rapidtide 3.1__py3-none-any.whl → 3.1.1__py3-none-any.whl

rapidtide/refineregressor.py

@@ -19,7 +19,7 @@
 import gc
 import logging
 import sys
-from typing import Any, Callable
+from typing import Any
 
 import numpy as np
 import statsmodels as sm
@@ -48,7 +48,7 @@ def _procOneVoxelTimeShift(
         "debug": False,
     }
     options.update(kwargs)
-    detrendorder = options["detrendorder"]
+    detrendorder = int(options["detrendorder"])
     offsettime = options["offsettime"]
     debug = options["debug"]
     if debug:
@@ -234,8 +234,7 @@ def alignvoxels(
     chunksize: int = 1000,
     padtrs: int = 60,
     debug: bool = False,
-    rt_floatset: type = np.float64,
-    rt_floattype: str = "float64",
+    rt_floattype: np.dtype = np.float64,
 ) -> int:
     """
     Apply temporal alignment (timeshift) to all voxels in fMRI data based on correlation peaks.
@@ -246,21 +245,21 @@ def alignvoxels(
 
     Parameters
     ----------
-    fmridata : 4D numpy.ndarray
+    fmridata : 4D NDArray
         fMRI data, filtered to the passband, with shape (nx, ny, nz, nt)
     fmritr : float
         Data repetition time (TR), in seconds
-    shiftedtcs : 4D numpy.ndarray
+    shiftedtcs : 4D NDArray
         Destination array for time-aligned voxel timecourses, shape (nx, ny, nz, nt)
-    weights : 4D numpy.ndarray
+    weights : 4D NDArray
         Weights for each timepoint in the final regressor, shape (nx, ny, nz, nt)
-    paddedshiftedtcs : 4D numpy.ndarray
+    paddedshiftedtcs : 4D NDArray
         Time-aligned voxel timecourses with padding, shape (nx, ny, nz, nt + 2*padtrs)
-    paddedweights : 4D numpy.ndarray
+    paddedweights : 4D NDArray
         Weights for each timepoint in the padded regressor, shape (nx, ny, nz, nt + 2*padtrs)
-    lagtimes : 3D numpy.ndarray
+    lagtimes : 3D NDArray
         Time delay of maximum crosscorrelation in seconds, shape (nx, ny, nz)
-    lagmask : 3D numpy.ndarray
+    lagmask : 3D NDArray
         Mask of voxels with successful correlation fits, shape (nx, ny, nz)
     detrendorder : int, optional
         Order of polynomial used to detrend the data (default is 1)
@@ -278,10 +277,8 @@ def alignvoxels(
         Number of timepoints to pad on each end of the timecourses (default is 60)
     debug : bool, optional
         If True, enable additional debugging output (default is False)
-    rt_floatset : type, optional
+    rt_floattype : np.dtype, optional
         Function to coerce variable types (default is np.float64)
-    rt_floattype : str, optional
-        Data type for internal variables ('float32' or 'float64') (default is 'float64')
 
     Returns
     -------
@@ -378,8 +375,7 @@ def makerefinemask(
     excludemask: NDArray | None = None,
     fixdelay: bool = False,
     debug: bool = False,
-    rt_floatset: type = np.float64,
-    rt_floattype: str = "float64",
+    rt_floattype: np.dtype = np.float64,
 ) -> tuple[int, NDArray | None, int, int, int, int, int]:
     """
     Determine which voxels should be used for regressor refinement based on correlation strength,
@@ -426,10 +422,8 @@ def makerefinemask(
         If True, uses the raw `lagmask` without applying delay thresholds. Default is False.
     debug : bool, optional
         Enable additional debugging output. Default is False.
-    rt_floatset : callable, optional
-        Function to coerce variable types. Default is `np.float64`.
-    rt_floattype : str, optional
-        Data type for internal variables. Must be 'float32' or 'float64'. Default is 'float64'.
+    rt_floattype : np.dtype, optional
+        Data type for internal arrays. Default is `np.float64`.
 
