rapidtide 2.9.5__py3-none-any.whl → 3.1.3__py3-none-any.whl

rapidtide/tests/test_refinedelay.py

@@ -0,0 +1,296 @@
+#!/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 copy
+import os
+
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+import numpy as np
+
+import rapidtide.io as tide_io
+import rapidtide.miscmath as tide_math
+import rapidtide.refinedelay as tide_refinedelay
+import rapidtide.resample as tide_resample
+from rapidtide.filter import NoncausalFilter
+from rapidtide.tests.utils import get_examples_path, get_test_temp_path, mse
+
+
+def eval_refinedelay(
+    sampletime=0.72,
+    tclengthinsecs=300.0,
+    mindelay=-5.0,
+    maxdelay=5.0,
+    lagpad=0.0,
+    numpoints=501,
+    smoothpts=3,
+    nativespaceshape=(10, 10, 10),
+    displayplots=False,
+    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)
+
+    Fs = 1.0 / sampletime
+    print("Testing transfer function:")
+    lowestfreq = 1.0 / (sampletime * tclen)
+    nyquist = 0.5 / sampletime
+    print(
+        "    sampletime=",
+        sampletime,
+        ", timecourse length=",
+        tclengthinsecs,
+        "s,  possible frequency range:",
+        lowestfreq,
+        nyquist,
+    )
+
+    # make an sLFO timecourse
+    timeaxis = np.linspace(0.0, sampletime * tclen, num=tclen, endpoint=False)
+    rawgms = tide_math.stdnormalize(np.random.normal(size=tclen))
+    testfilter = NoncausalFilter(filtertype="lfo")
+    sLFO = tide_math.stdnormalize(testfilter.apply(Fs, rawgms))
+    if displayplots:
+        fig = plt.figure()
+        ax = fig.add_subplot(111)
+        ax.set_title("Initial regressor")
+        plt.plot(timeaxis, rawgms)
+        plt.plot(timeaxis, sLFO)
+        plt.show()
+
+    # now turn it into a lagtc generator
+    numpadtrs = int(padtime // sampletime)
+    padtime = sampletime * numpadtrs
+    lagtcgenerator = tide_resample.FastResampler(timeaxis, sLFO, padtime=padtime)
+
+    # find the mapping of derivative ratios to delays
+    tide_refinedelay.trainratiotooffset(
+        lagtcgenerator,
+        timeaxis,
+        os.path.join(testtemproot, "refinedelaytest" + outputsuffix),
+        "norm",
+        mindelay=mindelay,
+        maxdelay=maxdelay,
+        numpoints=numpoints,
+        smoothpts=smoothpts,
+        debug=debug,
+    )
+
+    # make a delay map
+    numlags = nativespaceshape[0] * nativespaceshape[1] * nativespaceshape[2]
+    lagtimes = np.linspace(mindelay - lagpad, maxdelay + lagpad, numlags, endpoint=True)
+    if debug:
+        print("    lagtimes=", lagtimes)
+
+    # now make synthetic fMRI data
+    internalvalidfmrishape = (numlags, tclen)
+    fmridata = np.zeros(internalvalidfmrishape, dtype=float)
+    fmrimask = np.ones(numlags, dtype=float)
+    validvoxels = np.where(fmrimask > 0)[0]
+    for i in range(numlags):
+        noisevec = tide_math.stdnormalize(
+            testfilter.apply(Fs, tide_math.stdnormalize(np.random.normal(size=tclen)))
+        )
+        fmridata[i, :] = lagtcgenerator.yfromx(timeaxis - lagtimes[i]) + noiselevel * noisevec
+
+    """if displayplots:
+        fig = plt.figure()
+        ax = fig.add_subplot(111)
+        ax.set_title("Timecourses")
+        for i in range(0, numlags, 200):
+            plt.plot(timeaxis, fmridata[i, :])
+        plt.show()"""
+
+    # make a fake header
+    nim, nim_data, nim_hdr, thedims, thesizes = tide_io.readfromnifti(
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_brainmask.nii.gz")
+    )
+    xdim, ydim, slicedim, fmritr = tide_io.parseniftisizes(thesizes)
+    theheader = copy.copy(nim_hdr)
+    theheader["dim"][0] = 3
+    theheader["dim"][1] = nativespaceshape[0]
+    theheader["dim"][2] = nativespaceshape[1]
+    theheader["dim"][3] = nativespaceshape[2]
+    theheader["pixdim"][1] = 1.0
+    theheader["pixdim"][2] = 1.0
+    theheader["pixdim"][3] = 1.0
+    theheader["pixdim"][4] = 1.0
+
+    rt_floattype = "float64"
+    sLFOfitmean = np.zeros(numlags, dtype=rt_floattype)
+    rvalue = np.zeros(numlags, dtype=rt_floattype)
+    r2value = np.zeros(numlags, dtype=rt_floattype)
