rapidtide 3.0a6__py3-none-any.whl → 3.0a7__py3-none-any.whl

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/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

@@ -145,7 +145,7 @@ 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 +182,7 @@ 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 +196,22 @@ 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 +219,7 @@ 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 +1241,51 @@ 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/io.py

@@ -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/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)

rapidtide/util.py

@@ -26,8 +26,7 @@ import subprocess
 import sys
 import time
 from datetime import datetime
-from multiprocessing import RawArray, shared_memory
-from os.path import split
+from multiprocessing import shared_memory
 
 import matplotlib.pyplot as plt
 import numpy as np

rapidtide/workflows/happy.py

@@ -236,8 +236,10 @@ def happy_main(argparsingfunc):
     # filter out motion regressors here
     if args.motionfilename is not None:
         timings.append(["Motion filtering start", time.time(), None, None])
+        motiondict = tide_io.readmotion(args.motionfilename, tr=tr)
         confoundregressors, confoundregressorlabels = tide_fit.calcexpandedregressors(
-            tide_io.readconfounds(args.motionfilename),
+            motiondict,
+            labels=["xtrans", "ytrans", "ztrans", "xrot", "yrot", "zrot"],
             deriv=args.motfilt_deriv,
             order=args.motfilt_order,
         )
@@ -284,10 +286,21 @@ def happy_main(argparsingfunc):
             timings.append(["Motion filtered data saved", time.time(), numspatiallocs, "voxels"])
 
     # get slice times
-    slicetimes, normalizedtotr = tide_io.getslicetimesfromfile(slicetimename)
+    slicetimes, normalizedtotr, fileisbidsjson = tide_io.getslicetimesfromfile(slicetimename)
     if normalizedtotr and not args.slicetimesareinseconds:
         slicetimes *= tr
-
+    if args.teoffset is not None:
+        teoffset = float(args.teoffset)
+    else:
+        if fileisbidsjson:
+            jsoninfodict = tide_io.readdictfromjson(slicetimename)
+            try:
+                teoffset = jsoninfodict["EchoTime"]
+            except KeyError:
+                teoffset = 0.0
+        else:
+            teoffset = 0.0
+    infodict["teoffset"] = teoffset
     timings.append(["Slice times determined", time.time(), None, None])
 
     # normalize the input data
@@ -317,30 +330,32 @@ def happy_main(argparsingfunc):
     tide_io.savetonifti(mads.reshape((xsize, ysize, numslices)), theheader, madsfilename)
 
     # read in estimation mask if present. Otherwise, otherwise use intensity mask.
-    infodict["estmaskname"] = args.estmaskname
+    infodict["estweightsname"] = args.estweightsname
     if args.debug:
-        print(args.estmaskname)
-    if args.estmaskname is not None:
-        tide_util.logmem("before reading in estmask")
-        estmask = happy_support.readextmask(
-            args.estmaskname, nim_hdr, xsize, ysize, numslices, args.debug
+        print(args.estweightsname)
+    if args.estweightsname is not None:
+        tide_util.logmem("before reading in estweights")
+        estweights = happy_support.readextmask(
+            args.estweightsname, nim_hdr, xsize, ysize, numslices, args.debug
         )
-        # * np.float64(mask_byslice)
-        estmask_byslice = estmask.reshape(xsize * ysize, numslices)
-        print("using estmask from file", args.estmaskname)
+        estweights_byslice = estweights.reshape(xsize * ysize, numslices)
+        print("using estweights from file", args.estweightsname)
         numpasses = 1
     else:
         # just fall back to the intensity mask
-        estmask_byslice = mask_byslice.astype("float64")
+        estweights_byslice = mask_byslice.astype("float64")
         numpasses = 2
         print("Not using separate estimation mask - doing initial estimate using intensity mask")
-    if args.fliparteries:
-        # add another pass to refine the waveform after getting the new appflips
+
+    # add another pass to refine the waveform after getting the new appflips
+    if args.fliparteries or args.doaliasedcorrelation:
         numpasses += 1
-        print("Adding a pass to regenerate cardiac waveform using better appflips")
+        print("Adding a pass to regenerate cardiac waveform using better vessel specification")
 