     Returns
     -------
@@ -693,8 +687,7 @@ def dorefine(
     cleanrefined: bool = False,
     bipolar: bool = False,
     debug: bool = False,
-    rt_floatset: type = np.float64,
-    rt_floattype: str = "float64",
+    rt_floattype: np.dtype = np.float64,
 ) -> tuple[int, NDArray]:
     """
     Refine timecourses using specified method (ICA, PCA, weighted average, or unweighted average).
@@ -748,10 +741,8 @@ def dorefine(
         If True, flip sign of negative lag strengths (default is False).
     debug : bool, optional
         If True, print debug information (default is False).
-    rt_floatset : type, optional
+    rt_floattype : np.dtype, optional
         Data type for floating-point numbers (default is np.float64).
-    rt_floattype : str, optional
-        String representation of floating-point data type (default is "float64").
 
     Returns
     -------
@@ -883,7 +874,7 @@ def dorefine(
             theprefilter.apply(fmrifreq, icadata),
             detrendorder=detrendorder,
         )
-        thepxcorr = pearsonr(filteredavg, filteredica)[0]
+        thepxcorr = pearsonr(filteredavg, filteredica).statistic
         LGR.info(f"ica/avg correlation = {thepxcorr}")
         if thepxcorr > 0.0:
             outputdata = 1.0 * icadata
@@ -918,7 +909,7 @@ def dorefine(
             theprefilter.apply(fmrifreq, pcadata),
             detrendorder=detrendorder,
         )
-        thepxcorr = pearsonr(filteredavg, filteredpca)[0]
+        thepxcorr = pearsonr(filteredavg, filteredpca).statistic
         LGR.info(f"pca/avg correlation = {thepxcorr}")
         if thepxcorr > 0.0:
             outputdata = 1.0 * pcadata
@@ -934,8 +925,8 @@ def dorefine(
     if cleanrefined:
         thefit, R2 = tide_fit.mlregress(averagediscard, averagedata)
 
-        fitcoff = rt_floatset(thefit[0, 1])
-        datatoremove = rt_floatset(fitcoff * averagediscard)
+        fitcoff = thefit[0, 1]
+        datatoremove = (fitcoff * averagediscard).astype(rt_floattype)
         outputdata -= datatoremove
 
     # garbage collect

rapidtide/scripts/showxcorr_legacy.py

@@ -79,7 +79,7 @@ def getNullDistributionData(
         corrlist[i] = theshuffledxcorr_trim[argmax(theshuffledxcorr_trim)]
 
         # find and tabulate correlation coefficient at 0 lag
-        corrlist_pear[i] = pearsonr(filteredindata, filteredshuffleddata)[0]
+        corrlist_pear[i] = pearsonr(filteredindata, filteredshuffleddata).statistic
 
         # progress
         # tide_util.progressbar(i + 1, numreps, label='Percent complete')
@@ -455,7 +455,7 @@ def main():
 
     # report the pearson correlation
     if showpearson and verbose:
-        print("Pearson_R:\t", thepxcorr[0])
+        print("Pearson_R:\t", thepxcorr.statistic)
         if estimate_significance:
             for idx, percentile in enumerate(thepercentiles):
                 print(
@@ -467,7 +467,7 @@ def main():
         print("")
 
     if debug:
-        print(thepxcorr)
+        print(thepxcorr.statistic, thepxcorr.pvalue)
 
