rapidtide 3.0a9__tar.gz → 3.0a11__tar.gz

{rapidtide-3.0a9 → rapidtide-3.0a11}/CHANGELOG.md

@@ -1,5 +1,19 @@
 # Release history
 
+## Version 3.0alpha11 (3/5/25)
+* (tidepool) Substantial speed improvement switching datasets.
+* (tidepool) Colormap radio button is now set correctly.
+* (tidepool) Mask menu label is now set correctly when restoring a loaded dataset.
+* (versioneer) Updated to 0.29.
+* (docs) Tidepool's new functionality is now described.
+
+## 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...``.

{rapidtide-3.0a9/rapidtide.egg-info → rapidtide-3.0a11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: rapidtide
-Version: 3.0a9
+Version: 3.0a11
 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-3.0a9 → rapidtide-3.0a11}/TODO.md

@@ -2,9 +2,10 @@ To do list
 ----------
 
 1. (package) Expand automated testing
-4. (tidepool) Implement ASPECTS averaging
+4. (tidepool) Implement ASPECTS/JHU averaging
 7. (rapidtide) Implement a dispersive delay model
 8. (rapidtide) Add a sinc peak fit
+9. (tidepool) Fix the weird limit resetting bug when some panes are activated.
 
 Implement new argument parsing:
 rapidtide/experimental/highresmotion

{rapidtide-3.0a9 → rapidtide-3.0a11}/pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
-requires = ['setuptools>=42', 'cffi>=1.0.0', 'versioneer[toml]']
-build-backend = 'setuptools.build_meta'
+requires = ['setuptools>=42', 'cffi>=1.0.0', 'versioneer[toml]==0.29']
+build-backend = "setuptools.build_meta"
 
 [project]
 name = 'rapidtide'
@@ -41,8 +41,7 @@ dependencies = [
   'tqdm',
   'versioneer',
 ]
-#dynamic = ['version', 'license', 'keywords']
-dynamic = ['version']
+dynamic = ["version"]
 authors = [
     {name = 'Blaise deB. Frederick', email='blaise.frederick@gmail.com'},
     {name = 'Taylor Salo'},

{rapidtide-3.0a9 → rapidtide-3.0a11}/rapidtide/Colortables.py

@@ -63,37 +63,55 @@ def setendalpha(thestate, alpha, debug=False):
 def gen_thermal_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["thermal"]
+    thegradient = Gradients["thermal"]
+    thegradient["name"] = "thermal"
+    return thegradient
+    #return Gradients["thermal"]
 
 
 def gen_flame_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["flame"]
+    thegradient = Gradients["flame"]
+    thegradient["name"] = "flame"
+    return thegradient
+    #return Gradients["flame"]
 
 
 def gen_yellowy_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["yellowy"]
+    thegradient = Gradients["yellowy"]
+    thegradient["name"] = "yellowy"
+    return thegradient
+    #return Gradients["yellowy"]
 
 
 def gen_bipolar_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["bipolar"]
+    thegradient = Gradients["bipolar"]
+    thegradient["name"] = "bipolar"
+    return thegradient
+    #return Gradients["bipolar"]
 
 
 def gen_spectrum_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["spectrum"]
+    thegradient = Gradients["spectrum"]
+    thegradient["name"] = "spectrum"
+    return thegradient
+    #return Gradients["spectrum"]
 
 
 def gen_turbo_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["turbo"]
+    thegradient = Gradients["turbo"]
+    thegradient["name"] = "turbo"
+    return thegradient
+    #return Gradients["turbo"]
 
 
 def gen_gray_state():
@@ -103,6 +121,7 @@ def gen_gray_state():
             (1.0000, (255, 255, 255, 255)),
         ],
         "mode": "rgb",
+        "name": "gray",
     }
 
 
@@ -113,31 +132,44 @@ def gen_grey_state():
             (1.0000, (255, 255, 255, 255)),
         ],
         "mode": "rgb",
+        "name": "grey",
     }
 
 
 def gen_viridis_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["viridis"]
+    thegradient = Gradients["viridis"]
+    thegradient["name"] = "viridis"
+    return thegradient
+    #return Gradients["viridis"]
 
 
 def gen_inferno_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["inferno"]
+    thegradient = Gradients["inferno"]
+    thegradient["name"] = "inferno"
+    return thegradient
+    #return Gradients["inferno"]
 
 
 def gen_plasma_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["plasma"]
+    thegradient = Gradients["plasma"]
+    thegradient["name"] = "plasma"
+    return thegradient
+    #return Gradients["plasma"]
 
 
 def gen_magma_state():
     from pyqtgraph.graphicsItems.GradientEditorItem import Gradients
 
-    return Gradients["magma"]
+    thegradient = Gradients["magma"]
+    thegradient["name"] = "magma"
+    return thegradient
+    #return Gradients["magma"]
 
 
 def gen_g2y2r_state():
@@ -150,6 +182,7 @@ def gen_g2y2r_state():
             (1.0000, (255, 0, 0, 0)),
         ],
         "mode": "rgb",
+        "name": "g2y2r",
     }
 
 
@@ -157,6 +190,7 @@ def gen_mask_state():
     return {
         "ticks": [(0.0000, (0, 0, 0, 255)), (1.0000, (255, 255, 255, 0))],
         "mode": "rgb",
+        "name": "mask",
     }
 
