niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/fat_proc_dwi_to_dt.py

@@ -0,0 +1,522 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FAT_PROC_DWI_TO_DT_METADATA = Metadata(
+    id="c5a2942f4ac3b0a68c89864b914dd62d776684d1.boutiques",
+    name="fat_proc_dwi_to_dt",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FatProcDwiToDtParameters = typing.TypedDict('FatProcDwiToDtParameters', {
+    "__STYX_TYPE__": typing.Literal["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],
+})
+
+
+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(...)`.
+    """
+    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(
+    in_dwi: InputPathType,
+    in_gradmat: InputPathType,
+    prefix: str,
+    in_bvals: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    mask_from_struc: bool = False,
+    in_struc_res: InputPathType | None = None,
+    in_ref_orig: InputPathType | None = None,
+    prefix_dti: str | None = None,
+    flip_x: bool = False,
+    flip_y: bool = False,
+    flip_z: bool = False,
+    no_flip: bool = False,
+    no_scale_out_1000: bool = False,
+    no_reweight: bool = False,
+    no_cumulative_wts: bool = False,
+    qc_fa_thr: float | None = None,
+    qc_fa_max: float | None = None,
+    qc_fa_unc_max: float | None = None,
+    qc_v12_unc_max: float | None = None,
+    qc_prefix: str | None = None,
+    no_qc_view: bool = False,
+    no_cmd_out: bool = False,
+    workdir: str | None = None,
+    no_clean: bool = False,
+    uncert_off: bool = False,
+    uncert_iters: float | None = None,
+    uncert_extra_cmds: str | None = None,
+    check_abs_min: float | None = None,
+) -> FatProcDwiToDtParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_dwi: 4D volume of N DWIs. Required.
+        in_gradmat: Input text file of N gradient vectors or bmatrices.
+        prefix: Set prefix for output DWI data.
+        in_bvals: Optional, if bvalue information is in a separate file from\
+            the b-vectors or matrices.
+        mask: Optional whole brain mask can be input; otherwise, automasking is\
+            performed.
+        mask_from_struc: Flag to make a mask using 3dSkullStrip+3dmask_tool\
+            from the structural file.
+        in_struc_res: Alignment of the output DWI to the REF data set via\
+            anatomical reference; a version of the anatomical that has been\
+            resampled to match the DWI set.
+        in_ref_orig: Use another data set to adjust the DWI and subsequent\
+            parameter dsets' orientation and origin.
+        prefix_dti: Set prefix for output DTI data; default is 'dt'. Do not\
+            include path information here.
+        flip_x: Flip the DW gradients in the x-direction.
+        flip_y: Flip the DW gradients in the y-direction.
+        flip_z: Flip the DW gradients in the z-direction.
+        no_flip: Do not flip the DW gradients.
+        no_scale_out_1000: Turn off scaling of physical length units by 1000\
+            for tensor fitting.
+        no_reweight: Turn off reweighting and refitting of tensors during\
+            estimation.
+        no_cumulative_wts: Turn off displaying overall weight factors for each\
+            gradient.
+        qc_fa_thr: Set threshold for overlay FA volume in QC image.
+        qc_fa_max: Set cbar max for overlay FA volume in QC image.
+        qc_fa_unc_max: Set cbar max for overlay uncertainty (stdev) of FA in QC\
+            image.
+        qc_v12_unc_max: Set cbar max for overlay uncertainty (stdev) of V1\
+            towards V2 direction for DTs in QC image.
+        qc_prefix: Set the prefix of the QC image files separately.
+        no_qc_view: Turn off generating QC image files.
+        no_cmd_out: Don't save the command line call of this program and the\
+            location where it was run.
+        workdir: Specify a working directory, which can be removed.
+        no_clean: Do not remove the working directory.
+        uncert_off: Don't perform uncertainty calculation.
+        uncert_iters: Set the number of Monte Carlo iterations for the\
+            uncertainty calculation (default: 300).
