rapidtide 3.0.7.1__py3-none-any.whl → 3.0.9__py3-none-any.whl

rapidtide/simfuncfit.py

@@ -208,10 +208,10 @@ def fitcorr(
                         break
 
                     # process and send the data
-                    if (lagmask is None) or (initiallags is None):
+                    if (themask is None) or (initiallags is None):
                         thislag = None
                     else:
-                        if lagmask[val] > 0:
+                        if themask[val] > 0:
                             thislag = initiallags[val]
                         else:
                             thislag = None
@@ -289,32 +289,23 @@ def fitcorr(
             unit="voxels",
             disable=(not showprogressbar),
         ):
-            if themask is None:
-                dothisone = True
+            # process and send the data
+            if (themask is None) or (initiallags is None):
                 thislag = None
-            elif themask[vox] > 0:
                 dothisone = True
-                thislag = initiallags[vox]
             else:
-                dothisone = False
-                thislag = None
+                if themask[vox] > 0:
+                    thislag = initiallags[vox]
+                    dothisone = True
+                else:
+                    thislag = None
+                    dothisone = False
             if isinstance(initialdelayvalue, np.ndarray):
                 thisinitialdelayvalue = initialdelayvalue[vox]
             else:
                 thisinitialdelayvalue = initialdelayvalue
             if dothisone:
-                (
-                    dummy,
-                    volumetotalinc,
-                    lagtimes[vox],
-                    lagstrengths[vox],
-                    lagsigma[vox],
-                    gaussout[vox, :],
-                    windowout[vox, :],
-                    R2[vox],
-                    lagmask[vox],
-                    failreason,
-                ) = _procOneVoxelFitcorr(
+                voxel = _procOneVoxelFitcorr(
                     vox,
                     corrout[vox, :],
                     thefitter,
@@ -326,29 +317,38 @@ def fitcorr(
                     rt_floatset=rt_floatset,
                     rt_floattype=rt_floattype,
                 )
-                volumetotal += volumetotalinc
                 if (
                     thefitter.FML_INITAMPLOW
                     | thefitter.FML_INITAMPHIGH
                     | thefitter.FML_FITAMPLOW
                     | thefitter.FML_FITAMPHIGH
-                ) & failreason:
+                ) & voxel[9]:
                     ampfails += 1
-                if (thefitter.FML_INITWIDTHLOW | thefitter.FML_FITWIDTHLOW) & failreason:
+                if (thefitter.FML_INITWIDTHLOW | thefitter.FML_FITWIDTHLOW) & voxel[9]:
                     lowwidthfails += 1
-                if (thefitter.FML_INITWIDTHHIGH | thefitter.FML_FITWIDTHHIGH) & failreason:
+                if (thefitter.FML_INITWIDTHHIGH | thefitter.FML_FITWIDTHHIGH) & voxel[9]:
                     highwidthfails += 1
-                if (thefitter.FML_INITLAGLOW | thefitter.FML_INITLAGHIGH) & failreason:
+                if (thefitter.FML_INITLAGLOW | thefitter.FML_FITLAGLOW) & voxel[9]:
                     lowlagfails += 1
-                if (thefitter.FML_INITLAGLOW | thefitter.FML_FITLAGLOW) & failreason:
-                    lowlagfails += 1
-                if (thefitter.FML_INITLAGHIGH | thefitter.FML_FITLAGHIGH) & failreason:
+                if (thefitter.FML_INITLAGHIGH | thefitter.FML_FITLAGHIGH) & voxel[9]:
                     highlagfails += 1
-                if thefitter.FML_INITFAIL & failreason:
+                if thefitter.FML_INITFAIL & voxel[9]:
                     initfails += 1
-                if thefitter.FML_FITFAIL & failreason:
+                if thefitter.FML_FITFAIL & voxel[9]:
                     fitfails += 1
 