     if verbose:
         if uselabel:
@@ -497,7 +497,7 @@ def main():
                         "xcorr_R(P=0.05)",
                         "xcorr_maxdelay",
                     )
-                print(thelabel, thepxcorr[0], pearpcts_fit[0], R, pcts_fit[0], -maxdelay)
+                print(thelabel, thepxcorr.statistic, pearpcts_fit[0], R, pcts_fit[0], -maxdelay)
             else:
                 if labelline:
                     print(
@@ -507,7 +507,7 @@ def main():
                         "xcorr_R(P=0.05)",
                         "xcorr_maxdelay",
                     )
-                print(thepxcorr[0], pearpcts_fit[0], R, pcts_fit[0], -maxdelay)
+                print(thepxcorr.statistic, pearpcts_fit[0], R, pcts_fit[0], -maxdelay)
         else:
             if uselabel:
                 if labelline:
@@ -518,11 +518,11 @@ def main():
                         "xcorr_R",
                         "xcorr_maxdelay",
                     )
-                print(thelabel, thepxcorr[0], thepxcorr[1], R, -maxdelay)
+                print(thelabel, thepxcorr.statistic, thepxcorr.pvalue, R, -maxdelay)
             else:
                 if labelline:
                     print("pearson_r\tpearson_p\txcorr_R\txcorr_t\txcorr_maxdelay")
-                print(thepxcorr[0], "\t", thepxcorr[1], "\t", R, "\t", -maxdelay)
+                print(thepxcorr.statistic, "\t", thepxcorr.pvalue, "\t", R, "\t", -maxdelay)
 
     if displayplots:
         fig = figure()

rapidtide/scripts/stupidramtricks.py

@@ -102,19 +102,15 @@ def stupidramtricks(args):
         args.nprocs = tide_multiproc.maxcpus()
 
     if args.internalprecision == "double":
-        rt_floattype = "float64"
-        rt_floatset = np.float64
+        rt_floattype = np.float64
     else:
-        rt_floattype = "float32"
-        rt_floatset = np.float32
+        rt_floattype = np.float32
 
     # set the output precision
     if args.outputprecision == "double":
-        rt_outfloattype = "float64"
-        rt_outfloatset = np.float64
+        rt_outfloattype = np.float64
     else:
-        rt_outfloattype = "float32"
-        rt_outfloatset = np.float32
+        rt_outfloattype = np.float32
 
     # select the voxels in the mask
     print("setting sizes")
@@ -139,23 +135,25 @@ def stupidramtricks(args):
             print("allocating shared memory")
         # first move fmridata into shared memory
         fmridata, fmridata_shm = tide_util.numpy2shared(
-            fmridata, rt_floatset, name=f"fmridata_{args.pid}"
+            fmridata, rt_floattype, name=f"fmridata_{args.pid}"
         )
         sLFOfitmean, sLFOfitmean_shm = tide_util.allocshared(
-            internalvalidspaceshape, rt_outfloatset
+            internalvalidspaceshape, rt_outfloattype
+        )
+        rvalue, rvalue_shm = tide_util.allocshared(internalvalidspaceshape, rt_outfloattype)
+        r2value, r2value_shm = tide_util.allocshared(internalvalidspaceshape, rt_outfloattype)
+        fitNorm, fitNorm_shm = tide_util.allocshared(
+            internalvalidspaceshapederivs, rt_outfloattype
         )
-        rvalue, rvalue_shm = tide_util.allocshared(internalvalidspaceshape, rt_outfloatset)
-        r2value, r2value_shm = tide_util.allocshared(internalvalidspaceshape, rt_outfloatset)
-        fitNorm, fitNorm_shm = tide_util.allocshared(internalvalidspaceshapederivs, rt_outfloatset)
         fitcoeff, fitcoeff_shm = tide_util.allocshared(
-            internalvalidspaceshapederivs, rt_outfloatset
+            internalvalidspaceshapederivs, rt_outfloattype
         )
         movingsignal, movingsignal_shm = tide_util.allocshared(
-            internalvalidfmrishape, rt_outfloatset
+            internalvalidfmrishape, rt_outfloattype
         )
-        lagtc, lagtc_shm = tide_util.allocshared(internalvalidfmrishape, rt_floatset)
+        lagtc, lagtc_shm = tide_util.allocshared(internalvalidfmrishape, rt_floattype)
         filtereddata, filtereddata_shm = tide_util.allocshared(
-            internalvalidfmrishape, rt_outfloatset
+            internalvalidfmrishape, rt_outfloattype
         )
 
         location = "in shared memory"

rapidtide/simFuncClasses.py

@@ -158,7 +158,7 @@ class SimilarityFunctionator:
 
