rapidtide 3.0a13__py3-none-any.whl → 3.0a15__py3-none-any.whl

rapidtide/workflows/delayvar.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   Copyright 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.
@@ -27,6 +27,7 @@ from pathlib import Path
 import numpy as np
 from scipy.stats import pearsonr
 from sklearn.decomposition import PCA
+from tf_keras.src.dtensor.integration_test_utils import train_step
 
 import rapidtide.filter as tide_filt
 import rapidtide.io as tide_io
@@ -61,7 +62,8 @@ DEFAULT_DELAYOFFSETSPATIALFILT = -1
 DEFAULT_WINDOWSIZE = 30.0
 DEFAULT_SYSTEMICFITTYPE = "pca"
 DEFAULT_PCACOMPONENTS = 1
-DEFAULT_TRAINWIDTH = 0.0
+DEFAULT_LAGMIN = 0.0
+DEFAULT_LAGMAX = 0.0
 DEFAULT_TRAINSTEP = 0.5
 
 
@@ -146,19 +148,19 @@ def _get_parser():
         default=True,
     )
     parser.add_argument(
-        "--trainwidth",
-        dest="trainwidth",
-        action="store",
+        "--trainrange",
+        dest="lag_extrema",
+        action=pf.IndicateSpecifiedAction,
+        nargs=2,
         type=float,
-        metavar="WIDTH",
+        metavar=("LAGMIN", "LAGMAX"),
         help=(
-            "Train the ratio offset function over this range of central delays (in seconds).  The derivative "
+            "Set the range of delay offset center frequencies to span LAGMIN to LAGMAX. The derivative "
             "ratio calculation only works over a narrow range, so if the static offset is large, "
             "you need to train the ratio calculation with a central delay close to that value. "
-            "Set negative to select the width automatically. "
-            f"Default is {DEFAULT_TRAINWIDTH}"
+            f"LAGMAX.  Default is {DEFAULT_LAGMIN} to {DEFAULT_LAGMAX} seconds. "
         ),
-        default=DEFAULT_TRAINWIDTH,
+        default=(DEFAULT_LAGMIN, DEFAULT_LAGMAX),
     )
     parser.add_argument(
         "--trainstep",
@@ -209,6 +211,13 @@ def _get_parser():
         help="Use NCOMP components for PCA fit of delay offset.",
         default=DEFAULT_PCACOMPONENTS,
     )
+    parser.add_argument(
+        "--verbose",
+        dest="verbose",
+        action="store_true",
+        help=("Be wicked chatty."),
+        default=False,
+    )
     parser.add_argument(
         "--debug",
         dest="debug",
@@ -259,6 +268,9 @@ def delayvar(args):
     # get the pid of the parent process
     args.pid = os.getpid()
 
+    args.lagmin = args.lag_extrema[0]
+    args.lagmax = args.lag_extrema[1]
+
     # specify the output name
     if args.alternateoutput is None:
         outputname = args.datafileroot
@@ -502,6 +514,16 @@ def delayvar(args):
     # windowed delay deviation estimation
     lagstouse_valid = lagtimes_valid
 
+    # find the robust range of the static delays
+    (
+        pct02,
+        pct98,
+    ) = tide_stats.getfracvals(lagstouse_valid, [0.02, 0.98], debug=args.debug)
+    if args.lagmin == -999:
+        args.lagmin = np.round(pct02 / args.trainstep, 0) * args.trainstep
+    if args.lagmax == -999:
+        args.lagmax = np.round(pct98 / args.trainstep, 0) * args.trainstep
+
     print("\n\nWindowed delay estimation")
     TimingLGR.info("Windowed delay estimation start")
     LGR.info("\n\nWindowed delay estimation")
@@ -537,7 +559,7 @@ def delayvar(args):
             thehpf.apply(genlagsamplerate, reference_y),
             padtime=thepadtime,
         )
-        genlagtc.save(f"{outputname}_desc-lagtcgenerator_timeseries")
+        genlagtc.save(f"{outputname}_desc-hpflagtcgenerator_timeseries")
 
     # and filter the data if necessary
     if args.hpf:
@@ -582,7 +604,7 @@ def delayvar(args):
         numwins,
     )
     internalwinfmrishape = (numvalidspatiallocs, wintrs)
-    if args.debug or args.focaldebug:
+    if args.debug:
         print(f"window space shape = {internalwinspaceshape}")
         print(f"internalwindowfmrishape shape = {internalwinfmrishape}")
 
