rapidtide 3.0a12__py3-none-any.whl → 3.0a14__py3-none-any.whl

rapidtide/tests/test_delayestimation.py

@@ -24,8 +24,8 @@ import numpy as np
 
 import rapidtide.calcsimfunc as tide_calcsimfunc
 import rapidtide.filter as tide_filt
-import rapidtide.glmpass as tide_glmpass
 import rapidtide.helper_classes as tide_classes
+import rapidtide.linfitfiltpass as tide_linfitfiltpass
 import rapidtide.miscmath as tide_math
 import rapidtide.peakeval as tide_peakeval
 import rapidtide.resample as tide_resample
@@ -335,7 +335,7 @@ def test_delayestimation(displayplots=False, debug=False):
         filteredwaveforms[i, :] = theprefilter.apply(Fs, waveforms[i, :])
 
     for nprocs in [4, 1]:
-        voxelsprocessed_glm = tide_glmpass.glmpass(
+        voxelsprocessed_regressionfilt = tide_linfitfiltpass.linfitfiltpass(
             numlocs,
             waveforms[:, :],
             threshval,
@@ -366,7 +366,7 @@ def test_delayestimation(displayplots=False, debug=False):
         ax.legend()
         plt.show()
 
-        print(proctype, "glmpass", np.mean(diffsignal), np.max(np.fabs(diffsignal)))
+        print(proctype, "linfitfiltpass", np.mean(diffsignal), np.max(np.fabs(diffsignal)))
 
     # clean up shared memory
     tide_util.cleanup_shm(waveforms_shm)

rapidtide/tests/test_fastresampler.py

@@ -23,8 +23,7 @@ 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
+from rapidtide.tests.utils import get_test_temp_path, mse
 
 
 def test_FastResampler(debug=False):

rapidtide/tests/test_fullrunhappy_v1.py

@@ -25,15 +25,23 @@ 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",
+        "--spatialregression",
         "--model",
         "model_revised",
     ]
@@ -42,4 +50,4 @@ def test_fullrunhappy_v1(debug=False, displayplots=False):
 
 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

@@ -25,25 +25,33 @@ 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"),
+        os.path.join(exampleroot, "sub-HAPPYTEST.nii.gz"),
+        os.path.join(exampleroot, "sub-HAPPYTEST.json"),
+        os.path.join(testtemproot, "happyout2"),
         "--estweights",
-        os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),
+        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 +62,4 @@ 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

@@ -25,16 +25,24 @@ import rapidtide.workflows.happy_parser as happy_parser
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def test_fullrunhappy_v3(debug=False, displayplots=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()
+
     # 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"),
+        os.path.join(exampleroot, "sub-HAPPYTEST.nii.gz"),
+        os.path.join(exampleroot, "sub-HAPPYTEST.json"),
+        os.path.join(testtemproot, "happyout3"),
         "--estweights",
-        os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),
+        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",
@@ -42,10 +50,10 @@ def test_fullrunhappy_v3(debug=False, displayplots=False):
         "--cardcalconly",
     ]
     # "--motionfile",
-    # os.path.join(get_examples_path(), "sub-HAPPYTEST_mcf.par"),
+    # os.path.join(exampleroot, "sub-HAPPYTEST_mcf.par"),
     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)

rapidtide/tests/test_fullrunhappy_v4.py

@@ -25,22 +25,30 @@ import rapidtide.workflows.happy_parser as happy_parser
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def test_fullrunhappy_v4(debug=False, displayplots=False):
+def test_fullrunhappy_v4(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(), "happyout4"),
+        os.path.join(exampleroot, "sub-HAPPYTEST.nii.gz"),
+        os.path.join(exampleroot, "sub-HAPPYTEST.json"),
+        os.path.join(testtemproot, "happyout4"),
         "--estweights",
-        os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),
+        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",
         "--motionfile",
-        os.path.join(get_examples_path(), "sub-HAPPYTEST_mcf.par"),
+        os.path.join(exampleroot, "sub-HAPPYTEST_mcf.par"),
         "--aliasedcorrelation",
     ]
     happy_workflow.happy_main(happy_parser.process_args(inputargs=inputargs))
@@ -48,4 +56,4 @@ def test_fullrunhappy_v4(debug=False, displayplots=False):
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunhappy_v4(debug=True, displayplots=True)
+    test_fullrunhappy_v4(debug=True, local=True, displayplots=True)