 
@@ -168,6 +202,7 @@ def gen_greyclip_state():
             (1.0, (255, 0, 0, 255)),
         ],
         "mode": "rgb",
+        "name": "greyclip",
     }
 
 

{rapidtide-3.0a9 → rapidtide-3.0a11}/rapidtide/OrthoImageItem.py

@@ -19,8 +19,6 @@
 """
 A widget for orthographically displaying 3 and 4 dimensional data
 """
-
-import copy
 import os
 
 import numpy as np
@@ -34,6 +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
@@ -514,7 +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-3.0a9 → rapidtide-3.0a11}/rapidtide/RapidtideDataset.py

@@ -81,6 +81,7 @@ class Timecourse:
         label=None,
         report=False,
         isbids=False,
+        limits=None,
         verbose=0,
     ):
         self.verbose = verbose
@@ -91,6 +92,7 @@ class Timecourse:
         self.displaysamplerate = displaysamplerate
         self.starttime = starttime
         self.isbids = isbids
+        self.limits = limits
 
         if label is None:
             self.label = name
@@ -117,11 +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))
@@ -149,6 +161,7 @@ class Timecourse:
 
 class Overlay:
     "Store a data overlay and some information about it"
+    LUTname = None
 
     def __init__(
         self,
@@ -163,6 +176,7 @@ class Overlay:
         alpha=128,
         endalpha=0,
         display_state=True,
+        invertonload=False,
         isaMask=False,
         init_LUT=True,
         verbose=1,
@@ -180,6 +194,8 @@ class Overlay:
         self.namebase = namebase
         if self.verbose > 1:
             print("reading map ", self.name, " from ", self.filename, "...")
+        self.maskhash = 0
+        self.invertonload = invertonload
         self.readImageData(isaMask=isaMask)
         self.mask = None
         self.maskeddata = None
@@ -263,6 +279,7 @@ class Overlay:
 
     def updateStats(self):
         calcmaskeddata = self.data[np.where(self.mask != 0)]
+
         self.minval = calcmaskeddata.min()
         self.maxval = calcmaskeddata.max()
         (
@@ -276,6 +293,7 @@ class Overlay:
             calcmaskeddata, bins=np.linspace(self.minval, self.maxval, 200)
         )
         self.quartiles = [self.pct25, self.pct50, self.pct75]
+
         if self.verbose > 1:
             print(
                 self.name,
@@ -298,6 +316,8 @@ 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
@@ -386,9 +406,17 @@ class Overlay:
 
     def maskData(self):
         self.mask = self.geommask * self.funcmask
-        self.maskeddata = self.data.copy()
-        self.maskeddata[np.where(self.mask < 0.5)] = 0.0
-        self.updateStats()
+        maskhash = hash(self.mask.tostring())
+        # these operations are expensive, so only do them if the mask is changed
+        if (maskhash == self.maskhash) and (self.verbose > 1):
+            print("mask has not changed")
+        else:
+            if self.verbose > 1:
+                print("mask changed - recalculating")
+            self.maskeddata = self.data.copy()
+            self.maskeddata[np.where(self.mask < 0.5)] = 0.0
+            self.updateStats()
+            self.maskhash = maskhash
 
     def setReport(self, report):
         self.report = report
@@ -417,6 +445,7 @@ class Overlay:
             self.lut_state = setendalpha(lut_state, endalpha)
         self.gradient.restoreState(self.lut_state)
         self.theLUT = self.gradient.getLookupTable(512, alpha=True)
+        self.LUTname = lut_state["name"]
 
     def setisdisplayed(self, display_state):
         self.display_state = display_state
@@ -489,6 +518,7 @@ class RapidtideDataset:
         fileroot,
         anatname=None,
         geommaskname=None,
+        funcmaskname=None,
         graymaskspec=None,
         whitemaskspec=None,
         userise=False,
@@ -500,13 +530,14 @@ class RapidtideDataset:
         coordinatespace="unspecified",
         offsettime=0.0,
         init_LUT=True,
-        verbose=1,
+        verbose=0,
     ):
         self.verbose = verbose
         self.name = name
         self.fileroot = fileroot
         self.anatname = anatname
         self.geommaskname = geommaskname
+        self.funcmaskname = funcmaskname
         self.graymaskspec = graymaskspec
         self.whitemaskspec = whitemaskspec
         self.userise = userise
@@ -556,6 +587,7 @@ class RapidtideDataset:
                     label=thisregressor[1],
                     starttime=thisregressor[5],
                     isbids=self.bidsformat,
+                    limits=self.regressorsimcalclimits,
                     verbose=self.verbose,
                 )
                 if theregressor.timedata is not None:
@@ -573,6 +605,7 @@ class RapidtideDataset:
                     )
 
     def _loadfuncmaps(self):
+        mapstoinvert = ["varChange"]
         self.loadedfuncmaps = []
         xdim = 0
         ydim = 0
@@ -588,12 +621,17 @@ 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:
@@ -1108,6 +1146,11 @@ 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"],
@@ -1200,6 +1243,7 @@ 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):
@@ -1326,3 +1370,6 @@ class RapidtideDataset:
             self.focusmap = whichmap
         except KeyError:
             self.focusmap = "lagtimes"
+
+    def setFuncMaskName(self, maskname):
+        self.funcmaskname = maskname

rapidtide-3.0a11/rapidtide/__init__.py

@@ -0,0 +1,3 @@
+# -*- coding: utf-8 -*-
+from . import _version
+__version__ = _version.get_versions()['version']