allenai / deepfigures-open Goto Github PK
View Code? Open in Web Editor NEWCompanion code to the paper "Extracting Scientific Figures with Distantly Supervised Neural Networks" ๐ค
License: Apache License 2.0
deepfigures-open's Issues
Dockerfile broken with tensorflow-latest
tensorflow-latest throws errors attempting to install the enumerated packages
training dataset with images
Hello, can you provide a download link of trai ning images?
Server access Error
Would you be able to explain what might cause this problem during installation ?
:: problems summary :: :::: ERRORS Server access Error: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target url=https://repo.typesafe.com/typesafe/ivy-releases/org.sonatype.oss/oss-parent/9/jars/oss-parent.jar
Thanks
Error: Page 2 is an image and allow OCR is turned off
10:40:30.718 [main] DEBUG o.a.pdffigures2.GraphicsExtractor$ - Page 2 is an image and allow OCR is false, giving up
Exception in thread "main" org.allenai.pdffigures2.FigureExtractor$OcredPdfException: Page 2 is an image and allow OCR is turned off
at org.allenai.pdffigures2.GraphicsExtractor$.extractRawGraphics(GraphicsExtractor.scala:66)
at org.allenai.pdffigures2.GraphicsExtractor$.extractGraphics(GraphicsExtractor.scala:32)
at org.allenai.pdffigures2.FigureExtractor$$anonfun$7.apply(FigureExtractor.scala:133)
Did anyone get this error?
Subjectively large false positive rate w.r.t text
link dead
unfortunately the link in the research paper http://labs.semanticscholar.org/deepfigures is dead.
A docker file would be also greatly appreciated as it is time consuming to replicate some historic code.
Invalid value for "PDF_PATH": File "/work/host-input/paper.pdf" does not exist.
Docker build has succeeded.
Usage: rundetection.py [OPTIONS] OUTPUT_DIRECTORY PDF_PATH
Try "rundetection.py -h" for help.
Error: Invalid value for "PDF_PATH": File "/work/host-input/paper.pdf" does not exist.
Traceback (most recent call last):
File "manage.py", line 70, in
manage()
File "/media/amax/Masters/liupengxue/lpx/lib/python3.5/site-packages/click/core.py", line 722, in call
return self.main(*args, **kwargs)
File "/media/amax/Masters/liupengxue/lpx/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/media/amax/Masters/liupengxue/lpx/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/media/amax/Masters/liupengxue/lpx/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/media/amax/Masters/liupengxue/lpx/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/media/amax/Masters/liupengxue/deepfigures/deepfigures-open-master/scripts/detectfigures.py", line 79, in detectfigures
raise_error=True)
File "/media/amax/Masters/liupengxue/deepfigures/deepfigures-open-master/scripts/init.py", line 54, in execute
cmd=command)
subprocess.CalledProcessError: Command 'docker run --rm --env-file deepfigures-local.env --volume /media/amax/Masters/liupengxue/deepfigures/deepfigures-open-master/results:/work/host-output/ --volume /media/amax/Masters/liupengxue/deepfigures/deepfigures-open-master:/work/host-input/ deepfigures-cpu:0.0.1 python3 /work/scripts/rundetection.py /work/host-output/ /work/host-input/paper.pdf' returned non-zero exit status 2
Failed to access the docker container while running the code.
2018-12-12 17:51:48,308:INFO:scripts.build:Executing: docker build --tag deepfigures-cpu:0.0.1 --file
Failed to access the docker container while running the code. Kindly let me know how to resolve this error.
Error Log:
/home/saravanan/deepfigures-open/dockerfiles/cpu/Dockerfile .
Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post http://%2Fvar%2Frun%2Fdocker.sock/v1.38/build?buildargs=%7B%7D&cachefrom=%5B%5D&cgroupparent=&cpuperiod=0&cpuquota=0&cpusetcpus=&cpusetmems=&cpushares=0&dockerfile=dockerfiles%2Fcpu%2FDockerfile&labels=%7B%7D&memory=0&memswap=0&networkmode=default&rm=1&session=o7k4ifza9sfm8p1y323f64cp9&shmsize=0&t=deepfigures-cpu%3A0.0.1&target=&ulimits=null&version=1: dial unix /var/run/docker.sock: connect: permission denied
Traceback (most recent call last):
File "manage.py", line 70, in
manage()
File "/home/saravanan/anaconda3/lib/python3.7/site-packages/click/core.py", line 722, in call
return self.main(*args, **kwargs)
File "/home/saravanan/anaconda3/lib/python3.7/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/saravanan/anaconda3/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/saravanan/anaconda3/lib/python3.7/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/saravanan/anaconda3/lib/python3.7/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/saravanan/deepfigures-open/scripts/detectfigures.py", line 49, in detectfigures
build.build.callback()
File "/home/saravanan/deepfigures-open/scripts/build.py", line 34, in build
logger)
File "/home/saravanan/deepfigures-open/scripts/init.py", line 54, in execute
cmd=command)
subprocess.CalledProcessError: Command 'docker build --tag deepfigures-cpu:0.0.1 --file /home/saravanan/deepfigures-open/dockerfiles/cpu/Dockerfile .' returned non-zero exit status 1.
java.lang.NullPointerException while installing pdffigures2
I installed Scala and tried to install pdffigures2, but it failed:
richard@pito ๎ฐ ~/src ๎ฐ rm -rf pdffigures*
richard@pito ๎ฐ ~/src ๎ฐ git clone https://github.com/allenai/pdffigures2
Cloning into 'pdffigures2'...
remote: Enumerating objects: 392, done.
remote: Total 392 (delta 0), reused 0 (delta 0), pack-reused 392
Receiving objects: 100% (392/392), 6.43 MiB | 2.48 MiB/s, done.
Resolving deltas: 100% (111/111), done.
richard@pito ๎ฐ ~/src ๎ฐ cd pdffigures2
richard@pito ๎ฐ ~/src/pdffigures2 ๎ฐ ๎ master ๎ฐ sbt assembly
[info] Loading project definition from /home/richard/src/pdffigures2/project
[info] Updating {file:/home/richard/src/pdffigures2/project/}pdffigures2-build...
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by sbt.ivyint.ErrorMessageAuthenticator$ (file:/home/richard/.sbt/boot/scala-2.10.4/org.scala-sbt/sbt/0.13.8/ivy-0.13.8.jar) to field java.net.Authenticator.theAuthenticator
WARNING: Please consider reporting this to the maintainers of sbt.ivyint.ErrorMessageAuthenticator$
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
[info] Resolving org.fusesource.jansi#jansi;1.4 ...
[info] Done updating.
