rapidtide 3.0a10__py3-none-any.whl → 3.0a12__py3-none-any.whl

rapidtide/workflows/rapidtide_parser.py

@@ -80,6 +80,7 @@ DEFAULT_REFINE_PRENORM = "var"
 DEFAULT_REFINE_WEIGHTING = "None"
 DEFAULT_REFINE_PCACOMPONENTS = 0.8
 DEFAULT_GLMDERIVS = 0
+DEFAULT_REFINEGLMDERIVS = 1
 
 DEFAULT_DENOISING_LAGMIN = -10.0
 DEFAULT_DENOISING_LAGMAX = 10.0
@@ -309,7 +310,7 @@ def _get_parser():
         dest="realtr",
         action="store",
         metavar="TSTEP",
-        type=lambda x: pf.is_float(parser, x),
+        type=lambda x: pf.is_float(parser, x, minval=0.0),
         help=(
             "Set the timestep of the data file to TSTEP. "
             "This will override the TR in an "
@@ -395,7 +396,7 @@ def _get_parser():
         "--detrendorder",
         dest="detrendorder",
         action="store",
-        type=int,
+        type=lambda x: pf.is_int(parser, x, minval=0),
         metavar="ORDER",
         help=(f"Set order of trend removal (0 to disable). Default is {DEFAULT_DETREND_ORDER}."),
         default=DEFAULT_DETREND_ORDER,
@@ -514,7 +515,7 @@ def _get_parser():
         "--confoundpowers",
         dest="confound_power",
         metavar="N",
-        type=int,
+        type=lambda x: pf.is_int(parser, x, minval=1),
         help=(
             "Include powers of each confound regressor up to order N. Default is 1 (no expansion). "
         ),
@@ -580,7 +581,7 @@ def _get_parser():
         "--numskip",
         dest="preprocskip",
         action="store",
-        type=int,
+        type=lambda x: pf.is_int(parser, x, minval=0),
         metavar="SKIP",
         help=(
             "SKIP TRs were previously deleted during "
@@ -672,7 +673,7 @@ def _get_parser():
         "--regressorfreq",
         dest="inputfreq",
         action="store",
-        type=lambda x: pf.is_float(parser, x),
+        type=lambda x: pf.is_float(parser, x, minval=0.0),
         metavar="FREQ",
         help=(
             "Probe regressor in file has sample "
@@ -888,7 +889,7 @@ def _get_parser():
         "--despecklepasses",
         dest="despeckle_passes",
         action=pf.IndicateSpecifiedAction,
-        type=int,
+        type=lambda x: pf.is_int(parser, x, minval=0),
         metavar="PASSES",
         help=(
             "Detect and refit suspect correlations to "
@@ -943,7 +944,7 @@ def _get_parser():
         "--passes",
         dest="passes",
         action=pf.IndicateSpecifiedAction,
-        type=int,
+        type=lambda x: pf.is_int(parser, x, minval=1),
         metavar="PASSES",
         help=("Set the number of processing passes to PASSES.  " f"Default is {DEFAULT_PASSES}."),
         default=DEFAULT_PASSES,
@@ -1157,7 +1158,7 @@ def _get_parser():
         "--maxpasses",
         dest="maxpasses",
         action="store",
-        type=int,
+        type=lambda x: pf.is_int(parser, x, minval=1),
         metavar="MAXPASSES",
         help=(
             "Terminate refinement after MAXPASSES passes, whether or not convergence has occurred. "
@@ -1203,7 +1204,7 @@ def _get_parser():
         "--glmderivs",
         dest="glmderivs",
         action="store",
-        type=int,
+        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}"
@@ -1221,7 +1222,9 @@ def _get_parser():
         "--refinedelay",
         dest="dummy",
         action="store_true",
-        help=("Calculate a refined delay map using GLM information. ***DEPRECATED*** - this is now on by default."),
+        help=(
+            "Calculate a refined delay map using GLM information. ***DEPRECATED*** - this is now on by default."
+        ),
         default=True,
     )
     glm.add_argument(
@@ -1297,7 +1300,7 @@ def _get_parser():
         "--histlen",  # was -h
         dest="histlen",
         action="store",
-        type=int,
+        type=lambda x: pf.is_int(parser, x, minval=5),
         metavar="HISTLEN",
         help=(f"Change the histogram length to HISTLEN.  Default is {DEFAULT_HISTLEN}."),
         default=DEFAULT_HISTLEN,
@@ -1349,7 +1352,7 @@ def _get_parser():
         "--mklthreads",
         dest="mklthreads",
         action="store",
-        type=int,
+        type=lambda x: pf.is_int(parser, x, minval=1),
         metavar="MKLTHREADS",
         help=(
             "If mkl library is installed, use no more than MKLTHREADS worker "
@@ -1463,6 +1466,25 @@ def _get_parser():
     experimental = parser.add_argument_group(
         "Experimental options (not fully tested, or not tested at all, may not work).  Beware!"
     )
+    experimental.add_argument(
+        "--refineglmderivs",
+        dest="refineglmderivs",
+        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}"
+        ),
+        default=DEFAULT_REFINEGLMDERIVS,
+    )
+    experimental.add_argument(
+        "--dofinalrefine",
+        dest="dofinalrefine",
+        action="store_true",
+        help=("Do regressor refinement on the final pass."),
+        default=False,
+    )
     experimental.add_argument(
         "--territorymap",
         dest="territorymap",
@@ -1542,7 +1564,7 @@ def _get_parser():
         "--noisefreq",
         dest="noisefreq",
         action="store",
-        type=lambda x: pf.is_float(parser, x),
+        type=lambda x: pf.is_float(parser, x, minval=0.0),
         metavar="FREQ",
         help=(
             "Noise timecourse in file has sample "

