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

rapidtide-2.9.6.data/scripts/showxcorr_legacy

@@ -1,536 +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 getopt
-import sys
-
-import numpy as np
-from matplotlib.pyplot import figure, plot, show
-from numpy import argmax, r_, zeros
-from numpy.random import permutation
-from scipy.stats import pearsonr
-
-import rapidtide.correlate as tide_corr
-import rapidtide.filter as tide_filt
-import rapidtide.fit as tide_fit
-import rapidtide.io as tide_io
-import rapidtide.miscmath as tide_math
-import rapidtide.stats as tide_stats
-
-
-def getNullDistributionData(
-    indata,
-    xcorr_x,
-    thefilter,
-    windowfunc,
-    detrendorder,
-    searchstart,
-    searchend,
-    numreps=1000,
-):
-    print("estimating significance distribution using ", numreps, " repetitions")
-    corrlist = zeros(numreps, dtype="float")
-    corrlist_pear = zeros(numreps, dtype="float")
-    xcorr_x_trim = xcorr_x[searchstart : searchend + 1]
-
-    filteredindata = tide_math.corrnormalize(
-        thefilter.apply(Fs, indata), windowfunc=windowfunc, detrendorder=detrendorder
-    )
-    for i in range(0, numreps):
-        # make a shuffled copy of the regressors
-        shuffleddata = permutation(indata)
-
-        # filter it
-        filteredshuffleddata = tide_math.corrnormalize(
-            thefilter.apply(Fs, shuffleddata),
-            windowfunc=windowfunc,
-            detrendorder=detrendorder,
-        )
-
-        # crosscorrelate with original
-        if gccphat:
-            theshuffledxcorr = tide_corr.fastcorrelate(
-                filteredindata, filteredshuffleddata, usefft=dofftcorr, weighting="phat"
-            )
-
-        else:
-            theshuffledxcorr = tide_corr.fastcorrelate(
-                filteredindata, filteredshuffleddata, usefft=dofftcorr
-            )
-
-        # find and tabulate correlation coefficient at optimal lag
-        theshuffledxcorr_trim = theshuffledxcorr[searchstart : searchend + 1]
-        maxdelay = xcorr_x_trim[argmax(theshuffledxcorr_trim)]
-        corrlist[i] = theshuffledxcorr_trim[argmax(theshuffledxcorr_trim)]
-
-        # find and tabulate correlation coefficient at 0 lag
-        corrlist_pear[i] = pearsonr(filteredindata, filteredshuffleddata)[0]
-
-        # progress
-        # tide_util.progressbar(i + 1, numreps, label='Percent complete')
-
-    # jump to line after progress bar
-    print()
-
-    # return the distribution data
-    return corrlist, corrlist_pear
-
-
-def usage():
-    print("showxcorr - calculate and display crosscorrelation between two timeseries")
-    print("")
-    print(
-        "usage: showxcorr timecourse1 timecourse2 samplerate [-l LABEL] [-s STARTTIME] [-D DURATION] [-d] [-F LOWERFREQ,UPPERFREQ[,LOWERSTOP,UPPERSTOP]] [-V] [-L] [-R] [-C] [-t] [-w] [-f] [-z FILENAME] [-N TRIALS]"
-    )
-    print("")
-    print("required arguments:")
-    print("	timcoursefile1:	text file containing a timeseries")
-    print("	timcoursefile2:	text file containing a timeseries")
-    print("	samplerate:	the sample rate of the timecourses, in Hz")
-    print("")
-    print("optional arguments:")
-    print("    -t            - detrend the data")
-    print("    -w            - window the data with a hamming function")
-    print("    -l LABEL      - label for the delay value")
-    print("    -s STARTTIME  - time of first datapoint to use in seconds in the first file")
-    print("    -D DURATION   - amount of data to use in seconds")
-    print("    -r RANGE      - restrict peak search range to +/- RANGE seconds (default is ")
-    print("                    +/-15)")
-    print("    -d            - turns off display of graph")
-    print("    -F            - filter data and regressors from LOWERFREQ to UPPERFREQ.")
-    print("                    LOWERSTOP and UPPERSTOP can be specified, or will be ")
-    print("                    calculated automatically")
-    print("    -V            - filter data and regressors to VLF band")
-    print("    -L            - filter data and regressors to LFO band")
-    print("    -R            - filter data and regressors to respiratory band")
-    print("    -C            - filter data and regressors to cardiac band")
-    print("    -T            - trim data to match")
-    print("    -A            - print data on a single summary line")
-    print("    -a            - if summary mode is on, add a header line showing what values ")
-    print("                    mean")
-    print("    -f            - negate (flip) second regressor")
-    print("    -z FILENAME   - use the columns of FILENAME as controlling variables and ")
