niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/fat_proc_filter_dwis.py

@@ -0,0 +1,321 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FAT_PROC_FILTER_DWIS_METADATA = Metadata(
+    id="f1ab079defa2b7a6a0437c119ce099f8d81cc812.boutiques",
+    name="fat_proc_filter_dwis",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FatProcFilterDwisParameters = typing.TypedDict('FatProcFilterDwisParameters', {
+    "__STYX_TYPE__": typing.Literal["fat_proc_filter_dwis"],
+    "input_dwi": InputPathType,
+    "input_gradient": InputPathType,
+    "select_string": str,
+    "select_file": typing.NotRequired[InputPathType | None],
+    "output_prefix": str,
+    "input_bvals": typing.NotRequired[InputPathType | None],
+    "unit_mag_out": bool,
+    "qc_prefix": typing.NotRequired[str | None],
+    "no_qc_view": bool,
+    "no_cmd_out": bool,
+    "do_movie": typing.NotRequired[typing.Literal["AGIF", "MPEG"] | 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_filter_dwis": fat_proc_filter_dwis_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_filter_dwis": fat_proc_filter_dwis_outputs,
+    }.get(t)
+
+
+class FatProcFilterDwisOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fat_proc_filter_dwis(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    filtered_dwi: OutputPathType
+    """Filtered 4D DWI dataset."""
+    filtered_bvecs: OutputPathType
+    """Filtered gradient file matching input format."""
+    filtered_bvals: OutputPathType
+    """Filtered b-values file, if provided."""
+
+
+def fat_proc_filter_dwis_params(
+    input_dwi: InputPathType,
+    input_gradient: InputPathType,
+    select_string: str,
+    output_prefix: str,
+    select_file: InputPathType | None = None,
+    input_bvals: InputPathType | None = None,
+    unit_mag_out: bool = False,
+    qc_prefix: str | None = None,
+    no_qc_view: bool = False,
+    no_cmd_out: bool = False,
+    do_movie: typing.Literal["AGIF", "MPEG"] | None = None,
+) -> FatProcFilterDwisParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dwi: Name of a 4D file of DWIs (required).
+        input_gradient: Bvec/bmat file from the gradients. Required. One of\
+            these options must be used: -in_col_matA, -in_col_matT, -in_col_vec,\
+            -in_row_vec.
+        select_string: A string of indices and index ranges for selecting which\
+            volumes/grads/bvals to keep. This string gets applied to the volume,\
+            bval|bvec|bmat files for an input set. Either this or -select_file is\
+            required.
+        output_prefix: Output prefix for all the volumes and text files.\
+            Required.
+        select_file: A file containing a string of indices and index ranges for\
+            selecting which volumes/grads/bvals to keep. This string gets applied\
+            to the volume, bval|bvec|bmat files for an input set. Either this or\
+            -select is required.
+        input_bvals: If the bvec/bmat is a file of unit-magnitude values, then\
+            the bvalues can be input.
+        unit_mag_out: Ensure that the output grad information is unit\
+            magnitude.
+        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.
