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

niwrap_afni/afni/{epi_b0_correct.py → epi_b0_correct_py.py}

@@ -5,16 +5,43 @@ import typing
 import pathlib
 from styxdefs import *
 
-EPI_B0_CORRECT_METADATA = Metadata(
-    id="a6677e9e92afc1f84d2e14c41fd7dc5daf44fd9c.boutiques",
-    name="epi_b0_correct",
+EPI_B0_CORRECT_PY_METADATA = Metadata(
+    id="3754a6613428decb4ca608a0210df3417d707879.boutiques",
+    name="epi_b0_correct.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
 )
 
 
-EpiB0CorrectParameters = typing.TypedDict('EpiB0CorrectParameters', {
-    "__STYXTYPE__": typing.Literal["epi_b0_correct"],
+EpiB0CorrectPyParameters = typing.TypedDict('EpiB0CorrectPyParameters', {
+    "@type": typing.NotRequired[typing.Literal["afni/epi_b0_correct.py"]],
+    "prefix": str,
+    "input_freq": InputPathType,
+    "input_epi": InputPathType,
+    "input_mask": typing.NotRequired[InputPathType | None],
+    "input_magn": typing.NotRequired[InputPathType | None],
+    "input_anat": typing.NotRequired[InputPathType | None],
+    "input_json": typing.NotRequired[InputPathType | None],
+    "epi_pe_dir": str,
+    "epi_pe_bwpp": typing.NotRequired[float | None],
+    "epi_pe_echo_sp": typing.NotRequired[float | None],
+    "epi_pe_vox_dim": typing.NotRequired[float | None],
+    "scale_freq": typing.NotRequired[float | None],
+    "out_cmds": typing.NotRequired[str | None],
+    "out_pars": typing.NotRequired[str | None],
+    "wdir_name": typing.NotRequired[str | None],
+    "blur_sigma": typing.NotRequired[float | None],
+    "do_recenter_freq": typing.NotRequired[str | None],
+    "mask_dilate": typing.NotRequired[list[float] | None],
+    "no_clean": bool,
+    "qc_box_focus_ulay": bool,
+    "no_qc_image": bool,
+    "help": bool,
+    "ver": bool,
+    "date": bool,
+})
+EpiB0CorrectPyParametersTagged = typing.TypedDict('EpiB0CorrectPyParametersTagged', {
+    "@type": typing.Literal["afni/epi_b0_correct.py"],
     "prefix": str,
     "input_freq": InputPathType,
     "input_epi": InputPathType,
@@ -42,41 +69,9 @@ EpiB0CorrectParameters = typing.TypedDict('EpiB0CorrectParameters', {
 })
 
 
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "epi_b0_correct": epi_b0_correct_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 {
-        "epi_b0_correct": epi_b0_correct_outputs,
-    }.get(t)
-
-
-class EpiB0CorrectOutputs(typing.NamedTuple):
+class EpiB0CorrectPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `epi_b0_correct(...)`.
+    Output object returned when calling `EpiB0CorrectPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -92,7 +87,7 @@ class EpiB0CorrectOutputs(typing.NamedTuple):
     """Directory containing QC images."""
 
 
-def epi_b0_correct_params(
+def epi_b0_correct_py_params(
     prefix: str,
     input_freq: InputPathType,
     input_epi: InputPathType,
@@ -117,7 +112,7 @@ def epi_b0_correct_params(
     help_: bool = False,
     ver: bool = False,
     date: bool = False,
-) -> EpiB0CorrectParameters:
+) -> EpiB0CorrectPyParametersTagged:
     """
     Build parameters.
     
