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

niwrap_afni/afni/fat_proc_dwi_to_dt.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FAT_PROC_DWI_TO_DT_METADATA = Metadata(
-    id="802161f8f0acfd7af6348446316cf5b2c086b7ef.boutiques",
+    id="cfd7cb46a3baf5aaf831020bf3b5b8f725006223.boutiques",
     name="fat_proc_dwi_to_dt",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,39 @@ FAT_PROC_DWI_TO_DT_METADATA = Metadata(
 
 
 FatProcDwiToDtParameters = typing.TypedDict('FatProcDwiToDtParameters', {
-    "__STYXTYPE__": typing.Literal["fat_proc_dwi_to_dt"],
+    "@type": typing.NotRequired[typing.Literal["afni/fat_proc_dwi_to_dt"]],
+    "in_dwi": InputPathType,
+    "in_gradmat": InputPathType,
+    "prefix": str,
+    "in_bvals": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "mask_from_struc": bool,
+    "in_struc_res": typing.NotRequired[InputPathType | None],
+    "in_ref_orig": typing.NotRequired[InputPathType | None],
+    "prefix_dti": typing.NotRequired[str | None],
+    "flip_x": bool,
+    "flip_y": bool,
+    "flip_z": bool,
+    "no_flip": bool,
+    "no_scale_out_1000": bool,
+    "no_reweight": bool,
+    "no_cumulative_wts": bool,
+    "qc_fa_thr": typing.NotRequired[float | None],
+    "qc_fa_max": typing.NotRequired[float | None],
+    "qc_fa_unc_max": typing.NotRequired[float | None],
+    "qc_v12_unc_max": typing.NotRequired[float | None],
+    "qc_prefix": typing.NotRequired[str | None],
+    "no_qc_view": bool,
+    "no_cmd_out": bool,
+    "workdir": typing.NotRequired[str | None],
+    "no_clean": bool,
+    "uncert_off": bool,
+    "uncert_iters": typing.NotRequired[float | None],
+    "uncert_extra_cmds": typing.NotRequired[str | None],
+    "check_abs_min": typing.NotRequired[float | None],
+})
+FatProcDwiToDtParametersTagged = typing.TypedDict('FatProcDwiToDtParametersTagged', {
+    "@type": typing.Literal["afni/fat_proc_dwi_to_dt"],
     "in_dwi": InputPathType,
     "in_gradmat": InputPathType,
     "prefix": str,
@@ -45,48 +77,14 @@ FatProcDwiToDtParameters = typing.TypedDict('FatProcDwiToDtParameters', {
     "uncert_extra_cmds": typing.NotRequired[str | None],
     "check_abs_min": 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 {
-        "fat_proc_dwi_to_dt": fat_proc_dwi_to_dt_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_dwi_to_dt": fat_proc_dwi_to_dt_outputs,
-    }.get(t)
 
 
 class FatProcDwiToDtOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fat_proc_dwi_to_dt(...)`.
+    Output object returned when calling `FatProcDwiToDtParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    output_files: OutputPathType
-    """Output files generated with the specified prefix."""
 
 
 def fat_proc_dwi_to_dt_params(
@@ -119,7 +117,7 @@ def fat_proc_dwi_to_dt_params(
     uncert_iters: float | None = None,
     uncert_extra_cmds: str | None = None,
     check_abs_min: float | None = None,
-) -> FatProcDwiToDtParameters:
+) -> FatProcDwiToDtParametersTagged:
     """
     Build parameters.
     