+                # if this is a despeckle pass, only accept the new values if the fit did not fail
+                if (voxel[9] == 0) or not despeckling:
+                    volumetotal += voxel[1]
+                    lagtimes[vox] = voxel[2]
+                    lagstrengths[vox] = voxel[3]
+                    lagsigma[vox] = voxel[4]
+                    gaussout[vox, :] = voxel[5]
+                    windowout[vox, :] = voxel[6]
+                    R2[vox] = voxel[7]
+                    lagmask[vox] = voxel[8]
+                    failimage[vox] = voxel[9] & 0xFFFF
+
     LGR.info(f"\nSimilarity function fitted in {volumetotal} voxels")
     LGR.info(
         f"\tampfails: {ampfails}"

rapidtide/stats.py

@@ -269,7 +269,7 @@ def sigFromDistributionData(
     # check to make sure there are nonzero values first
     if len(np.where(vallist != 0.0)[0]) == 0:
         print("no nonzero values - skipping percentile calculation")
-        return None, 0, 0
+        return None, None, None
     thehistogram, peakheight, peakloc, peakwidth, centerofmass, peakpercentile = makehistogram(
         np.abs(vallist), histlen, therange=[0.0, 1.0]
     )
@@ -300,7 +300,10 @@ def sigFromDistributionData(
         pcts_fit = getfracvalsfromfit(histfit, thepercentiles)
         return pcts_data, pcts_fit, histfit
     else:
-        return pcts_data, 0, 0
+        pcts_fit = []
+        for i in len(pcts_data):
+            pcts_fit.append(None)
+        return pcts_data, pcts_fit, None
 
 
 global neglogpfromr_interpolator, minrforneglogp, maxrforneglogp

rapidtide/tests/.coveragerc

@@ -22,9 +22,15 @@ omit =
 exclude_lines = 
     # Don't complain if non-runnable code isn't run:
     if displayplots:
+    if args.displayplots:
+    if args.display:
     if doplot:
+    if args.doplot:
     if args.displayplots:
     if debug:
+    if optiondict["debug"]:
+    if optiondict['debug']:
+    if args.debug:
     if self.debug:
     if False:
     if __name__ == .__main__.:

rapidtide/tests/cleanposttest

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

rapidtide/tests/runlocaltest

@@ -18,8 +18,8 @@
 
 # make sure the test data is installed
 pushd ../data/examples/src
-cleanupdir
-installtestdatahere
+./cleanupdir
+./installtestdatahere
 popd
 
 # clean out old tests

rapidtide/tests/test_cleanregressor.py

@@ -22,9 +22,9 @@ import matplotlib as mpl
 import numpy as np
 
 import rapidtide.filter as tide_filt
-import rapidtide.helper_classes as tide_classes
 import rapidtide.miscmath as tide_math
 import rapidtide.resample as tide_resample
+import rapidtide.simFuncClasses as tide_simFuncClasses
 import rapidtide.workflows.cleanregressor as tide_cleanregressor
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path, mse
 
@@ -58,14 +58,14 @@ def test_cleanregressor(debug=False, local=False, displayplots=False):
     osvalidsimcalcstart = 0
     osvalidsimcalcend = tclen * oversampfac
 
-    theCorrelator = tide_classes.Correlator(
+    theCorrelator = tide_simFuncClasses.Correlator(
         Fs=oversampfreq,
         ncprefilter=theprefilter,
         detrendorder=1,
         windowfunc="hamming",
         corrweighting="phat",
     )
-    theFitter = tide_classes.SimilarityFunctionFitter(
+    theFitter = tide_simFuncClasses.SimilarityFunctionFitter(
         lagmod=lagmod,
         lagmin=lagmin,
         lagmax=lagmax,

rapidtide/tests/test_congrid.py

@@ -20,8 +20,8 @@ import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
 
-from rapidtide.resample import congrid
 from rapidtide.happy_supportfuncs import preloadcongrid
+from rapidtide.resample import congrid
 from rapidtide.tests.utils import mse
 
 

rapidtide/tests/test_corrpass.py

@@ -23,8 +23,8 @@ import numpy as np
 import rapidtide.calcsimfunc as tide_calcsimfunc
 import rapidtide.correlate as tide_corr
 import rapidtide.filter as tide_filt
-import rapidtide.helper_classes as tide_classes
 import rapidtide.resample as tide_resample
+import rapidtide.simFuncClasses as tide_simFuncClasses
 import rapidtide.simfuncfit as tide_simfuncfit
 from rapidtide.tests.utils import mse
 