@@ -164,7 +159,7 @@ def epi_b0_correct_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "epi_b0_correct",
+        "@type": "afni/epi_b0_correct.py",
         "prefix": prefix,
         "input_freq": input_freq,
         "input_epi": input_epi,
@@ -207,8 +202,8 @@ def epi_b0_correct_params(
     return params
 
 
-def epi_b0_correct_cargs(
-    params: EpiB0CorrectParameters,
+def epi_b0_correct_py_cargs(
+    params: EpiB0CorrectPyParameters,
     execution: Execution,
 ) -> list[str]:
     """
@@ -222,108 +217,108 @@ def epi_b0_correct_cargs(
     """
     cargs = []
     cargs.append("epi_b0_correct.py")
-    cargs.append(params.get("prefix"))
+    cargs.append(params.get("prefix", None))
     cargs.extend([
         "-in_freq",
-        execution.input_file(params.get("input_freq"))
+        execution.input_file(params.get("input_freq", None))
     ])
     cargs.extend([
         "-in_epi",
-        execution.input_file(params.get("input_epi"))
+        execution.input_file(params.get("input_epi", None))
     ])
-    if params.get("input_mask") is not None:
+    if params.get("input_mask", None) is not None:
         cargs.extend([
             "-in_mask",
-            execution.input_file(params.get("input_mask"))
+            execution.input_file(params.get("input_mask", None))
         ])
-    if params.get("input_magn") is not None:
+    if params.get("input_magn", None) is not None:
         cargs.extend([
             "-in_magn",
-            execution.input_file(params.get("input_magn"))
+            execution.input_file(params.get("input_magn", None))
         ])
-    if params.get("input_anat") is not None:
+    if params.get("input_anat", None) is not None:
         cargs.extend([
             "-in_anat",
-            execution.input_file(params.get("input_anat"))
+            execution.input_file(params.get("input_anat", None))
         ])
-    if params.get("input_json") is not None:
+    if params.get("input_json", None) is not None:
         cargs.extend([
             "-in_epi_json",
-            execution.input_file(params.get("input_json"))
+            execution.input_file(params.get("input_json", None))
         ])
     cargs.extend([
         "-epi_pe_dir",
-        params.get("epi_pe_dir")
+        params.get("epi_pe_dir", None)
     ])
-    if params.get("epi_pe_bwpp") is not None:
+    if params.get("epi_pe_bwpp", None) is not None:
         cargs.extend([
             "-epi_pe_bwpp",
-            str(params.get("epi_pe_bwpp"))
+            str(params.get("epi_pe_bwpp", None))
         ])
-    if params.get("epi_pe_echo_sp") is not None:
+    if params.get("epi_pe_echo_sp", None) is not None:
         cargs.extend([
             "-epi_pe_echo_sp",
-            str(params.get("epi_pe_echo_sp"))
+            str(params.get("epi_pe_echo_sp", None))
         ])
-    if params.get("epi_pe_vox_dim") is not None:
+    if params.get("epi_pe_vox_dim", None) is not None:
         cargs.extend([
             "-epi_pe_voxdim",
-            str(params.get("epi_pe_vox_dim"))
+            str(params.get("epi_pe_vox_dim", None))
         ])
-    if params.get("scale_freq") is not None:
+    if params.get("scale_freq", None) is not None:
         cargs.extend([
             "-scale_freq",
-            str(params.get("scale_freq"))
+            str(params.get("scale_freq", None))
         ])
-    if params.get("out_cmds") is not None:
+    if params.get("out_cmds", None) is not None:
         cargs.extend([
             "-out_cmds",
-            params.get("out_cmds")
+            params.get("out_cmds", None)
         ])
-    if params.get("out_pars") is not None:
+    if params.get("out_pars", None) is not None:
         cargs.extend([
             "-out_pars",
-            params.get("out_pars")
+            params.get("out_pars", None)
         ])
-    if params.get("wdir_name") is not None:
+    if params.get("wdir_name", None) is not None:
         cargs.extend([
             "-wdir_name",
-            params.get("wdir_name")
+            params.get("wdir_name", None)
         ])
-    if params.get("blur_sigma") is not None:
+    if params.get("blur_sigma", None) is not None:
         cargs.extend([
             "-blur_sigma",
-            str(params.get("blur_sigma"))
+            str(params.get("blur_sigma", None))
         ])
-    if params.get("do_recenter_freq") is not None:
+    if params.get("do_recenter_freq", None) is not None:
         cargs.extend([
             "-do_recenter_freq",
-            params.get("do_recenter_freq")
+            params.get("do_recenter_freq", None)
         ])
-    if params.get("mask_dilate") is not None:
+    if params.get("mask_dilate", None) is not None:
         cargs.extend([
             "-mask_dilate",
-            *map(str, params.get("mask_dilate"))
+            *map(str, params.get("mask_dilate", None))
         ])
-    if params.get("no_clean"):
+    if params.get("no_clean", False):
         cargs.append("-no_clean")
-    if params.get("qc_box_focus_ulay"):
+    if params.get("qc_box_focus_ulay", False):
         cargs.append("-qc_box_focus_ulay")
-    if params.get("no_qc_image"):
+    if params.get("no_qc_image", False):
         cargs.append("-no_qc_image")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("ver"):
+    if params.get("ver", False):
         cargs.append("-ver")
-    if params.get("date"):
+    if params.get("date", False):
         cargs.append("-date")
     return cargs
 
