niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_concat.py

@@ -0,0 +1,653 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_CONCAT_METADATA = Metadata(
+    id="fb2ef824b603c3920fd8a70883332abeb5fd81d4.boutiques",
+    name="mri_concat",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriConcatParameters = typing.TypedDict('MriConcatParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_concat"],
+    "input_files": list[InputPathType],
+    "output_file": str,
+    "file_list": typing.NotRequired[str | None],
+    "paired_sum": bool,
+    "paired_avg": bool,
+    "paired_diff": bool,
+    "paired_diff_norm": bool,
+    "paired_diff_norm1": bool,
+    "paired_diff_norm2": bool,
+    "norm_mean": bool,
+    "norm1": bool,
+    "matrix": typing.NotRequired[InputPathType | None],
+    "frame_weight": typing.NotRequired[InputPathType | None],
+    "norm_weight": bool,
+    "group_mean": typing.NotRequired[float | None],
+    "combine": bool,
+    "keep_datatype": bool,
+    "abs": bool,
+    "pos": bool,
+    "neg": bool,
+    "mean": bool,
+    "median": bool,
+    "mean_div_n": bool,
+    "sum": bool,
+    "var": bool,
+    "std": bool,
+    "max": bool,
+    "max_index": bool,
+    "max_index_prune": bool,
+    "max_index_add": typing.NotRequired[float | None],
+    "min": bool,
+    "replicate_times": typing.NotRequired[float | None],
+    "fnorm": bool,
+    "conjunction": bool,
+    "vote": bool,
+    "sort": bool,
+    "temporal_ar1": typing.NotRequired[float | None],
+    "prune": bool,
+    "pca": bool,
+    "pca_mask": typing.NotRequired[InputPathType | None],
+    "scm": bool,
+    "zconcat": typing.NotRequired[str | None],
+    "max_bonfcor": bool,
+    "multiply": typing.NotRequired[float | None],
+    "add": typing.NotRequired[float | None],
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "rms": bool,
+    "no_check": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mri_concat": mri_concat_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 {
+    }.get(t)
+
+
+class MriConcatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_concat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mri_concat_params(
+    input_files: list[InputPathType],
+    output_file: str,
+    file_list: str | None = None,
+    paired_sum: bool = False,
+    paired_avg: bool = False,
+    paired_diff: bool = False,
+    paired_diff_norm: bool = False,
+    paired_diff_norm1: bool = False,
+    paired_diff_norm2: bool = False,
+    norm_mean: bool = False,
+    norm1: bool = False,
+    matrix: InputPathType | None = None,
+    frame_weight: InputPathType | None = None,
+    norm_weight: bool = False,
+    group_mean: float | None = None,
+    combine: bool = False,
+    keep_datatype: bool = False,
+    abs_: bool = False,
+    pos: bool = False,
+    neg: bool = False,
+    mean: bool = False,
+    median: bool = False,
+    mean_div_n: bool = False,
+    sum_: bool = False,
+    var: bool = False,
+    std: bool = False,
+    max_: bool = False,
+    max_index: bool = False,
+    max_index_prune: bool = False,
+    max_index_add: float | None = None,
+    min_: bool = False,
+    replicate_times: float | None = None,
+    fnorm: bool = False,
+    conjunction: bool = False,
+    vote: bool = False,
+    sort: bool = False,
+    temporal_ar1: float | None = None,
+    prune: bool = False,
+    pca: bool = False,
+    pca_mask: InputPathType | None = None,
+    scm: bool = False,
+    zconcat: str | None = None,
+    max_bonfcor: bool = False,
+    multiply: float | None = None,
+    add: float | None = None,
+    mask_file: InputPathType | None = None,
+    rms: bool = False,
+    no_check: bool = False,
+) -> MriConcatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input image files (e.g. file1.mgh file2.mgh ...).
+        output_file: Output file name (e.g. output.mgh).
+        file_list: List file containing a text list of files to process (up to\
+            400000 files).
