rapidtide 3.0a6__py3-none-any.whl → 3.0a8__py3-none-any.whl

rapidtide/OrthoImageItem.py

@@ -25,6 +25,7 @@ import os
 
 import numpy as np
 import pyqtgraph as pg
+from more_itertools.more import first
 from pyqtgraph.Qt import QtCore, QtGui, QtWidgets
 
 try:
@@ -68,7 +69,16 @@ def newColorbar(left, top, impixpervoxx, impixpervoxy, imgsize):
     return thecolorbarfgwin, thecolorbarbgwin, theviewbox, colorbarvals
 
 
-def newViewWindow(view, left, top, impixpervoxx, impixpervoxy, imgsize, enableMouse=False):
+def setupViewWindow(
+    view,
+    left,
+    top,
+    impixpervoxx,
+    impixpervoxy,
+    imgsize,
+    enableMouse=False,
+):
+
     theviewbox = view.addViewBox(enableMouse=enableMouse, enableMenu=False, lockAspect=1.0)
     theviewbox.setAspectLocked()
     theviewbox.setRange(QtCore.QRectF(0, 0, imgsize, imgsize), padding=0.0, disableAutoRange=True)
@@ -146,6 +156,17 @@ class OrthoImageItem(QtWidgets.QWidget):
         self.offsetx = self.imgsize * (0.5 - self.xfov / (2.0 * self.maxfov))
         self.offsety = self.imgsize * (0.5 - self.yfov / (2.0 * self.maxfov))
         self.offsetz = self.imgsize * (0.5 - self.zfov / (2.0 * self.maxfov))
+        self.axviewbox = None
+        self.corviewbox = None
+        self.sagviewbox = None
+        self.axviewwin = None
+        self.corviewwin = None
+        self.sagviewwin = None
+        self.axviewbgwin = None
+        self.corviewbgwin = None
+        self.sagviewbgwin = None
+        self.debug = True
+        self.arrangement = arrangement
 
         if self.verbose > 1:
             print("OrthoImageItem initialization:")
@@ -162,7 +183,6 @@ class OrthoImageItem(QtWidgets.QWidget):
             print("    Offsets:", self.offsetx, self.offsety, self.offsetz)
         self.buttonisdown = False
 
-        self.arrangement = arrangement
         self.axview.setBackground(None)
         self.axview.setRange(padding=0.0)
         self.axview.ci.layout.setContentsMargins(0, 0, 0, 0)
@@ -182,7 +202,7 @@ class OrthoImageItem(QtWidgets.QWidget):
             self.axviewvLine,
             self.axviewhLine,
             self.axviewbox,
-        ) = newViewWindow(
+        ) = setupViewWindow(
             self.axview,
             self.offsetx,
             self.offsety,
@@ -197,7 +217,7 @@ class OrthoImageItem(QtWidgets.QWidget):
             self.corviewvLine,
             self.corviewhLine,
             self.corviewbox,
-        ) = newViewWindow(
+        ) = setupViewWindow(
             self.corview,
             self.offsetx,
             self.offsetz,
@@ -212,7 +232,7 @@ class OrthoImageItem(QtWidgets.QWidget):
             self.sagviewvLine,
             self.sagviewhLine,
             self.sagviewbox,
-        ) = newViewWindow(
+        ) = setupViewWindow(
             self.sagview,
             self.offsety,
             self.offsetz,

rapidtide/RapidtideDataset.py

@@ -432,6 +432,7 @@ class Overlay:
 
 class RapidtideDataset:
     "Store all the data associated with a rapidtide dataset"
+    fileroot = None
     focusregressor = None
     regressorfilterlimits = None
     regressorsimcalclimits = None

rapidtide/correlate.py

@@ -703,9 +703,12 @@ class AliasedCorrelator:
     """
 
