bob.bio.base merge requestshttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests2018-03-01T07:08:08Zhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/125Included metadata during the feature extraction.2018-03-01T07:08:08ZTiago de Freitas PereiraIncluded metadata during the feature extraction.Hi guys,
I have a feature extractor that needs to use some meta information that is stored in `bob.bio.base.database.BioFile`.
In this MR, I added in the preprocessor.__call__ and extractor.__call__ a keyword called metadata that w...Hi guys,
I have a feature extractor that needs to use some meta information that is stored in `bob.bio.base.database.BioFile`.
In this MR, I added in the preprocessor.__call__ and extractor.__call__ a keyword called metadata that will ship an instance of `bob.bio.base.database.BioFile`.
Some design decisions, that will may generate discussion, are commented in the MR diff. Please have a look there.
Extending this to other elements in the toolchain (enrolling, scoring), could provide a solution to !111.
@mguenther, do you have some time to review this one?
Thanks in advance.Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/124Fixed the exception that is raised when score file is not found2018-01-03T08:52:07ZManuel Günthersiebenkopf@googlemail.comFixed the exception that is raised when score file is not foundTiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/123Fix debug message (closes #103)2017-12-22T18:59:55ZAndré AnjosFix debug message (closes #103)Manuel Günthersiebenkopf@googlemail.comManuel Günthersiebenkopf@googlemail.comhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/121chain loading: following not preceding config file2017-12-05T11:00:49ZAmir MOHAMMADIchain loading: following not preceding config fileTiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/120Enabled the assignment of the variable env via config files2017-12-04T15:12:30ZTiago de Freitas PereiraEnabled the assignment of the variable env via config filesThis feature is just an extension of an existent feature.
Today the only way to send environment variables to SGE via `bob.bio.base` is setting the optional argument `--environment`.
This MR allows us to set that via configuration files ...This feature is just an extension of an existent feature.
Today the only way to send environment variables to SGE via `bob.bio.base` is setting the optional argument `--environment`.
This MR allows us to set that via configuration files by adding `env=MY_VAR=VALUE`.
Before any complains, I can't come up with test case for that one.
This is injected directly in the Namespace object (argparse) AND this object is not visible when we I call verify.main().https://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/119Integrate the new bob.extension loading config mechanism2018-01-03T09:24:48ZTiago de Freitas PereiraIntegrate the new bob.extension loading config mechanismCan we have this feature integrated with bob.bio.base?
I've done some effort with this MR, but I haven't integrated with this https://gitlab.idiap.ch/bob/bob.extension/merge_requests/58Can we have this feature integrated with bob.bio.base?
I've done some effort with this MR, but I haven't integrated with this https://gitlab.idiap.ch/bob/bob.extension/merge_requests/58Amir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/118Do not use **kwargs for pretty printing in databases2017-12-04T17:06:33ZAmir MOHAMMADIDo not use **kwargs for pretty printing in databasesbob.db.base.Database is deprecated Use bob.db.base.FileDatabase insteadbob.db.base.Database is deprecated Use bob.db.base.FileDatabase insteadAmir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/117Improves verbosity for preprocessing, extraction and enrollment; Adds more…2017-11-17T16:49:45ZAndré AnjosImproves verbosity for preprocessing, extraction and enrollment; Adds more…Improves verbosity for preprocessing, extraction and enrollment; Adds more verbosity for scoring (closes #98)Improves verbosity for preprocessing, extraction and enrollment; Adds more verbosity for scoring (closes #98)Manuel Günthersiebenkopf@googlemail.comManuel Günthersiebenkopf@googlemail.comhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/116Allow for comment lines in file-lists2017-11-14T11:26:25ZAmir MOHAMMADIAllow for comment lines in file-listsAmir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/115Stacks of extractors: Fix when no extractor requires training2017-11-14T17:45:30ZAmir MOHAMMADIStacks of extractors: Fix when no extractor requires trainingManuel Günthersiebenkopf@googlemail.comManuel Günthersiebenkopf@googlemail.comhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/7'extracted' is the correct name not 'features'2016-03-09T15:40:14ZAndré Anjos'extracted' is the correct name not 'features'*Created by: 183amir*
The error I was getting while using the bob.bio.base verify.py script before
this commit. My invoke command was:
```
'bob.example.facevoice/bin/verify.py' -vv --grid 'grid' --preprocessor 'inorm-lbp-cro p' --e...*Created by: 183amir*
The error I was getting while using the bob.bio.base verify.py script before
this commit. My invoke command was:
```
'bob.example.facevoice/bin/verify.py' -vv --grid 'grid' --preprocessor 'inorm-lbp-cro p' --extractor 'grid-graph' --algorithm 'gabor-jet' -d 'mobio-male' --zt-norm --groups 'eval' --sub-directory 'baselines/gabor-graph' --sub-task 'compute-scores' --group 'eval' --score-type 'C'
```
the error:
```python
bob.bio.base@2016-03-09 14:36:22,159 -- ERROR: During the execution, an exception was raised: The given directory type 'features' is not supported.
