rapidtide 3.0.8__py3-none-any.whl → 3.0.10__py3-none-any.whl

rapidtide/io.py

@@ -1263,6 +1263,10 @@ def readlabelledtsv(inputfilename, compressed=False):
         theext = ".tsv.gz"
     else:
         theext = ".tsv"
+
+    if not os.path.isfile(inputfilename + theext):
+        raise FileNotFoundError(f"Labelled tsv file {inputfilename + theext} does not exist")
+
     df = pd.read_csv(inputfilename + theext, sep="\t", quotechar='"')
 
     # replace nans with 0
@@ -1290,6 +1294,9 @@ def readcsv(inputfilename, debug=False):
     NOTE:  If file does not exist or is not valid, return an empty dictionary
 
     """
+    if not os.path.isfile(inputfilename + ".csv"):
+        raise FileNotFoundError(f"csv file {inputfilename}.csv does not exist")
+
     timeseriesdict = {}
 
     # Read the data in initially with no header
@@ -1341,6 +1348,9 @@ def readfslmat(inputfilename, debug=False):
     NOTE:  If file does not exist or is not valid, return an empty dictionary
 
     """
+    if not os.path.isfile(inputfilename + ".mat"):
+        raise FileNotFoundError(f"FSL mat file {inputfilename}.mat does not exist")
+
     timeseriesdict = {}
 
     # Read the data in with no header
@@ -1364,8 +1374,7 @@ def readoptionsfile(inputfileroot):
         # options saved as text
         thedict = readdict(inputfileroot + ".txt")
     else:
-        print("no valid options file found")
-        return {}
+        raise FileNotFoundError(f"options file {inputfileroot}(.json/.txt) does not exist")
 
     # correct behavior for older options files
     try:
@@ -1476,7 +1485,7 @@ def writebidstsv(
         reshapeddata = data
     if append:
         insamplerate, instarttime, incolumns, indata, incompressed, incolsource = readbidstsv(
-            outputfileroot + ".json", debug=debug
+            outputfileroot + ".json", neednotexist=True, debug=debug,
         )
         if debug:
             print("appending")
@@ -1723,7 +1732,7 @@ def readvectorsfromtextfile(fullfilespec, onecol=False, debug=False):
     return thesamplerate, thestarttime, thecolumns, thedata, compressed, filetype
 
 
-def readbidstsv(inputfilename, colspec=None, warn=True, debug=False):
+def readbidstsv(inputfilename, colspec=None, warn=True, neednotexist=False, debug=False):
     r"""Read time series out of a BIDS tsv file
 
     Parameters
@@ -1890,11 +1899,13 @@ def readbidstsv(inputfilename, colspec=None, warn=True, debug=False):
                 columnsource,
             )
     else:
-        print("file pair does not exist")
-        return [None, None, None, None, None, None]
+        if neednotexist:
+            return [None, None, None, None, None, None]
+        else:
+            raise FileNotFoundError(f"file pair {thefileroot}(.json/.tsv[.gz]) does not exist")
 
 
-def readcolfrombidstsv(inputfilename, columnnum=0, columnname=None, debug=False):
+def readcolfrombidstsv(inputfilename, columnnum=0, columnname=None, neednotexist=False, debug=False):
     r"""
 
     Parameters
@@ -1908,7 +1919,7 @@ def readcolfrombidstsv(inputfilename, columnnum=0, columnname=None, debug=False)
 
     """
     samplerate, starttime, columns, data, compressed, colsource = readbidstsv(
-        inputfilename, debug=debug
+        inputfilename, neednotexist=neednotexist, debug=debug
     )
     if data is None:
         print("no valid datafile found")

rapidtide/linfitfiltpass.py

@@ -91,11 +91,12 @@ def linfitfiltpass(
     filtereddata,
     nprocs=1,
     alwaysmultiproc=False,
+    voxelspecific=True,
     confoundregress=False,
-    ratiosonly=False,
+    coefficientsonly=False,
     procbyvoxel=True,
     showprogressbar=True,
-    mp_chunksize=1000,
+    chunksize=1000,
     rt_floatset=np.float64,
     rt_floattype="float64",
     verbose=True,
@@ -142,7 +143,7 @@ def linfitfiltpass(
 
