rapidtide 3.0.5__py3-none-any.whl → 3.0.7__py3-none-any.whl

rapidtide/tests/test_externaltools.py

@@ -0,0 +1,69 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+#   Copyright 2016-2025 Blaise Frederick
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
+#
+import os
+
+import matplotlib as mpl
+
+import rapidtide.externaltools as tide_exttools
+from rapidtide.tests.utils import get_examples_path, get_test_temp_path, mse
+
+
+def test_externaltools(debug=False, local=False):
+    # set input and output directories
+    if local:
+        exampleroot = "../data/examples/src"
+        testtemproot = "./tmp"
+    else:
+        exampleroot = get_examples_path()
+        testtemproot = get_test_temp_path()
+
+    thefsldir = tide_exttools.fslinfo()
+    if debug:
+        print(f"{thefsldir=}")
+
+    if not local:
+        os.environ["FSLDIR"] = "/plausible_FSLDIR"
+
+    thefsldir = tide_exttools.fslinfo()
+    if debug:
+        print(f"{thefsldir=}")
+
+    fslexists, c3dexists, antsexists = tide_exttools.whatexists()
+    if debug:
+        print(f"{fslexists=}, {c3dexists=}, {antsexists=}")
+
+    fslsubcmd, flirtcmd, applywarpcmd = tide_exttools.getfslcmds()
+    if debug:
+        print(f"{fslsubcmd=}, {flirtcmd=}, {applywarpcmd=}")
+
+    tide_exttools.runflirt(
+        "inputname", "targetname", "xform", "outputname", warpfile="thewarp", fake=True
+    )
+    tide_exttools.runflirt("inputname", "targetname", "xform", "outputname", fake=True)
+
+    tide_exttools.n4correct("inputname", "outputdir", fake=True)
+
+    tide_exttools.antsapply(
+        "inputname", "targetname", "outputroot", ["transform1", "transform2"], fake=True
+    )
+
+
+if __name__ == "__main__":
+    mpl.use("TkAgg")
+    test_externaltools(debug=True, local=True)

rapidtide/tests/test_fastresampler.py

@@ -45,6 +45,7 @@ def test_FastResampler(debug=False):
     if debug:
         print(f"{genlaggedtc.initstart=}, {genlaggedtc.initend=}, {genlaggedtc.initstep=}")
         print(f"{genlaggedtc.hiresstart=}, {genlaggedtc.hiresend=}, {genlaggedtc.hiresstep=}")
+    genlaggedtc.info()
 
     # save and reload with another name
     resamplername = os.path.join(get_test_temp_path(), "savedresampler")

rapidtide/tests/test_fullrunrapidtide_v2.py

@@ -68,6 +68,7 @@ def test_fullrunrapidtide_v2(debug=False, local=False, displayplots=False):
         "--outputlevel",
         "max",
         "--calccoherence",
+        "--cleanrefined",
         "--dispersioncalc",
         "--nprocs",
         "1",

rapidtide/tests/test_nullcorr.py

@@ -128,14 +128,11 @@ def test_nullsimfunc(debug=False, displayplots=False):
     histograms = []
     for thenprocs in [1, -1]:
         for i in range(numpasses):
-            corrlist = tide_nullsimfunc.getNullDistributionDatax(
-                sourcedata,
+            corrlist = tide_nullsimfunc.getNullDistributionData(
                 Fs,
                 theCorrelator,
                 thefitter,
-                despeckle_thresh=5.0,
-                fixdelay=False,
-                initialdelayvalue=0.0,
+                None,
                 numestreps=optiondict["numestreps"],
                 nprocs=thenprocs,
                 showprogressbar=optiondict["showprogressbar"],

rapidtide/tests/test_parserfuncs.py

@@ -16,11 +16,27 @@
 #   limitations under the License.
 #
 #
-import os
 import argparse
+import os
+
+import rapidtide.io as tide_io
 import rapidtide.workflows.parser_funcs as pf
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
+
+def proccolspec(thecolspec):
+    if thecolspec is not None:
+        # see if this is a numeric or text list
+        tokenlist = (thecolspec.split(",")[0]).split("-")
+        try:
+            firstelement = int(tokenlist[0])
+            return tide_io.colspectolist(thecolspec)
+        except ValueError:
+            return thecolspec.split(",")
+    else:
+        return [None]
+
+
 def _get_parser():
     """
     Argument parser for adjust offset
@@ -41,7 +57,7 @@ def _get_parser():
     return parser
 
