niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__shift_volume.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__SHIFT_VOLUME_METADATA = Metadata(
+    id="8632323dd36a0ba5f059c998ffcd7826b058d4be.boutiques",
+    name="@Shift_Volume",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VShiftVolumeParameters = typing.TypedDict('VShiftVolumeParameters', {
+    "__STYX_TYPE__": typing.Literal["@Shift_Volume"],
+    "rai_shift_vector": typing.NotRequired[list[float] | None],
+    "mni_anat_to_mni": bool,
+    "mni_to_mni_anat": bool,
+    "dset": InputPathType,
+    "no_cp": bool,
+    "prefix": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@Shift_Volume": v__shift_volume_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 {
+        "@Shift_Volume": v__shift_volume_outputs,
+    }.get(t)
+
+
+class VShiftVolumeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__shift_volume(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Shifted output dataset."""
+
+
+def v__shift_volume_params(
+    dset: InputPathType,
+    prefix: str,
+    rai_shift_vector: list[float] | None = None,
+    mni_anat_to_mni: bool = False,
+    mni_to_mni_anat: bool = False,
+    no_cp: bool = False,
+) -> VShiftVolumeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dset: Input dataset, typically an anatomical dataset to be aligned to\
+            BASE.
+        prefix: Prefix for the output dataset.
+        rai_shift_vector: Move dataset by dR, dA, dI mm (RAI coordinate system).
+        mni_anat_to_mni: Move dataset from MNI Anatomical space to MNI space\
+            (equivalent to -rai_shift 0 -4 -5).
+        mni_to_mni_anat: Move dataset from MNI space to MNI Anatomical space\
+            (equivalent to -rai_shift 0 4 5).
+        no_cp: Do not create new data, shift the existing ones (use with\
+            caution).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@Shift_Volume",
+        "mni_anat_to_mni": mni_anat_to_mni,
+        "mni_to_mni_anat": mni_to_mni_anat,
+        "dset": dset,
+        "no_cp": no_cp,
+        "prefix": prefix,
+    }
+    if rai_shift_vector is not None:
+        params["rai_shift_vector"] = rai_shift_vector
+    return params
+
+
+def v__shift_volume_cargs(
+    params: VShiftVolumeParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("@Shift_Volume")
+    if params.get("rai_shift_vector") is not None:
+        cargs.extend([
+            "-rai_shift",
+            *map(str, params.get("rai_shift_vector"))
+        ])
+    if params.get("mni_anat_to_mni"):
+        cargs.append("-MNI_Anat_to_MNI")
+    if params.get("mni_to_mni_anat"):
+        cargs.append("-MNI_to_MNI_Anat")
+    cargs.extend([
+        "-dset",
+        execution.input_file(params.get("dset"))
+    ])
+    if params.get("no_cp"):
+        cargs.append("-no_cp")
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    return cargs
+
+
+def v__shift_volume_outputs(
+    params: VShiftVolumeParameters,
+    execution: Execution,
+) -> VShiftVolumeOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = VShiftVolumeOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + ".nii.gz"),
+    )
+    return ret
+
+
+def v__shift_volume_execute(
+    params: VShiftVolumeParameters,
+    execution: Execution,
+) -> VShiftVolumeOutputs:
+    """
+    Tool to shift a dataset in the RAI coordinate system or between MNI anatomical
+    space and MNI space.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VShiftVolumeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__shift_volume_cargs(params, execution)
+    ret = v__shift_volume_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__shift_volume(
+    dset: InputPathType,
+    prefix: str,
+    rai_shift_vector: list[float] | None = None,
+    mni_anat_to_mni: bool = False,
+    mni_to_mni_anat: bool = False,
+    no_cp: bool = False,
+    runner: Runner | None = None,
+) -> VShiftVolumeOutputs:
+    """
+    Tool to shift a dataset in the RAI coordinate system or between MNI anatomical
+    space and MNI space.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dset: Input dataset, typically an anatomical dataset to be aligned to\
+            BASE.
+        prefix: Prefix for the output dataset.
+        rai_shift_vector: Move dataset by dR, dA, dI mm (RAI coordinate system).