@@ -173,7 +171,7 @@ def fat_proc_dwi_to_dt_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fat_proc_dwi_to_dt",
+        "@type": "afni/fat_proc_dwi_to_dt",
         "in_dwi": in_dwi,
         "in_gradmat": in_gradmat,
         "prefix": prefix,
@@ -236,108 +234,108 @@ def fat_proc_dwi_to_dt_cargs(
     """
     cargs = []
     cargs.append("fat_proc_dwi_to_dt")
-    cargs.append(execution.input_file(params.get("in_dwi")))
+    cargs.append(execution.input_file(params.get("in_dwi", None)))
     cargs.extend([
         "-in_col_matA | -in_col_matT | -in_col_vec | -in_row_vec",
-        execution.input_file(params.get("in_gradmat"))
+        execution.input_file(params.get("in_gradmat", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("in_bvals") is not None:
+    if params.get("in_bvals", None) is not None:
         cargs.extend([
             "-in_bvals",
-            execution.input_file(params.get("in_bvals"))
+            execution.input_file(params.get("in_bvals", None))
         ])
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
-    if params.get("mask_from_struc"):
+    if params.get("mask_from_struc", False):
         cargs.append("-mask_from_struc")
-    if params.get("in_struc_res") is not None:
+    if params.get("in_struc_res", None) is not None:
         cargs.extend([
             "-in_struc_res",
-            execution.input_file(params.get("in_struc_res"))
+            execution.input_file(params.get("in_struc_res", None))
         ])
-    if params.get("in_ref_orig") is not None:
+    if params.get("in_ref_orig", None) is not None:
         cargs.extend([
             "-in_ref_orig",
-            execution.input_file(params.get("in_ref_orig"))
+            execution.input_file(params.get("in_ref_orig", None))
         ])
-    if params.get("prefix_dti") is not None:
+    if params.get("prefix_dti", None) is not None:
         cargs.extend([
             "-prefix_dti",
-            params.get("prefix_dti")
+            params.get("prefix_dti", None)
         ])
-    if params.get("flip_x"):
+    if params.get("flip_x", False):
         cargs.append("-flip_x")
-    if params.get("flip_y"):
+    if params.get("flip_y", False):
         cargs.append("-flip_y")
-    if params.get("flip_z"):
+    if params.get("flip_z", False):
         cargs.append("-flip_z")
-    if params.get("no_flip"):
+    if params.get("no_flip", False):
         cargs.append("-no_flip")
-    if params.get("no_scale_out_1000"):
+    if params.get("no_scale_out_1000", False):
         cargs.append("-no_scale_out_1000")
-    if params.get("no_reweight"):
+    if params.get("no_reweight", False):
         cargs.append("-no_reweight")
-    if params.get("no_cumulative_wts"):
+    if params.get("no_cumulative_wts", False):
         cargs.append("-no_cumulative_wts")
-    if params.get("qc_fa_thr") is not None:
+    if params.get("qc_fa_thr", None) is not None:
         cargs.extend([
             "-qc_fa_thr",
-            str(params.get("qc_fa_thr"))
+            str(params.get("qc_fa_thr", None))
         ])
-    if params.get("qc_fa_max") is not None:
+    if params.get("qc_fa_max", None) is not None:
         cargs.extend([
             "-qc_fa_max",
-            str(params.get("qc_fa_max"))
+            str(params.get("qc_fa_max", None))
         ])
-    if params.get("qc_fa_unc_max") is not None:
+    if params.get("qc_fa_unc_max", None) is not None:
         cargs.extend([
             "-qc_fa_unc_max",
-            str(params.get("qc_fa_unc_max"))
+            str(params.get("qc_fa_unc_max", None))
         ])
-    if params.get("qc_v12_unc_max") is not None:
+    if params.get("qc_v12_unc_max", None) is not None:
         cargs.extend([
             "-qc_v12_unc_max",
-            str(params.get("qc_v12_unc_max"))
+            str(params.get("qc_v12_unc_max", None))
         ])
-    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_qc_view"):
+    if params.get("no_qc_view", False):
         cargs.append("-no_qc_view")
-    if params.get("no_cmd_out"):
+    if params.get("no_cmd_out", False):
         cargs.append("-no_cmd_out")
-    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("no_clean"):
+    if params.get("no_clean", False):
         cargs.append("-no_clean")
-    if params.get("uncert_off"):
+    if params.get("uncert_off", False):
         cargs.append("-uncert_off")
-    if params.get("uncert_iters") is not None:
+    if params.get("uncert_iters", None) is not None:
         cargs.extend([
             "-uncert_iters",
-            str(params.get("uncert_iters"))
+            str(params.get("uncert_iters", None))
         ])
-    if params.get("uncert_extra_cmds") is not None:
+    if params.get("uncert_extra_cmds", None) is not None:
         cargs.extend([
             "-uncert_extra_cmds",
-            params.get("uncert_extra_cmds")
+            params.get("uncert_extra_cmds", None)
         ])
-    if params.get("check_abs_min") is not None:
+    if params.get("check_abs_min", None) is not None:
         cargs.extend([
             "-check_abs_min",
-            str(params.get("check_abs_min"))
+            str(params.get("check_abs_min", None))
         ])
     return cargs
 
@@ -357,18 +355,19 @@ def fat_proc_dwi_to_dt_outputs(
     """
     ret = FatProcDwiToDtOutputs(
         root=execution.output_file("."),
-        output_files=execution.output_file(params.get("prefix") + "*"),
     )
     return ret
 
 
 def fat_proc_dwi_to_dt_execute(
     params: FatProcDwiToDtParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FatProcDwiToDtOutputs:
     """
-    This program fits tensors and DT parameters, as well as the uncertainty of DT
-    parameters needed for tractography.
+    fat_proc_dwi_to_dt
+    
+    This program fits tensors and DT parameters, as well as the uncertainty of
+    DT parameters needed for tractography.
     