+        do_movie: Output a movie of the newly created dataset (AGIF or MPEG).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fat_proc_filter_dwis",
+        "input_dwi": input_dwi,
+        "input_gradient": input_gradient,
+        "select_string": select_string,
+        "output_prefix": output_prefix,
+        "unit_mag_out": unit_mag_out,
+        "no_qc_view": no_qc_view,
+        "no_cmd_out": no_cmd_out,
+    }
+    if select_file is not None:
+        params["select_file"] = select_file
+    if input_bvals is not None:
+        params["input_bvals"] = input_bvals
+    if qc_prefix is not None:
+        params["qc_prefix"] = qc_prefix
+    if do_movie is not None:
+        params["do_movie"] = do_movie
+    return params
+
+
+def fat_proc_filter_dwis_cargs(
+    params: FatProcFilterDwisParameters,
+    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_filter_dwis")
+    cargs.extend([
+        "-in_dwi",
+        execution.input_file(params.get("input_dwi"))
+    ])
+    cargs.extend([
+        "-in_col_matA|-in_col_matT|-in_col_vec|-in_row_vec",
+        execution.input_file(params.get("input_gradient"))
+    ])
+    cargs.extend([
+        "-select",
+        params.get("select_string")
+    ])
+    if params.get("select_file") is not None:
+        cargs.extend([
+            "-select_file",
+            execution.input_file(params.get("select_file"))
+        ])
+    cargs.extend([
+        "-prefix",
+        params.get("output_prefix")
+    ])
+    if params.get("input_bvals") is not None:
+        cargs.extend([
+            "-in_bvals",
+            execution.input_file(params.get("input_bvals"))
+        ])
+    if params.get("unit_mag_out"):
+        cargs.append("-unit_mag_out")
+    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("do_movie") is not None:
+        cargs.extend([
+            "-do_movie",
+            params.get("do_movie")
+        ])
+    return cargs
+
+
+def fat_proc_filter_dwis_outputs(
+    params: FatProcFilterDwisParameters,
+    execution: Execution,
+) -> FatProcFilterDwisOutputs:
+    """
+    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 = FatProcFilterDwisOutputs(
+        root=execution.output_file("."),
+        filtered_dwi=execution.output_file(params.get("output_prefix") + "_filtered.nii.gz"),
+        filtered_bvecs=execution.output_file(params.get("output_prefix") + "_filtered.bvecs"),
+        filtered_bvals=execution.output_file(params.get("output_prefix") + "_filtered.bvals"),
+    )
+    return ret
+
+
+def fat_proc_filter_dwis_execute(
+    params: FatProcFilterDwisParameters,
+    execution: Execution,
+) -> FatProcFilterDwisOutputs:
+    """
+    Filter out user-found and user-defined bad volumes from DWI data sets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FatProcFilterDwisOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fat_proc_filter_dwis_cargs(params, execution)
+    ret = fat_proc_filter_dwis_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fat_proc_filter_dwis(
+    input_dwi: InputPathType,
+    input_gradient: InputPathType,
+    select_string: str,
+    output_prefix: str,
+    select_file: InputPathType | None = None,
+    input_bvals: InputPathType | None = None,
+    unit_mag_out: bool = False,
+    qc_prefix: str | None = None,
+    no_qc_view: bool = False,
+    no_cmd_out: bool = False,
+    do_movie: typing.Literal["AGIF", "MPEG"] | None = None,
+    runner: Runner | None = None,
+) -> FatProcFilterDwisOutputs:
+    """
+    Filter out user-found and user-defined bad volumes from DWI data sets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dwi: Name of a 4D file of DWIs (required).
+        input_gradient: Bvec/bmat file from the gradients. Required. One of\
+            these options must be used: -in_col_matA, -in_col_matT, -in_col_vec,\
+            -in_row_vec.
+        select_string: A string of indices and index ranges for selecting which\
+            volumes/grads/bvals to keep. This string gets applied to the volume,\
+            bval|bvec|bmat files for an input set. Either this or -select_file is\
+            required.
+        output_prefix: Output prefix for all the volumes and text files.\
+            Required.
+        select_file: A file containing a string of indices and index ranges for\
+            selecting which volumes/grads/bvals to keep. This string gets applied\
+            to the volume, bval|bvec|bmat files for an input set. Either this or\
+            -select is required.
+        input_bvals: If the bvec/bmat is a file of unit-magnitude values, then\
+            the bvalues can be input.
+        unit_mag_out: Ensure that the output grad information is unit\
+            magnitude.
+        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.
