rapidtide 3.0a12__py3-none-any.whl → 3.0a13__py3-none-any.whl

rapidtide/workflows/rapidtide_parser.py

@@ -79,8 +79,8 @@ DEFAULT_PEAKFIT_TYPE = "gauss"
 DEFAULT_REFINE_PRENORM = "var"
 DEFAULT_REFINE_WEIGHTING = "None"
 DEFAULT_REFINE_PCACOMPONENTS = 0.8
-DEFAULT_GLMDERIVS = 0
-DEFAULT_REFINEGLMDERIVS = 1
+DEFAULT_REGRESSIONFILTDERIVS = 0
+DEFAULT_REFINEREGRESSDERIVS = 1
 
 DEFAULT_DENOISING_LAGMIN = -10.0
 DEFAULT_DENOISING_LAGMAX = 10.0
@@ -160,7 +160,7 @@ def _get_parser():
             f"sets searchrange=({DEFAULT_DENOISING_LAGMIN}, {DEFAULT_DENOISING_LAGMAX}), "
             f"passes={DEFAULT_DENOISING_PASSES}, despeckle_passes={DEFAULT_DENOISING_DESPECKLE_PASSES}, "
             f"refineoffset=True, peakfittype={DEFAULT_DENOISING_PEAKFITTYPE}, "
-            f"gausssigma={DEFAULT_DENOISING_SPATIALFILT}, nofitfilt=True, doglmfilt=True. "
+            f"gausssigma={DEFAULT_DENOISING_SPATIALFILT}, nofitfilt=True, dolinfitfilt=True. "
             "Any of these options can be overridden with the appropriate "
             "additional arguments."
         ),
@@ -176,7 +176,7 @@ def _get_parser():
             f"passes={DEFAULT_DELAYMAPPING_PASSES}, despeckle_passes={DEFAULT_DELAYMAPPING_DESPECKLE_PASSES}, "
             f"gausssigma={DEFAULT_DELAYMAPPING_SPATIALFILT}, "
             "refineoffset=True, refinedelay=True, outputlevel='normal', "
-            "doglmfilt=False. "
+            "dolinfitfilt=False. "
             "Any of these options can be overridden with the appropriate "
             "additional arguments."
         ),
@@ -193,7 +193,7 @@ def _get_parser():
             f"passes=1, despeckle_passes={DEFAULT_CVRMAPPING_DESPECKLE_PASSES}, "
             f"searchrange=({DEFAULT_CVRMAPPING_LAGMIN}, {DEFAULT_CVRMAPPING_LAGMAX}), "
             f"filterfreqs=({DEFAULT_CVRMAPPING_FILTER_LOWERPASS}, {DEFAULT_CVRMAPPING_FILTER_UPPERPASS}), "
-            "and calculates a voxelwise GLM using the optimally delayed "
+            "and calculates a voxelwise regression fit using the optimally delayed "
             "input regressor and the percent normalized, demeaned BOLD data as inputs. This map is output as "
             "(XXX_desc-CVR_map.nii.gz).  If no input regressor is supplied, this will generate an error.  "
             "These options can be overridden with the appropriate additional arguments."
@@ -207,7 +207,7 @@ def _get_parser():
         help=(
             "Treat this run as an initial pass to locate good candidate voxels for global mean "
             "regressor generation.  This sets: passes=1, despecklepasses=0, "
-            "refinedespeckle=False, outputlevel='normal', doglmfilt=False, saveintermediatemaps=False."
+            "refinedespeckle=False, outputlevel='normal', dolinfitfilt=False, saveintermediatemaps=False."
         ),
         default=False,
     )
@@ -1065,15 +1065,6 @@ def _get_parser():
         help=("Disables selecting the leftmost delay peak when setting the refine offset."),
         default=True,
     )
-    reg_ref.add_argument(
-        "--pickleft",
-        dest="dummy",
-        action="store_true",
-        help=(
-            "DEPRECATED. pickleft is now on by default. Use 'nopickleft' to disable it instead."
-        ),
-        default=True,
-    )
     reg_ref.add_argument(
         "--pickleftthresh",
         dest="pickleftthresh",
@@ -1167,22 +1158,22 @@ def _get_parser():
         default=DEFAULT_MAXPASSES,
     )
 