                     # process and send the data
                     if procbyvoxel:
-                        if confoundregress:
+                        if confoundregress or (not voxelspecific):
                             outQ.put(
                                 _procOneRegressionFitItem(
                                     val,
@@ -163,7 +164,7 @@ def linfitfiltpass(
                                 )
                             )
                     else:
-                        if confoundregress:
+                        if confoundregress or (not voxelspecific):
                             outQ.put(
                                 _procOneRegressionFitItem(
                                     val,
@@ -197,7 +198,7 @@ def linfitfiltpass(
             indexaxis=indexaxis,
             procunit=procunit,
             showprogressbar=showprogressbar,
-            chunksize=mp_chunksize,
+            chunksize=chunksize,
         )
 
         # unpack the data
@@ -208,7 +209,7 @@ def linfitfiltpass(
                     r2value[voxel[0]] = voxel[3]
                     filtereddata[voxel[0], :] = voxel[7]
                     itemstotal += 1
-            elif ratiosonly:
+            elif coefficientsonly:
                 for voxel in data_out:
                     meanvalue[voxel[0]] = voxel[1]
                     rvalue[voxel[0]] = voxel[2]
@@ -240,7 +241,7 @@ def linfitfiltpass(
                     r2value[timepoint[0]] = timepoint[3]
                     filtereddata[:, timepoint[0]] = timepoint[7]
                     itemstotal += 1
-            elif ratiosonly:
+            elif coefficientsonly:
                 for timepoint in data_out:
                     meanvalue[timepoint[0]] = timepoint[1]
                     rvalue[timepoint[0]] = timepoint[2]
@@ -296,23 +297,41 @@ def linfitfiltpass(
                             rt_floatset=rt_floatset,
                             rt_floattype=rt_floattype,
                         )
-                    elif ratiosonly:
-                        (
-                            dummy,
-                            meanvalue[vox],
-                            rvalue[vox],
-                            r2value[vox],
-                            fitcoeff[vox],
-                            fitNorm[vox],
-                            dummy,
-                            dummy,
-                        ) = _procOneRegressionFitItem(
-                            vox,
-                            theevs[vox, :],
-                            thedata,
-                            rt_floatset=rt_floatset,
-                            rt_floattype=rt_floattype,
-                        )
+                    elif coefficientsonly:
+                        if voxelspecific:
+                            (
+                                dummy,
+                                meanvalue[vox],
+                                rvalue[vox],
+                                r2value[vox],
+                                fitcoeff[vox],
+                                fitNorm[vox],
+                                dummy,
+                                dummy,
+                            ) = _procOneRegressionFitItem(
+                                vox,
+                                theevs[vox, :],
+                                thedata,
+                                rt_floatset=rt_floatset,
+                                rt_floattype=rt_floattype,
+                            )
+                        else:
+                            (
+                                dummy,
+                                meanvalue[vox],
+                                rvalue[vox],
+                                r2value[vox],
+                                fitcoeff[vox],
+                                fitNorm[vox],
+                                dummy,
+                                dummy,
+                            ) = _procOneRegressionFitItem(
+                                vox,
+                                theevs,
+                                thedata,
+                                rt_floatset=rt_floatset,
+                                rt_floattype=rt_floattype,
+                            )
                     else:
                         (
                             dummy,
@@ -357,7 +376,7 @@ def linfitfiltpass(
                             rt_floatset=rt_floatset,
                             rt_floattype=rt_floattype,
                         )
-                    elif ratiosonly:
+                    elif coefficientsonly:
                         (
                             dummy,
                             meanvalue[timepoint],