-    print("                    return the partial correlation")
-    print("    -N TRIALS     - estimate significance thresholds by Monte Carlo with TRIALS ")
-    print("                    repetition")
-    print("    -Y            - turn on debugging")
-    print("")
-    return ()
-
-
-def main():
-    # get the command line parameters
-    searchrange = 15.0
-    uselabel = False
-    displayplots = True
-    gccphat = False
-    windowfunc = "None"
-    detrendorder = 0
-    dopartial = False
-    duration = 1000000.0
-    starttime = 0.0
-    doplot = False
-    thelabel = ""
-    trimdata = False
-    verbose = True
-    summarymode = False
-    dofftcorr = True
-    labelline = False
-    estimate_significance = False
-    writecorrlists = False
-    flipregressor = False
-
-    debug = False
-    if debug:
-        dumpfiltered = True
-    else:
-        dumpfiltered = False
-    showpearson = True
-
-    nargs = len(sys.argv)
-    if nargs < 4:
-        usage()
-        exit()
-    infilename1 = sys.argv[1]
-    infilename2 = sys.argv[2]
-    Fs = float(sys.argv[3])
-
-    theprefilter = tide_filt.NoncausalFilter()
-
-    inputdata1 = tide_io.readvec(infilename1)
-    inputdata2 = tide_io.readvec(infilename2)
-    numpoints = len(inputdata1)
-
-    # now scan for optional arguments
-    try:
-        opts, args = getopt.getopt(sys.argv[4:], "fN:r:z:aATtVLRCF:dl:s:D:wY", ["help"])
-    except getopt.GetoptError as err:
-        # print help information and exit:
-        print(str(err))  # will print something like "option -x not recognized"
-        usage()
-        sys.exit(2)
-
-    for o, a in opts:
-        if o == "-d":
-            displayplots = False
-            if verbose:
-                print("disable display")
-        elif o == "-Y":
-            debug = True
-            dumpfiltered = True
-            if verbose:
-                print("turning on debugging")
-        elif o == "-T":
-            trimdata = True
-            if verbose:
-                print("trimming data to match")
-        elif o == "-g":
-            gccphat = True
-            if verbose:
-                print("doing phase alignment transform")
-        elif o == "-f":
-            flipregressor = True
-            if verbose:
-                print("negating second regressor")
-        elif o == "-a":
-            labelline = True
-            if verbose:
-                print("turning on label line")
-        elif o == "-t":
-            detrendorder = 1
-            if verbose:
-                print("enabling linear detrending")
-        elif o == "-w":
-            windowfunc = "hamming"
-            if verbose:
-                print("enabling hamming windowing")
-        elif o == "-z":
-            controlvariablefile = a
-            dopartial = True
-            if verbose:
-                print("performing partial correlations")
-        elif o == "-l":
-            thelabel = a
-            uselabel = True
-            if verbose:
-                print("label set to", thelabel)
-        elif o == "-N":
-            numreps = int(a)
-            estimate_significance = True
-            if verbose:
-                print("estimating significance threshold with ", numreps, " trials")
-        elif o == "-r":
-            searchrange = float(a)
-            if verbose:
-                print("peak search restricted to +/-", searchrange, " seconds")
-        elif o == "-D":
-            duration = float(a)
-            if verbose:
-                print("duration set to", duration)
-        elif o == "-s":
-            starttime = float(a)
-            if verbose:
-                print("starttime set to", starttime)
-        elif o == "-V":
-            theprefilter.settype("vlf")
-            if verbose:
-                print("prefiltering to vlf band")
-        elif o == "-L":
-            theprefilter.settype("lfo")
-            if verbose:
-                print("prefiltering to lfo band")
-        elif o == "-R":
-            theprefilter.settype("resp")
-            if verbose:
-                print("prefiltering to respiratory band")
-        elif o == "-C":
-            theprefilter.settype("cardiac")
-            if verbose:
-                print("prefiltering to cardiac band")
-        elif o == "-A":
-            verbose = False
-            summarymode = True
-        elif o == "-F":
-            arbvec = a.split(",")
-            if len(arbvec) != 2 and len(arbvec) != 4:
-                usage()
-                sys.exit()
-            if len(arbvec) == 2:
-                arb_lower = float(arbvec[0])
-                arb_upper = float(arbvec[1])