     # output mask size
-    print(f"estmask has {len(np.where(estmask_byslice[:, :] > 0)[0])} voxels above threshold.")
+    print(
+        f"estweights has {len(np.where(estweights_byslice[:, :] > 0)[0])} voxels above threshold."
+    )
 
     infodict["numpasses"] = numpasses
 
@@ -369,7 +384,7 @@ def happy_main(argparsingfunc):
             slicenorms,
         ) = happy_support.cardiacfromimage(
             normdata_byslice,
-            estmask_byslice,
+            estweights_byslice,
             numslices,
             timepoints,
             tr,
@@ -396,43 +411,15 @@ def happy_main(argparsingfunc):
             ]
         )
         infodict["cardfromfmri_normfac"] = cardfromfmri_normfac
-        slicetimeaxis = np.linspace(
-            0.0, tr * timepoints, num=(timepoints * numsteps), endpoint=False
+        slicetimeaxis = (
+            np.linspace(0.0, tr * timepoints, num=(timepoints * numsteps), endpoint=False)
+            + teoffset
         )
         if (thispass == 0) and args.doupsampling:
-            # allocate the upsampled image
-            upsampleimage = np.zeros((xsize, ysize, numslices, numsteps * timepoints), dtype=float)
-            upsampleimage_byslice = upsampleimage.reshape(
-                xsize * ysize, numslices, numsteps * timepoints
+            happy_support.upsampleimage(
+                input_data, nim_hdr, numsteps, sliceoffsets, slicesamplerate, outputroot
             )
-
-            # drop in the raw data
-            for theslice in range(numslices):
-                upsampleimage[
-                    :, :, theslice, sliceoffsets[theslice] : timepoints * numsteps : numsteps
-                ] = fmri_data.reshape((xsize, ysize, numslices, timepoints))[:, :, theslice, :]
-
-            # interpolate along the slice direction
-            for thestep in range(numsteps):
-                print(f"interpolating step {thestep}")
-                thesrclocs = np.where(sliceoffsets == thestep)[0]
-                print(f"sourcelocs: {thesrclocs}")
-                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):
-                    print(f"timepoint: {thetimepoint}")
-                    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(nim_hdr)
-            theheader["dim"][4] = timepoints * numsteps
-            theheader["pixdim"][4] = 1.0 / slicesamplerate
-            tide_io.savetonifti(upsampleimage, theheader, outputroot + "_upsampled")
+            sys.exit(0)
 
         if thispass == numpasses - 1:
             tide_io.writebidstsv(
@@ -1171,20 +1158,12 @@ def happy_main(argparsingfunc):
         # construct the destination arrays
         tide_util.logmem("before making destination arrays")
         app = np.zeros((xsize, ysize, numslices, args.destpoints), dtype=np.float64)
-        app_byslice = app.reshape((xsize * ysize, numslices, args.destpoints))
         cine = np.zeros((xsize, ysize, numslices, args.destpoints), dtype=np.float64)
-        cine_byslice = cine.reshape((xsize * ysize, numslices, args.destpoints))
         rawapp = np.zeros((xsize, ysize, numslices, args.destpoints), dtype=np.float64)
-        rawapp_byslice = rawapp.reshape((xsize * ysize, numslices, args.destpoints))
         corrected_rawapp = np.zeros((xsize, ysize, numslices, args.destpoints), dtype=np.float64)
-        corrected_rawapp_byslice = rawapp.reshape((xsize * ysize, numslices, args.destpoints))
         normapp = np.zeros((xsize, ysize, numslices, args.destpoints), dtype=np.float64)
-        normapp_byslice = normapp.reshape((xsize * ysize, numslices, args.destpoints))
         weights = np.zeros((xsize, ysize, numslices, args.destpoints), dtype=np.float64)
-        weight_byslice = weights.reshape((xsize * ysize, numslices, args.destpoints))
         derivatives = np.zeros((xsize, ysize, numslices, 4), dtype=np.float64)
-        derivatives_byslice = derivatives.reshape((xsize * ysize, numslices, 4))
-
         timings.append(["Output arrays allocated" + passstring, time.time(), None, None])
 
         if args.centric:
@@ -1198,6 +1177,42 @@ def happy_main(argparsingfunc):
         # now do the phase projection
         #
         #
+        """app, rawapp, corrected_rawapp, normapp, weights, cine, derivatives = (
+            happy_support.phaseproject(
+                demeandata,
+                means,
+                args.destpoints,
+                numsteps,
+                timings,
+                cardfromfmri_sliceres,
+                instantaneous_cardiacphase,
+                thispass,
+                numpasses,
+                args,
+                outputroot,
+                slicesamplerate,
+                pleth_sliceres,
+                mrsamplerate,
+                projmask_byslice,
+                cardphasevals,
+                thetimes,
+                centric=True,
+                passstring="",
+                badpointlist=None,
+                congridbins=3.0,
+                gridkernel="kaiser",
+            )
+        )"""
+        app_byslice = app.reshape((xsize * ysize, numslices, args.destpoints))
+        rawapp_byslice = rawapp.reshape((xsize * ysize, numslices, args.destpoints))
+        corrected_rawapp_byslice = corrected_rawapp.reshape(
+            (xsize * ysize, numslices, args.destpoints)
+        )
+        normapp_byslice = normapp.reshape((xsize * ysize, numslices, args.destpoints))
+        weights_byslice = weights.reshape((xsize * ysize, numslices, args.destpoints))
+        cine_byslice = cine.reshape((xsize * ysize, numslices, args.destpoints))
+        derivatives_byslice = derivatives.reshape((xsize * ysize, numslices, 4))
+
         demeandata_byslice = demeandata.reshape((xsize * ysize, numslices, timepoints))
         means_byslice = means.reshape((xsize * ysize, numslices))
 