rapidtide/refinedelay.py

@@ -391,10 +391,10 @@ def getderivratios(
         nprocs_makelaggedtcs=optiondict["nprocs_makelaggedtcs"],
         nprocs_regressionfilt=optiondict["nprocs_regressionfilt"],
         regressderivs=regressderivs,
-        mp_chunksize=optiondict["mp_chunksize"],
+        chunksize=optiondict["mp_chunksize"],
         showprogressbar=optiondict["showprogressbar"],
         alwaysmultiproc=optiondict["alwaysmultiproc"],
-        ratiosonly=True,
+        coefficientsonly=True,
         debug=debug,
     )
 

rapidtide/refineregressor.py

@@ -590,7 +590,7 @@ def dorefine(
                 sys.exit()
         LGR.info(
             f"Using {len(thefit.components_)} component(s), accounting for "
-            + f"{100.0 * np.cumsum(thefit.explained_variance_ratio_)[len(thefit.components_) - 1]}% of the variance"
+            + f"{100.0 * np.cumsum(thefit.explained_variance_ratio_)[len(thefit.components_) - 1]:.2f}% of the variance"
         )
         reduceddata = thefit.inverse_transform(thefit.transform(refinevoxels))
         if debug:

rapidtide/resample.py

@@ -597,7 +597,7 @@ def arbresample(
         return resampled
 
 
-def upsample(inputdata, Fs_init, Fs_higher, method="univariate", intfac=False, debug=False):
+def upsample(inputdata, Fs_init, Fs_higher, method="univariate", intfac=False, dofilt=True, debug=False):
     starttime = time.time()
     if Fs_higher <= Fs_init:
         print("upsample: target frequency must be higher than initial frequency")
@@ -607,19 +607,19 @@ def upsample(inputdata, Fs_init, Fs_higher, method="univariate", intfac=False, d
     orig_x = np.linspace(0.0, (1.0 / Fs_init) * len(inputdata), num=len(inputdata), endpoint=False)
     endpoint = orig_x[-1] - orig_x[0]
     ts_higher = 1.0 / Fs_higher
-    numresamppts = int(endpoint // ts_higher + 1)
     if intfac:
         numresamppts = int(Fs_higher // Fs_init) * len(inputdata)
     else:
         numresamppts = int(endpoint // ts_higher + 1)
     upsampled_x = np.arange(0.0, ts_higher * numresamppts, ts_higher)
     upsampled_y = doresample(orig_x, inputdata, upsampled_x, method=method)
-    initfilter = tide_filt.NoncausalFilter(
-        filtertype="arb", transferfunc="trapezoidal", debug=debug
-    )
-    stopfreq = np.min([1.1 * Fs_init / 2.0, Fs_higher / 2.0])
-    initfilter.setfreqs(0.0, 0.0, Fs_init / 2.0, stopfreq)
-    upsampled_y = initfilter.apply(Fs_higher, upsampled_y)
+    if dofilt:
+        initfilter = tide_filt.NoncausalFilter(
+            filtertype="arb", transferfunc="trapezoidal", debug=debug
+        )
+        stopfreq = np.min([1.1 * Fs_init / 2.0, Fs_higher / 2.0])
+        initfilter.setfreqs(0.0, 0.0, Fs_init / 2.0, stopfreq)
+        upsampled_y = initfilter.apply(Fs_higher, upsampled_y)
     if debug:
         print("upsampling took", time.time() - starttime, "seconds")
     return upsampled_y

rapidtide/simFuncClasses.py

@@ -694,9 +694,9 @@ class SimilarityFunctionFitter:
                 while peakpoints[peakstart - 1] == 1:
                     peakstart -= 1
             else:
-                while thegrad[peakend + 1] <= 0.0 and peakpoints[peakend + 1] == 1:
+                while thegrad[peakend + 1] <= 0.0 and peakpoints[peakend + 1] == 1 and peakend < len(self.corrtimeaxis) - 2:
                     peakend += 1
-                while thegrad[peakstart - 1] >= 0.0 and peakpoints[peakstart - 1] == 1:
+                while thegrad[peakstart - 1] >= 0.0 and peakpoints[peakstart - 1] == 1 and peakstart >= 1:
                     peakstart -= 1
             if self.debug:
                 print("final peakstart, peakend:", peakstart, peakend)
@@ -819,12 +819,18 @@ class SimilarityFunctionFitter:
                 if self.debug:
                     print("fit input array:", p0)
                 try:
-                    plsq, dummy = sp.optimize.leastsq(
+                    plsq, ier = sp.optimize.leastsq(
                         tide_fit.gaussresiduals, p0, args=(data, X), maxfev=5000
                     )
-                    maxval = plsq[0] + baseline
-                    maxlag = np.fmod((1.0 * plsq[1]), self.lagmod)
-                    maxsigma = plsq[2]
+                    if ier not in [1, 2, 3, 4]:  # Check for successful convergence
+                        failreason |= self.FML_FITALGOFAIL
+                        maxval = np.float64(0.0)
+                        maxlag = np.float64(0.0)
+                        maxsigma = np.float64(0.0)
+                    else:
+                        maxval = plsq[0] + baseline
+                        maxlag = np.fmod((1.0 * plsq[1]), self.lagmod)
+                        maxsigma = plsq[2]
                 except:
                     failreason |= self.FML_FITALGOFAIL
                     maxval = np.float64(0.0)
@@ -929,7 +935,7 @@ class SimilarityFunctionFitter:
                 # different rules for mutual information peaks
                 if ((maxval - baseline) < self.lthreshval * baselinedev) or (maxval < baseline):
                     failreason |= self.FML_FITAMPLOW
-                    maxval_init = 0.0
+                    maxval = 0.0
                     if self.debug:
                         if (maxval - baseline) < self.lthreshval * baselinedev:
                             print(

rapidtide/tests/.coveragerc

@@ -6,17 +6,23 @@ sigterm = true
 source = .
 omit =
     __init__.py
-    ../__init__.py
-    ../scripts/__init__.py
-    ../OrthoImageItem.py
-    ../wiener2.py
-    ../tidepoolTemplate.py
-    ../tidepoolTemplate_qt6.py
-    ../tidepoolTemplate_alt.py
-    ../tidepoolTemplate_alt_qt6.py
-    ../tidepoolTemplate_big.py
-    ../tidepoolTemplate_big_qt6.py
-    ../notreadyforprimetime/*
+    scripts/__init__.py
+    OrthoImageItem.py
+    wiener2.py
+    fMRIData_class.py
+    tidepoolTemplate.py
+    tidepoolTemplate_qt6.py
+    tidepoolTemplate_alt.py
+    tidepoolTemplate_alt_qt6.py
+    tidepoolTemplate_big.py
+    tidepoolTemplate_big_qt6.py
+    */tidepool.py
+    */delayvar.py
+    */variabilityizer.py
+    */synthASL.py
+    */proj2flow.py
+    */adjustoffset.py
+    notreadyforprimetime/*
 
 [report]
 exclude_lines = 

rapidtide/tests/test_delayestimation.py

@@ -350,7 +350,7 @@ def test_delayestimation(displayplots=False, debug=False):
             nprocs=nprocs,
             alwaysmultiproc=False,
             showprogressbar=False,
-            mp_chunksize=chunksize,
+            chunksize=chunksize,
         )
 
         if nprocs == 1:

rapidtide/tests/test_findmaxlag.py

@@ -26,7 +26,7 @@ import numpy as np
 import rapidtide.fit as tide_fit
 import rapidtide.io as tide_io
 import rapidtide.simFuncClasses as tide_simFuncClasses
-from rapidtide.tests.utils import get_examples_path
+from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
 def dumplists(results, targets, failflags):
@@ -39,7 +39,12 @@ def dumplists(results, targets, failflags):
         print(results[i], targets[i], failflags[i])
 
 
-def eval_fml_result(absmin, absmax, testvalues, foundvalues, failflags, tolerance=0.0001):
+def eval_fml_result(absmin, absmax, testvalues, foundvalues, failflags, tolerance=0.0001, debug=False):
+    if debug:
+        print(f"{absmin=}, {absmax=}, {tolerance=}")
+        print(f"{testvalues=}")
+        print(f"{foundvalues=}")
+        print(f"{failflags=}")
     for i in range(len(testvalues)):
         if testvalues[i] < absmin:
             if foundvalues[i] != absmin:
@@ -61,12 +66,22 @@ def eval_fml_result(absmin, absmax, testvalues, foundvalues, failflags, toleranc
     return True
 
 
-def test_findmaxlag(displayplots=False, debug=False):
+def test_findmaxlag(displayplots=False, local=False, debug=False):
+    # set input and output directories
+    if local:
+        exampleroot = "../data/examples/src"
+        testtemproot = "./tmp"
+    else:
+        exampleroot = get_examples_path()
+        testtemproot = get_test_temp_path()
+
+    if debug:
+        print("debug flag is set")
     # for fittype in ["gauss", "quad", "fastquad", "COM", "None", "fastgauss", "gausscf"]:
     for fittype in ["gauss"]:
         print("*************************************")
         print(f"testing fittype: {fittype}")
-        textfilename = op.join(get_examples_path(), "lt_rt.txt")
+        textfilename = op.join(exampleroot, "lt_rt.txt")
 
         # set default variable values
         searchfrac = 0.75
@@ -172,16 +187,16 @@ def test_findmaxlag(displayplots=False, debug=False):
             for i in range(len(testlags)):
                 print(testlags[i], fml_maxlags[i], fml_lfailreasons[i])
 
-        assert eval_fml_result(lagmin, lagmax, testlags, fml_maxlags, fml_lfailreasons)
-        assert eval_fml_result(absminval, absmaxval, testvals, fml_maxvals, fml_lfailreasons)
+        assert eval_fml_result(lagmin, lagmax, testlags, fml_maxlags, fml_lfailreasons, debug=debug)
+        assert eval_fml_result(absminval, absmaxval, testvals, fml_maxvals, fml_lfailreasons, debug=debug)
         assert eval_fml_result(
-            absminsigma, absmaxsigma, testsigmas, fml_maxsigmas, fml_lfailreasons
+            absminsigma, absmaxsigma, testsigmas, fml_maxsigmas, fml_lfailreasons, debug=debug
         )
 
-        assert eval_fml_result(lagmin, lagmax, testlags, fmlc_maxlags, fmlc_lfailreasons)
-        assert eval_fml_result(absminval, absmaxval, testvals, fmlc_maxvals, fmlc_lfailreasons)
+        assert eval_fml_result(lagmin, lagmax, testlags, fmlc_maxlags, fmlc_lfailreasons, debug=debug)
+        assert eval_fml_result(absminval, absmaxval, testvals, fmlc_maxvals, fmlc_lfailreasons, debug=debug)
         assert eval_fml_result(
-            absminsigma, absmaxsigma, testsigmas, fmlc_maxsigmas, fmlc_lfailreasons
+            absminsigma, absmaxsigma, testsigmas, fmlc_maxsigmas, fmlc_lfailreasons, debug=debug
         )
 
         if displayplots:
@@ -315,19 +330,19 @@ def test_findmaxlag(displayplots=False, debug=False):
             ax.legend(["findmaxlag_gauss", "classes"])
             plt.show()
 
-        assert eval_fml_result(lagmin, lagmax, testlags, fml_maxlags, fml_wfailreasons)
+        assert eval_fml_result(lagmin, lagmax, testlags, fml_maxlags, fml_wfailreasons, debug=debug)
         # assert eval_fml_result(absminval, absmaxval, testvals, fml_maxvals, fml_wfailreasons)
         assert eval_fml_result(
-            absminsigma, absmaxsigma, testsigmas, fml_maxsigmas, fml_wfailreasons
+            absminsigma, absmaxsigma, testsigmas, fml_maxsigmas, fml_wfailreasons, debug=debug
         )
 