rapidtide/workflows/retroglm.py

@@ -57,6 +57,7 @@ DEFAULT_REFINEDELAYMINDELAY = -5.0
 DEFAULT_REFINEDELAYMAXDELAY = 5.0
 DEFAULT_REFINEDELAYNUMPOINTS = 501
 DEFAULT_DELAYOFFSETSPATIALFILT = -1
+DEFAULT_REFINEGLMDERIVS = 1
 
 
 def _get_parser():
@@ -91,7 +92,7 @@ def _get_parser():
         "--glmderivs",
         dest="glmderivs",
         action="store",
-        type=int,
+        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}"
@@ -115,7 +116,7 @@ def _get_parser():
         "--numskip",
         dest="numskip",
         action="store",
-        type=int,
+        type=lambda x: pf.is_int(parser, x, minval=0),
         metavar="NUMSKIP",
         help=("Skip NUMSKIP points at the beginning of the fmri file."),
         default=0,
@@ -213,6 +214,21 @@ def _get_parser():
         help=("Output lots of helpful information on a limited subset of operations."),
         default=False,
     )
+    experimental = parser.add_argument_group(
+        "Experimental options (not fully tested, or not tested at all, may not work).  Beware!"
+    )
+    experimental.add_argument(
+        "--refineglmderivs",
+        dest="refineglmderivs",
+        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}"
+        ),
+        default=DEFAULT_REFINEGLMDERIVS,
+    )
 
     return parser
 
@@ -430,7 +446,7 @@ def retroglm(args):
         print(f"{numvalidspatiallocs=}")
     internalvalidspaceshape = numvalidspatiallocs
     if args.refinedelay:
-        derivaxissize = np.max([2, args.glmderivs + 1])
+        derivaxissize = np.max([args.refineglmderivs + 1, args.glmderivs + 1])
     else:
         derivaxissize = args.glmderivs + 1
     internalvalidspaceshapederivs = (
@@ -505,6 +521,7 @@ def retroglm(args):
         threshval = therunoptions["glmthreshval"]
     except KeyError:
         threshval = 0.0
+        therunoptions["glmthreshval"] = threshval
     mode = "glm"
 
     if args.debug or args.focaldebug:
@@ -579,54 +596,94 @@ def retroglm(args):
             glmmean,
             rvalue,
             r2value,
-            fitNorm[:, :2],
-            fitcoeff[:, :2],
+            fitNorm[:, : (args.refineglmderivs + 1)],
+            fitcoeff[:, : (args.refineglmderivs + 1)],
             movingsignal,
             lagtc,
             filtereddata,
             LGR,
             TimingLGR,
             therunoptions,
+            glmderivs=args.refineglmderivs,
             debug=args.debug,
         )
 