 
-def epi_b0_correct_outputs(
-    params: EpiB0CorrectParameters,
+def epi_b0_correct_py_outputs(
+    params: EpiB0CorrectPyParameters,
     execution: Execution,
-) -> EpiB0CorrectOutputs:
+) -> EpiB0CorrectPyOutputs:
     """
     Build outputs object containing output file paths and possibly stdout/stderr.
     
@@ -333,22 +328,24 @@ def epi_b0_correct_outputs(
     Returns:
         Outputs object.
     """
-    ret = EpiB0CorrectOutputs(
+    ret = EpiB0CorrectPyOutputs(
         root=execution.output_file("."),
-        warp_dset=execution.output_file(params.get("prefix") + "_WARP.nii.gz"),
-        cmds_script=execution.output_file(params.get("prefix") + "_cmds.tcsh"),
-        params_txt=execution.output_file(params.get("prefix") + "_pars.txt"),
-        unwarped_epi=execution.output_file(params.get("prefix") + "_unwarped.nii.gz"),
-        qc_image_dir=execution.output_file(params.get("prefix") + "_QC/"),
+        warp_dset=execution.output_file(params.get("prefix", None) + "_WARP.nii.gz"),
+        cmds_script=execution.output_file(params.get("prefix", None) + "_cmds.tcsh"),
+        params_txt=execution.output_file(params.get("prefix", None) + "_pars.txt"),
+        unwarped_epi=execution.output_file(params.get("prefix", None) + "_unwarped.nii.gz"),
+        qc_image_dir=execution.output_file(params.get("prefix", None) + "_QC/"),
     )
     return ret
 
 
-def epi_b0_correct_execute(
-    params: EpiB0CorrectParameters,
-    execution: Execution,
-) -> EpiB0CorrectOutputs:
+def epi_b0_correct_py_execute(
+    params: EpiB0CorrectPyParameters,
+    runner: Runner | None = None,
+) -> EpiB0CorrectPyOutputs:
     """
+    epi_b0_correct.py
+    
     B0 distortion correction tool using an acquired frequency (phase) image.
     
     Author: AFNI Developers
@@ -357,18 +354,20 @@ def epi_b0_correct_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `EpiB0CorrectOutputs`).
+        NamedTuple of outputs (described in `EpiB0CorrectPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(EPI_B0_CORRECT_PY_METADATA)
     params = execution.params(params)
-    cargs = epi_b0_correct_cargs(params, execution)
-    ret = epi_b0_correct_outputs(params, execution)
+    cargs = epi_b0_correct_py_cargs(params, execution)
+    ret = epi_b0_correct_py_outputs(params, execution)
     execution.run(cargs)
     return ret
 
 
-def epi_b0_correct(
+def epi_b0_correct_py(
     prefix: str,
     input_freq: InputPathType,
     input_epi: InputPathType,
@@ -394,8 +393,10 @@ def epi_b0_correct(
     ver: bool = False,
     date: bool = False,
     runner: Runner | None = None,
-) -> EpiB0CorrectOutputs:
+) -> EpiB0CorrectPyOutputs:
     """
+    epi_b0_correct.py
+    
     B0 distortion correction tool using an acquired frequency (phase) image.
     
