rapidtide 3.0a11__py3-none-any.whl → 3.0a13__py3-none-any.whl

rapidtide/data/examples/src/testfmri

@@ -1,132 +1,11 @@
 #!/bin/bash
 
-#rapidtide \
-#    --spatialfilt 2 \
-#    --nprocs -1 \
-#    --simcalcrange 50 -1 \
-#    --outputlevel max \
-#    --glmderivs 1 \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST_norefine
-
 rapidtide \
     --spatialfilt -1 \
+    --delayoffsetspatialfilt -1 \
     --nprocs -1 \
     --searchrange -5 20 \
     --simcalcrange 50 -1 \
+    --outputlevel max \
     sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_defaultfilt
-
-rapidtide \
-    --spatialfilt 5 \
-    --nprocs -1 \
-    --searchrange -5 20 \
-    --simcalcrange 50 -1 \
-    sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_5mmfilt
-
-rapidtide \
-    --spatialfilt 0 \
-    --nprocs -1 \
-    --searchrange -5 20 \
-    --simcalcrange 50 -1 \
-    sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_nospatialfilt
-
-#rapidtide \
-#    --spatialfilt 5 \
-#    --nprocs -1 \
-#    --simcalcrange 50 -1 \
-#    --outputlevel max \
-#    --refinedelay \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST_corr
-
-#rapidtide \
-#    --spatialfilt 2 \
-#    --nprocs -1 \
-#    --passes 50 \
-#    --despecklepasses 50 \
-#    --simcalcrange 50 -1 \
-#    --outputlevel max \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST_spec
-#
-#rapidtide \
-#    --spatialfilt 2 \
-#    --nprocs -1 \
-#    --denoising \
-#    --passes 4 \
-#    --despecklepasses 5 \
-#    --simcalcrange 50 -1 \
-#    --outputlevel max \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST_denoisingspec
-#
-#rapidtide \
-#    --spatialfilt 2 \
-#    --nprocs -1 \
-#    --denoising \
-#    --simcalcrange 50 -1 \
-#    --outputlevel max \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST_denoisingnospec
-#rapidtide \
-    #--spatialfilt 2 \
-    #--nprocs -1 \
-    #--passes 3 \
-    #--simcalcrange 50 -1 \
-    #--padtype constant \
-    #--outputlevel max \
-    #sub-RAPIDTIDETEST.nii.gz \
-    #../dst/sub-RAPIDTIDETEST_constantpad
-
-#rapidtide \
-#    --spatialfilt 2 \
-#    --nprocs -1 \
-#    --passes 3 \
-#    --simcalcrange 50 -1 \
-#    --memprofile \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST_memprofile
-
-#rapidtide \
-    #--spatialfilt 2 \
-    #--nprocs -1 \
-    #--passes 3 \
-    #--simcalcrange 50 -1 \
-    #--texcludemask tmask3_exclude.txt \
-    #sub-RAPIDTIDETEST.nii.gz \
-    #../dst/sub-RAPIDTIDETEST_excludemask
-#
-#rapidtide \
-    #--spatialfilt 2 \
-    #--nprocs -1 \
-    #--passes 3 \
-    #--simcalcrange 50 -1 \
-    #--tincludemask tmask3.txt \
-    #--texcludemask tmask3_exclude.txt \
-    #sub-RAPIDTIDETEST.nii.gz \
-    #../dst/sub-RAPIDTIDETEST_bothmasks
-
-#for FILT in 1 2 4 8 16
-#do
-#    rapidtide \
-#        --spatialfilt ${FILT} \
-#        --nprocs -1 \
-#        --passes 3 \
-#        --simcalcrange 50 -1 \
-#        --outputlevel min \
-#        sub-RAPIDTIDETEST.nii.gz \
-#        ../dst/sub-RAPIDTIDETEST_${FILT}
-#done
-#
-#for MAP in maxtime maxcorr
-#do
-#    fslmerge -t ../dst/all_${MAP} \
-#        ../dst/sub-RAPIDTIDETEST_1_desc-${MAP}_map.nii.gz \
-#        ../dst/sub-RAPIDTIDETEST_2_desc-${MAP}_map.nii.gz \
-#        ../dst/sub-RAPIDTIDETEST_4_desc-${MAP}_map.nii.gz \
-#        ../dst/sub-RAPIDTIDETEST_8_desc-${MAP}_map.nii.gz \
-#        ../dst/sub-RAPIDTIDETEST_16_desc-${MAP}_map.nii.gz 
-#done
+    ../dst/sub-RAPIDTIDETEST

rapidtide/data/examples/src/testglmfilt

@@ -34,7 +34,9 @@ datavec = amp1 * evs[:, 0] + amp2 * evs[:, 1] + amp3 * evs[:, 2] + intercept
 noisevec = noiseamp * np.random.rand(arrlen)
 invec = datavec + noisevec
 
