rapidtide 3.0.1__tar.gz → 3.0.2__tar.gz

{rapidtide-3.0.1 → rapidtide-3.0.2}/CHANGELOG.md

@@ -1,5 +1,12 @@
 # Release history
 
+## Version 3.0.2 (4/28/25)
+* (rapidtide) Leaned harder into using the voxelData class, and beefed up its capabilities.
+* (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. 
+* (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-3.0.2}/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-3.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rapidtide
-Version: 3.0.1
+Version: 3.0.2
 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-3.0.2}/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-3.0.2}/rapidtide/data/examples/src/testretro

@@ -1,25 +1,21 @@
 #!/bin/bash
 
-#rapidtide \
-#    --nprocs -1 \
-#    --passes 3 \
-#    --refinetype unweighted_average \
-#    --numnull 0 \
-#    --outputlevel max \
-#    --regressderivs 1 \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST
+rapidtide \
+    --nprocs -1 \
+    --passes 3 \
+    --outputlevel max \
+    --regressderivs 1 \
+    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 onlyregressors
 
 #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-3.0.2}/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-3.0.2}/rapidtide/io.py

@@ -139,7 +139,7 @@ def parseniftidims(thedims):
     nx, ny, nz, nt : int
         Number of points along each dimension
     """
-    return thedims[1], thedims[2], thedims[3], thedims[4]
+    return int(thedims[1]), int(thedims[2]), int(thedims[3]), int(thedims[4])
 
 
 # sizes are the mapping between voxels and physical coordinates
@@ -263,32 +263,30 @@ def niftihdrfromarray(data):
 
 def makedestarray(
     destshape,
-    textio=False,
-    fileiscifti=False,
+    filetype="nifti",
     rt_floattype="float64",
 ):
-    if textio:
+    if filetype == "text":
         try:
             internalspaceshape = destshape[0]
             timedim = destshape[1]
         except TypeError:
             internalspaceshape = destshape
             timedim = None
+    elif filetype == "cifti":
+        spaceindex = len(destshape) - 1
+        timeindex = spaceindex - 1
+        internalspaceshape = destshape[spaceindex]
+        if destshape[timeindex] > 1:
+            timedim = destshape[timeindex]
+        else:
+            timedim = None
     else:
-        if fileiscifti:
-            spaceindex = len(destshape) - 1
-            timeindex = spaceindex - 1
-            internalspaceshape = destshape[spaceindex]
-            if destshape[timeindex] > 1:
-                timedim = destshape[timeindex]
-            else:
-                timedim = None
+        internalspaceshape = int(destshape[0]) * int(destshape[1]) * int(destshape[2])
+        if len(destshape) == 3:
+            timedim = None
         else:
-            internalspaceshape = int(destshape[0]) * int(destshape[1]) * int(destshape[2])
-            if len(destshape) == 3:
-                timedim = None
-            else:
-                timedim = destshape[3]
+            timedim = destshape[3]
     if timedim is None:
         outmaparray = np.zeros(internalspaceshape, dtype=rt_floattype)
     else:
@@ -329,8 +327,7 @@ def savemaplist(
     destshape,
     theheader,
     bidsbasedict,
-    textio=False,
-    fileiscifti=False,
+    filetype="nifti",
     rt_floattype="float64",
     cifti_hdr=None,
     savejson=True,
@@ -338,8 +335,7 @@ def savemaplist(
 ):
     outmaparray, internalspaceshape = makedestarray(
         destshape,
-        textio=textio,
-        fileiscifti=fileiscifti,
+        filetype=filetype,
         rt_floattype=rt_floattype,
     )
     for themap, mapsuffix, maptype, theunit, thedescription in maplist:
@@ -365,7 +361,7 @@ def savemaplist(
             bidsdict["Units"] = theunit
         if thedescription is not None:
             bidsdict["Description"] = thedescription
-        if textio:
+        if filetype == "text":
             writenpvecs(
                 outmaparray.reshape(destshape),
                 f"{outputname}_{mapsuffix}.txt",
@@ -374,7 +370,7 @@ def savemaplist(
             savename = f"{outputname}_desc-{mapsuffix}_{maptype}"
             if savejson:
                 writedicttojson(bidsdict, savename + ".json")
-            if not fileiscifti:
+            if filetype == "nifti":
                 savetonifti(outmaparray.reshape(destshape), theheader, savename)
             else:
                 isseries = len(outmaparray.shape) != 1