@@ -133,7 +133,7 @@ def test_calcsimfunc(debug=False, displayplots=False):
     }
 
     theprefilter = tide_filt.NoncausalFilter("lfo")
-    theCorrelator = tide_classes.Correlator(
+    theCorrelator = tide_simFuncClasses.Correlator(
         Fs=oversampfreq,
         ncprefilter=theprefilter,
         detrendorder=optiondict["detrendorder"],
@@ -141,7 +141,7 @@ def test_calcsimfunc(debug=False, displayplots=False):
         corrweighting=optiondict["corrweighting"],
     )
 
-    thefitter = tide_classes.SimilarityFunctionFitter(
+    thefitter = tide_simFuncClasses.SimilarityFunctionFitter(
         lagmod=optiondict["lagmod"],
         lthreshval=optiondict["lthreshval"],
         uthreshval=optiondict["uthreshval"],

rapidtide/tests/test_delayestimation.py

@@ -24,11 +24,11 @@ import numpy as np
 
 import rapidtide.calcsimfunc as tide_calcsimfunc
 import rapidtide.filter as tide_filt
-import rapidtide.helper_classes as tide_classes
 import rapidtide.linfitfiltpass as tide_linfitfiltpass
 import rapidtide.miscmath as tide_math
 import rapidtide.peakeval as tide_peakeval
 import rapidtide.resample as tide_resample
+import rapidtide.simFuncClasses as tide_simFuncClasses
 import rapidtide.simfuncfit as tide_simfuncfit
 import rapidtide.util as tide_util
 
@@ -130,7 +130,7 @@ def test_delayestimation(displayplots=False, debug=False):
     # set up theCorrelator
     if debug:
         print("\n\nsetting up theCorrelator")
-    theCorrelator = tide_classes.Correlator(
+    theCorrelator = tide_simFuncClasses.Correlator(
         Fs=oversampfreq,
         ncprefilter=theprefilter,
         detrendorder=detrendorder,
@@ -152,7 +152,7 @@ def test_delayestimation(displayplots=False, debug=False):
     # set up theMutualInformationator
     if debug:
         print("\n\nsetting up theMutualInformationator")
-    theMutualInformationator = tide_classes.MutualInformationator(
+    theMutualInformationator = tide_simFuncClasses.MutualInformationator(
         Fs=oversampfreq,
         smoothingtime=smoothingtime,
         ncprefilter=theprefilter,
@@ -170,7 +170,7 @@ def test_delayestimation(displayplots=False, debug=False):
     # set up thefitter
     if debug:
         print("\n\nsetting up thefitter")
-    thefitter = tide_classes.SimilarityFunctionFitter(
+    thefitter = tide_simFuncClasses.SimilarityFunctionFitter(
         lagmod=lagmod,
         lthreshval=0.0,
         uthreshval=1.0,
@@ -350,7 +350,7 @@ def test_delayestimation(displayplots=False, debug=False):
             nprocs=nprocs,
             alwaysmultiproc=False,
             showprogressbar=False,
-            mp_chunksize=chunksize,
+            chunksize=chunksize,
         )
 
         if nprocs == 1:
@@ -360,9 +360,10 @@ def test_delayestimation(displayplots=False, debug=False):
         diffsignal = filtereddata
         fig = plt.figure()
         ax = fig.add_subplot(1, 1, 1)
-        # ax.plot(timepoints, filtereddata[refnum, :], label='filtereddata')
-        ax.plot(oversamptimepoints, referencetc, label="referencetc")
-        ax.plot(timepoints, movingsignal[refnum, :], label="movingsignal")
+        # ax.plot(oversamptimepoints, referencetc, label="referencetc")
+        ax.plot(timepoints, waveforms[refnum, :], label="waveform")
+        ax.plot(timepoints, fitcoff[refnum] * movingsignal[refnum, :], label="movingsignal")
+        # ax.plot(timepoints, filtereddata[refnum, :], label="filtereddata")
         ax.legend()
         plt.show()
 

rapidtide/tests/test_findmaxlag.py

@@ -24,8 +24,8 @@ import matplotlib.pyplot as plt
 import numpy as np
 
 import rapidtide.fit as tide_fit
-import rapidtide.helper_classes as tide_classes
 import rapidtide.io as tide_io
+import rapidtide.simFuncClasses as tide_simFuncClasses
 from rapidtide.tests.utils import get_examples_path
 
 
@@ -101,7 +101,7 @@ def test_findmaxlag(displayplots=False, debug=False):
         fmlc_lfailreasons = np.zeros(len(testlags), dtype=np.uint16)
 
