rapidtide 2.9.6__py3-none-any.whl → 3.1.3__py3-none-any.whl

rapidtide/workflows/retrolagtcs.py

@@ -0,0 +1,442 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+#   Copyright 2016-2025 Blaise Frederick
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
+#
+import argparse
+import copy
+import logging
+import os
+import sys
+from argparse import Namespace
+from typing import Any, Callable, Dict, List, Optional, Tuple, Union
+
+import numpy as np
+from numpy.typing import NDArray
+
+import rapidtide.io as tide_io
+import rapidtide.linfitfiltpass as tide_linfitfiltpass
+import rapidtide.makelaggedtcs as tide_makelagged
+import rapidtide.multiproc as tide_multiproc
+import rapidtide.resample as tide_resample
+import rapidtide.util as tide_util
+import rapidtide.workflows.parser_funcs as pf
+
+LGR = logging.getLogger("GENERAL")
+ErrorLGR = logging.getLogger("ERROR")
+TimingLGR = logging.getLogger("TIMING")
+
+DEFAULT_REGRESSIONFILTDERIVS = 0
+
+
+def _get_parser() -> Any:
+    """
+    Argument parser for retrolagtcs.
+
+    This function constructs and returns an `argparse.ArgumentParser` object configured
+    for the `retrolagtcs` command-line tool. It defines all required and optional
+    arguments needed to generate voxel-specific lagged timecourses from rapidtide
+    analysis maps.
+
+    Returns
+    -------
+    argparse.ArgumentParser
+        Configured argument parser for retrolagtcs.
+
+    Notes
+    -----
+    The parser expects several input files and parameters to define the processing
+    pipeline. The function uses `pf.is_valid_file` to validate the existence of
+    the input 4D NIfTI file.
+
+    Examples
+    --------
+    >>> parser = _get_parser()
+    >>> args = parser.parse_args()
+    >>> print(args.fmrifile)
+    'sub-01_task-rest_bold.nii.gz'
+    """
+    parser = argparse.ArgumentParser(
+        prog="retrolagtcs",
+        description="Generate voxel specific lagged timecourses using the maps generated from a previous rapidtide analysis.",
+        allow_abbrev=False,
+    )
+
+    # Required arguments
+    parser.add_argument(
+        "fmrifile",
+        type=lambda x: pf.is_valid_file(parser, x),
+        help="The name of 4D nifti fmri target file.",
+    )
+    parser.add_argument(
+        "maskfile",
+        type=str,
+        help="The mask file to use (usually called XXX_desc-corrfit_mask.nii.gz)",
+    )
+    parser.add_argument(
+        "lagtimesfile",
+        type=str,
+        help="The  name of the lag times file (usually called XXX_desc-maxtime_map.nii.gz)",
+    )
+    parser.add_argument(
+        "lagtcgeneratorfile",
+        type=str,
+        help="The root name of the lagtc generator file (usually called XXX_desc-lagtcgenerator_timeseries)",
+    )
+    parser.add_argument(
+        "outputroot",
+        type=str,
+        help="Output root.",
+    )
+    parser.add_argument(
+        "--regressderivs",
+        dest="regressderivs",
+        action="store",
+        type=int,
+        metavar="NDERIVS",
+        help=(
+            f"When doing final GLM, include derivatives up to NDERIVS order. Default is {DEFAULT_REGRESSIONFILTDERIVS}"
+        ),
+        default=DEFAULT_REGRESSIONFILTDERIVS,
+    )
+    parser.add_argument(
+        "--nprocs",
+        dest="nprocs",
+        action="store",
+        type=int,
+        metavar="NPROCS",
+        help=(
+            "Use NPROCS worker processes for multiprocessing. "
+            "Setting NPROCS to less than 1 sets the number of "
+            "worker processes to n_cpus."
+        ),
+        default=1,
+    )
+    parser.add_argument(
+        "--numskip",
+        dest="numskip",
+        action="store",
+        type=int,
+        metavar="NUMSKIP",
+        help=("Skip NUMSKIP points at the beginning of the fmri file."),
+        default=0,
+    )
+    parser.add_argument(
+        "--noprogressbar",
+        dest="showprogressbar",
+        action="store_false",
+        help=("Will disable showing progress bars (helpful if stdout is going to a file)."),
+        default=True,
+    )
+
+    parser.add_argument(
+        "--debug",
+        dest="debug",
+        action="store_true",
+        help=("Output lots of helpful information."),
+        default=False,
+    )
+    return parser
+
+
+def retrolagtcs(args: Any) -> None:
+    """
+    Generate lagged time series regressors from fMRI data using a lag-time map and a generator file.
+
+    This function reads fMRI data, a mask, and a lag-time map to compute lagged time series
+    regressors for each voxel in the mask. It supports both single-process and multi-process
+    execution using shared memory. The computed regressors are saved as NIfTI files.