 
-def test_parserfuncs(debug=False, local=False, displayplots=False):
+def test_parserfuncs(debug=False, local=False):
     # set input and output directories
     if local:
         exampleroot = "../data/examples/src"
@@ -50,21 +66,36 @@ def test_parserfuncs(debug=False, local=False, displayplots=False):
         exampleroot = get_examples_path()
         testtemproot = get_test_temp_path()
 
-
     theparser = _get_parser()
 
-    filename = os.path.join(exampleroot,"sub-RAPIDTIDETEST_desc-oversampledmovingregressor_timeseries.json")
-    retval = pf.is_valid_file(theparser, filename)
-    print(filename, retval)
-
-    #filename = os.path.join(exampleroot,"sub-RAPIDTIDETEST_desc-oversampledmovingregressor_timeseriesxyz.json")
-    #retval = pf.is_valid_file(theparser, filename)
-    #print(filename, retval)
-
-    filename = os.path.join(exampleroot,"sub-RAPIDTIDETEST_desc-oversampledmovingregressor_timeseries.json:acolname")
-    retval = pf.is_valid_file(theparser, filename)
-    print(filename, retval)
+    testvecs = [
+        ["sub-RAPIDTIDETEST_desc-oversampledmovingregressor_timeseries.json", [None]],
+        [
+            "sub-RAPIDTIDETEST_desc-oversampledmovingregressor_timeseries.json:acolname",
+            ["acolname"],
+        ],
+        [
+            "sub-RAPIDTIDETEST_desc-oversampledmovingregressor_timeseries.json:acolname,bcolname",
+            ["acolname", "bcolname"],
+        ],
+        [
+            "sub-RAPIDTIDETEST_desc-oversampledmovingregressor_timeseries.tsv.gz:1,2,5-10",
+            [1, 2, 5, 6, 7, 8, 9, 10],
+        ],
+        [
+            "sub-RAPIDTIDETEST_desc-oversampledmovingregressor_timeseries.json:3,2,7,5-10,6-11",
+            [2, 3, 5, 6, 7, 8, 9, 10, 11],
+        ],
+    ]
+    for infile, expectedcols in testvecs:
+        filename = os.path.join(exampleroot, infile)
+        retval = pf.is_valid_file(theparser, filename)
+        thename, thecolspec = tide_io.parsefilespec(retval)
+        collist = proccolspec(thecolspec)
+        if debug:
+            print(filename, retval, thename, thecolspec, collist)
+        assert collist == expectedcols
 
 
 if __name__ == "__main__":
-    test_parserfuncs(debug=True, local=True, displayplots=True)
+    test_parserfuncs(debug=True, local=True)

rapidtide/tests/test_zRapidtideDataset.py

@@ -26,7 +26,7 @@ from rapidtide.RapidtideDataset import RapidtideDataset
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def main(runninglocally=False):
+def main(runninglocally=False, debug=False):
     # initialize default values
     if runninglocally:
         datafileroot = "../data/examples/dst/sub-RAPIDTIDETEST_"
@@ -74,4 +74,4 @@ def main(runninglocally=False):
 
 
 if __name__ == "__main__":
-    main(runninglocally=True)
+    main(runninglocally=True, debug=True)

rapidtide/voxelData.py

@@ -100,6 +100,7 @@ class VoxelData:
     ysize = None
     numslices = None
     timepoints = None
+    dimensions = None
     realtimepoints = None
     xdim = None
     ydim = None
@@ -160,6 +161,10 @@ class VoxelData:
                 self.xsize, self.ysize, self.numslices, self.timepoints = tide_io.parseniftidims(
                     self.thedims
                 )
+                if self.timepoints == 1:
+                    self.dimensions = 3
+                else:
+                    self.dimensions = 4
                 self.numslicelocs = int(self.xsize) * int(self.ysize)
                 self.numspatiallocs = int(self.xsize) * int(self.ysize) * int(self.numslices)
                 self.cifti_hdr = None
@@ -283,15 +288,24 @@ class VoxelData:
         if not self.resident:
             self.load()
         if self.filetype == "nifti":
-            return self.nim_data[:, :, :, self.validstart : self.validend + 1]
+            if self.dimensions == 4 or self.filetype == "cifti" or self.filetype == "text":
+                return self.nim_data[:, :, :, self.validstart : self.validend + 1]
+            else:
+                return self.nim_data[:, :, :]
         else:
             return self.nim_data[:, self.validstart : self.validend + 1]
 
