rapidtide 2.9.6__py3-none-any.whl → 3.1.3__py3-none-any.whl

rapidtide/data/examples/src/testhappy

@@ -1,70 +1,103 @@
 #!/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
+#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 \
-#    ../dst/happy_2comp \
-#    --cardiacfile happystdres_bids.tsv:normcardiac_25.0Hz \
-#    --mklthreads 8 \
-#    --hilbertcomponents 2 \
-#    --model model_revised
-#
+#    --prefillcongrid \
+#    --mpdetrend \
+#    ../dst/happy_mpdetrend_prefill \
+#    --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
+#    --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_legacy \
+#happy \
     #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 \
+    #../dst/happy_mask \
+    #--processmask sub-HAPPYTEST_mask.nii.gz \
+    #--nprocs -1
+
+#    --motionfile sub-HAPPYTEST_mcf.par \
+
+#happy \
+    #sub-HAPPYTEST.nii.gz \
+    #sub-HAPPYTEST.json \
+    #../dst/happy \
     #--increaseoutputlevel \
-    #--decreaseoutputlevel \
-    #--dodlfilter
+    #--model model_cnn_pytorch \
+    #--usepytorch \
+    #--nprocs -1
 
+happy \
+    sub-HAPPYTEST.nii.gz \
+    sub-HAPPYTEST.json \
+    ../dst/happy_attention \
+    --nprocs -1
 
 #happy \
-    #ses-060_bold_trunc.nii.gz \
-    #ses-060_bold_trunc.json \
-    #../dst/happy_motion \
-    #--mklthreads 8 \
-    #--motionfile ses-060_bold_trunc_prefiltered_func_data_mcf.par
+#    sub-HAPPYTEST.nii.gz \
+#    sub-HAPPYTEST.json \
+#    ../dst/happy_tensorflow \
+#    --increaseoutputlevel \
+#    --usenewvesselmethod \
+#    --usetensorflow \
+#    --nprocs -1

rapidtide/data/examples/src/testinitdelay

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_defaultfilt
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --regressor ../dst/sub-RAPIDTIDETEST_defaultfilt_desc-movingregressor_timeseries.json:pass3 \
+    --initialdelay ../dst/sub-RAPIDTIDETEST_defaultfilt_desc-maxtimerefined_map.nii.gz \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_startfromlast

rapidtide/data/examples/src/testmodels

@@ -0,0 +1,33 @@
+#!/bin/bash
+
+ROOTDIR=/data/frederic
+PCDIR=${ROOTDIR}/physioconn/output_2025
+
+rm ../dst/test_*txt
+
+#./144125/144125_REST1_RL_info.json,0.7202007666318957,0.8433922959142652,0.1885880669098923,0.16165008008446202,0.6377615782804948,-0.08267147123355054,2.6174440579296476,2.0755666381391205
+#./144125/144125_REST1_LR_info.json,0.808565698536329,0.9092988425552718,0.1964254075310612,0.14474567837066749,0.6483316301973894,-0.1649780161060566,2.675852113898243,1.9540795999118095
+#./144125/144125_REST2_RL_info.json,0.8797561606112176,0.9399168800183665,0.10131674249235224,0.14794551115545787,0.6022251227345572,-0.11661211769010084,2.594834129016148,1.9613812654056964
+#./144125/144125_REST2_LR_info.json,0.8945024253604358,0.9870236312805825,0.11015444842855743,0.15346602449619334,0.6273109523220333,-0.17124563603244516,2.3826604881557882,1.9571315095343715
+
+#for MODEL in model_revised_tf2 model_serdar_tf2 model_convautoencoder_en16_fn16 model_convautoencoder_en16_fn24 model_convautoencoder_en16_fn32
+#for MODEL in model_convautoencoder_en16_fn16 model_convautoencoder_en16_fn24 model_convautoencoder_en16_fn32
+#for MODEL in model_cnn_w112_l21_fn50_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w128_l21_fn50_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w032_l21_fn50_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w048_l21_fn50_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w064_l21_fn50_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w080_l21_fn50_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w096_l21_fn50_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned
+#for MODEL in model_cnn_w64_l21_fn35_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w64_l21_fn40_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w64_l21_fn45_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w64_l21_fn50_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w64_l21_fn55_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w64_l21_fn60_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned
+#for MODEL in model_cnn_w064_l21_fn20_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w064_l21_fn25_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w064_l21_fn30_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w064_l21_fn50_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w064_l21_fn60_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned
+
+for MODEL in model_cnn_w064_l03_fn20_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w064_l05_fn20_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w064_l07_fn20_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w064_l09_fn20_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w064_l11_fn20_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned model_cnn_w064_l13_fn20_fl5_e100_t4.0_ct0.72_s20_d1_relu_normaligned
+
+do
+    applydlfilter \
+        ${PCDIR}/144125/144125_REST1_LR_desc-stdrescardfromfmri_timeseries.json:cardiacfromfmri_25.0Hz \
+        ../dst/test_${MODEL}.txt \
+        --model ~/code/rapidtide/rapidtide/experimental/${MODEL} \
+        --nodisplay
+done
+
+showtc \
+    ../dst/test_model*txt \
+    ${PCDIR}/144125/144125_REST1_LR_desc-stdrescardfromfmri_timeseries.json:cardiacfromfmri_25.0Hz,pleth \
+    --samplerate 25.0 \
+    --format separate