-    # GLM noise removal options
-    glm = parser.add_argument_group("GLM noise removal options")
-    glm.add_argument(
-        "--noglm",
-        dest="doglmfilt",
+    # sLFO noise removal options
+    slfofilt = parser.add_argument_group("sLFO noise removal options")
+    slfofilt.add_argument(
+        "--nodenoise",
+        dest="dolinfitfilt",
         action="store_false",
         help=(
-            "Turn off GLM filtering to remove delayed "
+            "Turn off regression filtering to remove delayed "
             "regressor from each voxel (disables output of "
             "fitNorm)."
         ),
         default=True,
     )
-    glm.add_argument(
-        "--glmsourcefile",
-        dest="glmsourcefile",
+    slfofilt.add_argument(
+        "--denoisesourcefile",
+        dest="denoisesourcefile",
         action="store",
         type=lambda x: pf.is_valid_file(parser, x),
         metavar="FILE",
@@ -1193,48 +1184,39 @@ def _get_parser():
         ),
         default=None,
     )
-    glm.add_argument(
+    slfofilt.add_argument(
         "--preservefiltering",
         dest="preservefiltering",
         action="store_true",
-        help="Don't reread data prior to performing GLM.",
+        help="Don't reread data prior to performing sLFO filtering.",
         default=False,
     )
-    glm.add_argument(
-        "--glmderivs",
-        dest="glmderivs",
+    slfofilt.add_argument(
+        "--regressderivs",
+        dest="regressderivs",
         action="store",
         type=lambda x: pf.is_int(parser, x, minval=0),
         metavar="NDERIVS",
         help=(
-            f"When doing final GLM, include derivatives up to NDERIVS order. Default is {DEFAULT_GLMDERIVS}"
+            f"When doing final sLFO filtering, include derivatives up to NDERIVS order. Default is {DEFAULT_REGRESSIONFILTDERIVS}"
         ),
-        default=DEFAULT_GLMDERIVS,
+        default=DEFAULT_REGRESSIONFILTDERIVS,
     )
-    glm.add_argument(
+    slfofilt.add_argument(
         "--norefinedelay",
         dest="refinedelay",
         action="store_false",
-        help=("Do not calculate a refined delay map using GLM information."),
+        help=("Do not calculate a refined delay map using sLFO regression information."),
         default=True,
     )
-    glm.add_argument(
-        "--refinedelay",
-        dest="dummy",
-        action="store_true",
-        help=(
-            "Calculate a refined delay map using GLM information. ***DEPRECATED*** - this is now on by default."
-        ),
-        default=True,
-    )
-    glm.add_argument(
+    slfofilt.add_argument(
         "--nofilterwithrefineddelay",
         dest="filterwithrefineddelay",
         action="store_false",
-        help=("Do not use the refined delay in GLM filter."),
+        help=("Do not use the refined delay in sLFO filter."),
         default=True,
     )
-    glm.add_argument(
+    slfofilt.add_argument(
         "--delaypatchthresh",
         dest="delaypatchthresh",
         action="store",
@@ -1246,7 +1228,7 @@ def _get_parser():
         ),
         default=DEFAULT_PATCHTHRESH,
     )
-    glm.add_argument(
+    slfofilt.add_argument(
         "--delayoffsetspatialfilt",
         dest="delayoffsetgausssigma",
         action="store",
@@ -1271,7 +1253,7 @@ def _get_parser():
         choices=["min", "less", "normal", "more", "max"],
         help=(
             "The level of file output produced.  'min' produces only absolutely essential files, 'less' adds in "
-            "the GLM filtered data (rather than just filter efficacy metrics), 'normal' saves what you "
+            "the sLFO filtered data (rather than just filter efficacy metrics), 'normal' saves what you "
             "would typically want around for interactive data exploration, "
             "'more' adds files that are sometimes useful, and 'max' outputs anything you might possibly want. "
             "Selecting 'max' will produce ~3x your input datafile size as output.  "
@@ -1279,16 +1261,6 @@ def _get_parser():
         ),
         default=DEFAULT_OUTPUTLEVEL,
     )
-    output.add_argument(
-        "--nolimitoutput",
-        dest="limitoutput",
-        action="store_false",
-        help=(
-            "Save some of the large and rarely used files.  "
-            "NB: THIS IS NOW DEPRECATED: Use '--outputlevel max' instead."
-        ),
-        default=True,
-    )
     output.add_argument(
         "--savelags",
         dest="savecorrtimes",
@@ -1467,16 +1439,16 @@ def _get_parser():
         "Experimental options (not fully tested, or not tested at all, may not work).  Beware!"
     )
     experimental.add_argument(
-        "--refineglmderivs",
-        dest="refineglmderivs",
+        "--refineregressderivs",
+        dest="refineregressderivs",
         action="store",
         type=lambda x: pf.is_int(parser, x, minval=1),
         metavar="NDERIVS",
         help=(
-            f"When doing GLM for delay refinement, include derivatives up to NDERIVS order. Must be 1 or more.  "
-            f"Default is {DEFAULT_REFINEGLMDERIVS}"
+            f"When doing regression fit for delay refinement, include derivatives up to NDERIVS order. Must be 1 or more.  "
+            f"Default is {DEFAULT_REFINEREGRESSDERIVS}"
         ),
-        default=DEFAULT_REFINEGLMDERIVS,
+        default=DEFAULT_REFINEREGRESSDERIVS,
     )
     experimental.add_argument(
         "--dofinalrefine",
@@ -1670,6 +1642,51 @@ def _get_parser():
         default=False,
     )
 