         # initialize the correlation fitter
-        thefitter = tide_classes.SimilarityFunctionFitter(
+        thefitter = tide_simFuncClasses.SimilarityFunctionFitter(
             corrtimeaxis=xvecs,
             lagmin=lagmin,
             lagmax=lagmax,

rapidtide/tests/test_fullrunrapidtide_v3.py

@@ -22,8 +22,8 @@ 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
+from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
 def test_fullrunrapidtide_v3(debug=False, local=False, displayplots=False):
@@ -87,6 +87,7 @@ def test_fullrunrapidtide_v3(debug=False, local=False, displayplots=False):
     ]
     rapidtide_retroregress.retroregress(rapidtide_retroregress.process_args(inputargs=inputargs))
 
+
 if __name__ == "__main__":
     mpl.use("TkAgg")
     test_fullrunrapidtide_v3(debug=True, local=True, displayplots=True)

rapidtide/tests/test_fullrunrapidtide_v8.py

@@ -0,0 +1,66 @@
+#!/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.qualitycheck as rapidtide_quality
+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
+
+
+def test_fullrunrapidtide_v8(debug=False, local=False, displayplots=False):
+    # set input and output directories
+    if local:
+        exampleroot = "../data/examples/src"
+        testtemproot = "./tmp"
+    else:
+        exampleroot = get_examples_path()
+        testtemproot = get_test_temp_path()
+
+    # run rapidtide
+    inputargs = [
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST8"),
+        "--spatialfilt",
+        "2",
+        "--simcalcrange",
+        "4",
+        "-1",
+        "--searchrange",
+        "-5",
+        "10",
+        "--nprocs",
+        "-1",
+        "--passes",
+        "1",
+        "--despecklepasses",
+        "3",
+        "--similaritymetric",
+        "riptide",
+        "--riptidestep",
+        "1.5",
+    ]
+    rapidtide_workflow.rapidtide_main(rapidtide_parser.process_args(inputargs=inputargs))
+
+
+if __name__ == "__main__":
+    mpl.use("TkAgg")
+    test_fullrunrapidtide_v8(debug=True, local=True, displayplots=True)

rapidtide/tests/test_getparsers.py

@@ -33,18 +33,24 @@ from rapidtide.workflows.filtnifti import _get_parser as filtnifti_getparser
 from rapidtide.workflows.filttc import _get_parser as filttc_getparser
 from rapidtide.workflows.fixtr import _get_parser as fixtr_getparser
 from rapidtide.workflows.gmscalc import _get_parser as gmscalc_getparser
-from rapidtide.workflows.happy_parser import _get_parser as happy_parser_getparser
 from rapidtide.workflows.happy2std import _get_parser as happy2std_getparser
+from rapidtide.workflows.happy_parser import _get_parser as happy_parser_getparser
 from rapidtide.workflows.histnifti import _get_parser as histnifti_getparser
 from rapidtide.workflows.histtc import _get_parser as histtc_getparser
 from rapidtide.workflows.linfitfilt import _get_parser as linfitfilt_getparser
 from rapidtide.workflows.localflow import _get_parser as localflow_getparser
 from rapidtide.workflows.mergequality import _get_parser as mergequality_getparser
-from rapidtide.workflows.niftidecomp import _get_parser_temporal as niftidecomp_getparser_temporal
-from rapidtide.workflows.niftidecomp import _get_parser_spatial as niftidecomp_getparser_spatial
+from rapidtide.workflows.niftidecomp import (
+    _get_parser_spatial as niftidecomp_getparser_spatial,
+)
+from rapidtide.workflows.niftidecomp import (
+    _get_parser_temporal as niftidecomp_getparser_temporal,
+)
 from rapidtide.workflows.niftistats import _get_parser as niftistats_getparser
 from rapidtide.workflows.pairproc import _get_parser as pairproc_getparser
-from rapidtide.workflows.pairwisemergenifti import _get_parser as pairwisemergenifti_getparser
+from rapidtide.workflows.pairwisemergenifti import (
+    _get_parser as pairwisemergenifti_getparser,
+)
 from rapidtide.workflows.physiofreq import _get_parser as physiofreq_getparser
 from rapidtide.workflows.pixelcomp import _get_parser as pixelcomp_getparser
 from rapidtide.workflows.plethquality import _get_parser as plethquality_getparser
@@ -75,7 +81,8 @@ from rapidtide.workflows.variabilityizer import _get_parser as variabilityizer_g
 
