rapidtide 3.0.1__tar.gz → 3.0.3__tar.gz

{rapidtide-3.0.1 → rapidtide-3.0.3}/CHANGELOG.md

@@ -1,5 +1,22 @@
 # Release history
 
+## Version 3.0.3 (5/4/25)
+* (rapidtide, retroregress) If you supply a brain, GM, WM, or CSF mask, rapidtide extracts the matching timecourse from the mask at startup, and after filtering, if it's done.  retroregress extracts the timecourses after filtering.
+* (rapidtide) Fixed mask logic when gray matter mask is provided.
+* (rapidtide) Fixed a crash when ``--acfix`` is selected and a bad sidelobe is encountered if the similarity calculation range is not the entire timecourse (THAT was hard to pin down...).
+* (rapidtide, tidepool) Fixed a serious cosmetic bug in corrout files introduced in v3.0.2 - teoffset was not being set properly by rapidtide, so the tidepool similarity function display was very wrong.
+* (rapidtide) shiftedtcs file is now written during each pass if ``--saveintermediatemaps`` is set and ``--outputlevel`` is ``more`` or ``max`` (in response to a feature request).
+* (rapidtide) Added back the ability to have integral powers of the motion regressors.
+* (rapidtide) Added the ability to specify a CSF mask.
+
+
+## Version 3.0.2 (4/28/25)
+* (retroregress) Added a new argument to ``--outputlevel``, ``onlyregressors``.  When selected, retroregress generates the voxel specific sLFO regressor(s), saves them, and exits.  This option exists so that you can use the rapidtide voxel specific sLFO regressors in an external processing routine such as XCP-D without extraneous data storage or processing time. 
+* (rapidtide) Leaned harder into using the voxelData class, and beefed up its capabilities.
+* (happy) Updated to use voxelData.
+* (happy) Moved phase projection to an external routine.
+* (documentation) Fixed a few more typos.
+
 ## Version 3.0.1 (4/23/25)
 * (documentation) I missed a bunch of weird errors in the "Theory of Operation" section.  Are you surprised?  I'm not surprised.  You shouldn't be either.  These are now fixed.  This doesn't change any code - mostly affects online documentation.
 

{rapidtide-3.0.1 → rapidtide-3.0.3}/INSTALL.rst

@@ -115,7 +115,7 @@ This will use the most recent version on dockerhub, which is built automatically
 NOTE: I don't advise doing this unless you're helping debug something - 
 there's no guarantee that "latest" is functional at any given time.
 
-Now that the file is downloaded, you can run and rapidtide command in the Docker container.  For example, to run a simple
+Now that the file is downloaded, you can run any rapidtide command in the Docker container.  For example, to run a simple
 rapidtide analysis, you would use the following command (you can do this all in one step - it will just integrate the
 first pull into the run time if the version you request hasn't already been downloaded).
 

{rapidtide-3.0.1/rapidtide.egg-info → rapidtide-3.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rapidtide
-Version: 3.0.1
+Version: 3.0.3
 Summary: Tools for performing correlation analysis on fMRI data.
 Author: Taylor Salo, Daniel M. Drucker, Ph.D., Jeffrey N Stout, Yaroslav O. Halchenko, Derek Monroe
 Author-email: "Blaise deB. Frederick" <blaise.frederick@gmail.com>

{rapidtide-3.0.1 → rapidtide-3.0.3}/rapidtide/DerivativeDelay.py

@@ -135,8 +135,6 @@ class DerivativeDelay:
                     (xdim, ydim, slicedim),
                     gausssigma=args.delayoffsetgausssigma,
                     patchthresh=args.delaypatchthresh,
-                    fileiscifti=False,
-                    textio=False,
                     rt_floattype=rt_floattype,
                     debug=args.debug,
                 )
@@ -181,8 +179,6 @@ class DerivativeDelay:
                     (xdim, ydim, slicedim),
                     gausssigma=args.delayoffsetgausssigma,
                     patchthresh=args.delaypatchthresh,
-                    fileiscifti=False,
-                    textio=False,
                     rt_floattype=rt_floattype,
                     debug=args.debug,
                 )

