rapidtide 2.9.5__py3-none-any.whl → 3.1.3__py3-none-any.whl

{rapidtide-2.9.5.dist-info → rapidtide-3.1.3.dist-info}/METADATA

@@ -1,10 +1,9 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: rapidtide
-Version: 2.9.5
+Version: 3.1.3
 Summary: Tools for performing correlation analysis on fMRI data.
-Home-page: https://github.com/bbfrederick/rapidtide
-Author: Taylor Salo, Daniel M. Drucker, Ph.D., Jeffrey N Stout
-Author-email: Blaise deB Frederick <blaise.frederick@gmail.com>
+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>
 License: Apache Software License
 Project-URL: Homepage, https://github.com/bbfrederick/rapidtide
 Project-URL: Bug Tracker, https://github.com/bbfrederick/rapidtide/issues
@@ -17,12 +16,12 @@ Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Image Recognition
 Classifier: License :: OSI Approved :: Apache Software License
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Requires-Python: >=3.8
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.10
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: numpy
@@ -35,23 +34,17 @@ Requires-Dist: nibabel
 Requires-Dist: nilearn
 Requires-Dist: matplotlib
 Requires-Dist: pyqtgraph
-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: torch
 Requires-Dist: tqdm
-Provides-Extra: doc
-Requires-Dist: sphinx>=1.8.0; extra == "doc"
-Requires-Dist: sphinx-rtd-theme; extra == "doc"
-Requires-Dist: sphinx-argparse; extra == "doc"
-Requires-Dist: sphinx-gallery; extra == "doc"
-Requires-Dist: m2r; extra == "doc"
-Requires-Dist: numpydoc; extra == "doc"
-Requires-Dist: recommonmark; extra == "doc"
-Requires-Dist: mistune==0.8.4; extra == "doc"
-Requires-Dist: sphinx; extra == "doc"
-Requires-Dist: mistune; extra == "doc"
+Requires-Dist: versioneer
+Provides-Extra: tf
+Requires-Dist: tensorflow>=2.18.0; extra == "tf"
+Requires-Dist: tf-keras>=2.18.0; extra == "tf"
 Provides-Extra: test
 Requires-Dist: codecov; extra == "test"
 Requires-Dist: coverage; extra == "test"
@@ -59,13 +52,16 @@ Requires-Dist: coveralls; extra == "test"
 Requires-Dist: flake8-black; extra == "test"
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
-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: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: sphinx_rtd_theme; extra == "doc"
+Requires-Dist: sphinx-argparse; extra == "doc"
+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"
+Dynamic: license-file
 
 The rapidtide package
 =====================
@@ -210,14 +206,12 @@ new features and bug fixes!
 
 Python version compatibility
 ============================
-I switched over a while ago to using Python 3 as my daily driver, so I know
-that everything works there. However, I know that a lot of people can\'t
-or won\'t switch from Python 2x, so I kept Python 2.7 compatibility for
-quite some time.
-
-That said, the writing is on the wall, and since I depend on a number of
-packages that have dropped Python 2.x support, as of 2.0, so has rapidtide. However,
-as of version 1.9.0 I\'m also releasing the code in a docker
+Since I depend on a number of
+packages that have dropped Python 2.x support, as of rapidtide 2.0, so did rapidtide. And given that I use fairly
+modern constructs, I don't support anything prior to Python 3.9.  The current UPPER limit is 3.12, because
+tensorflow (needed for happy) does not yet support 3.13 or later.  In 2025, I don't imagine
+anybody is running rapidtide on a system that can't upgrade to a modern Python, but if you are,
+as of version 1.9.0 the package is also available in a docker
 container (fredericklab/rapidtide), which has everything nicely installed in
 a fully configured Python 3 environment, so there\'s really no need for me continue 2.x
 support.  So now it's f-strings all the way, kids!
@@ -302,193 +296,6 @@ Financial Support
 This code base is being developed and supported by grants from the US
 NIH (`1R01 NS097512 <http://grantome.com/grant/NIH/R01-NS097512-02>`__, RF1 MH130637-01)
 
