rapidtide 3.0.6__tar.gz → 3.0.7.1__tar.gz

{rapidtide-3.0.6 → rapidtide-3.0.7.1}/CHANGELOG.md

@@ -1,5 +1,21 @@
 # Release history
 
+## Version 3.0.7.1 (6/16/25)
+* (rapidtide) Disabled sLFO filtering by default.  Use ``sLFOfiltmask`` to turn it on.
+* (retroregress) Synced with sLFO filtering changes to rapidtide.
+
+## Version 3.0.7 (6/16/25)
+* (rapidtide) Save the full autocorrelation function of the probe regressor at each pass.
+* (rapidtide) Now save a version of the mean fMRI image prior to filtering
+* (rapidtide) Added the ability to disable masking of sLFO filter. Use ``--nosLFOfiltmask`` to disable.
+* (happy) Implemented multiprocessing for detrending, phase projection, and phase projection smoothing.
+* (happy) Precache convolution gridding kernel outputs to improve repeatability.
+* (happy) Early implementation of Wright's method for finding vessels.
+* (showarbcorr) Fixed some internal issues.
+* (simdata) Many changes to finetune the simulation and make the output more realistic.  Still in progress.
+* (Docker) Turned on provenance and sbom in Docker builds.
+* (package) Accepted several dependabot PRs.
+
 ## Version 3.0.6 (5/21/25)
 * (rapidtide) Made a generic, reusable multiprocessing module and moved many functions over to it.
 * (ccorrica) Samplerate is now set properly if input is a BIDS tsv file.

{rapidtide-3.0.6/rapidtide.egg-info → rapidtide-3.0.7.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rapidtide
-Version: 3.0.6
+Version: 3.0.7.1
 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>

{rapidtide-3.0.6 → rapidtide-3.0.7.1}/rapidtide/RapidtideDataset.py

@@ -903,6 +903,23 @@ class RapidtideDataset:
                 print("using ", self.fileroot + "meanvalue.nii.gz", " as background")
             # allloadedmaps.append('anatomic')
             return True
+        elif os.path.isfile(self.fileroot + "desc-unfiltmean_map.nii.gz"):
+            thepath, thebase = os.path.split(self.fileroot)
+            self.overlays["anatomic"] = Overlay(
+                "anatomic",
+                self.fileroot + "desc-unfiltmean_map.nii.gz",
+                thebase,
+                init_LUT=self.init_LUT,
+                verbose=self.verbose,
+            )
+            if self.verbose > 1:
+                print(
+                    "using ",
+                    self.fileroot + "desc-unfiltmean_map.nii.gz",
+                    " as background",
+                )
+            # allloadedmaps.append('anatomic')
+            return True
         elif os.path.isfile(self.fileroot + "desc-mean_map.nii.gz"):
             thepath, thebase = os.path.split(self.fileroot)
             self.overlays["anatomic"] = Overlay(

{rapidtide-3.0.6 → rapidtide-3.0.7.1}/rapidtide/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-05-21T09:46:09-0400",
+ "date": "2025-06-16T15:12:43-0400",
  "dirty": false,
  "error": null,
- "full-revisionid": "3f58d08c2a84ae41777dc6b9522b0e89da4cdaec",
- "version": "3.0.6"
+ "full-revisionid": "6dead8e554dd0464bdfc65de24889374508f920d",
+ "version": "3.0.7.1"
 }
 '''  # END VERSION_JSON
 

{rapidtide-3.0.6 → rapidtide-3.0.7.1}/rapidtide/correlate.py

@@ -761,18 +761,14 @@ class AliasedCorrelator:
         return corrfunc
 
 
-def arbcorr(
+def matchsamplerates(
     input1,
     Fs1,
     input2,
     Fs2,
-    start1=0.0,
-    start2=0.0,
-    windowfunc="hamming",
     method="univariate",
     debug=False,
 ):
-    """Calculate something."""
     if Fs1 > Fs2:
         corrFs = Fs1
         matchedinput1 = input1
@@ -782,9 +778,32 @@ def arbcorr(
         matchedinput1 = tide_resample.upsample(input1, Fs1, corrFs, method=method, debug=debug)
         matchedinput2 = input2
     else:
-        corrFs = Fs1
+        corrFs = Fs2
         matchedinput1 = input1
         matchedinput2 = input2
+    return matchedinput1, matchedinput2, corrFs
+
+
+def arbcorr(
+    input1,
+    Fs1,
+    input2,
+    Fs2,
+    start1=0.0,
+    start2=0.0,
+    windowfunc="hamming",
+    method="univariate",
+    debug=False,
+):
+    # upsample to the higher frequency of the two
+    matchedinput1, matchedinput2, corrFs = matchsamplerates(
+        input1,
+        Fs1,
+        input2,
+        Fs2,
+        method=method,
+        debug=debug,
+    )
     norm1 = tide_math.corrnormalize(matchedinput1, detrendorder=1, windowfunc=windowfunc)
     norm2 = tide_math.corrnormalize(matchedinput2, detrendorder=1, windowfunc=windowfunc)
     thexcorr_y = signal.fftconvolve(norm1, norm2[::-1], mode="full")