     def __init__(self, hiressignal, hires_Fs, numsteps):
-        self.hiressignal = tide_math.corrnormalize(hiressignal)
         self.hires_Fs = hires_Fs
         self.numsteps = numsteps
+        self.sethiressignal(hiressignal)
+
+    def sethiressignal(self, hiressignal):
+        self.hiressignal = tide_math.corrnormalize(hiressignal)
         self.corrlen = len(self.hiressignal) * 2 + 1
         self.corrx = (
             np.linspace(0.0, self.corrlen, num=self.corrlen) / self.hires_Fs
@@ -735,10 +738,9 @@ class AliasedCorrelator:
             print(offset, self.numsteps)
         osvec = self.hiressignal * 0.0
         osvec[offset :: self.numsteps] = loressignal[:]
-        corrfunc = (
-            tide_corr.fastcorrelate(tide_math.corrnormalize(osvec), self.hiressignal)
-            * self.numsteps
-        )
+        corrfunc = tide_corr.fastcorrelate(
+            tide_math.corrnormalize(osvec), self.hiressignal
+        ) * np.sqrt(self.numsteps)
         return corrfunc
 
 

rapidtide/data/examples/src/testfmri

@@ -14,29 +14,18 @@ rapidtide \
     --nprocs -1 \
     --searchrange -5 20 \
     --simcalcrange 50 -1 \
-    --outputlevel min \
     --refinedelay \
     sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_refinedelay
+    ../dst/sub-RAPIDTIDETEST_filt
 
 rapidtide \
-    --spatialfilt 5 \
+    --spatialfilt 0 \
     --nprocs -1 \
     --searchrange -5 20 \
     --simcalcrange 50 -1 \
-    --outputlevel min \
     --norefinedelay \
     sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_norefinedelay
-
-rapidtide \
-    --spatialfilt 5 \
-    --nprocs -1 \
-    --searchrange -5 20 \
-    --simcalcrange 50 -1 \
-    --outputlevel min \
-    sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_noption
+    ../dst/sub-RAPIDTIDETEST_nofilt
 
 #rapidtide \
 #    --spatialfilt 5 \

rapidtide/data/examples/src/testhappy

@@ -65,5 +65,10 @@
 happy \
     sub-HAPPYTEST.nii.gz \
     sub-HAPPYTEST.json \
-    ../dst/happy_motion \
-    --motionfile sub-HAPPYTEST_mcf.par
+    ../dst/happy
+
+happy \
+    sub-HAPPYTEST.nii.gz \
+    sub-HAPPYTEST.json \
+    ../dst/happy_aliasedcorrelation \
+    --aliasedcorrelation

rapidtide/happy_supportfuncs.py

@@ -134,6 +134,27 @@ def calc_3d_optical_flow(video, projmask, flowhdr, outputroot, window_size=3, de
     return flow_vectors
 
 
+def phasejolt(phaseimage):
+
+    # Compute the gradient of the window in x, y, and z directions
+    grad_x, grad_y, grad_z = np.gradient(phaseimage)
+
+    # Now compute the second order gradients of the window in x, y, and z directions
+    grad_xx, grad_xy, grad_xz = np.gradient(grad_x)
+    grad_yx, grad_yy, grad_yz = np.gradient(grad_y)
+    grad_zx, grad_zy, grad_zz = np.gradient(grad_z)
+
+    # Calculate our metrics of interest
+    jump = (np.fabs(grad_x) + np.fabs(grad_y) + np.fabs(grad_z)) / 3.0
+    jolt = (
+        (np.fabs(grad_xx) + np.fabs(grad_xy) + np.fabs(grad_xz))
+        + (np.fabs(grad_yx) + np.fabs(grad_yy) + np.fabs(grad_yz))
+        + (np.fabs(grad_zx) + np.fabs(grad_zy) + np.fabs(grad_zz))
+    ) / 9.0
+    laplacian = grad_xx + grad_yy + grad_zz
+    return (jump, jolt, laplacian)
+
+
 def cardiacsig(thisphase, amps=(1.0, 0.0, 0.0), phases=None, overallphase=0.0):
     total = 0.0
     if phases is None:
@@ -145,7 +166,7 @@ def cardiacsig(thisphase, amps=(1.0, 0.0, 0.0), phases=None, overallphase=0.0):
 
 def cardiacfromimage(
     normdata_byslice,
-    estmask_byslice,
+    estweights_byslice,
     numslices,
     timepoints,
     tr,
@@ -182,7 +203,7 @@ def cardiacfromimage(
 