+        paired_sum: Compute paired sum (1+2, 3+4, etc).
+        paired_avg: Compute paired average (1+2, 3+4, etc).
+        paired_diff: Compute paired difference (1-2, 3-4, etc).
+        paired_diff_norm: Compute paired difference normalized by TP1,2\
+            average.
+        paired_diff_norm1: Compute paired difference normalized by TP1.
+        paired_diff_norm2: Compute paired difference normalized by TP2.
+        norm_mean: Normalize frames by mean of all time points.
+        norm1: Normalize frames by first time point (TP1).
+        matrix: Multiply by matrix from ASCII file.
+        frame_weight: Weight each frame by values in ASCII file (one value per\
+            frame).
+        norm_weight: Normalize frames to sum to 1 after weighting.
+        group_mean: Create matrix to average Ng groups, Nper=Ntot/Ng.
+        combine: Average frames from non-zero voxels.
+        keep_datatype: Write output in the same datatype as input (default is\
+            Float format).
+        abs_: Take absolute value of input.
+        pos: Set input negatives to 0.
+        neg: Set input positives to 0.
+        mean: Compute mean of concatenated volumes.
+        median: Compute median of concatenated volumes.
+        mean_div_n: Compute mean divided by number of frames.
+        sum_: Compute sum of concatenated volumes.
+        var: Compute variance of concatenated volumes.
+        std: Compute standard deviation of concatenated volumes.
+        max_: Compute maximum of concatenated volumes.
+        max_index: Compute index of maximum of concatenated volumes.
+        max_index_prune: Set max index to 0 where all frames are 0.
+        max_index_add: Add value to non-zero max indices.
+        min_: Compute minimum of concatenated volumes.
+        replicate_times: Replicate N times over frames.
+        fnorm: Normalize time series at each voxel.
+        conjunction: Compute voxel-wise conjunction of concatenated volumes.
+        vote: Most frequent value at each voxel and fraction of occurrences.
+        sort: Sort each voxel by ascending frame value.
+        temporal_ar1: Compute temporal AR1 with degree of freedom adjustment.
+        prune: Set voxel value to 0 unless all frames are non-zero.
+        pca: Compute and output principal component analysis (PCA).
+        pca_mask: Mask used to select voxels for PCA (mask > 0.5).
+        scm: Compute spatial covariance matrix.
+        zconcat: Concatenate in slice direction skipping nskip slices.
+        max_bonfcor: Compute maximum and Bonferroni correct.
+        multiply: Multiply volumes by value.
+        add: Add value to volumes.
+        mask_file: Mask file used with vote or sort.
+        rms: Compute root mean square of concatenated volumes.
+        no_check: Do not check inputs.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_concat",
+        "input_files": input_files,
+        "output_file": output_file,
+        "paired_sum": paired_sum,
+        "paired_avg": paired_avg,
+        "paired_diff": paired_diff,
+        "paired_diff_norm": paired_diff_norm,
+        "paired_diff_norm1": paired_diff_norm1,
+        "paired_diff_norm2": paired_diff_norm2,
+        "norm_mean": norm_mean,
+        "norm1": norm1,
+        "norm_weight": norm_weight,
+        "combine": combine,
+        "keep_datatype": keep_datatype,
+        "abs": abs_,
+        "pos": pos,
+        "neg": neg,
+        "mean": mean,
+        "median": median,
+        "mean_div_n": mean_div_n,
+        "sum": sum_,
+        "var": var,
+        "std": std,
+        "max": max_,
+        "max_index": max_index,
+        "max_index_prune": max_index_prune,
+        "min": min_,
+        "fnorm": fnorm,
+        "conjunction": conjunction,
+        "vote": vote,
+        "sort": sort,
+        "prune": prune,
+        "pca": pca,
+        "scm": scm,
+        "max_bonfcor": max_bonfcor,
+        "rms": rms,
+        "no_check": no_check,
+    }
+    if file_list is not None:
+        params["file_list"] = file_list
+    if matrix is not None:
+        params["matrix"] = matrix