Traceback (most recent call last):
File "/home/miniconda2/envs/bob.example.facevoice/bin/verify.py", line 6, in <module>
sys.exit(bob.bio.base.script.verify.main())
File "/home/miniconda2/envs/bob.example.facevoice/lib/python2.7/site-packages/bob.bio.base-2.0.5-py2.7.egg/bob/bio/base/script/verify.py", line 435, in main
verify(args, command_line_parameters)
File "/home/miniconda2/envs/bob.example.facevoice/lib/python2.7/site-packages/bob.bio.base-2.0.5-py2.7.egg/bob/bio/base/script/verify.py", line 382, in verify
if not execute(args):
File "/home/miniconda2/envs/bob.example.facevoice/lib/python2.7/site-packages/bob.bio.base-2.0.5-py2.7.egg/bob/bio/base/script/verify.py", line 338, in execute
write_compressed = args.write_compressed_score_files)
File "/home/miniconda2/envs/bob.example.facevoice/lib/python2.7/site-packages/bob.bio.base-2.0.5-py2.7.egg/bob/bio/base/tools/scoring.py", line 273, in compute_scores
_scores_c(algorithm, t_model_ids, group, force)
File "/home/miniconda2/envs/bob.example.facevoice/lib/python2.7/site-packages/bob.bio.base-2.0.5-py2.7.egg/bob/bio/base/tools/scoring.py", line 163, in _scores_c
probe_files = fs.get_paths(probe_objects, 'projected' if algorithm.performs_projection else 'features')
File "/home/miniconda2/envs/bob.example.facevoice/lib/python2.7/site-packages/bob.bio.base-2.0.5-py2.7.egg/bob/bio/base/tools/FileSelector.py", line 103, in get_paths
raise ValueError("The given directory type '%s' is not supported." % directory_type)
ValueError: The given directory type 'features' is not supported.
```
`jman list` output:
```
$ jman list
job-id grid-id queue status job-name submitted command line
======== ==================== ============== ============== ==================== ===========================================
1 533393 [1-32:1] all.q success (0) enr-N-eval '/home..
2 533394 [1-32:1] all.q success (0) enr-T-eval '/home..
3 533395 [1-32:1] all.q success (0) score-A-eval '/home..
4 533396 [1-32:1] all.q success (0) score-B-eval '/home..
5 533397 [1-32:1] all.q failure (1) score-C-eval '/home..
6 533398 [1-32:1] all.q failure (1) score-D-eval '/home..
7 533399 extatix08 failure (1) score-Z-eval '/home..
8 533400 extatix08 failure (1) concat-eval '/home..
