niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3dmaskdump.py

@@ -0,0 +1,425 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DMASKDUMP_METADATA = Metadata(
+    id="9cb4c849a9357c37ec67fbe234f23f59f3a3a158.boutiques",
+    name="3dmaskdump",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dmaskdumpParameters = typing.TypedDict('V3dmaskdumpParameters', {
+    "__STYX_TYPE__": typing.Literal["3dmaskdump"],
+    "input_files": list[InputPathType],
+    "mask_dataset": typing.NotRequired[InputPathType | None],
+    "mask_range": typing.NotRequired[list[str] | None],
+    "output_index": bool,
+    "output_noijk": bool,
+    "output_xyz": bool,
+    "output_filename": typing.NotRequired[str | None],
+    "calc_mask_opts": typing.NotRequired[str | None],
+    "xbox_coords": typing.NotRequired[str | None],
+    "dbox_coords": typing.NotRequired[str | None],
+    "nbox_coords": typing.NotRequired[str | None],
+    "ibox_coords": typing.NotRequired[str | None],
+    "xball_coords": typing.NotRequired[str | None],
+    "dball_coords": typing.NotRequired[str | None],
+    "nball_coords": typing.NotRequired[str | None],
+    "nozero_output": bool,
+    "random_voxels": typing.NotRequired[float | None],
+    "random_seed": typing.NotRequired[float | None],
+    "output_niml": typing.NotRequired[str | None],
+    "quiet_mode": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dmaskdump": v_3dmaskdump_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 {
+        "3dmaskdump": v_3dmaskdump_outputs,
+    }.get(t)
+
+
+class V3dmaskdumpOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dmaskdump(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType | None
+    """Output ASCII file with voxel values"""
+
+
+def v_3dmaskdump_params(
+    input_files: list[InputPathType],
+    mask_dataset: InputPathType | None = None,
+    mask_range: list[str] | None = None,
+    output_index: bool = False,
+    output_noijk: bool = False,
+    output_xyz: bool = False,
+    output_filename: str | None = None,
+    calc_mask_opts: str | None = None,
+    xbox_coords: str | None = None,
+    dbox_coords: str | None = None,
+    nbox_coords: str | None = None,
+    ibox_coords: str | None = None,
+    xball_coords: str | None = None,
+    dball_coords: str | None = None,
+    nball_coords: str | None = None,
+    nozero_output: bool = False,
+    random_voxels: float | None = None,
+    random_seed: float | None = None,
+    output_niml: str | None = None,
+    quiet_mode: bool = False,
+) -> V3dmaskdumpParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input datasets to dump voxel values.
+        mask_dataset: Use the dataset as a mask. Only voxels with nonzero\
+            values in the mask will be printed from the input dataset.
+        mask_range: Further restrict the voxels from mask dataset to those mask\
+            values between 'a' and 'b' (inclusive).
+        output_index: Write out the dataset index values.
+        output_noijk: Do not write out the i,j,k values.
+        output_xyz: Write the x,y,z coordinates from the first input dataset at\
+            the start of each output line.
+        output_filename: Write output to specified file.
+        calc_mask_opts: Execute options enclosed as a 3dcalc-like program to\
+            produce a mask from the resulting 3D brick.
+        xbox_coords: Put a 'mask' at dataset coordinates 'x y z' mm.
+        dbox_coords: Put a 'mask' at RAI/DICOM coordinates of 'x y z' mm.
+        nbox_coords: Put a 'mask' at LPI/SPM coordinates of 'x y z' mm.
+        ibox_coords: Put a 'mask' at voxel indexes 'i j k'.
+        xball_coords: Put a ball (sphere) mask at dataset coordinates (x,y,z)\
+            with radius r.
+        dball_coords: Put a ball (sphere) mask at RAI/DICOM coordinates (x,y,z)\
+            with radius r.
+        nball_coords: Put a ball (sphere) mask at LPI/SPM coordinates (x,y,z)\
+            with radius r.
+        nozero_output: Skip output of any voxel where all the data values are\
+            zero.
+        random_voxels: Keep only N_RAND randomly selected voxels from what\
+            would have been the output.
+        random_seed: Seed the random number generator with SEED.