+    if frame_weight is not None:
+        params["frame_weight"] = frame_weight
+    if group_mean is not None:
+        params["group_mean"] = group_mean
+    if max_index_add is not None:
+        params["max_index_add"] = max_index_add
+    if replicate_times is not None:
+        params["replicate_times"] = replicate_times
+    if temporal_ar1 is not None:
+        params["temporal_ar1"] = temporal_ar1
+    if pca_mask is not None:
+        params["pca_mask"] = pca_mask
+    if zconcat is not None:
+        params["zconcat"] = zconcat
+    if multiply is not None:
+        params["multiply"] = multiply
+    if add is not None:
+        params["add"] = add
+    if mask_file is not None:
+        params["mask_file"] = mask_file
+    return params
+
+
+def mri_concat_cargs(
+    params: MriConcatParameters,
+    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("mri_concat")
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    cargs.extend([
+        "--o",
+        params.get("output_file")
+    ])
+    if params.get("file_list") is not None:
+        cargs.extend([
+            "--f",
+            params.get("file_list")
+        ])
+    if params.get("paired_sum"):
+        cargs.append("--paired-sum")
+    if params.get("paired_avg"):
+        cargs.append("--paired-avg")
+    if params.get("paired_diff"):
+        cargs.append("--paired-diff")
+    if params.get("paired_diff_norm"):
+        cargs.append("--paired-diff-norm")
+    if params.get("paired_diff_norm1"):
+        cargs.append("--paired-diff-norm1")
+    if params.get("paired_diff_norm2"):
+        cargs.append("--paired-diff-norm2")
+    if params.get("norm_mean"):
+        cargs.append("--norm-mean")
+    if params.get("norm1"):
+        cargs.append("--norm1")
+    if params.get("matrix") is not None:
+        cargs.extend([
+            "--mtx",
+            execution.input_file(params.get("matrix"))
+        ])
+    if params.get("frame_weight") is not None:
+        cargs.extend([
+            "--w",
+            execution.input_file(params.get("frame_weight"))
+        ])
+    if params.get("norm_weight"):
+        cargs.append("--wn")
+    if params.get("group_mean") is not None:
+        cargs.extend([
+            "--gmean",
+            str(params.get("group_mean"))
+        ])
+    if params.get("combine"):
+        cargs.append("--combine")
+    if params.get("keep_datatype"):
+        cargs.append("--keep-datatype")
+    if params.get("abs"):
+        cargs.append("--abs")
+    if params.get("pos"):
+        cargs.append("--pos")
+    if params.get("neg"):
+        cargs.append("--neg")
+    if params.get("mean"):
+        cargs.append("--mean")
+    if params.get("median"):
+        cargs.append("--median")
+    if params.get("mean_div_n"):
+        cargs.append("--mean-div-n")
+    if params.get("sum"):
+        cargs.append("--sum")
+    if params.get("var"):
+        cargs.append("--var")
+    if params.get("std"):
+        cargs.append("--std")
+    if params.get("max"):
+        cargs.append("--max")
+    if params.get("max_index"):
+        cargs.append("--max-index")
+    if params.get("max_index_prune"):
+        cargs.append("--max-index-prune")
+    if params.get("max_index_add") is not None:
+        cargs.extend([
+            "--max-index-add",
+            str(params.get("max_index_add"))
+        ])
+    if params.get("min"):
+        cargs.append("--min")
+    if params.get("replicate_times") is not None:
+        cargs.extend([
+            "--rep",
+            str(params.get("replicate_times"))
+        ])
+    if params.get("fnorm"):
+        cargs.append("--fnorm")
+    if params.get("conjunction"):
+        cargs.append("--conjunct")
+    if params.get("vote"):
+        cargs.append("--vote")
+    if params.get("sort"):
+        cargs.append("--sort")
+    if params.get("temporal_ar1") is not None:
+        cargs.extend([
+            "--tar1",
+            str(params.get("temporal_ar1"))
+        ])
+    if params.get("prune"):
+        cargs.append("--prune")
+    if params.get("pca"):