     Author: AFNI Developers
@@ -443,11 +444,9 @@ def epi_b0_correct(
         date: Display date of program's last update in terminal.
         runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `EpiB0CorrectOutputs`).
+        NamedTuple of outputs (described in `EpiB0CorrectPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(EPI_B0_CORRECT_METADATA)
-    params = epi_b0_correct_params(
+    params = epi_b0_correct_py_params(
         prefix=prefix,
         input_freq=input_freq,
         input_epi=input_epi,
@@ -473,13 +472,13 @@ def epi_b0_correct(
         ver=ver,
         date=date,
     )
-    return epi_b0_correct_execute(params, execution)
+    return epi_b0_correct_py_execute(params, runner)
 
 
 __all__ = [
-    "EPI_B0_CORRECT_METADATA",
-    "EpiB0CorrectOutputs",
-    "EpiB0CorrectParameters",
-    "epi_b0_correct",
-    "epi_b0_correct_params",
+    "EPI_B0_CORRECT_PY_METADATA",
+    "EpiB0CorrectPyOutputs",
+    "epi_b0_correct_py",
+    "epi_b0_correct_py_execute",
+    "epi_b0_correct_py_params",
 ]

niwrap_afni/afni/examine_xmat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 EXAMINE_XMAT_METADATA = Metadata(
-    id="41c6732fe776e16e30c04c5fc5c3167c839b8815.boutiques",
+    id="fc52de953fa604c168788487dd5836de626b94b0.boutiques",
     name="ExamineXmat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ EXAMINE_XMAT_METADATA = Metadata(
 
 
 ExamineXmatParameters = typing.TypedDict('ExamineXmatParameters', {
-    "__STYXTYPE__": typing.Literal["ExamineXmat"],
+    "@type": typing.NotRequired[typing.Literal["afni/ExamineXmat"]],
+    "input_file": typing.NotRequired[InputPathType | None],
+    "interactive": bool,
+    "prefix": typing.NotRequired[str | None],
+    "cprefix": typing.NotRequired[str | None],
+    "pprefix": typing.NotRequired[str | None],
+    "select": typing.NotRequired[str | None],
+    "msg_trace": bool,
+    "verbosity": typing.NotRequired[float | None],
+})
+ExamineXmatParametersTagged = typing.TypedDict('ExamineXmatParametersTagged', {
+    "@type": typing.Literal["afni/ExamineXmat"],
     "input_file": typing.NotRequired[InputPathType | None],
     "interactive": bool,
     "prefix": typing.NotRequired[str | None],
@@ -24,43 +35,11 @@ ExamineXmatParameters = typing.TypedDict('ExamineXmatParameters', {
     "msg_trace": bool,
     "verbosity": 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 {
-        "ExamineXmat": examine_xmat_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 {
-        "ExamineXmat": examine_xmat_outputs,
-    }.get(t)
 
 
 class ExamineXmatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `examine_xmat(...)`.
+    Output object returned when calling `ExamineXmatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -85,7 +64,7 @@ def examine_xmat_params(
     select_: str | None = None,
     msg_trace: bool = False,
     verbosity: float | None = None,
-) -> ExamineXmatParameters:
+) -> ExamineXmatParametersTagged:
     """
     Build parameters.
     
