rapidtide 3.0.7.1__py3-none-any.whl → 3.0.9__py3-none-any.whl

rapidtide/RapidtideDataset.py

@@ -408,7 +408,7 @@ class Overlay:
 
     def maskData(self):
         self.mask = self.geommask * self.funcmask
-        maskhash = hash(self.mask.tostring())
+        maskhash = hash(self.mask.tobytes())
         # these operations are expensive, so only do them if the mask is changed
         if (maskhash == self.maskhash) and (self.verbose > 1):
             print("mask has not changed")

rapidtide/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-06-16T15:12:43-0400",
+ "date": "2025-07-03T10:21:49-0400",
  "dirty": false,
  "error": null,
- "full-revisionid": "6dead8e554dd0464bdfc65de24889374508f920d",
- "version": "3.0.7.1"
+ "full-revisionid": "292e93bbd0a9c13e2d62a00746e14522b0783156",
+ "version": "3.0.9"
 }
 '''  # END VERSION_JSON
 

rapidtide/calcnullsimfunc.py

@@ -18,13 +18,11 @@
 #
 import sys
 
-
 import numpy as np
 
-
 import rapidtide.filter as tide_filt
-import rapidtide.miscmath as tide_math
 import rapidtide.genericmultiproc as tide_genericmultiproc
+import rapidtide.miscmath as tide_math
 
 
 # note: rawtimecourse has been filtered, but NOT windowed

rapidtide/data/examples/src/test_findmaxlag.py

@@ -24,8 +24,8 @@ import matplotlib.pyplot as plt
 import numpy as np
 
 import rapidtide.fit as tide_fit
-import rapidtide.helper_classes as tide_classes
 import rapidtide.io as tide_io
+import rapidtide.simFuncClasses as tide_classes
 from rapidtide.tests.utils import get_examples_path
 
 

rapidtide/data/examples/src/testfmri

@@ -1,24 +1,26 @@
 #!/bin/bash
 
 rapidtide \
-    --spatialfilt -1 \
+    --spatialfilt 2.5 \
     --nprocs -1 \
-    --searchrange -5 20 \
+    --searchrange -7.5 30 \
     --simcalcrange 50 -1 \
     --outputlevel more \
-    --sLFOfiltmask \
     --graymattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_GRAY \
     --brainmask sub-RAPIDTIDETEST_brainmask.nii.gz \
     --whitemattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_WHITE \
     --csfmask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_CSF \
     --cleanrefined \
+    --nofitfilt \
+    --refinedelayeachpass \
+    --similaritymetric correlation \
     sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST
+    ../dst/sub-RAPIDTIDETEST_simfunc
 
 rapidtide \
-    --spatialfilt -1 \
+    --spatialfilt 2.5 \
     --nprocs -1 \
-    --searchrange -5 20 \
+    --searchrange -7.5 30 \
     --simcalcrange 50 -1 \
     --outputlevel more \
     --graymattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_GRAY \
@@ -26,5 +28,15 @@ rapidtide \
     --whitemattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_WHITE \
     --csfmask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_CSF \
     --cleanrefined \
+    --nofitfilt \
+    --refinedelayeachpass \
+    --similaritymetric riptide \
+    --riptidestep 1.5 \
+    --ampthresh 0.0 \
+    --numnull 0 \
     sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_nosLFOfiltmask
+    ../dst/sub-RAPIDTIDETEST_riptide
+
+tidepool --uistyle big --dataset \
+    ../dst/sub-RAPIDTIDETEST_simfunc_ \
+    ../dst/sub-RAPIDTIDETEST_riptide_ &

rapidtide/data/examples/src/testnewrefine

@@ -6,28 +6,15 @@ rapidtide \
     --searchrange -5 20 \
     --simcalcrange 50 -1 \
     --outputlevel max \
-    --refineregressderivs 1 \
     sub-RAPIDTIDETEST.nii.gz \
     ../dst/sub-RAPIDTIDETEST_1deriv
 
-rapidtide \
-    --spatialfilt -1 \
-    --nprocs -1 \
-    --searchrange -5 20 \
-    --simcalcrange 50 -1 \
-    --outputlevel max \
-    --refineregressderivs 2 \
-    sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_2deriv
-
-
 retroregress \
     sub-RAPIDTIDETEST.nii.gz \
     ../dst/sub-RAPIDTIDETEST_1deriv \
     --alternateoutput ../dst/retrotest_1to1 \
     --nprocs -1 \
     --regressderivs 0 \
-    --refineregressderivs 1 \
     --outputlevel max
 
 retroregress \
@@ -36,14 +23,4 @@ retroregress \
     --alternateoutput ../dst/retrotest_2to1 \
     --nprocs -1 \
     --regressderivs 0 \
-    --refineregressderivs 1 \
-    --outputlevel max
-
-retroregress \
-    sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_1deriv \
-    --alternateoutput ../dst/retrotest_1to2 \
-    --nprocs -1 \
-    --regressderivs 0 \
-    --refineregressderivs 2 \
     --outputlevel max

rapidtide/fMRIData_class.py

@@ -16,21 +16,9 @@
 #   limitations under the License.
 #
 #
-import sys
-import warnings
-
-import matplotlib.pyplot as plt
 import numpy as np
-import scipy as sp
-from numpy.polynomial import Polynomial
-from scipy.optimize import curve_fit
-from statsmodels.robust import mad
 