+        cargs.append("--pca")
+    if params.get("pca_mask") is not None:
+        cargs.extend([
+            "--pca-mask",
+            execution.input_file(params.get("pca_mask"))
+        ])
+    if params.get("scm"):
+        cargs.append("--scm")
+    if params.get("zconcat") is not None:
+        cargs.extend([
+            "--zconcat",
+            params.get("zconcat")
+        ])
+    if params.get("max_bonfcor"):
+        cargs.append("--max-bonfcor")
+    if params.get("multiply") is not None:
+        cargs.extend([
+            "--mul",
+            str(params.get("multiply"))
+        ])
+    if params.get("add") is not None:
+        cargs.extend([
+            "--add",
+            str(params.get("add"))
+        ])
+    if params.get("mask_file") is not None:
+        cargs.extend([
+            "--mask",
+            execution.input_file(params.get("mask_file"))
+        ])
+    if params.get("rms"):
+        cargs.append("--rms")
+    if params.get("no_check"):
+        cargs.append("--no-check")
+    return cargs
+
+
+def mri_concat_outputs(
+    params: MriConcatParameters,
+    execution: Execution,
+) -> MriConcatOutputs:
+    """
+    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 = MriConcatOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mri_concat_execute(
+    params: MriConcatParameters,
+    execution: Execution,
+) -> MriConcatOutputs:
+    """
+    Concatenates input data sets.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriConcatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_concat_cargs(params, execution)
+    ret = mri_concat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_concat(
+    input_files: list[InputPathType],
+    output_file: str,
+    file_list: str | None = None,
+    paired_sum: bool = False,
+    paired_avg: bool = False,
+    paired_diff: bool = False,
+    paired_diff_norm: bool = False,
+    paired_diff_norm1: bool = False,
+    paired_diff_norm2: bool = False,
+    norm_mean: bool = False,
+    norm1: bool = False,
+    matrix: InputPathType | None = None,
+    frame_weight: InputPathType | None = None,
+    norm_weight: bool = False,
+    group_mean: float | None = None,
+    combine: bool = False,
+    keep_datatype: bool = False,
+    abs_: bool = False,
+    pos: bool = False,
+    neg: bool = False,
+    mean: bool = False,
+    median: bool = False,
+    mean_div_n: bool = False,
+    sum_: bool = False,
+    var: bool = False,
+    std: bool = False,
+    max_: bool = False,
+    max_index: bool = False,
+    max_index_prune: bool = False,
+    max_index_add: float | None = None,
+    min_: bool = False,
+    replicate_times: float | None = None,
+    fnorm: bool = False,
+    conjunction: bool = False,
+    vote: bool = False,
+    sort: bool = False,
+    temporal_ar1: float | None = None,
+    prune: bool = False,
+    pca: bool = False,
+    pca_mask: InputPathType | None = None,
+    scm: bool = False,
+    zconcat: str | None = None,
+    max_bonfcor: bool = False,
+    multiply: float | None = None,
+    add: float | None = None,
+    mask_file: InputPathType | None = None,
+    rms: bool = False,
+    no_check: bool = False,
+    runner: Runner | None = None,
+) -> MriConcatOutputs:
+    """
+    Concatenates input data sets.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_files: Input image files (e.g. file1.mgh file2.mgh ...).
+        output_file: Output file name (e.g. output.mgh).
+        file_list: List file containing a text list of files to process (up to\
+            400000 files).
+        paired_sum: Compute paired sum (1+2, 3+4, etc).
+        paired_avg: Compute paired average (1+2, 3+4, etc).
+        paired_diff: Compute paired difference (1-2, 3-4, etc).
+        paired_diff_norm: Compute paired difference normalized by TP1,2\
+            average.
+        paired_diff_norm1: Compute paired difference normalized by TP1.
+        paired_diff_norm2: Compute paired difference normalized by TP2.
+        norm_mean: Normalize frames by mean of all time points.
+        norm1: Normalize frames by first time point (TP1).
