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Resting state HRF estimation from BOLD-fMRI signal

Home Page: http://bids-apps.neuroimaging.io/rsHRF/

License: MIT License

Python 97.12% Dockerfile 0.75% MATLAB 2.12%

timeseries fmri-data-analysis fmri bids bidsapp

rshrf's Introduction

Resting state HRF estimation and deconvolution.

Please refer to https://github.com/compneuro-da/rsHRF for MATLAB version

The basic idea

This toolbox is aimed to retrieve the onsets of pseudo-events triggering an hemodynamic response from resting state fMRI BOLD voxel-wise signal. It is based on point process theory, and fits a model to retrieve the optimal lag between the events and the HRF onset, as well as the HRF shape, using a choice of basis functions (the canonical shape with two derivatives, (smoothed) Finite Impulse Response, mixture of gammas).

Once that the HRF has been retrieved for each voxel, it can be deconvolved from the time series (for example to improve lag-based connectivity estimates), or one can map the shape parameters everywhere in the brain (including white matter), and use the shape as a pathophysiological indicator.

How to use the toolbox

The input is voxelwise BOLD signal, already preprocessed according to your favorite recipe. Important thing are:

bandpass filter in the 0.01-0.08 Hz interval (or something like that)
z-score the voxel BOLD time series

To be on the safe side, these steps are performed again in the code.

The input can be images (3D or 4D), or directly matrices of [observation x voxels].

It is possible to use a temporal mask to exclude some time points (for example after scrubbing).

The demos allow you to run the analyses on several formats of input data.

Python Package and BIDS-app

A BIDS-App has been made for easy and reproducible analysis. Its documentation can be accessed at:

http://bids-apps.neuroimaging.io/rsHRF/

Collaborators

Guorong Wu
Nigel Colenbier
Sofie Van Den Bossche
Daniele Marinazzo
Madhur Tandon (Python - BIDS)
Asier Erramuzpe (Python - BIDS)
Amogh Johri (Python - BIDS)

References

Wu, G. R., Colenbier, N., Van Den Bossche, S., Clauw, K., Johri, A., Tandon, M., & Marinazzo, D. (2021). rsHRF: A toolbox for resting-state HRF estimation and deconvolution. Neuroimage, 244, 118591. open access journal page
Guo-Rong Wu, Wei Liao, Sebastiano Stramaglia, Ju-Rong Ding, Huafu Chen, Daniele Marinazzo*. "A blind deconvolution approach to recover effective connectivity brain networks from resting state fMRI data." Medical Image Analysis, 2013, 17:365-374. Open access institutional repo
Guo-Rong Wu, Daniele Marinazzo. "Sensitivity of the resting state hemodynamic response function estimation to autonomic nervous system fluctuations." Philosophical Transactions of the Royal Society A, 2016, 374: 20150190. Open access institutional repo

rshrf's People

Contributors

Stargazers

Watchers

Forkers

devhliu francopestilli sofievdbos amoghjohri peerherholz happybcloud remi-gau zhujunling65 omidvarnia

rshrf's Issues

Can't run GUI due to docker related error

I just installed rsHRF in a Linux machine with an Anaconda installation, using pip install rsHRF.

rsHRF was installed without a problem. However, if I run rsHRF --GUI, I get the error rsHRF: error: --GUI should not be used inside a Docker container, although, as far as I know, I'm not running rsHRF inside a Docker container.

Can't enter ".." in the input path?

Hello. I am having a problem specifying the input data path for rsHRF command line.

Due to the way we are executing this app, we need to reference our input data through "../" prefix.

$ singularity exec -e docker://bids/rshrf:1.0.0 rsHRF --input_file ../5cff8685503da13f7865f2da/5acab41cce736b3a7531808f/bold.nii.gz results --atlas ../5cff86ae503da13f7865f2dc/mask.nii.gz --estimation canon2dd

This results in the following error message.

WARNING: docker-extract failed, missing executable or libarchive
WARNING: Will use old layer extraction method - this does not handle whiteouts
�[33mWARNING: Non existent bind point (directory) in container: '/N/home'
�[0m�[33mWARNING: Non existent bind point (directory) in container: '/N/u'
�[0m�[33mWARNING: Non existent bind point (directory) in container: '/N/dc2'
�[0m�[33mWARNING: Non existent bind point (directory) in container: '/N/soft'
�[0m�[33mWARNING: Could not chdir to home: /N/u/brlife/Karst
�[0mTraceback (most recent call last):
  File "/usr/lib/python3.6/site-packages/nibabel/loadsave.py", line 40, in load
    stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/5cff8685503da13f7865f2da/5acab41cce736b3a7531808f/bold.nii.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/bin/rsHRF", line 11, in <module>
    sys.exit(main())
  File "/usr/lib/python3.6/site-packages/rsHRF/CLI.py", line 243, in main
    run_rsHRF()
  File "/usr/lib/python3.6/site-packages/rsHRF/CLI.py", line 128, in run_rsHRF
    TR = spm_dep.spm.spm_vol(args.input_file).header.get_zooms()[-1]
  File "/usr/lib/python3.6/site-packages/rsHRF/spm_dep/spm.py", line 12, in spm_vol
    v = nib.load(input_nii_file)
  File "/usr/lib/python3.6/site-packages/nibabel/loadsave.py", line 42, in load
    raise FileNotFoundError("No such file or no access: '%s'" % filename)
FileNotFoundError: No such file or no access: '/5cff8685503da13f7865f2da/5acab41cce736b3a7531808f/bold.nii.gz'

It looks like the CLI is stripping the ".." from the path, but I am not sure why it's failing. I have confirmed that the input data exists in the path that I am specifying.

Thank you!

ImportError: numpy.core.multiarray failed to import (v1.0.1)

(I sent an email for this but just for the record let me create this issue here!)

The Docker container with tag 1.0.1 fails to run with the following error message.

[0mModuleNotFoundError: No module named 'numpy.core._multiarray_umath'
Traceback (most recent call last):
  File "/usr/bin/rsHRF", line 6, in <module>
    from rsHRF.CLI import main
  File "/usr/lib/python3.6/site-packages/rsHRF/__init__.py", line 6, in <module>
    import rsHRF.fourD_rsHRF
  File "/usr/lib/python3.6/site-packages/rsHRF/fourD_rsHRF.py", line 5, in <module>
    import matplotlib.pyplot as plt
  File "/usr/lib/python3.6/site-packages/matplotlib/pyplot.py", line 32, in <module>
    import matplotlib.colorbar
  File "/usr/lib/python3.6/site-packages/matplotlib/colorbar.py", line 27, in <module>
    import matplotlib.artist as martist
  File "/usr/lib/python3.6/site-packages/matplotlib/artist.py", line 13, in <module>
    from .path import Path
  File "/usr/lib/python3.6/site-packages/matplotlib/path.py", line 17, in <module>
    from . import _path, cbook, rcParams
ImportError: numpy.core.multiarray failed to import

The new container seems to be using a slightly newer version of python, but apart from that I couldn't really tell why it's failing.