{rapidtide-3.0.1 → rapidtide-3.0.3}/rapidtide/calcsimfunc.py

@@ -69,6 +69,7 @@ def correlationpass(
     chunksize=1000,
     rt_floatset=np.float64,
     rt_floattype="float64",
+    debug=False,
 ):
     """
 
@@ -96,6 +97,8 @@ def correlationpass(
     -------
 
     """
+    if debug:
+        print(f"calling setreftc in calcsimfunc with length {len(referencetc)}")
     theCorrelator.setreftc(referencetc)
     theCorrelator.setlimits(lagmininpts, lagmaxinpts)
 

{rapidtide-3.0.1 → rapidtide-3.0.3}/rapidtide/correlate.py

@@ -86,11 +86,12 @@ def disablenumba():
 def check_autocorrelation(
     corrscale,
     thexcorr,
-    delta=0.1,
+    delta=0.05,
     acampthresh=0.1,
     aclagthresh=10.0,
     displayplots=False,
     detrendorder=1,
+    debug=False,
 ):
     """Check for autocorrelation in an array.
 
@@ -110,10 +111,23 @@ def check_autocorrelation(
     sidelobetime
     sidelobeamp
     """
+    if debug:
+        print("check_autocorrelation:")
+        print(f"delta: {delta}")
+        print(f"acampthresh: {acampthresh}")
+        print(f"aclagthresh: {aclagthresh}")
+        print(f"displayplots: {displayplots}")
     lookahead = 2
+    if displayplots:
+        print(f"check_autocorrelation: {displayplots=}")
+        plt.plot(corrscale, thexcorr)
+        plt.show()
     peaks = tide_fit.peakdetect(thexcorr, x_axis=corrscale, delta=delta, lookahead=lookahead)
     maxpeaks = np.asarray(peaks[0], dtype="float64")
     if len(peaks[0]) > 0:
+        if debug:
+            print(f"found {len(peaks[0])} peaks")
+            print(peaks)
         LGR.debug(peaks)
         zeropkindex = np.argmin(abs(maxpeaks[:, 0]))
         for i in range(zeropkindex + 1, maxpeaks.shape[0]):
@@ -155,6 +169,9 @@ def check_autocorrelation(
                     )
                     plt.show()
                 return sidelobetime, sidelobeamp
+    else:
+        if debug:
+            print("no peaks found")
     return None, None
 
 

rapidtide-3.0.3/rapidtide/data/examples/src/testfmri

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel more \
+    --dofinalrefine \
+    --graymattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_GRAY \
+    --brainmask sub-RAPIDTIDETEST_brainmask.nii.gz \
+    --whitemattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_WHITE \
+    --csfmask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_CSF \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST

{rapidtide-3.0.1 → rapidtide-3.0.3}/rapidtide/data/examples/src/testretro

@@ -1,25 +1,27 @@
 #!/bin/bash
 
-#rapidtide \
-#    --nprocs -1 \
-#    --passes 3 \
-#    --refinetype unweighted_average \
-#    --numnull 0 \
-#    --outputlevel max \
-#    --regressderivs 1 \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel more \
+    --dofinalrefine \
+    --graymattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_GRAY \
+    --brainmask sub-RAPIDTIDETEST_brainmask.nii.gz \
+    --whitemattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_WHITE \
+    --csfmask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_CSF \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST
 
 ##retroregress sub-RAPIDTIDETEST.nii.gz ../dst/sub-RAPIDTIDETEST --alternateoutput ../dst/0deriv --nprocs -1 
 
 retroregress \
     sub-RAPIDTIDETEST.nii.gz \
     ../dst/sub-RAPIDTIDETEST \
-    --alternateoutput ../dst/wintest \
+    --alternateoutput ../dst/specialtest \
     --nprocs -1 \
-    --outputlevel max \
-    --focaldebug \
-    --delayoffsetspatialfilt -1 
+    --outputlevel normal
 