 
 def test_parsers(debug=False):
-    parserlist = [ adjustoffset_getparser,
+    parserlist = [
+        adjustoffset_getparser,
         aligntcs_getparser,
         applydlfilter_getparser,
         atlasaverage_getparser,
@@ -128,7 +135,8 @@ def test_parsers(debug=False):
         synthASL_getparser,
         tcfrom2col_getparser,
         tcfrom3col_getparser,
-        variabilityizer_getparser ]
+        variabilityizer_getparser,
+    ]
 
     for thegetparser in parserlist:
         theusage = thegetparser().format_help()

rapidtide/tests/test_io.py

@@ -95,14 +95,10 @@ def test_io(debug=True, local=False, displayplots=False):
 
     # test fmritimeinfo
     fmritimeinfothresh = 1e-2
-    tr, timepoints = tide_io.fmritimeinfo(
-        os.path.join(exampleroot, "sub-HAPPYTEST.nii.gz")
-    )
+    tr, timepoints = tide_io.fmritimeinfo(os.path.join(exampleroot, "sub-HAPPYTEST.nii.gz"))
     assert np.fabs(tr - 1.16) < fmritimeinfothresh
     assert timepoints == 110
-    tr, timepoints = tide_io.fmritimeinfo(
-        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz")
-    )
+    tr, timepoints = tide_io.fmritimeinfo(os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"))
     assert np.fabs(tr - 1.5) < fmritimeinfothresh
     assert timepoints == 260
 

rapidtide/tests/test_nullcorr.py

@@ -25,8 +25,8 @@ import numpy as np
 import rapidtide.calcnullsimfunc as tide_nullsimfunc
 import rapidtide.correlate as tide_corr
 import rapidtide.filter as tide_filt
-import rapidtide.helper_classes as tide_classes
 import rapidtide.io as tide_io
+import rapidtide.simFuncClasses as tide_simFuncClasses
 import rapidtide.stats as tide_stats
 from rapidtide.tests.utils import get_test_data_path, get_test_temp_path
 
@@ -94,7 +94,7 @@ def test_nullsimfunc(debug=False, displayplots=False):
         "hardlimit": True,
     }
     theprefilter = tide_filt.NoncausalFilter("lfo")
-    theCorrelator = tide_classes.Correlator(
+    theCorrelator = tide_simFuncClasses.Correlator(
         Fs=Fs,
         ncprefilter=theprefilter,
         detrendorder=optiondict["detrendorder"],
@@ -102,7 +102,7 @@ def test_nullsimfunc(debug=False, displayplots=False):
         corrweighting=optiondict["corrweighting"],
     )
 
-    thefitter = tide_classes.SimilarityFunctionFitter(
+    thefitter = tide_simFuncClasses.SimilarityFunctionFitter(
         lagmod=optiondict["lagmod"],
         lthreshval=optiondict["lthreshval"],
         uthreshval=optiondict["uthreshval"],

rapidtide/tests/test_refinedelay.py

@@ -36,6 +36,7 @@ def eval_refinedelay(
     tclengthinsecs=300.0,
     mindelay=-5.0,
     maxdelay=5.0,
+    lagpad=0.0,
     numpoints=501,
     smoothpts=3,
     nativespaceshape=(10, 10, 10),
@@ -43,8 +44,17 @@ def eval_refinedelay(
     padtime=30.0,
     noiselevel=0.0,
     outputsuffix="",
+    local=False,
     debug=False,
 ):
+    # set input and output directories
+    if local:
+        exampleroot = "../data/examples/src"
+        testtemproot = "./tmp"
+    else:
+        exampleroot = get_examples_path()
+        testtemproot = get_test_temp_path()
+
     np.random.seed(12345)
     tclen = int(tclengthinsecs // sampletime)
 
@@ -84,7 +94,7 @@ def eval_refinedelay(
     tide_refinedelay.trainratiotooffset(
         lagtcgenerator,
         timeaxis,
-        os.path.join(get_test_temp_path(), "refinedelaytest" + outputsuffix),
+        os.path.join(testtemproot, "refinedelaytest" + outputsuffix),
         "norm",
         mindelay=mindelay,
         maxdelay=maxdelay,
@@ -95,7 +105,7 @@ def eval_refinedelay(
 