     Author: AFNI Developers
     
@@ -376,10 +375,12 @@ def fat_proc_dwi_to_dt_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FatProcDwiToDtOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_PROC_DWI_TO_DT_METADATA)
     params = execution.params(params)
     cargs = fat_proc_dwi_to_dt_cargs(params, execution)
     ret = fat_proc_dwi_to_dt_outputs(params, execution)
@@ -420,8 +421,10 @@ def fat_proc_dwi_to_dt(
     runner: Runner | None = None,
 ) -> FatProcDwiToDtOutputs:
     """
-    This program fits tensors and DT parameters, as well as the uncertainty of DT
-    parameters needed for tractography.
+    fat_proc_dwi_to_dt
+    
+    This program fits tensors and DT parameters, as well as the uncertainty of
+    DT parameters needed for tractography.
     
     Author: AFNI Developers
     
@@ -477,8 +480,6 @@ def fat_proc_dwi_to_dt(
     Returns:
         NamedTuple of outputs (described in `FatProcDwiToDtOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FAT_PROC_DWI_TO_DT_METADATA)
     params = fat_proc_dwi_to_dt_params(
         in_dwi=in_dwi,
         in_gradmat=in_gradmat,
@@ -510,13 +511,13 @@ def fat_proc_dwi_to_dt(
         uncert_extra_cmds=uncert_extra_cmds,
         check_abs_min=check_abs_min,
     )
-    return fat_proc_dwi_to_dt_execute(params, execution)
+    return fat_proc_dwi_to_dt_execute(params, runner)
 
 
 __all__ = [
     "FAT_PROC_DWI_TO_DT_METADATA",
     "FatProcDwiToDtOutputs",
-    "FatProcDwiToDtParameters",
     "fat_proc_dwi_to_dt",
+    "fat_proc_dwi_to_dt_execute",
     "fat_proc_dwi_to_dt_params",
 ]

niwrap_afni/afni/fat_proc_filter_dwis.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FAT_PROC_FILTER_DWIS_METADATA = Metadata(
-    id="3def8805da69fa90cfe590bc1ca23a15f6d16d00.boutiques",
+    id="9978a84be8a7011c9a5406c54e68397255149cfc.boutiques",
     name="fat_proc_filter_dwis",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,21 @@ FAT_PROC_FILTER_DWIS_METADATA = Metadata(
 
 
 FatProcFilterDwisParameters = typing.TypedDict('FatProcFilterDwisParameters', {
-    "__STYXTYPE__": typing.Literal["fat_proc_filter_dwis"],
+    "@type": typing.NotRequired[typing.Literal["afni/fat_proc_filter_dwis"]],
+    "input_dwi": InputPathType,
+    "input_gradient": InputPathType,
+    "select_string": str,
+    "select_file": typing.NotRequired[InputPathType | None],
+    "output_prefix": str,
+    "input_bvals": typing.NotRequired[InputPathType | None],
+    "unit_mag_out": bool,
+    "qc_prefix": typing.NotRequired[str | None],
+    "no_qc_view": bool,
+    "no_cmd_out": bool,
+    "do_movie": typing.NotRequired[typing.Literal["AGIF", "MPEG"] | None],
+})
+FatProcFilterDwisParametersTagged = typing.TypedDict('FatProcFilterDwisParametersTagged', {
+    "@type": typing.Literal["afni/fat_proc_filter_dwis"],
     "input_dwi": InputPathType,
     "input_gradient": InputPathType,
     "select_string": str,
@@ -27,43 +41,11 @@ FatProcFilterDwisParameters = typing.TypedDict('FatProcFilterDwisParameters', {
     "no_cmd_out": bool,
     "do_movie": typing.NotRequired[typing.Literal["AGIF", "MPEG"] | None],
 })
-
-
-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_filter_dwis": fat_proc_filter_dwis_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_filter_dwis": fat_proc_filter_dwis_outputs,
-    }.get(t)
 
 
 class FatProcFilterDwisOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fat_proc_filter_dwis(...)`.
+    Output object returned when calling `FatProcFilterDwisParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -87,7 +69,7 @@ def fat_proc_filter_dwis_params(
     no_qc_view: bool = False,
     no_cmd_out: bool = False,
     do_movie: typing.Literal["AGIF", "MPEG"] | None = None,
-) -> FatProcFilterDwisParameters:
+) -> FatProcFilterDwisParametersTagged:
     """
     Build parameters.
     