@@ -591,6 +613,7 @@ def delayvar(args):
     windowedmedfiltregressderivratios = np.zeros(internalwinspaceshape, dtype=float)
     windowedfilteredregressderivratios = np.zeros(internalwinspaceshape, dtype=float)
     windoweddelayoffset = np.zeros(internalwinspaceshape, dtype=float)
+    windowedclosestoffset = np.zeros(internalwinspaceshape, dtype=float)
     if usesharedmem:
         if args.debug:
             print("allocating shared memory")
@@ -626,17 +649,30 @@ def delayvar(args):
     if args.debug:
         print(f"wintrs={wintrs}, winskip={winskip}, numtrs={numtrs}, numwins={numwins}")
     thewindowprocoptions = therunoptions
+    if args.verbose:
+        thewindowprocoptions["showprogressbar"] = True
+    else:
+        thewindowprocoptions["showprogressbar"] = False
     if args.focaldebug:
         thewindowprocoptions["saveminimumsLFOfiltfiles"] = True
         winoutputlevel = "max"
     else:
         thewindowprocoptions["saveminimumsLFOfiltfiles"] = False
         winoutputlevel = "min"
+
+    # Now get the derivative ratios the individual windows
+    print("Finding derivative ratios:")
     for thewin in range(numwins):
-        print(f"Processing window {thewin + 1} of {numwins}")
+        print(f"\tProcessing window {thewin + 1} of {numwins}")
         starttr = thewin * winskip
         endtr = starttr + wintrs
         winlabel = f"_win-{str(thewin + 1).zfill(3)}"
+        if args.verbose:
+            thisLGR = LGR
+            thisTimingLGR = TimingLGR
+        else:
+            thisLGR = None
+            thisTimingLGR = None
 
         windowedregressderivratios[:, thewin], windowedregressrvalues[:, thewin] = (
             tide_refinedelay.getderivratios(
@@ -657,8 +693,8 @@ def delayvar(args):
                 winmovingsignal,
                 winlagtc,
                 winfiltereddata,
-                LGR,
-                TimingLGR,
+                thisLGR,
+                thisTimingLGR,
                 thewindowprocoptions,
                 regressderivs=1,
                 starttr=starttr,
@@ -666,7 +702,33 @@ def delayvar(args):
                 debug=args.debug,
             )
         )
+        if args.focaldebug:
+            theheader = copy.deepcopy(fmri_header)
+            theheader["dim"][4] = wintrs
+            theheader["toffset"] = winwidth / 2.0
+            maplist = [
+                (
+                    winlagtc,
+                    "windowedlagtcs",
+                    "bold",
+                    None,
+                    f"Lagtcs in each {winspace} second window",
+                ),
+            ]
+            tide_io.savemaplist(
+                outputname + winlabel,
+                maplist,
+                validvoxels,
+                (xsize, ysize, numslices, wintrs),
+                theheader,
+                bidsbasedict,
+                debug=args.debug,
+            )
 
+    # Filter the derivative ratios
+    print("Filtering derivative ratios:")
+    for thewin in range(numwins):
+        print(f"\tProcessing window {thewin + 1} of {numwins}")
         (
             windowedmedfiltregressderivratios[:, thewin],
             windowedfilteredregressderivratios[:, thewin],
@@ -681,34 +743,62 @@ def delayvar(args):
             fileiscifti=False,
             textio=False,
             rt_floattype=rt_floattype,
+            verbose=args.verbose,
             debug=args.debug,
         )
 
+    # Train the ratio offsets
+    print("Training ratio offsets:")
+    for thewin in range(numwins):
+        print(f"\tProcessing window {thewin + 1} of {numwins}")
+        starttr = thewin * winskip
+        endtr = starttr + wintrs
+        winlabel = f"_win-{str(thewin + 1).zfill(3)}"
         # find the mapping of glm ratios to delays
         tide_refinedelay.trainratiotooffset(
             genlagtc,
             initial_fmri_x[starttr:endtr],
             outputname + winlabel,
             winoutputlevel,
-            trainwidth=args.trainwidth,
-            trainstep=args.trainstep,
+            trainlagmin=args.lagmin,
+            trainlagmax=args.lagmax,
+            trainlagstep=args.trainstep,
             mindelay=args.mindelay,
             maxdelay=args.maxdelay,
             numpoints=args.numpoints,
-            debug=args.debug,
+            verbose=args.verbose,
+            debug=args.focaldebug,
         )
         TimingLGR.info("Refinement calibration end")
 
