rapidtide 3.0.8__tar.gz → 3.0.10__tar.gz

{rapidtide-3.0.8 → rapidtide-3.0.10}/CHANGELOG.md

@@ -1,11 +1,26 @@
 # Release history
 
+## Version 3.0.10 (8/18/25)
+* (tidepool) Do better checking on which required files exist so it's more clear why a dataset won't load.
+* (docs) Clarified that the sLFO filtered output of rapidtide has NO other filtering applied to is - the temporal, spatial, and confound filtering is all discarded prior to the final sLFO filtering step.
+* (package) Played with some coding models (qwen3-coder, Claude) to write some docstrings and check a few routines for bugs.  It generally worked well, but you definitely have to check their work.
+* (package) Adjusted coverage calculation.
+* (package) Added a test for data simulation.
+* (package) Accepted several dependabot PRs.
+
+## Version 3.0.9 (7/3/25)
+* (rapidtide) Added an alternative method for coarse delay estimation (set ``--similaritymetric riptide`` to select).  This uses a fit to a set of delayed regressors (actually, this is the original RIPTiDe method from ~2010).
+* (rapidtide) Separated coarse delay estimation and similarity function fitting into two separate workflows (they were together in v3.0.8).
+* (rapidtide) Fixed a stupid bug in the placement of the delay refinement code block for each pass.
+* (rapidtide) Laid most of the groundwork for dynamically switching delay estimation methods and parameters between passes.
+* (package) Accepted several dependabot PRs.
+
 ## Version 3.0.8 (6/26/25)
 * (rapidtide) Fix https://github.com/bbfrederick/rapidtide/issues/213 (thanks to https://github.com/tomosumi for reporting the bug).
 * (rapidtide) Split coarse delay estimation and fitting out into a separate workflow.
 * (rapidtide) Split delay refinement out into a separate workflow.
 * (rapidtide) Split regressor refinement out into a separate workflow.
-* (rapidtide) All this is in preparation for a new, modular workflow with more flexible control of the fitting process.  It's not done yet, butthis is getting all internal code blocks ready for it.  I want to pause here to make sure I haven't broken anything (all the automated tests pass, but I want to be careful).
+* (rapidtide) All this is in preparation for a new, modular workflow with more flexible control of the fitting process.  It's not done yet, but this is getting all internal code blocks ready for it.  I want to pause here to make sure I haven't broken anything (all the automated tests pass, but I want to be careful).
 * (docs) Some improvement to the tidepool section.
 * (package) Made a more streamlined and rational interface for allocating shared memory.
 * (package) Resolved incompatibility of statsmodels and scipy>1.15.3.

{rapidtide-3.0.8/rapidtide.egg-info → rapidtide-3.0.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rapidtide
-Version: 3.0.8
+Version: 3.0.10
 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>
@@ -38,8 +38,8 @@ Requires-Dist: pyqt6
 Requires-Dist: requests
 Requires-Dist: statsmodels
 Requires-Dist: pywavelets
-Requires-Dist: tensorflow>=2.10.0
-Requires-Dist: tf-keras
+Requires-Dist: tensorflow>=2.18.0
+Requires-Dist: tf-keras>=2.18.0
 Requires-Dist: tqdm
 Requires-Dist: versioneer
 Provides-Extra: tests

{rapidtide-3.0.8 → rapidtide-3.0.10}/pyproject.toml

@@ -36,8 +36,8 @@ dependencies = [
   'requests',
   'statsmodels',
   'pywavelets',
-  'tensorflow >= 2.10.0',
-  'tf-keras',
+  'tensorflow >= 2.18.0',
+  'tf-keras >= 2.18.0',
   'tqdm',
   'versioneer',
 ]

{rapidtide-3.0.8 → rapidtide-3.0.10}/rapidtide/OrthoImageItem.py

@@ -33,12 +33,17 @@ except ImportError:
     PILexists = False
 
 try:
-    from PyQt6.QtCore import QT_VERSION_STR
+    from PySide6.QtCore import __version__
 except ImportError:
-    pyqtversion = 5
+    try:
+        from PyQt6.QtCore import QT_VERSION_STR
+    except ImportError:
+        pyqtbinding = "pyqt5"
+    else:
+        pyqtbinding = "pyqt6"
 else:
-    pyqtversion = 6
-print(f"using {pyqtversion=}")
+    pyqtbinding = "pyside6"
+print(f"using {pyqtbinding=}")
 
 
 def newColorbar(left, top, impixpervoxx, impixpervoxy, imgsize):
@@ -520,10 +525,14 @@ class OrthoImageItem(QtWidgets.QWidget):
         if self.verbose > 1:
             print("saving main window")
         mydialog = QtWidgets.QFileDialog()
-        if pyqtversion == 5:
+        if pyqtbinding == "pyqt5":
             options = mydialog.Options()
-        else:
+        elif pyqtbinding == "pyqt6":
+            options = mydialog.options()
+        elif pyqtbinding == "pyside6":
             options = mydialog.options()
+        else:
+            print("unsupported qt binding")
         thedir = str(
             mydialog.getExistingDirectory(options=options, caption="Image output directory")
         )