rapidtide/tests/test_fullrunhappy_v5.py

@@ -25,16 +25,24 @@ import rapidtide.workflows.happy_parser as happy_parser
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def test_fullrunhappy_v4(debug=False, displayplots=False):
+def test_fullrunhappy_v4(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(), "happyout5"),
+        os.path.join(exampleroot, "sub-HAPPYTEST.nii.gz"),
+        os.path.join(exampleroot, "sub-HAPPYTEST.json"),
+        os.path.join(testtemproot, "happyout5"),
         "--model",
         "model_revised",
         "--motionfile",
-        os.path.join(get_examples_path(), "sub-HAPPYTEST_mcf.par"),
+        os.path.join(exampleroot, "sub-HAPPYTEST_mcf.par"),
         "--nomotderiv",
         "--nomotorthogonalize",
         "--motfiltorder",
@@ -53,4 +61,4 @@ def test_fullrunhappy_v4(debug=False, displayplots=False):
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunhappy_v4(debug=True, displayplots=True)
+    test_fullrunhappy_v4(debug=True, local=True, displayplots=True)

rapidtide/tests/test_fullrunrapidtide_v1.py

@@ -26,11 +26,19 @@ import rapidtide.workflows.rapidtide_parser as rapidtide_parser
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def test_fullrunrapidtide_v1(debug=False, displayplots=False):
+def test_fullrunrapidtide_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 rapidtide
     inputargs = [
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST1"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST1"),
         "--spatialfilt",
         "2",
         "--simcalcrange",
@@ -46,11 +54,11 @@ def test_fullrunrapidtide_v1(debug=False, displayplots=False):
         "4.0",
     ]
     rapidtide_workflow.rapidtide_main(rapidtide_parser.process_args(inputargs=inputargs))
-    rapidtide_quality.qualitycheck(os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST1"))
+    rapidtide_quality.qualitycheck(os.path.join(testtemproot, "sub-RAPIDTIDETEST1"))
 
     inputargs = [
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST1_fixval"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST1_fixval"),
         "--spatialfilt",
         "2",
         "--simcalcrange",
@@ -62,7 +70,7 @@ def test_fullrunrapidtide_v1(debug=False, displayplots=False):
         "1",
         "--despecklepasses",
         "3",
-        "--noglm",
+        "--nodenoise",
         "--norefinedelay",
         "--initialdelay",
         "0.0",
@@ -70,8 +78,8 @@ def test_fullrunrapidtide_v1(debug=False, displayplots=False):
     rapidtide_workflow.rapidtide_main(rapidtide_parser.process_args(inputargs=inputargs))
 
     inputargs = [
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST1_fixmap"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST1_fixmap"),
         "--spatialfilt",
         "2",
         "--simcalcrange",
@@ -83,13 +91,13 @@ def test_fullrunrapidtide_v1(debug=False, displayplots=False):
         "1",
         "--despecklepasses",
         "3",
-        "--noglm",
+        "--nodenoise",
         "--initialdelay",
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST1_desc-maxtime_map.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST1_desc-maxtime_map.nii.gz"),
     ]
     rapidtide_workflow.rapidtide_main(rapidtide_parser.process_args(inputargs=inputargs))
 
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunrapidtide_v1(debug=True, displayplots=True)
+    test_fullrunrapidtide_v1(debug=True, local=True, displayplots=True)

rapidtide/tests/test_fullrunrapidtide_v2.py

@@ -25,27 +25,35 @@ import rapidtide.workflows.rapidtide_parser as rapidtide_parser
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def test_fullrunrapidtide_v2(debug=False, displayplots=False):
+def test_fullrunrapidtide_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 rapidtide
     inputargs = [
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST2"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST2"),
         "--tincludemask",
-        os.path.join(get_examples_path(), "tmask3.txt"),
+        os.path.join(exampleroot, "tmask3.txt"),
         "--corrmask",
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST_restrictedmask.nii.gz"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_restrictedmask.nii.gz"),
         "--globalmeaninclude",
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST_brainmask.nii.gz"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_brainmask.nii.gz"),
         "--globalmeanexclude",
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST_nullmask.nii.gz"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_nullmask.nii.gz"),
         "--refineinclude",
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST_brainmask.nii.gz"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_brainmask.nii.gz"),
         "--refineexclude",
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST_nullmask.nii.gz"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_nullmask.nii.gz"),
         "--offsetinclude",
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST_brainmask.nii.gz"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_brainmask.nii.gz"),
         "--offsetexclude",
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST_nullmask.nii.gz"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_nullmask.nii.gz"),
         "--spatialfilt",
         "-1",
         "--savelags",
@@ -74,7 +82,7 @@ def test_fullrunrapidtide_v2(debug=False, displayplots=False):
         "--refineprenorm",
         "var",
         "--motionfile",
-        os.path.join(get_examples_path(), "fakemotion.par"),
+        os.path.join(exampleroot, "fakemotion.par"),
     ]
     if debug:
         print(inputargs)
@@ -83,4 +91,4 @@ def test_fullrunrapidtide_v2(debug=False, displayplots=False):
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunrapidtide_v2(debug=True, displayplots=True)
+    test_fullrunrapidtide_v2(debug=True, local=True, displayplots=True)

