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

niwrap_afni/afni/fat_proc_align_anat_pair.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FAT_PROC_ALIGN_ANAT_PAIR_METADATA = Metadata(
-    id="b574466715c601bd21ffc5b2deb0cf613a361f94.boutiques",
+    id="41ecad2a2d11a7e351eaa339de33b52bf2c115e4.boutiques",
     name="fat_proc_align_anat_pair",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,22 @@ FAT_PROC_ALIGN_ANAT_PAIR_METADATA = Metadata(
 
 
 FatProcAlignAnatPairParameters = typing.TypedDict('FatProcAlignAnatPairParameters', {
-    "__STYXTYPE__": typing.Literal["fat_proc_align_anat_pair"],
+    "@type": typing.NotRequired[typing.Literal["afni/fat_proc_align_anat_pair"]],
+    "input_t1w": InputPathType,
+    "input_t2w": InputPathType,
+    "output_prefix": str,
+    "output_grid": typing.NotRequired[float | None],
+    "out_t2w_grid": bool,
+    "input_t2w_mask": typing.NotRequired[InputPathType | None],
+    "do_ss_tmp_t1w": bool,
+    "warp": typing.NotRequired[str | None],
+    "matrix": typing.NotRequired[InputPathType | None],
+    "workdir": typing.NotRequired[str | None],
+    "no_cmd_out": bool,
+    "no_clean": bool,
+})
+FatProcAlignAnatPairParametersTagged = typing.TypedDict('FatProcAlignAnatPairParametersTagged', {
+    "@type": typing.Literal["afni/fat_proc_align_anat_pair"],
     "input_t1w": InputPathType,
     "input_t2w": InputPathType,
     "output_prefix": str,
@@ -28,43 +43,11 @@ FatProcAlignAnatPairParameters = typing.TypedDict('FatProcAlignAnatPairParameter
     "no_cmd_out": bool,
     "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_align_anat_pair": fat_proc_align_anat_pair_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_align_anat_pair": fat_proc_align_anat_pair_outputs,
-    }.get(t)
 
 
 class FatProcAlignAnatPairOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fat_proc_align_anat_pair(...)`.
+    Output object returned when calling `FatProcAlignAnatPairParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -89,7 +72,7 @@ def fat_proc_align_anat_pair_params(
     workdir: str | None = None,
     no_cmd_out: bool = False,
     no_clean: bool = False,
-) -> FatProcAlignAnatPairParameters:
+) -> FatProcAlignAnatPairParametersTagged:
     """
     Build parameters.
     
@@ -113,7 +96,7 @@ def fat_proc_align_anat_pair_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fat_proc_align_anat_pair",
+        "@type": "afni/fat_proc_align_anat_pair",
         "input_t1w": input_t1w,
         "input_t2w": input_t2w,
         "output_prefix": output_prefix,
@@ -152,48 +135,48 @@ def fat_proc_align_anat_pair_cargs(
     cargs.append("fat_proc_align_anat_pair")
     cargs.extend([
         "-in_t1w",
-        execution.input_file(params.get("input_t1w"))
+        execution.input_file(params.get("input_t1w", None))
     ])
     cargs.extend([
         "-in_t2w",
-        execution.input_file(params.get("input_t2w"))
+        execution.input_file(params.get("input_t2w", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("output_prefix")
+        params.get("output_prefix", None)
     ])
-    if params.get("output_grid") is not None:
+    if params.get("output_grid", None) is not None:
         cargs.extend([
             "-newgrid",
-            str(params.get("output_grid"))
+            str(params.get("output_grid", None))
         ])
-    if params.get("out_t2w_grid"):
+    if params.get("out_t2w_grid", False):
         cargs.append("-out_t2w_grid")
-    if params.get("input_t2w_mask") is not None:
+    if params.get("input_t2w_mask", None) is not None:
         cargs.extend([
             "-in_t2w_mask",
-            execution.input_file(params.get("input_t2w_mask"))
+            execution.input_file(params.get("input_t2w_mask", None))
         ])
-    if params.get("do_ss_tmp_t1w"):
+    if params.get("do_ss_tmp_t1w", False):
         cargs.append("-do_ss_tmp_t1w")
-    if params.get("warp") is not None:
+    if params.get("warp", None) is not None:
         cargs.extend([
             "-warp",
-            params.get("warp")
+            params.get("warp", None)
         ])
-    if params.get("matrix") is not None:
+    if params.get("matrix", None) is not None:
         cargs.extend([
             "-matrix",
-            execution.input_file(params.get("matrix"))
+            execution.input_file(params.get("matrix", 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("no_cmd_out"):
+    if params.get("no_cmd_out", False):
         cargs.append("-no_cmd_out")
-    if params.get("no_clean"):
+    if params.get("no_clean", False):
         cargs.append("-no_clean")
     return cargs
 
