rapidtide 3.0a7__tar.gz → 3.0a9__tar.gz

{rapidtide-3.0a7 → rapidtide-3.0a9}/CHANGELOG.md

@@ -1,5 +1,18 @@
 # Release history
 
+## 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.
+* (tidepool) Clarify how you specify the dataset name in the help text.
+* (tidepool) Fixed some typos in outputs.
+* (tidepool) Made some internal changes in preparation for allowing loading multiple files.
+
 ## Version 3.0alpha7 (2/11/25)
 * (happy) Trying out some new approaches for aliased correlation.
 * (happy) Put in some initial support for multiecho data.

{rapidtide-3.0a7/rapidtide.egg-info → rapidtide-3.0a9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: rapidtide
-Version: 3.0a7
+Version: 3.0a9
 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-3.0a7 → rapidtide-3.0a9}/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-3.0a7 → rapidtide-3.0a9}/rapidtide/OrthoImageItem.py

@@ -68,7 +68,16 @@ def newColorbar(left, top, impixpervoxx, impixpervoxy, imgsize):
     return thecolorbarfgwin, thecolorbarbgwin, theviewbox, colorbarvals
 
 
-def newViewWindow(view, left, top, impixpervoxx, impixpervoxy, imgsize, enableMouse=False):
+def setupViewWindow(
+    view,
+    left,
+    top,
+    impixpervoxx,
+    impixpervoxy,
+    imgsize,
+    enableMouse=False,
+):
+
     theviewbox = view.addViewBox(enableMouse=enableMouse, enableMenu=False, lockAspect=1.0)
     theviewbox.setAspectLocked()
     theviewbox.setRange(QtCore.QRectF(0, 0, imgsize, imgsize), padding=0.0, disableAutoRange=True)
@@ -146,6 +155,17 @@ class OrthoImageItem(QtWidgets.QWidget):
         self.offsetx = self.imgsize * (0.5 - self.xfov / (2.0 * self.maxfov))
         self.offsety = self.imgsize * (0.5 - self.yfov / (2.0 * self.maxfov))
         self.offsetz = self.imgsize * (0.5 - self.zfov / (2.0 * self.maxfov))
+        self.axviewbox = None
+        self.corviewbox = None
+        self.sagviewbox = None
+        self.axviewwin = None
+        self.corviewwin = None
+        self.sagviewwin = None
+        self.axviewbgwin = None
+        self.corviewbgwin = None
+        self.sagviewbgwin = None
+        self.debug = True
+        self.arrangement = arrangement
 
         if self.verbose > 1:
             print("OrthoImageItem initialization:")
@@ -162,7 +182,6 @@ class OrthoImageItem(QtWidgets.QWidget):
             print("    Offsets:", self.offsetx, self.offsety, self.offsetz)
         self.buttonisdown = False
 
-        self.arrangement = arrangement
         self.axview.setBackground(None)
         self.axview.setRange(padding=0.0)
         self.axview.ci.layout.setContentsMargins(0, 0, 0, 0)
@@ -182,7 +201,7 @@ class OrthoImageItem(QtWidgets.QWidget):
             self.axviewvLine,
             self.axviewhLine,
             self.axviewbox,
-        ) = newViewWindow(
+        ) = setupViewWindow(
             self.axview,
             self.offsetx,
             self.offsety,
@@ -197,7 +216,7 @@ class OrthoImageItem(QtWidgets.QWidget):
             self.corviewvLine,
             self.corviewhLine,
             self.corviewbox,
-        ) = newViewWindow(
+        ) = setupViewWindow(
             self.corview,
             self.offsetx,
             self.offsetz,
@@ -212,7 +231,7 @@ class OrthoImageItem(QtWidgets.QWidget):
             self.sagviewvLine,
             self.sagviewhLine,
             self.sagviewbox,
-        ) = newViewWindow(
+        ) = setupViewWindow(
             self.sagview,
             self.offsety,
             self.offsetz,

