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

rapidtide/workflows/retroglm.py

@@ -1,643 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-#   Copyright 2016-2024 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
-
-import numpy as np
-
-import rapidtide.filter as tide_filt
-import rapidtide.io as tide_io
-import rapidtide.miscmath as tide_math
-import rapidtide.multiproc as tide_multiproc
-import rapidtide.resample as tide_resample
-import rapidtide.util as tide_util
-import rapidtide.workflows.glmfrommaps as tide_glmfrommaps
-import rapidtide.workflows.parser_funcs as pf
-
-LGR = logging.getLogger("GENERAL")
-ErrorLGR = logging.getLogger("ERROR")
-TimingLGR = logging.getLogger("TIMING")
-
-DEFAULT_GLMDERIVS = 0
-
-
-def _get_parser():
-    """
-    Argument parser for glmfilt
-    """
-    parser = argparse.ArgumentParser(
-        prog="retroglm",
-        description="Do the rapidtide GLM filtering using the maps generated from a previous 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 file to filter.",
-    )
-    parser.add_argument(
-        "datafileroot",
-        type=str,
-        help="The root name of the previously run rapidtide dataset (everything up to but not including the underscore.)",
-    )
-    parser.add_argument(
-        "--alternateoutput",
-        dest="alternateoutput",
-        type=str,
-        help="Alternate output root (if not specified, will use the same root as the previous dataset).",
-        default=None,
-    )
-    parser.add_argument(
-        "--glmderivs",
-        dest="glmderivs",
-        action="store",
-        type=int,
-        metavar="NDERIVS",
-        help=(
-            f"When doing final GLM, include derivatives up to NDERIVS order. Default is {DEFAULT_GLMDERIVS}"
-        ),
-        default=DEFAULT_GLMDERIVS,
-    )
-    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(
-        "--outputlevel",
-        dest="outputlevel",
-        action="store",
-        type=str,
-        choices=["min", "less", "normal", "more", "max"],
-        help=(
-            "The level of file output produced.  'min' produces only absolutely essential files, 'less' adds in "
-            "the GLM filtered data (rather than just filter efficacy metrics), 'normal' saves what you "
-            "would typically want around for interactive data exploration, "
-            "'more' adds files that are sometimes useful, and 'max' outputs anything you might possibly want. "
-            "Selecting 'max' will produce ~3x your input datafile size as output.  "
-            f'Default is "normal".'
-        ),
-        default="normal",
-    )
-    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(
-        "--makepseudofile",
-        dest="makepseudofile",
-        action="store_true",
-        help=("Make a simulated input file from the mean and the movingsignal."),
-        default=False,
-    )
-    parser.add_argument(
-        "--debug",
-        dest="debug",
-        action="store_true",
-        help=("Output lots of helpful information."),
-        default=False,
-    )
-    return parser
-
-
-def retroglm(args):
-    rt_floatset = np.float64
-    rt_floattype = "float64"
-    rt_outfloatset = np.float64
-    rt_outfloattype = "float64"
-
-    if args.outputlevel == "min":
-        args.saveminimumglmfiles = False
-        args.savenormalglmfiles = False
-        args.savemovingsignal = False
-        args.saveallglmfiles = False
-    elif args.outputlevel == "less":
-        args.saveminimumglmfiles = True
-        args.savenormalglmfiles = False
-        args.savemovingsignal = False
-        args.saveallglmfiles = False
-    elif args.outputlevel == "normal":
-        args.saveminimumglmfiles = True
-        args.savenormalglmfiles = True
-        args.savemovingsignal = False
-        args.saveallglmfiles = False