java.lang.NullPointerException
at java.base/java.util.regex.Matcher.getTextLength(Matcher.java:1769)
at java.base/java.util.regex.Matcher.reset(Matcher.java:416)
at java.base/java.util.regex.Matcher.<init>(Matcher.java:253)
at java.base/java.util.regex.Pattern.matcher(Pattern.java:1130)
at java.base/java.util.regex.Pattern.split(Pattern.java:1249)
at java.base/java.util.regex.Pattern.split(Pattern.java:1322)
at sbt.IO$.pathSplit(IO.scala:744)
at sbt.IO$.parseClasspath(IO.scala:859)
at sbt.compiler.CompilerArguments.extClasspath(CompilerArguments.scala:62)
at sbt.compiler.MixedAnalyzingCompiler$.withBootclasspath(MixedAnalyzingCompiler.scala:189)
at sbt.compiler.MixedAnalyzingCompiler$.searchClasspathAndLookup(MixedAnalyzingCompiler.scala:167)
at sbt.compiler.MixedAnalyzingCompiler$.apply(MixedAnalyzingCompiler.scala:177)
at sbt.compiler.IC$.incrementalCompile(IncrementalCompiler.scala:138)
at sbt.Compiler$.compile(Compiler.scala:128)
at sbt.Compiler$.compile(Compiler.scala:114)
at sbt.Defaults$.sbt$Defaults$$compileIncrementalTaskImpl(Defaults.scala:814)
at sbt.Defaults$$anonfun$compileIncrementalTask$1.apply(Defaults.scala:805)
at sbt.Defaults$$anonfun$compileIncrementalTask$1.apply(Defaults.scala:803)
at scala.Function1$$anonfun$compose$1.apply(Function1.scala:47)
at sbt.$tilde$greater$$anonfun$$u2219$1.apply(TypeFunctions.scala:40)
at sbt.std.Transform$$anon$4.work(System.scala:63)
at sbt.Execute$$anonfun$submit$1$$anonfun$apply$1.apply(Execute.scala:226)
at sbt.Execute$$anonfun$submit$1$$anonfun$apply$1.apply(Execute.scala:226)
at sbt.ErrorHandling$.wideConvert(ErrorHandling.scala:17)
at sbt.Execute.work(Execute.scala:235)
at sbt.Execute$$anonfun$submit$1.apply(Execute.scala:226)
at sbt.Execute$$anonfun$submit$1.apply(Execute.scala:226)
at sbt.ConcurrentRestrictions$$anon$4$$anonfun$1.apply(ConcurrentRestrictions.scala:159)
at sbt.CompletionService$$anon$2.call(CompletionService.scala:28)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:514)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1135)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:844)
[error] (compile:compileIncremental) java.lang.NullPointerException
Project loading failed: (r)etry, (q)uit, (l)ast, or (i)gnore? r
[info] Loading project definition from /home/richard/src/pdffigures2/project
java.lang.NullPointerException
at java.base/java.util.regex.Matcher.getTextLength(Matcher.java:1769)
at java.base/java.util.regex.Matcher.reset(Matcher.java:416)
at java.base/java.util.regex.Matcher.<init>(Matcher.java:253)
at java.base/java.util.regex.Pattern.matcher(Pattern.java:1130)
at java.base/java.util.regex.Pattern.split(Pattern.java:1249)
at java.base/java.util.regex.Pattern.split(Pattern.java:1322)
at sbt.IO$.pathSplit(IO.scala:744)
at sbt.IO$.parseClasspath(IO.scala:859)
at sbt.compiler.CompilerArguments.extClasspath(CompilerArguments.scala:62)
at sbt.compiler.MixedAnalyzingCompiler$.withBootclasspath(MixedAnalyzingCompiler.scala:189)
at sbt.compiler.MixedAnalyzingCompiler$.searchClasspathAndLookup(MixedAnalyzingCompiler.scala:167)
at sbt.compiler.MixedAnalyzingCompiler$.apply(MixedAnalyzingCompiler.scala:177)
at sbt.compiler.IC$.incrementalCompile(IncrementalCompiler.scala:138)
at sbt.Compiler$.compile(Compiler.scala:128)
at sbt.Compiler$.compile(Compiler.scala:114)
at sbt.Defaults$.sbt$Defaults$$compileIncrementalTaskImpl(Defaults.scala:814)
at sbt.Defaults$$anonfun$compileIncrementalTask$1.apply(Defaults.scala:805)
at sbt.Defaults$$anonfun$compileIncrementalTask$1.apply(Defaults.scala:803)
at scala.Function1$$anonfun$compose$1.apply(Function1.scala:47)
at sbt.$tilde$greater$$anonfun$$u2219$1.apply(TypeFunctions.scala:40)
at sbt.std.Transform$$anon$4.work(System.scala:63)
at sbt.Execute$$anonfun$submit$1$$anonfun$apply$1.apply(Execute.scala:226)
at sbt.Execute$$anonfun$submit$1$$anonfun$apply$1.apply(Execute.scala:226)
at sbt.ErrorHandling$.wideConvert(ErrorHandling.scala:17)
at sbt.Execute.work(Execute.scala:235)
at sbt.Execute$$anonfun$submit$1.apply(Execute.scala:226)
at sbt.Execute$$anonfun$submit$1.apply(Execute.scala:226)
at sbt.ConcurrentRestrictions$$anon$4$$anonfun$1.apply(ConcurrentRestrictions.scala:159)
at sbt.CompletionService$$anon$2.call(CompletionService.scala:28)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:514)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1135)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:844)
[error] (compile:compileIncremental) java.lang.NullPointerException
Project loading failed: (r)etry, (q)uit, (l)ast, or (i)gnore? i
[warn] Ignoring load failure: no project loaded.