-                arb_lowerstop = 0.9 * float(arbvec[0])
-                arb_upperstop = 1.1 * float(arbvec[1])
-            if len(arbvec) == 4:
-                arb_lower = float(arbvec[0])
-                arb_upper = float(arbvec[1])
-                arb_lowerstop = float(arbvec[2])
-                arb_upperstop = float(arbvec[3])
-            theprefilter.settype("arb")
-            theprefilter.setfreqs(arb_lowerstop, arb_lower, arb_upper, arb_upperstop)
-            if verbose:
-                print(
-                    "prefiltering to ",
-                    arb_lower,
-                    arb_upper,
-                    "(stops at ",
-                    arb_lowerstop,
-                    arb_upperstop,
-                    ")",
-                )
-        else:
-            assert False, "unhandled option"
-
-    startpoint1 = max([int(starttime * Fs), 0])
-    if debug:
-        print("startpoint set to ", startpoint1)
-    endpoint1 = min([startpoint1 + int(duration * Fs), int(len(inputdata1))])
-    if debug:
-        print("endpoint set to ", endpoint1)
-    endpoint2 = min([int(duration * Fs), int(len(inputdata1)), int(len(inputdata2))])
-    trimdata1 = inputdata1[startpoint1:endpoint1]
-    trimdata2 = inputdata2[0:endpoint2]
-
-    if trimdata:
-        minlen = np.min([len(trimdata1), len(trimdata2)])
-        trimdata1 = trimdata1[0:minlen]
-        trimdata2 = trimdata2[0:minlen]
-
-    # band limit the regressor if that is needed
-    if theprefilter.gettype() != "None":
-        if verbose:
-            print("filtering to ", theprefilter.gettype(), " band")
-    filtereddata1 = tide_math.corrnormalize(
-        theprefilter.apply(Fs, trimdata1),
-        windowfunc=windowfunc,
-        detrendorder=detrendorder,
-    )
-    filtereddata2 = tide_math.corrnormalize(
-        theprefilter.apply(Fs, trimdata2),
-        windowfunc=windowfunc,
-        detrendorder=detrendorder,
-    )
-    if flipregressor:
-        filtereddata2 *= -1.0
-    if dumpfiltered:
-        tide_io.writenpvecs(filtereddata1, "filtereddata1.txt")
-        tide_io.writenpvecs(filtereddata2, "filtereddata2.txt")
-
-    if dopartial:
-        controlvars = tide_io.readvecs(controlvariablefile)
-        regressorvec = []
-        for j in range(0, controlvars.shape[0]):
-            regressorvec.append(
-                tide_math.corrnormalize(
-                    theprefilter.apply(Fs, controlvars[j, :]),
-                    windowfunc=windowfunc,
-                    detrendorder=detrendorder,
-                )
-            )
-        if (np.max(filtereddata1) - np.min(filtereddata1)) > 0.0:
-            thefit, filtereddata1 = tide_fit.mlregress(regressorvec, filtereddata1)
-        if (np.max(filtereddata2) - np.min(filtereddata2)) > 0.0:
-            thefit, filtereddata2 = tide_fit.mlregress(regressorvec, filtereddata2)
-
-    if gccphat:
-        thexcorr = tide_corr.fastcorrelate(
-            filtereddata1, filtereddata2, usefft=dofftcorr, weighting="phat"
-        )
-    else:
-        thexcorr = tide_corr.fastcorrelate(filtereddata1, filtereddata2, usefft=dofftcorr)
-    thepxcorr = pearsonr(filtereddata1, filtereddata2)
-
-    xcorrlen = len(thexcorr)
-    sampletime = 1.0 / Fs
-    xcorr_x = r_[0.0:xcorrlen] * sampletime - (xcorrlen * sampletime) / 2.0 + sampletime / 2.0
-    halfwindow = int(searchrange * Fs)
-    corrzero = xcorrlen // 2
-    searchstart = corrzero - halfwindow
-    searchend = corrzero + halfwindow
-    xcorr_x_trim = xcorr_x[searchstart : searchend + 1]
-    thexcorr_trim = thexcorr[searchstart : searchend + 1]
-    if debug:
-        print("searching for peak correlation over range ", searchstart, searchend)
-    maxdelay = xcorr_x_trim[argmax(thexcorr_trim)]
-    if debug:
-        print("maxdelay before refinement", maxdelay)
-    dofindmaxlag = True
-    if dofindmaxlag:
-        print("executing findmaxlag")
-        (
-            maxindex,
-            maxdelay,
-            maxval,
-            maxsigma,
-            maskval,
-            failreason,
-            peakstart,
-            peakend,
-        ) = tide_fit.findmaxlag_gauss(
-            xcorr_x_trim,
-            thexcorr_trim,
-            -searchrange,
-            searchrange,
-            1000.0,
-            refine=True,
-            useguess=False,
-            fastgauss=False,
-            displayplots=False,
-        )
-        print(maxindex, maxdelay, maxval, maxsigma, maskval, failreason)
-        R = maxval
-    if debug:
-        print("maxdelay after refinement", maxdelay)
-        if failreason > 0:
-            print("failreason =", failreason)
-    else:
-        R = thexcorr_trim[argmax(thexcorr_trim)]