-filtered, datatoremove, R, outcoffs, outintercept = tide_fit.glmfilt(invec, evs, returnintercept=True, debug=True)
+filtered, datatoremove, R, outcoffs, outintercept = tide_fit.linfitfilt(
+    invec, evs, returnintercept=True, debug=True
+)
 
 incoffs = [amp1, amp2, amp3]
 coffdiffs = outcoffs - incoffs
@@ -58,7 +60,7 @@ plt.plot(datavec - datatoremove + offset)
 print(R)
 plt.show()
 
-filtered, datatoremove, R, coffs = tide_fit.glmfilt(invec, evs[:, 0], debug=True)
+filtered, datatoremove, R, coffs = tide_fit.linfitfilt(invec, evs[:, 0], debug=True)
 
 """
 offset = 0.0
@@ -80,7 +82,7 @@ invec2 = (
     + noiseamp * np.random.rand(arrlen)
 )
 
-filtered, datatoremove, R, coffs = tide_fit.glmfilt(invec2, evs, debug=True)
+filtered, datatoremove, R, coffs = tide_fit.linfitfilt(invec2, evs, debug=True)
 
 """
 offset = 0.0
@@ -95,7 +97,7 @@ print(R)
 plt.show()
 """
 
-filtered, thenewevs, datatoremove, R, coffs = tide_fit.expandedglmfilt(
+filtered, thenewevs, datatoremove, R, coffs = tide_fit.expandedlinfitfilt(
     invec2, evs, ncomps=3, debug=True
 )
 
@@ -116,7 +118,7 @@ print(R)
 plt.show()
 """
 
-filtered, datatoremove, R, coffs = tide_fit.glmfilt(invec2, thenewevs, debug=True)
+filtered, datatoremove, R, coffs = tide_fit.linfitfilt(invec2, thenewevs, debug=True)
 """
 offset = 0.0
 plt.plot(invec2 + offset)
@@ -138,7 +140,7 @@ alignedev, maxdelay, maxval, failreason = tide_corr.aligntcwithref(
     verbose=True,
 )
 print(f"{maxdelay=}, {maxval=}, {failreason=}")
-filtered, datatoremove, R, coffs = tide_fit.glmfilt(invec3, alignedev, debug=True)
+filtered, datatoremove, R, coffs = tide_fit.linfitfilt(invec3, alignedev, debug=True)
 offset = 0.0
 plt.plot(evs[:, 0])
 offset += 1.0

rapidtide/data/examples/src/testhappy

@@ -65,5 +65,5 @@
 happy \
     sub-HAPPYTEST.nii.gz \
     sub-HAPPYTEST.json \
-    --spatialglm \
+    --spatialregression \
     ../dst/happy

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/testnewrefine

@@ -0,0 +1,49 @@
+#!/bin/bash
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel max \
+    --refineregressderivs 1 \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_1deriv
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel max \
+    --refineregressderivs 2 \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_2deriv
+
+
+retroregress \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_1deriv \
+    --alternateoutput ../dst/retrotest_1to1 \
+    --nprocs -1 \
+    --regressderivs 0 \
+    --refineregressderivs 1 \
+    --outputlevel max
+
+retroregress \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_2deriv \
+    --alternateoutput ../dst/retrotest_2to1 \
+    --nprocs -1 \
+    --regressderivs 0 \
+    --refineregressderivs 1 \
+    --outputlevel max
+
+retroregress \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_1deriv \
+    --alternateoutput ../dst/retrotest_1to2 \
+    --nprocs -1 \
+    --regressderivs 0 \
+    --refineregressderivs 2 \
+    --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/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

