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

niwrap_afni/afni/fim2.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIM2_METADATA = Metadata(
-    id="821c0c76727aa989e97731a04d2596a66d166df2.boutiques",
+    id="5a4e1f8896d5725c0337f94e013785705278b663.boutiques",
     name="fim2",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,33 @@ FIM2_METADATA = Metadata(
 
 
 Fim2Parameters = typing.TypedDict('Fim2Parameters', {
-    "__STYXTYPE__": typing.Literal["fim2"],
+    "@type": typing.NotRequired[typing.Literal["afni/fim2"]],
+    "image_files": list[InputPathType],
+    "pcnt": typing.NotRequired[float | None],
+    "pcthresh": typing.NotRequired[float | None],
+    "im1": typing.NotRequired[int | None],
+    "num": typing.NotRequired[int | None],
+    "non": bool,
+    "coef": typing.NotRequired[float | None],
+    "ort": typing.NotRequired[list[InputPathType] | None],
+    "ideal": typing.NotRequired[list[InputPathType] | None],
+    "polref": typing.NotRequired[int | None],
+    "fimfile": typing.NotRequired[str | None],
+    "corr": bool,
+    "corfile": typing.NotRequired[str | None],
+    "cnrfile": typing.NotRequired[str | None],
+    "sigfile": typing.NotRequired[str | None],
+    "fitfile": typing.NotRequired[str | None],
+    "subort": typing.NotRequired[str | None],
+    "flim": bool,
+    "clean": bool,
+    "clip": bool,
+    "q": bool,
+    "dfspace": bool,
+    "regbase": typing.NotRequired[str | None],
+})
+Fim2ParametersTagged = typing.TypedDict('Fim2ParametersTagged', {
+    "@type": typing.Literal["afni/fim2"],
     "image_files": list[InputPathType],
     "pcnt": typing.NotRequired[float | None],
     "pcthresh": typing.NotRequired[float | None],
@@ -39,43 +65,11 @@ Fim2Parameters = typing.TypedDict('Fim2Parameters', {
     "dfspace": bool,
     "regbase": 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 {
-        "fim2": fim2_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 {
-        "fim2": fim2_outputs,
-    }.get(t)
 
 
 class Fim2Outputs(typing.NamedTuple):
     """
-    Output object returned when calling `fim2(...)`.
+    Output object returned when calling `Fim2Parameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -117,7 +111,7 @@ def fim2_params(
     q: bool = False,
     dfspace: bool = False,
     regbase: str | None = None,
-) -> Fim2Parameters:
+) -> Fim2ParametersTagged:
     """
     Build parameters.
     