         Parameters
         ----------
-        thetc : numpy.ndarray
+        thetc : NDArray
             Input timecourse data to be prepared
         isreftc : bool, optional
             Flag indicating whether the input is a reference timecourse. If True, the timecourse
@@ -166,7 +166,7 @@ class SimilarityFunctionator:
 
         Returns
         -------
-        numpy.ndarray
+        NDArray
             Prepared and normalized timecourse data after filtering, normalization, detrending,
             and window function application
 

rapidtide/simfuncfit.py

@@ -40,8 +40,7 @@ def onesimfuncfit(
     lthreshval: float = 0.0,
     fixdelay: bool = False,
     initialdelayvalue: float = 0.0,
-    rt_floatset: type = np.float64,
-    rt_floattype: str = "float64",
+    rt_floattype: np.dtype = np.float64,
 ) -> Tuple[int, float, float, float, int, int, int, int]:
     """
     Perform a single fit on a correlation function using the provided fitter.
@@ -70,10 +69,8 @@ def onesimfuncfit(
         Default is False.
     initialdelayvalue : float, optional
         The fixed delay value to use when `fixdelay=True`. Default is 0.0.
-    rt_floatset : type, optional
+    rt_floattype : np.dtype, optional
         The data type to use for floating-point values. Default is `np.float64`.
-    rt_floattype : str, optional
-        String representation of the floating-point type. Default is "float64".
 
     Returns
     -------
@@ -96,7 +93,6 @@ def onesimfuncfit(
     Examples
     --------
     >>> import numpy as np
-    >>> from some_module import some_fitter_class
     >>> corr_func = np.random.rand(100)
     >>> fitter = some_fitter_class()
     >>> result = onesimfuncfit(corr_func, fitter)
@@ -128,10 +124,10 @@ def onesimfuncfit(
     else:
         # do something different
         failreason = np.uint32(0)
-        maxlag = rt_floatset(initialdelayvalue)
+        maxlag = initialdelayvalue
         maxindex = np.int16(bisect.bisect_left(thefitter.corrtimeaxis, initialdelayvalue))
-        maxval = rt_floatset(correlationfunc[maxindex])
-        maxsigma = rt_floatset(1.0)
+        maxval = correlationfunc[maxindex]
+        maxsigma = 1.0
         maskval = np.uint16(1)
         peakstart = maxindex
         peakend = maxindex
@@ -148,8 +144,7 @@ def _procOneVoxelFitcorr(
     initiallag: Optional[float] = None,
     fixdelay: bool = False,
     initialdelayvalue: float = 0.0,
-    rt_floatset: type = np.float64,
-    rt_floattype: str = "float64",
+    rt_floattype: np.dtype = np.float64,
 ) -> Tuple[int, int, float, float, float, NDArray, NDArray, float, int, int]:
     """
     Process a single voxel for correlation fitting.
@@ -176,10 +171,8 @@ def _procOneVoxelFitcorr(
         If True, fixes the delay during fitting. Default is False.
     initialdelayvalue : float, optional
         Initial delay value if `fixdelay` is True. Default is 0.0.
-    rt_floatset : type, optional
+    rt_floattype : np.dtype, optional
         Type to use for real-valued floating-point arrays. Default is `np.float64`.
-    rt_floattype : str, optional
-        String representation of the floating-point type. Default is "float64".
 