@@ -119,7 +101,7 @@ def fat_proc_filter_dwis_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fat_proc_filter_dwis",
+        "@type": "afni/fat_proc_filter_dwis",
         "input_dwi": input_dwi,
         "input_gradient": input_gradient,
         "select_string": select_string,
@@ -156,45 +138,45 @@ def fat_proc_filter_dwis_cargs(
     cargs.append("fat_proc_filter_dwis")
     cargs.extend([
         "-in_dwi",
-        execution.input_file(params.get("input_dwi"))
+        execution.input_file(params.get("input_dwi", None))
     ])
     cargs.extend([
         "-in_col_matA|-in_col_matT|-in_col_vec|-in_row_vec",
-        execution.input_file(params.get("input_gradient"))
+        execution.input_file(params.get("input_gradient", None))
     ])
     cargs.extend([
         "-select",
-        params.get("select_string")
+        params.get("select_string", None)
     ])
-    if params.get("select_file") is not None:
+    if params.get("select_file", None) is not None:
         cargs.extend([
             "-select_file",
-            execution.input_file(params.get("select_file"))
+            execution.input_file(params.get("select_file", None))
         ])
     cargs.extend([
         "-prefix",
-        params.get("output_prefix")
+        params.get("output_prefix", None)
     ])
-    if params.get("input_bvals") is not None:
+    if params.get("input_bvals", None) is not None:
         cargs.extend([
             "-in_bvals",
-            execution.input_file(params.get("input_bvals"))
+            execution.input_file(params.get("input_bvals", None))
         ])
-    if params.get("unit_mag_out"):
+    if params.get("unit_mag_out", False):
         cargs.append("-unit_mag_out")
-    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_qc_view"):
+    if params.get("no_qc_view", False):
         cargs.append("-no_qc_view")
-    if params.get("no_cmd_out"):
+    if params.get("no_cmd_out", False):
         cargs.append("-no_cmd_out")
-    if params.get("do_movie") is not None:
+    if params.get("do_movie", None) is not None:
         cargs.extend([
             "-do_movie",
-            params.get("do_movie")
+            params.get("do_movie", None)
         ])
     return cargs
 
@@ -214,18 +196,20 @@ def fat_proc_filter_dwis_outputs(
     """
     ret = FatProcFilterDwisOutputs(
         root=execution.output_file("."),
-        filtered_dwi=execution.output_file(params.get("output_prefix") + "_filtered.nii.gz"),
-        filtered_bvecs=execution.output_file(params.get("output_prefix") + "_filtered.bvecs"),
-        filtered_bvals=execution.output_file(params.get("output_prefix") + "_filtered.bvals"),
+        filtered_dwi=execution.output_file(params.get("output_prefix", None) + "_filtered.nii.gz"),
+        filtered_bvecs=execution.output_file(params.get("output_prefix", None) + "_filtered.bvecs"),
+        filtered_bvals=execution.output_file(params.get("output_prefix", None) + "_filtered.bvals"),
     )
     return ret
 
 
 def fat_proc_filter_dwis_execute(
     params: FatProcFilterDwisParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FatProcFilterDwisOutputs:
     """
+    fat_proc_filter_dwis
+    
     Filter out user-found and user-defined bad volumes from DWI data sets.
     
     Author: AFNI Developers
@@ -234,10 +218,12 @@ def fat_proc_filter_dwis_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FatProcFilterDwisOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_PROC_FILTER_DWIS_METADATA)
     params = execution.params(params)
     cargs = fat_proc_filter_dwis_cargs(params, execution)
     ret = fat_proc_filter_dwis_outputs(params, execution)
@@ -260,6 +246,8 @@ def fat_proc_filter_dwis(
     runner: Runner | None = None,
 ) -> FatProcFilterDwisOutputs:
     """
+    fat_proc_filter_dwis
+    
     Filter out user-found and user-defined bad volumes from DWI data sets.
     
     Author: AFNI Developers
@@ -294,8 +282,6 @@ def fat_proc_filter_dwis(
     Returns:
         NamedTuple of outputs (described in `FatProcFilterDwisOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FAT_PROC_FILTER_DWIS_METADATA)
     params = fat_proc_filter_dwis_params(
         input_dwi=input_dwi,
         input_gradient=input_gradient,
@@ -309,13 +295,13 @@ def fat_proc_filter_dwis(
         no_cmd_out=no_cmd_out,
         do_movie=do_movie,
     )
-    return fat_proc_filter_dwis_execute(params, execution)
+    return fat_proc_filter_dwis_execute(params, runner)
 
 
 __all__ = [
     "FAT_PROC_FILTER_DWIS_METADATA",
     "FatProcFilterDwisOutputs",
-    "FatProcFilterDwisParameters",
     "fat_proc_filter_dwis",
+    "fat_proc_filter_dwis_execute",
     "fat_proc_filter_dwis_params",
 ]