     # make sure there is an appflips array
     if appflips_byslice is None:
-        appflips_byslice = estmask_byslice * 0.0 + 1.0
+        appflips_byslice = estweights_byslice * 0.0 + 1.0
     else:
         if arteriesonly:
             appflips_byslice[np.where(appflips_byslice > 0.0)] = 0.0
@@ -196,22 +217,22 @@ def cardiacfromimage(
     if not verbose:
         print("Averaging slices...")
     if fliparteries:
-        thismask_byslice = appflips_byslice.astype(np.int64) * estmask_byslice
+        theseweights_byslice = appflips_byslice.astype(np.float64) * estweights_byslice
     else:
-        thismask_byslice = estmask_byslice
+        theseweights_byslice = estweights_byslice
     for theslice in range(numslices):
         if verbose:
             print("Averaging slice", theslice)
         if usemask:
-            validestvoxels = np.where(np.abs(thismask_byslice[:, theslice]) > 0)[0]
+            validestvoxels = np.where(np.abs(theseweights_byslice[:, theslice]) > 0)[0]
         else:
-            validestvoxels = np.where(np.abs(thismask_byslice[:, theslice] >= 0))[0]
+            validestvoxels = np.where(np.abs(theseweights_byslice[:, theslice] >= 0))[0]
         if len(validestvoxels) > 0:
             if madnorm:
                 sliceavs[theslice, :], slicenorms[theslice] = tide_math.madnormalize(
                     np.mean(
                         normdata_byslice[validestvoxels, theslice, :]
-                        * thismask_byslice[validestvoxels, theslice, np.newaxis],
+                        * theseweights_byslice[validestvoxels, theslice, np.newaxis],
                         axis=0,
                     ),
                     returnnormfac=True,
@@ -219,7 +240,7 @@ def cardiacfromimage(
             else:
                 sliceavs[theslice, :] = np.mean(
                     normdata_byslice[validestvoxels, theslice, :]
-                    * thismask_byslice[validestvoxels, theslice, np.newaxis],
+                    * theseweights_byslice[validestvoxels, theslice, np.newaxis],
                     axis=0,
                 )
                 slicenorms[theslice] = 1.0
@@ -1241,3 +1262,51 @@ def phaseproject(
         normapp_byslice[validlocs, theslice, :] = np.nan_to_num(
             app_byslice[validlocs, theslice, :] / means_byslice[validlocs, theslice, None]
         )
+    return app, rawapp, corrected_rawapp, normapp, weights, cine, derivatives
+
+
+def upsampleimage(input_data, input_hdr, numsteps, sliceoffsets, slicesamplerate, outputroot):
+    fmri_data = input_data.byvol()
+    timepoints = input_data.timepoints
+    xsize = input_data.xsize
+    ysize = input_data.ysize
+    numslices = input_data.numslices
+
+    # allocate the image
+    print(f"upsampling fmri data by a factor of {numsteps}")
+    upsampleimage = np.zeros((xsize, ysize, numslices, numsteps * timepoints), dtype=float)
+    upsampleimage_byslice = upsampleimage.reshape(xsize * ysize, numslices, numsteps * timepoints)
+
+    # demean the raw data
+    meanfmri = fmri_data.mean(axis=1)
+    demeaned_data = fmri_data - meanfmri[:, None]
+
+    # drop in the raw data
+    for theslice in range(numslices):
+        upsampleimage[
+            :, :, theslice, sliceoffsets[theslice] : timepoints * numsteps : numsteps
+        ] = demeaned_data.reshape((xsize, ysize, numslices, timepoints))[:, :, theslice, :]
+
+    upsampleimage_byslice = upsampleimage.reshape(xsize * ysize, numslices, timepoints * numsteps)
+
+    # interpolate along the slice direction
+    thedstlocs = np.linspace(0, numslices, num=len(sliceoffsets), endpoint=False)
+    print(f"len(destlocst), destlocs: {len(thedstlocs)}, {thedstlocs}")
+    for thetimepoint in range(0, timepoints * numsteps):
+        thestep = thetimepoint % numsteps
+        print(f"interpolating step {thestep}")
+        thesrclocs = np.where(sliceoffsets == thestep)[0]
+        print(f"timepoint: {thetimepoint}, sourcelocs: {thesrclocs}")
+        for thexyvoxel in range(xsize * ysize):
+            theinterps = np.interp(
+                thedstlocs,
+                1.0 * thesrclocs,
+                upsampleimage_byslice[thexyvoxel, thesrclocs, thetimepoint],
+            )
+            upsampleimage_byslice[thexyvoxel, :, thetimepoint] = 1.0 * theinterps
+
+    theheader = copy.deepcopy(input_hdr)
+    theheader["dim"][4] = timepoints * numsteps
+    theheader["pixdim"][4] = 1.0 / slicesamplerate
+    tide_io.savetonifti(upsampleimage, theheader, outputroot + "_upsampled")
+    print("upsampling complete")