@@ -213,18 +196,20 @@ def fat_proc_align_anat_pair_outputs(
     """
     ret = FatProcAlignAnatPairOutputs(
         root=execution.output_file("."),
-        aligned_t1w=execution.output_file(params.get("output_prefix") + "_t1w_aligned.nii.gz"),
-        qc_snapshot_t1w_on_t2w=execution.output_file(params.get("output_prefix") + "_QC_T1w_over_T2w.png"),
-        qc_snapshot_t1w_edges_on_t2w=execution.output_file(params.get("output_prefix") + "_QC_T1w_edges_over_T2w.png"),
+        aligned_t1w=execution.output_file(params.get("output_prefix", None) + "_t1w_aligned.nii.gz"),
+        qc_snapshot_t1w_on_t2w=execution.output_file(params.get("output_prefix", None) + "_QC_T1w_over_T2w.png"),
+        qc_snapshot_t1w_edges_on_t2w=execution.output_file(params.get("output_prefix", None) + "_QC_T1w_edges_over_T2w.png"),
     )
     return ret
 
 
 def fat_proc_align_anat_pair_execute(
     params: FatProcAlignAnatPairParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FatProcAlignAnatPairOutputs:
     """
+    fat_proc_align_anat_pair
+    
     A tool for aligning a T1w anatomical image to a T2w anatomical image using
     solid-body parameters (translation and rotation).
     
@@ -234,10 +219,12 @@ def fat_proc_align_anat_pair_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FatProcAlignAnatPairOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_PROC_ALIGN_ANAT_PAIR_METADATA)
     params = execution.params(params)
     cargs = fat_proc_align_anat_pair_cargs(params, execution)
     ret = fat_proc_align_anat_pair_outputs(params, execution)
@@ -261,6 +248,8 @@ def fat_proc_align_anat_pair(
     runner: Runner | None = None,
 ) -> FatProcAlignAnatPairOutputs:
     """
+    fat_proc_align_anat_pair
+    
     A tool for aligning a T1w anatomical image to a T2w anatomical image using
     solid-body parameters (translation and rotation).
     
@@ -288,8 +277,6 @@ def fat_proc_align_anat_pair(
     Returns:
         NamedTuple of outputs (described in `FatProcAlignAnatPairOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FAT_PROC_ALIGN_ANAT_PAIR_METADATA)
     params = fat_proc_align_anat_pair_params(
         input_t1w=input_t1w,
         input_t2w=input_t2w,
@@ -304,13 +291,13 @@ def fat_proc_align_anat_pair(
         no_cmd_out=no_cmd_out,
         no_clean=no_clean,
     )
-    return fat_proc_align_anat_pair_execute(params, execution)
+    return fat_proc_align_anat_pair_execute(params, runner)
 
 
 __all__ = [
     "FAT_PROC_ALIGN_ANAT_PAIR_METADATA",
     "FatProcAlignAnatPairOutputs",
-    "FatProcAlignAnatPairParameters",
     "fat_proc_align_anat_pair",
+    "fat_proc_align_anat_pair_execute",
     "fat_proc_align_anat_pair_params",
 ]

niwrap_afni/afni/fat_proc_axialize_anat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FAT_PROC_AXIALIZE_ANAT_METADATA = Metadata(
-    id="93b54cf4587e31bd1fe589e3220826cd9b89c2b5.boutiques",
+    id="0d6f50b1ea3cc4f04f960518e894745efed02768.boutiques",
     name="fat_proc_axialize_anat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,32 @@ FAT_PROC_AXIALIZE_ANAT_METADATA = Metadata(
 