@@ -1216,7 +1231,7 @@ def happy_main(argparsingfunc):
             procpoints = np.where(censorpoints < 1)[0]
 
         # do phase averaging
-        app_bypoint, weight_bypoint = happy_support.cardiaccycleaverage(
+        app_bypoint, weights_bypoint = happy_support.cardiaccycleaverage(
             instantaneous_cardiacphase,
             outphases,
             cardfromfmri_sliceres,
@@ -1238,7 +1253,7 @@ def happy_main(argparsingfunc):
             )
             tide_io.writebidstsv(
                 outputroot + "_desc-cardiaccycleweightfromfmri_timeseries",
-                weight_bypoint,
+                weights_bypoint,
                 1.0 / (outphases[1] - outphases[0]),
                 starttime=outphases[0],
                 columns=["cardiaccycleweightfromfmri"],
@@ -1295,7 +1310,7 @@ def happy_main(argparsingfunc):
         outtimes = np.linspace(
             0.0, maxtime, num=int(maxtime / args.pulsereconstepsize), endpoint=False
         )
-        atp_bypoint, atpweight_bypoint = happy_support.cardiaccycleaverage(
+        atp_bypoint, atpweights_bypoint = happy_support.cardiaccycleaverage(
             instantaneous_cardiactime,
             outtimes,
             cardfromfmri_sliceres,
@@ -1326,13 +1341,14 @@ def happy_main(argparsingfunc):
         appsmoothingfilter.setfreqs(0.0, 0.0, phaseFc, phaseFc)
 
         # setup for aliased correlation if we're going to do it
-        if args.doaliasedcorrelation and (thispass == numpasses - 1):
+        if args.doaliasedcorrelation:
             if args.cardiacfilename and False:
                 signal_sliceres = pleth_sliceres
-                # signal_stdres = pleth_stdres
             else:
                 signal_sliceres = cardfromfmri_sliceres
-                # signal_stdres = dlfilteredcard_stdres
+
+            # zero out bad points
+            signal_sliceres *= 1.0 - badpointlist
 
             theAliasedCorrelator = tide_corr.AliasedCorrelator(
                 signal_sliceres,
@@ -1345,16 +1361,21 @@ def happy_main(argparsingfunc):
             )
             correndloc = tide_util.valtoindex(thealiasedcorrx, args.aliasedcorrelationwidth / 2.0)
             aliasedcorrelationpts = correndloc - corrstartloc + 1
-            thecorrfunc = np.zeros(
-                (xsize, ysize, numslices, aliasedcorrelationpts), dtype=np.float64
-            )
-            thecorrfunc_byslice = thecorrfunc.reshape(
-                (xsize * ysize, numslices, aliasedcorrelationpts)
-            )
-            wavedelay = np.zeros((xsize, ysize, numslices), dtype=np.float64)
-            wavedelay_byslice = wavedelay.reshape((xsize * ysize, numslices))
-            waveamp = np.zeros((xsize, ysize, numslices), dtype=np.float64)
-            waveamp_byslice = waveamp.reshape((xsize * ysize, numslices))
+            if thispass == 0:
+                thecorrfunc = np.zeros(
+                    (xsize, ysize, numslices, aliasedcorrelationpts), dtype=np.float64
+                )
+                thecorrfunc_byslice = thecorrfunc.reshape(
+                    (xsize * ysize, numslices, aliasedcorrelationpts)
+                )
+                wavedelay = np.zeros((xsize, ysize, numslices), dtype=np.float64)
+                wavedelay_byslice = wavedelay.reshape((xsize * ysize, numslices))
+                waveamp = np.zeros((xsize, ysize, numslices), dtype=np.float64)
+                waveamp_byslice = waveamp.reshape((xsize * ysize, numslices))
+            else:
+                thecorrfunc *= 0.0
+                wavedelay *= 0.0
+                waveamp *= 0.0
 