@@ -157,7 +151,7 @@ def fim2_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fim2",
+        "@type": "afni/fim2",
         "image_files": image_files,
         "non": non,
         "corr": corr,
@@ -215,95 +209,95 @@ def fim2_cargs(
     """
     cargs = []
     cargs.append("fim2")
-    cargs.extend([execution.input_file(f) for f in params.get("image_files")])
-    if params.get("pcnt") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("image_files", None)])
+    if params.get("pcnt", None) is not None:
         cargs.extend([
             "-pcnt",
-            str(params.get("pcnt"))
+            str(params.get("pcnt", None))
         ])
-    if params.get("pcthresh") is not None:
+    if params.get("pcthresh", None) is not None:
         cargs.extend([
             "-pcthresh",
-            str(params.get("pcthresh"))
+            str(params.get("pcthresh", None))
         ])
-    if params.get("im1") is not None:
+    if params.get("im1", None) is not None:
         cargs.extend([
             "-im1",
-            str(params.get("im1"))
+            str(params.get("im1", None))
         ])
-    if params.get("num") is not None:
+    if params.get("num", None) is not None:
         cargs.extend([
             "-num",
-            str(params.get("num"))
+            str(params.get("num", None))
         ])
-    if params.get("non"):
+    if params.get("non", False):
         cargs.append("-non")
-    if params.get("coef") is not None:
+    if params.get("coef", None) is not None:
         cargs.extend([
             "-coef",
-            str(params.get("coef"))
+            str(params.get("coef", None))
         ])
-    if params.get("ort") is not None:
+    if params.get("ort", None) is not None:
         cargs.extend([
             "-ort",
-            *[execution.input_file(f) for f in params.get("ort")]
+            *[execution.input_file(f) for f in params.get("ort", None)]
         ])
-    if params.get("ideal") is not None:
+    if params.get("ideal", None) is not None:
         cargs.extend([
             "-ideal",
-            *[execution.input_file(f) for f in params.get("ideal")]
+            *[execution.input_file(f) for f in params.get("ideal", None)]
         ])
-    if params.get("polref") is not None:
+    if params.get("polref", None) is not None:
         cargs.extend([
             "-polref",
-            str(params.get("polref"))
+            str(params.get("polref", None))
         ])
-    if params.get("fimfile") is not None:
+    if params.get("fimfile", None) is not None:
         cargs.extend([
             "-fimfile",
-            params.get("fimfile")
+            params.get("fimfile", None)
         ])
-    if params.get("corr"):
+    if params.get("corr", False):
         cargs.append("-corr")
-    if params.get("corfile") is not None:
+    if params.get("corfile", None) is not None:
         cargs.extend([
             "-corfile",
-            params.get("corfile")
+            params.get("corfile", None)
         ])
-    if params.get("cnrfile") is not None:
+    if params.get("cnrfile", None) is not None:
         cargs.extend([
             "-cnrfile",
-            params.get("cnrfile")
+            params.get("cnrfile", None)
         ])
-    if params.get("sigfile") is not None:
+    if params.get("sigfile", None) is not None:
         cargs.extend([
             "-sigfile",
-            params.get("sigfile")
+            params.get("sigfile", None)
         ])
-    if params.get("fitfile") is not None:
+    if params.get("fitfile", None) is not None:
         cargs.extend([
             "-fitfile",
-            params.get("fitfile")
+            params.get("fitfile", None)
         ])
-    if params.get("subort") is not None:
+    if params.get("subort", None) is not None:
         cargs.extend([
             "-subort",
-            params.get("subort")
+            params.get("subort", None)
         ])
-    if params.get("flim"):
+    if params.get("flim", False):
         cargs.append("-flim")
-    if params.get("clean"):
+    if params.get("clean", False):
         cargs.append("-clean")
-    if params.get("clip"):
+    if params.get("clip", False):
         cargs.append("-clip")
-    if params.get("q"):
+    if params.get("q", False):
         cargs.append("-q")
-    if params.get("dfspace"):
+    if params.get("dfspace", False):
         cargs.append("-dfspace")
-    if params.get("regbase") is not None:
+    if params.get("regbase", None) is not None:
         cargs.extend([
             "-regbase",
-            params.get("regbase")
+            params.get("regbase", None)
         ])
     return cargs
 
@@ -323,21 +317,23 @@ def fim2_outputs(
     """
     ret = Fim2Outputs(
         root=execution.output_file("."),
-        activation_magnitudes=execution.output_file(params.get("fimfile")) if (params.get("fimfile") is not None) else None,
-        correlation_image=execution.output_file(params.get("corfile")) if (params.get("corfile") is not None) else None,
-        contrast_to_noise_image=execution.output_file(params.get("cnrfile")) if (params.get("cnrfile") is not None) else None,
-        std_deviation_image=execution.output_file(params.get("sigfile")) if (params.get("sigfile") is not None) else None,
-        ls_fit_coefficients=execution.output_file(params.get("fitfile")) if (params.get("fitfile") is not None) else None,
-        subtracted_references=execution.output_file(params.get("subort")) if (params.get("subort") is not None) else None,
+        activation_magnitudes=execution.output_file(params.get("fimfile", None)) if (params.get("fimfile") is not None) else None,
+        correlation_image=execution.output_file(params.get("corfile", None)) if (params.get("corfile") is not None) else None,
+        contrast_to_noise_image=execution.output_file(params.get("cnrfile", None)) if (params.get("cnrfile") is not None) else None,
+        std_deviation_image=execution.output_file(params.get("sigfile", None)) if (params.get("sigfile") is not None) else None,
+        ls_fit_coefficients=execution.output_file(params.get("fitfile", None)) if (params.get("fitfile") is not None) else None,
+        subtracted_references=execution.output_file(params.get("subort", None)) if (params.get("subort") is not None) else None,
     )
     return ret
 
 
 def fim2_execute(
     params: Fim2Parameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Fim2Outputs:
     """
+    fim2
+    
     Functional Imaging Mapping Tool.
     