Soichi

Broken links in the references section

The following links in the references section of the README file are broken:

https://github.com/guorongwu/rsHRF/raw/master/docs/2013_MIA.pdf

https://github.com/guorongwu/rsHRF/raw/master/docs/2016_PTA.pdf

https://github.com/guorongwu/rsHRF/raw/master/docs/poster_OHBM2016_HRF.pdf

small fix in the knee point estimation and deconvolution

Hi,

we have made a small modification to the matlab code in two scripts

https://github.com/compneuro-da/rsHRF/blob/master/rsHRF_knee_pt.m
https://github.com/compneuro-da/rsHRF/blob/master/rsHRF_iterative_wiener_deconv.m

Basically this is to make sure that the knee point is always found in the decreasing phase of the error, and not in the increasing one. The latter would happen not so often, but it could happen in extreme cases.

The fix should be pretty straightforward.

thanks!

to-do (wish)list for the python implementation

The current version is functioning and dockerized, thanks to @madhur-tandon .

The matlab version is a few functionalities ahead (apart from the SPM plugin, not applicable to python).

Here the changes implemented in the new version of the matlab toolbox.

https://github.com/compneuro-da/rsHRF/blob/a2eafb68a8c7e308f6776e680c36e857730d60a0/update_log.txt

pasted here with some comment for each of them

------ v2.2, 201909 -----------

Change the GUI (add surface analysis pannel and Display)
Nice to have a GUI also in Python, but low priority
add rsHRF_viwer.m for HRF shapes visualization
Same as before. Nice, but low priority
add a m-file (rsHRF_mvgc.m) for multivariate Granger causality analysis.
This is an important part, but something that comes after the HRF part. Also takes some work (and there could be other toolboxes doing it). Leave aside for now.
update HRF basis functions, add Gamma/Fourier basis function (more flexible, and supporting finer temporal grid).
Important addition, implemented here https://github.com/compneuro-da/rsHRF/blob/master/rsHRF_estimation_temporal_basis.m . To do
update (s)FIR model, using AR(k) for autocorrelated noise modeling
Important addition, implemented here https://github.com/compneuro-da/rsHRF/blob/master/rsHRF_estimation_FIR.m (subfunction glsco, where AR is mentioned, new input parameter para.AR)
add a m-file (rsHRF_estimation_impulseest.m, see code for help) for Nonparametric impulse response estimation (not included in rsHRF GUI).
Also important, here the demo https://github.com/compneuro-da/rsHRF/blob/master/demo_code/demo_rsHRF_impulseest.m) and the code
https://github.com/compneuro-da/rsHRF/blob/33edcb2ca677ab39518bd90156be1cf047fca932/rsHRF_estimation_impulseest.m

------ v2.1, 201908 -----------

add suface based analysis module.
Important to read another type of files (GIFTI). In this case what changes is the read/write part.
Here some python functions to do so https://github.com/nipy/nibabel/blob/master/nibabel/gifti/gifti.py. They should be included in the read/write part.

problem with dependency pyyawt on macos 12.4 on apple M1 arm processor

I'm trying to install rsHRF on a conda environment
The system is Apple M1 Pro, macOS v.12.4.
c compiler is gfortran. Suspect it may be an incompatibility issue with the ARM processing instruction set.

In a fresh (Python 3.6.8) environment with scikit-learn installed via conda, I tried the following

pip install rsHRF

That generates the following failed install log:

Collecting rsHRF
  Using cached rsHRF-1.5.8-py3-none-any.whl (60 kB)
Collecting joblib
  Downloading joblib-1.1.0-py2.py3-none-any.whl (306 kB)
     |████████████████████████████████| 306 kB 2.7 MB/s 
Requirement already satisfied: nibabel in /Users/localuser/anaconda/lib/python3.6/site-packages (from rsHRF) (2.1.0)
Requirement already satisfied: pandas in /Users/localuser/anaconda/lib/python3.6/site-packages (from rsHRF) (1.1.5)
Collecting duecredit
  Using cached duecredit-0.9.1-py3-none-any.whl (86 kB)
Requirement already satisfied: numpy in /Users/localuser/anaconda/lib/python3.6/site-packages (from rsHRF) (1.16.3)
Requirement already satisfied: patsy in /Users/localuser/anaconda/lib/python3.6/site-packages (from rsHRF) (0.4.1)
Requirement already satisfied: scipy in /Users/localuser/anaconda/lib/python3.6/site-packages (from rsHRF) (1.2.1)
Collecting pyyawt
  Using cached pyyawt-0.1.1.zip (450 kB)
Requirement already satisfied: matplotlib in /Users/localuser/anaconda/lib/python3.6/site-packages (from rsHRF) (2.0.2)
Collecting pybids==0.11.1
  Using cached pybids-0.11.1-py2.py3-none-any.whl (3.2 MB)
Collecting mpld3
  Using cached mpld3-0.5.8-py3-none-any.whl (201 kB)
Requirement already satisfied: python-dateutil>=2.7.3 in /Users/localuser/anaconda/lib/python3.6/site-packages (from pandas->rsHRF) (2.8.1)
Requirement already satisfied: pytz>=2017.2 in /Users/localuser/anaconda/lib/python3.6/site-packages (from pandas->rsHRF) (2017.2)
Requirement already satisfied: requests in /Users/localuser/.local/lib/python3.6/site-packages (from duecredit->rsHRF) (2.20.1)
Collecting citeproc-py>=0.4
  Using cached citeproc_py-0.6.0-py3-none-any.whl (179 kB)
Requirement already satisfied: six in /Users/localuser/anaconda/lib/python3.6/site-packages (from duecredit->rsHRF) (1.10.0)
Collecting importlib-metadata; python_version < "3.8"
  Downloading importlib_metadata-4.8.3-py3-none-any.whl (17 kB)
Requirement already satisfied: cycler>=0.10 in /Users/localuser/anaconda/lib/python3.6/site-packages (from matplotlib->rsHRF) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in /Users/localuser/anaconda/lib/python3.6/site-packages (from matplotlib->rsHRF) (2.1.4)
Collecting num2words
  Using cached num2words-0.5.12-py3-none-any.whl (125 kB)
Collecting bids-validator
  Using cached bids_validator-1.9.9-py2.py3-none-any.whl (21 kB)
Requirement already satisfied: sqlalchemy in /Users/localuser/anaconda/lib/python3.6/site-packages (from pybids==0.11.1->rsHRF) (1.1.9)
Requirement already satisfied: jinja2 in /Users/localuser/anaconda/lib/python3.6/site-packages (from mpld3->rsHRF) (2.9.6)
Requirement already satisfied: urllib3<1.25,>=1.21.1 in /Users/localuser/.local/lib/python3.6/site-packages (from requests->duecredit->rsHRF) (1.24.1)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /Users/localuser/.local/lib/python3.6/site-packages (from requests->duecredit->rsHRF) (3.0.4)
Requirement already satisfied: certifi>=2017.4.17 in /Users/localuser/anaconda/lib/python3.6/site-packages (from requests->duecredit->rsHRF) (2020.4.5.1)
Requirement already satisfied: idna<2.8,>=2.5 in /Users/localuser/.local/lib/python3.6/site-packages (from requests->duecredit->rsHRF) (2.7)
Requirement already satisfied: lxml in /Users/localuser/anaconda/lib/python3.6/site-packages (from citeproc-py>=0.4->duecredit->rsHRF) (3.7.3)
Collecting typing-extensions>=3.6.4; python_version < "3.8"
  Downloading typing_extensions-4.1.1-py3-none-any.whl (26 kB)
Collecting zipp>=0.5
  Downloading zipp-3.6.0-py3-none-any.whl (5.3 kB)
Collecting docopt>=0.6.2
  Using cached docopt-0.6.2.tar.gz (25 kB)
Requirement already satisfied: MarkupSafe>=0.23 in /Users/localuser/anaconda/lib/python3.6/site-packages (from jinja2->mpld3->rsHRF) (0.23)
Building wheels for collected packages: pyyawt, docopt
  **Building wheel for pyyawt (setup.py) ... error
  ERROR: Command errored out with exit status 1:**
   command: /Users/localuser/anaconda/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/cj/4mb6t1f906j397tj71pxfxz00000gn/T/pip-install-axmgy6_h/pyyawt/setup.py'"'"'; __file__='"'"'/private/var/folders/cj/4mb6t1f906j397tj71pxfxz00000gn/T/pip-install-axmgy6_h/pyyawt/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/cj/4mb6t1f906j397tj71pxfxz00000gn/T/pip-wheel-ukrm8ak7
       cwd: /private/var/folders/cj/4mb6t1f906j397tj71pxfxz00000gn/T/pip-install-axmgy6_h/pyyawt/
  Complete output (464 lines):
  running bdist_wheel
  running build
  running config_cc
  unifing config_cc, config, build_clib, build_ext, build commands --compiler options
  running config_fc
  unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
  running build_src
  build_src
  building py_modules sources
  creating build
  creating build/src.macosx-10.7-x86_64-3.6
  creating build/src.macosx-10.7-x86_64-3.6/pyyawt
  building extension "pyyawt._pyyawt" sources
  building data_files sources
  build_src: building npy-pkg config files
  running build_py
  creating build/lib.macosx-10.7-x86_64-3.6
  creating build/lib.macosx-10.7-x86_64-3.6/pyyawt
  copying pyyawt/dwt3d.py -> build/lib.macosx-10.7-x86_64-3.6/pyyawt
  copying pyyawt/dwt2d.py -> build/lib.macosx-10.7-x86_64-3.6/pyyawt
  copying pyyawt/dwt1d.py -> build/lib.macosx-10.7-x86_64-3.6/pyyawt
  copying pyyawt/dwt.py -> build/lib.macosx-10.7-x86_64-3.6/pyyawt
  copying pyyawt/version.py -> build/lib.macosx-10.7-x86_64-3.6/pyyawt
  copying pyyawt/denoising.py -> build/lib.macosx-10.7-x86_64-3.6/pyyawt
  copying pyyawt/cwt.py -> build/lib.macosx-10.7-x86_64-3.6/pyyawt
  copying pyyawt/utility.py -> build/lib.macosx-10.7-x86_64-3.6/pyyawt
  copying pyyawt/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/pyyawt
  copying pyyawt/__config__.py -> build/lib.macosx-10.7-x86_64-3.6/pyyawt
  copying pyyawt/setup.py -> build/lib.macosx-10.7-x86_64-3.6/pyyawt
  copying pyyawt/swt.py -> build/lib.macosx-10.7-x86_64-3.6/pyyawt
  copying pyyawt/cowt.py -> build/lib.macosx-10.7-x86_64-3.6/pyyawt
  copying build/src.macosx-10.7-x86_64-3.6/pyyawt/__config__.py -> build/lib.macosx-10.7-x86_64-3.6/pyyawt
  running build_ext
  customize UnixCCompiler
  customize UnixCCompiler using build_ext
  building 'pyyawt._pyyawt' extension
  compiling C sources
  C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/localuser/anaconda/include -arch x86_64 -I/Users/localuser/anaconda/include -arch x86_64
  
  creating build/temp.macosx-10.7-x86_64-3.6/pyyawt
  creating build/temp.macosx-10.7-x86_64-3.6/pyyawt/src
  compile options: '-DPY_EXTENSION -Ipyyawt/src -I/Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include -I/Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include -I/Users/localuser/anaconda/include/python3.6m -c'
  gcc: pyyawt/src/beylkin.c
  gcc: pyyawt/src/bior.c
  gcc: pyyawt/src/bathlets.c
  gcc: pyyawt/src/bior_t.c
  gcc: pyyawt/src/_pyyawt.c
  gcc: pyyawt/src/cowt.c
  gcc: pyyawt/src/coiflets.c
  gcc: pyyawt/src/cwt.c
  In file included from pyyawt/src/beylkin.c:24:
  In file included from pyyawt/src/bior_t.c:25:
  pyyawt/src/swtlib.h:In file included from pyyawt/src/cowt.c:23:
  pyyawt/src/swtlib.hpyyawt/src/swtlib.h:673:32:: 673:67332: :32: In file included from pyyawt/src/bathlets.c:24:
  pyyawt/src/swtlib.h:673:32: In file included from pyyawt/src/bior.c:24:
  pyyawt/src/swtlib.h:673:32: In file included from pyyawt/src/cwt.c:23:
  pyyawt/src/swtlib.h:673:32: In file included from pyyawt/src/coiflets.c:24:
  pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
  warning: this function declaration is not a prototype [-Wstrict-prototypes]
  warning: this function declaration is not a prototype [-Wstrict-prototypes]
               void filter_clear ();             void filter_clear ();
  
                                 ^                               ^
  
                                  void                                void
  
               void filter_clear ();
                                 ^
                                  voidwarning: warning: this function declaration is not a prototype [-Wstrict-prototypes]this function declaration is not a prototype [-Wstrict-prototypes]
  
  warning: this function declaration is not a prototype [-Wstrict-prototypes]
               void filter_clear ();             void filter_clear ();             void filter_clear ();
                                 ^
                                  void
  
                                 ^
                                  void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  
  warning:
  this function declaration is not a prototype [-Wstrict-prototypes]                               ^
                                  void
  
