rapidtide 3.0a5__tar.gz → 3.0a6__tar.gz

{rapidtide-3.0a5 → rapidtide-3.0a6}/CHANGELOG.md

@@ -1,5 +1,8 @@
 # Release history
 
+## Version 3.0alpha6 (1/28/25)
+* (happy) Fixed a major bug in motion filtering (thank you to Sukru Demiral for reporting it!)
+
 ## Version 3.0alpha5 (1/25/25)
 * (happy) Fixed a typo in argument description.
 * (atlasaverage) Added the ability to segment a template atlas based on values of the map being summarized.

{rapidtide-3.0a5 → rapidtide-3.0a6}/INSTALL.rst

@@ -7,7 +7,7 @@ Required dependencies
 `````````````````````
 
 The processing programs in rapidtide require the following to be
-installed first:
+installed:
 
 -  Python >= 3.9
 -  numpy
@@ -19,10 +19,10 @@ installed first:
 -  nibabel
 -  nilearn
 -  matplotlib >= 3.3.0
--  pyqt5-sip
+-  pyqt6-sip
+-  pyqt6
 -  pyqtgraph >= 0.13.4
 -  statsmodels
--  tomlkit
 -  tqdm
 
 Optional dependencies

{rapidtide-3.0a5/rapidtide.egg-info → rapidtide-3.0a6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: rapidtide
-Version: 3.0a5
+Version: 3.0a6
 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>
@@ -33,7 +33,8 @@ Requires-Dist: nibabel
 Requires-Dist: nilearn
 Requires-Dist: matplotlib>=3.3.0
 Requires-Dist: pyqtgraph>=0.13.4
-Requires-Dist: pyqt5-sip
+Requires-Dist: pyqt6-sip
+Requires-Dist: pyqt6
 Requires-Dist: requests
 Requires-Dist: statsmodels
 Requires-Dist: pywavelets

{rapidtide-3.0a5 → rapidtide-3.0a6}/pyproject.toml

@@ -1,12 +1,12 @@
 [build-system]
-requires = ["setuptools>=42", "cffi>=1.0.0", 'versioneer[toml]']
+requires = ['setuptools>=42', 'cffi>=1.0.0', 'versioneer[toml]']
 build-backend = 'setuptools.build_meta'
 
 [project]
 name = 'rapidtide'
 description = 'Tools for performing correlation analysis on fMRI data.'
-keywords = ["fMRI", "correlation", "RIPTiDe", "noise"]
-license = {text = "Apache Software License"}
+keywords = ['fMRI', 'correlation', 'RIPTiDe', 'noise']
+license = {text = 'Apache Software License'}
 readme = 'README.rst'
 classifiers = [
     'Operating System :: OS Independent',
@@ -31,7 +31,8 @@ dependencies = [
   'nilearn',
   'matplotlib>=3.3.0',
   'pyqtgraph>=0.13.4',
-  'pyqt5-sip',
+  'pyqt6-sip',
+  'pyqt6',
   'requests',
   'statsmodels',
   'pywavelets',
@@ -43,12 +44,12 @@ dependencies = [
 #dynamic = ['version', 'license', 'keywords']
 dynamic = ['version']
 authors = [
-    {name = "Blaise deB. Frederick", email="blaise.frederick@gmail.com"},
-    {name = "Taylor Salo"},
-    {name = "Daniel M. Drucker, Ph.D."},
-    {name = "Jeffrey N Stout"},
-    {name = "Yaroslav O. Halchenko"},
-    {name = "Derek Monroe"},
+    {name = 'Blaise deB. Frederick', email='blaise.frederick@gmail.com'},
+    {name = 'Taylor Salo'},
+    {name = 'Daniel M. Drucker, Ph.D.'},
+    {name = 'Jeffrey N Stout'},
+    {name = 'Yaroslav O. Halchenko'},
+    {name = 'Derek Monroe'},
 ]
 
 [project.urls]
@@ -151,7 +152,7 @@ include = ['rapidtide', 'cloud']
 rapidtide = ['rapidtide/*.py', 'rapidtide/workflows/*.py', 'rapidtide/scripts/*']
 
 [tool.setuptools.dynamic]
-version = {attr = "rapidtide.__version__"}
+version = {attr = 'rapidtide.__version__'}
 
 [tool.setuptools.exclude-package-data]
 rapidtide = ['.eggs', '.git', '.github', '.pytest_cache', 'rapidtide/candidatetests', 'rapidtide/disabledtests', 'rapidtide/data/examples']

{rapidtide-3.0a5 → rapidtide-3.0a6}/rapidtide/data/examples/src/testhappy

@@ -9,13 +9,13 @@
 #    --infotag tag2 value2 \
 #    --model model_revised
 
-happy \
-    sub-HAPPYTEST.nii.gz \
-    sub-HAPPYTEST.json \
-    ../dst/happy \
-    --mklthreads 8 \