```https://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/3Update requirements.txt2016-02-27T17:03:45ZAndré AnjosUpdate requirements.txt*Created by: 183amir*
This package depends on scipy but it is not listed in requirements.txt*Created by: 183amir*
This package depends on scipy but it is not listed in requirements.txthttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/114Test filelist databases when no zt files exist2017-11-10T18:40:53ZAmir MOHAMMADITest filelist databases when no zt files existAmir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/113Removed global variable results2017-11-08T16:43:15ZTiago de Freitas PereiraRemoved global variable resultsThe script `bob.bio.base.scripts.collect_results` has global variable called `results` whose role is to gather the results from several directories.
Would be cleaner and more easy to reuse this module if the results were passed throug...The script `bob.bio.base.scripts.collect_results` has global variable called `results` whose role is to gather the results from several directories.
Would be cleaner and more easy to reuse this module if the results were passed throught the recursions instead of being stored in global variable.
I've just done that.
Do you mind to review that @mguenther?
ThanksManuel Günthersiebenkopf@googlemail.comManuel Günthersiebenkopf@googlemail.comhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/30Refactoring 20162016-08-04T08:47:32ZAndré AnjosRefactoring 2016*Created by: 183amir*
*Created by: 183amir*
https://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/112SequentialExtractor: Apply extractor on training data always when apply=True2017-11-07T17:12:23ZAmir MOHAMMADISequentialExtractor: Apply extractor on training data always when apply=TrueManuel Günthersiebenkopf@googlemail.comManuel Günthersiebenkopf@googlemail.comhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/110Add configuration file for Hamming distance algorithm2017-11-03T16:23:05ZVedrana KRIVOKUCAAdd configuration file for Hamming distance algorithmHamming distance configuration file to supplement ``distance_euclidean.py`` and ``distance_cosine.py`` in ``bob.bio.base`` algorithm configs.Hamming distance configuration file to supplement ``distance_euclidean.py`` and ``distance_cosine.py`` in ``bob.bio.base`` algorithm configs.Manuel Günthersiebenkopf@googlemail.comManuel Günthersiebenkopf@googlemail.comhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/109Fix manifest file to avoid packaging warnings2017-11-03T15:56:21ZAndré AnjosFix manifest file to avoid packaging warningsA small update to `MANIFEST.in` to correct for packaging warnings. Nothing vital.
It also removes the outdated `bootstrap-buildout.py` script.A small update to `MANIFEST.in` to correct for packaging warnings. Nothing vital.
It also removes the outdated `bootstrap-buildout.py` script.Manuel Günthersiebenkopf@googlemail.comManuel Günthersiebenkopf@googlemail.comhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/108Fixed issue with --directory flag in evaluate.py2017-10-26T06:50:19ZManuel Günthersiebenkopf@googlemail.comFixed issue with --directory flag in evaluate.pyIn a93954e1, I had introduced a test for the existence of files before evaluation -- such that the crash happens at the beginning of the evaluation and not in the middle. In that, I disregarded the `--directory` flag, which made this fla...In a93954e1, I had introduced a test for the existence of files before evaluation -- such that the crash happens at the beginning of the evaluation and not in the middle. In that, I disregarded the `--directory` flag, which made this flag useless. Also, the tests for this flag were insufficient since the script was only tested with absolute paths.
This MR fixes the issue and updates the test case such that relative paths are passed to `evaluate.py`,Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/107Deleting partially concatenated score file when failing.2017-11-06T10:44:43ZManuel Günthersiebenkopf@googlemail.comDeleting partially concatenated score file when failing.When only parts of the score files per model in `nonorm/dev` (and similar for `ztnorm` and `eval`) are available, the score concatenation fails as expected. However, the partially written `nonorm/scores-dev` file still exists, which is o...When only parts of the score files per model in `nonorm/dev` (and similar for `ztnorm` and `eval`) are available, the score concatenation fails as expected. However, the partially written `nonorm/scores-dev` file still exists, which is obviously wrong since it contains only partial results.
This MR fixes this by removing the `nonorm/scores-dev` when an exception is raised during processing.André AnjosAndré Anjos