+    # Deprecated options
+    deprecated = parser.add_argument_group(
+        "Deprecated options.  These options will go away in the indeterminate future.  Don't use them."
+    )
+    deprecated.add_argument(
+        "--refinedelay",
+        dest="dummy",
+        action="store_true",
+        help=(
+            "Calculate a refined delay map using regression coefficient information. ***DEPRECATED***: refinedelay is now on by default."
+        ),
+        default=True,
+    )
+    deprecated.add_argument(
+        "--nolimitoutput",
+        dest="limitoutput",
+        action="store_false",
+        help=(
+            "Save some of the large and rarely used files.  "
+            "***DEPRECATED***: Use '--outputlevel max' instead."
+        ),
+        default=True,
+    )
+    deprecated.add_argument(
+        "--pickleft",
+        dest="dummy",
+        action="store_true",
+        help=(
+            "***DEPRECATED***: pickleft is now on by default. Use 'nopickleft' to disable it instead."
+        ),
+        default=True,
+    )
+    deprecated.add_argument(
+        "--noglm",
+        dest="dolinfitfilt",
+        action="store_false",
+        help=(
+            "Turn off regression filtering to remove delayed "
+            "regressor from each voxel (disables output of "
+            "fitNorm)."
+            "***DEPRECATED***: Use '--nodenoise' instead."
+        ),
+        default=True,
+    )
+
     # Debugging options
     debugging = parser.add_argument_group(
         "Debugging options.  You probably don't want to use any of these unless I ask you to to help diagnose a problem"
@@ -1759,10 +1776,10 @@ def _get_parser():
         default=False,
     )
     debugging.add_argument(
-        "--singleproc_glm",
-        dest="singleproc_glm",
+        "--singleproc_regressionfilt",
+        dest="singleproc_regressionfilt",
         action="store_true",
-        help=("Force single proc path for glm."),
+        help=("Force single proc path for regression filtering."),
         default=False,
     )
     debugging.add_argument(
@@ -2134,7 +2151,7 @@ def process_args(inputargs=None):
         args["refineoffset"] = True
         args["refinedelay"] = True
         args["outputlevel"] = "normal"
-        pf.setifnotset(args, "doglmfilt", True)
+        pf.setifnotset(args, "dolinfitfilt", True)
 
     if args["denoising"]:
         LGR.warning('Using "denoising" analysis mode. Overriding any affected arguments.')
@@ -2147,7 +2164,7 @@ def process_args(inputargs=None):
         args["refineoffset"] = True
         args["refinedelay"] = True
         args["zerooutbadfit"] = False
-        pf.setifnotset(args, "doglmfilt", True)
+        pf.setifnotset(args, "dolinfitfilt", True)
 
     if args["docvrmap"]:
         LGR.warning('Using "CVR" analysis mode. Overriding any affected arguments.')
@@ -2166,7 +2183,7 @@ def process_args(inputargs=None):
         args["preservefiltering"] = True
         args["passes"] = 1
         args["outputlevel"] = "min"
-        args["doglmfilt"] = False
+        args["dolinfitfilt"] = False
 
     if args["globalpreselect"]:
         LGR.warning('Using "globalpreselect" analysis mode. Overriding any affected arguments.')
@@ -2174,7 +2191,7 @@ def process_args(inputargs=None):
         args["despeckle_passes"] = 0
         args["refinedespeckle"] = False
         args["outputlevel"] = "normal"
-        pf.setifnotset(args, "doglmfilt", False)
+        pf.setifnotset(args, "dolinfitfilt", False)
         args["saveintermediatemaps"] = False
 
