rapidtide 3.0.11__py3-none-any.whl → 3.1.1__py3-none-any.whl

rapidtide/tests/test_fullrunhappy_v1.py

@@ -42,8 +42,6 @@ def test_fullrunhappy_v1(debug=False, local=False, displayplots=False):
         "--mklthreads",
         "-1",
         "--spatialregression",
-        "--model",
-        "model_revised_tf2",
     ]
     happy_workflow.happy_main(happy_parser.process_args(inputargs=inputargs))
 

rapidtide/tests/test_fullrunhappy_v2.py

@@ -45,8 +45,6 @@ def test_fullrunhappy_v2(debug=False, local=False, displayplots=False):
         os.path.join(exampleroot, "sub-HAPPYTEST_smallmask.nii.gz"),
         "--mklthreads",
         "-1",
-        "--model",
-        "model_revised_tf2",
         "--fliparteries",
         "--temporalregression",
         "--cardiacfile",

rapidtide/tests/test_fullrunhappy_v3.py

@@ -24,6 +24,13 @@ 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
@@ -45,12 +52,12 @@ def test_fullrunhappy_v3(debug=False, local=False, displayplots=False):
         os.path.join(exampleroot, "sub-HAPPYTEST_smallmask.nii.gz"),
         "--mklthreads",
         "-1",
-        "--model",
-        "model_revised_tf2",
         "--cardcalconly",
     ]
-    # "--motionfile",
-    # os.path.join(exampleroot, "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))
 
 

rapidtide/tests/test_fullrunhappy_v4.py

@@ -24,7 +24,14 @@ 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_v4(debug=False, local=False, displayplots=False):
     # set input and output directories
     if local:
@@ -45,12 +52,13 @@ def test_fullrunhappy_v4(debug=False, local=False, displayplots=False):
         os.path.join(exampleroot, "sub-HAPPYTEST_smallmask.nii.gz"),
         "--mklthreads",
         "-1",
-        "--model",
-        "model_revised_tf2",
+        "--usenewvesselmethod",
         "--motionfile",
         os.path.join(exampleroot, "sub-HAPPYTEST_mcf.par"),
         "--aliasedcorrelation",
     ]
+    if tensorflowexists:
+        inputargs.append("--usetensorflow")
     happy_workflow.happy_main(happy_parser.process_args(inputargs=inputargs))
 
 

rapidtide/tests/test_fullrunrapidtide_v7.py

@@ -81,7 +81,7 @@ def test_fullrunrapidtide_v7(debug=False, local=False, displayplots=False):
     rapidtide_retroregress.retroregress(rapidtide_retroregress.process_args(inputargs=inputargs))
 
     # check to see that rapidtide and retroregress output match
-    msethresh = 1e-6
+    msethresh = 2e-6
     aethresh = 2
     tclist = ["brain", "GM", "WM", "CSF"]
     for timecourse in tclist:

rapidtide/tests/test_getparsers.py

@@ -20,7 +20,6 @@ import numpy as np
 
 from rapidtide.workflows.adjustoffset import _get_parser as adjustoffset_getparser
 from rapidtide.workflows.aligntcs import _get_parser as aligntcs_getparser
-from rapidtide.workflows.applydlfilter import _get_parser as applydlfilter_getparser
 from rapidtide.workflows.atlasaverage import _get_parser as atlasaverage_getparser
 from rapidtide.workflows.atlastool import _get_parser as atlastool_getparser
 from rapidtide.workflows.calctexticc import _get_parser as calctexticc_getparser
@@ -84,7 +83,6 @@ def test_parsers(debug=False):
     parserlist = [
         adjustoffset_getparser,
         aligntcs_getparser,
-        applydlfilter_getparser,
         atlasaverage_getparser,
         atlastool_getparser,
         calctexticc_getparser,
@@ -137,7 +135,17 @@ def test_parsers(debug=False):
         tcfrom3col_getparser,
         variabilityizer_getparser,
     ]
-
+    try:
+        import tensorflow as tf
+        dlfilterloads = True
+    except ImportError:
+        dlfilterloads = False
+    if dlfilterloads:
+        from rapidtide.workflows.applydlfilter import (
+            _get_parser as applydlfilter_getparser,
+        )
+        parserlist.append(applydlfilter_getparser)
+    
     for thegetparser in parserlist:
         theusage = thegetparser().format_help()
         if debug:

rapidtide/tests/test_refinedelay.py

@@ -144,7 +144,6 @@ def eval_refinedelay(
     theheader["pixdim"][4] = 1.0
 
     rt_floattype = "float64"
-    rt_floatset = np.float64
     sLFOfitmean = np.zeros(numlags, dtype=rt_floattype)
     rvalue = np.zeros(numlags, dtype=rt_floattype)
     r2value = np.zeros(numlags, dtype=rt_floattype)

rapidtide/tests/test_simroundtrip.py

@@ -37,11 +37,14 @@ def test_simroundtrip(debug=False, local=False, displayplots=False):
         exampleroot = get_examples_path()
         testtemproot = get_test_temp_path()
 
-
     # run initial rapidtide
     inputargs = [
         os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
         os.path.join(testtemproot, "sub-RAPIDTIDETESTSIM"),
+        "--corrmask",
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_restrictedmask.nii.gz"),
+        "--globalmeaninclude",
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_brainmask.nii.gz"),
         "--spatialfilt",
         "2",
         "--simcalcrange",
@@ -58,24 +61,29 @@ def test_simroundtrip(debug=False, local=False, displayplots=False):
     ]
     rapidtide_workflow.rapidtide_main(rapidtide_parser.process_args(inputargs=inputargs))
 