-        # now calculate the delay offsets
+    # now calculate the delay offsets
+    print("Calculating delay offsets:")
+    for thewin in range(numwins):
+        print(f"\tProcessing window {thewin + 1} of {numwins}")
+        winlabel = f"_win-{str(thewin + 1).zfill(3)}"
         TimingLGR.info("Calculating delay offsets")
-        if args.focaldebug:
+        if args.debug:
             print(
                 f"calculating delayoffsets for {windowedfilteredregressderivratios.shape[0]} voxels"
             )
         for i in range(windowedfilteredregressderivratios.shape[0]):
-            windoweddelayoffset[i, thewin] = tide_refinedelay.ratiotodelay(
-                windowedfilteredregressderivratios[i, thewin]
+            (windoweddelayoffset[i, thewin], windowedclosestoffset[i, thewin]) = (
+                tide_refinedelay.ratiotodelay(
+                    windowedfilteredregressderivratios[i, thewin],
+                    offset=lagstouse_valid[i],
+                    debug=args.focaldebug,
+                )
             )
+        namesuffix = "_desc-delayoffset_hist"
+        tide_stats.makeandsavehistogram(
+            windoweddelayoffset[:, thewin],
+            therunoptions["histlen"],
+            1,
+            outputname + winlabel + namesuffix,
+            displaytitle="Histogram of delay offsets calculated from GLM",
+            dictvarname="delayoffsethist",
+            thedict=None,
+        )
 
     # now see if there are common timecourses in the delay offsets
     themean = np.mean(windoweddelayoffset, axis=1)
@@ -749,7 +839,7 @@ def delayvar(args):
         # unscale the PCA cleaned data
         for vox in range(0, windoweddelayoffset.shape[0]):
             reduceddata[vox, :] = reduceddata[vox, :] * thevar[vox] + themean[vox]
-        if args.focaldebug:
+        if args.debug:
             print("complex processing: reduceddata.shape =", scaledvoxels.shape)
         # pcadata = np.mean(reduceddata, axis=0)
         pcadata = thefit.components_[0]
@@ -850,22 +940,13 @@ def delayvar(args):
             nprocs_regressionfilt=args.nprocs,
             regressderivs=1,
             showprogressbar=args.showprogressbar,
-            debug=args.focaldebug,
+            debug=args.debug,
         )
 
-    namesuffix = f"_desc-delayoffsetwin{thewin}_hist"
-    tide_stats.makeandsavehistogram(
-        windoweddelayoffset[:, thewin],
-        therunoptions["histlen"],
-        1,
-        outputname + namesuffix,
-        displaytitle="Histogram of delay offsets calculated from GLM",
-        dictvarname="delayoffsethist",
-        thedict=None,
-    )
     theheader = copy.deepcopy(fmri_header)
     theheader["dim"][4] = numwins
     theheader["pixdim"][4] = winspace
+    theheader["toffset"] = winwidth / 2.0
     maplist = [
         (
             windoweddelayoffset,
@@ -874,6 +955,13 @@ def delayvar(args):
             None,
             f"Delay offsets in each {winspace} second window",
         ),
+        (
+            windowedclosestoffset,
+            "windowedclosestoffset",
+            "info",
+            None,
+            f"Closest delay offsets in each {winspace} second window",
+        ),
         (
             np.square(windowedregressrvalues),
             "windowedregressr2values",

rapidtide/workflows/diffrois.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.

rapidtide/workflows/endtidalproc.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.

rapidtide/workflows/fdica.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.

rapidtide/workflows/filtnifti.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.

rapidtide/workflows/filttc.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.

rapidtide/workflows/fixtr.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.

rapidtide/workflows/gmscalc.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.