         # now project the data
         fmri_data_byslice = input_data.byslice()
@@ -1381,20 +1402,21 @@ def happy_main(argparsingfunc):
                         cyclic=True,
                     )
                     for i in range(len(theindices)):
-                        weight_byslice[validlocs, theslice, theindices[i]] += theweights[i]
+                        weights_byslice[validlocs, theslice, theindices[i]] += theweights[i]
                         # rawapp_byslice[validlocs, theslice, theindices[i]] += (
                         #    theweights[i] * filteredmr
                         # )
                         rawapp_byslice[validlocs, theslice, theindices[i]] += filteredmr
                         cine_byslice[validlocs, theslice, theindices[i]] += theweights[i] * cinemr
                 for d in range(args.destpoints):
-                    if weight_byslice[validlocs[0], theslice, d] == 0.0:
-                        weight_byslice[validlocs, theslice, d] = 1.0
+                    if weights_byslice[validlocs[0], theslice, d] == 0.0:
+                        weights_byslice[validlocs, theslice, d] = 1.0
                 rawapp_byslice[validlocs, theslice, :] = np.nan_to_num(
-                    rawapp_byslice[validlocs, theslice, :] / weight_byslice[validlocs, theslice, :]
+                    rawapp_byslice[validlocs, theslice, :]
+                    / weights_byslice[validlocs, theslice, :]
                 )
                 cine_byslice[validlocs, theslice, :] = np.nan_to_num(
-                    cine_byslice[validlocs, theslice, :] / weight_byslice[validlocs, theslice, :]
+                    cine_byslice[validlocs, theslice, :] / weights_byslice[validlocs, theslice, :]
                 )
             else:
                 rawapp_byslice[:, theslice, :] = 0.0
@@ -1419,7 +1441,7 @@ def happy_main(argparsingfunc):
                 corrected_rawapp_byslice[validlocs, theslice, :] = (
                     rawapp_byslice[validlocs, theslice, :] - timecoursemean
                 ) * appflips_byslice[validlocs, theslice, None] + timecoursemean
-                if args.doaliasedcorrelation and (thispass == numpasses - 1):
+                if args.doaliasedcorrelation and (thispass > 0):
                     for theloc in validlocs:
                         thecorrfunc_byslice[theloc, theslice, :] = theAliasedCorrelator.apply(
                             -appflips_byslice[theloc, theslice]
@@ -1430,14 +1452,14 @@ def happy_main(argparsingfunc):
                         wavedelay_byslice[theloc, theslice] = (
                             thealiasedcorrx[corrstartloc : correndloc + 1]
                         )[maxloc]
-                        waveamp_byslice[theloc, theslice] = thecorrfunc_byslice[
-                            theloc, theslice, maxloc
-                        ]
+                        waveamp_byslice[theloc, theslice] = np.fabs(
+                            thecorrfunc_byslice[theloc, theslice, maxloc]
+                        )
             else:
                 corrected_rawapp_byslice[validlocs, theslice, :] = rawapp_byslice[
                     validlocs, theslice, :
                 ]
-                if args.doaliasedcorrelation and (thispass == numpasses - 1):
+                if args.doaliasedcorrelation and (thispass > 0):
                     for theloc in validlocs:
                         thecorrfunc_byslice[theloc, theslice, :] = theAliasedCorrelator.apply(
                             -demeandata_byslice[theloc, theslice, :],
@@ -1447,9 +1469,9 @@ def happy_main(argparsingfunc):
                         wavedelay_byslice[theloc, theslice] = (
                             thealiasedcorrx[corrstartloc : correndloc + 1]
                         )[maxloc]
-                        waveamp_byslice[theloc, theslice] = thecorrfunc_byslice[
-                            theloc, theslice, maxloc
-                        ]
+                        waveamp_byslice[theloc, theslice] = np.fabs(
+                            thecorrfunc_byslice[theloc, theslice, maxloc]
+                        )
             timecoursemin = np.min(
                 corrected_rawapp_byslice[validlocs, theslice, :], axis=1
             ).reshape((-1, 1))
@@ -1622,8 +1644,18 @@ def happy_main(argparsingfunc):
                 tide_io.savetonifti(veins, theheader, veinmapfilename)
         timings.append(["Masks saved" + passstring, time.time(), None, None])
 
+        # save the mask we used for this pass
+        tide_io.savetonifti(
+            estweights_byslice.reshape((xsize, ysize, numslices)),
+            theheader,
+            f"{outputroot}_desc-estweightspass{thispass}_map",
+        )
+
         # now get ready to start again with a new mask
-        estmask_byslice = vesselmask.reshape((xsize * ysize, numslices)) + 0
+        if args.doaliasedcorrelation and thispass > 0:
+            estweights_byslice = waveamp_byslice * vesselmask.reshape((xsize * ysize, numslices))
+        else:
+            estweights_byslice = vesselmask.reshape((xsize * ysize, numslices)) + 0
 