-import rapidtide.correlate as tide_corr
-import rapidtide.filter as tide_filt
-import rapidtide.fit as tide_fit
-import rapidtide.miscmath as tide_math
-import rapidtide.util as tide_util
+import rapidtide.io as tide_io
 
 
 class fMRIData:
@@ -42,9 +30,7 @@ class fMRIData:
     mask = None
     validvoxels = None
     filename = None
-    textio = False
-    fileiscifti = False
-    fileisnifti = False
+    filetype = None
 
     def __init__(
         self,
@@ -110,53 +96,44 @@ class fMRIData:
         ####################################################
         #  Read data
         ####################################################
-        # open the fmri datafil
+        # open the fmri datafile
         if tide_io.checkiftext(self.filename):
-            self.textio = True
-        else:
-            self.textio = False
-
-        if self.textio:
+            self.filetype = "text"
             self.data = tide_io.readvecs(self.filename)
             self.header = None
             theshape = np.shape(nim_data)
             self.xsize = theshape[0]
             self.ysize = 1
             self.numslices = 1
-            self.fileiscifti = False
             self.timepoints = theshape[1]
             self.thesizes = [0, int(self.xsize), 1, 1, int(self.timepoints)]
             self.numspatiallocs = int(self.xsize)
             self.nativespaceshape = self.xsize
             self.cifti_hdr = None
+        elif tide_io.checkifcifti(self.filename):
+            self.filetype = "cifti"
+            (
+                cifti,
+                cifti_hdr,
+                self.data,
+                self.header,
+                thedims,
+                thesizes,
+                dummy,
+            ) = tide_io.readfromcifti(self.filename)
+            self.isgrayordinate = True
+            self.timepoints = nim_data.shape[1]
+            numspatiallocs = nim_data.shape[0]
+            LGR.debug(f"cifti file has {timepoints} timepoints, {numspatiallocs} numspatiallocs")
+            slicesize = numspatiallocs
+            nativespaceshape = (1, 1, 1, 1, numspatiallocs)
         else:
-            self.fileiscifti = tide_io.checkifcifti(self.filename)
-            if self.fileiscifti:
-                (
-                    cifti,
-                    cifti_hdr,
-                    self.data,
-                    self.header,
-                    thedims,
-                    thesizes,
-                    dummy,
-                ) = tide_io.readfromcifti(self.filename)
-                self.isgrayordinate = True
-                self.timepoints = nim_data.shape[1]
-                numspatiallocs = nim_data.shape[0]
-                LGR.debug(
-                    f"cifti file has {timepoints} timepoints, {numspatiallocs} numspatiallocs"
-                )
-                slicesize = numspatiallocs
-                nativespaceshape = (1, 1, 1, 1, numspatiallocs)
-            else:
-                LGR.debug("input file is NIFTI")
-                nim, self.data, self.header, thedims, thesizes = tide_io.readfromnifti(
-                    fmrifilename
-                )
-                optiondict["isgrayordinate"] = False
-                xsize, ysize, numslices, timepoints = tide_io.parseniftidims(thedims)
-                numspatiallocs = int(xsize) * int(ysize) * int(numslices)
-                cifti_hdr = None
-                nativespaceshape = (xsize, ysize, numslices)
+            self.filetype = "nifti"
+            LGR.debug("input file is NIFTI")
+            nim, self.data, self.header, thedims, thesizes = tide_io.readfromnifti(fmrifilename)
+            optiondict["isgrayordinate"] = False
+            xsize, ysize, numslices, timepoints = tide_io.parseniftidims(thedims)
+            numspatiallocs = int(xsize) * int(ysize) * int(numslices)
+            cifti_hdr = None
+            nativespaceshape = (xsize, ysize, numslices)
             xdim, ydim, slicethickness, tr = tide_io.parseniftisizes(thesizes)

rapidtide/fit.py

@@ -1469,11 +1469,11 @@ def getpeaks(xvals, yvals, xrange=None, bipolar=False, displayplots=False):
         peaks = np.concatenate((peaks, negpeaks))
     procpeaks = []
     if xrange is None:
-        lagmin = xvals[0]
-        lagmax = xvals[-1]
+        lagmin = xvals[0] + 0.0
+        lagmax = xvals[-1] + 0.0
     else:
-        lagmin = xrange[0]
-        lagmax = xrange[1]
+        lagmin = xrange[0] + 0.0
+        lagmax = xrange[1] + 0.0
     originloc = tide_util.valtoindex(xvals, 0.0, discrete=False)
     for thepeak in peaks:
         if lagmin <= xvals[thepeak] <= lagmax:

rapidtide/happy_supportfuncs.py

@@ -22,7 +22,7 @@ import warnings
 
 import numpy as np
 from scipy.signal import savgol_filter, welch
-from scipy.stats import kurtosis, skew, pearsonr
+from scipy.stats import kurtosis, pearsonr, skew
 from statsmodels.robust import mad
 from tqdm import tqdm