{rapidtide-3.0a7 → rapidtide-3.0a9}/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"
 
@@ -159,6 +187,8 @@ 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 +272,6 @@ 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)
         )
@@ -432,6 +460,7 @@ class Overlay:
 
 class RapidtideDataset:
     "Store all the data associated with a rapidtide dataset"
+    fileroot = None
     focusregressor = None
     regressorfilterlimits = None
     regressorsimcalclimits = None
@@ -451,6 +480,8 @@ class RapidtideDataset:
     ysize = 0.0
     zsize = 0.0
     tr = 0.0
+    space = None
+    affine = None
 
     def __init__(
         self,
@@ -1057,7 +1088,11 @@ 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
@@ -1286,4 +1321,8 @@ 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-3.0a7 → rapidtide-3.0a9}/rapidtide/data/examples/src/testfmri

@@ -14,29 +14,18 @@ rapidtide \
     --nprocs -1 \
     --searchrange -5 20 \
     --simcalcrange 50 -1 \
-    --outputlevel min \
     --refinedelay \
     sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_refinedelay
+    ../dst/sub-RAPIDTIDETEST_filt
 
 rapidtide \
-    --spatialfilt 5 \
+    --spatialfilt 0 \
     --nprocs -1 \
     --searchrange -5 20 \
     --simcalcrange 50 -1 \
-    --outputlevel min \
-    --norefinedelay \
-    sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_norefinedelay
-
-rapidtide \
-    --spatialfilt 5 \
-    --nprocs -1 \
-    --searchrange -5 20 \
-    --simcalcrange 50 -1 \
-    --outputlevel min \
+    --refinedelay \
     sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_noption
+    ../dst/sub-RAPIDTIDETEST_nofilt
 
 #rapidtide \
 #    --spatialfilt 5 \

{rapidtide-3.0a7 → rapidtide-3.0a9}/rapidtide/happy_supportfuncs.py

@@ -134,6 +134,27 @@ def calc_3d_optical_flow(video, projmask, flowhdr, outputroot, window_size=3, de
     return flow_vectors
 
 
+def phasejolt(phaseimage):
+
+    # Compute the gradient of the window in x, y, and z directions
+    grad_x, grad_y, grad_z = np.gradient(phaseimage)
+
+    # Now compute the second order gradients of the window in x, y, and z directions
+    grad_xx, grad_xy, grad_xz = np.gradient(grad_x)
+    grad_yx, grad_yy, grad_yz = np.gradient(grad_y)
+    grad_zx, grad_zy, grad_zz = np.gradient(grad_z)
+
+    # Calculate our metrics of interest
+    jump = (np.fabs(grad_x) + np.fabs(grad_y) + np.fabs(grad_z)) / 3.0
+    jolt = (
+        (np.fabs(grad_xx) + np.fabs(grad_xy) + np.fabs(grad_xz))
+        + (np.fabs(grad_yx) + np.fabs(grad_yy) + np.fabs(grad_yz))
+        + (np.fabs(grad_zx) + np.fabs(grad_zy) + np.fabs(grad_zz))
+    ) / 9.0
+    laplacian = grad_xx + grad_yy + grad_zz
+    return (jump, jolt, laplacian)
+
+
 def cardiacsig(thisphase, amps=(1.0, 0.0, 0.0), phases=None, overallphase=0.0):
     total = 0.0
     if phases is None:

{rapidtide-3.0a7 → rapidtide-3.0a9}/rapidtide/helper_classes.py

@@ -691,6 +691,7 @@ class SimilarityFunctionFitter:
     FML_FITWIDTHHIGH = np.uint32(0x0800)
     FML_FITLAGLOW = np.uint32(0x1000)
     FML_FITLAGHIGH = np.uint32(0x2000)
+    FML_FITALGOFAIL = np.uint32(0x0400)
     FML_FITFAIL = (
         FML_FITAMPLOW
         | FML_FITAMPHIGH
@@ -698,6 +699,7 @@ class SimilarityFunctionFitter:
         | FML_FITWIDTHHIGH
         | FML_FITLAGLOW
         | FML_FITLAGHIGH
+        | FML_FITALGOFAIL
     )
 
     def __init__(
@@ -873,6 +875,8 @@ class SimilarityFunctionFitter:
             reasons.append("Fit Lag too low")
         if failreason.astype(np.uint32) & self.FML_FITLAGHIGH:
             reasons.append("Fit Lag too high")
+        if failreason.astype(np.uint32) & self.FML_FITALGOFAIL:
+            reasons.append("Nonlinear fit failed")
 
         if len(reasons) > 0:
             return ", ".join(reasons)
@@ -1119,6 +1123,7 @@ class SimilarityFunctionFitter:
                     maxlag = np.fmod((1.0 * plsq[1]), self.lagmod)
                     maxsigma = plsq[2]
                 except:
+                    failreason |= self.FML_FITALGOFAIL
                     maxval = np.float64(0.0)
                     maxlag = np.float64(0.0)
                     maxsigma = np.float64(0.0)
@@ -1139,6 +1144,7 @@ class SimilarityFunctionFitter:
                     maxlag = np.fmod((1.0 * plsq[1]), self.lagmod)
                     maxsigma = plsq[2]
                 except:
+                    failreason |= self.FML_FITALGOFAIL
                     maxval = np.float64(0.0)
                     maxlag = np.float64(0.0)
                     maxsigma = np.float64(0.0)
@@ -1173,6 +1179,7 @@ class SimilarityFunctionFitter:
                         print("poly coffs:", a, b, c)
                         print("maxlag, maxval, maxsigma:", maxlag, maxval, maxsigma)
                 except np.lib.polynomial.RankWarning:
+                    failreason |= self.FML_FITALGOFAIL
                     maxlag = 0.0
                     maxval = 0.0
                     maxsigma = 0.0
@@ -1219,6 +1226,7 @@ class SimilarityFunctionFitter:
                 # different rules for mutual information peaks
                 if ((maxval - baseline) < self.lthreshval * baselinedev) or (maxval < baseline):
                     failreason |= self.FML_FITAMPLOW
+                    maxval_init = 0.0
                     if self.debug:
                         if (maxval - baseline) < self.lthreshval * baselinedev:
                             print(
@@ -1229,7 +1237,6 @@ class SimilarityFunctionFitter:
                             )
                         if maxval < baseline:
                             print("FITAMPLOW: maxval < baseline:", maxval, baseline)
-                    maxval_init = 0.0
                     if self.debug:
                         print("bad fit amp: maxval is lower than lower limit")
             if (self.lagmin > maxlag) or (maxlag > self.lagmax):
@@ -1269,6 +1276,8 @@ class SimilarityFunctionFitter:
             maxsigma = np.float64(maxsigma_init)
             if failreason != self.FML_NOERROR:
                 maskval = np.uint16(0)
+            else:
+                maskval = np.uint16(1)
 
         if self.debug or self.displayplots:
             print(

{rapidtide-3.0a7 → rapidtide-3.0a9}/rapidtide/io.py

@@ -355,7 +355,7 @@ def savemaplist(
             themap,
             internalspaceshape,
             validvoxels,
-            outmaparray,
+            outmaparray.astype(themap.dtype),
             debug=False,
         )
 

{rapidtide-3.0a7 → rapidtide-3.0a9}/rapidtide/simfuncfit.py

@@ -43,7 +43,7 @@ def onesimfuncfit(
 ):
     if initiallag is not None:
         thefitter.setguess(True, maxguess=initiallag)
-        widthmax = despeckle_thresh
+        thefitter.setrange(-despeckle_thresh/2.0, despeckle_thresh/2.0)
     else:
         thefitter.setguess(False)