Python implementation of the 1D Total Variation Denoising algorithm A Direct Algorithm for 1D Total Variation Denoising (Sign. Proc. Letters, DOI:10.1109/LSP.2013.2278339) using xtensor and pybind11 to bind c++ and numpy.
License: BSD 3-Clause "New" or "Revised" License
Hi there,
I get error when trying to install the package. I'm on MacOS Big Sur running Python 3.8.9 in a virtualenv.
I cloned your repo, activated my virtualenv and ran pip install ./TVD_Condat2013
Processing /Users/martin/Desktop/TVD_Condat2013
Requirement already satisfied: pybind11>=2.0.1 in /Users/martin/.virtualenvs/myenv/lib/python3.8/site-packages (from TVDCondat2013==0.0.1) (2.9.0)
Requirement already satisfied: numpy in /Users/martin/.virtualenvs/myenv/lib/python3.8/site-packages (from TVDCondat2013==0.0.1) (1.19.5)
Building wheels for collected packages: TVDCondat2013
Building wheel for TVDCondat2013 (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /Users/martin/.virtualenvs/myenv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-req-build-65bjutj_/setup.py'"'"'; __file__='"'"'/private/var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-req-build-65bjutj_/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/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-wheel-wr43e01q
cwd: /private/var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-req-build-65bjutj_/
Complete output (20 lines):
running bdist_wheel
running build
running build_ext
creating var
creating var/folders
creating var/folders/49
creating var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn
creating var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -iwithsysroot/System/Library/Frameworks/System.framework/PrivateHeaders -iwithsysroot/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Headers -arch arm64 -arch x86_64 -Werror=implicit-function-declaration -I/Users/martin/.virtualenvs/myenv/include -I/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/include/python3.8 -c /var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/tmpo7e5_93b.cpp -o var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/tmpo7e5_93b.o -std=c++14
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -iwithsysroot/System/Library/Frameworks/System.framework/PrivateHeaders -iwithsysroot/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Headers -arch arm64 -arch x86_64 -Werror=implicit-function-declaration -I/Users/martin/.virtualenvs/myenv/include -I/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/include/python3.8 -c /var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/tmpifqhogfs.cpp -o var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/tmpifqhogfs.o -fvisibility=hidden
building 'TVDCondat2013' extension
creating build
creating build/temp.macosx-10.14-x86_64-3.8
creating build/temp.macosx-10.14-x86_64-3.8/src
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -iwithsysroot/System/Library/Frameworks/System.framework/PrivateHeaders -iwithsysroot/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Headers -arch arm64 -arch x86_64 -Werror=implicit-function-declaration -I/Users/martin/.virtualenvs/myenv/lib/python3.8/site-packages/pybind11/include -I/Users/martin/.virtualenvs/myenv/lib/python3.8/site-packages/pybind11/include -I/Users/martin/.virtualenvs/myenv/lib/python3.8/site-packages/numpy/core/include -I/Users/martin/.virtualenvs/myenv/include -I/Users/martin/.virtualenvs/myenv/Library/include -I/Users/martin/.virtualenvs/myenv/include -I/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/include/python3.8 -c src/main.cpp -o build/temp.macosx-10.14-x86_64-3.8/src/main.o -stdlib=libc++ -mmacosx-version-min=10.7 -DVERSION_INFO="0.0.1" -std=c++14 -fvisibility=hidden
src/main.cpp:3:10: fatal error: 'xtensor/xmath.hpp' file not found
#include "xtensor/xmath.hpp"
^~~~~~~~~~~~~~~~~~~
1 error generated.
error: command 'clang' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for TVDCondat2013
Running setup.py clean for TVDCondat2013
Failed to build TVDCondat2013
Installing collected packages: TVDCondat2013
Running setup.py install for TVDCondat2013 ... error
ERROR: Command errored out with exit status 1:
command: /Users/martin/.virtualenvs/myenv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-req-build-65bjutj_/setup.py'"'"'; __file__='"'"'/private/var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-req-build-65bjutj_/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/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-record-4d_79p_e/install-record.txt --single-version-externally-managed --compile --install-headers /Users/martin/.virtualenvs/myenv/include/site/python3.8/TVDCondat2013
cwd: /private/var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-req-build-65bjutj_/
Complete output (15 lines):
running install
running build
running build_ext
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -iwithsysroot/System/Library/Frameworks/System.framework/PrivateHeaders -iwithsysroot/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Headers -arch arm64 -arch x86_64 -Werror=implicit-function-declaration -I/Users/martin/.virtualenvs/myenv/include -I/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/include/python3.8 -c /var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/tmp9fwt3sy7.cpp -o var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/tmp9fwt3sy7.o -std=c++14
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -iwithsysroot/System/Library/Frameworks/System.framework/PrivateHeaders -iwithsysroot/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Headers -arch arm64 -arch x86_64 -Werror=implicit-function-declaration -I/Users/martin/.virtualenvs/myenv/include -I/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/include/python3.8 -c /var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/tmpeyanws0z.cpp -o var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/tmpeyanws0z.o -fvisibility=hidden
building 'TVDCondat2013' extension
creating build
creating build/temp.macosx-10.14-x86_64-3.8
creating build/temp.macosx-10.14-x86_64-3.8/src
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -iwithsysroot/System/Library/Frameworks/System.framework/PrivateHeaders -iwithsysroot/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Headers -arch arm64 -arch x86_64 -Werror=implicit-function-declaration -I/Users/martin/.virtualenvs/myenv/lib/python3.8/site-packages/pybind11/include -I/Users/martin/.virtualenvs/myenv/lib/python3.8/site-packages/pybind11/include -I/Users/martin/.virtualenvs/myenv/lib/python3.8/site-packages/numpy/core/include -I/Users/martin/.virtualenvs/myenv/include -I/Users/martin/.virtualenvs/myenv/Library/include -I/Users/martin/.virtualenvs/myenv/include -I/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/include/python3.8 -c src/main.cpp -o build/temp.macosx-10.14-x86_64-3.8/src/main.o -stdlib=libc++ -mmacosx-version-min=10.7 -DVERSION_INFO="0.0.1" -std=c++14 -fvisibility=hidden
src/main.cpp:3:10: fatal error: 'xtensor/xmath.hpp' file not found
#include "xtensor/xmath.hpp"
^~~~~~~~~~~~~~~~~~~
1 error generated.