[error] Not a valid command: assembly
[error] assembly
[error] ^
I also tried to sbt compile as per allenai/pdffigures2#16 (comment)
./vendor/tensorbox indicated but missing from repository
Docker build fails:
Step 8/14 : ADD ./vendor/tensorbox /work/vendor/tensorbox
ADD failed: stat /var/lib/docker/tmp/docker-builder498793371/vendor/tensorbox: no such file or directory
Traceback (most recent call last):
File "manage.py", line 70, in <module>
manage()
File "/usr/local/lib/python3.4/dist-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/usr/local/lib/python3.4/dist-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python3.4/dist-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/local/lib/python3.4/dist-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python3.4/dist-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/nconnor/Repos/deepfigures-open/scripts/detectfigures.py", line 49, in detectfigures
build.build.callback()
File "/home/nconnor/Repos/deepfigures-open/scripts/build.py", line 34, in build
logger)
File "/home/nconnor/Repos/deepfigures-open/scripts/__init__.py", line 54, in execute
cmd=command)
Weights are in tar format, not gzip
https://s3-us-west-2.amazonaws.com/ai2-s2-research-public/deepfigures/weights.tar.gz
Since this is a tar file, it would be helpful to fix the file name or provide a hint to this in the README
installation problem
hello,
Thanks for the work on deepfigure_open.
I have an installation problem when i try to install it on a virtual machine
The sbt assembly state return this output
[error] /home/opencv/pdffigures2/src/main/scala/org/allenai/pdffigures2/VisualLogger.scala:173:45: value EXIT_ON_CLOSE is not a member of object javax.swing.JFrame
[error] frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE)
[error] ^
[error] one error found
[error] (Compile / compileIncremental) Compilation failed
and my system is :
Openjdk 11.0.5 2019-10-15
OpenJDK Runtime Environment (build 11.0.5+10-post-Ubuntu-0ubuntu1.118.04)
OpenJDK 64-Bit Server VM (build 11.0.5+10-post-Ubuntu-0ubuntu1.118.04, mixed mode, sharing)
Maybe you can help me to figure what's wrong .
thanks for your help
Why does pipeline.py has both pdffigure and deepfigure in it? Only one of them should be used or it should be configurable?
installation problem
hello,
Thanks for the work on deepfigure_open.
I have an installation problem when i try to install it on a virtual machine
The sbt assembly state return this output
[error] /home/opencv/pdffigures2/src/main/scala/org/allenai/pdffigures2/VisualLogger.scala:173:45: value EXIT_ON_CLOSE is not a member of object javax.swing.JFrame
[error] frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE)
[error] ^
[error] one error found
[error] (Compile / compileIncremental) Compilation failed
and my system is :
Openjdk 11.0.5 2019-10-15
OpenJDK Runtime Environment (build 11.0.5+10-post-Ubuntu-0ubuntu1.118.04)
OpenJDK 64-Bit Server VM (build 11.0.5+10-post-Ubuntu-0ubuntu1.118.04, mixed mode, sharing)
Maybe you can help me to figure what's wrong .
thanks for your help
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