     Author: AFNI Developers
@@ -346,10 +342,12 @@ def fim2_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Fim2Outputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIM2_METADATA)
     params = execution.params(params)
     cargs = fim2_cargs(params, execution)
     ret = fim2_outputs(params, execution)
@@ -384,6 +382,8 @@ def fim2(
     runner: Runner | None = None,
 ) -> Fim2Outputs:
     """
+    fim2
+    
     Functional Imaging Mapping Tool.
     
     Author: AFNI Developers
@@ -426,8 +426,6 @@ def fim2(
     Returns:
         NamedTuple of outputs (described in `Fim2Outputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FIM2_METADATA)
     params = fim2_params(
         image_files=image_files,
         pcnt=pcnt,
@@ -453,13 +451,13 @@ def fim2(
         dfspace=dfspace,
         regbase=regbase,
     )
-    return fim2_execute(params, execution)
+    return fim2_execute(params, runner)
 
 
 __all__ = [
     "FIM2_METADATA",
     "Fim2Outputs",
-    "Fim2Parameters",
     "fim2",
+    "fim2_execute",
     "fim2_params",
 ]

niwrap_afni/afni/{find_variance_lines.py → find_variance_lines_tcsh.py}

@@ -5,16 +5,34 @@ import typing
 import pathlib
 from styxdefs import *
 
-FIND_VARIANCE_LINES_METADATA = Metadata(
-    id="46cc1bbfa68d9508d98e3c8d1703d0d91c133340.boutiques",
-    name="find_variance_lines",
+FIND_VARIANCE_LINES_TCSH_METADATA = Metadata(
+    id="3447eee105e11d76e6ca8bbc5dda2062c2674033.boutiques",
+    name="find_variance_lines.tcsh",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
 )
 
 
-FindVarianceLinesParameters = typing.TypedDict('FindVarianceLinesParameters', {
-    "__STYXTYPE__": typing.Literal["find_variance_lines"],
+FindVarianceLinesTcshParameters = typing.TypedDict('FindVarianceLinesTcshParameters', {
+    "@type": typing.NotRequired[typing.Literal["afni/find_variance_lines.tcsh"]],
+    "input_files": list[InputPathType],
+    "mask": typing.NotRequired[str | None],
+    "min_cvox": typing.NotRequired[int | None],
+    "min_nt": typing.NotRequired[int | None],
+    "nerode": typing.NotRequired[int | None],
+    "nfirst": typing.NotRequired[int | None],
+    "percentile": typing.NotRequired[int | None],
+    "polort": typing.NotRequired[str | None],
+    "output_dir": typing.NotRequired[str | None],
+    "do_clean": typing.NotRequired[int | None],
+    "do_img": typing.NotRequired[int | None],
+    "echo": bool,
+    "help": bool,
+    "hist": bool,
+    "ver": bool,
+})
+FindVarianceLinesTcshParametersTagged = typing.TypedDict('FindVarianceLinesTcshParametersTagged', {
+    "@type": typing.Literal["afni/find_variance_lines.tcsh"],
     "input_files": list[InputPathType],
     "mask": typing.NotRequired[str | None],
     "min_cvox": typing.NotRequired[int | None],
@@ -33,55 +51,17 @@ FindVarianceLinesParameters = typing.TypedDict('FindVarianceLinesParameters', {
 })
 
 
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "find_variance_lines": find_variance_lines_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 {
-        "find_variance_lines": find_variance_lines_outputs,
-    }.get(t)
-
-
-class FindVarianceLinesOutputs(typing.NamedTuple):
+class FindVarianceLinesTcshOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `find_variance_lines(...)`.
+    Output object returned when calling `FindVarianceLinesTcshParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    variance_maps: OutputPathType | None
-    """Variance maps per run"""
-    scaled_variance_maps: OutputPathType | None
-    """Scaled variance maps per run"""
-    cluster_reports: OutputPathType | None
-    """Cluster reports"""
-    jpeg_images: OutputPathType | None
-    """JPEG images showing locations of high variance"""
+    output_directory: OutputPathType | None
+    """Output directory containing maps and reports."""
 
