rapidtide 3.0.6__py3-none-any.whl → 3.0.7__py3-none-any.whl

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/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-05-21T09:46:09-0400",
+ "date": "2025-06-16T13:13:35-0400",
  "dirty": false,
  "error": null,
- "full-revisionid": "3f58d08c2a84ae41777dc6b9522b0e89da4cdaec",
- "version": "3.0.6"
+ "full-revisionid": "9e8ae750c70431c04a50473c749c451e996d490f",
+ "version": "3.0.7"
 }
 '''  # END VERSION_JSON
 

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/data/examples/src/testfmri

@@ -13,3 +13,18 @@ rapidtide \
     --cleanrefined \
     sub-RAPIDTIDETEST.nii.gz \
     ../dst/sub-RAPIDTIDETEST
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel more \
+    --nosLFOfiltmask \
+    --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/data/examples/src/testhappy

@@ -1,81 +1,77 @@
 #!/bin/csh -f
 
 #happy \
-#    ~/Dropbox_PHC/MR_data_2/physioconn/rfMRI_REST1_LR/100206_3T_rfMRI_REST1_LR.nii.gz \
-#    ~/Dropbox_PHC/MR_data_2/physioconn/rfMRI_REST1_LR/slicetimes.txt \
-#    ~/Dropbox_PHC/MR_data_2/physioconn/happytest/happyarm \
-#    --mklthreads -1 \
-#    --infotag tag1 value1 \
-#    --infotag tag2 value2 \
-#    --model model_revised
+#    sub-HAPPYTEST.nii.gz \
+#    sub-HAPPYTEST.json \
+#    ../dst/happy_vanilla \
+#    --nprocs 1
 
 #happy \
-    #sub-HAPPYTEST.nii.gz \
-    #sub-HAPPYTEST.json \
-    #../dst/happy \
-    #--mklthreads 8 \
-    #--model model_revised \
-    #--spatialglm --aliasedcorrelation
-
+#    sub-HAPPYTEST.nii.gz \
+#    sub-HAPPYTEST.json \
+#    --mpphaseproject \
+#    ../dst/happy_mpphaseproj \
+#    --nprocs -1
 
 #happy \
 #    sub-HAPPYTEST.nii.gz \
 #    sub-HAPPYTEST.json \
-#    ../dst/happy_2comp \
-#    --cardiacfile happystdres_bids.tsv:normcardiac_25.0Hz \
-#    --mklthreads 8 \
-#    --hilbertcomponents 2 \
-#    --model model_revised
-#
+#    --mpdetrend \
+#    ../dst/happy_mpdetrend \
+#    --nprocs -1
+
 #happy \
 #    sub-HAPPYTEST.nii.gz \
 #    sub-HAPPYTEST.json \
-#    ../dst/happy_3comp \
-#    --cardiacfile happystdres_bids.tsv:normcardiac_25.0Hz \
-#    --mklthreads 8 \
-#    --hilbertcomponents 3 \
-#    --model model_revised
+#    --mpphaseproject \
+#    --mpdetrend \
+#    ../dst/happy_mpdetrend_mpphaseproj \
+#    --nprocs -1
 
-#happy_legacy \
-    #sub-HAPPYTEST.nii.gz \
-    #sub-HAPPYTEST.json \
-    #../dst/happy_normaltest \
-    #--mklthreads=8 \
-    #--model=model_revised \
-    #--outputbins=40 \
-    #--gridbins=3.5 \
-    #--stdfreq=20.0 \
-    #--estmask=happytestvesselmask.nii.gz \
-    #--minhr=46 \
-    #--maxhr=131.2 \
-    #--minhrfilt=45.5 \
-    #--maxhrfilt=800.0 \
-    #--envcutoff=0.45 \
-    #--notchwidth=1.25 \
-    #--cardiacfile=happytestpleth.txt \
-    #--cardiacfreq=20.0 \
-    #--cardiacstart=0.0 \
-    #--aliasedcorrelation \
-    #--increaseoutputlevel \
-    #--increaseoutputlevel \
-    #--decreaseoutputlevel \
-    #--dodlfilter
+#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 \
-    ../dst/happy \
-    --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 \
-    #--model ~/code/rapidtide/rapidtide/data/models/model_cnn_w064_l13_fn20_fl08 \
-    #../dst/happy_newcnn
+#    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 \
-    #../dst/happy
-#
+    #--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/data/examples/src/testsimdata

@@ -1,36 +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 2 \
-        --nprocs -1 \
-        --passes 3 \
-        --nofitfilt \
-        --similaritymetric hybrid \
-        --norefinedespeckled \
-        --filterband lfo \
-        --corrtype linear \
-        sub-RAPIDTIDETEST.nii.gz \
-        ../dst/sub-RAPIDTIDETEST
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel more \
+    --nofitfilt \
+    --corrtype linear \
+    ../dst/simulatedfmri_vn05.nii.gz \
+    ../dst/simrapidtide_vn05
 
 simdata \
-    sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_desc-mean_map.nii.gz \
-    ../dst/simulatedfmri \
-    sub-RAPIDTIDETEST.json \
-    --lfopctfile ../dst/sub-RAPIDTIDETEST_desc-corrfit_mask.nii.gz \
-    --lfolagfile ../dst/sub-RAPIDTIDETEST_desc-maxtime_map.nii.gz \
+    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 2 \
-        --nprocs -1 \
-        --passes 3 \
-        --nofitfilt \
-        --similaritymetric hybrid \
-        --regressor ../dst/sub-RAPIDTIDETEST_desc-movingregressor_timeseries.json:pass3 \
-        --CVR \
-        --filterband lfo \
-        --corrtype linear \
-        ../dst/simulatedfmri.nii.gz \
-        ../dst/simrapidtide
-
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel more \
+    --nofitfilt \
+    --corrtype linear \
+    ../dst/simulatedfmri_sigfrac.nii.gz \
+    ../dst/simrapidtide_sigfrac