-    elif args.outputlevel == "more":
-        args.saveminimumglmfiles = True
-        args.savenormalglmfiles = True
-        args.savemovingsignal = True
-        args.saveallglmfiles = False
-    elif args.outputlevel == "max":
-        args.saveminimumglmfiles = True
-        args.savenormalglmfiles = True
-        args.savemovingsignal = True
-        args.saveallglmfiles = True
-    else:
-        print(f"illegal output level {args['outputlevel']}")
-        sys.exit()
-
-    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 runoptions file
-    print("reading runoptions")
-    runoptionsfile = f"{args.datafileroot}_desc-runoptions_info"
-    therunoptions = tide_io.readoptionsfile(runoptionsfile)
-    try:
-        candoretroglm = therunoptions["retroglmcompatible"]
-    except KeyError:
-        print("this rapidtide dataset does not support retrospective GLM calculation")
-        sys.exit()
-
-    # read the fmri input files
-    print("reading fmrifile")
-    fmri_input, fmri_data, fmri_header, fmri_dims, fmri_sizes = tide_io.readfromnifti(
-        args.fmrifile
-    )
-    if args.debug:
-        print(f"{fmri_data.shape=}")
-    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)
-    fmri_data_spacebytime = fmri_data.reshape((numspatiallocs, timepoints))
-    if args.debug:
-        print(f"{fmri_data_spacebytime.shape=}")
-
-    # read the processed mask
-    print("reading procfit maskfile")
-    procmaskfile = f"{args.datafileroot}_desc-processed_mask.nii.gz"
-    (
-        procmask_input,
-        procmask,
-        procmask_header,
-        procmask_dims,
-        procmask_sizes,
-    ) = tide_io.readfromnifti(procmaskfile)
-    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=}")
-
-    # read the corrfit mask
-    print("reading corrfit maskfile")
-    corrmaskfile = f"{args.datafileroot}_desc-corrfit_mask.nii.gz"
-    (
-        corrmask_input,
-        corrmask,
-        corrmask_header,
-        corrmask_dims,
-        corrmask_sizes,
-    ) = tide_io.readfromnifti(corrmaskfile)
-    if not tide_io.checkspacematch(fmri_header, corrmask_header):
-        raise ValueError("corrmask dimensions do not match fmri dimensions")
-    corrmask_spacebytime = corrmask.reshape((numspatiallocs))
-    if args.debug:
-        print(f"{corrmask_spacebytime.shape=}")
-
-    print("reading lagtimes")
-    lagtimesfile = f"{args.datafileroot}_desc-maxtime_map.nii.gz"
-    (
-        lagtimes_input,
-        lagtimes,
-        lagtimes_header,
-        lagtimes_dims,
-        lagtimes_sizes,
-    ) = tide_io.readfromnifti(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
-    )
-
-    if therunoptions["arbvec"] is not None:
-        # NOTE - this vector is LOWERPASS, UPPERPASS, LOWERSTOP, UPPERSTOP
-        # setfreqs expects LOWERSTOP, LOWERPASS, UPPERPASS, UPPERSTOP
-        theprefilter = tide_filt.NoncausalFilter(
-            "arb",
-            transferfunc=therunoptions["filtertype"],
-        )
-        theprefilter.setfreqs(
-            therunoptions["arbvec"][2],
-            therunoptions["arbvec"][0],
-            therunoptions["arbvec"][1],
-            therunoptions["arbvec"][3],
-        )
-    else:
-        theprefilter = tide_filt.NoncausalFilter(
-            therunoptions["filterband"],
-            transferfunc=therunoptions["filtertype"],
-            padtime=therunoptions["padseconds"],
-        )
-
-    # read the lagtc generator file
-    print("reading lagtc generator")
-    lagtcgeneratorfile = f"{args.datafileroot}_desc-lagtcgenerator_timeseries"
-    genlagtc = tide_resample.FastResamplerFromFile(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.glmderivs + 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")
-    fmri_data_valid = fmri_data_spacebytime[validvoxels, :]
-    lagtimes_valid = lagtimes_spacebytime[validvoxels]