-        medfiltglmderivratios, filteredglmderivratios, delayoffsetMAD = (
-            tide_refinedelay.filterderivratios(
-                glmderivratios,
-                (xsize, ysize, numslices),
-                validvoxels,
-                (xdim, ydim, slicedim),
-                gausssigma=args.delayoffsetgausssigma,
-                patchthresh=args.delaypatchthresh,
-                fileiscifti=False,
-                textio=False,
-                rt_floattype=rt_floattype,
+        if args.refineglmderivs == 1:
+            medfiltglmderivratios, filteredglmderivratios, delayoffsetMAD = (
+                tide_refinedelay.filterderivratios(
+                    glmderivratios,
+                    (xsize, ysize, numslices),
+                    validvoxels,
+                    (xdim, ydim, slicedim),
+                    gausssigma=args.delayoffsetgausssigma,
+                    patchthresh=args.delaypatchthresh,
+                    fileiscifti=False,
+                    textio=False,
+                    rt_floattype=rt_floattype,
+                    debug=args.debug,
+                )
+            )
+
+            # find the mapping of glm ratios to delays
+            tide_refinedelay.trainratiotooffset(
+                genlagtc,
+                initial_fmri_x,
+                outputname,
+                args.outputlevel,
+                mindelay=args.mindelay,
+                maxdelay=args.maxdelay,
+                numpoints=args.numpoints,
                 debug=args.debug,
             )
-        )
+            TimingLGR.info("Refinement calibration end")
+
+            # now calculate the delay offsets
+            TimingLGR.info("Calculating delay offsets")
+            delayoffset = np.zeros_like(filteredglmderivratios)
+            if args.focaldebug:
+                print(f"calculating delayoffsets for {filteredglmderivratios.shape[0]} voxels")
+            for i in range(filteredglmderivratios.shape[0]):
+                delayoffset[i] = tide_refinedelay.ratiotodelay(filteredglmderivratios[i])
+                """delayoffset[i] = tide_refinedelay.coffstodelay(
+                    np.asarray([filteredglmderivratios[i]]),
+                    mindelay=args.mindelay,
+                    maxdelay=args.maxdelay,
+                )"""
+
+            refinedvoxelstoreport = filteredglmderivratios.shape[0]
+        else:
+            medfiltglmderivratios = np.zeros_like(glmderivratios)
+            filteredglmderivratios = np.zeros_like(glmderivratios)
+            delayoffsetMAD = np.zeros(args.refineglmderivs, dtype=float)
+            for i in range(args.refineglmderivs):
+                medfiltglmderivratios[i, :], filteredglmderivratios[i, :], delayoffsetMAD[i] = (
+                    tide_refinedelay.filterderivratios(
+                        glmderivratios[i, :],
+                        (xsize, ysize, numslices),
+                        validvoxels,
+                        (xdim, ydim, slicedim),
+                        gausssigma=args.delayoffsetgausssigma,
+                        patchthresh=args.delaypatchthresh,
+                        fileiscifti=False,
+                        textio=False,
+                        rt_floattype=rt_floattype,
+                        debug=args.debug,
+                    )
+                )
+
+            # now calculate the delay offsets
+            delayoffset = np.zeros_like(filteredglmderivratios[0, :])
+            if args.debug:
+                print(f"calculating delayoffsets for {filteredglmderivratios.shape[1]} voxels")
+            for i in range(filteredglmderivratios.shape[1]):
+                delayoffset[i] = tide_refinedelay.coffstodelay(
+                    filteredglmderivratios[:, i],
+                    mindelay=args.mindelay,
+                    maxdelay=args.maxdelay,
+                )
+            refinedvoxelstoreport = filteredglmderivratios.shape[1]
 
