rapidtide 3.0a8__tar.gz → 3.0a10__tar.gz

{rapidtide-3.0a8 → rapidtide-3.0a10}/CHANGELOG.md

@@ -1,5 +1,18 @@
 # Release history
 
+## Version 3.0alpha10 (2/28/25)
+* (tidepool) Full support for multiple concurrent datasets.  Dataset loading and selection is now done through the File menu.
+* (tidepool) Load additional informational maps, and somewhat more intelligently.
+* (tidepool) Fixed pane loading to use all available panes.
+* (tidepool) Fixed image saving under pyqt6.
+* (tidepool) For the regressor spectrum, only do FFT of the portion of the regressor used for similarity calculation.
+
+## Version 3.0alpha9 (2/26/25)
+* (rapidtide) Fixed the calculation of the regressor autocorrelation width (used in estimating MTT).
+* (tidepool) First working version that allows loading multiple files. Use ``--dataset DATASET1 DATASET2...``.
+* (tidepool) Added new "big" template to let you see more information at once.  Select with ``--uistyle big``.
+* (tidepool) Pretty significant code cleanup under the hood.
+
 ## Version 3.0alpha8 (2/20/25)
 * (rapidtide) Enhanced fit failure reporting.
 * (rapidtide) Fixed map output type for non-float maps.

{rapidtide-3.0a8/rapidtide.egg-info → rapidtide-3.0a10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: rapidtide
-Version: 3.0a8
+Version: 3.0a10
 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>

{rapidtide-3.0a8 → rapidtide-3.0a10}/TODO.md

@@ -2,10 +2,9 @@ To do list
 ----------
 
 1. (package) Expand automated testing
-2. (package) Expand documentation A LOT
-3. (rapidtide) Finish implementing the --tmask option
 4. (tidepool) Implement ASPECTS averaging
 7. (rapidtide) Implement a dispersive delay model
+8. (rapidtide) Add a sinc peak fit
 
 Implement new argument parsing:
 rapidtide/experimental/highresmotion

{rapidtide-3.0a8 → rapidtide-3.0a10}/rapidtide/OrthoImageItem.py

@@ -19,13 +19,10 @@
 """
 A widget for orthographically displaying 3 and 4 dimensional data
 """
-
-import copy
 import os
 
 import numpy as np
 import pyqtgraph as pg
-from more_itertools.more import first
 from pyqtgraph.Qt import QtCore, QtGui, QtWidgets
 
 try:
@@ -35,6 +32,14 @@ try:
 except ImportError:
     PILexists = False
 
+try:
+    from PyQt6.QtCore import QT_VERSION_STR
+except ImportError:
+    pyqtversion = 5
+else:
+    pyqtversion = 6
+print(f"using {pyqtversion=}")
+
 
 def newColorbar(left, top, impixpervoxx, impixpervoxy, imgsize):
     cb_xdim = imgsize // 10
@@ -515,7 +520,10 @@ class OrthoImageItem(QtWidgets.QWidget):
         if self.verbose > 1:
             print("saving main window")
         mydialog = QtWidgets.QFileDialog()
-        options = mydialog.Options()
+        if pyqtversion == 5:
+            options = mydialog.Options()
+        else:
+            options = mydialog.options()
         thedir = str(
             mydialog.getExistingDirectory(options=options, caption="Image output directory")
         )

{rapidtide-3.0a8 → rapidtide-3.0a10}/rapidtide/RapidtideDataset.py

@@ -39,6 +39,34 @@ atlases = {
 }
 
 
+def check_rt_spatialmatch(dataset1, dataset2):
+    if (
+        (dataset1.xdim == dataset2.xdim)
+        and (dataset1.ydim == dataset2.ydim)
+        and (dataset1.zdim == dataset2.zdim)
+    ):
+        dimmatch = True
+    else:
+        dimmatch = False
+    if (
+        (dataset1.xsize == dataset2.xsize)
+        and (dataset1.ysize == dataset2.ysize)
+        and (dataset1.zsize == dataset2.zsize)
+    ):
+        sizematch = True
+    else:
+        sizematch = False
+    if dataset1.space == dataset2.space:
+        spacematch = True
+    else:
+        spacematch = False
+    if dataset1.affine == dataset2.affine:
+        affinematch = True
+    else:
+        affinematch = False
+    return dimmatch, sizematch, spacematch, affinematch
+
+
 class Timecourse:
     "Store a timecourse and some information about it"
 