+    fitNorm = np.zeros((numlags, 2), dtype=rt_floattype)
+    fitcoeff = np.zeros((numlags, 2), dtype=rt_floattype)
+    movingsignal = np.zeros(internalvalidfmrishape, dtype=rt_floattype)
+    lagtc = np.zeros(internalvalidfmrishape, dtype=rt_floattype)
+    filtereddata = np.zeros(internalvalidfmrishape, dtype=rt_floattype)
+    optiondict = {
+        "regressfiltthreshval": 0.0,
+        "saveminimumsLFOfiltfiles": False,
+        "nprocs_makelaggedtcs": 1,
+        "nprocs_regressionfilt": 1,
+        "mp_chunksize": 1000,
+        "showprogressbar": False,
+        "alwaysmultiproc": False,
+        "focaldebug": debug,
+        "fmrifreq": Fs,
+    }
+
+    regressderivratios, regressrvalues = tide_refinedelay.getderivratios(
+        fmridata,
+        validvoxels,
+        timeaxis,
+        0.0 * lagtimes,
+        fmrimask,
+        lagtcgenerator,
+        "glm",
+        "refinedelaytest",
+        sampletime,
+        sLFOfitmean,
+        rvalue,
+        r2value,
+        fitNorm[:, :2],
+        fitcoeff[:, :2],
+        movingsignal,
+        lagtc,
+        filtereddata,
+        None,
+        None,
+        optiondict,
+        debug=debug,
+    )
+
+    medfilt, filteredregressderivratios, themad = tide_refinedelay.filterderivratios(
+        regressderivratios,
+        nativespaceshape,
+        validvoxels,
+        (xdim, ydim, slicedim),
+        patchthresh=3.0,
+        rt_floattype="float64",
+        debug=debug,
+    )
+
+    delayoffset = np.zeros_like(filteredregressderivratios)
+    for i in range(filteredregressderivratios.shape[0]):
+        delayoffset[i], closestoffset = tide_refinedelay.ratiotodelay(
+            filteredregressderivratios[i]
+        )
+
+    # do the tests
+    msethresh = 0.1
+    aethresh = 2
+    print(f"{mse(lagtimes, delayoffset)=}")
+    assert mse(lagtimes, delayoffset) < msethresh
+    # np.testing.assert_almost_equal(lagtimes, delayoffset, aethresh)
+
+    if displayplots:
+        fig = plt.figure()
+        ax = fig.add_subplot(111)
+        ax.set_title("Lagtimes")
+        plt.plot(lagtimes)
+        plt.plot(delayoffset)
+        plt.legend(["Target", "Fit"])
+        plt.show()
+
+
+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,
+            tclengthinsecs=300.0,
+            mindelay=-3.0,
+            maxdelay=3.0,
+            numpoints=501,
+            smoothpts=9,
+            nativespaceshape=(10, 10, 10),
+            displayplots=displayplots,
+            outputsuffix="_1",
+            noiselevel=noiselevel,
+            local=local,
+            debug=debug,
+        )
+    eval_refinedelay(
+        sampletime=0.72,
+        tclengthinsecs=300.0,
+        mindelay=-3.0,
+        maxdelay=3.0,
+        numpoints=501,
+        smoothpts=9,
+        nativespaceshape=(10, 10, 10),
+        displayplots=displayplots,
+        outputsuffix="_2",
+        local=local,
+        debug=debug,
+    )
+    eval_refinedelay(
+        sampletime=0.72,
+        tclengthinsecs=300.0,
+        mindelay=-3.0,
+        maxdelay=3.0,
+        numpoints=501,
+        smoothpts=5,
+        nativespaceshape=(10, 10, 10),
+        displayplots=displayplots,
+        outputsuffix="_3",
+        local=local,
+        debug=debug,
+    )
+    eval_refinedelay(
+        sampletime=1.5,
+        tclengthinsecs=300.0,
+        mindelay=-3.0,
+        maxdelay=3.0,
+        numpoints=501,
+        smoothpts=3,
+        nativespaceshape=(10, 10, 10),
+        displayplots=displayplots,
+        outputsuffix="_1p5_501_3",
+        local=local,
+        debug=debug,
+    )
+    eval_refinedelay(
+        sampletime=3.0,
+        tclengthinsecs=300.0,
+        mindelay=-3.0,
+        maxdelay=3.0,
+        numpoints=501,
+        smoothpts=3,
+        nativespaceshape=(10, 10, 10),
+        displayplots=displayplots,
+        outputsuffix="_3p0_501_3",
+        local=local,
+        debug=debug,
+    )
+
+
+if __name__ == "__main__":
+    mpl.use("TkAgg")
+    test_refinedelay(displayplots=True, local=True, debug=True)