     Returns
     -------
@@ -212,8 +205,7 @@ def _procOneVoxelFitcorr(
     ...     despeckle_thresh=5.0,
     ...     fixdelay=False,
     ...     initialdelayvalue=0.0,
-    ...     rt_floatset=np.float64,
-    ...     rt_floattype="float64"
+    ...     rt_floattype=np.float64,
     ... )
     >>> print(result)
     (10, 1, 1.23, 0.95, 0.12, array([...]), array([...]), 0.90, 1, 0)
@@ -235,7 +227,6 @@ def _procOneVoxelFitcorr(
         fixdelay=fixdelay,
         initialdelayvalue=initialdelayvalue,
         initiallag=initiallag,
-        rt_floatset=rt_floatset,
         rt_floattype=rt_floattype,
     )
 
@@ -244,29 +235,29 @@ def _procOneVoxelFitcorr(
 
     # now tuck everything away in the appropriate output array
     volumetotalinc = 0
-    thewindowout = rt_floatset(0.0 * corr_y)
+    thewindowout = np.zeros_like(corr_y, rt_floattype)
     thewindowout[peakstart : peakend + 1] = 1.0
     if (maskval == 0) and thefitter.zerooutbadfit:
-        thetime = rt_floatset(0.0)
-        thestrength = rt_floatset(0.0)
-        thesigma = rt_floatset(0.0)
-        thegaussout = 0.0 * corr_y
-        theR2 = rt_floatset(0.0)
+        thetime = 0.0
+        thestrength = 0.0
+        thesigma = 0.0
+        thegaussout = np.zeros_like(corr_y, rt_floattype)
+        theR2 = 0.0
     else:
         volumetotalinc = 1
-        thetime = rt_floatset(np.fmod(maxlag, thefitter.lagmod))
-        thestrength = rt_floatset(maxval)
-        thesigma = rt_floatset(maxsigma)
-        thegaussout = rt_floatset(0.0 * corr_y)
-        thewindowout = rt_floatset(0.0 * corr_y)
+        thetime = np.fmod(maxlag, thefitter.lagmod)
+        thestrength = maxval
+        thesigma = maxsigma
+        thegaussout = np.zeros_like(corr_y, rt_floattype)
+        thewindowout = np.zeros_like(corr_y, rt_floattype)
         if (not fixdelay) and (maxsigma != 0.0):
-            thegaussout = rt_floatset(
-                tide_fit.gauss_eval(thefitter.corrtimeaxis, [maxval, maxlag, maxsigma])
-            )
+            thegaussout = tide_fit.gauss_eval(
+                thefitter.corrtimeaxis, [maxval, maxlag, maxsigma]
+            ).astype(rt_floattype)
         else:
-            thegaussout = rt_floatset(0.0)
-            thewindowout = rt_floatset(0.0)
-        theR2 = rt_floatset(thestrength * thestrength)
+            thegaussout = 0.0
+            thewindowout = 0.0
+        theR2 = thestrength * thestrength
 
     return (
         vox,
@@ -304,8 +295,7 @@ def fitcorr(
     chunksize: int = 1000,
     despeckle_thresh: float = 5.0,
     initiallags: Optional[NDArray] = None,
-    rt_floatset: type = np.float64,
-    rt_floattype: str = "float64",
+    rt_floattype: np.dtype = np.float64,
 ) -> int:
     """
     Fit correlation data to extract lag parameters and related statistics for each voxel.
@@ -358,10 +348,8 @@ def fitcorr(
         Threshold for despeckling, by default 5.0.
     initiallags : NDArray, optional
         Initial lag values for each voxel, by default None.
-    rt_floatset : type, optional
+    rt_floattype : np.dtype, optional
         Floating-point type for runtime, by default np.float64.
-    rt_floattype : str, optional
-        String representation of floating-point type, by default "float64".
 