rapidtide/helper_classes.py

@@ -691,6 +691,7 @@ class SimilarityFunctionFitter:
     FML_FITWIDTHHIGH = np.uint32(0x0800)
     FML_FITLAGLOW = np.uint32(0x1000)
     FML_FITLAGHIGH = np.uint32(0x2000)
+    FML_FITALGOFAIL = np.uint32(0x0400)
     FML_FITFAIL = (
         FML_FITAMPLOW
         | FML_FITAMPHIGH
@@ -698,6 +699,7 @@ class SimilarityFunctionFitter:
         | FML_FITWIDTHHIGH
         | FML_FITLAGLOW
         | FML_FITLAGHIGH
+        | FML_FITALGOFAIL
     )
 
     def __init__(
@@ -873,6 +875,8 @@ class SimilarityFunctionFitter:
             reasons.append("Fit Lag too low")
         if failreason.astype(np.uint32) & self.FML_FITLAGHIGH:
             reasons.append("Fit Lag too high")
+        if failreason.astype(np.uint32) & self.FML_FITALGOFAIL:
+            reasons.append("Nonlinear fit failed")
 
         if len(reasons) > 0:
             return ", ".join(reasons)
@@ -1119,6 +1123,7 @@ class SimilarityFunctionFitter:
                     maxlag = np.fmod((1.0 * plsq[1]), self.lagmod)
                     maxsigma = plsq[2]
                 except:
+                    failreason |= self.FML_FITALGOFAIL
                     maxval = np.float64(0.0)
                     maxlag = np.float64(0.0)
                     maxsigma = np.float64(0.0)
@@ -1139,6 +1144,7 @@ class SimilarityFunctionFitter:
                     maxlag = np.fmod((1.0 * plsq[1]), self.lagmod)
                     maxsigma = plsq[2]
                 except:
+                    failreason |= self.FML_FITALGOFAIL
                     maxval = np.float64(0.0)
                     maxlag = np.float64(0.0)
                     maxsigma = np.float64(0.0)
@@ -1173,6 +1179,7 @@ class SimilarityFunctionFitter:
                         print("poly coffs:", a, b, c)
                         print("maxlag, maxval, maxsigma:", maxlag, maxval, maxsigma)
                 except np.lib.polynomial.RankWarning:
+                    failreason |= self.FML_FITALGOFAIL
                     maxlag = 0.0
                     maxval = 0.0
                     maxsigma = 0.0
@@ -1219,6 +1226,7 @@ class SimilarityFunctionFitter:
                 # different rules for mutual information peaks
                 if ((maxval - baseline) < self.lthreshval * baselinedev) or (maxval < baseline):
                     failreason |= self.FML_FITAMPLOW
+                    maxval_init = 0.0
                     if self.debug:
                         if (maxval - baseline) < self.lthreshval * baselinedev:
                             print(
@@ -1229,7 +1237,6 @@ class SimilarityFunctionFitter:
                             )
                         if maxval < baseline:
                             print("FITAMPLOW: maxval < baseline:", maxval, baseline)
-                    maxval_init = 0.0
                     if self.debug:
                         print("bad fit amp: maxval is lower than lower limit")
             if (self.lagmin > maxlag) or (maxlag > self.lagmax):
@@ -1269,6 +1276,8 @@ class SimilarityFunctionFitter:
             maxsigma = np.float64(maxsigma_init)
             if failreason != self.FML_NOERROR:
                 maskval = np.uint16(0)
+            else:
+                maskval = np.uint16(1)
 
         if self.debug or self.displayplots:
             print(

rapidtide/io.py

@@ -355,7 +355,7 @@ def savemaplist(
             themap,
             internalspaceshape,
             validvoxels,
-            outmaparray,
+            outmaparray.astype(themap.dtype),
             debug=False,
         )
 
