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

rapidtide/tests/test_fullrunrapidtide_v7.py

@@ -0,0 +1,114 @@
+#!/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.io as tide_io
+import rapidtide.workflows.rapidtide as rapidtide_workflow
+import rapidtide.workflows.rapidtide_parser as rapidtide_parser
+import rapidtide.workflows.retroregress as rapidtide_retroregress
+from rapidtide.tests.utils import get_examples_path, get_test_temp_path, mse
+
+
+def test_fullrunrapidtide_v7(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()
+
+    # test anatomic masks
+    inputargs = [
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST_seg"),
+        "--nprocs",
+        "-1",
+        "--passes",
+        "3",
+        "--brainmask",
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_brainmask.nii.gz"),
+        "--graymattermask",
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_GRAY"),
+        "--whitemattermask",
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_WHITE"),
+        "--csfmask",
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_CSF"),
+    ]
+    rapidtide_workflow.rapidtide_main(rapidtide_parser.process_args(inputargs=inputargs))
+
+    inputargs = [
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST_seg"),
+        "--alternateoutput",
+        os.path.join(testtemproot, "segtest"),
+        "--nprocs",
+        "-1",
+        "--outputlevel",
+        "max",
+    ]
+    rapidtide_retroregress.retroregress(rapidtide_retroregress.process_args(inputargs=inputargs))
+
+    inputargs = [
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST_seg"),
+        "--alternateoutput",
+        os.path.join(testtemproot, "regressoronly"),
+        "--nprocs",
+        "-1",
+        "--outputlevel",
+        "onlyregressors",
+    ]
+    rapidtide_retroregress.retroregress(rapidtide_retroregress.process_args(inputargs=inputargs))
+
+    # check to see that rapidtide and retroregress output match
+    msethresh = 2e-6
+    aethresh = 2
+    tclist = ["brain", "GM", "WM", "CSF"]
+    for timecourse in tclist:
+        infilespec = os.path.join(
+            testtemproot,
+            f"sub-RAPIDTIDETEST_seg_desc-regionalpostfilter_timeseries.json:{timecourse}",
+        )
+        insamplerate, instarttime, incolumns, indata, incompressed, infiletype = (
+            tide_io.readvectorsfromtextfile(infilespec, onecol=True, debug=debug)
+        )
+        outfilespec = os.path.join(
+            testtemproot, f"segtest_desc-regionalpostfilter_timeseries.json:{timecourse}"
+        )
+        outsamplerate, outstarttime, outcolumns, outdata, outcompressed, outfiletype = (
+            tide_io.readvectorsfromtextfile(outfilespec, onecol=True, debug=debug)
+        )
+        assert insamplerate == outsamplerate
+        assert instarttime == outstarttime
+        assert incompressed == outcompressed
+        assert infiletype == outfiletype
+        assert incolumns == outcolumns
+        assert indata.shape == outdata.shape
+        assert indata.shape[0] == indata.shape[0]
+        assert mse(indata, outdata) < msethresh
+        np.testing.assert_almost_equal(indata, outdata, aethresh)
+
+
+if __name__ == "__main__":
+    mpl.use("TkAgg")
+    test_fullrunrapidtide_v7(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

