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

rapidtide/tests/test_externaltools.py

@@ -0,0 +1,69 @@
+#!/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.externaltools as tide_exttools
+from rapidtide.tests.utils import get_examples_path, get_test_temp_path, mse
+
+
+def test_externaltools(debug=False, local=False):
+    # set input and output directories
+    if local:
+        exampleroot = "../data/examples/src"
+        testtemproot = "./tmp"
+    else:
+        exampleroot = get_examples_path()
+        testtemproot = get_test_temp_path()
+
+    thefsldir = tide_exttools.fslinfo()
+    if debug:
+        print(f"{thefsldir=}")
+
+    if not local:
+        os.environ["FSLDIR"] = "/plausible_FSLDIR"
+
+    thefsldir = tide_exttools.fslinfo()
+    if debug:
+        print(f"{thefsldir=}")
+
+    fslexists, c3dexists, antsexists = tide_exttools.whatexists()
+    if debug:
+        print(f"{fslexists=}, {c3dexists=}, {antsexists=}")
+
+    fslsubcmd, flirtcmd, applywarpcmd = tide_exttools.getfslcmds()
+    if debug:
+        print(f"{fslsubcmd=}, {flirtcmd=}, {applywarpcmd=}")
+
+    tide_exttools.runflirt(
+        "inputname", "targetname", "xform", "outputname", warpfile="thewarp", fake=True
+    )
+    tide_exttools.runflirt("inputname", "targetname", "xform", "outputname", fake=True)
+
+    tide_exttools.n4correct("inputname", "outputdir", fake=True)
+
+    tide_exttools.antsapply(
+        "inputname", "targetname", "outputroot", ["transform1", "transform2"], fake=True
+    )
+
+
+if __name__ == "__main__":
+    mpl.use("TkAgg")
+    test_externaltools(debug=True, local=True)

rapidtide/tests/test_fastresampler.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.
@@ -16,12 +16,14 @@
 #   limitations under the License.
 #
 #
+import os
+
 import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
 
 from rapidtide.resample import FastResampler, FastResamplerFromFile
-from rapidtide.tests.utils import mse
+from rapidtide.tests.utils import get_test_temp_path, mse
 
 
 def test_FastResampler(debug=False):
@@ -29,7 +31,7 @@ def test_FastResampler(debug=False):
     padtime = 50.0
     testlen = 1000
     timeaxis = np.arange(0.0, 1.0 * testlen) * tr
-    timecoursein = np.float64(timeaxis * 0.0)
+    timecoursein = np.zeros_like(timeaxis, np.float64)
     midpoint = int(testlen // 2) + 1
     timecoursein[midpoint - 1] = np.float64(1.0)
     timecoursein[midpoint] = np.float64(1.0)
@@ -43,10 +45,12 @@ def test_FastResampler(debug=False):
     if debug:
         print(f"{genlaggedtc.initstart=}, {genlaggedtc.initend=}, {genlaggedtc.initstep=}")
         print(f"{genlaggedtc.hiresstart=}, {genlaggedtc.hiresend=}, {genlaggedtc.hiresstep=}")
+    genlaggedtc.info()
 
     # save and reload with another name
-    genlaggedtc.save("savedresampler")
-    genlaggedtc2 = FastResamplerFromFile("savedresampler", padtime=padtime, debug=debug)
+    resamplername = os.path.join(get_test_temp_path(), "savedresampler")
+    genlaggedtc.save(resamplername)
+    genlaggedtc2 = FastResamplerFromFile(resamplername, padtime=padtime, debug=debug)
     if debug:
         print(f"{genlaggedtc2.initstart=}, {genlaggedtc2.initend=}, {genlaggedtc2.initstep=}")
         print(f"{genlaggedtc2.hiresstart=}, {genlaggedtc2.hiresend=}, {genlaggedtc2.hiresstep=}")

rapidtide/tests/test_filter.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.
@@ -21,9 +21,51 @@ import matplotlib.pyplot as plt
 import numpy as np
 import scipy as sp
 
+from rapidtide.ffttools import showfftcache
 from rapidtide.filter import NoncausalFilter
 
 
+def maketestwaves(timeaxis):
+    tclen = len(timeaxis)
+    testwaves = []
+    testwaves.append(
+        {
+            "name": "constant high",
+            "timeaxis": 1.0 * timeaxis,
+            "waveform": np.ones((tclen), dtype="float"),
+        }
+    )
+    testwaves.append(
+        {
+            "name": "white noise",
+            "timeaxis": 1.0 * timeaxis,
+            "waveform": 0.3 * np.random.normal(size=tclen),
+        }
+    )
+
+    scratch = np.zeros_like(timeaxis)
+    scratch[int(tclen / 5) : int(2 * tclen / 5)] = 1.0
+    scratch[int(3 * tclen / 5) : int(4 * tclen / 5)] = 1.0
+    testwaves.append(
+        {
+            "name": "block regressor",
+            "timeaxis": 1.0 * timeaxis,
+            "waveform": 1.0 * scratch,
+        }
+    )
+
+    scratch = np.zeros_like(timeaxis)
+    scratch[int(tclen / 2) :] = 1.0
+    testwaves.append(
+        {
+            "name": "step regressor",
+            "timeaxis": 1.0 * timeaxis,
+            "waveform": 1.0 * scratch,
+        }
+    )
+    return testwaves
+
+
 def spectralfilterprops(thefilter, thefiltername, debug=False):
     lowerstop, lowerpass, upperpass, upperstop = thefilter["filter"].getfreqs()
     freqspace = thefilter["frequencies"][1] - thefilter["frequencies"][0]
@@ -33,6 +75,11 @@ def spectralfilterprops(thefilter, thefiltername, debug=False):
     upperstopindex = int(
         np.min([np.ceil(upperstop / freqspace), len(thefilter["frequencies"]) - 1])
     )
+    print(f"max allowable index: {len(thefilter['frequencies']) - 1}")
+    lowerstopindex = np.max([0, lowerstopindex])
+    lowerpassindex = np.max([0, lowerpassindex])
+    upperstopindex = np.min([len(thefilter["frequencies"]) - 1, upperstopindex])
+    upperpassindex = np.min([len(thefilter["frequencies"]) - 1, upperpassindex])
     if debug:
         print("filter name:", thefiltername)
         print("freqspace:", freqspace)
@@ -105,7 +152,7 @@ def eval_filterprops(
     allfilters = []
 
     # construct all the physiological filters
-    for filtertype in ["lfo", "resp", "cardiac", "hrv_lf", "hrv_hf", "hrv_vhf"]:
+    for filtertype in ["None", "lfo", "resp", "cardiac", "hrv_lf", "hrv_hf", "hrv_vhf"]:
         testfilter = NoncausalFilter(filtertype=filtertype)
         lstest, lptest, uptest, ustest = testfilter.getfreqs()
         if lptest < nyquist:
@@ -121,43 +168,59 @@ def eval_filterprops(
                     }
                 )
 
-    """'# make the lowpass filters
+    # make the lowpass filters
     for transferfunc in transferfunclist:
         testfilter = NoncausalFilter(
-                        filtertype='arb',
-                        transferfunc=transferfunc,
-                        initlowerstop=0.0, initlowerpass=0.0,
-                        initupperpass=0.1, initupperstop=0.11)
+            filtertype="arb",
+            transferfunc=transferfunc,
+            initlowerstop=0.0,
+            initlowerpass=0.0,
+            initupperpass=0.1,
+            initupperstop=0.11,
+        )
         lstest, lptest, uptest, ustest = testfilter.getfreqs()
         if lptest < nyquist:
             allfilters.append(
                 {
-                    'name': '0.1Hz LP ' + transferfunc,
-                    'filter': NoncausalFilter(
-                                filtertype='arb',
-                                transferfunc=transferfunc,
-                                initlowerstop=0.0, initlowerpass=0.0,
-                                initupperpass=0.1, initupperstop=0.11, debug=False)
-                })
+                    "name": "0.1Hz LP " + transferfunc,
+                    "filter": NoncausalFilter(
+                        filtertype="arb",
+                        transferfunc=transferfunc,
+                        initlowerstop=0.0,
+                        initlowerpass=0.0,
+                        initupperpass=0.1,
+                        initupperstop=0.11,
+                        debug=False,
+                    ),
+                }
+            )
 
     # make the highpass filters
     for transferfunc in transferfunclist:
         testfilter = NoncausalFilter(
-                        filtertype='arb',
-                        transferfunc=transferfunc,
-                        initlowerstop=0.09, initlowerpass=0.1,
-                        initupperpass=-1.0, initupperstop=-1.0)
+            filtertype="arb",
+            transferfunc=transferfunc,
+            initlowerstop=0.09,
+            initlowerpass=0.1,
+            initupperpass=1.0e20,
+            initupperstop=1.0e20,
+        )
         lstest, lptest, uptest, ustest = testfilter.getfreqs()
         if lptest < nyquist:
             allfilters.append(
                 {
-                    'name': '0.1Hz HP ' + transferfunc,
-                    'filter': NoncausalFilter(
-                                filtertype='arb',
-                                transferfunc=transferfunc,
-                                initlowerstop=0.09, initlowerpass=0.1,
-                                initupperpass=-1.0, initupperstop=-1.0, debug=False)
-                })"""
+                    "name": "0.1Hz HP " + transferfunc,
+                    "filter": NoncausalFilter(
+                        filtertype="arb",
+                        transferfunc=transferfunc,
+                        initlowerstop=0.09,
+                        initlowerpass=0.1,
+                        initupperpass=1.0e20,
+                        initupperstop=1.0e20,
+                        debug=False,
+                    ),
+                }
+            )
 
     # calculate the transfer functions for the filters
     for index in range(0, len(allfilters)):
@@ -204,50 +267,22 @@ def eval_filterprops(
         assert response["upperstopmean"] < 1e4
 
     # construct some test waveforms for end effects
-    testwaves = []
-    testwaves.append(
-        {
-            "name": "constant high",
-            "timeaxis": 1.0 * timeaxis,
-            "waveform": np.ones((tclen), dtype="float"),
-        }
-    )
-    testwaves.append(
-        {
-            "name": "white noise",
-            "timeaxis": 1.0 * timeaxis,
-            "waveform": 0.3 * np.random.normal(size=tclen),
-        }
-    )
-
-    scratch = timeaxis * 0.0
-    scratch[int(tclen / 5) : int(2 * tclen / 5)] = 1.0
-    scratch[int(3 * tclen / 5) : int(4 * tclen / 5)] = 1.0
-    testwaves.append(
-        {
-            "name": "block regressor",
-            "timeaxis": 1.0 * timeaxis,
-            "waveform": 1.0 * scratch,
-        }
-    )
+    testwaves = maketestwaves(timeaxis)
 
     # show the end effects waveforms
     if displayplots:
-        legend = []
         plt.figure()
         plt.ylim([-2.2, 2.2 * len(testwaves)])
-        offset = 0.0
         for thewave in testwaves:
+            legend = []
+            offset = 0.0
             for thefilter in allfilters:
                 plt.plot(
                     thewave["timeaxis"],
                     offset + thefilter["filter"].apply(1.0 / sampletime, thewave["waveform"]),
                 )
                 legend.append(thewave["name"] + ": " + thefilter["name"])
-                offset += 1.0
-            # plt.plot(thewave['timeaxis'], thewave['waveform'] + offset)
-            # legend.append(thewave['name'])
-            # offset += 2.2
+                offset += 1.25
             plt.legend(legend)
             plt.show()
 
@@ -262,6 +297,10 @@ def test_filterprops(displayplots=False, debug=False):
     eval_filterprops(
         sampletime=0.1, tclengthinsecs=30000.0, numruns=10, displayplots=displayplots, debug=debug
     )
+    eval_filterprops(
+        sampletime=0.1, tclengthinsecs=30000.1, numruns=10, displayplots=displayplots, debug=debug
+    )
+    showfftcache()
 
 
 if __name__ == "__main__":

rapidtide/tests/test_findmaxlag.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.
@@ -24,9 +24,9 @@ import matplotlib.pyplot as plt
 import numpy as np
 
 import rapidtide.fit as tide_fit
-import rapidtide.helper_classes as tide_classes
 import rapidtide.io as tide_io
-from rapidtide.tests.utils import get_examples_path
+import rapidtide.simFuncClasses as tide_simFuncClasses
+from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
 def dumplists(results, targets, failflags):
@@ -39,7 +39,14 @@ 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 +68,22 @@ 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
@@ -101,7 +118,7 @@ def test_findmaxlag(displayplots=False, debug=False):
         fmlc_lfailreasons = np.zeros(len(testlags), dtype=np.uint16)
 
         # initialize the correlation fitter
-        thefitter = tide_classes.SimilarityFunctionFitter(
+        thefitter = tide_simFuncClasses.SimilarityFunctionFitter(
             corrtimeaxis=xvecs,
             lagmin=lagmin,
             lagmax=lagmax,
@@ -172,16 +189,24 @@ 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(
-            absminsigma, absmaxsigma, testsigmas, fml_maxsigmas, fml_lfailreasons
+            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, 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(
-            absminsigma, absmaxsigma, testsigmas, fmlc_maxsigmas, fmlc_lfailreasons
+            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, debug=debug
         )
 
         if displayplots:
@@ -315,19 +340,25 @@ 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(
-            absminsigma, absmaxsigma, testsigmas, fmlc_maxsigmas, fmlc_wfailreasons
+            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, 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_fullrunhappy_v1.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.
@@ -25,22 +25,27 @@ import rapidtide.workflows.happy_parser as happy_parser
 from rapidtide.tests.utils import create_dir, get_examples_path, get_test_temp_path, mse
 
 
-def test_fullrunhappy_v1(debug=False, displayplots=False):
+def test_fullrunhappy_v1(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 happy
     inputargs = [
-        os.path.join(get_examples_path(), "sub-HAPPYTEST.nii.gz"),
-        os.path.join(get_examples_path(), "sub-HAPPYTEST.json"),
-        os.path.join(get_test_temp_path(), "happyout1"),
+        os.path.join(exampleroot, "sub-HAPPYTEST.nii.gz"),
+        os.path.join(exampleroot, "sub-HAPPYTEST.json"),
+        os.path.join(testtemproot, "happyout1"),
         "--mklthreads",
         "-1",
-        "--spatialglm",
-        "--model",
-        "model_revised",
-        "--aliasedcorrelation",
+        "--spatialregression",
     ]
     happy_workflow.happy_main(happy_parser.process_args(inputargs=inputargs))
 
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunhappy_v1(debug=True, displayplots=True)
+    test_fullrunhappy_v1(debug=True, local=True, displayplots=True)

rapidtide/tests/test_fullrunhappy_v2.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.
@@ -25,25 +25,31 @@ import rapidtide.workflows.happy_parser as happy_parser
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def test_fullrunhappy_v2(debug=False, displayplots=False):
+def test_fullrunhappy_v2(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 happy
     inputargs = [
-        os.path.join(get_examples_path(), "sub-HAPPYTEST.nii.gz"),
-        os.path.join(get_examples_path(), "sub-HAPPYTEST.json"),
-        os.path.join(get_test_temp_path(), "happyout2"),
-        "--estmask",
-        os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),
+        os.path.join(exampleroot, "sub-HAPPYTEST.nii.gz"),
+        os.path.join(exampleroot, "sub-HAPPYTEST.json"),
+        os.path.join(testtemproot, "happyout2"),
+        "--estweights",
+        os.path.join(exampleroot, "sub-HAPPYTEST_smallmask.nii.gz"),
         "--projmask",
-        os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),
+        os.path.join(exampleroot, "sub-HAPPYTEST_smallmask.nii.gz"),
         "--mklthreads",
         "-1",
-        "--model",
-        "model_revised",
         "--fliparteries",
-        "--temporalglm",
+        "--temporalregression",
         "--cardiacfile",
         os.path.join(
-            get_examples_path(),
+            exampleroot,
             "sub-HAPPYTEST_desc-slicerescardfromfmri_timeseries.json:cardiacfromfmri_dlfiltered",
         ),
         "--increaseoutputlevel",
@@ -54,4 +60,4 @@ def test_fullrunhappy_v2(debug=False, displayplots=False):
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunhappy_v2(debug=True, displayplots=True)
+    test_fullrunhappy_v2(debug=True, local=True, displayplots=True)

rapidtide/tests/test_fullrunhappy_v3.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.
@@ -24,28 +24,43 @@ import rapidtide.workflows.happy as happy_workflow
 import rapidtide.workflows.happy_parser as happy_parser
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
+try:
+    import tensorflow as tf
+
+    tensorflowexists = True
+except ImportError:
+    tensorflowexists = False
+
+
+def test_fullrunhappy_v3(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()
 
-def test_fullrunhappy_v3(debug=False, displayplots=False):
     # run happy
     inputargs = [
-        os.path.join(get_examples_path(), "sub-HAPPYTEST.nii.gz"),
-        os.path.join(get_examples_path(), "sub-HAPPYTEST.json"),
-        os.path.join(get_test_temp_path(), "happyout3"),
-        "--estmask",
-        os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),
+        os.path.join(exampleroot, "sub-HAPPYTEST.nii.gz"),
+        os.path.join(exampleroot, "sub-HAPPYTEST.json"),
+        os.path.join(testtemproot, "happyout3"),
+        "--estweights",
+        os.path.join(exampleroot, "sub-HAPPYTEST_smallmask.nii.gz"),
         "--projmask",
-        os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),
+        os.path.join(exampleroot, "sub-HAPPYTEST_smallmask.nii.gz"),
         "--mklthreads",
         "-1",
-        "--model",
-        "model_revised",
         "--cardcalconly",
     ]
-    # "--motionfile",
-    # os.path.join(get_examples_path(), "sub-HAPPYTEST_mcf.par"),
+    if tensorflowexists:
+        inputargs.append("--usetensorflow")
+        inputargs.append("--model")
+        inputargs.append("model_revised_tf2")
     happy_workflow.happy_main(happy_parser.process_args(inputargs=inputargs))
 
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunhappy_v3(debug=True, displayplots=True)
+    test_fullrunhappy_v3(debug=True, local=True, displayplots=True)