error: command 'clang' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /Users/martin/.virtualenvs/myenv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-req-build-65bjutj_/setup.py'"'"'; __file__='"'"'/private/var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-req-build-65bjutj_/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/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-record-4d_79p_e/install-record.txt --single-version-externally-managed --compile --install-headers /Users/martin/.virtualenvs/myenv/include/site/python3.8/TVDCondat2013 Check the logs for full command output.
Any idea how to resolve?
Regards,
Martin
Hi Boris,
I've succesfully used your implementation in the past, but I am unable to install it on Ubuntu 22. I have installed xtensor and xtensor-python with conda, but to no avail. I keep getting the same error. Any idea? I paste the output below:
Thanks,
Jose
ERROR: Command errored out with exit status 1:
command: /home/jri/anaconda3/envs/sqwavefit/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-lj27max8/setup.py'"'"'; file='"'"'/tmp/pip-req-build-lj27max8/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 /tmp/pip-wheel-nrz9fwef
cwd: /tmp/pip-req-build-lj27max8/
Complete output (33 lines):
running bdist_wheel
running build
running build_ext
gcc -pthread -B /home/jri/anaconda3/envs/sqwavefit/compiler_compat -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/jri/anaconda3/envs/sqwavefit/include/python3.5m -c /tmp/tmpk8dvo_4j.cpp -o tmp/tmpk8dvo_4j.o -std=c++14
cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/jri/anaconda3/envs/sqwavefit/compiler_compat -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/jri/anaconda3/envs/sqwavefit/include/python3.5m -c /tmp/tmpbx2g14hy.cpp -o tmp/tmpbx2g14hy.o -fvisibility=hidden
cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
building 'TVDCondat2013' extension
creating build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/src
gcc -pthread -B /home/jri/anaconda3/envs/sqwavefit/compiler_compat -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -Iinclude -I/home/jri/anaconda3/envs/sqwavefit/lib/python3.5/site-packages/numpy/core/include -I/home/jri/anaconda3/envs/sqwavefit/include -I/home/jri/anaconda3/envs/sqwavefit/Library/include -I/home/jri/anaconda3/envs/sqwavefit/include/python3.5m -c src/main.cpp -o build/temp.linux-x86_64-3.5/src/main.o -DVERSION_INFO="0.0.1" -std=c++14 -fvisibility=hidden
cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
src/main.cpp: In function ‘xt::pyarray TVD(xt::pyarray, double)’:
src/main.cpp:169:23: error: ‘adapt’ is not a member of ‘xt’; did you mean ‘xadapt’?
169 | auto output_2 = xt::adapt(output);
| ^~~~~
| xadapt
src/main.cpp: In function ‘xt::pyarray D_TVD_R(xt::pyarray, double)’:
src/main.cpp:328:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
328 | for(size_t i=1;i<size;i++)
| ~^~~~~
src/main.cpp:338:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
338 | for(size_t i=0;i<size;i++)
| ~^~~~~
src/main.cpp:350:21: error: ‘adapt’ is not a member of ‘xt’; did you mean ‘xadapt’?
350 | auto output = xt::adapt(retrend);
| ^~~~~
| xadapt
src/main.cpp: At global scope:
src/main.cpp:356:16: error: expected constructor, destructor, or type conversion before ‘(’ token
356 | PYBIND11_MODULE(TVDCondat2013, m)
| ^
error: command 'gcc' failed with exit status 1
hello I try to install 'TVDCondat 2013' with the following command (pip install TVDCondat2013) but when I run my program is give following result:
Error:
ModuleNotFoundError: No module named 'TVDCondat2013'
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