+    print("initial rapidtide run complete")
+
     # now simulate data from maps
     print(testtemproot)
     inputargs = [
         "1.5",
         "260",
-        os.path.join( testtemproot, "sub-RAPIDTIDETESTSIM_desc-unfiltmean_map.nii.gz"),
-        os.path.join( testtemproot, "simulatedfmri_vn05"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETESTSIM_desc-unfiltmean_map.nii.gz"),
+        os.path.join(testtemproot, "simulatedfmri_vn05"),
         "--lfopctfile",
-        os.path.join( testtemproot, "sub-RAPIDTIDETESTSIM_desc-maxcorr_map.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETESTSIM_desc-maxcorr_map.nii.gz"),
         "--lfolagfile",
-        os.path.join( testtemproot, "sub-RAPIDTIDETESTSIM_desc-maxtimerefined_map.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETESTSIM_desc-maxtimerefined_map.nii.gz"),
         "--lforegressor",
-        os.path.join(testtemproot, "sub-RAPIDTIDETESTSIM_desc-movingregressor_timeseries.json:pass2"),
+        os.path.join(
+            testtemproot, "sub-RAPIDTIDETESTSIM_desc-movingregressor_timeseries.json:pass2"
+        ),
         "--voxelnoiselevel",
-        "5.0"
+        "5.0",
     ]
 
     pf.generic_init(rapidtide_simdata._get_parser, rapidtide_simdata.simdata, inputargs=inputargs)
+    print("simulated dataset generated")
 
     # run repeat rapidtide
     inputargs = [
@@ -96,6 +104,7 @@ def test_simroundtrip(debug=False, local=False, displayplots=False):
         "4.0",
     ]
     rapidtide_workflow.rapidtide_main(rapidtide_parser.process_args(inputargs=inputargs))
+    print("repeat rapidtide completed")
 
     absthresh = 1e-10
     msethresh = 1e-12
@@ -118,7 +127,6 @@ def test_simroundtrip(debug=False, local=False, displayplots=False):
         )"""
 
 
-
 if __name__ == "__main__":
     mpl.use("TkAgg")
     test_simroundtrip(debug=True, local=True, displayplots=True)

rapidtide/tests/test_stcorrelate.py

@@ -58,6 +58,7 @@ def test_stcorrelate(debug=False):
     times, corrpertime, ppertime = shorttermcorr_1D(
         sig1, sig2, tr, windowtime, samplestep=int(stepsize // tr), detrendorder=0
     )
+    print(f"1D correlation: {corrpertime=}, {ppertime=}")
     # plength = len(times)
     times, xcorrpertime, Rvals, delayvals, valid = shorttermcorr_2D(
         sig1,
@@ -67,8 +68,9 @@ def test_stcorrelate(debug=False):
         samplestep=int(stepsize // tr),
         weighting=corrweighting,
         detrendorder=0,
-        displayplots=False,
+        displayplots=debug,
     )
+    print(f"2D correlation: {Rvals=}, {delayvals=}, {valid=}")
     # xlength = len(times)
     writenpvecs(corrpertime, outfilename + "_pearson.txt")
     writenpvecs(ppertime, outfilename + "_pvalue.txt")

rapidtide/tests/utils.py

@@ -23,9 +23,10 @@ Utility functions for testing rapidtide.
 import os
 
 import numpy as np
+import numpy.typing as npt
 
 
-def get_rapidtide_root():
+def get_rapidtide_root() -> str:
     """
     Returns the path to the base rapidtide directory, terminated with separator.
     Based on function by Yaroslav Halchenko used in Neurosynth Python package.
@@ -34,7 +35,7 @@ def get_rapidtide_root():
     return os.path.join(thisdir, "..") + os.path.sep
 
 
-def get_scripts_path():
+def get_scripts_path() -> str:
     """
     Returns the path to test datasets, terminated with separator. Test-related
     data are kept in tests folder in "testdata".
@@ -43,7 +44,7 @@ def get_scripts_path():
     return os.path.realpath(os.path.join(get_rapidtide_root(), "scripts")) + os.path.sep
 
 
-def get_test_data_path():
+def get_test_data_path() -> str:
     """
     Returns the path to test datasets, terminated with separator. Test-related
     data are kept in tests folder in "testdata".
@@ -52,7 +53,7 @@ def get_test_data_path():
     return os.path.realpath(os.path.join(get_rapidtide_root(), "tests", "testdata")) + os.path.sep
 
 
-def get_test_target_path():
+def get_test_target_path() -> str:
     """
     Returns the path to test comparison data, terminated with separator. Test-related
     data are kept in tests folder in "testtargets".
@@ -63,7 +64,7 @@ def get_test_target_path():
     )
 
 
-def get_test_temp_path():
+def get_test_temp_path() -> str:
     """
     Returns the path to test temporary directory, terminated with separator.
     Based on function by Yaroslav Halchenko used in Neurosynth Python package.
@@ -71,7 +72,7 @@ def get_test_temp_path():
     return os.path.realpath(os.path.join(get_rapidtide_root(), "tests", "tmp")) + os.path.sep
 
 
-def get_examples_path():
+def get_examples_path() -> str:
     """
     Returns the path to examples src directory, where larger test files live, terminated with separator. Test-related
     data are kept in tests folder in "data".
@@ -83,7 +84,7 @@ def get_examples_path():
     )
 
 
-def create_dir(thedir, debug=False):
+def create_dir(thedir: str, debug: bool = False) -> None:
     # create a directory if it doesn't exist
     try:
         os.makedirs(thedir)
@@ -96,7 +97,7 @@ def create_dir(thedir, debug=False):
             pass
 
 
-def mse(ndarr1, ndarr2):
+def mse(ndarr1: npt.NDArray, ndarr2: npt.NDArray) -> np.floating:
     """
     Compute mean-squared error.
     """