 
 FatProcAxializeAnatParameters = typing.TypedDict('FatProcAxializeAnatParameters', {
-    "__STYXTYPE__": typing.Literal["fat_proc_axialize_anat"],
+    "@type": typing.NotRequired[typing.Literal["afni/fat_proc_axialize_anat"]],
+    "in_file": InputPathType,
+    "ref_file": InputPathType,
+    "prefix": str,
+    "mode_t2w": bool,
+    "mode_t1w": bool,
+    "workdir": typing.NotRequired[str | None],
+    "out_match_ref": bool,
+    "do_ceil_out": bool,
+    "extra_al_wtmask": typing.NotRequired[InputPathType | None],
+    "extra_al_cost": typing.NotRequired[str | None],
+    "extra_al_opts": typing.NotRequired[str | None],
+    "focus_mask": typing.NotRequired[InputPathType | None],
+    "focus_by_ss": bool,
+    "remove_inf_sli": typing.NotRequired[float | None],
+    "pre_align_center_mass": bool,
+    "pre_center_mass": bool,
+    "post_lr_symm": bool,
+    "no_pre_lr_symm": bool,
+    "no_clean": bool,
+    "qc_ulay_range": typing.NotRequired[list[float] | None],
+    "no_qc_view": bool,
+    "qc_prefix": typing.NotRequired[str | None],
+})
+FatProcAxializeAnatParametersTagged = typing.TypedDict('FatProcAxializeAnatParametersTagged', {
+    "@type": typing.Literal["afni/fat_proc_axialize_anat"],
     "in_file": InputPathType,
     "ref_file": InputPathType,
     "prefix": str,
@@ -38,43 +63,11 @@ FatProcAxializeAnatParameters = typing.TypedDict('FatProcAxializeAnatParameters'
     "no_qc_view": bool,
     "qc_prefix": 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 {
-        "fat_proc_axialize_anat": fat_proc_axialize_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_axialize_anat": fat_proc_axialize_anat_outputs,
-    }.get(t)
 
 
 class FatProcAxializeAnatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fat_proc_axialize_anat(...)`.
+    Output object returned when calling `FatProcAxializeAnatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -108,7 +101,7 @@ def fat_proc_axialize_anat_params(
     qc_ulay_range: list[float] | None = None,
     no_qc_view: bool = False,
     qc_prefix: str | None = None,
-) -> FatProcAxializeAnatParameters:
+) -> FatProcAxializeAnatParametersTagged:
     """
     Build parameters.
     
@@ -146,7 +139,7 @@ def fat_proc_axialize_anat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fat_proc_axialize_anat",
+        "@type": "afni/fat_proc_axialize_anat",
         "in_file": in_file,
         "ref_file": ref_file,
         "prefix": prefix,
@@ -196,70 +189,70 @@ def fat_proc_axialize_anat_cargs(
     """
     cargs = []
     cargs.append("fat_proc_axialize_anat")
-    cargs.append(execution.input_file(params.get("in_file")))
-    cargs.append(execution.input_file(params.get("ref_file")))
-    cargs.append(params.get("prefix"))
-    if params.get("mode_t2w"):
+    cargs.append(execution.input_file(params.get("in_file", None)))
+    cargs.append(execution.input_file(params.get("ref_file", None)))
+    cargs.append(params.get("prefix", None))
+    if params.get("mode_t2w", False):
         cargs.append("-mode_t2w")
-    if params.get("mode_t1w"):
+    if params.get("mode_t1w", False):
         cargs.append("-mode_t1w")
-    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("out_match_ref"):
+    if params.get("out_match_ref", False):
         cargs.append("-out_match_ref")
-    if params.get("do_ceil_out"):
+    if params.get("do_ceil_out", False):
         cargs.append("-do_ceil_out")
-    if params.get("extra_al_wtmask") is not None:
+    if params.get("extra_al_wtmask", None) is not None:
         cargs.extend([
             "-extra_al_wtmask",
-            execution.input_file(params.get("extra_al_wtmask"))
+            execution.input_file(params.get("extra_al_wtmask", None))
         ])
-    if params.get("extra_al_cost") is not None:
+    if params.get("extra_al_cost", None) is not None:
         cargs.extend([
             "-extra_al_cost",
-            params.get("extra_al_cost")
+            params.get("extra_al_cost", None)
         ])
-    if params.get("extra_al_opts") is not None:
+    if params.get("extra_al_opts", None) is not None:
         cargs.extend([
             "-extra_al_opts",
-            params.get("extra_al_opts")
+            params.get("extra_al_opts", None)
         ])
-    if params.get("focus_mask") is not None:
+    if params.get("focus_mask", None) is not None:
         cargs.extend([
             "-focus_mask",
-            execution.input_file(params.get("focus_mask"))
+            execution.input_file(params.get("focus_mask", None))
         ])
-    if params.get("focus_by_ss"):
+    if params.get("focus_by_ss", False):
         cargs.append("-focus_by_ss")
-    if params.get("remove_inf_sli") is not None:
+    if params.get("remove_inf_sli", None) is not None:
         cargs.extend([
             "-remove_inf_sli",
-            str(params.get("remove_inf_sli"))
+            str(params.get("remove_inf_sli", None))
         ])
-    if params.get("pre_align_center_mass"):
+    if params.get("pre_align_center_mass", False):
         cargs.append("-pre_align_center_mass")
-    if params.get("pre_center_mass"):
+    if params.get("pre_center_mass", False):
         cargs.append("-pre_center_mass")
-    if params.get("post_lr_symm"):
+    if params.get("post_lr_symm", False):
         cargs.append("-post_lr_symm")
-    if params.get("no_pre_lr_symm"):
+    if params.get("no_pre_lr_symm", False):
         cargs.append("-no_pre_lr_symm")
-    if params.get("no_clean"):
+    if params.get("no_clean", False):
         cargs.append("-no_clean")
-    if params.get("qc_ulay_range") is not None:
+    if params.get("qc_ulay_range", None) is not None:
         cargs.extend([
             "-qc1_ulay_range",
-            *map(str, params.get("qc_ulay_range"))
+            *map(str, params.get("qc_ulay_range", None))
         ])
-    if params.get("no_qc_view"):
+    if params.get("no_qc_view", False):
         cargs.append("-no_qc_view")
-    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)
         ])
     return cargs
 
