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

rapidtide/tests/.coveragerc

@@ -6,18 +6,39 @@ sigterm = true
 source = .
 omit =
     __init__.py
-    ../__init__.py
-    ../scripts/__init__.py
-    ../OrthoImageItem.py
-    ../wiener2.py
-    ../tidepoolTemplate.py
-    ../tidepoolTemplate_alt.py
+    scripts/__init__.py
+    OrthoImageItem.py
+    wiener2.py
+    fMRIData_class.py
+    tidepoolTemplate.py
+    tidepoolTemplate_qt6.py
+    tidepoolTemplate_alt.py
+    tidepoolTemplate_alt_qt6.py
+    tidepoolTemplate_big.py
+    tidepoolTemplate_big_qt6.py
+    */tidepool.py
+    */delayvar.py
+    */variabilityizer.py
+    */synthASL.py
+    */proj2flow.py
+    */adjustoffset.py
+    notreadyforprimetime/*
 
 [report]
 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__.:
+    except np.lib.RankWarning:
+    except IndexError:

rapidtide-2.9.6.data/scripts/fdica → rapidtide/tests/cleanposttest

@@ -1,7 +1,6 @@
-#!python
-# -*- coding: utf-8 -*-
+#!/bin/sh
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   Copyright 2016-2021 Blaise Frederick
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.
@@ -16,7 +15,6 @@
 #   limitations under the License.
 #
 #
-import rapidtide.workflows.fdica as fdica_workflow
 
-if __name__ == "__main__":
-    fdica_workflow.main()
+rm tmp/*
+rm .coverage.*

rapidtide/tests/happycomp

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+cd tmp
+for NEWFILE in happyout1_desc*.nii.gz
+do
+   OLDFILE=`echo ${NEWFILE} | sed 's/happyout1_/happyout1t_/g'`
+   echo ${OLDFILE} ${NEWFILE}
+   diff ${OLDFILE} ${NEWFILE}
+done

rapidtide/tests/resethappytargets

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: latin-1 -*-
 #
-#   Copyright 2016-2021 Blaise Frederick
+#   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.

rapidtide/tests/resetrapidtidetargets

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: latin-1 -*-
 #
-#   Copyright 2016-2021 Blaise Frederick
+#   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.

rapidtide/tests/resettargets

@@ -1,6 +1,6 @@
 #!/bin/csh -f
 #
-#   Copyright 2016-2021 Blaise Frederick
+#   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.

rapidtide/tests/runlocaltest

@@ -1,6 +1,6 @@
 #!/bin/sh
 #
-#   Copyright 2016-2021 Blaise Frederick
+#   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.
@@ -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/showkernels

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: latin-1 -*-
 #
-#   Copyright 2016-2021 Blaise Frederick
+#   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.

rapidtide/tests/test_aliasedcorrelate.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.
@@ -62,7 +62,7 @@ def aliasedcorrelate(
     lowresaxis = np.arange(0.0, len(lowressignal)) * (1.0 / lowres_Fs) - lowresstarttime
     tcgenerator = tide_resample.FastResampler(highresaxis, hiressignal, padtime=padtime)
     targetsignal = tide_math.corrnormalize(lowressignal)
-    corrfunc = timerange * 0.0
+    corrfunc = np.zeros_like(timerange)
     for i in range(len(timerange)):
         aliasedhiressignal = tide_math.corrnormalize(tcgenerator.yfromx(lowresaxis + timerange[i]))
         corrfunc[i] = np.dot(aliasedhiressignal, targetsignal)
@@ -83,8 +83,8 @@ def test_aliasedcorrelate(displayplots=False):
     timerange = np.linspace(0.0, width, num=101) - width / 2.0
     hiaxis = np.linspace(0.0, 2.0 * np.pi * inlenhi / Fs_hi, num=inlenhi, endpoint=False)
     loaxis = np.linspace(0.0, 2.0 * np.pi * inlenlo / Fs_lo, num=inlenlo, endpoint=False)
-    sighi = hiaxis * 0.0
-    siglo = loaxis * 0.0
+    sighi = np.zeros_like(hiaxis)
+    siglo = np.zeros_like(loaxis)
     for theinfo in siginfo:
         sighi += theinfo[0] * np.sin(theinfo[1] * hiaxis)
         siglo += theinfo[0] * np.sin(theinfo[1] * loaxis)

rapidtide/tests/test_aligntcs.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.