-    corrmask_valid = corrmask_spacebytime[validvoxels]
-    procmask_valid = procmask_spacebytime[validvoxels]
-    if args.debug:
-        print(f"{fmri_data_valid.shape=}")
-
-    if usesharedmem:
-        if args.debug:
-            print("allocating shared memory")
-        glmmean, dummy, dummy = tide_util.allocshared(internalvalidspaceshape, rt_outfloatset)
-        rvalue, dummy, dummy = tide_util.allocshared(internalvalidspaceshape, rt_outfloatset)
-        r2value, dummy, dummy = tide_util.allocshared(internalvalidspaceshape, rt_outfloatset)
-        fitNorm, dummy, dummy = tide_util.allocshared(
-            internalvalidspaceshapederivs, rt_outfloatset
-        )
-        fitcoeff, dummy, dummy = tide_util.allocshared(
-            internalvalidspaceshapederivs, rt_outfloatset
-        )
-        movingsignal, dummy, dummy = tide_util.allocshared(internalvalidfmrishape, rt_outfloatset)
-        lagtc, dummy, dummy = tide_util.allocshared(internalvalidfmrishape, rt_floatset)
-        filtereddata, dummy, dummy = tide_util.allocshared(internalvalidfmrishape, rt_outfloatset)
-    else:
-        if args.debug:
-            print("allocating memory")
-        glmmean = np.zeros(internalvalidspaceshape, dtype=rt_outfloattype)
-        rvalue = np.zeros(internalvalidspaceshape, dtype=rt_outfloattype)
-        r2value = np.zeros(internalvalidspaceshape, dtype=rt_outfloattype)
-        fitNorm = np.zeros(internalvalidspaceshapederivs, dtype=rt_outfloattype)
-        fitcoeff = np.zeros(internalvalidspaceshapederivs, dtype=rt_outfloattype)
-        movingsignal = np.zeros(internalvalidfmrishape, dtype=rt_outfloattype)
-        lagtc = np.zeros(internalvalidfmrishape, dtype=rt_floattype)
-        filtereddata = np.zeros(internalvalidfmrishape, dtype=rt_outfloattype)
-
-    oversampfactor = int(therunoptions["oversampfactor"])
-    if args.alternateoutput is None:
-        outputname = therunoptions["outputname"]
-    else:
-        outputname = args.alternateoutput
-    if args.debug:
-        print(f"{outputname=}")
-    oversamptr = fmritr / oversampfactor
-    try:
-        threshval = therunoptions["glmthreshval"]
-    except KeyError:
-        threshval = 0.0
-    mode = "glm"
-
-    outputpath = os.path.dirname(outputname)
-    rawsources = [
-        os.path.relpath(args.fmrifile, start=outputpath),
-        os.path.relpath(lagtimesfile, start=outputpath),
-        os.path.relpath(corrmaskfile, start=outputpath),
-        os.path.relpath(procmaskfile, start=outputpath),
-        os.path.relpath(runoptionsfile, start=outputpath),
-        os.path.relpath(lagtcgeneratorfile, start=outputpath),
-    ]
-
-    bidsbasedict = {
-        "RawSources": rawsources,
-        "Units": "arbitrary",
-        "CommandLineArgs": thecommandline,
-    }
-
-    if args.debug:
-        # dump the fmri input file going to glm
-        theheader = copy.deepcopy(fmri_header)
-        theheader["dim"][4] = validtimepoints
-        theheader["pixdim"][4] = fmritr
-
-        maplist = [
-            (
-                fmri_data_valid,
-                "datatofilter",
-                "bold",
-                None,
-                "fMRI data that will be subjected to GLM filtering",
-            ),
-        ]
-        tide_io.savemaplist(
-            outputname,
-            maplist,
-            validvoxels,
-            (xsize, ysize, numslices, validtimepoints),
-            theheader,
-            bidsbasedict,
-            textio=False,
-            fileiscifti=False,
-            rt_floattype=rt_floattype,
-            cifti_hdr=None,
-        )
-
-    initialvariance = tide_math.imagevariance(fmri_data_valid, theprefilter, 1.0 / fmritr)
-
-    print("calling glmmfrommaps")
-    voxelsprocessed_glm, regressorset = tide_glmfrommaps.glmfrommaps(
-        fmri_data_valid,