-        assert eval_fml_result(lagmin, lagmax, testlags, fmlc_maxlags, fmlc_wfailreasons)
-        assert eval_fml_result(absminval, absmaxval, testvals, fmlc_maxvals, fmlc_wfailreasons)
+        assert eval_fml_result(lagmin, lagmax, testlags, fmlc_maxlags, fmlc_wfailreasons, debug=debug)
+        assert eval_fml_result(absminval, absmaxval, testvals, fmlc_maxvals, fmlc_wfailreasons, debug=debug)
         assert eval_fml_result(
-            absminsigma, absmaxsigma, testsigmas, fmlc_maxsigmas, fmlc_wfailreasons
+            absminsigma, absmaxsigma, testsigmas, fmlc_maxsigmas, fmlc_wfailreasons, debug=debug
         )
 
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_findmaxlag(displayplots=True, debug=True)
+    test_findmaxlag(displayplots=True, local=True, debug=True)

rapidtide/tests/test_fullrunrapidtide_v8.py

@@ -0,0 +1,66 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+#   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.
+#   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.qualitycheck as rapidtide_quality
+import rapidtide.workflows.rapidtide as rapidtide_workflow
+import rapidtide.workflows.rapidtide_parser as rapidtide_parser
+from rapidtide.tests.utils import get_examples_path, get_test_temp_path
+
+
+def test_fullrunrapidtide_v8(debug=False, local=False, displayplots=False):
+    # set input and output directories
+    if local:
+        exampleroot = "../data/examples/src"
+        testtemproot = "./tmp"
+    else:
+        exampleroot = get_examples_path()
+        testtemproot = get_test_temp_path()
+
+    # run rapidtide
+    inputargs = [
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST8"),
+        "--spatialfilt",
+        "2",
+        "--simcalcrange",
+        "4",
+        "-1",
+        "--searchrange",
+        "-5",
+        "10",
+        "--nprocs",
+        "-1",
+        "--passes",
+        "1",
+        "--despecklepasses",
+        "3",
+        "--similaritymetric",
+        "riptide",
+        "--riptidestep",
+        "1.5",
+    ]
+    rapidtide_workflow.rapidtide_main(rapidtide_parser.process_args(inputargs=inputargs))
+
+
+if __name__ == "__main__":
+    mpl.use("TkAgg")
+    test_fullrunrapidtide_v8(debug=True, local=True, displayplots=True)

rapidtide/tests/test_padvec.py

@@ -63,6 +63,23 @@ def maketestwaves(timeaxis):
             "waveform": 1.0 * scratch,
         }
     )
+
+    scratch = np.exp(-timeaxis / timeaxis[2])
+    testwaves.append(
+        {
+            "name": "damped exponential regressor",
+            "timeaxis": 1.0 * timeaxis,
+            "waveform": 1.0 * scratch,
+        }
+    )
+
+    testwaves.append(
+        {
+            "name": "white noise plus exponential",
+            "timeaxis": 1.0 * timeaxis,
+            "waveform": 0.3 * np.random.normal(size=tclen) + scratch,
+        }
+    )
     return testwaves
 
 
@@ -89,7 +106,7 @@ def eval_padvecprops(
     nperseg = np.min([tclen, 2048])
     f, dummy = sp.signal.welch(overall, fs=1.0 / sampletime, nperseg=nperseg)
 
-    padtypelist = ["reflect", "zero", "constant", "constant+"]
+    padtypelist = ["reflect", "zero", "cyclic", "constant", "constant+"]
     transferfunclist = ["brickwall", "trapezoidal", "butterworth"]
 
     # construct some test waveforms for end effects
@@ -184,6 +201,7 @@ def eval_padvecprops(
                     legend.append(thewave["name"] + ": " + thefilter["name"])
                     offset += 1.25
                 plt.legend(legend)
+                plt.title(padtype)
                 plt.show()