rapidtide/tests/test_calcicc.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.

rapidtide/tests/test_cleanregressor.py

@@ -0,0 +1,184 @@
+#!/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 numpy as np
+
+import rapidtide.filter as tide_filt
+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
+
+
+def test_cleanregressor(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()
+
+    outputname = os.path.join(testtemproot, "cleanregressortest")
+    thepass = 1
+    padtrs = 30
+    fmrifreq = 1.0
+    oversampfac = 2
+    oversampfreq = oversampfac * fmrifreq
+    theprefilter = tide_filt.NoncausalFilter("lfo")
+    lagmin = -30
+    lagmax = 30
+    lagmininpts = int((lagmin * oversampfreq) - 0.5)
+    lagmaxinpts = int((lagmax * oversampfreq) + 0.5)
+    lagmod = 1000.0
+    noiseamp = 0.25
+    detrendorder = 3
+    windowfunc = "hamming"
+
+    tclen = 500
+    osvalidsimcalcstart = 0
+    osvalidsimcalcend = tclen * oversampfac
+
+    theCorrelator = tide_simFuncClasses.Correlator(
+        Fs=oversampfreq,
+        ncprefilter=theprefilter,
+        detrendorder=1,
+        windowfunc="hamming",
+        corrweighting="phat",
+    )
+    theFitter = tide_simFuncClasses.SimilarityFunctionFitter(
+        lagmod=lagmod,
+        lagmin=lagmin,
+        lagmax=lagmax,
+        debug=debug,
+        allowhighfitamps=True,
+        enforcethresh=False,
+        zerooutbadfit=False,
+    )
+
+    # make a reference timecourse
+    rng = np.random.default_rng(seed=1234)
+    basewave = theprefilter.apply(fmrifreq, rng.normal(loc=0.0, scale=1.0, size=tclen))
+    noisewave = rng.normal(loc=0.0, scale=noiseamp, size=tclen)
+    theparamsets = [
+        [2.0, 0.0, False, 0],
+        [2.5, 0.8, True, 0],
+        [5.0, 0.5, True, 0],
+        [7.5, 0.25, True, 100],
+        [10.0, 0.1, True, 0],
+    ]
+    for paramset in theparamsets:
+        echotime = paramset[0]
+        echoamp = paramset[1]
+        check_autocorrelation = paramset[2]
+        osvalidsimcalcstart = paramset[3]
+        if debug:
+            print(
+                "**********Start******************************************************************"
+            )
+            print(f"{echotime=}, {echoamp=}, {check_autocorrelation=}, {osvalidsimcalcstart=}")
+            print(
+                "*********************************************************************************"
+            )
+        theechotc, dummy, dummy, dummy = tide_resample.timeshift(
+            basewave, echotime * oversampfreq, padtrs, doplot=displayplots, debug=debug
+        )
+        resampnonosref_y = basewave + echoamp * theechotc + noisewave
+        resampref_y = tide_resample.upsample(resampnonosref_y, fmrifreq, oversampfreq)