{rapidtide-3.0.1 → rapidtide-3.0.2}/rapidtide/refinedelay.py

@@ -110,7 +110,6 @@ def trainratiotooffset(
         "alwaysmultiproc": False,
         "focaldebug": debug,
         "fmrifreq": 1.0 / sampletime,
-        "textio": False,
     }
 
     if trainlagmax - trainlagmin > 0.0:
@@ -233,7 +232,7 @@ def trainratiotooffset(
         funcoffsets.append(trainoffsets[whichoffset] + 0.0)
     maplimits = (xaxis[0], xaxis[-1])
 
-    if outputlevel != "min":
+    if outputlevel != "min" and outputlevel != "onlyregressors":
         resampaxis = np.linspace(xaxis[0], xaxis[-1], num=len(xaxis), endpoint=True)
         outputfuncs = np.zeros((resampaxis.size, numoffsets), dtype=float)
         colnames = []
@@ -429,8 +428,7 @@ def filterderivratios(
     thedims,
     patchthresh=3.0,
     gausssigma=0,
-    fileiscifti=False,
-    textio=False,
+    filetype="nifti",
     rt_floattype="float64",
     verbose=True,
     debug=False,
@@ -448,8 +446,7 @@ def filterderivratios(
         print(f"MAD of regression fit derivative ratios = {themad}")
     outmaparray, internalspaceshape = tide_io.makedestarray(
         nativespaceshape,
-        textio=textio,
-        fileiscifti=fileiscifti,
+        filetype=filetype,
         rt_floattype=rt_floattype,
     )
     mappedregressderivratios = tide_io.populatemap(
@@ -459,7 +456,7 @@ def filterderivratios(
         outmaparray,
         debug=debug,
     )
-    if textio or fileiscifti:
+    if filetype != "nifti":
         medfilt = regressderivratios
         filteredarray = regressderivratios
     else:

{rapidtide-3.0.1 → rapidtide-3.0.2}/rapidtide/tests/cleanposttest

@@ -17,5 +17,4 @@
 #
 
 rm tmp/*
-#rm testdata/*
 rm .coveragerc.*

{rapidtide-3.0.1 → rapidtide-3.0.2}/rapidtide/tests/test_fullrunrapidtide_v3.py

@@ -23,6 +23,7 @@ import matplotlib as mpl
 import rapidtide.workflows.rapidtide as rapidtide_workflow
 import rapidtide.workflows.rapidtide_parser as rapidtide_parser
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
+import rapidtide.workflows.retroregress as rapidtide_retroregress
 
 
 def test_fullrunrapidtide_v3(debug=False, local=False, displayplots=False):
@@ -76,6 +77,15 @@ def test_fullrunrapidtide_v3(debug=False, local=False, displayplots=False):
     #    "--cleanrefined",
     rapidtide_workflow.rapidtide_main(rapidtide_parser.process_args(inputargs=inputargs))
 
+    inputargs = [
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST3"),
+        "--alternateoutput",
+        os.path.join(testtemproot, "onlyregressors"),
+        "--outputlevel",
+        "onlyregressors",
+    ]
+    rapidtide_retroregress.retroregress(rapidtide_retroregress.process_args(inputargs=inputargs))
 
 if __name__ == "__main__":
     mpl.use("TkAgg")

{rapidtide-3.0.1 → rapidtide-3.0.2}/rapidtide/tests/test_fullrunrapidtide_v6.py

@@ -17,7 +17,6 @@
 #
 #
 import os
-import subprocess
 
 import matplotlib as mpl
 

{rapidtide-3.0.1 → rapidtide-3.0.2}/rapidtide/tests/test_refinedelay.py

@@ -153,7 +153,6 @@ def eval_refinedelay(
         "alwaysmultiproc": False,
         "focaldebug": debug,
         "fmrifreq": Fs,
-        "textio": False,
     }
 
     regressderivratios, regressrvalues = tide_refinedelay.getderivratios(
@@ -186,8 +185,6 @@ def eval_refinedelay(
         validvoxels,
         (xdim, ydim, slicedim),
         patchthresh=3.0,
-        fileiscifti=False,
-        textio=False,
         rt_floattype="float64",
         debug=debug,
     )