     def byvoxel(self):
-        return self.byvoltrimmed().reshape(self.numspatiallocs, -1)
+        if self.dimensions == 4 or self.filetype == "cifti" or self.filetype == "text":
+            return self.byvoltrimmed().reshape(self.numspatiallocs, -1)
+        else:
+            return self.byvoltrimmed().reshape(self.numspatiallocs)
 
     def byslice(self):
-        return self.byvoltrimmed().reshape(self.numslicelocs, self.numslices, -1)
+        if self.dimensions == 4 or self.filetype == "cifti" or self.filetype == "text":
+            return self.byvoltrimmed().reshape(self.numslicelocs, self.numslices, -1)
+        else:
+            return self.byvoltrimmed().reshape(self.numslicelocs, self.numslices)
 
     def validdata(self):
         if self.validvoxels is None:

rapidtide/workflows/ccorrica.py

@@ -156,8 +156,7 @@ def ccorrica(args):
         else:
             Fs = args.samplerate
     else:
-        if args.samplerate != "auto":
-            Fs = args.samplerate
+        Fs = samplerate
 
     sampletime = 1.0 / Fs
     thedims = tcdata.shape

rapidtide/workflows/cleanregressor.py

@@ -103,8 +103,9 @@ def cleanregressor(
         theCorrelator.setlimits(acmininpts, acmaxinpts)
         # theCorrelator.setlimits(lagmininpts, lagmaxinpts)
         print("check_autocorrelation:", acmininpts, acmaxinpts, lagmininpts, lagmaxinpts)
-        thexcorr, accheckcorrscale, dummy = theCorrelator.run(
-            resampref_y[osvalidsimcalcstart : osvalidsimcalcend + 1]
+        thexcorr, accheckcorrscale, theglobalmax = theCorrelator.run(
+            resampref_y[osvalidsimcalcstart : osvalidsimcalcend + 1],
+            trim=False,
         )
         theFitter.setcorrtimeaxis(accheckcorrscale)
         (

rapidtide/workflows/happy.py

@@ -24,7 +24,7 @@ import warnings
 from pathlib import Path
 
 import numpy as np
-from tqdm import tqdm
+from scipy.stats import pearsonr
 
 import rapidtide.correlate as tide_corr
 import rapidtide.filter as tide_filt
@@ -314,7 +314,11 @@ def happy_main(argparsingfunc):
         validprojvoxels,
         time,
         timings,
+        LGR=None,
+        mpcode=args.mpdetrend,
+        nprocs=args.nprocs,
         showprogressbar=args.showprogressbar,
+        debug=args.debug,
     )
     normdata_byslice = normdata.reshape((xsize * ysize, numslices, timepoints))
 
@@ -1241,7 +1245,9 @@ def happy_main(argparsingfunc):
         demeandata_byslice = demeandata.reshape((xsize * ysize, numslices, timepoints))
         means_byslice = means.reshape((xsize * ysize, numslices))
 
-        timings.append(["Phase projection to image started" + passstring, time.time(), None, None])
+        timings.append(
+            ["Phase projection to image prep 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(
@@ -1255,6 +1261,14 @@ def happy_main(argparsingfunc):
             proctrs = np.where(censortrs < 1)[0]
             procpoints = np.where(censorpoints < 1)[0]
 
+        # preload congrid
+        if args.preloadcongrid:
+            print("Preloading congrid values...")
+            happy_support.preloadcongrid(
+                outphases, args.congridbins, gridkernel=args.gridkernel, cyclic=True, debug=False
+            )
+            print("done")
+
         # do phase averaging
         app_bypoint, weights_bypoint = happy_support.cardiaccycleaverage(
             instantaneous_cardiacphase,
@@ -1264,6 +1278,7 @@ def happy_main(argparsingfunc):
             args.congridbins,
             args.gridkernel,
             args.centric,
+            cache=args.congridcache,
             cyclic=True,
         )
         if thispass == numpasses - 1:
@@ -1356,9 +1371,53 @@ def happy_main(argparsingfunc):
                 debug=args.debug,
             )
 
+        timings.append(
+            ["Phase projection to image prep ended" + passstring, time.time(), None, None]
+        )
         if not args.verbose:
-            print("Phase projecting...")
+            print("Setting up for phase projection...")
 