+        uncert_extra_cmds: Extra commands for the uncertainty calculations.
+        check_abs_min: Help the program push through finding tiny negative\
+            values in columns that should contain numbers >=0. Provide a tolerance\
+            value VVV.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fat_proc_dwi_to_dt",
+        "in_dwi": in_dwi,
+        "in_gradmat": in_gradmat,
+        "prefix": prefix,
+        "mask_from_struc": mask_from_struc,
+        "flip_x": flip_x,
+        "flip_y": flip_y,
+        "flip_z": flip_z,
+        "no_flip": no_flip,
+        "no_scale_out_1000": no_scale_out_1000,
+        "no_reweight": no_reweight,
+        "no_cumulative_wts": no_cumulative_wts,
+        "no_qc_view": no_qc_view,
+        "no_cmd_out": no_cmd_out,
+        "no_clean": no_clean,
+        "uncert_off": uncert_off,
+    }
+    if in_bvals is not None:
+        params["in_bvals"] = in_bvals
+    if mask is not None:
+        params["mask"] = mask
+    if in_struc_res is not None:
+        params["in_struc_res"] = in_struc_res
+    if in_ref_orig is not None:
+        params["in_ref_orig"] = in_ref_orig
+    if prefix_dti is not None:
+        params["prefix_dti"] = prefix_dti
+    if qc_fa_thr is not None:
+        params["qc_fa_thr"] = qc_fa_thr
+    if qc_fa_max is not None:
+        params["qc_fa_max"] = qc_fa_max
+    if qc_fa_unc_max is not None:
+        params["qc_fa_unc_max"] = qc_fa_unc_max
+    if qc_v12_unc_max is not None:
+        params["qc_v12_unc_max"] = qc_v12_unc_max
+    if qc_prefix is not None:
+        params["qc_prefix"] = qc_prefix
+    if workdir is not None:
+        params["workdir"] = workdir
+    if uncert_iters is not None:
+        params["uncert_iters"] = uncert_iters
+    if uncert_extra_cmds is not None:
+        params["uncert_extra_cmds"] = uncert_extra_cmds
+    if check_abs_min is not None:
+        params["check_abs_min"] = check_abs_min
+    return params
+
+
+def fat_proc_dwi_to_dt_cargs(
+    params: FatProcDwiToDtParameters,
+    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("fat_proc_dwi_to_dt")
+    cargs.append(execution.input_file(params.get("in_dwi")))
+    cargs.extend([
+        "-in_col_matA | -in_col_matT | -in_col_vec | -in_row_vec",
+        execution.input_file(params.get("in_gradmat"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("in_bvals") is not None:
+        cargs.extend([
+            "-in_bvals",
+            execution.input_file(params.get("in_bvals"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("mask_from_struc"):
+        cargs.append("-mask_from_struc")
+    if params.get("in_struc_res") is not None:
+        cargs.extend([
+            "-in_struc_res",
+            execution.input_file(params.get("in_struc_res"))
+        ])
+    if params.get("in_ref_orig") is not None:
+        cargs.extend([
+            "-in_ref_orig",
+            execution.input_file(params.get("in_ref_orig"))
+        ])
+    if params.get("prefix_dti") is not None:
+        cargs.extend([
+            "-prefix_dti",
+            params.get("prefix_dti")
+        ])
+    if params.get("flip_x"):
+        cargs.append("-flip_x")
+    if params.get("flip_y"):
+        cargs.append("-flip_y")
+    if params.get("flip_z"):
+        cargs.append("-flip_z")
+    if params.get("no_flip"):
+        cargs.append("-no_flip")
+    if params.get("no_scale_out_1000"):
+        cargs.append("-no_scale_out_1000")
+    if params.get("no_reweight"):
+        cargs.append("-no_reweight")
+    if params.get("no_cumulative_wts"):
+        cargs.append("-no_cumulative_wts")
+    if params.get("qc_fa_thr") is not None:
+        cargs.extend([
+            "-qc_fa_thr",
+            str(params.get("qc_fa_thr"))
+        ])