-    --model model_revised \
-    --spatialglm --aliasedcorrelation
+#happy \
+    #sub-HAPPYTEST.nii.gz \
+    #sub-HAPPYTEST.json \
+    #../dst/happy \
+    #--mklthreads 8 \
+    #--model model_revised \
+    #--spatialglm --aliasedcorrelation
 
 
 #happy \
@@ -62,9 +62,8 @@ happy \
     #--dodlfilter
 
 
-#happy \
-    #ses-060_bold_trunc.nii.gz \
-    #ses-060_bold_trunc.json \
-    #../dst/happy_motion \
-    #--mklthreads 8 \
-    #--motionfile ses-060_bold_trunc_prefiltered_func_data_mcf.par
+happy \
+    sub-HAPPYTEST.nii.gz \
+    sub-HAPPYTEST.json \
+    ../dst/happy_motion \
+    --motionfile sub-HAPPYTEST_mcf.par

{rapidtide-3.0a5 → rapidtide-3.0a6}/rapidtide/workflows/happy.py

@@ -236,16 +236,21 @@ def happy_main(argparsingfunc):
     # filter out motion regressors here
     if args.motionfilename is not None:
         timings.append(["Motion filtering start", time.time(), None, None])
+        confoundregressors, confoundregressorlabels = tide_fit.calcexpandedregressors(
+            tide_io.readconfounds(args.motionfilename),
+            deriv=args.motfilt_deriv,
+            order=args.motfilt_order,
+        )
         (motionregressors, motionregressorlabels, filtereddata, confoundr2) = (
             tide_glmpass.confoundregress(
-                args.motionfilename,
+                confoundregressors,
+                confoundregressorlabels,
                 fmri_data[validprojvoxels, :],
                 tr,
                 orthogonalize=args.orthogonalize,
-                motstart=args.motskip,
-                motionhp=args.motionhp,
-                motionlp=args.motionlp,
-                deriv=args.motfilt_deriv,
+                tcstart=args.motskip,
+                tchp=args.motionhp,
+                tclp=args.motionlp,
             )
         )
         if confoundr2 is None:

{rapidtide-3.0a5 → rapidtide-3.0a6}/rapidtide/workflows/happy_parser.py

@@ -178,13 +178,6 @@ def _get_parser():
         ),
         default=True,
     )
-    preprocessing_opts.add_argument(
-        "--motpos",
-        dest="motfilt_pos",
-        action="store_true",
-        help=("Include motion position regressors. "),
-        default=False,
-    )
     preprocessing_opts.add_argument(
         "--nomotderiv",
         dest="motfilt_deriv",
@@ -192,6 +185,17 @@ def _get_parser():
         help=("Do not use motion derivative regressors. "),
         default=True,
     )
+    preprocessing_opts.add_argument(
+        "--motfiltorder",
+        dest="motfilt_order",
+        action="store",
+        metavar="N",
+        type=lambda x: pf.is_int(parser, x),
+        help=(
+            "Include powers of each confound regressor up to order N. Default is 1 (no expansion). "
+        ),
+        default=1,
+    )
     preprocessing_opts.add_argument(
         "--discardmotionfiltered",
         dest="savemotionglmfilt",

{rapidtide-3.0a5 → rapidtide-3.0a6/rapidtide.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: rapidtide
-Version: 3.0a5
+Version: 3.0a6
 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>
@@ -33,7 +33,8 @@ Requires-Dist: nibabel
 Requires-Dist: nilearn
 Requires-Dist: matplotlib>=3.3.0
 Requires-Dist: pyqtgraph>=0.13.4
-Requires-Dist: pyqt5-sip
+Requires-Dist: pyqt6-sip
+Requires-Dist: pyqt6
 Requires-Dist: requests
 Requires-Dist: statsmodels
 Requires-Dist: pywavelets

{rapidtide-3.0a5 → rapidtide-3.0a6}/rapidtide.egg-info/requires.txt

@@ -8,7 +8,8 @@ nibabel
 nilearn
 matplotlib>=3.3.0
 pyqtgraph>=0.13.4
-pyqt5-sip
+pyqt6-sip
+pyqt6
 requests
 statsmodels
 pywavelets