-
-    # set the significance threshold
-    if estimate_significance:
-        # generate a list of correlations from shuffled data
-        corrlist, corrlist_pear = getNullDistributionData(
-            trimdata1,
-            xcorr_x,
-            theprefilter,
-            windowfunc,
-            detrendorder,
-            searchstart,
-            searchend,
-            numreps=numreps,
-        )
-
-        # calculate percentiles for the crosscorrelation from the distribution data
-        histlen = 100
-        thepercentiles = [0.95, 0.99, 0.995]
-
-        pcts, pcts_fit, histfit = tide_stats.sigFromDistributionData(
-            corrlist, histlen, thepercentiles
-        )
-        if debug:
-            tide_stats.printthresholds(
-                pcts,
-                thepercentiles,
-                "Crosscorrelation significance thresholds from data:",
-            )
-            tide_stats.printthresholds(
-                pcts_fit,
-                thepercentiles,
-                "Crosscorrelation significance thresholds from fit:",
-            )
-
-        # calculate significance for the pearson correlation
-        pearpcts, pearpcts_fit, histfit = tide_stats.sigFromDistributionData(
-            corrlist_pear, histlen, thepercentiles
-        )
-        if debug:
-            tide_stats.printthresholds(
-                pearpcts,
-                thepercentiles,
-                "Pearson correlation significance thresholds from data:",
-            )
-            tide_stats.printthresholds(
-                pearpcts_fit,
-                thepercentiles,
-                "Pearson correlation significance thresholds from fit:",
-            )
-
-        if writecorrlists:
-            tide_io.writenpvecs(corrlist, "corrlist.txt")
-            tide_io.writenpvecs(corrlist_pear, "corrlist_pear.txt")
-
-    # report the pearson correlation
-    if showpearson and verbose:
-        print("Pearson_R:\t", thepxcorr[0])
-        if estimate_significance:
-            for idx, percentile in enumerate(thepercentiles):
-                print(
-                    "    pear_p(",
-                    "{:.3f}".format(1.0 - percentile),
-                    "):\t",
-                    pearpcts[idx],
-                )
-        print("")
-
-    if debug:
-        print(thepxcorr)
-
-    if verbose:
-        if uselabel:
-            print(thelabel, ":\t", maxdelay)
-        else:
-            print("Crosscorrelation_Rmax:\t", R)
-            print("Crosscorrelation_maxdelay:\t", maxdelay)
-            if estimate_significance:
-                for idx, percentile in enumerate(thepercentiles):
-                    print(
-                        "    xc_p(",
-                        "{:.3f}".format(1.0 - percentile),
-                        "):\t",
-                        pcts[idx],
-                    )
-            print(infilename1, "[0 seconds] == ", infilename2, "[", -maxdelay, " seconds]")
-
-    if summarymode:
-        if estimate_significance:
-            if uselabel:
-                if labelline:
-                    print(
-                        "thelabel",
-                        "pearson_R",
-                        "pearson_R(p=0.05)",
-                        "xcorr_R",
-                        "xcorr_R(P=0.05)",
-                        "xcorr_maxdelay",
-                    )
-                print(thelabel, thepxcorr[0], pearpcts_fit[0], R, pcts_fit[0], -maxdelay)
-            else:
-                if labelline:
-                    print(
-                        "pearson_R",
-                        "pearson_R(p=0.05)",
-                        "xcorr_R",
-                        "xcorr_R(P=0.05)",
-                        "xcorr_maxdelay",
-                    )
-                print(thepxcorr[0], pearpcts_fit[0], R, pcts_fit[0], -maxdelay)
-        else:
-            if uselabel:
-                if labelline:
-                    print(
-                        "thelabel",
-                        "pearson_r",
-                        "pearson_p",
-                        "xcorr_R",
-                        "xcorr_maxdelay",
-                    )
-                print(thelabel, thepxcorr[0], thepxcorr[1], R, -maxdelay)
-            else:
-                if labelline:
-                    print("pearson_r\tpearson_p\txcorr_R\txcorr_t\txcorr_maxdelay")
-                print(thepxcorr[0], "\t", thepxcorr[1], "\t", R, "\t", -maxdelay)
-
-    if displayplots:
-        fig = figure()
-        ax = fig.add_subplot(111)
-        # ax.set_title('GCC')
-        plot(xcorr_x, thexcorr, "k")
-        show()
-
-
-if __name__ == "__main__":
-    main()