rapidtide/data/examples/src/testnewrefine

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel max \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_1deriv
+
+retroregress \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_1deriv \
+    --alternateoutput ../dst/retrotest_1to1 \
+    --nprocs -1 \
+    --regressderivs 0 \
+    --outputlevel max
+
+retroregress \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_2deriv \
+    --alternateoutput ../dst/retrotest_2to1 \
+    --nprocs -1 \
+    --regressderivs 0 \
+    --outputlevel max

rapidtide/data/examples/src/testnoiseamp

@@ -1,9 +1,9 @@
 #!/usr/bin/env python
 
-import rapidtide.miscmath as tide_math
-import rapidtide.io as tide_io
 import matplotlib.pyplot as plt
 
+import rapidtide.io as tide_io
+import rapidtide.miscmath as tide_math
 
 windowsize = 40.0
 samplerate, starttime, inputdata = tide_io.readcolfrombidstsv("../dst/sub-RAPIDTIDETEST_desc-oversampledmovingregressor_timeseries.json", columnname="pass3")

rapidtide/data/examples/src/testppgproc

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+applyppgproc \
+    ../dst/happy_desc-slicerescardfromfmri_timeseries \
+    ppgtest \
+    --process_noise 0.001 \
+    --hr_estimate 65.0 \
+    --qual_thresh 0.7 \
+    --display --debug
+
+applyppgproc \
+    ../dst/happy_desc-stdrescardfromfmri_timeseries \
+    ppgtest \
+    --process_noise 0.001 \
+    --hr_estimate 65.0 \
+    --qual_thresh 0.7 \
+    --display --debug

rapidtide/data/examples/src/testrefineonly

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --passes 1 \
+    --nodelayfit \
+    --focaldebug \
+    --dofinalrefine \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_firstpass
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --nodelayfit \
+    --regressor ../dst/sub-RAPIDTIDETEST_firstpass_desc-refinedmovingregressor_timeseries.json:filtered_pass1 \
+    --initialdelay ../dst/sub-RAPIDTIDETEST_firstpass_desc-maxtimerefined_map.nii.gz \
+    --dofinalrefine \
+    --passes 1 \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_secondpass

rapidtide/data/examples/src/testretro

@@ -1,19 +1,32 @@
 #!/bin/bash
 
-#rapidtide \
-#    --nprocs -1 \
-#    --passes 3 \
-#    --refinetype unweighted_average \
-#    --numnull 0 \
-#    --outputlevel max \
-#    --glmderivs 1 \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel more \
+    --dofinalrefine \
+    --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 \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST
 