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               void filter_clear ();
                                 ^
                                  void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
               extend_method getdwtMode();
                                       ^
                                        void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  pyyawt/src/bior.c:248:11: warning: unused variable 'pFilterCoef' [-Wunused-variable]
    double *pFilterCoef, *pFilterCoefMirror;
            ^
  pyyawt/src/bior.c:248:25: warning: unused variable 'pFilterCoefMirror' [-Wunused-variable]
    double *pFilterCoef, *pFilterCoefMirror;
                          ^
  In file included from pyyawt/src/cwt.c:24:
  pyyawt/src/kiss_fft.h:8:10: fatal error: 'malloc.h' file not found
  #include <malloc.h>
           ^~~~~~~~~~
  pyyawt/src/bior_t.c:363:1: warning: unused function 'bspline_init' [-Wunused-function]
  bspline_init (const double **h1, const double **g1,
  ^
  2 warnings and 1 error generated.
  gcc: pyyawt/src/daubechies.c
  pyyawt/src/bathlets.c:466:11: warning: unused variable 'pFilterCoef' [-Wunused-variable]
    double *pFilterCoef;
            ^
  pyyawt/src/bior.c:433:11: warning: unused variable 'pFilterCoef' [-Wunused-variable]
    double *pFilterCoef, *pFilterCoefMirror;
            ^
  pyyawt/src/bior.c:433:25: warning: unused variable 'pFilterCoefMirror' [-Wunused-variable]
    double *pFilterCoef, *pFilterCoefMirror;
                          ^
  pyyawt/src/bior.c:619:11: warning: unused variable 'pFilterCoef' [-Wunused-variable]
    double *pFilterCoef, *pFilterCoefMirror;
            ^
  pyyawt/src/bior.c:619:25: warning: unused variable 'pFilterCoefMirror' [-Wunused-variable]
    double *pFilterCoef, *pFilterCoefMirror;
                          ^
  pyyawt/src/bior.c:804:25: warning: unused variable 'pFilterCoefMirror' [-Wunused-variable]
    double *pFilterCoef, *pFilterCoefMirror;
                          ^
  pyyawt/src/bior.c:804:11: warning: unused variable 'pFilterCoef' [-Wunused-variable]
    double *pFilterCoef, *pFilterCoefMirror;
            ^
  3 warnings generated.
  gcc: pyyawt/src/dmey.c
  In file included from pyyawt/src/_pyyawt.c:239:
  pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               void filter_clear ();
                                 ^
                                  void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  In file included from pyyawt/src/_pyyawt.c:244:
  In file included from /Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
  In file included from /Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
  In file included from /Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824:
  /Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
  #warning "Using deprecated NumPy API, disable it with " \
   ^
  In file included from pyyawt/src/daubechies.c:27:
  pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               void filter_clear ();
                                 ^
                                  void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  2 warnings generated.
  2 warnings generated.
  3 warnings generated.
  10 warnings generated.
  gcc: pyyawt/src/dwt1d.c
  gcc: pyyawt/src/dwt2d.c
  gcc: pyyawt/src/farras.c
  gcc: pyyawt/src/dwt3d.c
  2 warnings generated.
  In file included from pyyawt/src/dmey.c:25:
  pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               void filter_clear ();
                                 ^
                                  void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  gcc: pyyawt/src/haar.c
  2 warnings generated.
  gcc: pyyawt/src/kingsbury.c
  2 warnings generated.
  gcc: pyyawt/src/kiss_fft.c
  pyyawt/src/_pyyawt.c:17558:134: warning: code will never be executed [-Wunreachable-code]
      __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                                                                                                       ^~~~~~~
  In file included from pyyawt/src/dwt1d.c:23:
  pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               void filter_clear ();
                                 ^
                                  void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  pyyawt/src/dwt1d.c:28:26: warning: this old-style function definition is not preceded by a prototype [-Wstrict-prototypes]
   extend_method getdwtMode(){
                           ^
  pyyawt/src/dwt1d.c:38:14: warning: this old-style function definition is not preceded by a prototype [-Wstrict-prototypes]
  filter_clear ()
               ^
  pyyawt/src/dwt1d.c:99:11: error: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)' [-Werror,-Wimplicit-function-declaration]
        if (strcmp(wname,wi[count].wname) == 0)
            ^
  pyyawt/src/dwt1d.c:99:11: note: include the header <string.h> or explicitly provide a declaration for 'strcmp'
  pyyawt/src/dwt1d.c:235:4: error: implicitly declaring library function 'strcpy' with type 'char *(char *, const char *)' [-Werror,-Wimplicit-function-declaration]
            strcpy(*str1,ei[count].extMethodName);
            ^
  pyyawt/src/dwt1d.c:235:4: note: include the header <string.h> or explicitly provide a declaration for 'strcpy'
  In file included from pyyawt/src/dwt2d.c:24:
  pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               void filter_clear ();
                                 ^
                                  void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  pyyawt/src/dwt1d.c:1186:8: warning: unused variable 'c' [-Wunused-variable]
    char c='a';
         ^
  5 warnings and 2 errors generated.
  pyyawt/src/dwt2d.c:318:7: warning: variable 'filterOutLength' set but not used [-Wunused-but-set-variable]
    int filterOutLength;
        ^
  pyyawt/src/dwt2d.c:415:8: warning: unused variable 'c' [-Wunused-variable]
    char c='b';
         ^
  pyyawt/src/dwt2d.c:413:7: warning: variable 'filterOutLength' set but not used [-Wunused-but-set-variable]
    int filterOutLength;
        ^
  pyyawt/src/_pyyawt.c:21882:26: warning: code will never be executed [-Wunreachable-code]
                  module = PyImport_ImportModuleLevelObject(
                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  In file included from pyyawt/src/dwt3d.c:24:
  pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               void filter_clear ();
                                 ^
                                  void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  gcc: pyyawt/src/legendre.c
  In file included from pyyawt/src/farras.c:25:
  pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               void filter_clear ();
                                 ^
                                  void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  pyyawt/src/dwt2d.c:814:7: error: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)' [-Werror,-Wimplicit-function-declaration]
    if (strcmp (coefType, "h") == 0)
        ^
  pyyawt/src/dwt2d.c:814:7: note: include the header <string.h> or explicitly provide a declaration for 'strcmp'
  pyyawt/src/dwt2d.c:1396:7: warning: variable 'filterOutLength' set but not used [-Wunused-but-set-variable]
    int filterOutLength;
        ^
  pyyawt/src/dwt2d.c:1398:8: warning: unused variable 'c' [-Wunused-variable]
    char c='b';
         ^
  7 warnings and 1 error generated.
  In file included from pyyawt/src/haar.c:24:
  pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               void filter_clear ();
                                 ^
                                  void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  In file included from pyyawt/src/_pyyawt.c:244:
  In file included from /Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
  In file included from /Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:21:
  /Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: unused function '_import_array' [-Wunused-function]
  _import_array(void)
  ^
  pyyawt/src/_pyyawt.c:22960:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function]
  static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) {
                                 ^
  pyyawt/src/_pyyawt.c:23075:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function]
  static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
                                  ^
  pyyawt/src/_pyyawt.c:23137:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function]
  static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
                                  ^
  pyyawt/src/_pyyawt.c:22369:48: warning: unused function '__pyx_t_float_complex_from_parts' [-Wunused-function]
      static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
                                                 ^
  pyyawt/src/_pyyawt.c:22379:30: warning: unused function '__Pyx_c_eqf' [-Wunused-function]
      static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                               ^
  pyyawt/src/_pyyawt.c:22382:48: warning: unused function '__Pyx_c_sumf' [-Wunused-function]
      static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                                                 ^
  pyyawt/src/_pyyawt.c:22388:48: warning: unused function '__Pyx_c_difff' [-Wunused-function]
      static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                                                 ^
  pyyawt/src/_pyyawt.c:22400:48: warning: unused function '__Pyx_c_quotf' [-Wunused-function]
      static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                                                 ^
  pyyawt/src/_pyyawt.c:22407:48: warning: unused function '__Pyx_c_negf' [-Wunused-function]
      static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) {
                                                 ^