 
-def find_variance_lines_params(
+def find_variance_lines_tcsh_params(
     input_files: list[InputPathType],
     mask: str | None = None,
     min_cvox: int | None = None,
@@ -97,7 +77,7 @@ def find_variance_lines_params(
     help_: bool = False,
     hist: bool = False,
     ver: bool = False,
-) -> FindVarianceLinesParameters:
+) -> FindVarianceLinesTcshParametersTagged:
     """
     Build parameters.
     
@@ -121,7 +101,7 @@ def find_variance_lines_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "find_variance_lines",
+        "@type": "afni/find_variance_lines.tcsh",
         "input_files": input_files,
         "echo": echo,
         "help": help_,
@@ -151,8 +131,8 @@ def find_variance_lines_params(
     return params
 
 
-def find_variance_lines_cargs(
-    params: FindVarianceLinesParameters,
+def find_variance_lines_tcsh_cargs(
+    params: FindVarianceLinesTcshParameters,
     execution: Execution,
 ) -> list[str]:
     """
@@ -166,72 +146,72 @@ def find_variance_lines_cargs(
     """
     cargs = []
     cargs.append("find_variance_lines.tcsh")
-    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
-    if params.get("mask") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("input_files", None)])
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            params.get("mask")
+            params.get("mask", None)
         ])
-    if params.get("min_cvox") is not None:
+    if params.get("min_cvox", None) is not None:
         cargs.extend([
             "-min_cvox",
-            str(params.get("min_cvox"))
+            str(params.get("min_cvox", None))
         ])
-    if params.get("min_nt") is not None:
+    if params.get("min_nt", None) is not None:
         cargs.extend([
             "-min_nt",
-            str(params.get("min_nt"))
+            str(params.get("min_nt", None))
         ])
-    if params.get("nerode") is not None:
+    if params.get("nerode", None) is not None:
         cargs.extend([
             "-nerode",
-            str(params.get("nerode"))
+            str(params.get("nerode", None))
         ])
-    if params.get("nfirst") is not None:
+    if params.get("nfirst", None) is not None:
         cargs.extend([
             "-nfirst",
-            str(params.get("nfirst"))
+            str(params.get("nfirst", None))
         ])
-    if params.get("percentile") is not None:
+    if params.get("percentile", None) is not None:
         cargs.extend([
             "-perc",
-            str(params.get("percentile"))
+            str(params.get("percentile", None))
         ])
-    if params.get("polort") is not None:
+    if params.get("polort", None) is not None:
         cargs.extend([
             "-polort",
-            params.get("polort")
+            params.get("polort", None)
         ])
-    if params.get("output_dir") is not None:
+    if params.get("output_dir", None) is not None:
         cargs.extend([
             "-rdir",
-            params.get("output_dir")
+            params.get("output_dir", None)
         ])
-    if params.get("do_clean") is not None:
+    if params.get("do_clean", None) is not None:
         cargs.extend([
             "-do_clean",
-            str(params.get("do_clean"))
+            str(params.get("do_clean", None))
         ])
-    if params.get("do_img") is not None:
+    if params.get("do_img", None) is not None:
         cargs.extend([
             "-do_img",
-            str(params.get("do_img"))
+            str(params.get("do_img", None))
         ])
-    if params.get("echo"):
+    if params.get("echo", False):
         cargs.append("-echo")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("hist"):
+    if params.get("hist", False):
         cargs.append("-hist")
-    if params.get("ver"):
+    if params.get("ver", False):
         cargs.append("-ver")
     return cargs
 
 
-def find_variance_lines_outputs(
-    params: FindVarianceLinesParameters,
+def find_variance_lines_tcsh_outputs(
+    params: FindVarianceLinesTcshParameters,
     execution: Execution,
-) -> FindVarianceLinesOutputs:
+) -> FindVarianceLinesTcshOutputs:
     """
     Build outputs object containing output file paths and possibly stdout/stderr.
     