+        # make a vessel map using Wright's method
+        if args.wrightiterations > 0:
+            timings.append(
+                [
+                    "Wright mask generation started" + passstring,
+                    time.time(),
+                    None,
+                    None,
+                ]
+            )
+            wrightcorrs = happy_support.wrightmap(
+                input_data,
+                demeandata_byslice,
+                rawapp_byslice,
+                projmask_byslice,
+                outphases,
+                cardphasevals,
+                proctrs,
+                args.congridbins,
+                args.gridkernel,
+                args.destpoints,
+                iterations=args.wrightiterations,
+                nprocs=args.nprocs,
+                verbose=False,
+                debug=args.debug,
+            )
+
+            theheader = input_data.copyheader(numtimepoints=1)
+            wrightfilename = f"{outputroot}_desc-wrightcorrspass{thispass + 1}_map"
+            tide_io.writedicttojson(bidsbasedict, wrightfilename + ".json")
+            tide_io.savetonifti(wrightcorrs, theheader, wrightfilename)
+            timings.append(
+                [
+                    "Wright mask generation completed" + passstring,
+                    time.time(),
+                    None,
+                    None,
+                ]
+            )
+
+        timings.append(["Phase projection to image started" + passstring, time.time(), None, None])
         # 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

rapidtide/workflows/happy_parser.py

@@ -593,6 +593,14 @@ def _get_parser():
         help="Will disable showing progress bars (helpful if stdout is going to a file). ",
         default=True,
     )
+    misc_opts.add_argument(
+        "--wrightiterations",
+        dest="wrightiterations",
+        action="store",
+        type=lambda x: pf.is_int(parser, x),
+        help="Number of iterations for calculating Wright map. Set to 0 to disable.",
+        default=0,
+    )
     pf.addtagopts(
         misc_opts,
         helptext="Additional key, value pairs to add to the info json file (useful for tracking analyses).",
@@ -692,6 +700,34 @@ def _get_parser():
         help="Decrease the number of intermediate output files. ",
         default=0,
     )
+    debug_opts.add_argument(
+        "--nompdetrend",
+        dest="mpdetrend",
+        action="store_false",
+        help="Disable multiproc detrending.",
+        default=True,
+    )
+    debug_opts.add_argument(
+        "--nompphaseproject",
+        dest="mpphaseproject",
+        action="store_false",
+        help="Disable multiproc phase projection.",
+        default=True,
+    )
+    debug_opts.add_argument(
+        "--noprefillcongrid",
+        dest="preloadcongrid",
+        action="store_false",
+        help="Don't prefill the congrid value cache.",
+        default=True,
+    )
+    debug_opts.add_argument(
+        "--nocongridcache",
+        dest="congridcache",
+        action="store_false",
+        help="Disable the congrid value cache completely.",
+        default=True,
+    )
 
     return parser
 

rapidtide/workflows/rapidtide.py

@@ -16,7 +16,6 @@
 #   limitations under the License.
 #
 #
-import copy
 import gc
 import logging
 import os
@@ -28,8 +27,6 @@ from pathlib import Path
 import numpy as np
 from scipy import ndimage
 from scipy.stats import rankdata
-from sklearn.decomposition import PCA
-from tqdm import tqdm
 
 import rapidtide.calccoherence as tide_calccoherence
 import rapidtide.calcnullsimfunc as tide_nullsimfunc
@@ -55,7 +52,6 @@ import rapidtide.voxelData as tide_voxelData
 import rapidtide.wiener as tide_wiener
 import rapidtide.workflows.cleanregressor as tide_cleanregressor
 import rapidtide.workflows.regressfrommaps as tide_regressfrommaps
-from rapidtide.tests.utils import mse
 
 from .utils import setup_logger
 
@@ -395,6 +391,11 @@ def rapidtide_main(argparsingfunc):
     csfmask = anatomicmasks[3]
 