@@ -53,6 +81,7 @@ class Timecourse:
         label=None,
         report=False,
         isbids=False,
+        limits=None,
         verbose=0,
     ):
         self.verbose = verbose
@@ -63,6 +92,7 @@ class Timecourse:
         self.displaysamplerate = displaysamplerate
         self.starttime = starttime
         self.isbids = isbids
+        self.limits = limits
 
         if label is None:
             self.label = name
@@ -89,11 +119,21 @@ class Timecourse:
         self.timeaxis = (
             np.linspace(0.0, self.length, num=self.length, endpoint=False) / self.samplerate
         ) - self.starttime
+        if self.limits is not None:
+            startpoint = np.max((int(np.round(self.limits[0] * self.samplerate, 0)), 0))
+            endpoint = np.min((int(np.round(self.limits[1] * self.samplerate, 0)), self.length))
+        else:
+            startpoint = 0
+            endpoint = self.length
         self.specaxis, self.specdata = tide_filt.spectrum(
-            tide_math.corrnormalize(self.timedata), self.samplerate
+            tide_math.corrnormalize(self.timedata[startpoint:endpoint]), self.samplerate
+        )
+        self.kurtosis, self.kurtosis_z, self.kurtosis_p = tide_stats.kurtosisstats(
+            self.timedata[startpoint:endpoint]
+        )
+        self.skewness, self.skewness_z, self.skewness_p = tide_stats.skewnessstats(
+            self.timedata[startpoint:endpoint]
         )
-        self.kurtosis, self.kurtosis_z, self.kurtosis_p = tide_stats.kurtosisstats(self.timedata)
-        self.skewness, self.skewness_z, self.skewness_p = tide_stats.skewnessstats(self.timedata)
 
         if self.verbose > 1:
             print("Timecourse data range:", np.min(self.timedata), np.max(self.timedata))
@@ -135,6 +175,7 @@ class Overlay:
         alpha=128,
         endalpha=0,
         display_state=True,
+        invertonload=False,
         isaMask=False,
         init_LUT=True,
         verbose=1,
@@ -152,6 +193,7 @@ class Overlay:
         self.namebase = namebase
         if self.verbose > 1:
             print("reading map ", self.name, " from ", self.filename, "...")
+        self.invertonload = invertonload
         self.readImageData(isaMask=isaMask)
         self.mask = None
         self.maskeddata = None
@@ -159,6 +201,8 @@ class Overlay:
         self.setGeomMask(geommask, maskdata=False)
         self.maskData()
         self.updateStats()
+        self.dispmin = self.robustmin
+        self.dispmax = self.robustmax
         if init_LUT:
             self.gradient = getagradient()
             self.lut_state = lut_state
@@ -242,8 +286,6 @@ class Overlay:
             self.pct75,
             self.robustmax,
         ) = tide_stats.getfracvals(calcmaskeddata, [0.02, 0.25, 0.5, 0.75, 0.98], nozero=False)
-        self.dispmin = self.robustmin
-        self.dispmax = self.robustmax
         self.histy, self.histx = np.histogram(
             calcmaskeddata, bins=np.linspace(self.minval, self.maxval, 200)
         )
@@ -270,6 +312,8 @@ class Overlay:
         self.nim, self.data, self.header, self.dims, self.sizes = tide_io.readfromnifti(
             self.filename
         )
+        if self.invertonload:
+            self.data *= -1.0
         if isaMask:
             if self.filevals is None:
                 self.data[np.where(self.data < 0.5)] = 0.0
@@ -452,6 +496,8 @@ class RapidtideDataset:
     ysize = 0.0
     zsize = 0.0
     tr = 0.0
+    space = None
+    affine = None
 