{rapidtide-3.0.8 → rapidtide-3.0.10}/rapidtide/RapidtideDataset.py

@@ -408,7 +408,7 @@ class Overlay:
 
     def maskData(self):
         self.mask = self.geommask * self.funcmask
-        maskhash = hash(self.mask.tostring())
+        maskhash = hash(self.mask.tobytes())
         # 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")
@@ -600,12 +600,15 @@ class RapidtideDataset:
                 if self.focusregressor is None:
                     self.focusregressor = thisregressor[0]
             else:
-                if self.verbose > 1:
-                    print(
-                        "file: ",
-                        self.fileroot + thisregressor[2],
-                        " does not exist - skipping...",
-                    )
+                if thisregressor[6]:
+                    raise FileNotFoundError(f"regressor file {self.fileroot + thisregressor[2]} does not exist")
+                else:
+                    if self.verbose > 1:
+                        print(
+                            "file: ",
+                            self.fileroot + thisregressor[2],
+                            " does not exist - skipping...",
+                        )
 
     def _loadfuncmaps(self):
         mapstoinvert = ["varChange"]
@@ -1047,6 +1050,7 @@ class RapidtideDataset:
                     self.inputfreq,
                     self.inputfreq,
                     self.inputstarttime,
+                    True,
                 ],
                 [
                     "postfilt",
@@ -1055,6 +1059,7 @@ class RapidtideDataset:
                     self.inputfreq,
                     self.inputfreq,
                     self.inputstarttime,
+                    True,
                 ],
                 [
                     "pass1",
@@ -1063,6 +1068,7 @@ class RapidtideDataset:
                     self.fmrifreq * self.oversampfactor,
                     self.fmrifreq,
                     0.0,
+                    True,
                 ],
                 [
                     "pass2",
@@ -1071,6 +1077,7 @@ class RapidtideDataset:
                     self.fmrifreq * self.oversampfactor,
                     self.fmrifreq,
                     0.0,
+                    False,
                 ],
                 [
                     "pass3",
@@ -1079,6 +1086,7 @@ class RapidtideDataset:
                     self.fmrifreq * self.oversampfactor,
                     self.fmrifreq,
                     0.0,
+                    False,
                 ],
                 [
                     "pass4",
@@ -1087,6 +1095,7 @@ class RapidtideDataset:
                     self.fmrifreq * self.oversampfactor,
                     self.fmrifreq,
                     0.0,
+                    False,
                 ],
             ]
         else:
@@ -1098,6 +1107,7 @@ class RapidtideDataset:
                     self.inputfreq,
                     self.inputfreq,
                     self.inputstarttime,
+                    True,
                 ],
                 [
                     "postfilt",
@@ -1106,6 +1116,7 @@ class RapidtideDataset:
                     self.inputfreq,
                     self.inputfreq,
                     self.inputstarttime,
+                    True,
                 ],
                 [
                     "pass1",
@@ -1114,6 +1125,7 @@ class RapidtideDataset:
                     self.fmrifreq * self.oversampfactor,
                     self.fmrifreq,
                     0.0,
+                    True,
                 ],
                 [
                     "pass2",
@@ -1122,6 +1134,7 @@ class RapidtideDataset:
                     self.fmrifreq * self.oversampfactor,
                     self.fmrifreq,
                     0.0,
+                    False,
                 ],
                 [
                     "pass3",
@@ -1130,6 +1143,7 @@ class RapidtideDataset:
                     self.fmrifreq * self.oversampfactor,
                     self.fmrifreq,
                     0.0,
+                    False,
                 ],
                 [
                     "pass4",
@@ -1138,6 +1152,7 @@ class RapidtideDataset:
                     self.fmrifreq * self.oversampfactor,
                     self.fmrifreq,
                     0.0,
+                    False,
                 ],
             ]
         self._loadregressors()

{rapidtide-3.0.8 → rapidtide-3.0.10}/rapidtide/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-06-26T14:50:59-0400",
+ "date": "2025-08-18T17:30:20-0400",
  "dirty": false,
  "error": null,
- "full-revisionid": "d9a8fd9ab24057e4a74e43dccdc1117e3c6875a2",
- "version": "3.0.8"
+ "full-revisionid": "939d31d88a5839ee746b0f84f4d370248fe5b312",
+ "version": "3.0.10"
 }
 '''  # END VERSION_JSON
 

rapidtide-3.0.10/rapidtide/data/examples/src/testfmri

@@ -0,0 +1,42 @@
+#!/bin/bash
+
+rapidtide \
+    --spatialfilt 2.5 \
+    --nprocs -1 \
+    --searchrange -7.5 30 \
+    --simcalcrange 50 -1 \
+    --outputlevel more \
+    --graymattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_GRAY \
+    --brainmask sub-RAPIDTIDETEST_brainmask.nii.gz \
+    --whitemattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_WHITE \
+    --csfmask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_CSF \
+    --cleanrefined \
+    --nofitfilt \
+    --refinedelayeachpass \
+    --similaritymetric correlation \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_flexipass
+
+#rapidtide \
+    #--spatialfilt 2.5 \
+    #--nprocs -1 \
+    #--searchrange -7.5 30 \
+    #--simcalcrange 50 -1 \
+    #--outputlevel more \
+    #--graymattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_GRAY \
+    #--brainmask sub-RAPIDTIDETEST_brainmask.nii.gz \
+    #--whitemattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_WHITE \
+    #--csfmask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_CSF \
+    #--cleanrefined \
+    #--nofitfilt \
+    #--refinedelayeachpass \
+    #--similaritymetric riptide \
+    #--riptidestep 1.5 \
+    #--ampthresh 0.0 \
+    #--numnull 0 \
+    #sub-RAPIDTIDETEST.nii.gz \
+    #../dst/sub-RAPIDTIDETEST_riptide
+#
+#tidepool --uistyle big --dataset \
+    #../dst/sub-RAPIDTIDETEST_simfunc_ \
+    #../dst/sub-RAPIDTIDETEST_riptide_ &

{rapidtide-3.0.8 → rapidtide-3.0.10}/rapidtide/data/examples/src/testhappy

@@ -73,5 +73,4 @@ happy \
     sub-HAPPYTEST.nii.gz \
     sub-HAPPYTEST.json \
     ../dst/happy_newdefaults \
-    --aliasedcorrelation \
     --nprocs -1