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

rapidtide/workflows/rapidtide2std.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/rapidtide_parser.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.
@@ -29,14 +29,6 @@ import rapidtide.io as tide_io
 import rapidtide.util as tide_util
 import rapidtide.workflows.parser_funcs as pf
 
-try:
-    from memory_profiler import profile
-
-    memprofilerexists = True
-except ImportError:
-    memprofilerexists = False
-
-
 # Create a sentinel.
 # from https://stackoverflow.com/questions/58594956/find-out-which-arguments-were-passed-explicitly-in-argparse
 class _Sentinel:
@@ -70,7 +62,6 @@ DEFAULT_MAXPASSES = 15
 DEFAULT_REFINE_TYPE = "pca"
 DEFAULT_INTERPTYPE = "univariate"
 DEFAULT_WINDOW_TYPE = "hamming"
-DEFAULT_GLOBALMASK_METHOD = "mean"
 DEFAULT_GLOBALSIGNAL_METHOD = "sum"
 DEFAULT_CORRWEIGHTING = "phat"
 DEFAULT_CORRTYPE = "linear"
@@ -240,7 +231,7 @@ def _get_parser():
         action="store_true",
         help=(
             "This is a NIRS analysis - this is a macro that "
-            "sets nothresh, refineprenorm=var, ampthresh=0.7, and "
+            "sets nothresh, dataiszeromean=True, refineprenorm=var, ampthresh=0.7, and "
             "lagminthresh=0.1. "
         ),
         default=False,
@@ -382,6 +373,17 @@ def _get_parser():
         ),
         default=False,
     )
+    preproc.add_argument(
+        "--dataiszeromean",
+        dest="dataiszeromean",
+        action="store_true",
+        help=(
+            "Assume that the fMRI data is zero mean (this will be the case if you used AFNI for preprocessing).  "
+            "This affects how masks are generated.  Rapidtide will attempt to detect this, but set explicitly "
+            "if you know this is the case."
+        ),
+        default=False,
+    )
 
     # Add filter options
     pf.addfilteropts(parser, filtertarget="data and regressors", details=True)
@@ -444,19 +446,6 @@ def _get_parser():
         ),
         default=False,
     )
-    preproc.add_argument(
-        "--globalmaskmethod",
-        dest="globalmaskmethod",
-        action="store",
-        type=str,
-        choices=["mean", "variance"],
-        help=(
-            "Select whether to use timecourse mean or variance to "
-            "mask voxels prior to generating global mean. "
-            f'Default is "{DEFAULT_GLOBALMASK_METHOD}".'
-        ),
-        default=DEFAULT_GLOBALMASK_METHOD,
-    )
     preproc.add_argument(
         "--globalmeaninclude",
         dest="globalmeanincludespec",
@@ -1425,13 +1414,6 @@ def _get_parser():
         help=("Disable use of shared memory for large array storage."),
         default=True,
     )
-    misc.add_argument(
-        "--memprofile",
-        dest="memprofile",
-        action="store_true",
-        help=("Enable memory profiling - " "warning: this slows things down a lot."),
-        default=False,
-    )
     pf.addtagopts(misc)
 
     # Experimental options (not fully tested, may not work)
@@ -1519,68 +1501,6 @@ def _get_parser():
         help=("Attempt to detect and remove respiratory signal that strays into " "the LFO band."),
         default=False,
     )
-
-    experimental.add_argument(
-        "--noisetimecourse",
-        dest="noisetimecoursespec",
-        metavar="FILENAME[:VALSPEC]",
-        help=(
-            "Find and remove any instance of the timecourse supplied from any regressors used for analysis. "
-            "(if VALSPEC is given, and there are multiple timecourses in the file, use the indicated timecourse."
-            "This can be the name of the regressor if it's in the file, or the column number). "
-        ),
-        default=None,
-    )
-    noise_group = experimental.add_mutually_exclusive_group()
-    noise_group.add_argument(
-        "--noisefreq",
-        dest="noisefreq",
-        action="store",
-        type=lambda x: pf.is_float(parser, x, minval=0.0),
-        metavar="FREQ",
-        help=(
-            "Noise timecourse in file has sample "
-            "frequency FREQ (default is 1/tr) "
-            "NB: --noisefreq and --noisetstep) "
-            "are two ways to specify the same thing."
-        ),
-        default="auto",
-    )
-    noise_group.add_argument(
-        "--noisetstep",
-        dest="noisefreq",
-        action="store",
-        type=lambda x: pf.invert_float(parser, x),
-        metavar="TSTEP",
-        help=(
-            "Noise timecourse in file has sample "
-            "frequency FREQ (default is 1/tr) "
-            "NB: --noisefreq and --noisetstep) "
-            "are two ways to specify the same thing."
-        ),
-        default="auto",
-    )
-    experimental.add_argument(
-        "--noisestart",
-        dest="noisestarttime",
-        action="store",
-        type=float,
-        metavar="START",
-        help=(
-            "The time delay in seconds into the noise timecourse "
-            "file, corresponding in the first TR of the fMRI "
-            "file (default is 0.0)."
-        ),
-        default=0.0,
-    )
-    experimental.add_argument(
-        "--noiseinvert",
-        dest="noiseinvert",
-        action="store_true",
-        help=("Invert noise regressor prior to alignment."),
-        default=False,
-    )
-
     experimental.add_argument(
         "--acfix",
         dest="fix_autocorrelation",
@@ -1857,8 +1777,6 @@ def process_args(inputargs=None):
     args["absmaxsigma"] = 10000.0
     # width of the reference autocorrelation function
     args["absminsigma"] = 0.05
-    # search window width for noise regressor mutual information function
-    args["noisesearchwindow"] = 30.0
     # number of MADs away from the median to consider an outlier
     args["sigdistoutlierfac"] = 10.0
 
