Ideally, the version should be updated or can be made deprecated. But should not be removed from the repository(PyPi). Can you please upload them back with some new versions tags ?

I tried pip install catch22 and got a long error log. These are the last few lines:

    C/SP_Summaries.c:161:9: error: ‘for’ loop initial declarations are only allowed in C99 mode
             for(int i = 0; i < nWelch; i ++){
             ^
    C/SP_Summaries.c:173:9: error: ‘for’ loop initial declarations are only allowed in C99 mode
             for(int i=0; i<nWelch/5; i++){
             ^
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/username/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-kiwf2hln/catch22/setup.py'"'"'; __file__='"'"'/tmp/pip-install-kiwf2hln/catch22/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-jtj01ddj/install-record.txt --single-version-externally-managed --compile --install-headers /home/username/anaconda3/include/python3.7m/catch22 Check the logs for full command output.

System: Anaconda3, CentOS 7

Any ideas?

Hello!

We package and maintain catch22 for Fedora Linux. Now that pycatch22 has been split into its own repo and bundles the C sources, we were wondering if:

• it would make sense to compile the C sources from here and provide catch22 as a shared library (libcatch22.so.0 types on Linux)
• use the shared library to link against when building pycatch22 etc.

The advantage of this is that we won't need to bundle catch22 in pycatch22, and that catch22 is provided as a library for people using C to use.

@musicinmybrain has created a pull request that generates the shared library (by adding a Makefile and so on) here. The main question here, as you'll see from that pull request, is whether you (upstream) intend to provide it as a C library, and if you do, would you be committing to ABI/shared object versioning etc. to notify users of changes and so on?

Link to the libtool documentation on versioning: https://www.gnu.org/software/libtool/manual/html_node/Versioning.html#Versioning

I've modified the CO_f1ecac feature to use interpolation, making it a double (and equivalent to the HCTSA function). See HCTSA's CO_AutoCorr.m and BF_PointOfCrossing.m

Adds new .c and .h files for 2 new functions: DN_Mean and DN_Spread_Std which represent the mean and standard deviation, respectively. Adds a boolean argument to core function calls where users can specify if they want to compute catch24 or just catch22. Need to run tests to check everything is working properly, but I have made changes to C code, and R and Python wrappers. @benfulcher changes will need to be made to the MATLAB wrapper too, right?

I'll remove the drafting tag once I have worked through unit tests, but either of you can feel free to run the additions and check they work if you have time.

Hi,

First of all, thanks for this great package!

I noticed that when doing a lot of calls to catch22.catch22_all(data), the memory consumption of grows. This pull request frees C arrays in C/CO_AutoCorr.c, C/helper_functions.c and wrap_Python/catch22_wrap_P3.c. With these changes, the memory consumption is stable. You can test this for yourself by running the following code before and after applying the changes that I am proposing.

import catch22
import numpy as np
from memory_profiler import profile

@profile
def catch22_all(signal):
    catch22.catch22_all(signal)
    
for i in range(10000):
    signal = np.random.randn(1000)
    catch22_all(signal)

Referring to this code snippet in CO_AutoCorr.c

#define tau 2
#define numBins 5

double CO_HistogramAMI_even_2_5(const double y[], const int size)

Why tau is 2 and numBins is 5? Shouldn't it be vice-versa according to the implementation of hctsa feature

Hi,

I have problem to install your package from R...following errors occurred:

• installing source package 'catch22' ... ** libs c:/Rtools/mingw_64/bin/gcc -I"C:/PROGRA~1/R/R-35~1.1/include" -DNDEBUG -I../inst/include -I"C:/Users/PeterLaurinec/Documents/R/win-library/3.5/Rcpp/include" -O2 -Wall -std=gnu99 -mtune=generic -c CO_AutoCorr.c -o CO_AutoCorr.o In file included from CO_AutoCorr.c:8:0: CO_AutoCorr.c: In function 'CO_AutoCorr': fft.h:16:43: error: '_Imaginary_I' undeclared (first use in this function) #define CMPLX(x, y) ((cplx)((double)(x) + _Imaginary_I * (double)(y))) ^ CO_AutoCorr.c:63:16: note: in expansion of macro 'CMPLX' F[i] = CMPLX(y[i] - m, 0.0); ^ fft.h:16:43: note: each undeclared identifier is reported only once for each function it appears in #define CMPLX(x, y) ((cplx)((double)(x) + _Imaginary_I * (double)(y))) ^ CO_AutoCorr.c:63:16: note: in expansion of macro 'CMPLX' F[i] = CMPLX(y[i] - m, 0.0); ^ CO_AutoCorr.c: In function 'co_autocorrs': fft.h:16:43: error: '_Imaginary_I' undeclared (first use in this function) #define CMPLX(x, y) ((cplx)((double)(x) + _Imaginary_I * (double)(y))) ^ CO_AutoCorr.c:97:16: note: in expansion of macro 'CMPLX' F[i] = CMPLX(y[i] - m, 0.0); ^ CO_AutoCorr.c: In function 'CO_HistogramAMI_even_2_5': CO_AutoCorr.c:347:5: error: variable-sized object may not be initialized double binEdges[numBins+1] = {0}; ^ CO_AutoCorr.c:347:5: warning: excess elements in array initializer CO_AutoCorr.c:347:5: warning: (near initialization for 'binEdges') CO_AutoCorr.c:370:5: error: variable-sized object may not be initialized double binEdges12[(numBins + 1) * (numBins + 1)] = {0}; ^ CO_AutoCorr.c:370:5: warning: excess elements in array initializer CO_AutoCorr.c:370:5: warning: (near initialization for 'binEdges12') CO_AutoCorr.c:414:5: error: variable-sized object may not be initialized double pi[numBins] = {0}; ^ CO_AutoCorr.c:414:5: warning: excess elements in array initializer CO_AutoCorr.c:414:5: warning: (near initialization for 'pi') CO_AutoCorr.c:415:5: error: variable-sized object may not be initialized double pj[numBins] = {0}; ^ CO_AutoCorr.c:415:5: warning: excess elements in array initializer CO_AutoCorr.c:415:5: warning: (near initialization for 'pj') make: *** [C:/PROGRA~1/R/R-35~1.1/etc/x64/Makeconf:208: CO_AutoCorr.o] Error 1 ERROR: compilation failed for package 'catch22'

Any idea? Thx

There is a difficulty in compiling using python3. E.g., python3 setup.py build gives the following:

running build
running build_ext
building 'catch22_C' extension
creating build
creating build/temp.macosx-10.7-x86_64-3.7
creating build/C
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/alex/miniconda3/envs/pipe-516-ram-mating-behaviour/include -arch x86_64 -I/Users/alex/miniconda3/envs/pipe-516-ram-mating-behaviour/include -arch x86_64 -I../C/ -I/Users/alex/miniconda3/envs/pipe-516-ram-mating-behaviour/include/python3.7m -c catch22_wrap.c -o build/temp.macosx-10.7-x86_64-3.7/catch22_wrap.o
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/alex/miniconda3/envs/pipe-516-ram-mating-behaviour/include -arch x86_64 -I/Users/alex/miniconda3/envs/pipe-516-ram-mating-behaviour/include -arch x86_64 -I../C/ -I/Users/alex/miniconda3/envs/pipe-516-ram-mating-behaviour/include/python3.7m -c ../C/MD_hrv.c -o build/temp.macosx-10.7-x86_64-3.7/../C/MD_hrv.o
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/alex/miniconda3/envs/pipe-516-ram-mating-behaviour/include -arch x86_64 -I/Users/alex/miniconda3/envs/pipe-516-ram-mating-behaviour/include -arch x86_64 -I../C/ -I/Users/alex/miniconda3/envs/pipe-516-ram-mating-behaviour/include/python3.7m -c ../C/SP_Summaries.c -o build/temp.macosx-10.7-x86_64-3.7/../C/SP_Summaries.o
In file included from ../C/CO_AutoCorr.h:9:0,
                 from ../C/SP_Summaries.c:9:
../C/SP_Summaries.c: In function 'welch':
../C/fft.h:16:43: error: '_Imaginary_I' undeclared (first use in this function)
 #define CMPLX(x, y) ((cplx)((double)(x) + _Imaginary_I * (double)(y)))
                                           ^
../C/SP_Summaries.c:43:20: note: in expansion of macro 'CMPLX'
             F[i] = CMPLX(xw[i] - m, 0.0);
                    ^~~~~
../C/fft.h:16:43: note: each undeclared identifier is reported only once for each function it appears in
 #define CMPLX(x, y) ((cplx)((double)(x) + _Imaginary_I * (double)(y)))
                                           ^
../C/SP_Summaries.c:43:20: note: in expansion of macro 'CMPLX'
             F[i] = CMPLX(xw[i] - m, 0.0);
                    ^~~~~
../C/SP_Summaries.c:71:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
         if(i>0 & i < Nout-1){
            ~^~
error: command 'gcc' failed with exit status 1

Can fix? Or just limit to python2?