  pyyawt/src/_pyyawt.c:22413:30: warning: unused function '__Pyx_c_is_zerof' [-Wunused-function]
      static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) {
                               ^
  pyyawt/src/_pyyawt.c:22416:48: warning: unused function '__Pyx_c_conjf' [-Wunused-function]
      static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) {
                                                 ^
  pyyawt/src/_pyyawt.c:22430:52: warning: unused function '__Pyx_c_powf' [-Wunused-function]
          static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                                                     ^
  pyyawt/src/_pyyawt.c:22489:49: warning: unused function '__pyx_t_double_complex_from_parts' [-Wunused-function]
      static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
                                                  ^
  pyyawt/src/_pyyawt.c:22499:30: warning: unused function '__Pyx_c_eq' [-Wunused-function]
      static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                               ^
  pyyawt/src/_pyyawt.c:22502:49: warning: unused function '__Pyx_c_sum' [-Wunused-function]
      static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                                                  ^
  pyyawt/src/_pyyawt.c:22508:49: warning: unused function '__Pyx_c_diff' [-Wunused-function]
      static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                                                  ^
  pyyawt/src/_pyyawt.c:22520:49: warning: unused function '__Pyx_c_quot' [-Wunused-function]
      static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                                                  ^
  pyyawt/src/_pyyawt.c:22527:49: warning: unused function '__Pyx_c_neg' [-Wunused-function]
      static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) {
                                                  ^
  pyyawt/src/_pyyawt.c:22533:30: warning: unused function '__Pyx_c_is_zero' [-Wunused-function]
      static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) {
                               ^
  pyyawt/src/_pyyawt.c:22536:49: warning: unused function '__Pyx_c_conj' [-Wunused-function]
      static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) {
                                                  ^
  pyyawt/src/_pyyawt.c:22550:53: warning: unused function '__Pyx_c_pow' [-Wunused-function]
          static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                                                      ^
  pyyawt/src/_pyyawt.c:22624:32: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function]
  static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
                                 ^
  pyyawt/src/_pyyawt.c:22650:27: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration]
  static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
                            ^
  pyyawt/src/_pyyawt.c:17251:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew1' [-Wunused-function]
  static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__pyx_v_a) {
                                 ^
  pyyawt/src/_pyyawt.c:17301:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew2' [-Wunused-function]
  static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__pyx_v_a, PyObject *__pyx_v_b) {
                                 ^
  pyyawt/src/_pyyawt.c:17351:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew3' [-Wunused-function]
  static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c) {
                                 ^
  pyyawt/src/_pyyawt.c:17401:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew4' [-Wunused-function]
  static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d) {
                                 ^
  pyyawt/src/_pyyawt.c:17451:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew5' [-Wunused-function]
  static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d, PyObject *__pyx_v_e) {
                                 ^
  pyyawt/src/_pyyawt.c:18259:27: warning: unused function '__pyx_f_5numpy_set_array_base' [-Wunused-function]
  static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_arr, PyObject *__pyx_v_base) {
                            ^
  pyyawt/src/_pyyawt.c:18355:32: warning: unused function '__pyx_f_5numpy_get_array_base' [-Wunused-function]
  static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__pyx_v_arr) {
                                 ^
  gcc: pyyawt/src/swt.c
  2 warnings generated.
  gcc: pyyawt/src/symlets.c
  2 warnings generated.
  In file included from pyyawt/src/kingsbury.c:25:
  pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               void filter_clear ();
                                 ^
                                  void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  In file included from pyyawt/src/kiss_fft.c:16:
  In file included from pyyawt/src/_kiss_fft_guts.h:19:
  pyyawt/src/kiss_fft.h:8:10: fatal error: 'malloc.h' file not found
  #include <malloc.h>
           ^~~~~~~~~~
  gcc: pyyawt/src/utility.c
  1 error generated.
  gcc: pyyawt/src/vaidyanathan.c
  2 warnings generated.
  In file included from pyyawt/src/legendre.c:24:
  pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               void filter_clear ();
                                 ^
                                  void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  2 warnings generated.
  In file included from pyyawt/src/swt.c:23:
  pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               void filter_clear ();
                                 ^
                                  void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  In file included from pyyawt/src/symlets.c:24:
  pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               void filter_clear ();
                                 ^
                                  void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  In file included from pyyawt/src/utility.c:24:
  pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               void filter_clear ();
                                 ^
                                  void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  pyyawt/src/utility.c:554:11: error: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)' [-Werror,-Wimplicit-function-declaration]
        if (strcmp(mode,ei[count].extMethodName) == 0)
            ^
  pyyawt/src/utility.c:554:11: note: include the header <string.h> or explicitly provide a declaration for 'strcmp'
  2 warnings and 1 error generated.
  In file included from pyyawt/src/vaidyanathan.c:24:
  pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               void filter_clear ();
                                 ^
                                  void
  pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
               extend_method getdwtMode();
                                       ^
                                        void
  2 warnings generated.
  2 warnings generated.
  2 warnings generated.
  2 warnings generated.
  36 warnings generated.
  error: Command "gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/localuser/anaconda/include -arch x86_64 -I/Users/localuser/anaconda/include -arch x86_64 -DPY_EXTENSION -Ipyyawt/src -I/Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include -I/Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include -I/Users/localuser/anaconda/include/python3.6m -c pyyawt/src/cwt.c -o build/temp.macosx-10.7-x86_64-3.6/pyyawt/src/cwt.o -MMD -MF build/temp.macosx-10.7-x86_64-3.6/pyyawt/src/cwt.o.d" failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for pyyawt
  Running setup.py clean for pyyawt
  Building wheel for docopt (setup.py) ... done
  Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=19851 sha256=18c3f901fb65adc47f4e5f06cfe78cc400f3c1f839a3ea9049735ce10ea61ad5
  Stored in directory: /Users/localuser/Library/Caches/pip/wheels/3f/2a/fa/4d7a888e69774d5e6e855d190a8a51b357d77cc05eb1c097c9
Successfully built docopt
Failed to build pyyawt
Installing collected packages: joblib, citeproc-py, typing-extensions, zipp, importlib-metadata, duecredit, pyyawt, docopt, num2words, bids-validator, pybids, mpld3, rsHRF
    Running setup.py install for pyyawt ... error
    ERROR: Command errored out with exit status 1:
     command: /Users/localuser/anaconda/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/cj/4mb6t1f906j397tj71pxfxz00000gn/T/pip-install-axmgy6_h/pyyawt/setup.py'"'"'; __file__='"'"'/private/var/folders/cj/4mb6t1f906j397tj71pxfxz00000gn/T/pip-install-axmgy6_h/pyyawt/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/cj/4mb6t1f906j397tj71pxfxz00000gn/T/pip-record-ruoqk64x/install-record.txt --single-version-externally-managed --compile --install-headers /Users/localuser/anaconda/include/python3.6m/pyyawt
         cwd: /private/var/folders/cj/4mb6t1f906j397tj71pxfxz00000gn/T/pip-install-axmgy6_h/pyyawt/
    Complete output (447 lines):
    running install
    running build
    running config_cc
    unifing config_cc, config, build_clib, build_ext, build commands --compiler options
    running config_fc
    unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
    running build_src
    build_src
    building py_modules sources
    building extension "pyyawt._pyyawt" sources
    building data_files sources
    build_src: building npy-pkg config files
    running build_py
    copying pyyawt/version.py -> build/lib.macosx-10.7-x86_64-3.6/pyyawt
    copying build/src.macosx-10.7-x86_64-3.6/pyyawt/__config__.py -> build/lib.macosx-10.7-x86_64-3.6/pyyawt
    running build_ext
    customize UnixCCompiler
    customize UnixCCompiler using build_ext
    building 'pyyawt._pyyawt' extension
    compiling C sources
    C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/localuser/anaconda/include -arch x86_64 -I/Users/localuser/anaconda/include -arch x86_64
    