+    if params.get("qc_fa_max") is not None:
+        cargs.extend([
+            "-qc_fa_max",
+            str(params.get("qc_fa_max"))
+        ])
+    if params.get("qc_fa_unc_max") is not None:
+        cargs.extend([
+            "-qc_fa_unc_max",
+            str(params.get("qc_fa_unc_max"))
+        ])
+    if params.get("qc_v12_unc_max") is not None:
+        cargs.extend([
+            "-qc_v12_unc_max",
+            str(params.get("qc_v12_unc_max"))
+        ])
+    if params.get("qc_prefix") is not None:
+        cargs.extend([
+            "-qc_prefix",
+            params.get("qc_prefix")
+        ])
+    if params.get("no_qc_view"):
+        cargs.append("-no_qc_view")
+    if params.get("no_cmd_out"):
+        cargs.append("-no_cmd_out")
+    if params.get("workdir") is not None:
+        cargs.extend([
+            "-workdir",
+            params.get("workdir")
+        ])
+    if params.get("no_clean"):
+        cargs.append("-no_clean")
+    if params.get("uncert_off"):
+        cargs.append("-uncert_off")
+    if params.get("uncert_iters") is not None:
+        cargs.extend([
+            "-uncert_iters",
+            str(params.get("uncert_iters"))
+        ])
+    if params.get("uncert_extra_cmds") is not None:
+        cargs.extend([
+            "-uncert_extra_cmds",
+            params.get("uncert_extra_cmds")
+        ])
+    if params.get("check_abs_min") is not None:
+        cargs.extend([
+            "-check_abs_min",
+            str(params.get("check_abs_min"))
+        ])
+    return cargs
+
+
+def fat_proc_dwi_to_dt_outputs(
+    params: FatProcDwiToDtParameters,
+    execution: Execution,
+) -> FatProcDwiToDtOutputs:
+    """
+    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 = 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,
+) -> FatProcDwiToDtOutputs:
+    """
+    This program fits tensors and DT parameters, as well as the uncertainty of DT
+    parameters needed for tractography.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FatProcDwiToDtOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fat_proc_dwi_to_dt_cargs(params, execution)
+    ret = fat_proc_dwi_to_dt_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fat_proc_dwi_to_dt(
+    in_dwi: InputPathType,
+    in_gradmat: InputPathType,
+    prefix: str,
+    in_bvals: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    mask_from_struc: bool = False,
+    in_struc_res: InputPathType | None = None,
+    in_ref_orig: InputPathType | None = None,
+    prefix_dti: str | None = None,
+    flip_x: bool = False,
+    flip_y: bool = False,
+    flip_z: bool = False,
+    no_flip: bool = False,
+    no_scale_out_1000: bool = False,
+    no_reweight: bool = False,
+    no_cumulative_wts: bool = False,
+    qc_fa_thr: float | None = None,
+    qc_fa_max: float | None = None,
+    qc_fa_unc_max: float | None = None,
+    qc_v12_unc_max: float | None = None,
+    qc_prefix: str | None = None,
+    no_qc_view: bool = False,
+    no_cmd_out: bool = False,
+    workdir: str | None = None,
+    no_clean: bool = False,
+    uncert_off: bool = False,
+    uncert_iters: float | None = None,
+    uncert_extra_cmds: str | None = None,
+    check_abs_min: float | None = None,
+    runner: Runner | None = None,
+) -> FatProcDwiToDtOutputs:
+    """
+    This program fits tensors and DT parameters, as well as the uncertainty of DT
+    parameters needed for tractography.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_dwi: 4D volume of N DWIs. Required.
+        in_gradmat: Input text file of N gradient vectors or bmatrices.
+        prefix: Set prefix for output DWI data.
+        in_bvals: Optional, if bvalue information is in a separate file from\
+            the b-vectors or matrices.