@@ -1160,13 +1160,15 @@ def getslicetimesfromfile(slicetimename):
             for idx, thetime in enumerate(slicetimelist):
                 slicetimes[idx] = float(thetime)
             normalizedtotr = False
+            fileisbidsjson = True
         except KeyError:
             print(slicetimename, "is not a valid BIDS sidecar file")
             sys.exit()
     else:
         slicetimes = readvec(slicetimename)
         normalizedtotr = True
-    return slicetimes, normalizedtotr
+        fileisbidsjson = False
+    return slicetimes, normalizedtotr, fileisbidsjson
 
 
 def readbidssidecar(inputfilename):

rapidtide/simfuncfit.py

@@ -43,7 +43,7 @@ def onesimfuncfit(
 ):
     if initiallag is not None:
         thefitter.setguess(True, maxguess=initiallag)
-        widthmax = despeckle_thresh
+        thefitter.setrange(-despeckle_thresh/2.0, despeckle_thresh/2.0)
     else:
         thefitter.setguess(False)
 

rapidtide/tests/test_filter.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_fullrunhappy_v2.py

@@ -31,7 +31,7 @@ def test_fullrunhappy_v2(debug=False, displayplots=False):
         os.path.join(get_examples_path(), "sub-HAPPYTEST.nii.gz"),
         os.path.join(get_examples_path(), "sub-HAPPYTEST.json"),
         os.path.join(get_test_temp_path(), "happyout2"),
-        "--estmask",
+        "--estweights",
         os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),
         "--projmask",
         os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),

rapidtide/tests/test_fullrunhappy_v3.py

@@ -31,7 +31,7 @@ def test_fullrunhappy_v3(debug=False, displayplots=False):
         os.path.join(get_examples_path(), "sub-HAPPYTEST.nii.gz"),
         os.path.join(get_examples_path(), "sub-HAPPYTEST.json"),
         os.path.join(get_test_temp_path(), "happyout3"),
-        "--estmask",
+        "--estweights",
         os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),
         "--projmask",
         os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),

rapidtide/tests/test_fullrunhappy_v4.py

@@ -31,7 +31,7 @@ def test_fullrunhappy_v4(debug=False, displayplots=False):
         os.path.join(get_examples_path(), "sub-HAPPYTEST.nii.gz"),
         os.path.join(get_examples_path(), "sub-HAPPYTEST.json"),
         os.path.join(get_test_temp_path(), "happyout4"),
-        "--estmask",
+        "--estweights",
         os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),
         "--projmask",
         os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),
@@ -39,6 +39,8 @@ def test_fullrunhappy_v4(debug=False, displayplots=False):
         "-1",
         "--model",
         "model_revised",
+        "--motionfile",
+        os.path.join(get_examples_path(), "sub-HAPPYTEST_mcf.par"),
     ]
     happy_workflow.happy_main(happy_parser.process_args(inputargs=inputargs))
 

rapidtide/tests/test_fullrunhappy_v5.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+#   Copyright 2016-2024 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.workflows.happy as happy_workflow
+import rapidtide.workflows.happy_parser as happy_parser
+from rapidtide.tests.utils import get_examples_path, get_test_temp_path
+
+
+def test_fullrunhappy_v4(debug=False, displayplots=False):
+    # run happy
+    inputargs = [
+        os.path.join(get_examples_path(), "sub-HAPPYTEST.nii.gz"),
+        os.path.join(get_examples_path(), "sub-HAPPYTEST.json"),
+        os.path.join(get_test_temp_path(), "happyout5"),
+        "--model",
+        "model_revised",
+        "--motionfile",
+        os.path.join(get_examples_path(), "sub-HAPPYTEST_mcf.par"),
+        "--nomotderiv",
+        "--nomotorthogonalize",
+        "--motfiltorder",
+        "2",
+        "--numskip",
+        "5",
+        "--motskip",
+        "5",
+        "--motionhp",
+        "0.01",
+        "--motionlp",
+        "2.0",
+    ]
+    happy_workflow.happy_main(happy_parser.process_args(inputargs=inputargs))
+
+
+if __name__ == "__main__":
+    mpl.use("TkAgg")
+    test_fullrunhappy_v4(debug=True, displayplots=True)