    creating build/temp.macosx-10.7-x86_64-3.6/pyyawt
    creating build/temp.macosx-10.7-x86_64-3.6/pyyawt/src
    compile options: '-DPY_EXTENSION -Ipyyawt/src -I/Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include -I/Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include -I/Users/localuser/anaconda/include/python3.6m -c'
    gcc: pyyawt/src/_pyyawt.c
    gcc: pyyawt/src/bathlets.c
    gcc: pyyawt/src/beylkin.c
    gcc: pyyawt/src/bior.c
    gcc: pyyawt/src/coiflets.c
    gcc: pyyawt/src/cowt.c
    gcc: pyyawt/src/cwt.c
    gcc: pyyawt/src/bior_t.c
    In file included from pyyawt/src/bior.c:24:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    pyyawt/src/bior.c:248:25: warning: unused variable 'pFilterCoefMirror' [-Wunused-variable]
      double *pFilterCoef, *pFilterCoefMirror;
                            ^
    pyyawt/src/bior.c:248:11: warning: unused variable 'pFilterCoef' [-Wunused-variable]
      double *pFilterCoef, *pFilterCoefMirror;
              ^
    pyyawt/src/bior.c:433:25: warning: unused variable 'pFilterCoefMirror' [-Wunused-variable]
      double *pFilterCoef, *pFilterCoefMirror;
                            ^
    pyyawt/src/bior.c:433:11: warning: unused variable 'pFilterCoef' [-Wunused-variable]
      double *pFilterCoef, *pFilterCoefMirror;
              ^
    pyyawt/src/bior.c:619:11: warning: unused variable 'pFilterCoef' [-Wunused-variable]
      double *pFilterCoef, *pFilterCoefMirror;
              ^
    pyyawt/src/bior.c:619:25: warning: unused variable 'pFilterCoefMirror' [-Wunused-variable]
      double *pFilterCoef, *pFilterCoefMirror;
                            ^
    pyyawt/src/bior.c:804:25: warning: unused variable 'pFilterCoefMirror' [-Wunused-variable]
      double *pFilterCoef, *pFilterCoefMirror;
                            ^
    pyyawt/src/bior.c:804:11: warning: unused variable 'pFilterCoef' [-Wunused-variable]
      double *pFilterCoef, *pFilterCoefMirror;
              ^
    In file included from pyyawt/src/bior_t.c:25:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    pyyawt/src/bior_t.c:363:1: warning: unused function 'bspline_init' [-Wunused-function]
    bspline_init (const double **h1, const double **g1,
    ^
    3 warnings generated.
    In file included from pyyawt/src/coiflets.c:24:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    In file included from pyyawt/src/cwt.c:23:
    pyyawt/src/swtlib.hpyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    :673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    gcc: pyyawt/src/daubechies.c
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    In file included from pyyawt/src/cwt.c:24:
    pyyawt/src/kiss_fft.h:8:10: fatal error: 'malloc.h' file not found
    #include <malloc.h>
             ^~~~~~~~~~
    In file included from pyyawt/src/beylkin.c:24:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    2 warnings and 1 error generated.
    10 warnings generated.
    In file included from pyyawt/src/bathlets.c:24:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    gcc: pyyawt/src/dmey.c
    pyyawt/src/bathlets.c:466:11: warning: unused variable 'pFilterCoef' [-Wunused-variable]
      double *pFilterCoef;
              ^
    In file included from pyyawt/src/cowt.c:23:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    2 warnings generated.
    gcc: pyyawt/src/dwt1d.c
    2 warnings generated.
    gcc: pyyawt/src/dwt2d.c
    gcc: pyyawt/src/dwt3d.c
    3 warnings generated.
    gcc: pyyawt/src/farras.c
    In file included from pyyawt/src/_pyyawt.c:239:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    In file included from pyyawt/src/_pyyawt.c:244:
    In file included from /Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
    In file included from /Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
    In file included from /Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824:
    /Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
    #warning "Using deprecated NumPy API, disable it with " \
     ^
    2 warnings generated.
    In file included from pyyawt/src/daubechies.c:27:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    gcc: pyyawt/src/haar.c
    In file included from pyyawt/src/dmey.c:25:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    In file included from pyyawt/src/dwt1d.c:23:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    pyyawt/src/dwt1d.c:28:26: warning: this old-style function definition is not preceded by a prototype [-Wstrict-prototypes]
     extend_method getdwtMode(){
                             ^
    In file included from pyyawt/src/dwt3d.c:24:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    pyyawt/src/dwt1d.c:38:14: warning: this old-style function definition is not preceded by a prototype [-Wstrict-prototypes]
    filter_clear ()
                 ^
    pyyawt/src/dwt1d.c:99:11: error: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)' [-Werror,-Wimplicit-function-declaration]
          if (strcmp(wname,wi[count].wname) == 0)
              ^
    pyyawt/src/dwt1d.c:99:11: note: include the header <string.h> or explicitly provide a declaration for 'strcmp'
    pyyawt/src/dwt1d.c:235:4: error: implicitly declaring library function 'strcpy' with type 'char *(char *, const char *)' [-Werror,-Wimplicit-function-declaration]
              strcpy(*str1,ei[count].extMethodName);
              ^
    pyyawt/src/dwt1d.c:235:4: note: include the header <string.h> or explicitly provide a declaration for 'strcpy'
    In file included from pyyawt/src/dwt2d.c:24:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    2 warnings generated.
    pyyawt/src/dwt1d.c:1186:8: warning: unused variable 'c' [-Wunused-variable]
      char c='a';
           ^
    5 warnings and 2 errors generated.
    gcc: pyyawt/src/kingsbury.c
    pyyawt/src/dwt2d.c:318:7: warning: variable 'filterOutLength' set but not used [-Wunused-but-set-variable]
      int filterOutLength;
          ^
    pyyawt/src/dwt2d.c:413:7: warning: variable 'filterOutLength' set but not used [-Wunused-but-set-variable]
      int filterOutLength;
          ^
    pyyawt/src/dwt2d.c:415:8: warning: unused variable 'c' [-Wunused-variable]
      char c='b';
           ^
    2 warnings generated.
    pyyawt/src/dwt2d.c:814:7: error: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)' [-Werror,-Wimplicit-function-declaration]
      if (strcmp (coefType, "h") == 0)
          ^
    pyyawt/src/dwt2d.c:814:7: note: include the header <string.h> or explicitly provide a declaration for 'strcmp'
    gcc: pyyawt/src/kiss_fft.c
    pyyawt/src/dwt2d.c:1396:7: warning: variable 'filterOutLength' set but not used [-Wunused-but-set-variable]
      int filterOutLength;
          ^
    pyyawt/src/dwt2d.c:1398:8: warning: unused variable 'c' [-Wunused-variable]
      char c='b';
           ^
    7 warnings and 1 error generated.
    In file included from pyyawt/src/farras.c:25:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    gcc: pyyawt/src/legendre.c
    gcc: pyyawt/src/swt.c
    2 warnings generated.
    gcc: pyyawt/src/symlets.c
    pyyawt/src/_pyyawt.c:17558:134: warning: code will never be executed [-Wunreachable-code]
        __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                                                                                                         ^~~~~~~
    In file included from pyyawt/src/haar.c:24:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    2 warnings generated.
    In file included from pyyawt/src/kingsbury.c:25:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    gcc: pyyawt/src/utility.c
    In file included from pyyawt/src/kiss_fft.c:16:
    In file included from pyyawt/src/_kiss_fft_guts.h:19:
    pyyawt/src/kiss_fft.h:8:10: fatal error: 'malloc.h' file not found
    #include <malloc.h>
             ^~~~~~~~~~
    In file included from pyyawt/src/swt.c:23:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    pyyawt/src/_pyyawt.c:21882:26: warning: code will never be executed [-Wunreachable-code]
                    module = PyImport_ImportModuleLevelObject(
                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    1 error generated.
    In file included from pyyawt/src/legendre.c:24:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    gcc: pyyawt/src/vaidyanathan.c
    In file included from pyyawt/src/_pyyawt.c:244:
    In file included from /Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
    In file included from /Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:21:
    /Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: unused function '_import_array' [-Wunused-function]
    _import_array(void)
    ^
    pyyawt/src/_pyyawt.c:22960:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function]
    static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) {