+        output_niml: Output data in the XML/NIML format compatible with input\
+            back to AFNI via the READ_NIML_FILE command.
+        quiet_mode: Do not print progress messages to stderr.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dmaskdump",
+        "input_files": input_files,
+        "output_index": output_index,
+        "output_noijk": output_noijk,
+        "output_xyz": output_xyz,
+        "nozero_output": nozero_output,
+        "quiet_mode": quiet_mode,
+    }
+    if mask_dataset is not None:
+        params["mask_dataset"] = mask_dataset
+    if mask_range is not None:
+        params["mask_range"] = mask_range
+    if output_filename is not None:
+        params["output_filename"] = output_filename
+    if calc_mask_opts is not None:
+        params["calc_mask_opts"] = calc_mask_opts
+    if xbox_coords is not None:
+        params["xbox_coords"] = xbox_coords
+    if dbox_coords is not None:
+        params["dbox_coords"] = dbox_coords
+    if nbox_coords is not None:
+        params["nbox_coords"] = nbox_coords
+    if ibox_coords is not None:
+        params["ibox_coords"] = ibox_coords
+    if xball_coords is not None:
+        params["xball_coords"] = xball_coords
+    if dball_coords is not None:
+        params["dball_coords"] = dball_coords
+    if nball_coords is not None:
+        params["nball_coords"] = nball_coords
+    if random_voxels is not None:
+        params["random_voxels"] = random_voxels
+    if random_seed is not None:
+        params["random_seed"] = random_seed
+    if output_niml is not None:
+        params["output_niml"] = output_niml
+    return params
+
+
+def v_3dmaskdump_cargs(
+    params: V3dmaskdumpParameters,
+    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("3dmaskdump")
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    if params.get("mask_dataset") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask_dataset"))
+        ])
+    if params.get("mask_range") is not None:
+        cargs.extend([
+            "-mrange",
+            *params.get("mask_range")
+        ])
+    if params.get("output_index"):
+        cargs.append("-index")
+    if params.get("output_noijk"):
+        cargs.append("-noijk")
+    if params.get("output_xyz"):
+        cargs.append("-xyz")
+    if params.get("output_filename") is not None:
+        cargs.extend([
+            "-o",
+            params.get("output_filename")
+        ])
+    if params.get("calc_mask_opts") is not None:
+        cargs.extend([
+            "-cmask",
+            params.get("calc_mask_opts")
+        ])
+    if params.get("xbox_coords") is not None:
+        cargs.extend([
+            "-xbox",
+            params.get("xbox_coords")
+        ])
+    if params.get("dbox_coords") is not None:
+        cargs.extend([
+            "-dbox",
+            params.get("dbox_coords")
+        ])
+    if params.get("nbox_coords") is not None:
+        cargs.extend([
+            "-nbox",
+            params.get("nbox_coords")
+        ])
+    if params.get("ibox_coords") is not None:
+        cargs.extend([
+            "-ibox",
+            params.get("ibox_coords")
+        ])
+    if params.get("xball_coords") is not None:
+        cargs.extend([
+            "-xball",
+            params.get("xball_coords")
+        ])
+    if params.get("dball_coords") is not None:
+        cargs.extend([
+            "-dball",
+            params.get("dball_coords")
+        ])
+    if params.get("nball_coords") is not None:
+        cargs.extend([
+            "-nball",
+            params.get("nball_coords")
+        ])
+    if params.get("nozero_output"):
+        cargs.append("-nozero")
+    if params.get("random_voxels") is not None:
+        cargs.extend([
+            "-n_rand",
+            str(params.get("random_voxels"))
+        ])
+    if params.get("random_seed") is not None:
+        cargs.extend([
+            "-n_randseed",
+            str(params.get("random_seed"))
+        ])
+    if params.get("output_niml") is not None:
+        cargs.extend([
+            "-niml",
+            params.get("output_niml")
+        ])
+    if params.get("quiet_mode"):
+        cargs.append("-quiet")
+    return cargs
+
+
+def v_3dmaskdump_outputs(
+    params: V3dmaskdumpParameters,
+    execution: Execution,
+) -> V3dmaskdumpOutputs:
+    """
+    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 = V3dmaskdumpOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output_filename")) if (params.get("output_filename") is not None) else None,
+    )
+    return ret
+
+
+def v_3dmaskdump_execute(
+    params: V3dmaskdumpParameters,
+    execution: Execution,
+) -> V3dmaskdumpOutputs:
+    """
+    Outputs voxel values from AFNI datasets satisfying mask criteria to an ASCII
+    file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dmaskdumpOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dmaskdump_cargs(params, execution)
+    ret = v_3dmaskdump_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dmaskdump(
+    input_files: list[InputPathType],
+    mask_dataset: InputPathType | None = None,
+    mask_range: list[str] | None = None,
+    output_index: bool = False,
+    output_noijk: bool = False,
+    output_xyz: bool = False,
+    output_filename: str | None = None,
+    calc_mask_opts: str | None = None,
+    xbox_coords: str | None = None,
+    dbox_coords: str | None = None,
+    nbox_coords: str | None = None,
+    ibox_coords: str | None = None,
+    xball_coords: str | None = None,
+    dball_coords: str | None = None,
+    nball_coords: str | None = None,
+    nozero_output: bool = False,
+    random_voxels: float | None = None,
+    random_seed: float | None = None,
+    output_niml: str | None = None,
+    quiet_mode: bool = False,
+    runner: Runner | None = None,
+) -> V3dmaskdumpOutputs:
+    """
+    Outputs voxel values from AFNI datasets satisfying mask criteria to an ASCII
+    file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: Input datasets to dump voxel values.
+        mask_dataset: Use the dataset as a mask. Only voxels with nonzero\
+            values in the mask will be printed from the input dataset.
+        mask_range: Further restrict the voxels from mask dataset to those mask\
+            values between 'a' and 'b' (inclusive).
+        output_index: Write out the dataset index values.
+        output_noijk: Do not write out the i,j,k values.
+        output_xyz: Write the x,y,z coordinates from the first input dataset at\
+            the start of each output line.
+        output_filename: Write output to specified file.
+        calc_mask_opts: Execute options enclosed as a 3dcalc-like program to\
+            produce a mask from the resulting 3D brick.
+        xbox_coords: Put a 'mask' at dataset coordinates 'x y z' mm.
+        dbox_coords: Put a 'mask' at RAI/DICOM coordinates of 'x y z' mm.
+        nbox_coords: Put a 'mask' at LPI/SPM coordinates of 'x y z' mm.
+        ibox_coords: Put a 'mask' at voxel indexes 'i j k'.
+        xball_coords: Put a ball (sphere) mask at dataset coordinates (x,y,z)\
+            with radius r.
+        dball_coords: Put a ball (sphere) mask at RAI/DICOM coordinates (x,y,z)\
+            with radius r.
+        nball_coords: Put a ball (sphere) mask at LPI/SPM coordinates (x,y,z)\
+            with radius r.
+        nozero_output: Skip output of any voxel where all the data values are\
+            zero.
+        random_voxels: Keep only N_RAND randomly selected voxels from what\
+            would have been the output.
+        random_seed: Seed the random number generator with SEED.
+        output_niml: Output data in the XML/NIML format compatible with input\
+            back to AFNI via the READ_NIML_FILE command.
