rapidtide 3.0a5__tar.gz → 3.0a7__tar.gz

{rapidtide-3.0a5 → rapidtide-3.0a7}/CHANGELOG.md

@@ -1,5 +1,14 @@
 # Release history
 
+## Version 3.0alpha7 (2/11/25)
+* (happy) Trying out some new approaches for aliased correlation.
+* (happy) Put in some initial support for multiecho data.
+* (happy) Updated argument parser.
+* (package) Various modernizations and cleanups.
+
+## 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-3.0a7}/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
@@ -103,7 +103,7 @@ directory, and type the following:
 
 ::
 
-   python setup.py install
+   python install .
 
 
 to install all of the tools in the package. You should be able to run

{rapidtide-3.0a5/rapidtide.egg-info → rapidtide-3.0a7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: rapidtide
-Version: 3.0a5
+Version: 3.0a7
 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>
@@ -33,14 +33,15 @@ 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
-Requires-Dist: tomlkit
 Requires-Dist: tensorflow>=2.10.0
 Requires-Dist: tf-keras
 Requires-Dist: tqdm
+Requires-Dist: versioneer
 Provides-Extra: tests
 Requires-Dist: codecov; extra == "tests"
 Requires-Dist: coverage; extra == "tests"
@@ -56,6 +57,7 @@ Requires-Dist: sphinx-gallery; extra == "doc"
 Requires-Dist: myst-parser; extra == "doc"
 Requires-Dist: numpydoc; extra == "doc"
 Requires-Dist: sphinxcontrib-bibtex; extra == "doc"
+Requires-Dist: tomlkit; extra == "doc"
 
 The rapidtide package
 =====================

{rapidtide-3.0a5 → rapidtide-3.0a7}/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',
@@ -31,24 +31,25 @@ dependencies = [
   'nilearn',
   'matplotlib>=3.3.0',
   'pyqtgraph>=0.13.4',
-  'pyqt5-sip',
+  'pyqt6-sip',
+  'pyqt6',
   'requests',
   'statsmodels',
   'pywavelets',
-  'tomlkit',
   'tensorflow>=2.10.0',
   'tf-keras',
   'tqdm',
+  'versioneer',
 ]
 #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]
@@ -75,6 +76,7 @@ doc = [
   'myst-parser',
   'numpydoc',
   'sphinxcontrib-bibtex',
+  'tomlkit',
 ]
 
 [project.scripts]
@@ -151,7 +153,7 @@ 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']
@@ -203,4 +205,4 @@ parentdir_prefix = 'rapidtide-'
 skip = '.git*,versioneer.py,*.css,exportlist.txt,data,*.bib'
 check-hidden = true
 ignore-regex = '\bsubjeT\b'
-ignore-words-list = 'thex,normall'
+ignore-words-list = 'TE,thex,normall'

{rapidtide-3.0a5 → rapidtide-3.0a7}/rapidtide/correlate.py

@@ -703,9 +703,12 @@ class AliasedCorrelator:
     """
 
     def __init__(self, hiressignal, hires_Fs, numsteps):
-        self.hiressignal = tide_math.corrnormalize(hiressignal)
         self.hires_Fs = hires_Fs
         self.numsteps = numsteps
+        self.sethiressignal(hiressignal)
+
+    def sethiressignal(self, hiressignal):
+        self.hiressignal = tide_math.corrnormalize(hiressignal)
         self.corrlen = len(self.hiressignal) * 2 + 1
         self.corrx = (
             np.linspace(0.0, self.corrlen, num=self.corrlen) / self.hires_Fs
@@ -735,10 +738,9 @@ class AliasedCorrelator:
             print(offset, self.numsteps)
         osvec = self.hiressignal * 0.0
         osvec[offset :: self.numsteps] = loressignal[:]
-        corrfunc = (
-            tide_corr.fastcorrelate(tide_math.corrnormalize(osvec), self.hiressignal)
-            * self.numsteps
-        )
+        corrfunc = tide_corr.fastcorrelate(
+            tide_math.corrnormalize(osvec), self.hiressignal
+        ) * np.sqrt(self.numsteps)
         return corrfunc
 
 

{rapidtide-3.0a5 → rapidtide-3.0a7}/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 +62,13 @@ 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
+
+happy \
+    sub-HAPPYTEST.nii.gz \
+    sub-HAPPYTEST.json \
+    ../dst/happy_aliasedcorrelation \
+    --aliasedcorrelation

{rapidtide-3.0a5 → rapidtide-3.0a7}/rapidtide/happy_supportfuncs.py

@@ -145,7 +145,7 @@ def cardiacsig(thisphase, amps=(1.0, 0.0, 0.0), phases=None, overallphase=0.0):
 
 def cardiacfromimage(
     normdata_byslice,
-    estmask_byslice,
+    estweights_byslice,
     numslices,
     timepoints,
     tr,
@@ -182,7 +182,7 @@ def cardiacfromimage(
 