                                   ^
    pyyawt/src/_pyyawt.c:23075:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function]
    static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
                                    ^
    pyyawt/src/_pyyawt.c:23137:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function]
    static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
                                    ^
    pyyawt/src/_pyyawt.c:22369:48: warning: unused function '__pyx_t_float_complex_from_parts' [-Wunused-function]
        static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
                                                   ^
    pyyawt/src/_pyyawt.c:22379:30: warning: unused function '__Pyx_c_eqf' [-Wunused-function]
        static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                                 ^
    pyyawt/src/_pyyawt.c:22382:48: warning: unused function '__Pyx_c_sumf' [-Wunused-function]
        static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                                                   ^
    pyyawt/src/_pyyawt.c:22388:48: warning: unused function '__Pyx_c_difff' [-Wunused-function]
        static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                                                   ^
    pyyawt/src/_pyyawt.c:22400:48: warning: unused function '__Pyx_c_quotf' [-Wunused-function]
        static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                                                   ^
    pyyawt/src/_pyyawt.c:22407:48: warning: unused function '__Pyx_c_negf' [-Wunused-function]
        static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) {
                                                   ^
    pyyawt/src/_pyyawt.c:22413:30: warning: unused function '__Pyx_c_is_zerof' [-Wunused-function]
        static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) {
                                 ^
    pyyawt/src/_pyyawt.c:22416:48: warning: unused function '__Pyx_c_conjf' [-Wunused-function]
        static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) {
                                                   ^
    pyyawt/src/_pyyawt.c:22430:52: warning: unused function '__Pyx_c_powf' [-Wunused-function]
            static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
                                                       ^
    pyyawt/src/_pyyawt.c:22489:49: warning: unused function '__pyx_t_double_complex_from_parts' [-Wunused-function]
        static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
                                                    ^
    pyyawt/src/_pyyawt.c:22499:30: warning: unused function '__Pyx_c_eq' [-Wunused-function]
        static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                                 ^
    pyyawt/src/_pyyawt.c:22502:49: warning: unused function '__Pyx_c_sum' [-Wunused-function]
        static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                                                    ^
    pyyawt/src/_pyyawt.c:22508:49: warning: unused function '__Pyx_c_diff' [-Wunused-function]
        static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                                                    ^
    pyyawt/src/_pyyawt.c:22520:49: warning: unused function '__Pyx_c_quot' [-Wunused-function]
        static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                                                    ^
    pyyawt/src/_pyyawt.c:22527:49: warning: unused function '__Pyx_c_neg' [-Wunused-function]
        static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) {
                                                    ^
    pyyawt/src/_pyyawt.c:22533:30: warning: unused function '__Pyx_c_is_zero' [-Wunused-function]
        static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) {
                                 ^
    pyyawt/src/_pyyawt.c:22536:49: warning: unused function '__Pyx_c_conj' [-Wunused-function]
        static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) {
                                                    ^
    pyyawt/src/_pyyawt.c:22550:53: warning: unused function '__Pyx_c_pow' [-Wunused-function]
            static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) {
                                                        ^
    pyyawt/src/_pyyawt.c:22624:32: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function]
    static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
                                   ^
    pyyawt/src/_pyyawt.c:22650:27: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration]
    static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
                              ^
    pyyawt/src/_pyyawt.c:17251:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew1' [-Wunused-function]
    static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__pyx_v_a) {
                                   ^
    pyyawt/src/_pyyawt.c:17301:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew2' [-Wunused-function]
    static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__pyx_v_a, PyObject *__pyx_v_b) {
                                   ^
    pyyawt/src/_pyyawt.c:17351:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew3' [-Wunused-function]
    static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c) {
                                   ^
    pyyawt/src/_pyyawt.c:17401:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew4' [-Wunused-function]
    static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d) {
                                   ^
    pyyawt/src/_pyyawt.c:17451:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew5' [-Wunused-function]
    static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d, PyObject *__pyx_v_e) {
                                   ^
    pyyawt/src/_pyyawt.c:18259:27: warning: unused function '__pyx_f_5numpy_set_array_base' [-Wunused-function]
    static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_arr, PyObject *__pyx_v_base) {
                              ^
    pyyawt/src/_pyyawt.c:18355:32: warning: unused function '__pyx_f_5numpy_get_array_base' [-Wunused-function]
    static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__pyx_v_arr) {
                                   ^
    2 warnings generated.
    2 warnings generated.
    In file included from pyyawt/src/symlets.c:24:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    2 warnings generated.
    In file included from pyyawt/src/utility.c:24:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    In file included from pyyawt/src/vaidyanathan.c:24:
    pyyawt/src/swtlib.h:673:32: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 void filter_clear ();
                                   ^
                                    void
    pyyawt/src/swtlib.h:689:38: warning: this function declaration is not a prototype [-Wstrict-prototypes]
                 extend_method getdwtMode();
                                         ^
                                          void
    pyyawt/src/utility.c:554:11: error: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)' [-Werror,-Wimplicit-function-declaration]
          if (strcmp(mode,ei[count].extMethodName) == 0)
              ^
    pyyawt/src/utility.c:554:11: note: include the header <string.h> or explicitly provide a declaration for 'strcmp'
    2 warnings generated.
    2 warnings and 1 error generated.
    2 warnings generated.
    2 warnings generated.
    36 warnings generated.
    error: Command "gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/localuser/anaconda/include -arch x86_64 -I/Users/localuser/anaconda/include -arch x86_64 -DPY_EXTENSION -Ipyyawt/src -I/Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include -I/Users/localuser/anaconda/lib/python3.6/site-packages/numpy/core/include -I/Users/localuser/anaconda/include/python3.6m -c pyyawt/src/cwt.c -o build/temp.macosx-10.7-x86_64-3.6/pyyawt/src/cwt.o -MMD -MF build/temp.macosx-10.7-x86_64-3.6/pyyawt/src/cwt.o.d" failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /Users/localuser/anaconda/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/cj/4mb6t1f906j397tj71pxfxz00000gn/T/pip-install-axmgy6_h/pyyawt/setup.py'"'"'; __file__='"'"'/private/var/folders/cj/4mb6t1f906j397tj71pxfxz00000gn/T/pip-install-axmgy6_h/pyyawt/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/cj/4mb6t1f906j397tj71pxfxz00000gn/T/pip-record-ruoqk64x/install-record.txt --single-version-externally-managed --compile --install-headers /Users/localuser/anaconda/include/python3.6m/pyyawt Check the logs for full command output.
WARNING: You are using pip version 20.1.1; however, version 21.3.1 is available.
You should consider upgrading via the '/Users/localuser/anaconda/bin/python -m pip install --upgrade pip' command.