@@ -6,16 +6,25 @@
 #    --refinetype unweighted_average \
 #    --numnull 0 \
 #    --outputlevel max \
-#    --glmderivs 1 \
+#    --regressderivs 1 \
 #    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/0deriv --nprocs -1 --glmderivs 0 --makepseudofile --outputlevel max
-retroglm sub-RAPIDTIDETEST.nii.gz ../dst/sub-RAPIDTIDETEST --alternateoutput ../dst/0deriv_refined --nprocs -1 --glmderivs 0 --makepseudofile --outputlevel max --refinedelay --nofilterwithrefineddelay
-retroglm sub-RAPIDTIDETEST.nii.gz ../dst/sub-RAPIDTIDETEST --alternateoutput ../dst/0deriv_refinedfit --nprocs -1 --glmderivs 0 --makepseudofile --outputlevel max --refinedelay
-##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/wintest \
+    --nprocs -1 \
+    --outputlevel max \
+    --focaldebug \
+    --delayoffsetspatialfilt -1 
+
+#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

@@ -13,4 +13,4 @@ retrolagtcs \
     ../dst/sub-RAPIDTIDETEST_1deriv_desc-maxtime_map.nii.gz \
     ../dst/sub-RAPIDTIDETEST_1deriv_desc-lagtcgenerator_timeseries \
     ../dst/retrolag_1deriv \
-    --glmderivs 1 
+    --regressderivs 1

rapidtide/dlfilter.py

@@ -77,7 +77,6 @@ from tensorflow.keras.layers import (
     TimeDistributed,
     UpSampling1D,
 )
-
 from tensorflow.keras.models import Sequential, load_model
 from tensorflow.keras.optimizers import RMSprop
 

rapidtide/fit.py

@@ -23,6 +23,7 @@ import matplotlib.pyplot as plt
 import numpy as np
 import scipy as sp
 import scipy.special as sps
+import statsmodels.api as sm
 import tqdm
 from numpy.polynomial import Polynomial
 from scipy.optimize import curve_fit
@@ -1105,6 +1106,37 @@ def mlproject(thefit, theevs, intercept):
     return thedest
 
 
+def olsregress(X, y, intercept=True, debug=False):
+    """
+
+    Parameters
+    ----------
+    X
+    y
+    intercept
+
+    Returns
+    -------
+
+    """
+    """Return the coefficients from a multiple linear regression, along with R, the coefficient of determination.
+
+    X: The independent variables (nxp).
+    y: The dependent variable (1xn or nx1).
+    intercept: Specifies whether or not the slope intercept should be considered.
+
+    The routine computes the coefficients (b_0, b_1, ..., b_p) from the data (x,y) under
+    the assumption that y = b0 + b_1 * x_1 + b_2 * x_2 + ... + b_p * x_p.
+
+    If intercept is False, the routine assumes that b0 = 0 and returns (b_1, b_2, ..., b_p).
+    """
+    if intercept:
+        X = sm.add_constant(X, prepend=True)
+    model = sm.OLS(y, exog=X)
+    thefit = model.fit()
+    return thefit.params, np.sqrt(thefit.rsquared)
+
+
 def mlregress(X, y, intercept=True, debug=False):
     """
 
@@ -1223,9 +1255,9 @@ def calcexpandedregressors(
     return outputregressors, outlabels
 
 
-def derivativeglmfilt(thedata, theevs, nderivs=1, debug=False):
+def derivativelinfitfilt(thedata, theevs, nderivs=1, debug=False):
     r"""First perform multicomponent expansion on theevs (each ev replaced by itself,
-    its square, its cube, etc.).  Then perform a glm fit of thedata using the vectors
+    its square, its cube, etc.).  Then perform a linear fit of thedata using the vectors
     in thenewevs and return the result.
 
     Parameters
@@ -1269,16 +1301,16 @@ def derivativeglmfilt(thedata, theevs, nderivs=1, debug=False):
     if debug:
         print(f"{nderivs=}")
         print(f"{thenewevs.shape=}")
-    filtered, datatoremove, R, coffs = glmfilt(thedata, thenewevs, debug=debug)
+    filtered, datatoremove, R, coffs = linfitfilt(thedata, thenewevs, debug=debug)
     if debug:
         print(f"{R=}")
 
     return filtered, thenewevs, datatoremove, R, coffs
 
 
-def expandedglmfilt(thedata, theevs, ncomps=1, debug=False):
+def expandedlinfitfilt(thedata, theevs, ncomps=1, debug=False):
     r"""First perform multicomponent expansion on theevs (each ev replaced by itself,
-    its square, its cube, etc.).  Then perform a glm fit of thedata using the vectors
+    its square, its cube, etc.).  Then perform a multiple regression fit of thedata using the vectors
     in thenewevs and return the result.
 