+        quiet_mode: Do not print progress messages to stderr.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dmaskdumpOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DMASKDUMP_METADATA)
+    params = v_3dmaskdump_params(
+        input_files=input_files,
+        mask_dataset=mask_dataset,
+        mask_range=mask_range,
+        output_index=output_index,
+        output_noijk=output_noijk,
+        output_xyz=output_xyz,
+        output_filename=output_filename,
+        calc_mask_opts=calc_mask_opts,
+        xbox_coords=xbox_coords,
+        dbox_coords=dbox_coords,
+        nbox_coords=nbox_coords,
+        ibox_coords=ibox_coords,
+        xball_coords=xball_coords,
+        dball_coords=dball_coords,
+        nball_coords=nball_coords,
+        nozero_output=nozero_output,
+        random_voxels=random_voxels,
+        random_seed=random_seed,
+        output_niml=output_niml,
+        quiet_mode=quiet_mode,
+    )
+    return v_3dmaskdump_execute(params, execution)
+
+
+__all__ = [
+    "V3dmaskdumpOutputs",
+    "V3dmaskdumpParameters",
+    "V_3DMASKDUMP_METADATA",
+    "v_3dmaskdump",
+    "v_3dmaskdump_params",
+]

niwrap_afni/afni/v_3dmatcalc.py

@@ -0,0 +1,221 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DMATCALC_METADATA = Metadata(
+    id="9c4d323b9663dd4eadd79fdc472de04da567e563.boutiques",
+    name="3dmatcalc",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dmatcalcParameters = typing.TypedDict('V3dmatcalcParameters', {
+    "__STYX_TYPE__": typing.Literal["3dmatcalc"],
+    "input_dataset": InputPathType,
+    "input_matrix": InputPathType,
+    "output_dataset": str,
+    "mask": typing.NotRequired[InputPathType | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dmatcalc": v_3dmatcalc_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 {
+        "3dmatcalc": v_3dmatcalc_outputs,
+    }.get(t)
+
+
+class V3dmatcalcOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dmatcalc(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_header: OutputPathType
+    """Output dataset header file."""
+    output_brick: OutputPathType
+    """Output dataset brick file."""
+
+
+def v_3dmatcalc_params(
+    input_dataset: InputPathType,
+    input_matrix: InputPathType,
+    output_dataset: str,
+    mask: InputPathType | None = None,
+) -> V3dmatcalcParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input dataset to be processed.
+        input_matrix: The matrix to be applied, specified as a .1D file or as\
+            an expression in the syntax of 1dmatcalc.
+        output_dataset: Prefix for the output dataset.
+        mask: Apply the matrix only to voxels in the mask; other voxels will be\
+            set to all zeroes.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dmatcalc",
+        "input_dataset": input_dataset,
+        "input_matrix": input_matrix,
+        "output_dataset": output_dataset,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    return params
+
+
+def v_3dmatcalc_cargs(
+    params: V3dmatcalcParameters,
+    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("3dmatcalc")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_dataset"))
+    ])
+    cargs.extend([
+        "-matrix",
+        execution.input_file(params.get("input_matrix"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("output_dataset")
+    ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    return cargs
+
+
+def v_3dmatcalc_outputs(
+    params: V3dmatcalcParameters,
+    execution: Execution,
+) -> V3dmatcalcOutputs:
+    """
+    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 = V3dmatcalcOutputs(
+        root=execution.output_file("."),
+        output_header=execution.output_file(params.get("output_dataset") + "+tlrc.HEAD"),
+        output_brick=execution.output_file(params.get("output_dataset") + "+tlrc.BRIK"),
+    )
+    return ret
+
+
+def v_3dmatcalc_execute(
+    params: V3dmatcalcParameters,
+    execution: Execution,
+) -> V3dmatcalcOutputs:
+    """
+    Apply a matrix to a dataset, voxel-by-voxel, to produce a new dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dmatcalcOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dmatcalc_cargs(params, execution)
+    ret = v_3dmatcalc_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dmatcalc(
+    input_dataset: InputPathType,
+    input_matrix: InputPathType,
+    output_dataset: str,
+    mask: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> V3dmatcalcOutputs:
+    """
+    Apply a matrix to a dataset, voxel-by-voxel, to produce a new dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input dataset to be processed.
+        input_matrix: The matrix to be applied, specified as a .1D file or as\
+            an expression in the syntax of 1dmatcalc.
+        output_dataset: Prefix for the output dataset.
+        mask: Apply the matrix only to voxels in the mask; other voxels will be\
+            set to all zeroes.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dmatcalcOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DMATCALC_METADATA)
+    params = v_3dmatcalc_params(
+        input_dataset=input_dataset,
+        input_matrix=input_matrix,
+        output_dataset=output_dataset,
+        mask=mask,
+    )
+    return v_3dmatcalc_execute(params, execution)
+
+
+__all__ = [
+    "V3dmatcalcOutputs",
+    "V3dmatcalcParameters",
+    "V_3DMATCALC_METADATA",
+    "v_3dmatcalc",
+    "v_3dmatcalc_params",
+]