     # configure the filter
@@ -2211,50 +2228,50 @@ def process_args(inputargs=None):
         args["savecorrtimes"] = False
         args["savelagregressors"] = False
         args["savedespecklemasks"] = False
-        args["saveminimumglmfiles"] = False
-        args["savenormalglmfiles"] = False
+        args["saveminimumsLFOfiltfiles"] = False
+        args["savenormalsLFOfiltfiles"] = False
         args["savemovingsignal"] = False
-        args["saveallglmfiles"] = False
+        args["saveallsLFOfiltfiles"] = False
     elif args["outputlevel"] == "less":
         args["saveconfoundfiltered"] = False
         args["savegaussout"] = False
         args["savecorrtimes"] = False
         args["savelagregressors"] = False
         args["savedespecklemasks"] = False
-        args["saveminimumglmfiles"] = True
-        args["savenormalglmfiles"] = False
+        args["saveminimumsLFOfiltfiles"] = True
+        args["savenormalsLFOfiltfiles"] = False
         args["savemovingsignal"] = False
-        args["saveallglmfiles"] = False
+        args["saveallsLFOfiltfiles"] = False
     elif args["outputlevel"] == "normal":
         args["saveconfoundfiltered"] = False
         args["savegaussout"] = False
         args["savecorrtimes"] = False
         args["savelagregressors"] = False
         args["savedespecklemasks"] = False
-        args["saveminimumglmfiles"] = True
-        args["savenormalglmfiles"] = True
+        args["saveminimumsLFOfiltfiles"] = True
+        args["savenormalsLFOfiltfiles"] = True
         args["savemovingsignal"] = False
-        args["saveallglmfiles"] = False
+        args["saveallsLFOfiltfiles"] = False
     elif args["outputlevel"] == "more":
         args["saveconfoundfiltered"] = False
         args["savegaussout"] = False
         args["savecorrtimes"] = False
         args["savelagregressors"] = True
         args["savedespecklemasks"] = False
-        args["saveminimumglmfiles"] = True
-        args["savenormalglmfiles"] = True
+        args["saveminimumsLFOfiltfiles"] = True
+        args["savenormalsLFOfiltfiles"] = True
         args["savemovingsignal"] = True
-        args["saveallglmfiles"] = False
+        args["saveallsLFOfiltfiles"] = False
     elif args["outputlevel"] == "max":
         args["saveconfoundfiltered"] = True
         args["savegaussout"] = True
         args["savecorrtimes"] = True
         args["savelagregressors"] = True
         args["savedespecklemasks"] = True
-        args["saveminimumglmfiles"] = True
-        args["savenormalglmfiles"] = True
+        args["saveminimumsLFOfiltfiles"] = True
+        args["savenormalsLFOfiltfiles"] = True
         args["savemovingsignal"] = True
-        args["saveallglmfiles"] = True
+        args["saveallsLFOfiltfiles"] = True
     else:
         print(f"illegal output level {args['outputlevel']}")
         sys.exit()
@@ -2286,8 +2303,8 @@ def process_args(inputargs=None):
         args["territorymapname"] = None
         args["territorymapincludevals"] = None
 
-    # this is new enough to do retrospective GLM
-    args["retroglmcompatible"] = True
+    # this is new enough to do retrospective regression filtering
+    args["retroregresscompatible"] = True
 
     LGR.debug("\nafter postprocessing\n{}".format(args))
 

rapidtide/workflows/{glmfrommaps.py → regressfrommaps.py}

@@ -19,8 +19,8 @@
 
 import numpy as np
 
-import rapidtide.glmpass as tide_glmpass
 import rapidtide.io as tide_io
+import rapidtide.linfitfiltpass as tide_linfitfiltpass
 import rapidtide.makelaggedtcs as tide_makelagged
 import rapidtide.util as tide_util
 