     # save a vessel image
     if args.unnormvesselmap:

rapidtide/workflows/happy_parser.py

@@ -17,13 +17,14 @@
 #
 #
 import argparse
-import sys
 
 import numpy as np
 
 import rapidtide.io as tide_io
 import rapidtide.workflows.parser_funcs as pf
 
+DEFAULT_ALIASEDCORRELATIONWIDTH = 5.0
+
 
 def _get_parser():
     """
@@ -207,10 +208,10 @@ def _get_parser():
     # Cardiac estimation tuning
     cardiac_est_tuning = parser.add_argument_group("Cardiac estimation tuning")
     cardiac_est_tuning.add_argument(
-        "--estmask",
-        dest="estmaskname",
+        "--estweights",
+        dest="estweightsname",
         action="store",
-        metavar="MASKNAME",
+        metavar="WEIGHTSNAME",
         help=(
             "Generation of cardiac waveform from data will be restricted to "
             "voxels in MASKNAME and weighted by the mask intensity.  If this is "
@@ -292,6 +293,15 @@ def _get_parser():
         ),
         default=False,
     )
+    cardiac_est_tuning.add_argument(
+        "--teoffset",
+        dest="teoffset",
+        action="store",
+        metavar="TE",
+        type=lambda x: pf.is_float(parser, x),
+        help="Specify the echo time in seconds.  This is used when combining multiecho data.  Default is 0. ",
+        default=None,
+    )
 
     # External cardiac waveform options
     external_cardiac_opts = parser.add_argument_group("External cardiac waveform options")
@@ -538,6 +548,15 @@ def _get_parser():
         help="Attempt to calculate absolute delay using an aliased correlation (experimental).",
         default=False,
     )
+    misc_opts.add_argument(
+        "--aliasedcorrelationwidth",
+        dest="aliasedcorrelationwidth",
+        metavar="WIDTH",
+        action="store",
+        type=lambda x: pf.is_float(parser, x),
+        help=f"Width of the aliased correlation calculation (default is {DEFAULT_ALIASEDCORRELATIONWIDTH}). ",
+        default=DEFAULT_ALIASEDCORRELATIONWIDTH,
+    )
     misc_opts.add_argument(
         "--upsample",
         dest="doupsampling",
@@ -666,23 +685,7 @@ def process_args(inputargs=None):
     """
     Compile arguments for rapidtide workflow.
     """
-    if inputargs is None:
-        print("processing command line arguments")
-        # write out the command used
-        try:
-            args = _get_parser().parse_args()
-            argstowrite = sys.argv
-        except SystemExit:
-            _get_parser().print_help()
-            raise
-    else:
-        print("processing passed argument list:")
-        try:
-            args = _get_parser().parse_args(inputargs)
-            argstowrite = inputargs
-        except SystemExit:
-            print("Use --help option for detailed information on options.")
-            raise
+    args, argstowrite = pf.setargs(_get_parser, inputargs=inputargs)
 
     # save the raw and formatted command lines
     args.commandline = " ".join(argstowrite)
@@ -723,7 +726,6 @@ def process_args(inputargs=None):
     args.upsamplefac = 100
     args.centric = True
     args.pulsereconstepsize = 0.01
-    args.aliasedcorrelationwidth = 3.0
     args.unnormvesselmap = True
     args.histlen = 100
     args.softvesselfrac = 0.4

rapidtide/workflows/simdata.py

@@ -308,7 +308,9 @@ def simdata(args):
         _get_parser().print_help()
         sys.exit()
 
-    sliceoffsettimes, normalizedtotr = tide_io.getslicetimesfromfile(args.slicetimefile)
+    sliceoffsettimes, normalizedtotr, fileisjson = tide_io.getslicetimesfromfile(
+        args.slicetimefile
+    )
 
     fmritr, numtrs = tide_io.fmritimeinfo(args.fmrifilename)
     if normalizedtotr:

{rapidtide-3.0a6.dist-info → rapidtide-3.0a7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: rapidtide
-Version: 3.0a6
+Version: 3.0a7
 Summary: Tools for performing correlation analysis on fMRI data.
 Author: Taylor Salo, Daniel M. Drucker, Ph.D., Jeffrey N Stout, Yaroslav O. Halchenko, Derek Monroe
 Author-email: "Blaise deB. Frederick" <blaise.frederick@gmail.com>
@@ -38,10 +38,10 @@ Requires-Dist: pyqt6
 Requires-Dist: requests
 Requires-Dist: statsmodels
 Requires-Dist: pywavelets
-Requires-Dist: tomlkit
 Requires-Dist: tensorflow>=2.10.0
 Requires-Dist: tf-keras
 Requires-Dist: tqdm
+Requires-Dist: versioneer
 Provides-Extra: tests
 Requires-Dist: codecov; extra == "tests"
 Requires-Dist: coverage; extra == "tests"
@@ -57,6 +57,7 @@ Requires-Dist: sphinx-gallery; extra == "doc"
 Requires-Dist: myst-parser; extra == "doc"
 Requires-Dist: numpydoc; extra == "doc"
 Requires-Dist: sphinxcontrib-bibtex; extra == "doc"
+Requires-Dist: tomlkit; extra == "doc"
 
