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sciai-lab / mutex-watershed

The mutex watershed for image segmentation.
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unable to install #2

Closed ChuxiJ closed 5 years ago

ChuxiJ commented 5 years ago

when I run python setup.py install, I get: running install running bdist_egg running egg_info writing mutex_watershed.egg-info/PKG-INFO writing dependency_links to mutex_watershed.egg-info/dependency_links.txt writing requirements to mutex_watershed.egg-info/requires.txt writing top-level names to mutex_watershed.egg-info/top_level.txt reading manifest file 'mutex_watershed.egg-info/SOURCES.txt' writing manifest file 'mutex_watershed.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_ext gcc -pthread -B /opt/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/opt/anaconda3/include/python3.7m -c /tmp/tmph205w3zf.cpp -o tmp/tmph205w3zf.o -std=c++14 cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ gcc -pthread -B /opt/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/opt/anaconda3/include/python3.7m -c /tmp/tmpmpj2kmxf.cpp -o tmp/tmpmpj2kmxf.o -fvisibility=hidden cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ building 'mutex_watershed' extension creating build creating build/temp.linux-x86_64-3.7 creating build/temp.linux-x86_64-3.7/src gcc -pthread -B /opt/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/opt/anaconda3/include/python3.7m -I/home/jupyter/.local/include/python3.7m -I/opt/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/opt/anaconda3/include -I/opt/anaconda3/Library/include -I/opt/anaconda3/include/python3.7m -c src/main.cpp -o build/temp.linux-x86_64-3.7/src/main.o -DVERSION_INFO="0.1.1" -std=c++14 -fvisibility=hidden cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ src/main.cpp:7:29: fatal error: xtensor/xmath.hpp: No such file or directory

include "xtensor/xmath.hpp"

                         ^

compilation terminated. error: command 'gcc' failed with exit status 1

How can I fix it?

constantinpape commented 5 years ago

The compiler does not find xtensor. Did you follow the steps described in installation? If you did, your conda environment should contain xtensor. You can check this with conda list.

ChuxiJ commented 5 years ago

Thanks for the response, it works now! I can run your code, but the results seem different. WE really want to reproduce your experiments. image image

It seems that we need to do an extra edge detection process. Also, I found the result is not good as the paper says

constantinpape commented 5 years ago

Could you elaborate a bit? How did you obtain the images you show here. What experiments exactly did you run?

It seems that we need to do an extra edge detection process.

The mutex watershed will output a label image. It's trivial to translate this to an edge image, e.g. using this functions.

Also, I found the result is not good as the paper says

Based on which criterion? Note that the algorithm's quality depends on the input predictions, so improving network predictions is usually the best way to improve results.

ChuxiJ commented 5 years ago

image Thanks, I know how it works now!!

constantinpape commented 5 years ago

Thanks, I know how it works now!!

You're welcome. I am closing this for now, feel free to raise another issue if you have more questions.