+        do_movie: Output a movie of the newly created dataset (AGIF or MPEG).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FatProcFilterDwisOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_PROC_FILTER_DWIS_METADATA)
+    params = fat_proc_filter_dwis_params(
+        input_dwi=input_dwi,
+        input_gradient=input_gradient,
+        select_string=select_string,
+        select_file=select_file,
+        output_prefix=output_prefix,
+        input_bvals=input_bvals,
+        unit_mag_out=unit_mag_out,
+        qc_prefix=qc_prefix,
+        no_qc_view=no_qc_view,
+        no_cmd_out=no_cmd_out,
+        do_movie=do_movie,
+    )
+    return fat_proc_filter_dwis_execute(params, execution)
+
+
+__all__ = [
+    "FAT_PROC_FILTER_DWIS_METADATA",
+    "FatProcFilterDwisOutputs",
+    "FatProcFilterDwisParameters",
+    "fat_proc_filter_dwis",
+    "fat_proc_filter_dwis_params",
+]

niwrap_afni/afni/fat_proc_imit2w_from_t1w.py

@@ -0,0 +1,283 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FAT_PROC_IMIT2W_FROM_T1W_METADATA = Metadata(
+    id="6e7211eeaf18937b51ec873d5287062ff3f44746.boutiques",
+    name="fat_proc_imit2w_from_t1w",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FatProcImit2wFromT1wParameters = typing.TypedDict('FatProcImit2wFromT1wParameters', {
+    "__STYX_TYPE__": typing.Literal["fat_proc_imit2w_from_t1w"],
+    "t1_file": InputPathType,
+    "prefix": str,
+    "workdir": typing.NotRequired[str | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "ss_blur_fwhm": typing.NotRequired[float | None],
+    "no_clean": bool,
+    "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_imit2w_from_t1w": fat_proc_imit2w_from_t1w_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_imit2w_from_t1w": fat_proc_imit2w_from_t1w_outputs,
+    }.get(t)
+
+
+class FatProcImit2wFromT1wOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fat_proc_imit2w_from_t1w(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    t2w_contrast_volume: OutputPathType
+    """Volume with T2w-like tissue contrast from T1w"""
+    cleaned_t1w_volume: OutputPathType
+    """Cleaned/processed version of the input T1w volume with scaled skull and
+    noise outside the brain"""
+    skull_stripped_t1w: OutputPathType
+    """Skull-stripped version of the T1w volume"""
+    qc_images: OutputPathType
+    """QC images of the skull-stripped T1w volume and the final imitation-T2w
+    volume"""
+
+
+def fat_proc_imit2w_from_t1w_params(
+    t1_file: InputPathType,
+    prefix: str,
+    workdir: str | None = None,
+    mask: InputPathType | None = None,
+    ss_blur_fwhm: float | None = None,
+    no_clean: bool = False,
+    no_qc_view: bool = False,
+    qc_prefix: str | None = None,
+) -> FatProcImit2wFromT1wParameters:
+    """
+    Build parameters.
+    
+    Args:
+        t1_file: Full name of the input T1w volume.
+        prefix: Output prefix for files and snapshots.
+        workdir: Specify a working directory, which can be removed (default:\
+            __WORKING_imit2w_from_t1w).
+        mask: Optional input of a pre-skullstripped T1_FILE (either mask or\
+            skull-stripped volume).
+        ss_blur_fwhm: Optional, add in blurring during the 3dSkullStrip part\
+            (in mm, default: 2 FWHM).
+        no_clean: Optional switch to NOT remove working directory\
+            '__WORKING_imit2w_from_t1w' (default: remove working dir).
+        no_qc_view: Turn off the automatic creation of QC montages (default:\
+            on).