-        validvoxels,
-        initial_fmri_x,
-        lagtimes_valid,
-        corrmask_valid,
-        genlagtc,
-        mode,
-        outputname,
-        oversamptr,
-        glmmean,
-        rvalue,
-        r2value,
-        fitNorm,
-        fitcoeff,
-        movingsignal,
-        lagtc,
-        filtereddata,
-        LGR,
-        TimingLGR,
-        threshval,
-        args.saveminimumglmfiles,
-        nprocs_makelaggedtcs=args.nprocs,
-        nprocs_glm=args.nprocs,
-        glmderivs=args.glmderivs,
-        showprogressbar=args.showprogressbar,
-        debug=args.debug,
-    )
-
-    print(f"filtered {voxelsprocessed_glm} voxels")
-    finalvariance = tide_math.imagevariance(filtereddata, theprefilter, 1.0 / fmritr)
-    divlocs = np.where(finalvariance > 0.0)
-    varchange = initialvariance * 0.0
-    varchange[divlocs] = 100.0 * (finalvariance[divlocs] / initialvariance[divlocs] - 1.0)
-
-    theheader = copy.deepcopy(lagtimes_header)
-    if mode == "glm":
-        maplist = [
-            (
-                initialvariance,
-                "lfofilterInbandVarianceBefore",
-                "map",
-                None,
-                "Inband variance prior to filtering",
-            ),
-            (
-                finalvariance,
-                "lfofilterInbandVarianceAfter",
-                "map",
-                None,
-                "Inband variance after filtering",
-            ),
-            (
-                varchange,
-                "lfofilterInbandVarianceChange",
-                "map",
-                "percent",
-                "Change in inband variance after filtering, in percent",
-            ),
-        ]
-        if args.saveminimumglmfiles:
-            maplist += [
-                (
-                    r2value,
-                    "lfofilterR2",
-                    "map",
-                    None,
-                    "Squared R value of the GLM fit (proportion of variance explained)",
-                ),
-            ]
-        if args.savenormalglmfiles:
-            maplist += [
-                (rvalue, "lfofilterR", "map", None, "R value of the GLM fit"),
-                (glmmean, "lfofilterMean", "map", None, "Intercept from GLM fit"),
-            ]
-    else:
-        maplist = [
-            (initialvariance, "lfofilterInbandVarianceBefore", "map", None),
-            (finalvariance, "lfofilterInbandVarianceAfter", "map", None),
-            (varchange, "CVRVariance", "map", None),
-        ]
-        if args.savenormalglmfiles:
-            maplist += [
-                (rvalue, "CVRR", "map", None),
-                (r2value, "CVRR2", "map", None),
-                (fitcoeff, "CVR", "map", "percent"),
-            ]
-
-    bidsdict = bidsbasedict.copy()
-
-    if args.debug:
-        maplist += [
-            (
-                lagtimes_valid,
-                "maxtimeREAD",
-                "map",
-                "second",
-                "Lag time in seconds used for calculation",
-            ),
-            (corrmask_valid, "corrfitREAD", "mask", None, "Correlation mask used for calculation"),
-            (procmask_valid, "processedREAD", "mask", None, "Processed mask used for calculation"),
-        ]
-    if args.savenormalglmfiles:
-        if args.glmderivs > 0:
-            maplist += [
-                (fitcoeff[:, 0], "lfofilterCoeff", "map", None, "Fit coefficient"),
-                (fitNorm[:, 0], "lfofilterNorm", "map", None, "Normalized fit coefficient"),
-            ]
-            for thederiv in range(1, args.glmderivs + 1):
-                maplist += [
-                    (
-                        fitcoeff[:, thederiv],
-                        f"lfofilterCoeffDeriv{thederiv}",
-                        "map",
-                        None,
-                        f"Fit coefficient for temporal derivative {thederiv}",