+        theCorrelator.setreftc(resampnonosref_y)
+        referencetc = tide_math.corrnormalize(
+            resampref_y[osvalidsimcalcstart:],
+            detrendorder=detrendorder,
+            windowfunc=windowfunc,
+        )
+
+        resampref_y = tide_resample.upsample(resampnonosref_y, fmrifreq, oversampfreq)
+
+        (
+            cleaned_resampref_y,
+            cleaned_referencetc,
+            cleaned_nonosreferencetc,
+            despeckle_thresh,
+            sidelobeamp,
+            sidelobetime,
+            lagmod,
+            acwidth,
+            absmaxsigma,
+        ) = tide_cleanregressor.cleanregressor(
+            outputname,
+            thepass,
+            referencetc,
+            resampref_y,
+            resampnonosref_y,
+            fmrifreq,
+            oversampfreq,
+            osvalidsimcalcstart,
+            osvalidsimcalcend,
+            lagmininpts,
+            lagmaxinpts,
+            theFitter,
+            theCorrelator,
+            lagmin,
+            lagmax,
+            LGR=None,
+            check_autocorrelation=check_autocorrelation,
+            fix_autocorrelation=True,
+            despeckle_thresh=5.0,
+            lthreshval=0.0,
+            fixdelay=False,
+            detrendorder=detrendorder,
+            windowfunc=windowfunc,
+            respdelete=False,
+            displayplots=displayplots,
+            debug=debug,
+            rt_floattype=np.float64,
+        )
+        print(f"\t{len(referencetc)=}")
+        print(f"\t{len(resampref_y)=}")
+        print(f"\t{len(resampnonosref_y)=}")
+        print(f"\t{len(cleaned_resampref_y)=}")
+        print(f"\t{len(cleaned_referencetc)=}")
+        print(f"\t{len(cleaned_nonosreferencetc)=}")
+        print(f"\t{check_autocorrelation=}")
+        print(f"\t{despeckle_thresh=}")
+        print(f"\t{sidelobeamp=}")
+        print(f"\t{sidelobetime=}")
+        print(f"\t{lagmod=}")
+        print(f"\t{acwidth=}")
+        print(f"\t{absmaxsigma=}")
+        assert len(referencetc) == len(cleaned_referencetc)
+        assert len(resampref_y) == len(cleaned_resampref_y)
+        assert len(resampnonosref_y) == len(cleaned_nonosreferencetc)
+
+        if debug:
+            print(
+                "*********************************************************************************"
+            )
+            print(f"{echotime=}, {echoamp=}, {check_autocorrelation=}, {osvalidsimcalcstart=}")
+            print(
+                "**************End****************************************************************"
+            )
+
+
+if __name__ == "__main__":
+    mpl.use("TkAgg")
+    test_cleanregressor(debug=True, local=True, displayplots=True)

