rapidtide 3.0a10__tar.gz → 3.0a12__tar.gz

{rapidtide-3.0a10 → rapidtide-3.0a12}/CHANGELOG.md

@@ -1,5 +1,20 @@
 # Release history
 
+## Version 3.0alpha12 (3/19/25)
+* (rapidtide) Added option to perform refine on last pass.
+* (rapidtide) Moved refinement out into its own class to make things more modular.
+* (refinedelay) Put in some experimental code to do multiderivative delay fits.  Currently doesn't work very well.
+* (tidepool) Changed default colormaps for similarity widty, MTT.
+* (package) Made a script to compile qt templates.
+* (package) Added the ability to set value limits to some parser functions.
+
+## 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 documentation has been updated to reflect the current state of the program.
+
 ## 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.

{rapidtide-3.0a10/rapidtide.egg-info → rapidtide-3.0a12}/PKG-INFO

@@ -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>

rapidtide-3.0a12/TODO.md

@@ -0,0 +1,17 @@
+To do list
+----------
+
+1. (package) Expand automated testing
+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.
+10. (tidepool)
+
+Implement new argument parsing:
+vi \
+rapidtide/scripts/showxcorr_legacy.py \
+rapidtide/scripts/threeD.py \
+rapidtide/experimental/highresmotion \
+rapidtide/experimental/harmonogram \
+rapidtide/workflows/rapidtide2x_parser.py

{rapidtide-3.0a10 → rapidtide-3.0a12}/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-3.0a10 → rapidtide-3.0a12}/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-3.0a10 → rapidtide-3.0a12}/rapidtide/RapidtideDataset.py

@@ -161,6 +161,7 @@ class Timecourse:
 
 class Overlay:
     "Store a data overlay and some information about it"
+    LUTname = None
 
     def __init__(
         self,
@@ -193,6 +194,7 @@ 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
@@ -277,6 +279,7 @@ class Overlay:
 
     def updateStats(self):
         calcmaskeddata = self.data[np.where(self.mask != 0)]
+
         self.minval = calcmaskeddata.min()
         self.maxval = calcmaskeddata.max()
         (
@@ -290,6 +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,
@@ -402,9 +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
@@ -433,6 +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
@@ -505,6 +518,7 @@ class RapidtideDataset:
         fileroot,
         anatname=None,
         geommaskname=None,
+        funcmaskname=None,
         graymaskspec=None,
         whitemaskspec=None,
         userise=False,
@@ -523,6 +537,7 @@ class RapidtideDataset:
         self.fileroot = fileroot
         self.anatname = anatname
         self.geommaskname = geommaskname
+        self.funcmaskname = funcmaskname
         self.graymaskspec = graymaskspec
         self.whitemaskspec = whitemaskspec
         self.userise = userise
@@ -1355,3 +1370,6 @@ class RapidtideDataset:
             self.focusmap = whichmap
         except KeyError:
             self.focusmap = "lagtimes"
+
+    def setFuncMaskName(self, maskname):
+        self.funcmaskname = maskname