 #retroregress sub-RAPIDTIDETEST.nii.gz ../dst/sub-RAPIDTIDETEST --alternateoutput ../dst/0deriv_refined --nprocs -1 --regressderivs 0 --makepseudofile --outputlevel max --refinedelay --nofilterwithrefineddelay
 #retroregress sub-RAPIDTIDETEST.nii.gz ../dst/sub-RAPIDTIDETEST --alternateoutput ../dst/0deriv_refinedfit --nprocs -1 --regressderivs 0 --makepseudofile --outputlevel max --refinedelay

{rapidtide-3.0.1 → rapidtide-3.0.3}/rapidtide/happy_supportfuncs.py

@@ -999,211 +999,42 @@ def circularderivs(timecourse):
 
 
 def phaseproject(
-    datatoproject,
-    means,
-    destpoints,
-    numsteps,
-    timings,
-    cardfromfmri_sliceres,
-    instantaneous_cardiacphase,
+    input_data,
+    demeandata_byslice,
+    means_byslice,
+    rawapp_byslice,
+    app_byslice,
+    normapp_byslice,
+    weights_byslice,
+    cine_byslice,
+    projmask_byslice,
+    derivatives_byslice,
+    proctrs,
     thispass,
-    numpasses,
     args,
-    outputroot,
-    slicesamplerate,
-    pleth_sliceres,
-    mrsamplerate,
-    projmask_byslice,
+    sliceoffsets,
     cardphasevals,
-    thetimes,
-    centric=True,
-    passstring="",
-    badpointlist=None,
-    congridbins=3.0,
-    gridkernel="kaiser",
+    outphases,
+    appsmoothingfilter,
+    phaseFs,
+    thecorrfunc_byslice,
+    waveamp_byslice,
+    wavedelay_byslice,
+    wavedelayCOM_byslice,
+    corrected_rawapp_byslice,
+    corrstartloc,
+    correndloc,
+    thealiasedcorrx,
+    theAliasedCorrelator,
 ):
-    xsize, ysize, numslices, timepoints = datatoproject.shape
-    # construct the destination arrays
-    tide_util.logmem("before making destination arrays")
-    app = np.zeros((xsize, ysize, numslices, destpoints), dtype=np.float64)
-    app_byslice = app.reshape((xsize * ysize, numslices, destpoints))
-    cine = np.zeros((xsize, ysize, numslices, destpoints), dtype=np.float64)
-    cine_byslice = cine.reshape((xsize * ysize, numslices, destpoints))
-    rawapp = np.zeros((xsize, ysize, numslices, destpoints), dtype=np.float64)
-    rawapp_byslice = rawapp.reshape((xsize * ysize, numslices, destpoints))
-    corrected_rawapp = np.zeros((xsize, ysize, numslices, destpoints), dtype=np.float64)
-    corrected_rawapp_byslice = rawapp.reshape((xsize * ysize, numslices, destpoints))
-    normapp = np.zeros((xsize, ysize, numslices, destpoints), dtype=np.float64)
-    normapp_byslice = normapp.reshape((xsize * ysize, numslices, destpoints))
-    weights = np.zeros((xsize, ysize, numslices, destpoints), dtype=np.float64)
-    weight_byslice = weights.reshape((xsize * ysize, numslices, destpoints))
-    derivatives = np.zeros((xsize, ysize, numslices, 4), dtype=np.float64)
-    derivatives_byslice = derivatives.reshape((xsize * ysize, numslices, 4))
-
-    timings.append(["Output arrays allocated" + passstring, time.time(), None, None])
-
-    if centric:
-        outphases = np.linspace(-np.pi, np.pi, num=destpoints, endpoint=False)
-    else:
-        outphases = np.linspace(0.0, 2.0 * np.pi, num=destpoints, endpoint=False)