     # make a delay map
     numlags = nativespaceshape[0] * nativespaceshape[1] * nativespaceshape[2]
-    lagtimes = np.linspace(mindelay, maxdelay, numlags, endpoint=True)
+    lagtimes = np.linspace(mindelay - lagpad, maxdelay + lagpad, numlags, endpoint=True)
     if debug:
         print("    lagtimes=", lagtimes)
 
@@ -120,7 +130,7 @@ def eval_refinedelay(
 
     # make a fake header
     nim, nim_data, nim_hdr, thedims, thesizes = tide_io.readfromnifti(
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST_brainmask.nii.gz")
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_brainmask.nii.gz")
     )
     xdim, ydim, slicedim, fmritr = tide_io.parseniftisizes(thesizes)
     theheader = copy.copy(nim_hdr)
@@ -212,7 +222,7 @@ def eval_refinedelay(
         plt.show()
 
 
-def test_refinedelay(displayplots=False, debug=False):
+def test_refinedelay(displayplots=False, local=False, debug=False):
     for noiselevel in np.linspace(0.0, 0.5, num=5, endpoint=True):
         eval_refinedelay(
             sampletime=0.72,
@@ -225,6 +235,7 @@ def test_refinedelay(displayplots=False, debug=False):
             displayplots=displayplots,
             outputsuffix="_1",
             noiselevel=noiselevel,
+            local=local,
             debug=debug,
         )
     eval_refinedelay(
@@ -237,6 +248,7 @@ def test_refinedelay(displayplots=False, debug=False):
         nativespaceshape=(10, 10, 10),
         displayplots=displayplots,
         outputsuffix="_2",
+        local=local,
         debug=debug,
     )
     eval_refinedelay(
@@ -249,6 +261,7 @@ def test_refinedelay(displayplots=False, debug=False):
         nativespaceshape=(10, 10, 10),
         displayplots=displayplots,
         outputsuffix="_3",
+        local=local,
         debug=debug,
     )
     eval_refinedelay(
@@ -261,6 +274,7 @@ def test_refinedelay(displayplots=False, debug=False):
         nativespaceshape=(10, 10, 10),
         displayplots=displayplots,
         outputsuffix="_1p5_501_3",
+        local=local,
         debug=debug,
     )
     eval_refinedelay(
@@ -273,10 +287,11 @@ def test_refinedelay(displayplots=False, debug=False):
         nativespaceshape=(10, 10, 10),
         displayplots=displayplots,
         outputsuffix="_3p0_501_3",
+        local=local,
         debug=debug,
     )
 
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_refinedelay(displayplots=True, debug=True)
+    test_refinedelay(displayplots=True, local=True, debug=True)

rapidtide/tidepoolTemplate_alt.py

@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'tidepoolTemplate_alt.ui'
 #
-# Created by: PyQt5 UI code generator 5.15.10
+# Created by: PyQt5 UI code generator 5.15.11
 #
 # WARNING: Any manual changes made to this file will be lost when pyuic5 is
 # run again.  Do not edit this file unless you know what you are doing.

rapidtide/util.py

@@ -1106,6 +1106,13 @@ def allocshared(theshape, thetype, name=None):
     return outarray, shm  # Return both the array and the shared memory object
 
 
+def allocarray(theshape, thetype, shared=False, name=None):
+    if shared:
+        return allocshared(theshape, thetype, name)
+    else:
+        return np.zeros(theshape, dtype=thetype), None
+
+
 def cleanup_shm(shm):
     # Cleanup
     pass

rapidtide/voxelData.py

@@ -61,12 +61,9 @@ class dataVolume:
             print(f"illegal shape: {shape}")
         self.numspatiallocs = self.xsize * self.ysize * self.numslices
         self.dtype = dtype
-        if not shared:
-            self.data = np.zeros(shape, dtype=dtype)
-        else:
-            self.data, self.data_shm = tide_util.allocshared(
-                shape, self.dtype, name=f"filtereddata_{thepid}"
-            )
+        self.data, self.data_shm = tide_util.allocarray(
+            shape, self.dtype, shared=shared, name=f"filtereddata_{thepid}"
+        )
         return self.data
 
     def byvol(self):