rapidtide/tests/test_runmisc.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.
@@ -22,7 +22,7 @@ import matplotlib as mpl
 
 import rapidtide.workflows.parser_funcs as pf
 import rapidtide.workflows.showtc as showtc
-from rapidtide.tests.utils import get_examples_path
+from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
 def test_runmisc(debug=False, displayplots=False):
@@ -35,7 +35,7 @@ def test_runmisc(debug=False, displayplots=False):
         "--sampletime",
         "12.5",
         "--tofile",
-        "showtcout1.jpg",
+        os.path.join(get_test_temp_path(), "showtcout1.jpg"),
         "--starttime",
         "100",
         "--endtime",
@@ -55,7 +55,7 @@ def test_runmisc(debug=False, displayplots=False):
         "--displaytype",
         "power",
         "--tofile",
-        "showtcout2.jpg",
+        os.path.join(get_test_temp_path(), "showtcout2.jpg"),
         "--noxax",
         "--noyax",
         "--nolegend",
@@ -90,7 +90,7 @@ def test_runmisc(debug=False, displayplots=False):
         "--displaytype",
         "phase",
         "--tofile",
-        "showtcout3.jpg",
+        os.path.join(get_test_temp_path(), "showtcout3.jpg"),
     ]
     pf.generic_init(showtc._get_parser, showtc.showtc, inputargs=inputargs)
 

rapidtide/tests/test_sharedmem.py

@@ -0,0 +1,60 @@
+#!/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 numpy as np
+
+import rapidtide.util as tide_util
+
+
+def test_numpy2shared(debug=False):
+    vectorlen = 1000
+    for intype in [np.float32, np.float64]:
+        sourcevector = np.random.normal(size=vectorlen).astype(intype)
+        if debug:
+            print(f"{intype=}, {sourcevector.size=}, {sourcevector.dtype=}")
+        for outtype in [np.float32, np.float64]:
+
+            destvector, shm = tide_util.numpy2shared(sourcevector, outtype)
+            if debug:
+                print(f"\t{outtype=}, {destvector.size=}, {destvector.dtype=}")
+
+            # check everything
+            assert destvector.dtype == outtype
+            assert destvector.size == sourcevector.size
+            np.testing.assert_almost_equal(sourcevector, destvector, 3)
+
+            # clean up
+            tide_util.cleanup_shm(shm)
+
+
+def test_allocshared(debug=False):
+    datashape = (10, 10, 10)
+    for outtype in [np.float32, np.float64]:
+        destarray, shm = tide_util.allocshared(datashape, outtype)
+        if debug:
+            print(f"{outtype=}, {destarray.size=}, {destarray.dtype=}")
+
+        # check everything
+        assert destarray.dtype == outtype
+        assert destarray.size == np.prod(datashape)
+
+        # clean up if needed
+        tide_util.cleanup_shm(shm)
+
+
+if __name__ == "__main__":
+    test_numpy2shared(debug=True)
+    test_allocshared(debug=True)