-        # find the mapping of glm ratios to delays
-        tide_refinedelay.trainratiotooffset(
-            genlagtc,
-            initial_fmri_x,
-            outputname,
-            args.outputlevel,
-            mindelay=args.mindelay,
-            maxdelay=args.maxdelay,
-            numpoints=args.numpoints,
-            debug=args.debug,
-        )
-        TimingLGR.info("Refinement calibration end")
-
-        # now calculate the delay offsets
-        TimingLGR.info("Calculating delay offsets")
-        delayoffset = filteredglmderivratios * 0.0
-        if args.focaldebug:
-            print(f"calculating delayoffsets for {filteredglmderivratios.shape[0]} voxels")
-        for i in range(filteredglmderivratios.shape[0]):
-            delayoffset[i] = tide_refinedelay.ratiotodelay(filteredglmderivratios[i])
         namesuffix = "_desc-delayoffset_hist"
-
         tide_stats.makeandsavehistogram(
             delayoffset,
             therunoptions["histlen"],
@@ -641,7 +698,7 @@ def retroglm(args):
         TimingLGR.info(
             "Delay offset calculation done",
             {
-                "message2": filteredglmderivratios.shape[0],
+                "message2": refinedvoxelstoreport,
                 "message3": "voxels",
             },
         )
@@ -824,28 +881,56 @@ def retroglm(args):
             ]
 
     if args.refinedelay:
+        if args.refineglmderivs > 1:
+            for i in range(args.refineglmderivs):
+                maplist += [
+                    (
+                        glmderivratios[i, :],
+                        f"glmderivratios_{i}",
+                        "map",
+                        None,
+                        f"Ratio of derivative {i+1} of delayed sLFO to the delayed sLFO",
+                    ),
+                    (
+                        medfiltglmderivratios[i, :],
+                        f"medfiltglmderivratios_{i}",
+                        "map",
+                        None,
+                        f"Median filtered version of the glmderivratios_{i} map",
+                    ),
+                    (
+                        filteredglmderivratios[i, :],
+                        f"filteredglmderivratios_{i}",
+                        "map",
+                        None,
+                        f"glmderivratios_{i}, with outliers patched using median filtered data",
+                    ),
+                ]
+        else:
+            maplist += [
+                (
+                    glmderivratios,
+                    "glmderivratios",
+                    "map",
+                    None,
+                    "Ratio of the first derivative of delayed sLFO to the delayed sLFO",
+                ),
+                (
+                    medfiltglmderivratios,
+                    "medfiltglmderivratios",
+                    "map",
+                    None,
+                    "Median filtered version of the glmderivratios map",
+                ),
+                (
+                    filteredglmderivratios,
+                    "filteredglmderivratios",
+                    "map",
+                    None,
+                    "glmderivratios, with outliers patched using median filtered data",
+                ),
+            ]
         maplist += [
-            (
-                glmderivratios,
-                "glmderivratios",
-                "map",
-                None,
-                "Ratio of the first derivative of delayed sLFO to the delayed sLFO",
-            ),
-            (
-                medfiltglmderivratios,
-                "medfiltglmderivratios",
-                "map",
-                None,
-                "Median filtered version of the glmderivratios map",
-            ),
-            (
-                filteredglmderivratios,
-                "filteredglmderivratios",
-                "map",
-                None,
-                "glmderivratios, with outliers patched using median filtered data",
-            ),
             (
                 delayoffset,
                 "delayoffset",