rapidtide/tests/test_congrid.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.
@@ -20,6 +20,7 @@ import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
 
+from rapidtide.happy_supportfuncs import preloadcongrid
 from rapidtide.resample import congrid
 from rapidtide.tests.utils import mse
 
@@ -56,7 +57,7 @@ def test_congrid(debug=False, displayplots=False):
         binslist = [1.5, 2.0, 2.5, 3.0]
 
     for cycles in cyclist:
-        timecoursein = np.float64(sourceaxis * 0.0)
+        timecoursein = np.zeros_like(sourceaxis, np.float64)
         for i in range(len(sourceaxis)):
             timecoursein[i] = funcvalue2(sourceaxis[i], frequency=cycles)
 
@@ -74,86 +75,74 @@ def test_congrid(debug=False, displayplots=False):
         weights = np.zeros((gridlen), dtype=float)
         griddeddata = np.zeros((gridlen), dtype=float)
 
-        for gridkernel in kernellist:
-            for congridbins in binslist:
-                print("about to grid")
-
-                # reinitialize grid outputs
-                weights *= 0.0
-                griddeddata *= 0.0
-
-                for i in range(numsamples):
-                    thevals, theweights, theindices = congrid(
-                        gridaxis,
-                        testvals[i],
-                        funcvalue2(testvals[i], frequency=cycles),
-                        congridbins,
-                        kernel=gridkernel,
-                        debug=False,
-                    )
-                    for i in range(len(theindices)):
-                        weights[theindices[i]] += theweights[i]
-                        griddeddata[theindices[i]] += thevals[i]
-
-                griddeddata = np.where(weights > 0.0, griddeddata / weights, 0.0)
-
-                target = np.float64(gridaxis * 0.0)
-                for i in range(len(gridaxis)):
-                    target[i] = funcvalue2(gridaxis[i], frequency=cycles)
-
-                print("gridding done")
-                print("debug:", debug)
-
-                # plot if we are doing that
-                if displayplots:
-                    offset = 0.0
-                    legend = []
-                    plt.plot(sourceaxis, timecoursein)
-                    legend.append("Original")
-                    # offset += 1.0
-                    plt.plot(gridaxis, target + offset)
-                    legend.append("Target")
-                    # offset += 1.0
-                    plt.plot(gridaxis, griddeddata + offset)
-                    legend.append("Gridded")
-                    plt.plot(gridaxis, weights)
-                    legend.append("Weights")
-                    plt.legend(legend)
-                    plt.show()
-
-                # do the tests
-                msethresh = 6.0e-2
-                themse = mse(target, griddeddata)
-                if debug:
-                    if themse >= msethresh:
-                        extra = "FAIL"
-                    else:
-                        extra = ""
-                    print(
-                        "mse for",
-                        cycles,
-                        "cycles:",
-                        gridkernel,
-                        str(congridbins),
-                        ":",
-                        themse,
-                        extra,
-                    )
-                    outputlines.append(
-                        " ".join(
-                            [
-                                "mse for",
-                                str(cycles),
-                                "cycles:",
-                                gridkernel,
-                                str(congridbins),
-                                ":",
-                                str(themse),
-                            ]
+        for prefill in [True, False]:
+            for gridkernel in kernellist:
+                for congridbins in binslist:
+                    print("about to grid")
+
+                    # reinitialize grid outputs
+                    weights *= 0.0
+                    griddeddata *= 0.0
+
+                    if prefill:
+                        preloadcongrid(
+                            gridaxis, congridbins, gridkernel=gridkernel, cyclic=True, debug=False
+                        )
+                    for i in range(numsamples):
+                        thevals, theweights, theindices = congrid(
+                            gridaxis,
+                            testvals[i],
+                            funcvalue2(testvals[i], frequency=cycles),
+                            congridbins,
+                            kernel=gridkernel,
+                            debug=False,
+                        )
+                        for i in range(len(theindices)):
+                            weights[theindices[i]] += theweights[i]
+                            griddeddata[theindices[i]] += thevals[i]
+
+                    griddeddata = np.where(weights > 0.0, griddeddata / weights, 0.0)
+
+                    target = np.zeros_like(gridaxis, np.float64)
+                    for i in range(len(gridaxis)):
+                        target[i] = funcvalue2(gridaxis[i], frequency=cycles)
+
+                    print("gridding done")
+                    print("debug:", debug)
+
+                    # plot if we are doing that
+                    if displayplots:
+                        offset = 0.0
+                        legend = []
+                        plt.plot(sourceaxis, timecoursein)
+                        legend.append("Original")
+                        # offset += 1.0
+                        plt.plot(gridaxis, target + offset)
+                        legend.append("Target")
+                        # offset += 1.0
+                        plt.plot(gridaxis, griddeddata + offset)
+                        legend.append("Gridded")
+                        plt.plot(gridaxis, weights)
+                        legend.append("Weights")
+                        plt.legend(legend)
+                        plt.show()
+
+                    # do the tests
+                    msethresh = 6.0e-2
+                    themse = mse(target, griddeddata)
+                    if debug:
+                        if themse >= msethresh:
+                            extra = "FAIL"
+                        else:
+                            extra = ""
+                        print(
+                            f"mse for {cycles} cycles: {prefill=}, {gridkernel} {congridbins}: {themse} {extra}"
+                        )
+                        outputlines.append(
+                            f"mse for {cycles} cycles: {prefill=}, {gridkernel} {congridbins}: {themse}"
                         )
-                    )
-                if not debug:
-                    assert themse < msethresh
+                    if not debug:
+                        assert themse < msethresh
     if debug:
         for theline in outputlines:
             print(theline)

rapidtide/tests/test_correlate.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.

rapidtide/tests/test_corrpass.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.
@@ -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"],