bob issueshttps://gitlab.idiap.ch/groups/bob/-/issues2017-10-21T16:05:52Zhttps://gitlab.idiap.ch/bob/bob.bio.video/-/issues/3Failing nightly builds2017-10-21T16:05:52ZAndré AnjosFailing nightly builds*Created by: anjos*
Possibly, after the change of `bob.ip.flandmark` to suppress the opencv dependence this package (and also bob.bio.face) require new references for their failing tests. Example:
https://gitlab.idiap.ch/biometric/bo...*Created by: anjos*
Possibly, after the change of `bob.ip.flandmark` to suppress the opencv dependence this package (and also bob.bio.face) require new references for their failing tests. Example:
https://gitlab.idiap.ch/biometric/bob.nightlies/builds/3077
Could you please fix this and push it into the nightlies? Thanks.https://gitlab.idiap.ch/bob/bob.bio.video/-/issues/2AttributeError: 'bob.learn.em.GMMStats' object has no attribute 'copy'2017-10-21T16:05:52ZAndré AnjosAttributeError: 'bob.learn.em.GMMStats' object has no attribute 'copy'*Created by: 183amir*
I am trying to run an experiment with `bob.bio.video` and a `gmm` algorithm and I am seeing this error:
```
<Job: 4 (1281753) [1-32:1] - 'project'> | q_1day : failure (1) -- 'antispoofing.experiment/bin/verify.py...*Created by: 183amir*
I am trying to run an experiment with `bob.bio.video` and a `gmm` algorithm and I am seeing this error:
```
<Job: 4 (1281753) [1-32:1] - 'project'> | q_1day : failure (1) -- 'antispoofing.experiment/bin/verify.py' -vv -d 'replay-licit' -p 'bob.bio.video.preprocessor.Wrapper(bob
.bio.face.preprocessor.TanTriggs(bob.bio.face.preprocessor.FaceCrop(cropped_image_size=(80,64),cropped_positions={"topleft":(0,0),"bottomright":(80,64)})))' -e 'bob.bio.video.extractor.Wrapper("dct-blocks")' -a
'bob.bio.video.algorithm.Wrapper("gmm")' -s 'replay-licit' --groups 'dev' 'eval' --grid 'demanding' -I 'bob.bio.base' 'bob.bio.video' 'bob.bio.face' --sub-task 'project'
Array Job 1 (helvetix10) :
bob.bio.base@2016-05-17 19:58:48,292 -- INFO: - Projection: splitting of index range (0, 10)
bob.bio.base@2016-05-17 19:58:48,293 -- INFO: - Projection: projecting 10 features from directory '/idiap_temp/amohammadi/replay/replay-licit/./extracted' to directory '/idiap_temp/amohammadi/replay/replay-licit
/./projected'
--------------------
bob.bio.base@2016-05-17 19:58:40,133 -- WARNING: Under the desired name 'demanding', there are multiple entry points defined, we return the first one: ['bob.bio.base.config.grid.demanding', 'bob.bio.spear.config
.grid.demanding']
bob.bio.base@2016-05-17 19:58:51,275 -- ERROR: During the execution, an exception was raised: 'bob.learn.em.GMMStats' object has no attribute 'copy'
Traceback (most recent call last):
File "antispoofing.experiment/bin/verify.py", line 29, in <module>
sys.exit(bob.bio.base.script.verify.main())
File "/idiap/bob-stable/py27/local/lib/python2.7/site-packages/bob/bio/base/script/verify.py", line 435, in main
verify(args, command_line_parameters)
File "/idiap/bob-stable/py27/local/lib/python2.7/site-packages/bob/bio/base/script/verify.py", line 382, in verify
if not execute(args):
File "/idiap/bob-stable/py27/local/lib/python2.7/site-packages/bob/bio/base/script/verify.py", line 287, in execute
force = args.force)
File "/idiap/bob-stable/py27/local/lib/python2.7/site-packages/bob/bio/base/tools/algorithm.py", line 116, in project
projected = algorithm.project(feature)
File "antispoofing.experiment/src/bob.bio.video/bob/bio/video/algorithm/Wrapper.py", line 127, in project
features = projected if isinstance(projected, (list,tuple)) else projected.copy()
AttributeError: 'bob.learn.em.GMMStats' object has no attribute 'copy'
```https://gitlab.idiap.ch/bob/bob.learn.libsvm/-/issues/9SVM in sequence segmenation fault2017-10-21T19:07:03ZTiago de Freitas PereiraSVM in sequence segmenation faultWhen you try to train several SVMs in sequence we have segmentation fault.