-                    ),
-                    (
-                        fitNorm[:, thederiv],
-                        f"lfofilterNormDeriv{thederiv}",
-                        "map",
-                        None,
-                        f"Normalized fit coefficient for temporal derivative {thederiv}",
-                    ),
-                ]
-        else:
-            maplist += [
-                (fitcoeff, "lfofilterCoeff", "map", None, "Fit coefficient"),
-                (fitNorm, "lfofilterNorm", "map", None, "Normalized fit coefficient"),
-            ]
-
-    # write the 3D maps
-    tide_io.savemaplist(
-        outputname,
-        maplist,
-        validvoxels,
-        (xsize, ysize, numslices),
-        theheader,
-        bidsdict,
-        debug=args.debug,
-    )
-
-    # write the 4D maps
-    theheader = copy.deepcopy(fmri_header)
-    maplist = []
-    if args.saveminimumglmfiles:
-        maplist = [
-            (
-                filtereddata,
-                "lfofilterCleaned",
-                "bold",
-                None,
-                "fMRI data with sLFO signal filtered out",
-            ),
-        ]
-    if args.savemovingsignal:
-        maplist += [
-            (
-                movingsignal,
-                "lfofilterRemoved",
-                "bold",
-                None,
-                "sLFO signal filtered out of this voxel",
-            )
-        ]
-
-    if args.saveallglmfiles:
-        if args.glmderivs > 0:
-            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.glmderivs + 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:
-            if args.debug:
-                print("going down the single EV path")
-            maplist += [
-                (
-                    regressorset,
-                    "lfofilterEV",
-                    "bold",
-                    None,
-                    "Shifted sLFO regressor to filter",
-                ),
-            ]
-    if args.debug:
-        maplist.append((fmri_data_valid, "inputdata", "bold", None, None))
-    if args.makepseudofile:
-        print("reading mean image")
-        meanfile = f"{args.datafileroot}_desc-mean_map.nii.gz"
-        (
-            mean_input,
-            mean,
-            mean_header,
-            mean_dims,
-            mean_sizes,
-        ) = tide_io.readfromnifti(meanfile)
-        if not tide_io.checkspacematch(fmri_header, mean_header):
-            raise ValueError("mean dimensions do not match fmri dimensions")
-        if args.debug:
-            print(f"{mean.shape=}")
-        mean_spacebytime = mean.reshape((numspatiallocs))
-        if args.debug:
-            print(f"{mean_spacebytime.shape=}")
-        pseudofile = mean_spacebytime[validvoxels, None] + movingsignal[:, :]
-        maplist.append((pseudofile, "pseudofile", "bold", None, None))
-    tide_io.savemaplist(
-        outputname,
-        maplist,
-        validvoxels,
-        (xsize, ysize, numslices, validtimepoints),
-        theheader,
-        bidsdict,
-        debug=args.debug,
-    )

rapidtide-2.9.6.data/scripts/adjustoffset

@@ -1,23 +0,0 @@
-#!python
-# -*- coding: utf-8 -*-
-#
-#   Copyright 2016-2024 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 rapidtide.workflows.adjustoffset as theworkflow
-import rapidtide.workflows.parser_funcs as pf
-
-if __name__ == "__main__":
-    pf.generic_init(theworkflow._get_parser, theworkflow.adjustoffset)

rapidtide-2.9.6.data/scripts/aligntcs

@@ -1,23 +0,0 @@
-#!python
-# -*- coding: utf-8 -*-
-#
-#   Copyright 2016-2024 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 rapidtide.workflows.aligntcs as theworkflow
-import rapidtide.workflows.parser_funcs as pf
-
-if __name__ == "__main__":
-    pf.generic_init(theworkflow._get_parser, theworkflow.aligntcs)