Installing the dependency pyyawt seems to be the problm (see bolded text above)

Error running rshrf toolbox through docker image bids/rshrf:latest

Hi,

I tried running the toolbox through the docker image using the latest version. Following the instructions for the docker version
I used the following commands and encountered the following error.

docker pull bids/rshrf
docker run -ti --rm bids/rshrf --GUI

Gives the following error :

  File "/usr/bin/rsHRF", line 5, in <module>
    from rsHRF.CLI import main
  File "/usr/lib/python3.6/site-packages/rsHRF/__init__.py", line 7, in <module>
    import rsHRF.CLI
  File "/usr/lib/python3.6/site-packages/rsHRF/CLI.py", line 8, in <module>
    from .rsHRF_GUI import run
  File "/usr/lib/python3.6/site-packages/rsHRF/rsHRF_GUI/__init__.py", line 4, in <module>
    from . import gui_windows
  File "/usr/lib/python3.6/site-packages/rsHRF/rsHRF_GUI/gui_windows/__init__.py", line 1, in <module>
    from . import inputWindow
  File "/usr/lib/python3.6/site-packages/rsHRF/rsHRF_GUI/gui_windows/inputWindow.py", line 2, in <module>
    from tkinter       import Toplevel, Checkbutton, IntVar, Button, filedialog, NORMAL, DISABLED, OptionMenu, StringVar, Label
ModuleNotFoundError: No module named 'tkinter'

The same is true for :

docker run -ti --rm bids/rsHRF --help

Tested using Docker image using the latest version on both a Windows 10 and Linux ubuntu 16.04 system.

I wonder if there's something I'm doing wrong or there's an issue with the latest docker image.

Thanks,

Nigel

Limit number of CPUs

Hello.

Is there a way to limit the number of CPU/processes used to run this app?

It seems to always run up-to 8 cores according to my monitoring.

Does it always require 8 cores?

[BUG] Compromised credentials

What version of the bids app were you using?

No response

Describe your problem in detail.

CircleCI has alerted everyone to cycle credentials stored in their environment variables: https://circleci.com/blog/january-4-2023-security-alert/

A PYPI_PASSWORD environment variable was set in CircleCI (I have deleted it). I believe this belongs to @AmoghJohri and needs to be changed immediately. In the future, we should use tokens, and this can be done by setting TWINE_USER to __token__ and TWINE_PASSWORD to a token that is scoped to this one package only. The twine tool will automatically pick these up.

See https://pypi.org/help/#apitoken for additional guidance.

What command did you run?

No response

Describe what you expected.

No response

dockerfile uses pypi release

I am fixing the circle CI workflows of a lot of bids apps and having a quick look at the one of rsHRF.

Ideally we want the unit test to run regularly (with every push or merge to master) and not just on release.

Also we want to test the docker build regularly and possibly push an "unstable" image to docker hub that corresponds to the HEAD of the master branch.

Currently the dockerfile is set to install rsHRF from pypi which means that even if we make changes on the master branch the "unstable" docker image will be lagging behind.

One possible solution is to modify the dockerfile to copy the rsHRF code in it and install the package there.

Premature return in rest_IdealFilter ?

The return statement in the rest_IdealFilter function is inside the for loop.

See https://github.com/BIDS-Apps/rsHRF/blob/cf3410664a3a2eda1707f5ee7dc5a7f23fa21492/rsHRF/processing/rest_filter.py#L18

This looks odd to me since that implies that the for loop only executes once, independently of the value of nbin.

I must admit that I don't quite understand what the function does, so it is possible that this is OK.

No module named 'bids.grabbids'

Hi,
it seems there is some confusion with PyBIDS.
I am using Python3.7 and installing pybids as
pip3 install bids
Unfortunately when try something e.g. python3 CLI.py I get

No module named 'bids.grabbids'

googleing people suggest pip3 install pybids==0.6.5
which doesn't work and creates even more mess in my environment. Do you confirm everything is fine in the pybids use?

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