Follow a code that reproduces the issue (2 SVMs in sequence):
```
import bob.learn.libsvm
import numpy
numpy.random.seed(10)
for i in range(2):
pos = numpy....When you try to train several SVMs in sequence we have segmentation fault.
Follow a code that reproduces the issue (2 SVMs in sequence):
```
import bob.learn.libsvm
import numpy
numpy.random.seed(10)
for i in range(2):
pos = numpy.random.normal(0., 1, size=(100, 2))
neg = numpy.random.normal(1., 1, size=(100, 2))
data = [pos, neg]
trainer = bob.learn.libsvm.Trainer()
trainer.kernel_type = 'LINEAR'
trainer.cost = 1
trainer.train(data)
```
However, if you free the data variables in the end of loop for, everything runs fine
```
import bob.learn.libsvm
import numpy
numpy.random.seed(10)
for i in range(2):
pos = numpy.random.normal(0., 1, size=(100, 2))
neg = numpy.random.normal(1., 1, size=(100, 2))
data = [pos, neg]
trainer = bob.learn.libsvm.Trainer()
trainer.kernel_type = 'LINEAR'
trainer.cost = 1
trainer.train(data)
del data
del pos
del neg
```
I'm still debugging, but it seems that the issue is somewhere here in the bindings (https://gitlab.idiap.ch/bob/bob.learn.libsvm/blob/master/bob/learn/libsvm/trainer.cpp#L616)Bob 2.7.x releaseTiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.learn.libsvm/-/issues/8Segmentation fault when printing bob.learn.libsvm.Machine2017-10-21T19:07:03ZAndré AnjosSegmentation fault when printing bob.learn.libsvm.Machine*Created by: 183amir*
Here is the code that leads to the segmentation fault:
```python
import bob.io.base
import bob.learn.libsvm
fin = bob.io.base.HDF5File('scores/svm/regular/svm_machine.hdf5', 'r')
fin.cd('svm_machine')
s...*Created by: 183amir*
Here is the code that leads to the segmentation fault:
```python
import bob.io.base
import bob.learn.libsvm
fin = bob.io.base.HDF5File('scores/svm/regular/svm_machine.hdf5', 'r')
fin.cd('svm_machine')
svm_machine = bob.learn.libsvm.Machine(fin)
fin.cd('/')
fin.close()
print(svm_machine) # < -- it happens here!
```
Here is the back trace:
```
bin/gdb-python test.py
GNU gdb (Debian 7.7.1+dfsg-5) 7.7.1
Copyright (C) 2014 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from /bob-stable/py27/bin/python...(no debugging symbols found)...done.
Starting program: /bob-stable-2016-05-09/py27/bin/python test.py
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
[New Thread 0x7ffff1403700 (LWP 16549)]
[New Thread 0x7ffff0c02700 (LWP 16550)]
[New Thread 0x7fffee401700 (LWP 16551)]
[New Thread 0x7fffebc00700 (LWP 16552)]
[New Thread 0x7fffe93ff700 (LWP 16553)]
Program received signal SIGSEGV, Segmentation fault.
__memcpy_sse2_unaligned () at ../sysdeps/x86_64/multiarch/memcpy-sse2-unaligned.S:33
33 ../sysdeps/x86_64/multiarch/memcpy-sse2-unaligned.S: No such file or directory.