@@ -104,7 +83,7 @@ def examine_xmat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "ExamineXmat",
+        "@type": "afni/ExamineXmat",
         "interactive": interactive,
         "msg_trace": msg_trace,
     }
@@ -138,39 +117,39 @@ def examine_xmat_cargs(
     """
     cargs = []
     cargs.append("ExamineXmat")
-    if params.get("input_file") is not None:
+    if params.get("input_file", None) is not None:
         cargs.extend([
             "-input",
-            execution.input_file(params.get("input_file"))
+            execution.input_file(params.get("input_file", None))
         ])
-    if params.get("interactive"):
+    if params.get("interactive", False):
         cargs.append("-interactive")
-    if params.get("prefix") is not None:
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("cprefix") is not None:
+    if params.get("cprefix", None) is not None:
         cargs.extend([
             "-cprefix",
-            params.get("cprefix")
+            params.get("cprefix", None)
         ])
-    if params.get("pprefix") is not None:
+    if params.get("pprefix", None) is not None:
         cargs.extend([
             "-pprefix",
-            params.get("pprefix")
+            params.get("pprefix", None)
         ])
-    if params.get("select") is not None:
+    if params.get("select", None) is not None:
         cargs.extend([
             "-select",
-            params.get("select")
+            params.get("select", None)
         ])
-    if params.get("msg_trace"):
+    if params.get("msg_trace", False):
         cargs.append("-msg.trace")
-    if params.get("verbosity") is not None:
+    if params.get("verbosity", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verbosity"))
+            str(params.get("verbosity", None))
         ])
     return cargs
 
@@ -190,20 +169,22 @@ def examine_xmat_outputs(
     """
     ret = ExamineXmatOutputs(
         root=execution.output_file("."),
-        plot_image=execution.output_file(params.get("prefix") + ".jpg") if (params.get("prefix") is not None) else None,
-        plot_image_png=execution.output_file(params.get("prefix") + ".png") if (params.get("prefix") is not None) else None,
-        plot_image_pdf=execution.output_file(params.get("prefix") + ".pdf") if (params.get("prefix") is not None) else None,
-        cor_image=execution.output_file(params.get("cprefix") + ".jpg") if (params.get("cprefix") is not None) else None,
-        plot_image_prefix=execution.output_file(params.get("pprefix") + ".jpg") if (params.get("pprefix") is not None) else None,
+        plot_image=execution.output_file(params.get("prefix", None) + ".jpg") if (params.get("prefix") is not None) else None,
+        plot_image_png=execution.output_file(params.get("prefix", None) + ".png") if (params.get("prefix") is not None) else None,
+        plot_image_pdf=execution.output_file(params.get("prefix", None) + ".pdf") if (params.get("prefix") is not None) else None,
+        cor_image=execution.output_file(params.get("cprefix", None) + ".jpg") if (params.get("cprefix") is not None) else None,
+        plot_image_prefix=execution.output_file(params.get("pprefix", None) + ".jpg") if (params.get("pprefix") is not None) else None,
     )
     return ret
 
 
 def examine_xmat_execute(
     params: ExamineXmatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ExamineXmatOutputs:
     """
+    ExamineXmat
+    
     A program for examining the design matrix generated by 3dDeconvolve.
     
     Author: AFNI Developers
@@ -212,10 +193,12 @@ def examine_xmat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ExamineXmatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(EXAMINE_XMAT_METADATA)
     params = execution.params(params)
     cargs = examine_xmat_cargs(params, execution)
     ret = examine_xmat_outputs(params, execution)
@@ -235,6 +218,8 @@ def examine_xmat(
     runner: Runner | None = None,
 ) -> ExamineXmatOutputs:
     """
+    ExamineXmat
+    
     A program for examining the design matrix generated by 3dDeconvolve.
     
     Author: AFNI Developers
@@ -256,8 +241,6 @@ def examine_xmat(
     Returns:
         NamedTuple of outputs (described in `ExamineXmatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(EXAMINE_XMAT_METADATA)
     params = examine_xmat_params(
         input_file=input_file,
         interactive=interactive,
@@ -268,13 +251,13 @@ def examine_xmat(
         msg_trace=msg_trace,
         verbosity=verbosity,
     )
-    return examine_xmat_execute(params, execution)
+    return examine_xmat_execute(params, runner)
 
 
 __all__ = [
     "EXAMINE_XMAT_METADATA",
     "ExamineXmatOutputs",
-    "ExamineXmatParameters",
     "examine_xmat",
+    "examine_xmat_execute",
     "examine_xmat_params",
 ]