     # do spatial filtering if requested
+    if theinputdata.filetype == "nifti":
+        unfiltmeanvalue = np.mean(
+            theinputdata.byvoxel(),
+            axis=1,
+        )
     optiondict["gausssigma"] = theinputdata.smooth(
         optiondict["gausssigma"],
         brainmask=brainmask,
@@ -1731,18 +1732,17 @@ def rapidtide_main(argparsingfunc):
             else:
                 theSimFunc = theCorrelator
             tide_util.disablemkl(optiondict["nprocs_getNullDist"], debug=threaddebug)
-            simdistdata = tide_nullsimfunc.getNullDistributionDatax(
-                cleaned_resampref_y,
+            simdistdata = tide_nullsimfunc.getNullDistributionData(
                 oversampfreq,
                 theSimFunc,
                 theFitter,
+                LGR,
                 numestreps=optiondict["numestreps"],
                 nprocs=optiondict["nprocs_getNullDist"],
                 alwaysmultiproc=optiondict["alwaysmultiproc"],
                 showprogressbar=optiondict["showprogressbar"],
                 chunksize=optiondict["mp_chunksize"],
                 permutationmethod=optiondict["permutationmethod"],
-                fixdelay=optiondict["fixdelay"],
                 rt_floatset=np.float64,
                 rt_floattype="float64",
             )
@@ -2572,8 +2572,6 @@ def rapidtide_main(argparsingfunc):
             chunksize=optiondict["mp_chunksize"],
             nprocs=1,
             alwaysmultiproc=optiondict["alwaysmultiproc"],
-            rt_floatset=rt_floatset,
-            rt_floattype=rt_floattype,
         )
         tide_util.enablemkl(optiondict["mklthreads"], debug=threaddebug)
 
@@ -2658,6 +2656,9 @@ def rapidtide_main(argparsingfunc):
     optiondict["currentstage"] = "presLFOfit"
     tide_io.writedicttojson(optiondict, f"{outputname}_desc-runoptions_info.json")
     if optiondict["dolinfitfilt"] or optiondict["docvrmap"] or optiondict["refinedelay"]:
+        sLFOfiltmask = fitmask + 0.0
+        if optiondict["nosLFOfiltmask"]:
+            sLFOfiltmask = sLFOfiltmask * 0.0 + 1.0
         if optiondict["dolinfitfilt"]:
             if optiondict["refinedelay"]:
                 TimingLGR.info("Setting up for delay refinement and sLFO filtering")
@@ -2837,7 +2838,7 @@ def rapidtide_main(argparsingfunc):
                 validvoxels,
                 initial_fmri_x,
                 lagtimes,
-                fitmask,
+                sLFOfiltmask,
                 genlagtc,
                 mode,
                 outputname,
@@ -2933,7 +2934,7 @@ def rapidtide_main(argparsingfunc):
             namesuffix = "_desc-delayoffset_hist"
             if optiondict["dolinfitfilt"]:
                 tide_stats.makeandsavehistogram(
-                    delayoffset[np.where(fitmask > 0)],
+                    delayoffset[np.where(sLFOfiltmask > 0)],
                     optiondict["histlen"],
                     1,
                     outputname + namesuffix,
@@ -2971,7 +2972,7 @@ def rapidtide_main(argparsingfunc):
                     validvoxels,
                     initial_fmri_x,
                     lagstouse,
-                    fitmask,
+                    sLFOfiltmask,
                     genlagtc,
                     mode,
                     outputname,
@@ -3477,7 +3478,7 @@ def rapidtide_main(argparsingfunc):
                 validvoxels,
                 initial_fmri_x,
                 lagstouse,
-                fitmask,
+                sLFOfiltmask,
                 genlagtc,
                 mode,
                 outputname,
@@ -3545,7 +3546,10 @@ def rapidtide_main(argparsingfunc):
             tide_util.cleanup_shm(fitNorm_shm)
 
     # write the 3D maps that don't need to be remapped
+    if theinputdata.filetype != "nifti":
+        unfiltmeanvalue = meanvalue
     maplist = [
+        (unfiltmeanvalue, "unfiltmean", "map", None, "Voxelwise mean of fmri data before smoothing"),
         (meanvalue, "mean", "map", None, "Voxelwise mean of fmri data"),
         (stddevvalue, "std", "map", None, "Voxelwise standard deviation of fmri data"),
         (covvalue, "CoV", "map", None, "Voxelwise coefficient of variation of fmri data"),
@@ -3570,6 +3574,7 @@ def rapidtide_main(argparsingfunc):
         cifti_hdr=theinputdata.cifti_hdr,
     )
     del meanvalue
+    del unfiltmeanvalue
 
     if optiondict["numestreps"] > 0:
         masklist = []