@@ -0,0 +1,158 @@
+#!/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
+
+from rapidtide.workflows.adjustoffset import _get_parser as adjustoffset_getparser
+from rapidtide.workflows.aligntcs import _get_parser as aligntcs_getparser
+from rapidtide.workflows.atlasaverage import _get_parser as atlasaverage_getparser
+from rapidtide.workflows.atlastool import _get_parser as atlastool_getparser
+from rapidtide.workflows.calctexticc import _get_parser as calctexticc_getparser
+from rapidtide.workflows.ccorrica import _get_parser as ccorrica_getparser
+from rapidtide.workflows.delayvar import _get_parser as delayvar_getparser
+from rapidtide.workflows.diffrois import _get_parser as diffrois_getparser
+from rapidtide.workflows.endtidalproc import _get_parser as endtidalproc_getparser
+from rapidtide.workflows.fdica import _get_parser as fdica_getparser
+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.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_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.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
+from rapidtide.workflows.polyfitim import _get_parser as polyfitim_getparser
+from rapidtide.workflows.proj2flow import _get_parser as proj2flow_getparser
+from rapidtide.workflows.rankimage import _get_parser as rankimage_getparser
+from rapidtide.workflows.rapidtide2std import _get_parser as rapidtide2std_getparser
+from rapidtide.workflows.resamplenifti import _get_parser as resamplenifti_getparser
+from rapidtide.workflows.resampletc import _get_parser as resampletc_getparser
+from rapidtide.workflows.retrolagtcs import _get_parser as retrolagtcs_getparser
+from rapidtide.workflows.retroregress import _get_parser as retroregress_getparser
+from rapidtide.workflows.roisummarize import _get_parser as roisummarize_getparser
+from rapidtide.workflows.runqualitycheck import _get_parser as runqualitycheck_getparser
+from rapidtide.workflows.showarbcorr import _get_parser as showarbcorr_getparser
+from rapidtide.workflows.showhist import _get_parser as showhist_getparser
+from rapidtide.workflows.showstxcorr import _get_parser as showstxcorr_getparser
+from rapidtide.workflows.showtc import _get_parser as showtc_getparser
+from rapidtide.workflows.showxcorrx import _get_parser as showxcorrx_getparser
+from rapidtide.workflows.showxy import _get_parser as showxy_getparser
+from rapidtide.workflows.simdata import _get_parser as simdata_getparser
+from rapidtide.workflows.spatialfit import _get_parser as spatialfit_getparser
+from rapidtide.workflows.spatialmi import _get_parser as spatialmi_getparser
+from rapidtide.workflows.spectrogram import _get_parser as spectrogram_getparser
+from rapidtide.workflows.synthASL import _get_parser as synthASL_getparser
+from rapidtide.workflows.tcfrom2col import _get_parser as tcfrom2col_getparser
+from rapidtide.workflows.tcfrom3col import _get_parser as tcfrom3col_getparser
+from rapidtide.workflows.variabilityizer import _get_parser as variabilityizer_getparser
+
+
+def test_parsers(debug=False):
+    parserlist = [
+        adjustoffset_getparser,
+        aligntcs_getparser,
+        atlasaverage_getparser,
+        atlastool_getparser,
+        calctexticc_getparser,
+        ccorrica_getparser,
+        delayvar_getparser,
+        diffrois_getparser,
+        endtidalproc_getparser,
+        fdica_getparser,
+        filtnifti_getparser,
+        filttc_getparser,
+        fixtr_getparser,
+        gmscalc_getparser,
+        happy_parser_getparser,
+        happy2std_getparser,
+        histnifti_getparser,
+        histtc_getparser,
+        linfitfilt_getparser,
+        localflow_getparser,
+        mergequality_getparser,
+        niftidecomp_getparser_temporal,
+        niftidecomp_getparser_spatial,
+        niftistats_getparser,
+        pairproc_getparser,
+        pairwisemergenifti_getparser,
+        physiofreq_getparser,
+        pixelcomp_getparser,
+        plethquality_getparser,
+        polyfitim_getparser,
+        proj2flow_getparser,
+        rankimage_getparser,
+        rapidtide2std_getparser,
+        resamplenifti_getparser,
+        resampletc_getparser,
+        retrolagtcs_getparser,
+        retroregress_getparser,
+        roisummarize_getparser,
+        runqualitycheck_getparser,
+        showarbcorr_getparser,
+        showhist_getparser,
+        showstxcorr_getparser,
+        showtc_getparser,
+        showxcorrx_getparser,
+        showxy_getparser,
+        simdata_getparser,
+        spatialfit_getparser,
+        spatialmi_getparser,
+        spectrogram_getparser,
+        synthASL_getparser,
+        tcfrom2col_getparser,
+        tcfrom3col_getparser,
+        variabilityizer_getparser,
+    ]
+    try:
+        import tensorflow as tf
+
+        dlfilterloads = True
+    except ImportError:
+        dlfilterloads = False
+    if dlfilterloads:
+        from rapidtide.workflows.applydlfilter import (
+            _get_parser as applydlfilter_getparser,
+        )
+
+        parserlist.append(applydlfilter_getparser)
+
+    for thegetparser in parserlist:
+        theusage = thegetparser().format_help()
+        if debug:
+            print(theusage)
+
+
+if __name__ == "__main__":
+    test_parsers(debug=True)

rapidtide/tests/test_io.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.
@@ -25,9 +25,17 @@ import rapidtide.io as tide_io
 from rapidtide.tests.utils import create_dir, get_examples_path, get_test_temp_path, mse
 
 
-def test_io(debug=True, displayplots=False):
+def test_io(debug=True, 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()
+
     # create outputdir if it doesn't exist
-    create_dir(get_test_temp_path())
+    create_dir(testtemproot)
 
     # test checkifnifti
     assert tide_io.checkifnifti("test.nii") == True
@@ -87,24 +95,20 @@ def test_io(debug=True, displayplots=False):
 
     # test fmritimeinfo
     fmritimeinfothresh = 1e-2
-    tr, timepoints = tide_io.fmritimeinfo(
-        os.path.join(get_examples_path(), "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(get_examples_path(), "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
 
     # test niftifile reading
     sizethresh = 1e-3
     happy_img, happy_data, happy_hdr, happydims, happysizes = tide_io.readfromnifti(
-        os.path.join(get_examples_path(), "sub-HAPPYTEST.nii.gz")
+        os.path.join(exampleroot, "sub-HAPPYTEST.nii.gz")
     )
     fmri_img, fmri_data, fmri_hdr, fmridims, fmrisizes = tide_io.readfromnifti(
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz")
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz")
     )
     targetdims = [4, 65, 89, 64, 110, 1, 1, 1]
     targetsizes = [-1.00, 2.39583, 2.395830, 2.4, 1.16, 0.00, 0.00, 0.00]
@@ -120,7 +124,7 @@ def test_io(debug=True, displayplots=False):
     # test file writing
     datathresh = 2e-3  # relaxed threshold because sub-RAPIDTIDETEST has been converted to INT16
     tide_io.savetonifti(
-        fmri_data, fmri_hdr, os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST_copy.nii.gz")
+        fmri_data, fmri_hdr, os.path.join(testtemproot, "sub-RAPIDTIDETEST_copy.nii.gz")
     )
     (
         fmricopy_img,
@@ -128,7 +132,7 @@ def test_io(debug=True, displayplots=False):
         fmricopy_hdr,
         fmricopydims,
         fmricopysizes,
-    ) = tide_io.readfromnifti(os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST_copy.nii.gz"))
+    ) = tide_io.readfromnifti(os.path.join(testtemproot, "sub-RAPIDTIDETEST_copy.nii.gz"))
     assert tide_io.checkspacematch(fmri_hdr, fmricopy_hdr)
     assert tide_io.checktimematch(fmridims, fmridims)
     assert mse(fmri_data, fmricopy_data) < datathresh
@@ -141,10 +145,10 @@ def test_io(debug=True, displayplots=False):
 
     # test writing and reading text files
     debug = False
-    DESTDIR = get_test_temp_path()
-    SOURCEDIR = get_examples_path()
+    DESTDIR = testtemproot
+    SOURCEDIR = exampleroot
     EPSILON = 1e-5
-    numpoints = 10
+    numpoints = 100
     the2darray = np.zeros((6, numpoints), dtype=float)
     the2darray[0, :] = np.linspace(0, 1.0, numpoints, endpoint=False)
     the2darray[1, :] = np.sin(the2darray[0, :] * 2.0 * np.pi)
@@ -174,7 +178,7 @@ def test_io(debug=True, displayplots=False):
         ["plaintsv", True, ".tsv.gz"],
     ]
 
-    print("writing files")
+    print("writing files as a unit")
     for thistest in thetests:
         thetype = thistest[0]
         compressed = thistest[1]
@@ -218,6 +222,43 @@ def test_io(debug=True, displayplots=False):
             debug=debug,
         )
 
+    theappendtests = [
+        ["bidscontinuous", False, ".tsv"],
+        ["bidscontinuous", True, ".tsv.gz"],
+    ]
+
+    print("writing files with append")
+    for thistest in theappendtests:
+        thetype = thistest[0]
+        compressed = thistest[1]
+        if compressed:
+            compname = "compressed"
+        else:
+            compname = "uncompressed"
+
+        print(f"{the2darray.shape=}")
+        thefileroot = os.path.join(DESTDIR, f"testout_withcol_{thetype}_{compname}")
+        print(f"\t writing: {thefileroot}")
+        tide_io.writebidstsv(
+            thefileroot + "_append",
+            the2darray[:5, :],
+            inputsamplerate,
+            starttime=inputstarttime,
+            columns=thecols[:5],
+            compressed=compressed,
+            debug=debug,
+        )
+        tide_io.writebidstsv(
+            thefileroot + "_append",
+            the2darray[5, :],
+            inputsamplerate,
+            starttime=inputstarttime,
+            columns=[thecols[5]],
+            compressed=compressed,
+            append=True,
+            debug=debug,
+        )
+
     print("reading complete files")
     for thistest in thetests:
         thetype = thistest[0]
@@ -456,4 +497,4 @@ def test_io(debug=True, displayplots=False):
 
 
 if __name__ == "__main__":
-    test_io(debug=True, displayplots=True)
+    test_io(debug=True, local=True, displayplots=True)

rapidtide/tests/{test_glmpass.py → test_linfitfiltpass.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.
@@ -20,7 +20,7 @@ import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
 
-import rapidtide.glmpass as tide_glmpass
+import rapidtide.linfitfiltpass as tide_linfitfiltpass
 from rapidtide.tests.utils import mse
 
 
@@ -41,7 +41,7 @@ def gen2d(xsize=150, xcycles=11, tsize=200, tcycles=13, mean=10.0):
     return thearray, xwaves, twaves
 
 
-def test_glmpass(debug=True, displayplots=False):
+def test_linfitfiltpass(debug=True, displayplots=False):
     np.random.seed(12345)
     xsize = 150
     xcycles = 7
@@ -77,8 +77,8 @@ def test_glmpass(debug=True, displayplots=False):
     fitcoffs_x = np.zeros((xsize, tsize), dtype=np.float64)
     fitNorm_x = np.zeros((xsize, tsize), dtype=np.float64)
 
-    for confoundglm in [True, False]:
-        if confoundglm:
+    for confoundregress in [True, False]:
+        if confoundregress:
             twaveformrange = np.transpose(twaveforms[:6, :])
             xwaveformrange = xwaveforms[:, :6]
             print(f"{twaveformrange.shape=} - {xwaveformrange.shape=}")
@@ -115,9 +115,9 @@ def test_glmpass(debug=True, displayplots=False):
 
                     if debug:
                         print(
-                            f"confoundglm={confoundglm}, proc by {direction}, {procstring} proc, {maskstatus}"
+                            f"confoundregress={confoundregress}, proc by {direction}, {procstring} proc, {maskstatus}"
                         )
-                    tide_glmpass.glmpass(
+                    tide_linfitfiltpass.linfitfiltpass(
                         xsize,
                         testarray,
                         thisthreshval,
@@ -132,7 +132,7 @@ def test_glmpass(debug=True, displayplots=False):
                         showprogressbar=False,
                         procbyvoxel=procbyvoxel,
                         nprocs=nprocs,
-                        confoundglm=confoundglm,
+                        confoundregress=confoundregress,
                     )
                     if displayplots:
                         plt.figure()
@@ -142,10 +142,10 @@ def test_glmpass(debug=True, displayplots=False):
                         plt.show()
                     if debug:
                         print(f"\tMSE: {mse(datatoremove, targetarray)}\n")
-                    if not confoundglm:
+                    if not confoundregress:
                         assert mse(datatoremove, targetarray) < 1e-3
 
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_glmpass(debug=True, displayplots=True)
+    test_linfitfiltpass(debug=True, displayplots=True)

rapidtide/tests/test_mi.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_miscmath.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_motionregress.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.
@@ -21,8 +21,8 @@ import matplotlib.pyplot as plt
 import numpy as np
 
 import rapidtide.fit as tide_fit
-import rapidtide.glmpass as tide_glmpass
 import rapidtide.io as tide_io
+import rapidtide.linfitfiltpass as tide_linfitfiltpass
 from rapidtide.tests.utils import mse
 
 
@@ -130,9 +130,9 @@ def test_motionregress(debug=False, displayplots=False):
 
                 thedataarray = makedataarray(motionregressors)
                 numprocitems = thedataarray.shape[0]
-                filtereddata = thedataarray * 0.0
+                filtereddata = np.zeros_like(thedataarray)
                 r2value = np.zeros(numprocitems)
-                dummy = tide_glmpass.glmpass(
+                dummy = tide_linfitfiltpass.linfitfiltpass(
                     numprocitems,
                     thedataarray,
                     None,
@@ -144,7 +144,7 @@ def test_motionregress(debug=False, displayplots=False):
                     None,
                     None,
                     filtereddata,
-                    confoundglm=True,
+                    confoundregress=True,
                     nprocs=1,
                     showprogressbar=debug,
                     procbyvoxel=True,

rapidtide/tests/test_nullcorr.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.
@@ -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"],
@@ -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,
-                fixeddelayvalue=0.0,
+                None,
                 numestreps=optiondict["numestreps"],
                 nprocs=thenprocs,
                 showprogressbar=optiondict["showprogressbar"],