-    phasestep = outphases[1] - outphases[0]
-
-    #######################################################################################################
-    #
-    # now do the phase projection
-    #
-    #
-    datatoproject_byslice = datatoproject.reshape((xsize * ysize, numslices, timepoints))
-    means_byslice = means.reshape((xsize * ysize, numslices))
-
-    timings.append(["Phase projection to image started" + passstring, time.time(), None, None])
-    print("Starting phase projection")
-    proctrs = range(timepoints)  # proctrs is the list of all fmri trs to be projected
-    procpoints = range(
-        timepoints * numsteps
-    )  # procpoints is the list of all sliceres datapoints to be projected
-    if badpointlist is not None:
-        censortrs = np.zeros(timepoints, dtype="int")
-        censorpoints = np.zeros(timepoints * numsteps, dtype="int")
-        censortrs[np.where(badpointlist > 0.0)[0] // numsteps] = 1
-        censorpoints[np.where(badpointlist > 0.0)[0]] = 1
-        proctrs = np.where(censortrs < 1)[0]
-        procpoints = np.where(censorpoints < 1)[0]
-
-    # do phase averaging
-    app_bypoint = cardiaccycleaverage(
-        instantaneous_cardiacphase,
-        outphases,
-        cardfromfmri_sliceres,
-        procpoints,
-        congridbins,
-        gridkernel,
-        centric,
-        cyclic=True,
-    )
-    if thispass == numpasses - 1:
-        tide_io.writebidstsv(
-            outputroot + "_desc-cardiaccyclefromfmri_timeseries",
-            app_bypoint,
-            1.0 / (outphases[1] - outphases[0]),
-            starttime=outphases[0],
-            columns=["cardiaccyclefromfmri"],
-            append=False,
-            debug=args.debug,
-        )
-
-    # now do time averaging
-    lookaheadval = int(slicesamplerate / 4.0)
-    print("lookaheadval = ", lookaheadval)
-    wrappedcardiacphase = tide_math.phasemod(instantaneous_cardiacphase, centric=centric)
-    max_peaks, min_peaks = tide_fit.peakdetect(wrappedcardiacphase, lookahead=lookaheadval)
-    # start on a maximum
-    if max_peaks[0][0] > min_peaks[0][0]:
-        min_peaks = min_peaks[1:]
-    # work only with pairs
-    if len(max_peaks) > len(min_peaks):
-        max_peaks = max_peaks[:-1]
-
-    zerophaselocs = []
-    for idx, peak in enumerate(max_peaks):
-        minloc = min_peaks[idx][0]
-        maxloc = max_peaks[idx][0]
-        minval = min_peaks[idx][1]
-        maxval = max_peaks[idx][1]
-        if minloc > 0:
-            if wrappedcardiacphase[minloc - 1] < wrappedcardiacphase[minloc]:
-                minloc -= 1
-                minval = wrappedcardiacphase[minloc]
-        phasediff = minval - (maxval - 2.0 * np.pi)
-        timediff = minloc - maxloc
-        zerophaselocs.append(1.0 * minloc - (minval - outphases[0]) * timediff / phasediff)
-        # print(idx, [maxloc, maxval], [minloc, minval], phasediff, timediff, zerophaselocs[-1])
-    instantaneous_cardiactime = instantaneous_cardiacphase * 0.0
-
-    whichpeak = 0
-    for t in procpoints:
-        if whichpeak < len(zerophaselocs) - 1:
-            if t > zerophaselocs[whichpeak + 1]:
-                whichpeak += 1
-        if t > zerophaselocs[whichpeak]:
-            instantaneous_cardiactime[t] = (t - zerophaselocs[whichpeak]) / slicesamplerate
-        # print(t, whichpeak, zerophaselocs[whichpeak], instantaneous_cardiactime[t])
-    maxtime = (
-        np.ceil(
-            int(
-                1.02
-                * tide_stats.getfracval(instantaneous_cardiactime, 0.98)
-                // args.pulsereconstepsize
-            )
-        )
-        * args.pulsereconstepsize
-    )
-    outtimes = np.linspace(
-        0.0, maxtime, num=int(maxtime / args.pulsereconstepsize), endpoint=False
-    )
-    atp_bypoint = cardiaccycleaverage(
-        instantaneous_cardiactime,
-        outtimes,
-        cardfromfmri_sliceres,
-        procpoints,
-        congridbins,
-        gridkernel,
-        False,
-        cyclic=True,
-    )
-    if thispass == numpasses - 1:
-        tide_io.writebidstsv(
-            outputroot + "_desc-cardpulsefromfmri_timeseries",
-            atp_bypoint,
-            1.0 / (outtimes[1] - outtimes[0]),
-            starttime=outtimes[0],
-            columns=["pulsefromfmri"],
-            append=False,
-            debug=args.debug,
-        )
-
-    if not args.verbose:
-        print("Phase projecting...")
-
-    # make a lowpass filter for the projected data. Limit frequency to 3 cycles per 2pi (1/6th Fs)
-    phaseFs = 1.0 / phasestep
-    phaseFc = phaseFs / 6.0
-    appsmoothingfilter = tide_filt.NoncausalFilter("arb", cyclic=True, padtime=0.0)
-    appsmoothingfilter.setfreqs(0.0, 0.0, phaseFc, phaseFc)
-
-    # setup for aliased correlation if we're going to do it
-    if args.doaliasedcorrelation and (thispass == numpasses - 1):
-        if args.cardiacfilename:
-            signal_sliceres = pleth_sliceres
-            # signal_stdres = pleth_stdres
-        else:
-            signal_sliceres = cardfromfmri_sliceres
-            # signal_stdres = dlfilteredcard_stdres
-        corrsearchvals = (
-            np.linspace(0.0, args.aliasedcorrelationwidth, num=args.aliasedcorrelationpts)
-            - args.aliasedcorrelationwidth / 2.0
-        )
-        theAliasedCorrelator = tide_corr.AliasedCorrelator(
-            signal_sliceres,
-            slicesamplerate,
-            numsteps,
-        )
-        thecorrfunc = np.zeros(
-            (xsize, ysize, numslices, args.aliasedcorrelationpts), dtype=np.float64
-        )
-        thecorrfunc_byslice = thecorrfunc.reshape(
-            (xsize * ysize, numslices, args.aliasedcorrelationpts)
-        )
-        wavedelay = np.zeros((xsize, ysize, numslices), dtype=np.float64)
-        wavedelay_byslice = wavedelay.reshape((xsize * ysize, numslices))
-        waveamp = np.zeros((xsize, ysize, numslices), dtype=np.float64)
-        waveamp_byslice = waveamp.reshape((xsize * ysize, numslices))
+    xsize, ysize, numslices, timepoints = input_data.getdims()
+    fmri_data_byslice = input_data.byslice()
 