+        mask: Optional whole brain mask can be input; otherwise, automasking is\
+            performed.
+        mask_from_struc: Flag to make a mask using 3dSkullStrip+3dmask_tool\
+            from the structural file.
+        in_struc_res: Alignment of the output DWI to the REF data set via\
+            anatomical reference; a version of the anatomical that has been\
+            resampled to match the DWI set.
+        in_ref_orig: Use another data set to adjust the DWI and subsequent\
+            parameter dsets' orientation and origin.
+        prefix_dti: Set prefix for output DTI data; default is 'dt'. Do not\
+            include path information here.
+        flip_x: Flip the DW gradients in the x-direction.
+        flip_y: Flip the DW gradients in the y-direction.
+        flip_z: Flip the DW gradients in the z-direction.
+        no_flip: Do not flip the DW gradients.
+        no_scale_out_1000: Turn off scaling of physical length units by 1000\
+            for tensor fitting.
+        no_reweight: Turn off reweighting and refitting of tensors during\
+            estimation.
+        no_cumulative_wts: Turn off displaying overall weight factors for each\
+            gradient.
+        qc_fa_thr: Set threshold for overlay FA volume in QC image.
+        qc_fa_max: Set cbar max for overlay FA volume in QC image.
+        qc_fa_unc_max: Set cbar max for overlay uncertainty (stdev) of FA in QC\
+            image.
+        qc_v12_unc_max: Set cbar max for overlay uncertainty (stdev) of V1\
+            towards V2 direction for DTs in QC image.
+        qc_prefix: Set the prefix of the QC image files separately.
+        no_qc_view: Turn off generating QC image files.
+        no_cmd_out: Don't save the command line call of this program and the\
+            location where it was run.
+        workdir: Specify a working directory, which can be removed.
+        no_clean: Do not remove the working directory.
+        uncert_off: Don't perform uncertainty calculation.
+        uncert_iters: Set the number of Monte Carlo iterations for the\
+            uncertainty calculation (default: 300).
+        uncert_extra_cmds: Extra commands for the uncertainty calculations.
+        check_abs_min: Help the program push through finding tiny negative\
+            values in columns that should contain numbers >=0. Provide a tolerance\
+            value VVV.
+        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 = fat_proc_dwi_to_dt_params(
+        in_dwi=in_dwi,
+        in_gradmat=in_gradmat,
+        prefix=prefix,
+        in_bvals=in_bvals,
+        mask=mask,
+        mask_from_struc=mask_from_struc,
+        in_struc_res=in_struc_res,
+        in_ref_orig=in_ref_orig,
+        prefix_dti=prefix_dti,
+        flip_x=flip_x,
+        flip_y=flip_y,
+        flip_z=flip_z,
+        no_flip=no_flip,
+        no_scale_out_1000=no_scale_out_1000,
+        no_reweight=no_reweight,
+        no_cumulative_wts=no_cumulative_wts,
+        qc_fa_thr=qc_fa_thr,
+        qc_fa_max=qc_fa_max,
+        qc_fa_unc_max=qc_fa_unc_max,
+        qc_v12_unc_max=qc_v12_unc_max,
+        qc_prefix=qc_prefix,
+        no_qc_view=no_qc_view,
+        no_cmd_out=no_cmd_out,
+        workdir=workdir,
+        no_clean=no_clean,
+        uncert_off=uncert_off,
+        uncert_iters=uncert_iters,
+        uncert_extra_cmds=uncert_extra_cmds,
+        check_abs_min=check_abs_min,
+    )
+    return fat_proc_dwi_to_dt_execute(params, execution)
+
+
+__all__ = [
+    "FAT_PROC_DWI_TO_DT_METADATA",
+    "FatProcDwiToDtOutputs",
+    "FatProcDwiToDtParameters",
+    "fat_proc_dwi_to_dt",
+    "fat_proc_dwi_to_dt_params",
+]