+        mni_anat_to_mni: Move dataset from MNI Anatomical space to MNI space\
+            (equivalent to -rai_shift 0 -4 -5).
+        mni_to_mni_anat: Move dataset from MNI space to MNI Anatomical space\
+            (equivalent to -rai_shift 0 4 5).
+        no_cp: Do not create new data, shift the existing ones (use with\
+            caution).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VShiftVolumeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SHIFT_VOLUME_METADATA)
+    params = v__shift_volume_params(
+        rai_shift_vector=rai_shift_vector,
+        mni_anat_to_mni=mni_anat_to_mni,
+        mni_to_mni_anat=mni_to_mni_anat,
+        dset=dset,
+        no_cp=no_cp,
+        prefix=prefix,
+    )
+    return v__shift_volume_execute(params, execution)
+
+
+__all__ = [
+    "VShiftVolumeOutputs",
+    "VShiftVolumeParameters",
+    "V__SHIFT_VOLUME_METADATA",
+    "v__shift_volume",
+    "v__shift_volume_params",
+]

niwrap_afni/afni/v__show_dynamic_range.py

@@ -0,0 +1,183 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__SHOW_DYNAMIC_RANGE_METADATA = Metadata(
+    id="d0ec3925ed417e46aad2070bdc6ba2ddd1248eca.boutiques",
+    name="@ShowDynamicRange",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VShowDynamicRangeParameters = typing.TypedDict('VShowDynamicRangeParameters', {
+    "__STYX_TYPE__": typing.Literal["@ShowDynamicRange"],
+    "infile": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@ShowDynamicRange": v__show_dynamic_range_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 {
+        "@ShowDynamicRange": v__show_dynamic_range_outputs,
+    }.get(t)
+
+
+class VShowDynamicRangeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__show_dynamic_range(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    minpercchange_file: OutputPathType
+    """Dataset showing the percent signal change that an increment of 1
+    digitized value in the time series corresponds to."""
+    range_file: OutputPathType
+    """Dataset showing the number of discrete levels used to represent the time
+    series."""
+
+
+def v__show_dynamic_range_params(
+    infile: InputPathType,
+) -> VShowDynamicRangeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Input EPI time series dataset (e.g. epi.nii.gz).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@ShowDynamicRange",
+        "infile": infile,
+    }
+    return params
+
+
+def v__show_dynamic_range_cargs(
+    params: VShowDynamicRangeParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("@ShowDynamicRange")
+    cargs.append(execution.input_file(params.get("infile")))
+    return cargs
+
+
+def v__show_dynamic_range_outputs(
+    params: VShowDynamicRangeParameters,
+    execution: Execution,
+) -> VShowDynamicRangeOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = VShowDynamicRangeOutputs(
+        root=execution.output_file("."),
+        minpercchange_file=execution.output_file(pathlib.Path(params.get("infile")).name + "_minpercchange.nii.gz"),
+        range_file=execution.output_file(pathlib.Path(params.get("infile")).name + ".range.nii.gz"),
+    )
+    return ret
+
+
+def v__show_dynamic_range_execute(
+    params: VShowDynamicRangeParameters,
+    execution: Execution,
+) -> VShowDynamicRangeOutputs:
+    """
+    The script checks the dynamic range of the time series data at locations inside
+    the brain.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VShowDynamicRangeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__show_dynamic_range_cargs(params, execution)
+    ret = v__show_dynamic_range_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__show_dynamic_range(
+    infile: InputPathType,
+    runner: Runner | None = None,
+) -> VShowDynamicRangeOutputs:
+    """
+    The script checks the dynamic range of the time series data at locations inside
+    the brain.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Input EPI time series dataset (e.g. epi.nii.gz).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VShowDynamicRangeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SHOW_DYNAMIC_RANGE_METADATA)
+    params = v__show_dynamic_range_params(
+        infile=infile,
+    )
+    return v__show_dynamic_range_execute(params, execution)
+
+
+__all__ = [
+    "VShowDynamicRangeOutputs",
+    "VShowDynamicRangeParameters",
+    "V__SHOW_DYNAMIC_RANGE_METADATA",
+    "v__show_dynamic_range",
+    "v__show_dynamic_range_params",
+]