-    # now project the data
     for theslice in tqdm(
         range(numslices),
         desc="Slice",
         unit="slices",
+        disable=(not args.showprogressbar),
     ):
         if args.verbose:
             print("Phase projecting for slice", theslice)
@@ -1211,33 +1042,31 @@ def phaseproject(
         # indexlist = range(0, len(cardphasevals[theslice, :]))
         if len(validlocs) > 0:
             for t in proctrs:
-                filteredmr = -datatoproject_byslice[validlocs, theslice, t]
-                cinemr = (
-                    datatoproject_byslice[validlocs, theslice, t]
-                    + means_byslice[validlocs, theslice, t]
-                )
+                filteredmr = -demeandata_byslice[validlocs, theslice, t]
+                cinemr = fmri_data_byslice[validlocs, theslice, t]
                 thevals, theweights, theindices = tide_resample.congrid(
                     outphases,
                     cardphasevals[theslice, t],
                     1.0,
-                    congridbins,
-                    kernel=gridkernel,
+                    args.congridbins,
+                    kernel=args.gridkernel,
                     cyclic=True,
                 )
                 for i in range(len(theindices)):
-                    weight_byslice[validlocs, theslice, theindices[i]] += theweights[i]
-                    rawapp_byslice[validlocs, theslice, theindices[i]] += (
-                        theweights[i] * filteredmr
-                    )
+                    weights_byslice[validlocs, theslice, theindices[i]] += theweights[i]
+                    # rawapp_byslice[validlocs, theslice, theindices[i]] += (
+                    #    theweights[i] * filteredmr
+                    # )
+                    rawapp_byslice[validlocs, theslice, theindices[i]] += filteredmr
                     cine_byslice[validlocs, theslice, theindices[i]] += theweights[i] * cinemr
-            for d in range(destpoints):
-                if weight_byslice[validlocs[0], theslice, d] == 0.0:
-                    weight_byslice[validlocs, theslice, d] = 1.0
+            for d in range(args.destpoints):
+                if weights_byslice[validlocs[0], theslice, d] == 0.0:
+                    weights_byslice[validlocs, theslice, d] = 1.0
             rawapp_byslice[validlocs, theslice, :] = np.nan_to_num(
-                rawapp_byslice[validlocs, theslice, :] / weight_byslice[validlocs, theslice, :]
+                rawapp_byslice[validlocs, theslice, :] / weights_byslice[validlocs, theslice, :]
             )
             cine_byslice[validlocs, theslice, :] = np.nan_to_num(
-                cine_byslice[validlocs, theslice, :] / weight_byslice[validlocs, theslice, :]
+                cine_byslice[validlocs, theslice, :] / weights_byslice[validlocs, theslice, :]
             )
         else:
             rawapp_byslice[:, theslice, :] = 0.0
@@ -1260,33 +1089,41 @@ def phaseproject(
             corrected_rawapp_byslice[validlocs, theslice, :] = (
                 rawapp_byslice[validlocs, theslice, :] - timecoursemean
             ) * appflips_byslice[validlocs, theslice, None] + timecoursemean
-            if args.doaliasedcorrelation and (thispass == numpasses - 1):
+            if args.doaliasedcorrelation and (thispass > 0):
                 for theloc in validlocs:
                     thecorrfunc_byslice[theloc, theslice, :] = theAliasedCorrelator.apply(
                         -appflips_byslice[theloc, theslice]
-                        * datatoproject_byslice[theloc, theslice, :],
-                        -thetimes[theslice][0],
-                    )
+                        * demeandata_byslice[theloc, theslice, :],
+                        int(sliceoffsets[theslice]),
+                    )[corrstartloc : correndloc + 1]
                     maxloc = np.argmax(thecorrfunc_byslice[theloc, theslice, :])
-                    wavedelay_byslice[theloc, theslice] = corrsearchvals[maxloc]
-                    waveamp_byslice[theloc, theslice] = thecorrfunc_byslice[
-                        theloc, theslice, maxloc
-                    ]
+                    wavedelay_byslice[theloc, theslice] = (
+                        thealiasedcorrx[corrstartloc : correndloc + 1]
+                    )[maxloc]
+                    waveamp_byslice[theloc, theslice] = np.fabs(
+                        thecorrfunc_byslice[theloc, theslice, maxloc]
+                    )
+                    wavedelayCOM_byslice[theloc, theslice] = theCOM(
+                        thealiasedcorrx[corrstartloc : correndloc + 1],
+                        np.fabs(thecorrfunc_byslice[theloc, theslice, :]),
+                    )
         else:
             corrected_rawapp_byslice[validlocs, theslice, :] = rawapp_byslice[
                 validlocs, theslice, :
             ]
-            if args.doaliasedcorrelation and (thispass == numpasses - 1):
+            if args.doaliasedcorrelation and (thispass > 0):
                 for theloc in validlocs:
                     thecorrfunc_byslice[theloc, theslice, :] = theAliasedCorrelator.apply(
-                        -datatoproject_byslice[theloc, theslice, :],
-                        -thetimes[theslice][0],
-                    )
+                        -demeandata_byslice[theloc, theslice, :],
+                        int(sliceoffsets[theslice]),
+                    )[corrstartloc : correndloc + 1]
                     maxloc = np.argmax(np.abs(thecorrfunc_byslice[theloc, theslice, :]))
-                    wavedelay_byslice[theloc, theslice] = corrsearchvals[maxloc]
-                    waveamp_byslice[theloc, theslice] = thecorrfunc_byslice[
-                        theloc, theslice, maxloc
-                    ]
+                    wavedelay_byslice[theloc, theslice] = (
+                        thealiasedcorrx[corrstartloc : correndloc + 1]
+                    )[maxloc]
+                    waveamp_byslice[theloc, theslice] = np.fabs(
+                        thecorrfunc_byslice[theloc, theslice, maxloc]
+                    )
         timecoursemin = np.min(corrected_rawapp_byslice[validlocs, theslice, :], axis=1).reshape(
             (-1, 1)
         )
@@ -1296,10 +1133,10 @@ def phaseproject(
         normapp_byslice[validlocs, theslice, :] = np.nan_to_num(
             app_byslice[validlocs, theslice, :] / means_byslice[validlocs, theslice, None]
         )
-    return app, rawapp, corrected_rawapp, normapp, weights, cine, derivatives
+    return appflips_byslice
 