rapidtide/tests/test_fullrunrapidtide_v3.py

@@ -25,13 +25,21 @@ import rapidtide.workflows.rapidtide_parser as rapidtide_parser
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def test_fullrunrapidtide_v3(debug=False, displayplots=False):
+def test_fullrunrapidtide_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()
+
     # run rapidtide
     inputargs = [
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST3"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST3"),
         "--corrmask",
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST_restrictedmask.nii.gz:1"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_restrictedmask.nii.gz:1"),
         "--maxpasses",
         "2",
         "--numnull",
@@ -40,7 +48,7 @@ def test_fullrunrapidtide_v3(debug=False, displayplots=False):
         "pca",
         "--convergencethresh",
         "0.5",
-        "--noglm",
+        "--nodenoise",
         "--nprocs",
         "-1",
         "--similaritymetric",
@@ -60,7 +68,7 @@ def test_fullrunrapidtide_v3(debug=False, displayplots=False):
         "R",
         "--regressor",
         os.path.join(
-            get_examples_path(),
+            exampleroot,
             "sub-RAPIDTIDETEST_desc-oversampledmovingregressor_timeseries.json:pass3",
         ),
     ]
@@ -71,4 +79,4 @@ def test_fullrunrapidtide_v3(debug=False, displayplots=False):
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunrapidtide_v3(debug=True, displayplots=True)
+    test_fullrunrapidtide_v3(debug=True, local=True, displayplots=True)

rapidtide/tests/test_fullrunrapidtide_v4.py

@@ -25,18 +25,25 @@ import rapidtide.workflows.rapidtide_parser as rapidtide_parser
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def test_fullrunrapidtide_v4(debug=False, displayplots=False):
+def test_fullrunrapidtide_v4(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(get_examples_path(), "sub-NIRSRAPIDTIDETEST.txt"),
-        os.path.join(get_test_temp_path(), "sub-NIRSRAPIDTIDETEST4"),
+        os.path.join(exampleroot, "sub-NIRSRAPIDTIDETEST.txt"),
+        os.path.join(testtemproot, "sub-NIRSRAPIDTIDETEST4"),
         "--globalmeaninclude",
-        os.path.join(get_examples_path(), "sub-NIRSRAPIDTIDETEST_mask.txt"),
+        os.path.join(exampleroot, "sub-NIRSRAPIDTIDETEST_mask.txt"),
         "--nirs",
         "--datatstep",
         "0.2560",
-        "--globalmaskmethod",
-        "variance",
+        "--dataiszeromean",
         "--norefinedelay",
         "--despecklepasses",
         "0",
@@ -59,4 +66,4 @@ def test_fullrunrapidtide_v4(debug=False, displayplots=False):
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunrapidtide_v4(debug=True, displayplots=True)
+    test_fullrunrapidtide_v4(debug=True, local=True, displayplots=True)

rapidtide/tests/test_fullrunrapidtide_v5.py

@@ -25,17 +25,25 @@ import rapidtide.workflows.rapidtide_parser as rapidtide_parser
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def test_fullrunrapidtide_v5(debug=False, displayplots=False):
+def test_fullrunrapidtide_v5(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(get_examples_path(), "sub-RAPIDTIDETEST_cifti.ptseries.nii"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST5"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_cifti.ptseries.nii"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST5"),
         "--nprocs",
         "-1",
         "--passes",
         "2",
         "--numnull",
-        "0",
+        "10000",
         "--pickleft",
         "--norefinedelay",
         "--refineprenorm",
@@ -46,4 +54,4 @@ def test_fullrunrapidtide_v5(debug=False, displayplots=False):
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunrapidtide_v5(debug=True, displayplots=True)
+    test_fullrunrapidtide_v5(debug=True, local=True, displayplots=True)