+
+    Parameters
+    ----------
+    args : Any
+        An object containing the following attributes:
+        - fmrifile : str
+            Path to the input fMRI NIfTI file.
+        - maskfile : str
+            Path to the processing mask NIfTI file.
+        - lagtimesfile : str
+            Path to the lag times NIfTI file.
+        - lagtcgeneratorfile : str
+            Path to the lagtc generator file (used for resampling).
+        - outputroot : str
+            Root path for output files.
+        - nprocs : int
+            Number of processes to use for parallel execution. If less than 1, defaults to max CPU count.
+        - numskip : int
+            Number of initial time points to skip.
+        - regressderivs : int
+            Number of time derivatives to include in the regressor set.
+        - showprogressbar : bool
+            Whether to display a progress bar during processing.
+        - debug : bool
+            Whether to enable debug mode for additional logging.
+
+    Returns
+    -------
+    None
+        This function does not return a value but writes output files to disk.
+
+    Notes
+    -----
+    - The function requires the input files to have matching spatial dimensions.
+    - Shared memory is used for multi-process execution to improve performance.
+    - Output files include:
+        - Regressor time series (4D NIfTI)
+        - Optional mask and lag time maps (3D NIfTI)
+
+    Examples
+    --------
+    >>> import argparse
+    >>> args = argparse.Namespace(
+    ...     fmrifile='fmri.nii.gz',
+    ...     maskfile='mask.nii.gz',
+    ...     lagtimesfile='lagtimes.nii.gz',
+    ...     lagtcgeneratorfile='generator.txt',
+    ...     outputroot='output',
+    ...     nprocs=4,
+    ...     numskip=5,
+    ...     regressderivs=2,
+    ...     showprogressbar=True,
+    ...     debug=False
+    ... )
+    >>> retrolagtcs(args)
+    """
+    rt_floattype = np.float64
+    rt_outfloattype = np.float64
+
+    # get the pid of the parent process
+    args.pid = os.getpid()
+
+    thecommandline = " ".join(sys.argv[1:])
+
+    if args.nprocs < 1:
+        args.nprocs = tide_multiproc.maxcpus()
+    # don't use shared memory if there is only one process
+    if args.nprocs == 1:
+        usesharedmem = False
+    else:
+        usesharedmem = True
+
+    # read the fmri input files
+    print("reading fmrifile header")
+    fmri_input, dummy, fmri_header, fmri_dims, fmri_sizes = tide_io.readfromnifti(
+        args.fmrifile,
+        headeronly=True,
+    )
+    xdim, ydim, slicedim, fmritr = tide_io.parseniftisizes(fmri_sizes)
+    xsize, ysize, numslices, timepoints = tide_io.parseniftidims(fmri_dims)
+    numspatiallocs = int(xsize) * int(ysize) * int(numslices)
+
+    # read the processed mask
+    print("reading procfit maskfile")
+    (
+        procmask_input,
+        procmask,
+        procmask_header,
+        procmask_dims,
+        procmask_sizes,
+    ) = tide_io.readfromnifti(args.maskfile)
+    if not tide_io.checkspacematch(fmri_header, procmask_header):
+        raise ValueError("procmask dimensions do not match fmri dimensions")
+    procmask_spacebytime = procmask.reshape((numspatiallocs))
+    if args.debug:
+        print(f"{procmask_spacebytime.shape=}")
+
+    print("reading lagtimes")
+    (
+        lagtimes_input,
+        lagtimes,
+        lagtimes_header,
+        lagtimes_dims,
+        lagtimes_sizes,
+    ) = tide_io.readfromnifti(args.lagtimesfile)
+    if not tide_io.checkspacematch(fmri_header, lagtimes_header):
+        raise ValueError("lagtimes dimensions do not match fmri dimensions")
+    if args.debug:
+        print(f"{lagtimes.shape=}")
+    lagtimes_spacebytime = lagtimes.reshape((numspatiallocs))
+    if args.debug:
+        print(f"{lagtimes_spacebytime.shape=}")
+
+    startpt = args.numskip
+    endpt = timepoints - 1
+    validtimepoints = endpt - startpt + 1
+    skiptime = startpt * fmritr
+    initial_fmri_x = (
+        np.linspace(0.0, validtimepoints * fmritr, num=validtimepoints, endpoint=False) + skiptime
+    )
+
+    # read the lagtc generator file
+    print("reading lagtc generator")
+    genlagtc = tide_resample.FastResamplerFromFile(args.lagtcgeneratorfile)
+
+    # select the voxels in the mask
+    print("figuring out valid voxels")
+    validvoxels = np.where(procmask_spacebytime > 0)[0]
+    if args.debug:
+        print(f"{validvoxels.shape=}")
+    numvalidspatiallocs = np.shape(validvoxels)[0]
+    if args.debug:
+        print(f"{numvalidspatiallocs=}")
+    internalvalidspaceshape = numvalidspatiallocs