(gdb) bt
#0 __memcpy_sse2_unaligned () at ../sysdeps/x86_64/multiarch/memcpy-sse2-unaligned.S:33
#1 0x000000000047da9f in ?? ()
#2 0x00000000005e9b69 in PyUnicodeUCS4_FromFormat ()
#3 0x00007fffe209cf0a in PyBobLearnLibsvmMachine_Repr(PyBobLearnLibsvmMachineObject*) ()
from /bob-stable-2016-05-09/py27/local/lib/python2.7/site-packages/bob/learn/libsvm/_library.so
#4 0x000000000052ef8c in PyObject_Str ()
#5 0x000000000052db50 in ?? ()
#6 0x000000000052cd3b in PyFile_WriteObject ()
#7 0x00000000004d08a7 in PyEval_EvalFrameEx ()
#8 0x00000000004c87a1 in PyEval_EvalCodeEx ()
#9 0x00000000005030ef in ?? ()
#10 0x00000000004f8c72 in PyRun_FileExFlags ()
#11 0x00000000004f7d77 in PyRun_SimpleFileExFlags ()
#12 0x00000000004982f2 in Py_Main ()
#13 0x00007ffff6f12b45 in __libc_start_main (main=0x497d80 <main>, argc=2, argv=0x7fffffffdd88, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffdd78)
at libc-start.c:287
#14 0x0000000000497ca0 in _start ()
```https://gitlab.idiap.ch/bob/bob.learn.libsvm/-/issues/4ONE-CLASS SVM is not supported2017-10-21T19:07:03ZAndré AnjosONE-CLASS SVM is not supported*Created by: acostapazo*
It would be interesting that the package had implemented this feature. It will allow us to train svm machines using only one class data.
I am going to fork the repo in order to submit a pull-request for OC-SV...*Created by: acostapazo*
It would be interesting that the package had implemented this feature. It will allow us to train svm machines using only one class data.
I am going to fork the repo in order to submit a pull-request for OC-SVM support.
https://gitlab.idiap.ch/bob/bob.learn.libsvm/-/issues/2Number of support vectors for a SVM model2017-10-21T19:07:03ZAndré AnjosNumber of support vectors for a SVM model*Created by: tiagofrepereira2012*
Today is not possible to check the number of support vectors using the bob.learn.libsvm.Machine class.
Would be useful to have this feature.*Created by: tiagofrepereira2012*
Today is not possible to check the number of support vectors using the bob.learn.libsvm.Machine class.
Would be useful to have this feature.https://gitlab.idiap.ch/bob/bob.learn.libsvm/-/issues/1Failing (crashing) nosetests in debug mode2017-10-21T19:07:03ZAndré AnjosFailing (crashing) nosetests in debug mode*Created by: siebenkopf*
When compiled in debug mode, the following nose test:
``` sh
$ bin/nosetests bob.learn.libsvm.test_machine:test_data_loading -vs
```
will crash with a:
``` sh
[Blitz++] Precondition failure: Module /remo...*Created by: siebenkopf*
When compiled in debug mode, the following nose test:
``` sh
$ bin/nosetests bob.learn.libsvm.test_machine:test_data_loading -vs
```
will crash with a:
``` sh
[Blitz++] Precondition failure: Module /remote/idiap.svm/group.torch5spro/externals/py27-debug/usr/include/blitz/array/slicing.cc line 303
Slice is out of range for array: index=270 rank=0
Possible range for index: [0, 269]
python: /remote/idiap.svm/group.torch5spro/externals/py27-debug/usr/include/blitz/array/slicing.cc:303: void blitz::Array<P_numtype, N_rank>::slice(int&, int, blitz::Array<P_numtype, N_rank2>&, blitz::TinyVector<int, N_rank>&, int) [with int N_rank2 = 2; P_numtype = double; int N_rank = 1]: Assertion `0' failed.