rapidtide/workflows/happy.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2018-2024 Blaise Frederick
+#   Copyright 2018-2025 Blaise Frederick
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.
@@ -205,7 +205,6 @@ def happy_main(argparsingfunc):
     tide_util.logmem("before mask creation")
     # mask = np.uint16(masking.compute_epi_mask(nim).dataobj.reshape(numspatiallocs))
     mask = np.uint16(tide_mask.makeepimask(nim).dataobj.reshape(numspatiallocs))
-    validvoxels = np.where(mask > 0)[0]
     theheader = copy.deepcopy(nim_hdr)
     theheader["dim"][4] = 1
     timings.append(["Mask created", time.time(), None, None])
@@ -236,13 +235,14 @@ def happy_main(argparsingfunc):
     # filter out motion regressors here
     if args.motionfilename is not None:
         timings.append(["Motion filtering start", time.time(), None, None])
-        motiondict = tide_io.readmotion(args.motionfilename, tr=tr)
+        motiondict = tide_io.readmotion(args.motionfilename, tr=tr, colspec=args.motionfilecolspec)
         confoundregressors, confoundregressorlabels = tide_fit.calcexpandedregressors(
             motiondict,
             labels=["xtrans", "ytrans", "ztrans", "xrot", "yrot", "zrot"],
             deriv=args.motfilt_deriv,
             order=args.motfilt_order,
         )
+        tide_util.disablemkl(args.nprocs)
         (motionregressors, motionregressorlabels, filtereddata, confoundr2) = (
             tide_linfitfiltpass.confoundregress(
                 confoundregressors,
@@ -253,8 +253,10 @@ def happy_main(argparsingfunc):
                 tcstart=args.motskip,
                 tchp=args.motionhp,
                 tclp=args.motionlp,
+                nprocs=args.nprocs,
             )
         )
+        tide_util.enablemkl(args.mklthreads)
         if confoundr2 is None:
             print("There are no nonzero confound regressors - exiting")
             sys.exit()
@@ -273,6 +275,17 @@ def happy_main(argparsingfunc):
             append=False,
             debug=args.debug,
         )
+        # save motionr2 map
+        theheader = copy.deepcopy(nim_hdr)
+        theheader["dim"][4] = 1
+        motionr2filename = outputroot + "_desc-motionr2_map"
+        bidsdict = bidsbasedict.copy()
+        tide_io.writedicttojson(bidsdict, motionr2filename + ".json")
+        outarray = np.zeros((xsize, ysize, numslices), dtype=float)
+        outarray.reshape(numspatiallocs)[validprojvoxels] = confoundr2
+        tide_io.savetonifti(
+            outarray.reshape((xsize, ysize, numslices)), theheader, motionr2filename
+        )
         if args.savemotionglmfilt:
             motionfilteredfilename = outputroot + "_desc-motionfiltered_bold"
             bidsdict = bidsbasedict.copy()
@@ -372,6 +385,7 @@ def happy_main(argparsingfunc):
         # now get an estimate of the cardiac signal
         print("estimating cardiac signal from fmri data")
         tide_util.logmem("before cardiacfromimage")
+        tide_util.disablemkl(args.nprocs)
         (
             cardfromfmri_sliceres,
             cardfromfmri_normfac,
@@ -402,6 +416,7 @@ def happy_main(argparsingfunc):
             debug=args.debug,
             verbose=args.verbose,
         )
+        tide_util.enablemkl(args.mklthreads)
         timings.append(
             [
                 "Cardiac signal generated from image data" + passstring,
@@ -602,6 +617,15 @@ def happy_main(argparsingfunc):
                 )
                 thedlfilter = tide_dlfilt.DeepLearningFilter(modelpath=modelpath)
                 thedlfilter.loadmodel(args.modelname)
+                updatemodels = False
+                if updatemodels:
+                    updatedmodelname = f"{args.modelname}_tf2"
+                    newmodeldir = os.path.join(
+                        "/Users/frederic/code/rapidtide/rapidtide/data/models", updatedmodelname
+                    )
+                    print(f"creating {newmodeldir}")
+                    tide_util.makeadir(newmodeldir)
+                    thedlfilter.savemodel(altname=newmodeldir)
                 infodict["dlfiltermodel"] = args.modelname
                 normdlfilteredcard_stdres = thedlfilter.apply(normcardfromfmri_stdres)
                 dlfilteredcard_stdres = thedlfilter.apply(cardfromfmri_stdres)
@@ -966,6 +990,24 @@ def happy_main(argparsingfunc):
                     append=True,
                     debug=args.debug,
                 )
+                badpointlist_stdres = np.round(
+                    tide_resample.arbresample(
+                        badpointlist,
+                        slicesamplerate,
+                        args.stdfreq,
+                        decimate=True,
+                        debug=False,
+                    ),
+                    0,
+                )
+                tide_io.writebidstsv(
+                    outputroot + "_desc-stdrescardfromfmri_timeseries",
+                    badpointlist_stdres,
+                    args.stdfreq,
+                    columns=["badpts"],
+                    append=True,
+                    debug=args.debug,
+                )
 