-##retroglm sub-RAPIDTIDETEST.nii.gz ../dst/sub-RAPIDTIDETEST --alternateoutput ../dst/0deriv --nprocs -1 
-retroglm sub-RAPIDTIDETEST.nii.gz ../dst/sub-RAPIDTIDETEST --alternateoutput ../dst/1deriv --nprocs -1 --glmderivs 1 --makepseudofile --outputlevel max
-##retroglm sub-RAPIDTIDETEST.nii.gz ../dst/sub-RAPIDTIDETEST --alternateoutput ../dst/2deriv --nprocs -1 --glmderivs 2
-##retroglm sub-RAPIDTIDETEST.nii.gz ../dst/sub-RAPIDTIDETEST --alternateoutput ../dst/3deriv --nprocs -1 --glmderivs 3
+##retroregress sub-RAPIDTIDETEST.nii.gz ../dst/sub-RAPIDTIDETEST --alternateoutput ../dst/0deriv --nprocs -1 
+
+retroregress \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST \
+    --alternateoutput ../dst/specialtest \
+    --nprocs -1 \
+    --outputlevel normal
+
+#retroregress sub-RAPIDTIDETEST.nii.gz ../dst/sub-RAPIDTIDETEST --alternateoutput ../dst/0deriv_refined --nprocs -1 --regressderivs 0 --makepseudofile --outputlevel max --refinedelay --nofilterwithrefineddelay
+#retroregress sub-RAPIDTIDETEST.nii.gz ../dst/sub-RAPIDTIDETEST --alternateoutput ../dst/0deriv_refinedfit --nprocs -1 --regressderivs 0 --makepseudofile --outputlevel max --refinedelay
+##retroregress sub-RAPIDTIDETEST.nii.gz ../dst/sub-RAPIDTIDETEST --alternateoutput ../dst/2deriv --nprocs -1 --regressderivs 2
+##retroregress sub-RAPIDTIDETEST.nii.gz ../dst/sub-RAPIDTIDETEST --alternateoutput ../dst/3deriv --nprocs -1 --regressderivs 3
 
 ALTNAME=1deriv
 

rapidtide/data/examples/src/testretrolagtcs

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+retrolagtcs \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_0deriv_desc-corrfit_mask.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_0deriv_desc-maxtime_map.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_0deriv_desc-lagtcgenerator_timeseries \
+    ../dst/retrolag_0deriv
+
+retrolagtcs \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_1deriv_desc-corrfit_mask.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_1deriv_desc-maxtime_map.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_1deriv_desc-lagtcgenerator_timeseries \
+    ../dst/retrolag_1deriv \
+    --regressderivs 1

rapidtide/data/examples/src/testrolloff

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+for STOP in 2 3 4 5 6 7 8
+do
+    filttc ../dst/happy_desc-stdrescardfromfmri_timeseries.json:cardiacfromfmri_25.0Hz \
+    ../dst/stopfreq_${STOP} \
+    --filterfreqs 0.0 1.0 \
+    --filterstopfreqs 0.0 ${STOP}
+done
+
+showtc ../dst/stopfreq*.json --format separate

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

rapidtide/data/models/model_cnn_pytorch/loss.txt

@@ -0,0 +1 @@
+model_cnn_w060_l19_fn50_fl05_e025_t4.0_ct0.72_s20_d1_relu_normaligned: Prediction Error: 0.6981142062735153 Raw Error: 0.3174055677061575

rapidtide/data/models/model_cnn_pytorch/model_meta.json

@@ -0,0 +1,68 @@
+{
+    "dofft":false,
+    "dropout_rate":0.3,
+    "excludethresh":4.0,
+    "loss":[
+        0.30441974932999954,
+        0.18183457710591377,
+        0.16851514196375392,
+        0.16202728616720213,
+        0.15842841755073914,
+        0.1564911107478273,
+        0.15509463905571252,
+        0.15409289958448344,
+        0.15318550205312645,
+        0.15253183263581233,
+        0.15208946124896972,
+        0.15148001061784444,
+        0.1511366076229774,
+        0.15075672873619086,
+        0.15030987919196231,
+        0.15001051545245542,
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rapidtide/data/models/model_cnn_pytorch_fulldata/loss.txt

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rapidtide/data/models/model_cnn_pytorch_fulldata/model_meta.json

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rapidtide/data/models/model_cnnbp_pytorch_fullldata/loss.txt

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