@@ -54,7 +54,7 @@ def addmemprofiling(thefunc, memprofile, themessage):
         return thefunc
 
 
-def glmfrommaps(
+def regressfrommaps(
     fmri_data_valid,
     validvoxels,
     initial_fmri_x,
@@ -64,7 +64,7 @@ def glmfrommaps(
     mode,
     outputname,
     oversamptr,
-    glmmean,
+    sLFOfitmean,
     rvalue,
     r2value,
     fitNorm,
@@ -74,11 +74,11 @@ def glmfrommaps(
     filtereddata,
     LGR,
     TimingLGR,
-    glmthreshval,
-    saveminimumglmfiles,
+    regressfiltthreshval,
+    saveminimumsLFOfiltfiles,
     nprocs_makelaggedtcs=1,
-    nprocs_glm=1,
-    glmderivs=0,
+    nprocs_regressionfilt=1,
+    regressderivs=0,
     mp_chunksize=50000,
     showprogressbar=True,
     alwaysmultiproc=False,
@@ -86,10 +86,10 @@ def glmfrommaps(
     debug=False,
 ):
     if debug:
-        print("GLMFROMMAPS: Starting")
+        print("regressfrommaps: Starting")
         print(f"{nprocs_makelaggedtcs=}")
-        print(f"{nprocs_glm=}")
-        print(f"{glmderivs=}")
+        print(f"{nprocs_regressionfilt=}")
+        print(f"{regressderivs=}")
         print(f"{mp_chunksize=}")
         print(f"{showprogressbar=}")
         print(f"{alwaysmultiproc=}")
@@ -97,7 +97,7 @@ def glmfrommaps(
         print(f"{mode=}")
         print(f"{outputname=}")
         print(f"{oversamptr=}")
-        print(f"{glmthreshval=}")
+        print(f"{regressfiltthreshval=}")
     rt_floatset = np.float64
     rt_floattype = "float64"
     numvalidspatiallocs = np.shape(validvoxels)[0]
@@ -150,18 +150,20 @@ def glmfrommaps(
     if TimingLGR is not None:
         TimingLGR.info("Start filtering operation")
     if memprofile:
-        glmpass_func = addmemprofiling(tide_glmpass.glmpass, memprofile, "before glmpass")
+        linfitfiltpass_func = addmemprofiling(
+            tide_linfitfiltpass.linfitfiltpass, memprofile, "before linfitfiltpass"
+        )
     else:
-        glmpass_func = tide_glmpass.glmpass
+        linfitfiltpass_func = tide_linfitfiltpass.linfitfiltpass
 
-    if glmderivs > 0:
+    if regressderivs > 0:
         if debug:
-            print(f"adding derivatives up to order {glmderivs} prior to regression")
-        regressorset = tide_glmpass.makevoxelspecificderivs(lagtc, glmderivs)
+            print(f"adding derivatives up to order {regressderivs} prior to regression")
+        regressorset = tide_linfitfiltpass.makevoxelspecificderivs(lagtc, regressderivs)
         baseev = rt_floatset(genlagtc.yfromx(initial_fmri_x))
-        evset = tide_glmpass.makevoxelspecificderivs(baseev.reshape((1, -1)), glmderivs).reshape(
-            (-1, 2)
-        )
+        evset = tide_linfitfiltpass.makevoxelspecificderivs(
+            baseev.reshape((1, -1)), regressderivs
+        ).reshape((-1, 2))
     else:
         if debug:
             print(f"using raw lagged regressors for regression")
@@ -170,19 +172,19 @@ def glmfrommaps(
 