rapidtide/workflows/rapidtide_parser.py

@@ -1462,6 +1462,13 @@ def _get_parser():
         help=("Do regressor refinement on the final pass."),
         default=False,
     )
+    experimental.add_argument(
+        "--nosLFOfiltmask",
+        dest="nosLFOfiltmask",
+        action="store_true",
+        help=("Don't spatially limit sLFO filter to fit voxels."),
+        default=False,
+    )
     experimental.add_argument(
         "--territorymap",
         dest="territorymap",
@@ -1810,7 +1817,7 @@ def process_args(inputargs=None):
     args["hardlimit"] = True
     # The fraction of the main peak over which points are included in the peak
     args["searchfrac"] = 0.5
-    args["mp_chunksize"] = 50000
+    args["mp_chunksize"] = 500
     args["patchminsize"] = DEFAULT_PATCHMINSIZE
     args["patchfwhm"] = DEFAULT_PATCHFWHM
 

rapidtide/workflows/regressfrommaps.py

@@ -22,7 +22,6 @@ import numpy as np
 import rapidtide.io as tide_io
 import rapidtide.linfitfiltpass as tide_linfitfiltpass
 import rapidtide.makelaggedtcs as tide_makelagged
-import rapidtide.util as tide_util
 
 
 def regressfrommaps(
@@ -133,7 +132,6 @@ def regressfrommaps(
     if TimingLGR is not None:
         TimingLGR.info("Start filtering operation")
 
-
     voxelsprocessed_regressionfilt = tide_linfitfiltpass.linfitfiltpass(
         numvalidspatiallocs,
         fmri_data_valid,

rapidtide/workflows/showarbcorr.py

@@ -297,6 +297,8 @@ def showarbcorr(args):
         sys.exit()
     if starttime1 == None:
         starttime1 = 0.0
+    endtime1 = starttime1 + len(inputdata1) / Fs1
+    print(f"inputdata1 goes from {starttime1} to {endtime1}")
 
     if args.samplerate2 is not None:
         Fs2 = args.samplerate2
@@ -305,9 +307,19 @@ def showarbcorr(args):
         sys.exit()
     if starttime2 == None:
         starttime2 = 0.0
+    endtime2 = starttime2 + len(inputdata2) / Fs2
+    print(f"inputdata2 goes from {starttime2} to {endtime2}")
 
-    trimdata1 = inputdata1
-    trimdata2 = inputdata2
+    matchedinput1, matchedinput2, commonFs = tide_corr.matchsamplerates(
+        inputdata1,
+        Fs1,
+        inputdata2,
+        Fs2,
+        method="univariate",
+        debug=args.debug,
+    )
+    trimdata1 = matchedinput1
+    trimdata2 = matchedinput2
 
     if args.trimdata:
         minlen = np.min([len(trimdata1), len(trimdata2)])
@@ -324,12 +336,12 @@ def showarbcorr(args):
         if args.verbose:
             print("filtering to ", theprefilter.gettype(), " band")
     filtereddata1 = tide_math.corrnormalize(
-        theprefilter.apply(Fs1, trimdata1),
+        theprefilter.apply(commonFs, trimdata1),
         detrendorder=args.detrendorder,
         windowfunc=args.windowfunc,
     )
     filtereddata2 = tide_math.corrnormalize(
-        theprefilter.apply(Fs2, trimdata2),
+        theprefilter.apply(commonFs, trimdata2),
         detrendorder=args.detrendorder,
         windowfunc=args.windowfunc,
     )
@@ -341,9 +353,9 @@ def showarbcorr(args):
         print(f"{Fs1=}, {Fs2=}, {starttime1=}, {starttime2=}, {args.windowfunc=}")
     xcorr_x, thexcorr, corrFs, zeroloc = tide_corr.arbcorr(
         filtereddata1,
-        Fs1,
+        commonFs,
         filtereddata2,
-        Fs2,
+        commonFs,
         start1=starttime1,
         start2=starttime2,
         windowfunc=args.windowfunc,
@@ -375,6 +387,7 @@ def showarbcorr(args):
     thexcorr_trim = thexcorr[lowerlim:upperlim]
     print("trimmed Correlator lengths (x, y):", len(xcorr_x_trim), len(thexcorr_trim))
 
+    print(f"{len(filtereddata1)=}, {len(filtereddata2)=}")
     thepxcorr = pearsonr(filtereddata1, filtereddata2)
 
     # initialize the correlation fitter