rapidtide-2.9.6.data/scripts/showxcorrx

@@ -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.parser_funcs as pf
-import rapidtide.workflows.showxcorrx as theworkflow
-
-if __name__ == "__main__":
-    pf.generic_init(theworkflow._get_parser, theworkflow.showxcorrx)

rapidtide-2.9.6.data/scripts/showxy

@@ -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.parser_funcs as pf
-import rapidtide.workflows.showxy as theworkflow
-
-if __name__ == "__main__":
-    pf.generic_init(theworkflow._get_parser, theworkflow.showxy)

rapidtide-2.9.6.data/scripts/simdata

@@ -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.parser_funcs as pf
-import rapidtide.workflows.simdata as theworkflow
-
-if __name__ == "__main__":
-    pf.generic_init(theworkflow._get_parser, theworkflow.simdata)

rapidtide-2.9.6.data/scripts/spatialdecomp

@@ -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.niftidecomp as theworkflow
-import rapidtide.workflows.parser_funcs as pf
-
-if __name__ == "__main__":
-    pf.generic_init(theworkflow._get_parser_spatial, theworkflow.main_spatial)

rapidtide-2.9.6.data/scripts/spatialfit

@@ -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.parser_funcs as pf
-import rapidtide.workflows.spatialfit as theworkflow
-
-if __name__ == "__main__":
-    pf.generic_init(theworkflow._get_parser, theworkflow.spatialfit)

rapidtide-2.9.6.data/scripts/spatialmi

@@ -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.parser_funcs as pf
-import rapidtide.workflows.spatialmi as theworkflow
-
-if __name__ == "__main__":
-    pf.generic_init(theworkflow._get_parser, theworkflow.spatialmi)