     # make sure there is an appflips array
     if appflips_byslice is None:
-        appflips_byslice = estmask_byslice * 0.0 + 1.0
+        appflips_byslice = estweights_byslice * 0.0 + 1.0
     else:
         if arteriesonly:
             appflips_byslice[np.where(appflips_byslice > 0.0)] = 0.0
@@ -196,22 +196,22 @@ def cardiacfromimage(
     if not verbose:
         print("Averaging slices...")
     if fliparteries:
-        thismask_byslice = appflips_byslice.astype(np.int64) * estmask_byslice
+        theseweights_byslice = appflips_byslice.astype(np.float64) * estweights_byslice
     else:
-        thismask_byslice = estmask_byslice
+        theseweights_byslice = estweights_byslice
     for theslice in range(numslices):
         if verbose:
             print("Averaging slice", theslice)
         if usemask:
-            validestvoxels = np.where(np.abs(thismask_byslice[:, theslice]) > 0)[0]
+            validestvoxels = np.where(np.abs(theseweights_byslice[:, theslice]) > 0)[0]
         else:
-            validestvoxels = np.where(np.abs(thismask_byslice[:, theslice] >= 0))[0]
+            validestvoxels = np.where(np.abs(theseweights_byslice[:, theslice] >= 0))[0]
         if len(validestvoxels) > 0:
             if madnorm:
                 sliceavs[theslice, :], slicenorms[theslice] = tide_math.madnormalize(
                     np.mean(
                         normdata_byslice[validestvoxels, theslice, :]
-                        * thismask_byslice[validestvoxels, theslice, np.newaxis],
+                        * theseweights_byslice[validestvoxels, theslice, np.newaxis],
                         axis=0,
                     ),
                     returnnormfac=True,
@@ -219,7 +219,7 @@ def cardiacfromimage(
             else:
                 sliceavs[theslice, :] = np.mean(
                     normdata_byslice[validestvoxels, theslice, :]
-                    * thismask_byslice[validestvoxels, theslice, np.newaxis],
+                    * theseweights_byslice[validestvoxels, theslice, np.newaxis],
                     axis=0,
                 )
                 slicenorms[theslice] = 1.0
@@ -1241,3 +1241,51 @@ def phaseproject(
         normapp_byslice[validlocs, theslice, :] = np.nan_to_num(
             app_byslice[validlocs, theslice, :] / means_byslice[validlocs, theslice, None]
         )
+    return app, rawapp, corrected_rawapp, normapp, weights, cine, derivatives
+
+
+def upsampleimage(input_data, input_hdr, numsteps, sliceoffsets, slicesamplerate, outputroot):
+    fmri_data = input_data.byvol()
+    timepoints = input_data.timepoints
+    xsize = input_data.xsize
+    ysize = input_data.ysize
+    numslices = input_data.numslices
+
+    # allocate the image
+    print(f"upsampling fmri data by a factor of {numsteps}")
+    upsampleimage = np.zeros((xsize, ysize, numslices, numsteps * timepoints), dtype=float)
+    upsampleimage_byslice = upsampleimage.reshape(xsize * ysize, numslices, numsteps * timepoints)
+
+    # demean the raw data
+    meanfmri = fmri_data.mean(axis=1)
+    demeaned_data = fmri_data - meanfmri[:, None]
+
+    # drop in the raw data
+    for theslice in range(numslices):
+        upsampleimage[
+            :, :, theslice, sliceoffsets[theslice] : timepoints * numsteps : numsteps
+        ] = demeaned_data.reshape((xsize, ysize, numslices, timepoints))[:, :, theslice, :]
+
+    upsampleimage_byslice = upsampleimage.reshape(xsize * ysize, numslices, timepoints * numsteps)
+
+    # interpolate along the slice direction
+    thedstlocs = np.linspace(0, numslices, num=len(sliceoffsets), endpoint=False)
+    print(f"len(destlocst), destlocs: {len(thedstlocs)}, {thedstlocs}")
+    for thetimepoint in range(0, timepoints * numsteps):
+        thestep = thetimepoint % numsteps
+        print(f"interpolating step {thestep}")
+        thesrclocs = np.where(sliceoffsets == thestep)[0]
+        print(f"timepoint: {thetimepoint}, sourcelocs: {thesrclocs}")
+        for thexyvoxel in range(xsize * ysize):
+            theinterps = np.interp(
+                thedstlocs,
+                1.0 * thesrclocs,
+                upsampleimage_byslice[thexyvoxel, thesrclocs, thetimepoint],
+            )
+            upsampleimage_byslice[thexyvoxel, :, thetimepoint] = 1.0 * theinterps
+
+    theheader = copy.deepcopy(input_hdr)
+    theheader["dim"][4] = timepoints * numsteps
+    theheader["pixdim"][4] = 1.0 / slicesamplerate
+    tide_io.savetonifti(upsampleimage, theheader, outputroot + "_upsampled")
+    print("upsampling complete")