@@ -279,19 +272,21 @@ def fat_proc_axialize_anat_outputs(
     """
     ret = FatProcAxializeAnatOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + ".nii.gz"),
-        working_directory=execution.output_file(params.get("workdir")) if (params.get("workdir") is not None) else None,
+        output_file=execution.output_file(params.get("prefix", None) + ".nii.gz"),
+        working_directory=execution.output_file(params.get("workdir", None)) if (params.get("workdir") is not None) else None,
     )
     return ret
 
 
 def fat_proc_axialize_anat_execute(
     params: FatProcAxializeAnatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FatProcAxializeAnatOutputs:
     """
-    Helps align the major axes of an anatomical volume to those of the volumetric
-    field of view.
+    fat_proc_axialize_anat
+    
+    Helps align the major axes of an anatomical volume to those of the
+    volumetric field of view.
     
     Author: AFNI Developers
     
@@ -299,10 +294,12 @@ def fat_proc_axialize_anat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FatProcAxializeAnatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_PROC_AXIALIZE_ANAT_METADATA)
     params = execution.params(params)
     cargs = fat_proc_axialize_anat_cargs(params, execution)
     ret = fat_proc_axialize_anat_outputs(params, execution)
@@ -336,8 +333,10 @@ def fat_proc_axialize_anat(
     runner: Runner | None = None,
 ) -> FatProcAxializeAnatOutputs:
     """
-    Helps align the major axes of an anatomical volume to those of the volumetric
-    field of view.
+    fat_proc_axialize_anat
+    
+    Helps align the major axes of an anatomical volume to those of the
+    volumetric field of view.
     
     Author: AFNI Developers
     
@@ -377,8 +376,6 @@ def fat_proc_axialize_anat(
     Returns:
         NamedTuple of outputs (described in `FatProcAxializeAnatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FAT_PROC_AXIALIZE_ANAT_METADATA)
     params = fat_proc_axialize_anat_params(
         in_file=in_file,
         ref_file=ref_file,
@@ -403,13 +400,13 @@ def fat_proc_axialize_anat(
         no_qc_view=no_qc_view,
         qc_prefix=qc_prefix,
     )
-    return fat_proc_axialize_anat_execute(params, execution)
+    return fat_proc_axialize_anat_execute(params, runner)
 
 
 __all__ = [
     "FAT_PROC_AXIALIZE_ANAT_METADATA",
     "FatProcAxializeAnatOutputs",
-    "FatProcAxializeAnatParameters",
     "fat_proc_axialize_anat",
+    "fat_proc_axialize_anat_execute",
     "fat_proc_axialize_anat_params",
 ]