rapidtide/workflows/tidepool.py

@@ -87,7 +87,7 @@ def _get_parser():
         "--dataset",
         nargs="*",
         help=(
-            "Use this dataset root name (skip initial selection step).  The root name is the entire path "
+            "Specify one or more dataset root names (skip initial selection step).  The root name is the entire path "
             "to the rapidtide output data (including the underscore) that precedes 'desc-maxtime_map.nii.gz'"
         ),
         dest="datafileroot",
@@ -106,8 +106,12 @@ def _get_parser():
         "--uistyle",
         action="store",
         type=str,
-        choices=["normal", "old", "big"],
-        help="Set the window layout style.  Default is 'normal'.",
+        choices=["normal", "big"],
+        help=(
+            "Set the window layout style.  The 'normal' uistyle loads 8 data maps into display panes, "
+            "and fits comfortably on the screen of a 14in MacbookPro screen.  The 'big' uistyle has 16 display "
+            "panes, and fits on a 16in MBP screen.  Default is 'normal'."
+        ),
         default="normal",
     )
     parser.add_argument(
@@ -120,7 +124,7 @@ def _get_parser():
     )
     parser.add_argument(
         "--ignoredimmatch",
-        help="Do not check to see if dataset sizes match",
+        help="Do not check to see if dataset sizes match.  This is almost certainly a terrible idea.",
         dest="ignoredimmatch",
         action="store_true",
         default=False,
@@ -1114,6 +1118,7 @@ def setMask(maskname):
         }
     print(maskinfodicts[maskname]["msg"])
     ui.setMask_Button.setText(maskinfodicts[maskname]["label"])
+    currentdataset.setFuncMaskName(maskname)
     for themap in currentdataset.loadedfuncmaps:
         if maskname == "nomask":
             overlays[themap].setFuncMask(None)
@@ -1149,16 +1154,19 @@ def overlay_radioButton_clicked(which, enabled):
                 thedispmin = overlays[currentdataset.focusmap].dispmin
                 thedispmax = overlays[currentdataset.focusmap].dispmax
             if verbosity > 1:
-                print("currentdataset.focusmap set to ", currentdataset.focusmap)
-            if overlays[currentdataset.focusmap].lut_state == gen_gray_state():
+                print(f"currentdataset.focusmap set to {currentdataset.focusmap}")
+                print(
+                    f"overlays[currentdataset.focusmap].LUTname set to {overlays[currentdataset.focusmap].LUTname}"
+                )
+            if overlays[currentdataset.focusmap].LUTname == "gray":
                 ui.gray_radioButton.setChecked(True)
-            elif overlays[currentdataset.focusmap].lut_state == gen_thermal_state():
+            elif overlays[currentdataset.focusmap].LUTname == "thermal":
                 ui.thermal_radioButton.setChecked(True)
-            elif overlays[currentdataset.focusmap].lut_state == gen_plasma_state():
+            elif overlays[currentdataset.focusmap].LUTname == "plasma":
                 ui.plasma_radioButton.setChecked(True)
-            elif overlays[currentdataset.focusmap].lut_state == gen_viridis_state():
+            elif overlays[currentdataset.focusmap].LUTname == "viridis":
                 ui.viridis_radioButton.setChecked(True)
-            elif overlays[currentdataset.focusmap].lut_state == gen_turbo_state():
+            elif overlays[currentdataset.focusmap].LUTname == "turbo":
                 ui.turbo_radioButton.setChecked(True)
             else:
                 ui.rainbow_radioButton.setChecked(True)
@@ -1563,9 +1571,10 @@ def activateDataset(currentdataset, ui, win, defaultdict, overlayGraphicsViews,
         overlays["atlas"].setGeomMask(thegeommask)
         overlays["atlas"].setFuncMask(overlays["atlasmask"].data)
 
-    if verbosity > 0:
-        for theoverlay in overlays:
-            overlays[theoverlay].summarize()
+    if not panesinitialized:
+        if verbosity > 0:
+            for theoverlay in overlays:
+                overlays[theoverlay].summarize()
 
     if verbosity > 1:
         print("focusmap is:", currentdataset.focusmap, "bgmap is:", bgmap)
@@ -1668,6 +1677,11 @@ def activateDataset(currentdataset, ui, win, defaultdict, overlayGraphicsViews,
         updateRegressor()
         updateRegressorSpectrum()
 
+        # update the mask menu
+        if currentdataset.funcmaskname is not None:
+            print(f"updating the mask menu to {currentdataset.funcmaskname}")
+            setMask(currentdataset.funcmaskname)
+
 
 def loadpane(
     themap,
@@ -1968,13 +1982,13 @@ def tidepool(args):
             "funcmask": "p_lt_0p050_mask",
         },
         "lagsigma": {
-            "colormap": gen_spectrum_state(),
+            "colormap": gen_plasma_state(),
             "label": "Similarity width",
             "display": True,
             "funcmask": "p_lt_0p050_mask",
         },
         "MTT": {
-            "colormap": gen_spectrum_state(),
+            "colormap": gen_plasma_state(),
             "label": "MTT",
             "display": extramaps,
             "funcmask": "p_lt_0p050_mask",
@@ -2457,4 +2471,9 @@ def tidepool(args):
     updateRegressorSpectrum()
     uiinitialized = True
 
+    # for profiling
+    """for i in range(20):
+        selectDataset((i + 1) % 2)
+    sys.exit(0)"""
+
     QtWidgets.QApplication.instance().exec()

{rapidtide-3.0a10.dist-info → rapidtide-3.0a12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: rapidtide
-Version: 3.0a10
+Version: 3.0a12
 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>