Aborted
```
The issue seems to be located in https://github.com/bioidiap/bob.learn.libsvm/blob/master/bob/learn/libsvm/file.cpp#L492, where the k index is getting too high.
To reproduce the issue, checkout bob.learn.libsvm, bootstrap with the debug python version, e.g.:
``` sh
$ /idiap/group/torch5spro/externals/py27-debug/usr/bin/python bootstrap-buildout.py
```
and run the command above.
Happy debugging!https://gitlab.idiap.ch/bob/bob.db.iris/-/issues/2The requiremnets are rather much for a database2017-10-22T03:49:17ZAndré AnjosThe requiremnets are rather much for a database*Created by: 183amir*
This requirements are too much for a database:
```
setuptools
bob.io.base
bob.measure
bob.learn.linear
bob.db.base
matplotlib
```
Can we move some code/documentation somewhere else?
This database is part ...*Created by: 183amir*
This requirements are too much for a database:
```
setuptools
bob.io.base
bob.measure
bob.learn.linear
bob.db.base
matplotlib
```
Can we move some code/documentation somewhere else?
This database is part of bob core packages.Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.db.voxforge/-/issues/9Error by running ./bin/verify.py with voxforge2017-10-22T18:34:52ZMilos CERNAKError by running ./bin/verify.py with voxforgeHi,
I run a ./bin/verify.py with voxforge:
```
./bin/verify.py -g 'demanding' -d 'voxforge' -p 'energy-2gauss' -e 'mfcc-60' --algorithm 'gmm' -s $exp --groups {dev,eval} -R '/idiap/user/mcernak/Projects/bob_dev2/' -T $tempdir -vvv
```
A...Hi,
I run a ./bin/verify.py with voxforge:
```
./bin/verify.py -g 'demanding' -d 'voxforge' -p 'energy-2gauss' -e 'mfcc-60' --algorithm 'gmm' -s $exp --groups {dev,eval} -R '/idiap/user/mcernak/Projects/bob_dev2/' -T $tempdir -vvv
```
And I got this error:
```
bob.bio.base@2017-05-16 23:08:14,932 -- ERROR: During the execution, an exception was raised: 'module' object has no attribute 'FileListBioDatabase'
Traceback (most recent call last):
File "./bin/verify.py", line 66, in <module>
sys.exit(bob.bio.base.script.verify.main())
File "/remote/idiap.svm/user.active/mcernak/Projects/bob_dev2/src/bob.bio.base/bob/bio/base/script/verify.py", line 451, in main
args = parse_arguments(command_line_parameters)
File "/remote/idiap.svm/user.active/mcernak/Projects/bob_dev2/src/bob.bio.base/bob/bio/base/script/verify.py", line 34, in parse_arguments
skips = ['preprocessing', 'extractor-training', 'extraction', 'projector-training', 'projection', 'enroller-training', 'enrollment', 'score-computation', 'concatenation', 'calibration'])
File "/remote/idiap.svm/user.active/mcernak/Projects/bob_dev2/src/bob.bio.base/bob/bio/base/tools/command_line.py", line 226, in initialize
parser.get_default(keyword))
File "/remote/idiap.svm/user.active/mcernak/Projects/bob_dev2/src/bob.bio.base/bob/bio/base/tools/command_line.py", line 160, in _take_from_config_or_command_line
setattr(args, keyword, utils.load_resource(' '.join(getattr(args, keyword)), keyword, imports = args.imports, preferred_package = args.preferred_package))
File "/remote/idiap.svm/user.active/mcernak/Projects/bob_dev2/src/bob.bio.base/bob/bio/base/utils/resources.py", line 201, in load_resource
return entry_points[index].load()
File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2291, in load
File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2297, in resolve
File "/remote/idiap.svm/user.active/mcernak/Projects/bob_dev2/src/bob.db.voxforge/bob/db/voxforge/__init__.py", line 25, in <module>
from .query import Database
File "/remote/idiap.svm/user.active/mcernak/Projects/bob_dev2/src/bob.db.voxforge/bob/db/voxforge/query.py", line 24, in <module>
class Database(bob.bio.base.database.FileListBioDatabase):
AttributeError: 'module' object has no attribute 'FileListBioDatabase'
```
@akomaty do you know what this could mean?