 The rapidtide package
 =====================

{rapidtide-3.0a6.dist-info → rapidtide-3.0a7.dist-info}/RECORD

@@ -15,16 +15,16 @@ rapidtide/calcandfitcorrpairs.py,sha256=UmCp9eSU--HCYd7frdO9ctnMeDK32D1Eb53b1hdz
 rapidtide/calccoherence.py,sha256=SjSWcqbyATKu5Hya5LgRCTfq2w9l7G9L_kZbol802sk,4512
 rapidtide/calcnullsimfunc.py,sha256=_L5Gxr1CI0GKmGmEjHzrYNufAzDchDsruYCzboSgw3s,7150
 rapidtide/calcsimfunc.py,sha256=Jw_589HsH4ErYzI54jPezSRzBW7_xjxc71sstDbalng,5198
-rapidtide/correlate.py,sha256=FNkFEFaZsW13kG9O1LklBXD-t1G3WD81co5BP13lt9w,36186
+rapidtide/correlate.py,sha256=iZzJa2QV7Le1_Vr9l8Zj2QS0_ZV-EXKtWkOAcICI8ec,36266
 rapidtide/dlfilter.py,sha256=8hmOCyGSMQqT2p_rAwOrvs2FaafqbQBEpvFkHAKlxew,55505
 rapidtide/externaltools.py,sha256=YhxuSn5z3v5E7PzB07yftXJGw95rs95Nmxbq4Wo2fhU,3965
 rapidtide/fMRIData_class.py,sha256=TrR-MyIBEzbUgUq8oQVmjkddnrhxeN_rHlX-En0p4Ao,5102
 rapidtide/filter.py,sha256=Ci62Vcw_qKX--Hzut9kb6XmBLjEe773JyGkGJtnH2g4,71773
 rapidtide/fit.py,sha256=lAzLc19VAhq3QJFSbaCbAWCNDefxSCsJfjW5WLHABMk,67130
 rapidtide/glmpass.py,sha256=Krdgj-pP2Vtelr6qYtMgh2u2C-9thJGwp2FKiEzo-7M,15681
-rapidtide/happy_supportfuncs.py,sha256=yYVmEmNYNjp3WluNWagVzdLNGSNgKfekgeL2zbkMH8I,44847
+rapidtide/happy_supportfuncs.py,sha256=z1Tw6JEgffCQZCubgHYXDM9cZJjA5kZ-H_jZ0c7Wvnw,47032
 rapidtide/helper_classes.py,sha256=NBCmrxEqui-SnaKnJBISC3sJUJwZL45W5dTH9zDmKHY,50998
-rapidtide/io.py,sha256=TFOFsxqo-jor23T5aPy5dYAh-pHh_1lYTTGCIp7jn30,74319
+rapidtide/io.py,sha256=CCb0IVGKfW-z2uaFyfVB8nDwN9JRVj62u1fZeXmrle8,74400
 rapidtide/makelaggedtcs.py,sha256=GsJ3svPSRJIHzJ9F5ZpT0eW3k6rIUCGXgq4o-sK4R-E,3889
 rapidtide/maskutil.py,sha256=noqFZzAvyAy0ZzEa1nmEIGzWA0zaPoNSIP3ck1cFKcE,6089
 rapidtide/miscmath.py,sha256=Wj3GXNkXbvGlsdxYGUMTZ3H5a3a1uhfTWZV73XtUYx4,14044
@@ -44,7 +44,7 @@ rapidtide/tidepoolTemplate_alt.ui,sha256=ruxCjdY3GQtLRYunqSyN9t2ye551fdTM3ZNLDDo
 rapidtide/tidepoolTemplate_alt_qt6.py,sha256=T4ZKrERqhT3OFWehiOUk-pfNYqKzecEfuYRofwSOoHg,52104
 rapidtide/tidepoolTemplate_qt6.py,sha256=NtwaX-sAnZC9fPPNVeL1tt6t_OYVorsTx_iBY93taS4,46333
 rapidtide/transformerdlfilter.py,sha256=oODhn4CVtlT7ua72ADWw0LYmkJznDfH8gB3YmlY_w00,4551
-rapidtide/util.py,sha256=ZKTlsUlSyUHow9ADv-TkFAowKouR6799BX7KJdnQv3Q,35962
+rapidtide/util.py,sha256=Su9SUUR3_KVUzLyzTfCzXO9mDbdO-AD99MlIrn_YPoA,35926
 rapidtide/wiener.py,sha256=ls3jJvuTRlyJl1qL8SxYdct1vZD3yQ9Mhp8hb2lpx1E,4128
 rapidtide/wiener2.py,sha256=CSsNRqeSCrCJgD-FqOJ8RVoGKbdb-PW8e0cQfD3QyfY,3746