 
-def upsampleimage(input_data, input_hdr, numsteps, sliceoffsets, slicesamplerate, outputroot):
+def upsampleimage(input_data, numsteps, sliceoffsets, slicesamplerate, outputroot):
     fmri_data = input_data.byvol()
     timepoints = input_data.timepoints
     xsize = input_data.xsize
@@ -1309,7 +1146,6 @@ def upsampleimage(input_data, input_hdr, numsteps, sliceoffsets, slicesamplerate
     # allocate the image
     print(f"upsampling fmri data by a factor of {numsteps}")
     upsampleimage = np.zeros((xsize, ysize, numslices, numsteps * timepoints), dtype=float)
-    upsampleimage_byslice = upsampleimage.reshape(xsize * ysize, numslices, numsteps * timepoints)
 
     # demean the raw data
     meanfmri = fmri_data.mean(axis=1)
@@ -1339,8 +1175,8 @@ def upsampleimage(input_data, input_hdr, numsteps, sliceoffsets, slicesamplerate
             )
             upsampleimage_byslice[thexyvoxel, :, thetimepoint] = 1.0 * theinterps
 
-    theheader = copy.deepcopy(input_hdr)
-    theheader["dim"][4] = timepoints * numsteps
-    theheader["pixdim"][4] = 1.0 / slicesamplerate
+    theheader = input_data.copyheader(
+        numtimepoints=(timepoints * numsteps), tr=(1.0 / slicesamplerate)
+    )
     tide_io.savetonifti(upsampleimage, theheader, outputroot + "_upsampled")
     print("upsampling complete")

{rapidtide-3.0.1 → rapidtide-3.0.3}/rapidtide/helper_classes.py

@@ -310,7 +310,7 @@ class MutualInformationator(SimilarityFunctionator):
     def run(self, thetc, locs=None, trim=True, gettimeaxis=True):
         if len(thetc) != len(self.reftc):
             print(
-                "timecourses are of different sizes:",
+                "MutualInformationator: timecourses are of different sizes:",
                 len(thetc),
                 "!=",
                 len(self.reftc),
@@ -434,7 +434,7 @@ class Correlator(SimilarityFunctionator):
     def run(self, thetc, trim=True):
         if len(thetc) != len(self.reftc):
             print(
-                "timecourses are of different sizes:",
+                "Correlator: timecourses are of different sizes:",
                 len(thetc),
                 "!=",
                 len(self.reftc),
@@ -580,7 +580,7 @@ class Coherer:
     def run(self, thetc, trim=True, alt=False):
         if len(thetc) != len(self.reftc):
             print(
-                "timecourses are of different sizes:",
+                "Coherer: timecourses are of different sizes:",
                 len(thetc),
                 "!=",
                 len(self.reftc),
@@ -1076,7 +1076,7 @@ class SimilarityFunctionFitter:
                     maxval_init = 0.0
                     if self.debug:
                         print("bad initial amp:", maxval_init, "is less than 0.0")
-                if maxval_init > 1.0:
+                if (maxval_init > 1.0) and self.enforcethresh:
                     failreason |= self.FML_INITAMPHIGH
                     maxval_init = 1.0
                     if self.debug: