rapidtide 3.0.2__py3-none-any.whl → 3.0.4__py3-none-any.whl

rapidtide/tests/test_getparsers.py

@@ -0,0 +1,140 @@
+#!/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.applydlfilter import _get_parser as applydlfilter_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.happy_parser import _get_parser as happy_parser_getparser
+from rapidtide.workflows.happy2std import _get_parser as happy2std_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.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,
+        applydlfilter_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 ]
+
+    for thegetparser in parserlist:
+        theusage = thegetparser().format_help()
+        if debug:
+            print(theusage)
+
+
+if __name__ == "__main__":
+    test_parsers(debug=True)

rapidtide/tests/test_io.py

@@ -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
@@ -88,12 +96,12 @@ 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")
+        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")
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz")
     )
     assert np.fabs(tr - 1.5) < fmritimeinfothresh
     assert timepoints == 260
@@ -101,10 +109,10 @@ def test_io(debug=True, displayplots=False):
     # 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 +128,7 @@ 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 +136,7 @@ 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 +149,10 @@ 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 +182,7 @@ 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 +226,43 @@ 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 +501,4 @@ 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_parserfuncs.py

@@ -0,0 +1,70 @@
+#!/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 argparse
+import rapidtide.workflows.parser_funcs as pf
+from rapidtide.tests.utils import get_examples_path, get_test_temp_path
+
+def _get_parser():
+    """
+    Argument parser for adjust offset
+    """
+    parser = argparse.ArgumentParser(
+        prog="dummy",
+        description="dummy",
+        allow_abbrev=False,
+    )
+
+    # Required arguments
+    parser.add_argument(
+        "inputmap",
+        type=lambda x: pf.is_valid_file(parser, x),
+        help="The name of the rapidtide maxtime map.",
+    )
+
+    return parser
+
+
+def test_parserfuncs(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()
+
+
+    theparser = _get_parser()
+
+    filename = os.path.join(exampleroot,"sub-RAPIDTIDETEST_desc-oversampledmovingregressor_timeseries.json")
+    retval = pf.is_valid_file(theparser, filename)
+    print(filename, retval)
+
+    #filename = os.path.join(exampleroot,"sub-RAPIDTIDETEST_desc-oversampledmovingregressor_timeseriesxyz.json")
+    #retval = pf.is_valid_file(theparser, filename)
+    #print(filename, retval)
+
+    filename = os.path.join(exampleroot,"sub-RAPIDTIDETEST_desc-oversampledmovingregressor_timeseries.json:acolname")
+    retval = pf.is_valid_file(theparser, filename)
+    print(filename, retval)
+
+
+if __name__ == "__main__":
+    test_parserfuncs(debug=True, local=True, displayplots=True)

rapidtide/tests/test_zRapidtideDataset.py

@@ -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"

rapidtide/voxelData.py

@@ -128,6 +128,7 @@ class VoxelData:
         self.readdata(timestep, validstart, validend)
 
     def readdata(self, timestep, validstart, validend):
+        # load the data
         self.load()
 
         if tide_io.checkiftext(self.filename):

rapidtide/workflows/cleanregressor.py

@@ -51,10 +51,32 @@ def cleanregressor(
     detrendorder=3,
     windowfunc="hamming",
     respdelete=False,
+    displayplots=False,
     debug=False,
     rt_floattype="float64",
     rt_floatset=np.float64,
 ):
+    # print debugging info
+    if debug:
+        print("cleanregressor:")
+        print(f"\t{thepass=}")
+        print(f"\t{lagmininpts=}")
+        print(f"\t{lagmaxinpts=}")
+        print(f"\t{lagmin=}")
+        print(f"\t{lagmax=}")
+        print(f"\t{detrendorder=}")
+        print(f"\t{windowfunc=}")
+        print(f"\t{respdelete=}")
+        print(f"\t{check_autocorrelation=}")
+        print(f"\t{fix_autocorrelation=}")
+        print(f"\t{despeckle_thresh=}")
+        print(f"\t{lthreshval=}")
+        print(f"\t{fixdelay=}")
+        print(f"\t{check_autocorrelation=}")
+        print(f"\t{displayplots=}")
+        print(f"\t{rt_floattype=}")
+        print(f"\t{rt_floatset=}")
+
     # check the regressor for periodic components in the passband
     dolagmod = True
     doreferencenotch = True
@@ -121,21 +143,33 @@ def cleanregressor(
                 f"searching for sidelobes with amplitude > {theampthresh} "
                 f"with abs(lag) < {thelagthresh} s"
             )
+        if debug:
+            print(
+                (
+                    f"searching for sidelobes with amplitude > {theampthresh} "
+                    f"with abs(lag) < {thelagthresh} s"
+                )
+            )
         sidelobetime, sidelobeamp = tide_corr.check_autocorrelation(
             accheckcorrscale,
             thexcorr,
             acampthresh=theampthresh,
             aclagthresh=thelagthresh,
             detrendorder=detrendorder,
+            displayplots=displayplots,
+            debug=debug,
         )
+        if debug:
+            print(f"check_autocorrelation returned: {sidelobetime=}, {sidelobeamp=}")
         absmaxsigma = acwidth * 10.0
         passsuffix = "_pass" + str(thepass)
         if sidelobetime is not None:
             despeckle_thresh = np.max([despeckle_thresh, sidelobetime / 2.0])
-            LGR.warning(
-                f"\n\nWARNING: check_autocorrelation found bad sidelobe at {sidelobetime} "
-                f"seconds ({1.0 / sidelobetime} Hz)..."
-            )
+            if LGR is not None:
+                LGR.warning(
+                    f"\n\nWARNING: check_autocorrelation found bad sidelobe at {sidelobetime} "
+                    f"seconds ({1.0 / sidelobetime} Hz)..."
+                )
             # bidsify
             """tide_io.writebidstsv(
                 f"{outputname}_desc-movingregressor_timeseries",
@@ -160,7 +194,7 @@ def cleanregressor(
                         LGR.info("removing spectral component at sidelobe frequency")
                     acstopfreq = 1.0 / sidelobetime
                     acfixfilter = tide_filt.NoncausalFilter(
-                        debug=debug,
+                        debug=False,
                     )
                     acfixfilter.settype("arb_stop")
                     acfixfilter.setfreqs(
@@ -175,7 +209,7 @@ def cleanregressor(
                         detrendorder=detrendorder,
                     )
                     cleaned_referencetc = tide_math.corrnormalize(
-                        cleaned_resampref_y,
+                        cleaned_resampref_y[osvalidsimcalcstart : osvalidsimcalcend + 1],
                         detrendorder=detrendorder,
                         windowfunc=windowfunc,
                     )
@@ -222,6 +256,9 @@ def cleanregressor(
             cleaned_referencetc = 1.0 * referencetc
             cleaned_nonosreferencetc = 1.0 * resampnonosref_y
     else:
+        sidelobetime = None
+        sidelobeamp = None
+        lagmod = 1000.0
         acwidth = None
         absmaxsigma = None
         cleaned_resampref_y = 1.0 * tide_math.corrnormalize(