Merge branch 'main' of https://github.com/bbfrederick/rapidtide

.github/workflows/python-publish.yml

@@ -17,7 +17,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.12'
         ref: ${{ github.head_ref }}   # checkout the correct branch name
         fetch-depth: 0
 

Dockerfile

@@ -1,5 +1,6 @@
 # Start from the fredericklab base container
-FROM fredericklab/basecontainer_plus:latest-release
+#FROM fredericklab/basecontainer_plus:latest-release
+FROM fredericklab/basecontainer:latest-release
 
 # get build arguments
 ARG BUILD_TIME
@@ -9,8 +10,8 @@ ARG GITSHA
 ARG GITDATE
 
 # set and echo environment variables
-ENV BUILD_TIME $BUILD_TIME
-ENV BRANCH $BRANCH
+ENV BUILD_TIME=$BUILD_TIME
+ENV BRANCH=$BRANCH
 ENV GITVERSION=${GITVERSION}
 ENV GITSHA=${GITSHA}
 ENV GITDATE=${GITDATE}
@@ -22,6 +23,7 @@ RUN echo "GITSHA: "$GITSHA
 RUN echo "GITDATE: "$GITDATE
 
 # Install rapidtide
+USER root
 COPY . /src/rapidtide
 RUN echo $GITVERSION > /src/rapidtide/VERSION
 RUN cd /src/rapidtide && \
@@ -47,6 +49,8 @@ WORKDIR /tmp/
 RUN ln -s /src/rapidtide/cloud /
 ENTRYPOINT ["/cloud/mount-and-run"]
 
+USER rapidtide
+
 LABEL org.label-schema.build-date=$BUILD_TIME \
       org.label-schema.name="rapidtide" \
       org.label-schema.description="rapidtide - a set of tools for delay processing" \

README.rst

@@ -287,6 +287,18 @@ nibabel:
    nibabel
 
 
+scikit-image:
+-------------
+
+:cite:empty:`van2014scikit`
+
+.. bibliography::
+   :filter: False
+   :style: unsrt
+
+   van2014scikit
+
+
 scikit-learn:
 -------------
 
@@ -299,6 +311,18 @@ scikit-learn:
    scikitlearn
 
 
+statsmodels:
+-------------
+
+:cite:empty:`seabold2010statsmodels`
+
+.. bibliography::
+   :filter: False
+   :style: unsrt
+
+   seabold2010statsmodels
+
+
 pandas:
 -------
 
@@ -323,6 +347,18 @@ nilearn:
    nilearn
 
 
+pyqtgraph:
+-------------
+
+:cite:empty:`pyqtgraph`
+
+.. bibliography::
+   :filter: False
+   :style: unsrt
+
+   pyqtgraph
+
+
 References
 ==========
 

docs/references.bib

@@ -1,3 +1,10 @@
+@inproceedings{seabold2010statsmodels,
+  title={statsmodels: Econometric and statistical modeling with python},
+  author={Seabold, Skipper and Perktold, Josef},
+  booktitle={9th Python in Science Conference},
+  year={2010},
+}
+
 @article{numpy,
  title         = {Array programming with {NumPy}},
  author        = {Charles R. Harris and K. Jarrod Millman and St{\'{e}}fan J.
@@ -62,6 +69,22 @@ @misc{scipy
   url          = {https://doi.org/10.5281/zenodo.13352243}
 }
 
+@article{van2014scikit,
+  title={scikit-image: image processing in Python},
+  author={Van der Walt, Stefan and Sch{\"o}nberger, Johannes L and Nunez-Iglesias, Juan and Boulogne, Fran{\c{c}}ois and Warner, Joshua D and Yager, Neil and Gouillart, Emmanuelle and Yu, Tony},
+  journal={PeerJ},
+  volume={2},
+  pages={e453},
+  year={2014},
+  publisher={PeerJ Inc.}
+}
+
+@misc{pyqtgraph,
+  author       = {The pyqtgraph developers},
+  title        = {pyqtgraph},
+  url          = {https://www.pyqtgraph.org}
+}
+
 @misc{scikitlearn,
   author       = {The scikit-learn developers},
   title        = {scikit-learn},

rapidtide/stats.py

@@ -582,7 +582,7 @@ def gethistprops(
         i = 1
         started = False
         finished = False
-        while i < len(thestore[1, :] - 2) and not finished:
+        while i < len(thestore[1, :] - 3) and not finished:
             if thestore[1, i] > peakthresh * overallmax:
                 started = True
             if thestore[1, i] > thestore[1, peakindex]:

rapidtide/workflows/rapidtide_parser.py

@@ -461,7 +461,7 @@ def _get_parser():
         default=None,
     )
     preproc.add_argument(
-        "--motderiv",
+        "--nomotderiv",
         dest="mot_deriv",
         action="store_false",
         help=("Toggle whether derivatives will be used in motion regression.  Default is True."),
@@ -490,7 +490,7 @@ def _get_parser():
         default=1,
     )
     preproc.add_argument(
-        "--confoundderiv",
+        "--noconfoundderiv",
         dest="confound_deriv",
         action="store_false",
         help=(