-Additional packages used
-========================
-
-Rapidtide would not be possible without many additional open source packages.
-These include:
-
-numpy:
-------
-
-1) Stéfan van der Walt, S. Chris Colbert and Gaël Varoquaux. The NumPy Array:
-   A Structure for Efficient Numerical Computation, Computing in Science
-   & Engineering, 13, 22-30 (2011) \| https://doi.org/10.1109/MCSE.2011.37
-
-scipy:
-------
-
-1) Pauli Virtanen, Ralf Gommers, Travis E. Oliphant, Matt Haberland, Tyler Reddy,
-   David Cournapeau, Evgeni Burovski, Pearu Peterson, Warren Weckesser,
-   Jonathan Bright, Stéfan J. van der Walt, Matthew Brett, Joshua Wilson,
-   K. Jarrod Millman, Nikolay Mayorov, Andrew R. J. Nelson, Eric Jones,
-   Robert Kern, Eric Larson, CJ Carey, İlhan Polat, Yu Feng, Eric W. Moore,
-   Jake VanderPlas, Denis Laxalde, Josef Perktold, Robert Cimrman,
-   Ian Henriksen, E.A. Quintero, Charles R Harris, Anne M. Archibald,
-   Antônio H. Ribeiro, Fabian Pedregosa, Paul van Mulbregt,
-   and SciPy 1.0 Contributors. (2020) SciPy 1.0: Fundamental Algorithms for
-   Scientific Computing in Python. Nature Methods, 17, 261–272 (2020) \|
-   https://doi.org/10.1038/s41592-019-0686-2
-
-matplotlib:
------------
-
-1) John D. Hunter. Matplotlib: A 2D Graphics Environment, Computing in Science
-   & Engineering, 9, 90-95 (2007) \| https://doi.org/10.1109/MCSE.2007.55
-
-nibabel:
---------
-
-1) https://github.com/nipy/nibabel \| https://doi.org/10.5281/zenodo.591597
-
-scikit-learn:
--------------
-
-1) Pedregosa, F., Varoquaux, G., Gramfort, A., Michel, V., Thirion, B.,
-   Grisel, O., Blondel, M., Prettenhofer, P., Weiss, R., Dubourg, V.,
-   Vanderplas, J., Passos, A., Cournapeau, D., Brucher, M., Perrot, M.,
-   and Duchesnay, E., Scikit-learn: Machine Learning in Python.
-   Journal of Machine Learning Research, 2011. 12: p. 2825-2830. \| https://scikit-learn.org
-
-pandas:
--------
-
-1) McKinney, W., pandas: a foundational Python library for data analysis
-   and statistics. Python for High Performance and Scientific Computing, 2011. 14.
-
-nilearn:
---------
-
-1) https://github.com/nilearn/nilearn
-
-
-References
-==========
-
-Links to PDFs of all papers mentioned here can be found on the OMG
-website: https://www.nirs-fmri.net/home/publications
-
-General overview of systemic low frequency oscillations in fMRI data
---------------------------------------------------------------------
-
-1) Tong Y, Hocke LM, Frederick BB. (2019) Low Frequency Systemic
-   Hemodynamic \"Noise\" in Resting State BOLD fMRI: Characteristics,
-   Causes, Implications, Mitigation Strategies, and Applications. Front.
-   Neurosci., 14 August 2019 \| https://doi.org/10.3389/fnins.2019.00787
-
-Multimodal Cerebral Circulation Imaging
----------------------------------------
-
-1)  Tong Y, Frederick BD. (2010) Time lag dependent multimodal
-    processing of concurrent fMRI and near-infrared spectroscopy (NIRS)
-    data suggests a global circulatory origin for low-frequency
-    oscillation signals in human brain. Neuroimage, 53(2), 553-64.
-
-2)  Tong Y, Hocke L, Frederick BD. (2011) Isolating the sources of
-    widespread physiological fluctuations in fNIRS signals. J Biomed
-    Opt. 16(10), 106005.
-
-3)  Tong Y, Bergethon PR, Frederick BD. (2011c) An improved method for
-    mapping cerebrovascular reserve using concurrent fMRI and
-    near-infrared spectroscopy with Regressor Interpolation at
-    Progressive Time Delays (RIPTiDe). Neuroimage, 56(4), 2047-2057.
-
-4)  Tong Y, Frederick BD. (2012) Concurrent fNIRS and fMRI processing
-    allows independent visualization of the propagation of pressure
-    waves and bulk blood flow in the cerebral vasculature. Neuroimage,
-    Jul 16;61(4): 1419-27.
-
-5)  Tong Y, Hocke LM, Licata SC, Frederick BD. (2012) Low frequency
-    oscillations measured in the periphery with near infrared
-    spectroscopy (NIRS) are strongly correlated with blood oxygen
-    level-dependent functional magnetic resonance imaging (BOLD fMRI)
-    signals. J Biomed Opt, 2012;17(10):106004. doi:
-    10.1117/1.JBO.17.10.106004. PubMed PMID: 23224003; PMCID: 3461094.
-
-6)  Tong Y, Hocke LM, Frederick BD. (2013) Short repetition time
-    multiband EPI with simultaneous pulse recording allows dynamic
