackID
+    
     FACTID-based tractography code for AFNI, part of FATCAT.
     
     Author: AFNI Developers
@@ -444,10 +461,12 @@ def v_3d_track_id_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dTrackIdOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TRACK_ID_METADATA)
     params = execution.params(params)
     cargs = v_3d_track_id_cargs(params, execution)
     ret = v_3d_track_id_outputs(params, execution)
@@ -503,6 +522,8 @@ def v_3d_track_id(
     runner: Runner | None = None,
 ) -> V3dTrackIdOutputs:
     """
+    3dTrackID
+    
     FACTID-based tractography code for AFNI, part of FATCAT.
     
     Author: AFNI Developers
@@ -568,8 +589,6 @@ def v_3d_track_id(
     Returns:
         NamedTuple of outputs (described in `V3dTrackIdOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_TRACK_ID_METADATA)
     params = v_3d_track_id_params(
         mode=mode,
         netrois=netrois,
@@ -616,13 +635,13 @@ def v_3d_track_id(
         pair_out_power=pair_out_power,
         verb=verb,
     )
-    return v_3d_track_id_execute(params, execution)
+    return v_3d_track_id_execute(params, runner)
 
 
 __all__ = [
     "V3dTrackIdOutputs",
-    "V3dTrackIdParameters",
     "V_3D_TRACK_ID_METADATA",
     "v_3d_track_id",
+    "v_3d_track_id_execute",
     "v_3d_track_id_params",
 ]

niwrap_afni/afni/v_3d_trfix.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TRFIX_METADATA = Metadata(
-    id="a4d956a40d63cb24aa10d171635193de75a94468.boutiques",
+    id="139e0d97fc0cdd073b2a15ae7c848174e17c4f57.boutiques",
     name="3dTRfix",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,50 +14,26 @@ V_3D_TRFIX_METADATA = Metadata(
 
 
 V3dTrfixParameters = typing.TypedDict('V3dTrfixParameters', {
-    "__STYXTYPE__": typing.Literal["3dTRfix"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dTRfix"]],
+    "input_file": InputPathType,
+    "tr_list": typing.NotRequired[InputPathType | None],
+    "time_list": typing.NotRequired[InputPathType | None],
+    "prefix": str,
+    "output_tr": typing.NotRequired[float | None],
+})
+V3dTrfixParametersTagged = typing.TypedDict('V3dTrfixParametersTagged', {
+    "@type": typing.Literal["afni/3dTRfix"],
     "input_file": InputPathType,
     "tr_list": typing.NotRequired[InputPathType | None],
     "time_list": typing.NotRequired[InputPathType | None],
     "prefix": str,
     "output_tr": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dTRfix": v_3d_trfix_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 {
-        "3dTRfix": v_3d_trfix_outputs,
-    }.get(t)
 
 
 class V3dTrfixOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_trfix(...)`.
+    Output object returned when calling `V3dTrfixParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +49,7 @@ def v_3d_trfix_params(
     tr_list: InputPathType | None = None,
     time_list: InputPathType | None = None,
     output_tr: float | None = None,
-) -> V3dTrfixParameters:
+) -> V3dTrfixParametersTagged:
     """
     Build parameters.
     
@@ -87,7 +63,7 @@ def v_3d_trfix_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dTRfix",
+        "@type": "afni/3dTRfix",
         "input_file": input_file,
         "prefix": prefix,
     }
@@ -117,26 +93,26 @@ def v_3d_trfix_cargs(
     cargs.append("3dTRfix")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
-    if params.get("tr_list") is not None:
+    if params.get("tr_list", None) is not None:
         cargs.extend([
             "-TRlist",
-            execution.input_file(params.get("tr_list"))
+            execution.input_file(params.get("tr_list", None))
         ])
-    if params.get("time_list") is not None:
+    if params.get("time_list", None) is not None:
         cargs.extend([
             "-TIMElist",
-            execution.input_file(params.get("time_list"))
+            execution.input_file(params.get("time_list", None))
         ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("output_tr") is not None:
+    if params.get("output_tr", None) is not None:
         cargs.extend([
             "-TRout",
-            str(params.get("output_tr"))
+            str(params.get("output_tr", None))
         ])
     return cargs
 
@@ -156,17 +132,19 @@ def v_3d_trfix_outputs(
     """
     ret = V3dTrfixOutputs(
         root=execution.output_file("."),
-        output_file_head=execution.output_file(params.get("prefix") + "+orig.HEAD"),
-        output_file_brik=execution.output_file(params.get("prefix") + "+orig.BRIK"),
+        output_file_head=execution.output_file(params.get("prefix", None) + "+orig.HEAD"),
+        output_file_brik=execution.output_file(params.get("prefix", None) + "+orig.BRIK"),
     )
     return ret
 
 
 def v_3d_trfix_execute(
     params: V3dTrfixParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dTrfixOutputs:
     """
+    3dTRfix
+    
     Re-sample dataset with irregular time grid to regular time grid via linear
     interpolation.
     
@@ -176,10 +154,12 @@ def v_3d_trfix_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dTrfixOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TRFIX_METADATA)
     params = execution.params(params)
     cargs = v_3d_trfix_cargs(params, execution)
     ret = v_3d_trfix_outputs(params, execution)
@@ -196,6 +176,8 @@ def v_3d_trfix(
     runner: Runner | None = None,
 ) -> V3dTrfixOutputs:
     """
+    3dTRfix
+    
     Re-sample dataset with irregular time grid to regular time grid via linear
     interpolation.
     
@@ -213,8 +195,6 @@ def v_3d_trfix(
     Returns:
         NamedTuple of outputs (described in `V3dTrfixOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_TRFIX_METADATA)
     params = v_3d_trfix_params(
         input_file=input_file,
         tr_list=tr_list,
@@ -222,13 +202,13 @@ def v_3d_trfix(
         prefix=prefix,
         output_tr=output_tr,
     )
-    return v_3d_trfix_execute(params, execution)
+    return v_3d_trfix_execute(params, runner)
 
 
 __all__ = [
     "V3dTrfixOutputs",
-    "V3dTrfixParameters",
     "V_3D_TRFIX_METADATA",
     "v_3d_trfix",
+    "v_3d_trfix_execute",
     "v_3d_trfix_params",
 ]