rapidtide/tests/test_fullrunrapidtide_v6.py

@@ -24,15 +24,23 @@ import matplotlib as mpl
 import rapidtide.io as tide_io
 import rapidtide.workflows.rapidtide as rapidtide_workflow
 import rapidtide.workflows.rapidtide_parser as rapidtide_parser
-import rapidtide.workflows.retroglm as rapidtide_retroglm
+import rapidtide.workflows.retroregress as rapidtide_retroregress
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def test_fullrunrapidtide_v6(debug=False, displayplots=False):
+def test_fullrunrapidtide_v6(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(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST6"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST6"),
         "--spatialfilt",
         "2",
         "--simcalcrange",
@@ -44,7 +52,7 @@ def test_fullrunrapidtide_v6(debug=False, displayplots=False):
         "1",
         "--despecklepasses",
         "3",
-        "--glmderivs",
+        "--regressderivs",
         "0",
         "--delaypatchthresh",
         "4.0",
@@ -54,59 +62,59 @@ def test_fullrunrapidtide_v6(debug=False, displayplots=False):
     rapidtide_workflow.rapidtide_main(rapidtide_parser.process_args(inputargs=inputargs))
 
     inputargs = [
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST6"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST6"),
         "--alternateoutput",
-        os.path.join(get_test_temp_path(), "2deriv"),
+        os.path.join(testtemproot, "2deriv"),
         "--nprocs",
         "-1",
-        "--glmderivs",
+        "--regressderivs",
         "2",
         "--makepseudofile",
         "--outputlevel",
         "max",
     ]
-    rapidtide_retroglm.retroglm(rapidtide_retroglm.process_args(inputargs=inputargs))
+    rapidtide_retroregress.retroregress(rapidtide_retroregress.process_args(inputargs=inputargs))
 
     inputargs = [
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST6"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST6"),
         "--alternateoutput",
-        os.path.join(get_test_temp_path(), "1deriv_refined_corrected"),
+        os.path.join(testtemproot, "1deriv_refined_corrected"),
         "--nprocs",
         "1",
-        "--glmderivs",
+        "--regressderivs",
         "1",
         "--makepseudofile",
         "--outputlevel",
         "max",
         "--nofilterwithrefineddelay",
     ]
-    rapidtide_retroglm.retroglm(rapidtide_retroglm.process_args(inputargs=inputargs))
+    rapidtide_retroregress.retroregress(rapidtide_retroregress.process_args(inputargs=inputargs))
 
     inputargs = [
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST6"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST6"),
         "--alternateoutput",
-        os.path.join(get_test_temp_path(), "concordance"),
+        os.path.join(testtemproot, "concordance"),
         "--nprocs",
         "-1",
-        "--glmderivs",
+        "--regressderivs",
         "0",
         "--delaypatchthresh",
         "4.0",
         "--outputlevel",
         "max",
     ]
-    rapidtide_retroglm.retroglm(rapidtide_retroglm.process_args(inputargs=inputargs))
+    rapidtide_retroregress.retroregress(rapidtide_retroregress.process_args(inputargs=inputargs))
 
     absthresh = 1e-10
     msethresh = 1e-12
     spacetolerance = 1e-3
     for map in [
-        "glmderivratios",
-        "medfiltglmderivratios",
-        "filteredglmderivratios",
+        "regressderivratios",
+        "medfiltregressderivratios",
+        "filteredregressderivratios",
         "maxtimerefined",
         "lfofilterInbandVarianceBefore",
         "lfofilterInbandVarianceAfter",
@@ -118,8 +126,8 @@ def test_fullrunrapidtide_v6(debug=False, displayplots=False):
         "lfofilterR",
     ]:
         print(f"Testing map={map}")
-        filename1 = os.path.join(get_test_temp_path(), f"sub-RAPIDTIDETEST6_desc-{map}_map.nii.gz")
-        filename2 = os.path.join(get_test_temp_path(), f"concordance_desc-{map}_map.nii.gz")
+        filename1 = os.path.join(testtemproot, f"sub-RAPIDTIDETEST6_desc-{map}_map.nii.gz")
+        filename2 = os.path.join(testtemproot, f"concordance_desc-{map}_map.nii.gz")
         assert tide_io.checkniftifilematch(
             filename1,
             filename2,
@@ -132,4 +140,4 @@ def test_fullrunrapidtide_v6(debug=False, displayplots=False):
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunrapidtide_v6(debug=True, displayplots=True)
+    test_fullrunrapidtide_v6(debug=True, local=True, displayplots=True)