@@ -1993,18 +1911,6 @@ def process_args(inputargs=None):
     else:
         args["inputfreq_nondefault"] = True
 
-    if args["noisetimecoursespec"] is not None:
-        (
-            args["noisetimecoursename"],
-            args["noisetimecoursevals"],
-        ) = tide_io.parsefilespec(args["noisetimecoursespec"])
-    else:
-        args["noisetimecoursename"] = None
-        args["noisetimecoursevals"] = None
-
-    if args["noisefreq"] == "auto":
-        args["noisefreq"] = 1.0 / fmri_tr
-
     # mask processing
     if args["corrmaskincludespec"] is not None:
         (
@@ -2211,6 +2117,7 @@ def process_args(inputargs=None):
         LGR.warning('Using "nirs" macro. Overriding any affected arguments.')
         args["nothresh"] = True
         pf.setifnotset(args, "preservefiltering", False)
+        args["dataiszeromean"] = True
         args["refineprenorm"] = "var"
         args["ampthresh"] = 0.7
         args["ampthreshfromsig"] = False
@@ -2276,12 +2183,6 @@ def process_args(inputargs=None):
         print(f"illegal output level {args['outputlevel']}")
         sys.exit()
 
-    # disable memory profiling if necessary
-    if not memprofilerexists:
-        if args["memprofile"]:
-            LGR.info("memprofiler is not installed - disabling memory profiling")
-            args["memprofile"] = False
-
     # dispersion calculation
     args["dispersioncalc_lower"] = args["lagmin"]
     args["dispersioncalc_upper"] = args["lagmax"]

rapidtide/workflows/regressfrommaps.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.
@@ -24,35 +24,6 @@ import rapidtide.linfitfiltpass as tide_linfitfiltpass
 import rapidtide.makelaggedtcs as tide_makelagged
 import rapidtide.util as tide_util
 
-try:
-    from memory_profiler import profile
-
-    memprofilerexists = True
-except ImportError:
-    memprofilerexists = False
-
-
-def conditionalprofile():
-    def resdec(f):
-        if memprofilerexists:
-            return profile(f)
-        return f
-
-    return resdec
-
-
-@conditionalprofile()
-def memcheckpoint(message):
-    pass
-
-
-def addmemprofiling(thefunc, memprofile, themessage):
-    if memprofile:
-        return profile(thefunc, precision=2)
-    else:
-        tide_util.logmem(themessage)
-        return thefunc
-
 
 def regressfrommaps(
     fmri_data_valid,
@@ -82,7 +53,6 @@ def regressfrommaps(
     mp_chunksize=50000,
     showprogressbar=True,
     alwaysmultiproc=False,
-    memprofile=False,
     debug=False,
 ):
     if debug:
@@ -93,7 +63,6 @@ def regressfrommaps(
         print(f"{mp_chunksize=}")
         print(f"{showprogressbar=}")
         print(f"{alwaysmultiproc=}")
-        print(f"{memprofile=}")
         print(f"{mode=}")
         print(f"{outputname=}")
         print(f"{oversamptr=}")
@@ -107,20 +76,14 @@ def regressfrommaps(
         LGR.info("Start lagged timecourse creation")
     if TimingLGR is not None:
         TimingLGR.info("Start lagged timecourse creation")
-    if memprofile:
-        makelagged_func = addmemprofiling(
-            tide_makelagged.makelaggedtcs,
-            memprofile,
-            "before making lagged timecourses",
-        )
-    else:
-        makelagged_func = tide_makelagged.makelaggedtcs
-    voxelsprocessed_makelagged = makelagged_func(
+
+    voxelsprocessed_makelagged = tide_makelagged.makelaggedtcs(
         genlagtc,
         initial_fmri_x,
         fitmask,
         lagtimes,
         lagtc,
+        LGR=LGR,
         nprocs=nprocs_makelaggedtcs,
         alwaysmultiproc=alwaysmultiproc,
         showprogressbar=showprogressbar,
@@ -149,12 +112,6 @@ def regressfrommaps(
         LGR.info("Start filtering operation")
     if TimingLGR is not None:
         TimingLGR.info("Start filtering operation")
-    if memprofile:
-        linfitfiltpass_func = addmemprofiling(
-            tide_linfitfiltpass.linfitfiltpass, memprofile, "before linfitfiltpass"
-        )
-    else:
-        linfitfiltpass_func = tide_linfitfiltpass.linfitfiltpass
 