     Returns
     -------
@@ -443,7 +431,6 @@ def fitcorr(
                             initiallag=thislag,
                             fixdelay=fixdelay,
                             initialdelayvalue=thisinitialdelayvalue,
-                            rt_floatset=rt_floatset,
                             rt_floattype=rt_floattype,
                         )
                     )
@@ -528,7 +515,6 @@ def fitcorr(
                     initiallag=thislag,
                     fixdelay=fixdelay,
                     initialdelayvalue=thisinitialdelayvalue,
-                    rt_floatset=rt_floatset,
                     rt_floattype=rt_floattype,
                 )
                 if (

rapidtide/tests/test_cleanregressor.py

@@ -150,8 +150,7 @@ def test_cleanregressor(debug=False, local=False, displayplots=False):
             respdelete=False,
             displayplots=displayplots,
             debug=debug,
-            rt_floattype="float64",
-            rt_floatset=np.float64,
+            rt_floattype=np.float64,
         )
         print(f"\t{len(referencetc)=}")
         print(f"\t{len(resampref_y)=}")

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
@@ -45,13 +52,12 @@ def test_fullrunhappy_v3(debug=False, local=False, displayplots=False):
         os.path.join(exampleroot, "sub-HAPPYTEST_smallmask.nii.gz"),
         "--mklthreads",
         "-1",
-        "--usetensorflow",
-        "--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",
-        "--usetensorflow",
         "--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_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

@@ -41,6 +41,10 @@ def test_simroundtrip(debug=False, local=False, displayplots=False):
     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",
@@ -57,6 +61,8 @@ 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 = [
@@ -77,6 +83,7 @@ def test_simroundtrip(debug=False, local=False, displayplots=False):
     ]
 
     pf.generic_init(rapidtide_simdata._get_parser, rapidtide_simdata.simdata, inputargs=inputargs)
+    print("simulated dataset generated")
 
     # run repeat rapidtide
     inputargs = [
@@ -97,6 +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

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/util.py

@@ -2022,7 +2022,7 @@ def comparehappyruns(root1: str, root2: str, debug: bool = False) -> dict[str, A
 
 # shared memory routines
 def numpy2shared(
-    inarray: NDArray, theouttype: type, name: str | None = None
+    inarray: NDArray, theouttype: np.dtype, name: str | None = None
 ) -> tuple[NDArray, shared_memory.SharedMemory]:
     """
     Convert a numpy array to a shared memory array.
@@ -2033,9 +2033,9 @@ def numpy2shared(
 
     Parameters
     ----------
-    inarray : numpy.ndarray
+    inarray : NDArray
         Input numpy array to be converted to shared memory.
-    theouttype : type
+    theouttype : dtype
         Data type of the output shared memory array.
     name : str, optional
         Name of the shared memory block. If None, an anonymous shared memory
@@ -2043,7 +2043,7 @@ def numpy2shared(
 
     Returns
     -------
-    tuple[numpy.ndarray, multiprocessing.shared_memory.SharedMemory]
+    tuple[NDArray, multiprocessing.shared_memory.SharedMemory]
         A tuple containing:
         - The shared memory array with the same shape as input array
         - The shared memory object that manages the memory block
@@ -2078,7 +2078,7 @@ def numpy2shared(
 
 
 def allocshared(
-    theshape: tuple[int, ...], thetype: type, name: str | None = None
+    theshape: tuple[int, ...], thetype: np.dtype, name: str | None = None
 ) -> tuple[NDArray, shared_memory.SharedMemory]:
     """
     Allocate shared memory for a numpy array.
@@ -2137,7 +2137,7 @@ def allocshared(
 
 
 def allocarray(
-    theshape: tuple[int, ...], thetype: type, shared: bool = False, name: str | None = None
+    theshape: tuple[int, ...], thetype: np.dtype, shared: bool = False, name: str | None = None
 ) -> tuple[NDArray, shared_memory.SharedMemory | None]:
     """
     Allocate and return a numpy array with specified shape and type.

rapidtide/voxelData.py

@@ -681,7 +681,7 @@ class VoxelData:
 
         Parameters
         ----------
-        validvoxels : numpy.ndarray
+        validvoxels : NDArray
             Array containing the valid voxel coordinates. The first dimension
             represents the number of valid spatial locations.