+    internalvalidspaceshapederivs = (
+        internalvalidspaceshape,
+        args.regressderivs + 1,
+    )
+    internalvalidfmrishape = (numvalidspatiallocs, np.shape(initial_fmri_x)[0])
+    if args.debug:
+        print(f"validvoxels shape = {numvalidspatiallocs}")
+        print(f"internalvalidfmrishape shape = {internalvalidfmrishape}")
+
+    # slicing to valid voxels
+    print("selecting valid voxels")
+    lagtimes_valid = lagtimes_spacebytime[validvoxels]
+    procmask_valid = procmask_spacebytime[validvoxels]
+    if args.debug:
+        print(f"{lagtimes_valid.shape=}")
+
+    if usesharedmem:
+        if args.debug:
+            print("allocating shared memory")
+    else:
+        if args.debug:
+            print("allocating memory")
+    fitNorm, fitNorm_shm = tide_util.allocarray(
+        internalvalidspaceshapederivs, rt_outfloattype, shared=usesharedmem
+    )
+    fitcoeff, fitcoeff_shm = tide_util.allocarray(
+        internalvalidspaceshapederivs, rt_outfloattype, shared=usesharedmem
+    )
+    lagtc, lagtc_shm = tide_util.allocarray(
+        internalvalidfmrishape, rt_floattype, shared=usesharedmem
+    )
+
+    outputpath = os.path.dirname(args.outputroot)
+    rawsources = [
+        os.path.relpath(args.fmrifile, start=outputpath),
+        os.path.relpath(args.lagtimesfile, start=outputpath),
+        os.path.relpath(args.maskfile, start=outputpath),
+        os.path.relpath(args.lagtcgeneratorfile, start=outputpath),
+    ]
+
+    bidsbasedict = {
+        "RawSources": rawsources,
+        "Units": "arbitrary",
+        "CommandLineArgs": thecommandline,
+    }
+
+    print("calling makelaggedtcs")
+    voxelsprocessed_makelagged = tide_makelagged.makelaggedtcs(
+        genlagtc,
+        initial_fmri_x,
+        procmask_valid,
+        lagtimes_valid,
+        lagtc,
+        LGR=LGR,
+        nprocs=args.nprocs,
+        showprogressbar=args.showprogressbar,
+    )
+
+    print(f"generated regressors for {voxelsprocessed_makelagged} voxels")
+
+    theheader = copy.deepcopy(lagtimes_header)
+    bidsdict = bidsbasedict.copy()
+
+    if args.debug:
+        maplist = [
+            (
+                lagtimes_valid,
+                "maxtimeREAD",
+                "map",
+                "second",
+                "Lag time in seconds used for calculation",
+            ),
+            (procmask_valid, "maskREAD", "mask", None, "Mask used for calculation"),
+        ]
+
+        # write the 3D maps
+        tide_io.savemaplist(
+            args.outputroot,
+            maplist,
+            validvoxels,
+            (xsize, ysize, numslices),
+            theheader,
+            bidsdict,
+            debug=args.debug,
+        )
+
+    # write the 4D maps
+    theheader = copy.deepcopy(fmri_header)
+    maplist = []
+
+    if args.regressderivs > 0:
+        if args.debug:
+            print(f"adding derivatives up to order {args.regressderivs} prior to regression")
+        regressorset = tide_linfitfiltpass.makevoxelspecificderivs(lagtc, args.regressderivs)
+
+        if args.debug:
+            print("going down the multiple EV path")
+            print(f"{regressorset[:, :, 0].shape=}")
+        maplist += [
+            (
+                regressorset[:, :, 0],
+                "lfofilterEV",
+                "bold",
+                None,
+                "Shifted sLFO regressor to filter",
+            ),
+        ]
+        for thederiv in range(1, args.regressderivs + 1):
+            if args.debug:
+                print(f"{regressorset[:, :, thederiv].shape=}")
+            maplist += [
+                (
+                    regressorset[:, :, thederiv],
+                    f"lfofilterEVDeriv{thederiv}",
+                    "bold",
+                    None,
+                    f"Time derivative {thederiv} of shifted sLFO regressor",
+                ),
+            ]
+    else:
+        regressorset = lagtc
+        if args.debug:
+            print("going down the single EV path")
+        maplist += [
+            (
+                regressorset,
+                "lfofilterEV",
+                "bold",
+                None,
+                "Shifted sLFO regressor to filter",
+            ),
+        ]
+    tide_io.savemaplist(
+        args.outputroot,
+        maplist,
+        validvoxels,
+        (xsize, ysize, numslices, validtimepoints),
+        theheader,
+        bidsdict,
+        debug=args.debug,
+    )
+
+    # clean up shared memory
+    if usesharedmem:
+        tide_util.cleanup_shm(fitNorm_shm)
+        tide_util.cleanup_shm(fitcoeff_shm)
+        tide_util.cleanup_shm(lagtc_shm)