In release 0.4.0, the Python package instead has version 0.3.1.

https://github.com/DynamicsAndNeuralSystems/catch22/blob/2e1a271c6a7437b6a4a754e1adc7e34d7a224c01/wrap_Python/setup.py#L17

https://github.com/DynamicsAndNeuralSystems/catch22/blob/2e1a271c6a7437b6a4a754e1adc7e34d7a224c01/wrap_Python/setup_P3.py#L17

Been trying to install the R wrapper without much success (though more success than I've had with the Python and Matlab wrappers!). I noticed a few issues with the documentation along the way, and have noted them here along with the error I get:

The install docs refer to./C_functions, but this directory appears to be./C in current builds.

I think the .c and .h files are supposed to be moved to ./wrap_R/catch22/src, rather than ./wrap_R/src (which is specified in the install instructions, but does not actually exist unless I manually create it).

Running R CMD INSTALL catch22_x.y.tar.gz only “works” in the latter case, and then only if R CMD build catch22 was run after the .c and .h files are copied to ./wrap_R/catch22/src. Attempting to build with these files in ./wrap_R/src causes the following error:

catch22_wrap.cpp:5:25: fatal error: CO_AutoCorr.h: No such file or directory

The docs should clarify that users should replace catch22_x.y.tar.gz with the tar file generated by the previous step. The name of this fill will depend on their version of catch22.

Fixing the error related to the location of the C files got me as far as the following error. Any advice would be appreciated:

(r-environment) # [email protected] in ~/Software/catch22/wrap_R [17:55:06]
$ R CMD INSTALL catch22_0.1.tar.gz
* installing to library \u2018/home/despoB/dlurie/anaconda3/envs/r-environment/lib/R/library\u2019
* installing *source* package \u2018catch22\u2019 ...
** libs
gcc -std=gnu99 -I/home/despoB/dlurie/anaconda3/envs/r-environment/lib/R/include -DNDEBUG -I../inst/include -I"/home/despoB/dlurie/anaconda3/envs/r-environment/lib/R/library/Rcpp/include" -I/home/despoB/dlurie/anaconda3/envs/r-environment/include   -fpic  -I/home/despoB/dlurie/anaconda3/envs/r-environment/include  -c CO_AutoCorr.c -o CO_AutoCorr.o
In file included from CO_AutoCorr.c:8:0:
CO_AutoCorr.c: In function \u2018CO_AutoCorr\u2019:
fft.h:16:43: error: \u2018_Imaginary_I\u2019 undeclared (first use in this function)
 #define CMPLX(x, y) ((cplx)((double)(x) + _Imaginary_I * (double)(y)))
                                           ^
CO_AutoCorr.c:63:16: note: in expansion of macro \u2018CMPLX\u2019
         F[i] = CMPLX(y[i] - m, 0.0);
                ^
fft.h:16:43: note: each undeclared identifier is reported only once for each function it appears in
 #define CMPLX(x, y) ((cplx)((double)(x) + _Imaginary_I * (double)(y)))
                                           ^
CO_AutoCorr.c:63:16: note: in expansion of macro \u2018CMPLX\u2019
         F[i] = CMPLX(y[i] - m, 0.0);
                ^
CO_AutoCorr.c: In function \u2018co_autocorrs\u2019:
fft.h:16:43: error: \u2018_Imaginary_I\u2019 undeclared (first use in this function)
 #define CMPLX(x, y) ((cplx)((double)(x) + _Imaginary_I * (double)(y)))
                                           ^
CO_AutoCorr.c:97:16: note: in expansion of macro \u2018CMPLX\u2019
         F[i] = CMPLX(y[i] - m, 0.0);
                ^
make: *** [CO_AutoCorr.o] Error 1
ERROR: compilation failed for package \u2018catch22\u2019
* removing \u2018/home/despoB/dlurie/anaconda3/envs/r-environment/lib/R/library/catch22\u2019