         #  extract the fundamental
         if args.forcedhr is not None:
@@ -1755,6 +1797,7 @@ def happy_main(argparsingfunc):
             fitNorm = np.zeros(timepoints, dtype=np.float64)
             datatoremove = 0.0 * fmri_data
             print("Running spatial regression on", timepoints, "timepoints")
+            tide_util.disablemkl(args.nprocs)
             tide_linfitfiltpass.linfitfiltpass(
                 timepoints,
                 fmri_data[validlocs, :],
@@ -1771,6 +1814,7 @@ def happy_main(argparsingfunc):
                 procbyvoxel=False,
                 nprocs=args.nprocs,
             )
+            tide_util.enablemkl(args.mklthreads)
             print(datatoremove.shape, cardiacnoise.shape, fitcoffs.shape)
             # datatoremove[validlocs, :] = np.multiply(cardiacnoise[validlocs, :], fitcoffs[:, None])
             filtereddata = fmri_data - datatoremove
@@ -1815,6 +1859,7 @@ def happy_main(argparsingfunc):
             fitNorm = np.zeros(numspatiallocs, dtype=np.float64)
             datatoremove = 0.0 * fmri_data
             print("Running temporal regression on", numvalidspatiallocs, "voxels")
+            tide_util.disablemkl(args.nprocs)
             tide_linfitfiltpass.linfitfiltpass(
                 numvalidspatiallocs,
                 fmri_data[validlocs, :],
@@ -1830,6 +1875,7 @@ def happy_main(argparsingfunc):
                 procbyvoxel=True,
                 nprocs=args.nprocs,
             )
+            tide_util.enablemkl(args.mklthreads)
             datatoremove[validlocs, :] = np.multiply(
                 cardiacnoise[validlocs, :], fitcoffs[validlocs, None]
             )

rapidtide/workflows/happy2std.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.

rapidtide/workflows/happy_parser.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2019-2024 Blaise Frederick
+#   Copyright 2019-2025 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 +21,11 @@ import argparse
 import numpy as np
 
 import rapidtide.io as tide_io
+import rapidtide.multiproc as tide_multiproc
 import rapidtide.workflows.parser_funcs as pf
 
 DEFAULT_ALIASEDCORRELATIONWIDTH = 5.0
+DEFAULT_DL_MODEL = "model_revised_tf2"
 
 
 def _get_parser():
@@ -99,10 +101,10 @@ def _get_parser():
         dest="modelname",
         metavar="MODELNAME",
         help=(
-            "Use model MODELNAME for dl filter (default is model_revised - "
+            f"Use model MODELNAME for dl filter (default is {DEFAULT_DL_MODEL} - "
             "from the revised NeuroImage paper.) "
         ),
-        default="model_revised",
+        default=DEFAULT_DL_MODEL,
     )
 
     # Performance
@@ -120,7 +122,20 @@ def _get_parser():
         ),
         default=1,
     )
-
+    performance_opts.add_argument(
+        "--nprocs",
+        dest="nprocs",
+        action="store",
+        metavar="NPROCS",
+        type=lambda x: pf.is_int(parser, x),
+        help=(
+            "Use NPROCS CPUs to accelerate processing (defaults to 1 - more "
+            "CPUs up to the number of cores can accelerate processing a lot, but "
+            "you need to remember to ask for this many CPUs on clusters.)  Entering a mulitprocessor "
+            "routine disables mklthreads (otherwise there's chaos)."
+        ),
+        default=1,
+    )
     # Preprocessing
     preprocessing_opts = parser.add_argument_group("Preprocessing")
     preprocessing_opts.add_argument(
@@ -143,7 +158,7 @@ def _get_parser():
     )
     preprocessing_opts.add_argument(
         "--motionfile",
-        dest="motionfilename",
+        dest="motionfilespec",
         metavar="MOTFILE",
         help=(
             "Read 6 columns of motion regressors out of MOTFILE file (.par or BIDS .json) "
@@ -719,7 +734,6 @@ def process_args(inputargs=None):
     args.outputlevel = 1
     args.maskthreshpct = 10.0
     args.domadnorm = True
-    args.nprocs = 1
     args.verbose = False
     args.smoothlen = 101
     args.envthresh = 0.2
@@ -738,6 +752,16 @@ def process_args(inputargs=None):
     if args.disablenotch:
         args.notchpct = None
 
+    # process motionfile information
+    if args.motionfilespec is not None:
+        (args.motionfilename, args.motionfilecolspec) = tide_io.parsefilespec(args.motionfilespec)
+    else:
+        args.motionfilename = None
+
+    # set the number of worker processes if multiprocessing
+    if args.nprocs < 1:
+        args.nprocs = tide_multiproc.maxcpus()
+
     # process infotags
     args = pf.postprocesstagopts(args)
 

rapidtide/workflows/histnifti.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.

rapidtide/workflows/histtc.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.

rapidtide/workflows/linfitfilt.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.

rapidtide/workflows/localflow.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.

rapidtide/workflows/mergequality.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2024-2024 Blaise Frederick
+#   Copyright 2024-2025 Blaise Frederick
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.