rapidtide 3.0.2__py3-none-any.whl → 3.0.3__py3-none-any.whl

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/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(