Miloshttps://gitlab.idiap.ch/bob/bob.db.voxforge/-/issues/8buildout.cfg is not up to date2017-10-22T18:34:52ZAlain KOMATYbuildout.cfg is not up to datebuildout.cfg file is missing the line:
```
dependent-scripts = true
```buildout.cfg file is missing the line:
```
dependent-scripts = true
```Alain KOMATYAlain KOMATYhttps://gitlab.idiap.ch/bob/bob.db.voxforge/-/issues/7Nightly/Stable builds are broken because of this package2017-10-22T18:34:52ZAndré AnjosNightly/Stable builds are broken because of this packageIt's been too long since the last release and now the documentation of the stable package does not seem to be conforming to our build constraints:
Example: https://gitlab.idiap.ch/bob/bob.nightlies/builds/47425
It is probably suffi...It's been too long since the last release and now the documentation of the stable package does not seem to be conforming to our build constraints:
Example: https://gitlab.idiap.ch/bob/bob.nightlies/builds/47425
It is probably sufficient to just release a new version of this package to PyPI since the nightlies/unstable are passing, meaning all necessary mods are already applied to the HEAD of the master branch.
@pkorshunov: are you the responsible for this package? Could you just release a new version when possible to unblock the situation? Otherwise, please re-assign to the responsible party. Thanks in advance.Pavel KORSHUNOVPavel KORSHUNOVhttps://gitlab.idiap.ch/bob/bob.db.voxforge/-/issues/5Database still depends on bob.bio.base2017-10-22T18:34:52ZAndré AnjosDatabase still depends on bob.bio.baseThis database still depends on bob.bio.base, which means it has not been ported to the new scheme of things.
Until it is the case, it has been removed from the nightlies.
Does it interest any of you? @akomaty, @amohammadi, @pkorshunov....This database still depends on bob.bio.base, which means it has not been ported to the new scheme of things.
Until it is the case, it has been removed from the nightlies.
Does it interest any of you? @akomaty, @amohammadi, @pkorshunov. Otherwise, we should archive it.https://gitlab.idiap.ch/bob/bob.db.voxforge/-/issues/4Aborting and resuming the download script2017-10-22T18:34:52ZAndré AnjosAborting and resuming the download script*Created by: 1kastner*
The download and untar script checks whether a directory already exists and in that case it skips it. So generally speaking the script is capable of being aborted and resumed at a later point. Only one problem exi...*Created by: 1kastner*
The download and untar script checks whether a directory already exists and in that case it skips it. So generally speaking the script is capable of being aborted and resumed at a later point. Only one problem exists: if you start to download the same file the second time, wget adds ".[number]" at the end of the file, so "file.tgz.1" for the second attempt and so on. That means, the script in its current implementation processes the first download attempt and hence the broken file.
One fix which is customized for my personal needs can be found at https://gist.github.com/1kastner/46a6e8510c47901cb55d - I am not that well in shell scripting. It should take the file name "name.tgz.[HIGHEST_NUMBER]" instead of the first download attempt.