rapidtide/tests/test_simroundtrip.py

@@ -0,0 +1,132 @@
+#!/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.io as tide_io
+import rapidtide.workflows.parser_funcs as pf
+import rapidtide.workflows.rapidtide as rapidtide_workflow
+import rapidtide.workflows.rapidtide_parser as rapidtide_parser
+import rapidtide.workflows.simdata as rapidtide_simdata
+from rapidtide.tests.utils import get_examples_path, get_test_temp_path
+
+
+def test_simroundtrip(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 initial rapidtide
+    inputargs = [
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETESTSIM"),
+        "--corrmask",
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_restrictedmask.nii.gz"),
+        "--globalmeaninclude",
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_brainmask.nii.gz"),
+        "--spatialfilt",
+        "2",
+        "--simcalcrange",
+        "4",
+        "-1",
+        "--nprocs",
+        "-1",
+        "--passes",
+        "2",
+        "--despecklepasses",
+        "3",
+        "--delaypatchthresh",
+        "4.0",
+    ]
+    rapidtide_workflow.rapidtide_main(rapidtide_parser.process_args(inputargs=inputargs))
+
+    print("initial rapidtide run complete")
+
+    # now simulate data from maps
+    print(testtemproot)
+    inputargs = [
+        "1.5",
+        "260",
+        os.path.join(testtemproot, "sub-RAPIDTIDETESTSIM_desc-unfiltmean_map.nii.gz"),
+        os.path.join(testtemproot, "simulatedfmri_vn05"),
+        "--lfopctfile",
+        os.path.join(testtemproot, "sub-RAPIDTIDETESTSIM_desc-maxcorr_map.nii.gz"),
+        "--lfolagfile",
+        os.path.join(testtemproot, "sub-RAPIDTIDETESTSIM_desc-maxtimerefined_map.nii.gz"),
+        "--lforegressor",
+        os.path.join(
+            testtemproot, "sub-RAPIDTIDETESTSIM_desc-movingregressor_timeseries.json:pass2"
+        ),
+        "--voxelnoiselevel",
+        "5.0",
+    ]
+
+    pf.generic_init(rapidtide_simdata._get_parser, rapidtide_simdata.simdata, inputargs=inputargs)
+    print("simulated dataset generated")
+
+    # run repeat rapidtide
+    inputargs = [
+        os.path.join(testtemproot, "simulatedfmri_vn05.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETESTSIMRERUN"),
+        "--spatialfilt",
+        "2",
+        "--simcalcrange",
+        "4",
+        "-1",
+        "--nprocs",
+        "-1",
+        "--passes",
+        "2",
+        "--despecklepasses",
+        "3",
+        "--delaypatchthresh",
+        "4.0",
+    ]
+    rapidtide_workflow.rapidtide_main(rapidtide_parser.process_args(inputargs=inputargs))
+    print("repeat rapidtide completed")
+
+    absthresh = 1e-10
+    msethresh = 1e-12
+    spacetolerance = 1e-3
+    """for map in [
+        "maxtime",
+        "maxtimerefined",
+        "lfofilterCoeff",
+    ]:
+        print(f"Testing map={map}")
+        filename1 = os.path.join(testtemproot, f"sub-RAPIDTIDETESTSIM_desc-{map}_map.nii.gz")
+        filename2 = os.path.join(testtemproot, f"sub-RAPIDTIDETESTSIMRERUN_desc-{map}_map.nii.gz")
+        assert tide_io.checkniftifilematch(
+            filename1,
+            filename2,
+            absthresh=absthresh,
+            msethresh=msethresh,
+            spacetolerance=spacetolerance,
+            debug=debug,
+        )"""
+
+
+if __name__ == "__main__":
+    mpl.use("TkAgg")
+    test_simroundtrip(debug=True, local=True, displayplots=True)

rapidtide/tests/test_simulate.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2017-2024 Blaise Frederick
+#   Copyright 2017-2025 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_stcorrelate.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.
@@ -58,6 +58,7 @@ def test_stcorrelate(debug=False):
     times, corrpertime, ppertime = shorttermcorr_1D(
         sig1, sig2, tr, windowtime, samplestep=int(stepsize // tr), detrendorder=0
     )
+    print(f"1D correlation: {corrpertime=}, {ppertime=}")
     # plength = len(times)
     times, xcorrpertime, Rvals, delayvals, valid = shorttermcorr_2D(
         sig1,
@@ -67,8 +68,9 @@ def test_stcorrelate(debug=False):
         samplestep=int(stepsize // tr),
         weighting=corrweighting,
         detrendorder=0,
-        displayplots=False,
+        displayplots=debug,
     )
+    print(f"2D correlation: {Rvals=}, {delayvals=}, {valid=}")
     # xlength = len(times)
     writenpvecs(corrpertime, outfilename + "_pearson.txt")
     writenpvecs(ppertime, outfilename + "_pvalue.txt")

rapidtide/tests/test_timeshift.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.
@@ -32,7 +32,7 @@ def test_timeshift(debug=False):
     shiftdist = 30
     timeaxis = np.arange(0.0, 1.0 * testlen) * tr
     # timecoursein = np.zeros((testlen), dtype='float64')
-    timecoursein = np.float64(timeaxis * 0.0)
+    timecoursein = np.zeros_like(timeaxis, np.float64)
     midpoint = int(testlen // 2) + 1
     timecoursein[midpoint - 1] = np.float64(1.0)
     timecoursein[midpoint] = np.float64(1.0)

rapidtide/tests/test_valtoindex.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_zRapidtideDataset.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.
@@ -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_"
@@ -59,7 +59,9 @@ def main(runninglocally=False):
         verbose=verbose,
     )
 
+    print("getting overlays")
     theoverlays = thesubject.getoverlays()
+    print("getting regressors")
     theregressors = thesubject.getregressors()
 
     assert thesubject.focusregressor == "prefilt"
@@ -72,4 +74,4 @@ def main(runninglocally=False):
 
 
 if __name__ == "__main__":
-    main(runninglocally=True)
+    main(runninglocally=True, debug=True)