 rapidtide/data/examples/src/installtestdata,sha256=ummRjxxmArheODnzRHwb6DL9Sxhay6ulJpETEMVy-fs,205
@@ -64,7 +64,7 @@ rapidtide/data/examples/src/testfmridocker,sha256=jjL7bK29rrcog6uO9BtvcyAU3Sv8_5
 rapidtide/data/examples/src/testfrozen,sha256=K3qUWDRKPPiCXRgIFuPdwUUjUTzf4QBW8UUhR75NzDM,283
 rapidtide/data/examples/src/testfuncs,sha256=QmVJP8vjr-HqKCAaIz7McdADVZru6Nvwq16h5KPs9ek,1551
 rapidtide/data/examples/src/testglmfilt,sha256=LD2cTB-7yyCc31jAr8UtYksf-Cn-YLC3ScnV3olvpFE,3333
-rapidtide/data/examples/src/testhappy,sha256=4x97KdWaHJ_HcSy_0wIPrRMRf-xYmJMKgK3IFnCFehU,1741
+rapidtide/data/examples/src/testhappy,sha256=Qo-hNofuIYOj522PPtqR_5pePTTTyJTaOdAA18G3bkg,1817
 rapidtide/data/examples/src/testlinfit,sha256=oPnkHJ6lcwsuJhnSMMK7Gx3DHSCf6JK7CIYuIMHbyNA,471
 rapidtide/data/examples/src/testlocalflow,sha256=hEwstisbWVuALr_29fBJ2nHETKkEF_9qK8wJ4kzuiJk,596
 rapidtide/data/examples/src/testnoiseamp,sha256=ZRu3GstBhdnwZmDF7ExZynOXFFMElWiZuod8LbUKa-I,612
@@ -210,12 +210,13 @@ rapidtide/tests/test_corrpass.py,sha256=eBNw1KBvjo9WgorR-7aPga3WIeQxckTGjPwv-kn6
 rapidtide/tests/test_delayestimation.py,sha256=2AeQcT_cFvvNvH0R-K9WNDDp66S-UjybfAqdfG0REYU,13460
 rapidtide/tests/test_doresample.py,sha256=ILQxH6UXtHZ9OwgTpbZE_bek_QKYGmmA6D70r6NqAoc,2716
 rapidtide/tests/test_fastresampler.py,sha256=UOWk2_GXEp0xT_gOkVnvg7yuQbbkZGHdljB6zh28OJQ,3763
-rapidtide/tests/test_filter.py,sha256=gVo9I_i7pH0waMAUkhNXrFmBT3YRK4G_w-8y_B43aqY,10891
+rapidtide/tests/test_filter.py,sha256=_xhk3rbYFtuKgrDdgrrrlITtmQhOUUi5EhFcnxVUioA,10891
 rapidtide/tests/test_findmaxlag.py,sha256=x9mKQ8TmWW4jq8CrlfrX8zwO3n4pYa7aPgF3F1e0aPc,11551
 rapidtide/tests/test_fullrunhappy_v1.py,sha256=XuK90R4Ef7PIvJfyyXHqL__SvRjJUHtHX8PZYuJjEKo,1502
-rapidtide/tests/test_fullrunhappy_v2.py,sha256=4S61nuz_S-chlI8zScby3R0RpJdoFcIS0eFH9Ed5LU4,1932
-rapidtide/tests/test_fullrunhappy_v3.py,sha256=JrfMW4gqSxd01mnvKuImMToyhzqQl1R_mtQpLG67EVw,1740
-rapidtide/tests/test_fullrunhappy_v4.py,sha256=QaWkK8bZppz9i97g31K25Yg0HKnsdnCWbfzCTzsbCRU,1626
+rapidtide/tests/test_fullrunhappy_v2.py,sha256=9_1sjtTP-4YVv-d86iL0hkm8T8ODQ1Ckumu-iFu2W8s,1935
+rapidtide/tests/test_fullrunhappy_v3.py,sha256=sEWV-Qf_13gJ9BnUmgIu-JtMAh1Jp0Qn8EhTEBU4YmU,1743
+rapidtide/tests/test_fullrunhappy_v4.py,sha256=_8ax0oEEdaSSRa-N-lGquWP4MfLj6DR-xy-NUZ3kuhM,1721
+rapidtide/tests/test_fullrunhappy_v5.py,sha256=1otOjGN7PADurvB3PUqHq_FxCpd5vr3Q1KD8FrPGXlU,1721
 rapidtide/tests/test_fullrunrapidtide_v1.py,sha256=jO2PyPTvxfIYyzydQgxD812DRuzotCTFmnBqShRpa0M,2864