@@ -241,23 +221,22 @@ def find_variance_lines_outputs(
     Returns:
         Outputs object.
     """
-    ret = FindVarianceLinesOutputs(
+    ret = FindVarianceLinesTcshOutputs(
         root=execution.output_file("."),
-        variance_maps=execution.output_file(params.get("output_dir") + "/variance_map_run*.nii.gz") if (params.get("output_dir") is not None) else None,
-        scaled_variance_maps=execution.output_file(params.get("output_dir") + "/scaled_variance_map_run*.nii.gz") if (params.get("output_dir") is not None) else None,
-        cluster_reports=execution.output_file(params.get("output_dir") + "/cluster_report_run*.txt") if (params.get("output_dir") is not None) else None,
-        jpeg_images=execution.output_file(params.get("output_dir") + "/*.jpg") if (params.get("output_dir") is not None) else None,
+        output_directory=execution.output_file(params.get("output_dir", None)) if (params.get("output_dir") is not None) else None,
     )
     return ret
 
 
-def find_variance_lines_execute(
-    params: FindVarianceLinesParameters,
-    execution: Execution,
-) -> FindVarianceLinesOutputs:
+def find_variance_lines_tcsh_execute(
+    params: FindVarianceLinesTcshParameters,
+    runner: Runner | None = None,
+) -> FindVarianceLinesTcshOutputs:
     """
-    Look for bars of high variance that might suggest scanner interference in EPI
-    datasets.
+    find_variance_lines.tcsh
+    
+    Look for bars of high variance that might suggest scanner interference in
+    EPI datasets.
     
     Author: AFNI Developers
     
@@ -265,18 +244,20 @@ def find_variance_lines_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `FindVarianceLinesOutputs`).
+        NamedTuple of outputs (described in `FindVarianceLinesTcshOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIND_VARIANCE_LINES_TCSH_METADATA)
     params = execution.params(params)
-    cargs = find_variance_lines_cargs(params, execution)
-    ret = find_variance_lines_outputs(params, execution)
+    cargs = find_variance_lines_tcsh_cargs(params, execution)
+    ret = find_variance_lines_tcsh_outputs(params, execution)
     execution.run(cargs)
     return ret
 
 
-def find_variance_lines(
+def find_variance_lines_tcsh(
     input_files: list[InputPathType],
     mask: str | None = None,
     min_cvox: int | None = None,
@@ -293,10 +274,12 @@ def find_variance_lines(
     hist: bool = False,
     ver: bool = False,
     runner: Runner | None = None,
-) -> FindVarianceLinesOutputs:
+) -> FindVarianceLinesTcshOutputs:
     """
-    Look for bars of high variance that might suggest scanner interference in EPI
-    datasets.
+    find_variance_lines.tcsh
+    
+    Look for bars of high variance that might suggest scanner interference in
+    EPI datasets.
     
     Author: AFNI Developers
     
@@ -320,11 +303,9 @@ def find_variance_lines(
         ver: Show the current version.
         runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `FindVarianceLinesOutputs`).
+        NamedTuple of outputs (described in `FindVarianceLinesTcshOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FIND_VARIANCE_LINES_METADATA)
-    params = find_variance_lines_params(
+    params = find_variance_lines_tcsh_params(
         input_files=input_files,
         mask=mask,
         min_cvox=min_cvox,
@@ -341,13 +322,13 @@ def find_variance_lines(
         hist=hist,
         ver=ver,
     )
-    return find_variance_lines_execute(params, execution)
+    return find_variance_lines_tcsh_execute(params, runner)
 
 
 __all__ = [
-    "FIND_VARIANCE_LINES_METADATA",
-    "FindVarianceLinesOutputs",
-    "FindVarianceLinesParameters",
-    "find_variance_lines",
-    "find_variance_lines_params",
+    "FIND_VARIANCE_LINES_TCSH_METADATA",
+    "FindVarianceLinesTcshOutputs",
+    "find_variance_lines_tcsh",
+    "find_variance_lines_tcsh_execute",
+    "find_variance_lines_tcsh_params",
 ]