rapidtide 3.0a14__py3-none-any.whl → 3.0a15__py3-none-any.whl

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.

rapidtide/workflows/niftidecomp.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/niftistats.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/pairproc.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/pairwisemergenifti.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/parser_funcs.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.

rapidtide/workflows/physiofreq.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2020-2024 Blaise Frederick
+#   Copyright 2020-2025 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/pixelcomp.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/plethquality.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/polyfitim.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/proj2flow.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/rankimage.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.