 rapidtide/tests/test_fullrunrapidtide_v2.py,sha256=RsMCrq-A4WzVzQxFnyvuotKCT4ipfyepM1RxGBpmMys,2881
 rapidtide/tests/test_fullrunrapidtide_v3.py,sha256=xdwJJyAzup2Jimidb0y-l2Sw7Kwq2WBL6Tw-BQdyzBg,2223
@@ -281,9 +282,9 @@ rapidtide/workflows/fixtr.py,sha256=UuePpVA01YmU4sGiiRcBzMZG1jfNM8TA6xkFyBJdMc8,
 rapidtide/workflows/glmfilt.py,sha256=ys37_Xpo-LUaOzif9t2BSH-AJlxWkYtYm54REdxFsjg,9995
 rapidtide/workflows/glmfrommaps.py,sha256=bajR4JBaLaA6REPwBd9S421-0G3ozgaD-gHERxLbEEU,6006
 rapidtide/workflows/gmscalc.py,sha256=Vz5GnK2WM1PXkFkQSV8KFc1kKJoJ0Q4XW8srLKpsAUg,6258
-rapidtide/workflows/happy.py,sha256=trQbCq9S7ET7OEiaJ7jx66g9vJb5NwJBJpZsXAeCCT8,77030
+rapidtide/workflows/happy.py,sha256=znW3IVNjaQVPTUsILYFjOMEawA3o1_zldCNFHmloE8A,77412
 rapidtide/workflows/happy2std.py,sha256=aLr8j7qODB_laLNozmI_txKXqGZsuFZp-De8USEiSWE,8132
-rapidtide/workflows/happy_parser.py,sha256=oMgh-UOFmZjVwvb2pBGLFTz8mZqgB1W6ZD16eKpqesk,25110
+rapidtide/workflows/happy_parser.py,sha256=4wVkuqMvA8YbgsanMMbNppKFbmlHMJyLpjZgJaCQO20,25283
 rapidtide/workflows/histnifti.py,sha256=DtRWkN43GPIuXRCgvCvLrIoeVAjo0AIk1qmrBRBQjJI,11197
 rapidtide/workflows/histtc.py,sha256=rlTUsiXB1rBv4noNmjKmHajonuhkqSicp98k2JxiPj0,4561
 rapidtide/workflows/localflow.py,sha256=TvdoUdz_1zIn79UsaPWDPCgrRzy_Yp8wHi7ASdVA1XY,23542
@@ -314,7 +315,7 @@ rapidtide/workflows/showstxcorr.py,sha256=GbOvoKCqyTaGl5EMPpNTyejnBb5mUYbsdyV7lR
 rapidtide/workflows/showtc.py,sha256=h2eKhJXn30_lDpiBgWF6TZG60L-WZn931_SSjVZpM_M,18835
 rapidtide/workflows/showxcorrx.py,sha256=-KIv1nqf7knHyxgrEsDvHfhRInDRrdhXGjvWrNJAzmw,31370
 rapidtide/workflows/showxy.py,sha256=4eq1Ft8z9V-JTgjcnhWqGhFKR-dsXTeU0cArJmiWmVg,10532
-rapidtide/workflows/simdata.py,sha256=54Fq95y7-WYnONfWgP7EWZEdRp6NnJSw4cnebD-F3OQ,13894
+rapidtide/workflows/simdata.py,sha256=hd-A8bvmPX1Zn5EX6vYz40s64mYDtWzLRljYN23gcIA,13920
 rapidtide/workflows/spatialfit.py,sha256=AHwXlqxD6FsjpIVGYaF2ONyZ_AJdwuWwFPoiSxfLH20,9136
 rapidtide/workflows/spatialmi.py,sha256=m_gafDOAJOyRjXV-LO9UTckU_07MkdadPGcsKU3fzAw,13407
 rapidtide/workflows/spectrogram.py,sha256=ATe6baNL-Rv6rvV6rCcxcBO2naFu0v4UDJ2hX6T8BrA,6452
@@ -324,9 +325,9 @@ rapidtide/workflows/tcfrom3col.py,sha256=6tV2lGEtXpI4dn_8kcTCVzZxpJzmopuDwpXvOIE
 rapidtide/workflows/tidepool.py,sha256=7_MK2Sx72-MvkCnTh_Cg_jBaJpNnVdDjTLgdoKlpvdY,78516
 rapidtide/workflows/utils.py,sha256=k2m2F1-tWxhcUYvk5geO1yl-c5bKcDX7Jv7ohvJZaOk,5379
 rapidtide/workflows/variabilityizer.py,sha256=yQFDTBcGehxW44R_FQHeeKrTpeYrrh96xcW1uWbPtYo,3167
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