fedora/pass300/20220906/catch22.spec.out:IN_AutoMutualInfoStats.c:44:19: warning: suggest parentheses around comp arison in operand of '&' [-Wparentheses] fedora/pass300/20220906/catch22.spec.out:PD_PeriodicityWang.c:66:20: warning: suggest parentheses around comparis on in operand of '&' [-Wparentheses] fedora/pass300/20220906/catch22.spec.out:PD_PeriodicityWang.c:72:25: warning: suggest parentheses around comparis on in operand of '&' [-Wparentheses] fedora/pass300/20220906/catch22.spec.out:SB_BinaryStats.c:40:20: warning: suggest parentheses around comparison i n operand of '|' [-Wparentheses] fedora/pass300/20220906/catch22.spec.out:SB_BinaryStats.c:78:20: warning: suggest parentheses around comparison i n operand of '|' [-Wparentheses] fedora/pass300/20220906/catch22.spec.out:SP_Summaries.c:86:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] fedora/pass300/20220906/catch22.spec.out:splinefit.c:606:14: warning: suggest parentheses around comparison in op erand of '&' [-Wparentheses] fedora/pass300/20220906/catch22.spec.out:../C/IN_AutoMutualInfoStats.c:44:19: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] fedora/pass300/20220906/catch22.spec.out:../C/PD_PeriodicityWang.c:66:20: warning: suggest parentheses around com parison in operand of ‘&’ [-Wparentheses] fedora/pass300/20220906/catch22.spec.out:../C/PD_PeriodicityWang.c:72:25: warning: suggest parentheses around com parison in operand of ‘&’ [-Wparentheses] fedora/pass300/20220906/catch22.spec.out:../C/SB_BinaryStats.c:40:20: warning: suggest parentheses around compari son in operand of ‘|’ [-Wparentheses] fedora/pass300/20220906/catch22.spec.out:../C/SB_BinaryStats.c:78:20: warning: suggest parentheses around compari son in operand of ‘|’ [-Wparentheses] fedora/pass300/20220906/catch22.spec.out:../C/SP_Summaries.c:86:13: warning: suggest parentheses around compariso n in operand of ‘&’ [-Wparentheses] fedora/pass300/20220906/catch22.spec.out:../C/splinefit.c:606:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]

I checked the first two, presumably the rest are the same.

When running pip install catch22, the C compilation seems to complain. I tried it with python 3.7-3.9.

 C/CO_AutoCorr.c:531:9: error: ‘for’ loop initial declarations are only allowed in C99 mode
             for(int j = 0; j < numBins; j++){
             ^
    error: command '/usr/bin/gcc' failed with exit code 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/cxx579/anaconda3/envs/test_env/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-l6lnk30h/catch22_0230d4e651e84fa1a6f4489c53513e34/setup.py'"'"'; __file__='"'"'/tmp/pip-install-l6lnk30h/catch22_0230d4e651e84fa1a6f4489c53513e34/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-g8rdn06o/install-record.txt --single-version-externally-managed --compile --install-headers /home/cxx579/anaconda3/envs/test_env/include/python3.9/catch22 Check the logs for full command output.

I am not an expert in C and how it tights up with the Python wrapper but it might. have to do with this? Any ideas how to fix this. Thx :D

This issue can be fixed by

export CFLAGS="-std=c99"

However, it might be good to change the for loop instantiation that is more compatible by declaring the the iteration variable outside the loop like:

int i;
for (i=0;i<10;i++) { ..

What Happened

Get a segmentation fault when running catch22.catch22_all on short lists/numpy.arrays.

What I Expected to Happen

Returns a dictionary of features (perhaps with a lot of NaN-types due to the short timeseries)

Minimum Complete Verifable Example

>>> import catch22
>>> catch22.catch22_all([1,2])
Segmentation fault

Further Details

Can check that this doesn't happen with longer arrays like so:

import catch22
timeseries = list(range(10))
while timeseries:
    print(len(timeseries))
    catch22.catch22_all(timeseries)
    timeseries = timeseries[:-1]

I am using Sagemaker notebook and failed to install catch22 package.

Tried to add 'extra_compile_args = ['-std=c99']' before running 'pip install catch22'. Getting the following error:

C/SC_FluctAnal.c:12:5: note: use option -std=c99 or -std=gnu99 to compile your code

or else the compilation will fail in Linux. setup_P3.py :

the c++ extension module
extension_mod = Extension("catch22_C",
        sources=["catch22_wrap_P3.c"] + sourceFileList,
        include_dirs=[sourceDir],
        extra_compile_args = ['-std=c99']
)

Python:

    active environment : base
    active env location : /opt/anaconda
            shell level : 1
       user config file : /root/.condarc
 populated config files : /root/.condarc
          conda version : 4.9.2
    conda-build version : 3.17.8
         python version : 3.7.3.final.0
       virtual packages : __glibc=2.27=0
                          __unix=0=0
                          __archspec=1=x86_64

gcc

Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 7.5.0-3ubuntu1~18.04' --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-7 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu1~18.04)

Hi, I failed to install it in Python, would you mind checking out what is the problem? And how to use catch22? Is there a GUI or maybe a handbook for detailed method?