-    imaging of the cardiac pulsation signal. Magn Reson Med
-    2014;72(5):1268-76. Epub Nov 22, 2013. doi: 10.1002/mrm.25041.
-    PubMed PMID: 24272768.
-
-7)  Tong Y, Frederick B. (2014) Studying the Spatial Distribution of
-    Physiological Effects on BOLD Signals using Ultrafast fMRI. Front
-    Hum Neurosci 2014;5(196). doi: doi: 10.3389/fnhum.2014.00196.
-
-8)  Tong Y, Frederick B. (2014) Tracking cerebral blood flow in BOLD
-    fMRI using recursively generated regressors. Hum Brain Mapp.
-    2014;35(11):5471-85. doi: 10.1002/hbm.22564. PubMed PMID: 24954380;
-    PMCID: PMC4206590.
-
-9)  Donahue M, Strother M, Lindsey K, Hocke L, Tong Y, Frederick B.
-    (2015) Time delay processing of hypercapnic fMRI allows quantitative
-    parameterization of cerebrovascular reactivity and blood flow
-    delays. Journal of Cerebral Blood Flow & Metabolism.  2015. PubMed 
-    PMID: 26661192. Epub October 19, 2015. doi: 10.1177/0271678X15608643.
-
-10) Hocke L, Cayetano K, Tong Y, Frederick B. (2015) An optimized
-    multimodal fMRI/NIRS probe for ultra-high resolution mapping.
-    Neurophotonics. 2(4), 045004 (Oct-Dec 2015). doi:
-    10.1117/1.NPh.2.4.0450004.
-
-11) Tong Y, Hocke LM, Fan X, Janes AC, Frederick B (2015). Can apparent
-    resting state connectivity arise from systemic fluctuations?
-    Frontiers in human neuroscience. 2015;9. doi:
-    10.3389/fnhum.2015.00285.
-
-12) Tong Y, Lindsey KP, Hocke LM, Vitaliano G, Mintzopoulos D, Frederick
-    B. (2016) Perfusion information extracted from resting state
-    functional magnetic resonance imaging. Journal of cerebral blood
-    flow and metabolism : official journal of the International Society
-    of Cerebral Blood Flow and Metabolism. 2016. doi:
-    10.1177/0271678X16631755. PubMed PMID: 26873885.
-
-Cardiac waveform extraction and refinement
-------------------------------------------
-
-1) Aslan S, Hocke L, Schwarz N, Frederick B. (2019) Extraction of the
-   cardiac waveform from simultaneous multislice fMRI data using slice
-   sorted averaging and a deep learning reconstruction filter.
-   NeuroImage 198, 303–316 (2019).
-
-Physiological noise identification and removal using time delay methods
------------------------------------------------------------------------
-
-1) Tong Y, Lindsey KP, Frederick BD. (2011b) Partitioning of
-   physiological noise signals in the brain with concurrent
-   near-infrared spectroscopy (NIRS) and fMRI. J Cereb Blood Flow Metab.
-   31(12), 2352-62.
-
-2) Frederick BD, Nickerson LD, Tong Y. (2012) Physiological denoising of
-   BOLD fMRI data using Regressor Interpolation at Progressive Time
-   Delays (RIPTiDe) processing of concurrent fMRI and near-infrared
-   spectroscopy (NIRS). Neuroimage, Apr 15;60(3): 1419-27.
-
-3) Tong Y, Hocke LM, Nickerson LD, Licata SC, Lindsey KP, Frederick BB
-   (2013) Evaluating the effects of systemic low frequency oscillations
-   measured in the periphery on the independent component analysis
-   results of resting state networks. NeuroImage. 2013;76C:202-15. doi:
-   10.1016/j.neuroimage.2013.03.019. PubMed PMID: 23523805; PMCID:
-   PMC3652630.
-
-4) Hocke LM, Tong Y, Lindsey KP, Frederick BB (2016). Comparison of
-   peripheral near-infrared spectroscopy low-frequency oscillations to
-   other denoising methods in resting state functional MRI with
-   ultrahigh temporal resolution. Magnetic resonance in medicine :
-   official journal of the Society of Magnetic Resonance in Medicine /
-   Society of Magnetic Resonance in Medicine. 2016.
-   \| http://dx.doi.org/10.1002/mrm.26038. PubMed PMID: 26854203.
-
-5) Erdoğan S, Tong Y, Hocke L, Lindsey K, Frederick B (2016). Correcting
-   resting state fMRI-BOLD signals for blood arrival time enhances
-   functional connectivity analysis. Front. Hum. Neurosci., 28 June 2016
-   \| http://dx.doi.org/10.3389/fnhum.2016.00311
-
-6) Tong, Y, Hocke, LM, and Frederick, BB, Low Frequency
-   Systemic Hemodynamic \"Noise\" in Resting State BOLD fMRI: Characteristics,
-   Causes, Implications, Mitigation Strategies, and Applications.
-   Front Neurosci, 2019. 13: p. 787.
-   \| http://dx.doi.org/10.3389/fnins.2019.00787
 
 .. |PyPi Latest Version| image:: https://img.shields.io/pypi/v/rapidtide.svg
    :target: https://pypi.python.org/pypi/rapidtide/