     if debug:
         print(f"{regressorset.shape=}")
-    voxelsprocessed_glm = glmpass_func(
+    voxelsprocessed_regressionfilt = linfitfiltpass_func(
         numvalidspatiallocs,
         fmri_data_valid,
-        glmthreshval,
+        regressfiltthreshval,
         regressorset,
-        glmmean,
+        sLFOfitmean,
         rvalue,
         r2value,
         fitcoeff,
         fitNorm,
         movingsignal,
         filtereddata,
-        nprocs=nprocs_glm,
+        nprocs=nprocs_regressionfilt,
         alwaysmultiproc=alwaysmultiproc,
         showprogressbar=showprogressbar,
         mp_chunksize=mp_chunksize,
@@ -197,7 +199,7 @@ def glmfrommaps(
     # determine what was removed
     removeddata = fmri_data_valid - filtereddata
     noiseremoved = np.var(removeddata, axis=0)
-    if saveminimumglmfiles:
+    if saveminimumsLFOfiltfiles:
         tide_io.writebidstsv(
             f"{outputname}_desc-lfofilterNoiseRemoved_timeseries",
             noiseremoved,
@@ -205,9 +207,9 @@ def glmfrommaps(
             starttime=0.0,
             columns=[f"removedbyglm"],
             extraheaderinfo={
-                "Description": "Variance over space of data removed by GLM filter at each timepoint"
+                "Description": "Variance over space of data removed by the sLFO filter at each timepoint"
             },
             append=False,
         )
 
-    return voxelsprocessed_glm, regressorset, evset
+    return voxelsprocessed_regressionfilt, regressorset, evset

rapidtide/workflows/retrolagtcs.py

@@ -24,8 +24,8 @@ import sys
 
 import numpy as np
 
-import rapidtide.glmpass as tide_glmpass
 import rapidtide.io as tide_io
+import rapidtide.linfitfiltpass as tide_linfitfiltpass
 import rapidtide.makelaggedtcs as tide_makelagged
 import rapidtide.multiproc as tide_multiproc
 import rapidtide.resample as tide_resample
@@ -36,7 +36,7 @@ LGR = logging.getLogger("GENERAL")
 ErrorLGR = logging.getLogger("ERROR")
 TimingLGR = logging.getLogger("TIMING")
 
-DEFAULT_GLMDERIVS = 0
+DEFAULT_REGRESSIONFILTDERIVS = 0
 
 
 def _get_parser():
@@ -76,15 +76,15 @@ def _get_parser():
         help="Output root.",
     )
     parser.add_argument(
-        "--glmderivs",
-        dest="glmderivs",
+        "--regressderivs",
+        dest="regressderivs",
         action="store",
         type=int,
         metavar="NDERIVS",
         help=(
-            f"When doing final GLM, include derivatives up to NDERIVS order. Default is {DEFAULT_GLMDERIVS}"
+            f"When doing final GLM, include derivatives up to NDERIVS order. Default is {DEFAULT_REGRESSIONFILTDERIVS}"
         ),
-        default=DEFAULT_GLMDERIVS,
+        default=DEFAULT_REGRESSIONFILTDERIVS,
     )
     parser.add_argument(
         "--nprocs",
@@ -209,7 +209,7 @@ def retrolagtcs(args):
     internalvalidspaceshape = numvalidspatiallocs
     internalvalidspaceshapederivs = (
         internalvalidspaceshape,
-        args.glmderivs + 1,
+        args.regressderivs + 1,
     )
     internalvalidfmrishape = (numvalidspatiallocs, np.shape(initial_fmri_x)[0])
     if args.debug:
@@ -250,7 +250,7 @@ def retrolagtcs(args):
         "CommandLineArgs": thecommandline,
     }
 
-    print("calling glmmfrommaps")
+    print("calling makelaggedtcs")
     voxelsprocessed_makelagged = tide_makelagged.makelaggedtcs(
         genlagtc,
         initial_fmri_x,
@@ -293,10 +293,10 @@ def retrolagtcs(args):
     theheader = copy.deepcopy(fmri_header)
     maplist = []
 
-    if args.glmderivs > 0:
+    if args.regressderivs > 0:
         if args.debug:
-            print(f"adding derivatives up to order {args.glmderivs} prior to regression")
-        regressorset = tide_glmpass.makevoxelspecificderivs(lagtc, args.glmderivs)
+            print(f"adding derivatives up to order {args.regressderivs} prior to regression")
+        regressorset = tide_linfitfiltpass.makevoxelspecificderivs(lagtc, args.regressderivs)
 
         if args.debug:
             print("going down the multiple EV path")
@@ -310,7 +310,7 @@ def retrolagtcs(args):
                 "Shifted sLFO regressor to filter",
             ),
         ]
-        for thederiv in range(1, args.glmderivs + 1):
+        for thederiv in range(1, args.regressderivs + 1):
             if args.debug:
                 print(f"{regressorset[:, :, thederiv].shape=}")
             maplist += [