I hope I could make my point clear.https://gitlab.idiap.ch/bob/bob.db.voxforge/-/issues/3script/download_and_untar.sh incompatible with zc.buildout installation2017-10-22T18:34:52ZAndré Anjosscript/download_and_untar.sh incompatible with zc.buildout installation*Created by: 1kastner*
Like this the shell script does not work in case you used zc.buildout. Even the shell script is not shipped. I could use it and modified it for my purpose like this:
https://gist.github.com/1kastner/587ec3b395be7...*Created by: 1kastner*
Like this the shell script does not work in case you used zc.buildout. Even the shell script is not shipped. I could use it and modified it for my purpose like this:
https://gist.github.com/1kastner/587ec3b395be715c3461
If it could be shipped in the normal bob buildout process and further adjusted for that, that could be great!https://gitlab.idiap.ch/bob/bob.db.voxforge/-/issues/2VoxForge data are expected in a subdirectory 'audio'2017-10-22T18:34:52ZAndré AnjosVoxForge data are expected in a subdirectory 'audio'*Created by: laurentes*
The original VoxForge data are currently expected in a subdirectory 'audio/'. This is not required and it would even be better not to have this. We just need to update the lists to fix this issue.*Created by: laurentes*
The original VoxForge data are currently expected in a subdirectory 'audio/'. This is not required and it would even be better not to have this. We just need to update the lists to fix this issue.https://gitlab.idiap.ch/bob/bob.db.voxforge/-/issues/1Use python script to download the data instead of ./download_and_untar.sh2017-10-22T18:34:52ZAndré AnjosUse python script to download the data instead of ./download_and_untar.sh*Created by: khoury*
It would be better to write a python script to download the data and untar.
This will make it compatible to Windows users.*Created by: khoury*
It would be better to write a python script to download the data and untar.
This will make it compatible to Windows users.https://gitlab.idiap.ch/bob/bob.db.utfvp/-/issues/1WARNINGS2017-10-22T20:32:04ZTiago de Freitas PereiraWARNINGSI created this branch to do some updates
https://gitlab.idiap.ch/bob/bob.db.utfvp/commits/fixing-warnings
, but I have a lot of warnings
https://gitlab.idiap.ch/bob/bob.db.utfvp/builds/18427
Could you please help me?
I still h...I created this branch to do some updates
https://gitlab.idiap.ch/bob/bob.db.utfvp/commits/fixing-warnings
, but I have a lot of warnings
https://gitlab.idiap.ch/bob/bob.db.utfvp/builds/18427
Could you please help me?
I still have a lot of packages to do
Thanks
Refactoring 2016 and gitlab migration milestoneAndré AnjosAndré Anjoshttps://gitlab.idiap.ch/bob/bob.learn.linear/-/issues/9unchecked functions from `bob::math` are used2017-10-22T20:35:41ZManuel Günthersiebenkopf@googlemail.comunchecked functions from `bob::math` are usedsee bob/bob.math!13see bob/bob.math!13Manuel Günthersiebenkopf@googlemail.comManuel Günthersiebenkopf@googlemail.comhttps://gitlab.idiap.ch/bob/bob.learn.linear/-/issues/8please drop the dependency of bob.io.matlab2017-10-22T20:35:41ZAmir MOHAMMADIplease drop the dependency of bob.io.matlabalso please remove it form here when you do: https://gitlab.idiap.ch/bob/bob.conda/blob/master/recipes/bob.learn.linear/meta.yaml#L27also please remove it form here when you do: https://gitlab.idiap.ch/bob/bob.conda/blob/master/recipes/bob.learn.linear/meta.yaml#L27Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.learn.linear/-/issues/7Implement an automatic way to compute the number of subspaces2017-10-22T20:35:42ZTiago de Freitas PereiraImplement an automatic way to compute the number of subspacesIn `Gong, Boqing, et al. "Geodesic flow kernel for unsupervised domain adaptation." Computer Vision and Pattern Recognition (CVPR), 2012 IEEE Conference on. IEEE, 2012.` Section 3.4 describes a way to compute the optimum value for the n...In `Gong, Boqing, et al. "Geodesic flow kernel for unsupervised domain adaptation." Computer Vision and Pattern Recognition (CVPR), 2012 IEEE Conference on. IEEE, 2012.` Section 3.4 describes a way to compute the optimum value for the number of subspaces (called Subspace disagreement measure).
Would be nice to have that.Tiago de Freitas PereiraTiago de Freitas Pereira