     if regressderivs > 0:
         if debug:
@@ -172,7 +129,7 @@ def regressfrommaps(
 
     if debug:
         print(f"{regressorset.shape=}")
-    voxelsprocessed_regressionfilt = linfitfiltpass_func(
+    voxelsprocessed_regressionfilt = tide_linfitfiltpass.linfitfiltpass(
         numvalidspatiallocs,
         fmri_data_valid,
         regressfiltthreshval,
@@ -187,6 +144,7 @@ def regressfrommaps(
         nprocs=nprocs_regressionfilt,
         alwaysmultiproc=alwaysmultiproc,
         showprogressbar=showprogressbar,
+        verbose=(LGR is not None),
         mp_chunksize=mp_chunksize,
         rt_floatset=rt_floatset,
         rt_floattype=rt_floattype,

rapidtide/workflows/resamplenifti.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/resampletc.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/retrolagtcs.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.
@@ -257,6 +257,7 @@ def retrolagtcs(args):
         procmask_valid,
         lagtimes_valid,
         lagtc,
+        LGR=LGR,
         nprocs=args.nprocs,
         showprogressbar=args.showprogressbar,
     )

rapidtide/workflows/retroregress.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 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.
@@ -295,7 +295,29 @@ def retroregress(args):
         print(f"illegal output level {args['outputlevel']}")
         sys.exit()
 
+    # save the raw and formatted command lines
+    argstowrite = sys.argv
     thecommandline = " ".join(sys.argv[1:])
+    tide_io.writevec([thecommandline], f"{outputname}_retrocommandline.txt")
+    formattedcommandline = []
+    for thetoken in argstowrite[0:3]:
+        formattedcommandline.append(thetoken)
+    for thetoken in argstowrite[3:]:
+        if thetoken[0:2] == "--":
+            formattedcommandline.append(thetoken)
+        else:
+            formattedcommandline[-1] += " " + thetoken
+    for i in range(len(formattedcommandline)):
+        if i > 0:
+            prefix = "    "
+        else:
+            prefix = ""
+        if i < len(formattedcommandline) - 1:
+            suffix = " \\"
+        else:
+            suffix = ""
+        formattedcommandline[i] = prefix + formattedcommandline[i] + suffix
+    tide_io.writevec(formattedcommandline, f"{outputname}_retroformattedcommandline.txt")
 
     if args.nprocs < 1:
         args.nprocs = tide_multiproc.maxcpus()
@@ -659,7 +681,9 @@ def retroregress(args):
             if args.debug:
                 print(f"calculating delayoffsets for {filteredregressderivratios.shape[0]} voxels")
             for i in range(filteredregressderivratios.shape[0]):
-                delayoffset[i] = tide_refinedelay.ratiotodelay(filteredregressderivratios[i])
+                delayoffset[i], closestoffset = tide_refinedelay.ratiotodelay(
+                    filteredregressderivratios[i]
+                )
                 """delayoffset[i] = tide_refinedelay.coffstodelay(
                     np.asarray([filteredregressderivratios[i]]),
                     mindelay=args.mindelay,

rapidtide/workflows/roisummarize.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2021-2024 Blaise Frederick
+#   Copyright 2021-2025 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/runqualitycheck.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/showarbcorr.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/showhist.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/showstxcorr.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/showtc.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/showxcorrx.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/showxy.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/simdata.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/spatialfit.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/spatialmi.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/spectrogram.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/synthASL.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/tcfrom2col.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/tcfrom3col.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/tidepool.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.
@@ -262,6 +262,7 @@ def selectDataset(thesubject):
 
 class xyztlocation(QtWidgets.QWidget):
     "Manage a location in time and space"
+
     updatedXYZ = QtCore.pyqtSignal()
     updatedT = QtCore.pyqtSignal()
     movieTimer = QtCore.QTimer()

rapidtide/workflows/utils.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2021-2024 Blaise Frederick
+#   Copyright 2021-2025 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/variabilityizer.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-3.0a13.dist-info → rapidtide-3.0a15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rapidtide
-Version: 3.0a13
+Version: 3.0a15
 Summary: Tools for performing correlation analysis on fMRI data.
 Author: Taylor Salo, Daniel M. Drucker, Ph.D., Jeffrey N Stout, Yaroslav O. Halchenko, Derek Monroe
 Author-email: "Blaise deB. Frederick" <blaise.frederick@gmail.com>