+        qc_prefix: Change the prefix of the QC images (default: use prefix of\
+            volumes).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fat_proc_imit2w_from_t1w",
+        "t1_file": t1_file,
+        "prefix": prefix,
+        "no_clean": no_clean,
+        "no_qc_view": no_qc_view,
+    }
+    if workdir is not None:
+        params["workdir"] = workdir
+    if mask is not None:
+        params["mask"] = mask
+    if ss_blur_fwhm is not None:
+        params["ss_blur_fwhm"] = ss_blur_fwhm
+    if qc_prefix is not None:
+        params["qc_prefix"] = qc_prefix
+    return params
+
+
+def fat_proc_imit2w_from_t1w_cargs(
+    params: FatProcImit2wFromT1wParameters,
+    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_imit2w_from_t1w")
+    cargs.extend([
+        "-inset",
+        execution.input_file(params.get("t1_file"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("workdir") is not None:
+        cargs.extend([
+            "-workdir",
+            params.get("workdir")
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("ss_blur_fwhm") is not None:
+        cargs.extend([
+            "-ss_blur_fwhm",
+            str(params.get("ss_blur_fwhm"))
+        ])
+    if params.get("no_clean"):
+        cargs.append("-no_clean")
+    if params.get("no_qc_view"):
+        cargs.append("-no_qc_view")
+    if params.get("qc_prefix") is not None:
+        cargs.extend([
+            "-qc_prefix",
+            params.get("qc_prefix")
+        ])
+    return cargs
+
+
+def fat_proc_imit2w_from_t1w_outputs(
+    params: FatProcImit2wFromT1wParameters,
+    execution: Execution,
+) -> FatProcImit2wFromT1wOutputs:
+    """
+    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 = FatProcImit2wFromT1wOutputs(
+        root=execution.output_file("."),
+        t2w_contrast_volume=execution.output_file(params.get("prefix") + ".nii.gz"),
+        cleaned_t1w_volume=execution.output_file(params.get("prefix") + "_orig.nii.gz"),
+        skull_stripped_t1w=execution.output_file(params.get("prefix") + "_orig_ss.nii.gz"),
+        qc_images=execution.output_file(params.get("prefix") + "_qc*.nii.gz"),
+    )
+    return ret
+
+
+def fat_proc_imit2w_from_t1w_execute(
+    params: FatProcImit2wFromT1wParameters,
+    execution: Execution,
+) -> FatProcImit2wFromT1wOutputs:
+    """
+    Process T1w anatomical images to generate an imitation T2w-contrast image.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FatProcImit2wFromT1wOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fat_proc_imit2w_from_t1w_cargs(params, execution)
+    ret = fat_proc_imit2w_from_t1w_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fat_proc_imit2w_from_t1w(
+    t1_file: InputPathType,
+    prefix: str,
+    workdir: str | None = None,
+    mask: InputPathType | None = None,
+    ss_blur_fwhm: float | None = None,
+    no_clean: bool = False,
+    no_qc_view: bool = False,
+    qc_prefix: str | None = None,
+    runner: Runner | None = None,
+) -> FatProcImit2wFromT1wOutputs:
+    """
+    Process T1w anatomical images to generate an imitation T2w-contrast image.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        t1_file: Full name of the input T1w volume.
+        prefix: Output prefix for files and snapshots.
+        workdir: Specify a working directory, which can be removed (default:\
+            __WORKING_imit2w_from_t1w).
+        mask: Optional input of a pre-skullstripped T1_FILE (either mask or\
+            skull-stripped volume).
+        ss_blur_fwhm: Optional, add in blurring during the 3dSkullStrip part\
+            (in mm, default: 2 FWHM).
+        no_clean: Optional switch to NOT remove working directory\
+            '__WORKING_imit2w_from_t1w' (default: remove working dir).
+        no_qc_view: Turn off the automatic creation of QC montages (default:\
+            on).
+        qc_prefix: Change the prefix of the QC images (default: use prefix of\
+            volumes).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FatProcImit2wFromT1wOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_PROC_IMIT2W_FROM_T1W_METADATA)
+    params = fat_proc_imit2w_from_t1w_params(
+        t1_file=t1_file,
+        prefix=prefix,
+        workdir=workdir,
+        mask=mask,
+        ss_blur_fwhm=ss_blur_fwhm,
+        no_clean=no_clean,
+        no_qc_view=no_qc_view,
+        qc_prefix=qc_prefix,
+    )
+    return fat_proc_imit2w_from_t1w_execute(params, execution)
+
+
+__all__ = [
+    "FAT_PROC_IMIT2W_FROM_T1W_METADATA",
+    "FatProcImit2wFromT1wOutputs",
+    "FatProcImit2wFromT1wParameters",
+    "fat_proc_imit2w_from_t1w",
+    "fat_proc_imit2w_from_t1w_params",
+]