+        matrix: Multiply by matrix from ASCII file.
+        frame_weight: Weight each frame by values in ASCII file (one value per\
+            frame).
+        norm_weight: Normalize frames to sum to 1 after weighting.
+        group_mean: Create matrix to average Ng groups, Nper=Ntot/Ng.
+        combine: Average frames from non-zero voxels.
+        keep_datatype: Write output in the same datatype as input (default is\
+            Float format).
+        abs_: Take absolute value of input.
+        pos: Set input negatives to 0.
+        neg: Set input positives to 0.
+        mean: Compute mean of concatenated volumes.
+        median: Compute median of concatenated volumes.
+        mean_div_n: Compute mean divided by number of frames.
+        sum_: Compute sum of concatenated volumes.
+        var: Compute variance of concatenated volumes.
+        std: Compute standard deviation of concatenated volumes.
+        max_: Compute maximum of concatenated volumes.
+        max_index: Compute index of maximum of concatenated volumes.
+        max_index_prune: Set max index to 0 where all frames are 0.
+        max_index_add: Add value to non-zero max indices.
+        min_: Compute minimum of concatenated volumes.
+        replicate_times: Replicate N times over frames.
+        fnorm: Normalize time series at each voxel.
+        conjunction: Compute voxel-wise conjunction of concatenated volumes.
+        vote: Most frequent value at each voxel and fraction of occurrences.
+        sort: Sort each voxel by ascending frame value.
+        temporal_ar1: Compute temporal AR1 with degree of freedom adjustment.
+        prune: Set voxel value to 0 unless all frames are non-zero.
+        pca: Compute and output principal component analysis (PCA).
+        pca_mask: Mask used to select voxels for PCA (mask > 0.5).
+        scm: Compute spatial covariance matrix.
+        zconcat: Concatenate in slice direction skipping nskip slices.
+        max_bonfcor: Compute maximum and Bonferroni correct.
+        multiply: Multiply volumes by value.
+        add: Add value to volumes.
+        mask_file: Mask file used with vote or sort.
+        rms: Compute root mean square of concatenated volumes.
+        no_check: Do not check inputs.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriConcatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_CONCAT_METADATA)
+    params = mri_concat_params(
+        input_files=input_files,
+        output_file=output_file,
+        file_list=file_list,
+        paired_sum=paired_sum,
+        paired_avg=paired_avg,
+        paired_diff=paired_diff,
+        paired_diff_norm=paired_diff_norm,
+        paired_diff_norm1=paired_diff_norm1,
+        paired_diff_norm2=paired_diff_norm2,
+        norm_mean=norm_mean,
+        norm1=norm1,
+        matrix=matrix,
+        frame_weight=frame_weight,
+        norm_weight=norm_weight,
+        group_mean=group_mean,
+        combine=combine,
+        keep_datatype=keep_datatype,
+        abs_=abs_,
+        pos=pos,
+        neg=neg,
+        mean=mean,
+        median=median,
+        mean_div_n=mean_div_n,
+        sum_=sum_,
+        var=var,
+        std=std,
+        max_=max_,
+        max_index=max_index,
+        max_index_prune=max_index_prune,
+        max_index_add=max_index_add,
+        min_=min_,
+        replicate_times=replicate_times,
+        fnorm=fnorm,
+        conjunction=conjunction,
+        vote=vote,
+        sort=sort,
+        temporal_ar1=temporal_ar1,
+        prune=prune,
+        pca=pca,
+        pca_mask=pca_mask,
+        scm=scm,
+        zconcat=zconcat,
+        max_bonfcor=max_bonfcor,
+        multiply=multiply,
+        add=add,
+        mask_file=mask_file,
+        rms=rms,
+        no_check=no_check,
+    )
+    return mri_concat_execute(params, execution)
+
+
+__all__ = [
+    "MRI_CONCAT_METADATA",
+    "MriConcatOutputs",
+    "MriConcatParameters",
+    "mri_concat",
+    "mri_concat_params",
+]