     Parameters
@@ -1322,15 +1354,15 @@ def expandedglmfilt(thedata, theevs, ncomps=1, debug=False):
     if debug:
         print(f"{ncomps=}")
         print(f"{thenewevs.shape=}")
-    filtered, datatoremove, R, coffs = glmfilt(thedata, thenewevs, debug=debug)
+    filtered, datatoremove, R, coffs = linfitfilt(thedata, thenewevs, debug=debug)
     if debug:
         print(f"{R=}")
 
     return filtered, thenewevs, datatoremove, R, coffs
 
 
-def glmfilt(thedata, theevs, returnintercept=False, debug=False):
-    r"""Performs a glm fit of thedata using the vectors in theevs
+def linfitfilt(thedata, theevs, returnintercept=False, debug=False):
+    r"""Performs a multiple regression fit of thedata using the vectors in theevs
     and returns the result.
 
     Parameters
@@ -1383,7 +1415,7 @@ def glmfilt(thedata, theevs, returnintercept=False, debug=False):
         return filtered, datatoremove, R2, retcoffs
 
 
-def confoundglm(
+def confoundregress(
     data,
     regressors,
     debug=False,

rapidtide/happy_supportfuncs.py

@@ -290,6 +290,11 @@ def cardiacfromimage(
     )
 
 
+def theCOM(X, data):
+    # return the center of mass
+    return np.sum(X * data) / np.sum(data)
+
+
 def savgolsmooth(data, smoothlen=101, polyorder=3):
     return savgol_filter(data, smoothlen, polyorder)
 

rapidtide/io.py

@@ -1426,6 +1426,8 @@ def writebidstsv(
     extraheaderinfo=None,
     compressed=True,
     columns=None,
+    xaxislabel="time",
+    yaxislabel="arbitrary value",
     starttime=0.0,
     append=False,
     colsinjson=True,
@@ -1447,6 +1449,8 @@ def writebidstsv(
     :param samplerate:
     :param compressed:
     :param columns:
+    :param xaxislabel:
+    :param yaxislabel:
     :param starttime:
     :param append:
     :param colsinjson:
@@ -1462,6 +1466,8 @@ def writebidstsv(
         print("\tsamplerate:", samplerate)
         print("\tcompressed:", compressed)
         print("\tcolumns:", columns)
+        print("\txaxislabel:", xaxislabel)
+        print("\tyaxislabel:", yaxislabel)
         print("\tstarttime:", starttime)
         print("\tappend:", append)
     if len(data.shape) == 1:
@@ -1538,6 +1544,8 @@ def writebidstsv(
     headerdict = {}
     headerdict["SamplingFrequency"] = float(samplerate)
     headerdict["StartTime"] = float(starttime)
+    headerdict["XAxisLabel"] = xaxislabel
+    headerdict["YAxisLabel"] = yaxislabel
     if colsinjson:
         if startcol == 0:
             headerdict["Columns"] = columns
@@ -1991,8 +1999,11 @@ def colspectolist(colspec, debug=False):
         ("APARC_SUBCORTGRAY", "8-13,17-20,26-28,47-56,58-60,96,97"),
         ("APARC_CORTGRAY", "1000-1035,2000-2035"),
         ("APARC_GRAY", "8-13,17-20,26-28,47-56,58-60,96,97,1000-1035,2000-2035"),
-        ("APARC_WHITE", "2,7,41,46,177,219"),
-        ("APARC_ALLBUTCSF", "2,7-13,17-20,26-28,41,46-56,58-60,96,97,177,219,1000-1035,2000-2035"),
+        ("APARC_WHITE", "2,7,41,46,177,219,3000-3035,4000-4035,5001,5002"),
+        (
+            "APARC_ALLBUTCSF",
+            "2,7-13,17-20,26-28,41,46-56,58-60,96,97,177,219,1000-1035,2000-2035,3000-3035,4000-4035,5001,5002",
+        ),
         ("SSEG_GRAY", "3,8,10-13,16-18,26,42,47,49-54,58"),
         ("SSEG_WHITE", "2,7,41,46"),
     )