rapidtide-3.0.7.1/rapidtide/data/examples/src/testfmri

@@ -0,0 +1,30 @@
+#!/bin/bash
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --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 \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel more \
+    --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 \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_nosLFOfiltmask

rapidtide-3.0.7.1/rapidtide/data/examples/src/testhappy

@@ -0,0 +1,77 @@
+#!/bin/csh -f
+
+#happy \
+#    sub-HAPPYTEST.nii.gz \
+#    sub-HAPPYTEST.json \
+#    ../dst/happy_vanilla \
+#    --nprocs 1
+
+#happy \
+#    sub-HAPPYTEST.nii.gz \
+#    sub-HAPPYTEST.json \
+#    --mpphaseproject \
+#    ../dst/happy_mpphaseproj \
+#    --nprocs -1
+
+#happy \
+#    sub-HAPPYTEST.nii.gz \
+#    sub-HAPPYTEST.json \
+#    --mpdetrend \
+#    ../dst/happy_mpdetrend \
+#    --nprocs -1
+
+#happy \
+#    sub-HAPPYTEST.nii.gz \
+#    sub-HAPPYTEST.json \
+#    --mpphaseproject \
+#    --mpdetrend \
+#    ../dst/happy_mpdetrend_mpphaseproj \
+#    --nprocs -1
+
+#happy \
+#    sub-HAPPYTEST.nii.gz \
+#    sub-HAPPYTEST.json \
+#    --prefillcongrid \
+#    ../dst/happy_vanilla_prefill \
+#    --nprocs 1
+
+#happy \
+#    sub-HAPPYTEST.nii.gz \
+#    sub-HAPPYTEST.json \
+#    --prefillcongrid \
+#    --mpphaseproject \
+#    ../dst/happy_mpphaseproj_prefill \
+#    --nprocs -1
+
+#happy \
+#    sub-HAPPYTEST.nii.gz \
+#    sub-HAPPYTEST.json \
+#    --prefillcongrid \
+#    --mpdetrend \
+#    ../dst/happy_mpdetrend_prefill \
+#    --nprocs -1
+
+#happy \
+#    sub-HAPPYTEST.nii.gz \
+#    sub-HAPPYTEST.json \
+#    --prefillcongrid \
+#    --mpphaseproject \
+#    --mpdetrend \
+#    ../dst/happy_mpdetrend_mpphaseproj_prefill \
+#    --nprocs -1
+
+#happy \
+    #sub-HAPPYTEST.nii.gz \
+    #sub-HAPPYTEST.json \
+    #--mpphaseproject \
+    #--mpdetrend \
+    #--nocongridcache \
+    #../dst/happy_mpdetrend_mpphaseproj_nocache \
+    #--nprocs -1
+
+happy \
+    sub-HAPPYTEST.nii.gz \
+    sub-HAPPYTEST.json \
+    ../dst/happy_newdefaults \
+    --aliasedcorrelation \
+    --nprocs -1

rapidtide-3.0.7.1/rapidtide/data/examples/src/testsimdata

@@ -0,0 +1,53 @@
+#!/bin/bash
+
+#rapidtide \
+#    --spatialfilt -1 \
+#    --nprocs -1 \
+#    --searchrange -5 20 \
+#    --simcalcrange 50 -1 \
+#    --outputlevel more \
+#    --nofitfilt \
+#    --corrtype linear \
+#    sub-RAPIDTIDETEST.nii.gz \
+#    ../dst/sub-RAPIDTIDETEST
+
+simdata \
+    1.5 \
+    260 \
+    ../dst/sub-RAPIDTIDETEST_desc-unfiltmean_map.nii.gz \
+    ../dst/simulatedfmri_vn05 \
+    --lfopctfile ../dst/sub-RAPIDTIDETEST_desc-maxcorr_map.nii.gz \
+    --lfolagfile ../dst/sub-RAPIDTIDETEST_desc-maxtimerefined_map.nii.gz \
+    --lforegressor ../dst/sub-RAPIDTIDETEST_desc-movingregressor_timeseries.json:pass3 \
+    --voxelnoiselevel 5.0
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel more \
+    --nofitfilt \
+    --corrtype linear \
+    ../dst/simulatedfmri_vn05.nii.gz \
+    ../dst/simrapidtide_vn05
+
+simdata \
+    1.5 \
+    260 \
+    ../dst/sub-RAPIDTIDETEST_desc-unfiltmean_map.nii.gz \
+    ../dst/simulatedfmri_sigfrac \
+    --lfosignalfraction ../dst/sub-RAPIDTIDETEST_desc-lfofilterInbandVarianceChange_map.nii.gz \
+    --lfolagfile ../dst/sub-RAPIDTIDETEST_desc-maxtimerefined_map.nii.gz \
+    --lforegressor ../dst/sub-RAPIDTIDETEST_desc-movingregressor_timeseries.json:pass3 
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel more \
+    --nofitfilt \
+    --corrtype linear \
+    ../dst/simulatedfmri_sigfrac.nii.gz \
+    ../dst/simrapidtide_sigfrac