{rapidtide-3.0a5 → rapidtide-3.0a7}/rapidtide/io.py

@@ -1160,13 +1160,15 @@ def getslicetimesfromfile(slicetimename):
             for idx, thetime in enumerate(slicetimelist):
                 slicetimes[idx] = float(thetime)
             normalizedtotr = False
+            fileisbidsjson = True
         except KeyError:
             print(slicetimename, "is not a valid BIDS sidecar file")
             sys.exit()
     else:
         slicetimes = readvec(slicetimename)
         normalizedtotr = True
-    return slicetimes, normalizedtotr
+        fileisbidsjson = False
+    return slicetimes, normalizedtotr, fileisbidsjson
 
 
 def readbidssidecar(inputfilename):

{rapidtide-3.0a5 → rapidtide-3.0a7}/rapidtide/tests/test_filter.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   Copyright 2016-2025 Blaise Frederick
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

{rapidtide-3.0a5 → rapidtide-3.0a7}/rapidtide/tests/test_fullrunhappy_v2.py

@@ -31,7 +31,7 @@ def test_fullrunhappy_v2(debug=False, displayplots=False):
         os.path.join(get_examples_path(), "sub-HAPPYTEST.nii.gz"),
         os.path.join(get_examples_path(), "sub-HAPPYTEST.json"),
         os.path.join(get_test_temp_path(), "happyout2"),
-        "--estmask",
+        "--estweights",
         os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),
         "--projmask",
         os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),

{rapidtide-3.0a5 → rapidtide-3.0a7}/rapidtide/tests/test_fullrunhappy_v3.py

@@ -31,7 +31,7 @@ def test_fullrunhappy_v3(debug=False, displayplots=False):
         os.path.join(get_examples_path(), "sub-HAPPYTEST.nii.gz"),
         os.path.join(get_examples_path(), "sub-HAPPYTEST.json"),
         os.path.join(get_test_temp_path(), "happyout3"),
-        "--estmask",
+        "--estweights",
         os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),
         "--projmask",
         os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),

{rapidtide-3.0a5 → rapidtide-3.0a7}/rapidtide/tests/test_fullrunhappy_v4.py

@@ -31,7 +31,7 @@ def test_fullrunhappy_v4(debug=False, displayplots=False):
         os.path.join(get_examples_path(), "sub-HAPPYTEST.nii.gz"),
         os.path.join(get_examples_path(), "sub-HAPPYTEST.json"),
         os.path.join(get_test_temp_path(), "happyout4"),
-        "--estmask",
+        "--estweights",
         os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),
         "--projmask",
         os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),
@@ -39,6 +39,8 @@ def test_fullrunhappy_v4(debug=False, displayplots=False):
         "-1",
         "--model",
         "model_revised",
+        "--motionfile",
+        os.path.join(get_examples_path(), "sub-HAPPYTEST_mcf.par"),
     ]
     happy_workflow.happy_main(happy_parser.process_args(inputargs=inputargs))
 

rapidtide-3.0a7/rapidtide/tests/test_fullrunhappy_v5.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+#   Copyright 2016-2024 Blaise Frederick
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
+#
+import os
+
+import matplotlib as mpl
+
+import rapidtide.workflows.happy as happy_workflow
+import rapidtide.workflows.happy_parser as happy_parser
+from rapidtide.tests.utils import get_examples_path, get_test_temp_path
+
+
+def test_fullrunhappy_v4(debug=False, displayplots=False):
+    # run happy
+    inputargs = [
+        os.path.join(get_examples_path(), "sub-HAPPYTEST.nii.gz"),
+        os.path.join(get_examples_path(), "sub-HAPPYTEST.json"),
+        os.path.join(get_test_temp_path(), "happyout5"),
+        "--model",
+        "model_revised",
+        "--motionfile",
+        os.path.join(get_examples_path(), "sub-HAPPYTEST_mcf.par"),
+        "--nomotderiv",
+        "--nomotorthogonalize",
+        "--motfiltorder",
+        "2",
+        "--numskip",
+        "5",
+        "--motskip",
+        "5",
+        "--motionhp",
+        "0.01",
+        "--motionlp",
+        "2.0",
+    ]
+    happy_workflow.happy_main(happy_parser.process_args(inputargs=inputargs))
+
+
+if __name__ == "__main__":
+    mpl.use("TkAgg")
+    test_fullrunhappy_v4(debug=True, displayplots=True)

{rapidtide-3.0a5 → rapidtide-3.0a7}/rapidtide/util.py

@@ -26,8 +26,7 @@ import subprocess
 import sys
 import time
 from datetime import datetime
-from multiprocessing import RawArray, shared_memory
-from os.path import split
+from multiprocessing import shared_memory
 
 import matplotlib.pyplot as plt
 import numpy as np