rapidtide 3.0.9__tar.gz → 3.0.11__tar.gz

{rapidtide-3.0.9 → rapidtide-3.0.11}/CHANGELOG.md

@@ -1,5 +1,22 @@
 # Release history
 
+## Version 3.0.11 (8/27/25)
+* (Docker) Fixed a critical bug in building the container.
+* (happy) Added the ability to specify an overall processing mask.
+* (docs) Revised the singularity/apptainer installation section.
+* (reference) Added MNI152NLin2009cAsym versions of the JHU atlases.
+* (package) Miscellaneous code cleanups.
+* (package) More dependabot PRs.
+
+## 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.
+* (tidepool) Add support for PySide6 (in addition to PyQt5 and PyQt6).
+* (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-3.0.9 → rapidtide-3.0.11}/INSTALL.rst

@@ -65,7 +65,7 @@ source code, and type:
 
    git clone https://github.com/bbfrederick/rapidtide.git
    cd rapidtide
-   refresh
+   ./refresh
 
 
 to install all of the tools in the package. You should be able to run
@@ -74,11 +74,11 @@ subdirectories).
 
 If you’ve made edits to the code, or want to sync up with the current version on Github,
 cd into the
-package directory and type ``refresh``:
+package directory and type ``./refresh``:
 
 ::
 
-   refresh
+   ./refresh
 
 
 This will uninstall the current version, sync up to github, and reinstall
@@ -190,22 +190,23 @@ Then the following command will work (you can replace 'tidepool' with any of the
 Singularity installation
 ------------------------
 
-Many times you can't use Docker, because of security concerns.  Singularity, from LBL, offers containerized computing
-that runs entirely in user space, so the amount of mischief you can get up to is significantly less.  Singularity
+Many times you can't use Docker, because of security concerns.  Apptainer (formerly singularity), from LBL, offers containerized computing
+that runs entirely in user space, so the amount of mischief you can get up to is significantly less.  Apptainer
 containers can be created from Docker containers as follows (stealing from the fMRIprep documentation):
 ::
 
-    singularity build /my_images/rapidtide.simg docker://fredericklab/rapidtide:latest-release
+    apptainer build \
+        /my_image_directory/rapidtide.sif \
+        docker://fredericklab/rapidtide:latest-release
 
 
 Running the container is similar to Docker.  The "-B" option is used to bind filesystems to mountpoints in the container.
-For example, to run the simple rapidtide2x analysis above, type the following:
+For example, to run the simple rapidtide analysis above, type the following:
 ::
 
-    singularity run \
-        --cleanenv \
+    apptainer run \
         -B INPUTDIRECTORY:/data_in,OUTPUTDIRECTORY:/data_out \
-        rapidtide.simg \
+        rapidtide.sif \
             rapidtide \
                 /data_in/YOURNIFTIFILE.nii.gz \
                 /data_out/outputname \

{rapidtide-3.0.9/rapidtide.egg-info → rapidtide-3.0.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rapidtide
-Version: 3.0.9
+Version: 3.0.11
 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>
@@ -38,17 +38,17 @@ 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
-Requires-Dist: codecov; extra == "tests"
-Requires-Dist: coverage; extra == "tests"
-Requires-Dist: coveralls; extra == "tests"
-Requires-Dist: flake8-black; extra == "tests"
-Requires-Dist: pytest; extra == "tests"
-Requires-Dist: pytest-cov; extra == "tests"
+Provides-Extra: test
+Requires-Dist: codecov; extra == "test"
+Requires-Dist: coverage; extra == "test"
+Requires-Dist: coveralls; extra == "test"
+Requires-Dist: flake8-black; extra == "test"
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
 Provides-Extra: doc
 Requires-Dist: sphinx; extra == "doc"
 Requires-Dist: sphinx_rtd_theme; extra == "doc"

{rapidtide-3.0.9 → rapidtide-3.0.11}/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',
 ]
@@ -59,7 +59,7 @@ authors = [
 'Changelog' = 'https://github.com/bbfrederick/rapidtide/blob/main/CHANGELOG.md'
 
 [project.optional-dependencies]
-tests = [
+test = [
   'codecov',
   'coverage',
   'coveralls',
@@ -161,7 +161,7 @@ rapidtide = ['.eggs', '.git', '.github', '.pytest_cache', 'rapidtide/candidatete
 # Aliases
 docs = ['rapidtide[doc]']
 tests = ['rapidtide[test]']
-all = ['rapidtide[docs,tests]']
+all = ['rapidtide[doc,test]']
 
 [tool.black]
 line-length = 99

{rapidtide-3.0.9 → rapidtide-3.0.11}/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):
@@ -132,6 +137,7 @@ class OrthoImageItem(QtWidgets.QWidget):
     ):
         QtWidgets.QWidget.__init__(self)
         self.map = map
+        self.mapname = self.map.label
         self.bgmap = bgmap
         self.axview = axview
         self.corview = corview
@@ -175,6 +181,7 @@ class OrthoImageItem(QtWidgets.QWidget):
 
         if self.verbose > 1:
             print("OrthoImageItem initialization:")
+            print("    Map name:", self.mapname)
             print("    Dimensions:", self.xdim, self.ydim, self.zdim)
             print("    Voxel sizes:", self.xsize, self.ysize, self.zsize)
             print("    FOVs:", self.xfov, self.yfov, self.zfov)
@@ -356,6 +363,7 @@ class OrthoImageItem(QtWidgets.QWidget):
     def setMap(self, themap):
         self.map = themap
         self.tdim = self.map.tdim
+        self.mapname = self.map.label
 
     def enableView(self):
         if self.button is not None:
@@ -520,10 +528,14 @@ 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-3.0.9 → rapidtide-3.0.11}/rapidtide/RapidtideDataset.py

@@ -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-3.0.9 → rapidtide-3.0.11}/rapidtide/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-07-03T10:21:49-0400",
+ "date": "2025-08-27T10:21:33-0400",
  "dirty": false,
  "error": null,
- "full-revisionid": "292e93bbd0a9c13e2d62a00746e14522b0783156",
- "version": "3.0.9"
+ "full-revisionid": "078ea587f66134f5bb1f53817240da52156cf7f1",
+ "version": "3.0.11"
 }
 '''  # END VERSION_JSON
 

rapidtide-3.0.11/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-3.0.9 → rapidtide-3.0.11}/rapidtide/data/examples/src/testhappy

@@ -72,6 +72,12 @@
 happy \
     sub-HAPPYTEST.nii.gz \
     sub-HAPPYTEST.json \
-    ../dst/happy_newdefaults \
-    --aliasedcorrelation \
+    ../dst/happy_mask \
+    --processmask sub-HAPPYTEST_mask.nii.gz \
+    --nprocs -1
+
+happy \
+    sub-HAPPYTEST.nii.gz \
+    sub-HAPPYTEST.json \
+    ../dst/happy \
     --nprocs -1