     def __init__(
         self,
@@ -470,7 +516,7 @@ class RapidtideDataset:
         coordinatespace="unspecified",
         offsettime=0.0,
         init_LUT=True,
-        verbose=1,
+        verbose=0,
     ):
         self.verbose = verbose
         self.name = name
@@ -526,6 +572,7 @@ class RapidtideDataset:
                     label=thisregressor[1],
                     starttime=thisregressor[5],
                     isbids=self.bidsformat,
+                    limits=self.regressorsimcalclimits,
                     verbose=self.verbose,
                 )
                 if theregressor.timedata is not None:
@@ -543,6 +590,7 @@ class RapidtideDataset:
                     )
 
     def _loadfuncmaps(self):
+        mapstoinvert = ["varChange"]
         self.loadedfuncmaps = []
         xdim = 0
         ydim = 0
@@ -558,12 +606,17 @@ class RapidtideDataset:
                         " exists - reading...",
                     )
                 thepath, thebase = os.path.split(self.fileroot)
+                if mapname in mapstoinvert:
+                    invertthismap = True
+                else:
+                    invertthismap = False
                 self.overlays[mapname] = Overlay(
                     mapname,
                     self.fileroot + mapfilename + ".nii.gz",
                     thebase,
                     init_LUT=self.init_LUT,
                     report=True,
+                    invertonload=invertthismap,
                     verbose=self.verbose,
                 )
                 if xdim == 0:
@@ -1058,7 +1111,11 @@ class RapidtideDataset:
         return self.regressors
 
     def setfocusregressor(self, whichregressor):
-        self.focusregressor = whichregressor
+        try:
+            testregressor = self.regressors[whichregressor]
+            self.focusregressor = whichregressor
+        except KeyError:
+            self.focusregressor = "prefilt"
 
     def setupoverlays(self):
         # load the overlays
@@ -1074,6 +1131,11 @@ class RapidtideDataset:
                 ["lagsigma", "desc-maxwidth_map"],
                 ["MTT", "desc-MTT_map"],
                 ["R2", "desc-lfofilterR2_map"],
+                ["CoV", "desc-CoV_map"],
+                ["confoundR2", "desc-confoundfilterR2_map"],
+                ["varBefore", "desc-lfofilterInbandVarianceBefore_map"],
+                ["varAfter", "desc-lfofilterInbandVarianceAfter_map"],
+                ["varChange", "desc-lfofilterInbandVarianceChange_map"],
                 ["fitNorm", "desc-lfofilterNorm_map"],
                 ["fitcoff", "desc-lfofilterCoeff_map"],
                 ["neglog10p", "desc-neglog10p_map"],
@@ -1166,6 +1228,7 @@ class RapidtideDataset:
                 ["lagmask", "desc-corrfit_mask"],
                 ["refinemask", "desc-refine_mask"],
                 ["meanmask", "desc-globalmean_mask"],
+                ["brainmask", "desc-brainmask_mask"],
                 ["preselectmask", "desc-globalmeanpreselect_mask"],
             ]
             if not ("neglog10p" in self.loadedfuncmaps):
@@ -1287,4 +1350,8 @@ class RapidtideDataset:
         return self.overlays
 
     def setfocusmap(self, whichmap):
-        self.focusmap = whichmap
+        try:
+            testmap = self.overlays[whichmap]
+            self.focusmap = whichmap
+        except KeyError:
+            self.focusmap = "lagtimes"

{rapidtide-3.0a8 → rapidtide-3.0a10}/rapidtide/data/examples/src/testfmri

@@ -23,7 +23,7 @@ rapidtide \
     --nprocs -1 \
     --searchrange -5 20 \
     --simcalcrange 50 -1 \
-    --norefinedelay \
+    --refinedelay \
     sub-RAPIDTIDETEST.nii.gz \
     ../dst/sub-RAPIDTIDETEST_nofilt