bob issueshttps://gitlab.idiap.ch/groups/bob/-/issues2018-10-14T08:56:41Zhttps://gitlab.idiap.ch/bob/bob.extension/-/issues/63Activating auto-complete in bash for `bob`2018-10-14T08:56:41ZAndré AnjosActivating auto-complete in bash for `bob`It would be very cool if we could activate the automated bash-completion available in click (http://click.pocoo.org/5/bashcomplete/) when a conda environment containing `bob.extension` is installed.
The recipe is simple.
@amohammadi: d...It would be very cool if we could activate the automated bash-completion available in click (http://click.pocoo.org/5/bashcomplete/) when a conda environment containing `bob.extension` is installed.
The recipe is simple.
@amohammadi: do you think we could hook this into the recipe?André AnjosAndré Anjoshttps://gitlab.idiap.ch/bob/bob.extension/-/issues/62Moving `bob_dependency_graph.py` to `bob` driver2020-02-14T16:15:22ZAndré AnjosMoving `bob_dependency_graph.py` to `bob` driverThis script still seems to work, though I'm unsure of its usefulness nowadays.
Is anybody still using it? @mguenther?
If so, it would be nice to move it to the new command-line interface.This script still seems to work, though I'm unsure of its usefulness nowadays.
Is anybody still using it? @mguenther?
If so, it would be nice to move it to the new command-line interface.Amir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/18Nightlies failing because of this one..2018-07-08T07:19:20ZTiago de Freitas PereiraNightlies failing because of this one..check it out here.
https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/142510check it out here.
https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/142510https://gitlab.idiap.ch/bob/bob.bio.base/-/issues/125vstack_features is not optimized2020-02-27T09:22:42ZSaeed SARFJOOvstack_features is not optimizedI checked the time for loading data via `vstack_features` and directly from `bob.io.base.HDF5File`. Direct loading was 19.3 times faster than `vstack_features`. The code for testing is shown below:
``` python
import functools
import nump...I checked the time for loading data via `vstack_features` and directly from `bob.io.base.HDF5File`. Direct loading was 19.3 times faster than `vstack_features`. The code for testing is shown below:
``` python
import functools
import numpy as np
import time
import bob.bio.gmm.script.verify_ivector
import bob.bio.base
from bob.bio.gmm import tools, algorithm
from bob.bio.base import tools as base_tools
from bob.bio.gmm.script.verify_ivector import parse_arguments, execute
from bob.bio.gmm.tools.utils import read_feature
from bob.bio.base.utils.io import vstack_features
from bob.bio.base.tools.FileSelector import FileSelector
command_line_parameters = None
args = parse_arguments(command_line_parameters)
fs = FileSelector.instance()
limit_files = 100
reader = functools.partial(read_feature, args.extractor)
training_list = fs.training_list('extracted', 'train_projector')
training_list = training_list[:limit_files]
t1 = time.time()
data = vstack_features(reader, training_list, allow_missing_files=True)
t2 = time.time()
print('vstack time: ' + str(t2-t1))
t3 = time.time()
data2 = []
for i in range(len(training_list)):
f = bob.io.base.HDF5File(training_list[i])
data2.append(f.read('array'))
data2 = np.array(data2)
t4 = time.time()
print('direct time: ' + str(t4-t3))
```
and the output is:
```
vstack time: 5.793696880340576
direct time: 0.30901122093200684
```
Even for caching I tested them separately and the result was the same.https://gitlab.idiap.ch/bob/bob.learn.mlp/-/issues/10conda build is not using bob-devel2018-07-06T12:59:43ZTiago de Freitas Pereiraconda build is not using bob-develSame as in bob.measure#55
https://gitlab.idiap.ch/bob/bob.learn.mlp/-/jobs/142252
ping @andre.anjos @amohammadiSame as in bob.measure#55
https://gitlab.idiap.ch/bob/bob.learn.mlp/-/jobs/142252
ping @andre.anjos @amohammadihttps://gitlab.idiap.ch/bob/bob.learn.linear/-/issues/10conda build is not using bob-devel2018-07-06T12:56:53ZTiago de Freitas Pereiraconda build is not using bob-develSome as in bob.measure#55
https://gitlab.idiap.ch/bob/bob.learn.linear/-/jobs/142247
ping @andre.anjos @amohammadiSome as in bob.measure#55
https://gitlab.idiap.ch/bob/bob.learn.linear/-/jobs/142247
ping @andre.anjos @amohammadihttps://gitlab.idiap.ch/bob/bob.ip.base/-/issues/13conda build is not using bob-devel2018-07-06T12:55:09ZTiago de Freitas Pereiraconda build is not using bob-develSame issue as in bob.measure#55
https://gitlab.idiap.ch/bob/bob.ip.base/-/jobs/142232
I need help. Probably the solution is simple
ping @amohammadi @andre.anjos
thanksSame issue as in bob.measure#55
https://gitlab.idiap.ch/bob/bob.ip.base/-/jobs/142232
I need help. Probably the solution is simple
ping @amohammadi @andre.anjos
thankshttps://gitlab.idiap.ch/bob/bob.measure/-/issues/55conda build is not using bob-devel2018-07-06T12:53:09ZTiago de Freitas Pereiraconda build is not using bob-develCan I have the eyes of someone on this, please?
https://gitlab.idiap.ch/bob/bob.measure/-/jobs/142196
There's an issue with `bob.measure` when it tries to link against `openblas`.
Looking at the log you can see that, for some reason, ...Can I have the eyes of someone on this, please?
https://gitlab.idiap.ch/bob/bob.measure/-/jobs/142196
There's an issue with `bob.measure` when it tries to link against `openblas`.
Looking at the log you can see that, for some reason, `bob-devel` (which pins openblas) is not being installed during the conda build and conda-build downloads `blas mkl. Hence, we can't link it.
ThanksAmir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.pad.face/-/issues/23Follow-up from "WIP: rPPG as features for PAD"2018-07-06T08:57:29ZAmir MOHAMMADIFollow-up from "WIP: rPPG as features for PAD"The following discussions from !53 should be addressed:
- [x] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pad.face/merge_requests/53#note_32312):
> pls clean up the code here and change prints to logger.debu...The following discussions from !53 should be addressed:
- [x] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pad.face/merge_requests/53#note_32312):
> pls clean up the code here and change prints to logger.debug information.
- [x] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pad.face/merge_requests/53#note_32313):
> There is no code under these comments.
- [x] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pad.face/merge_requests/53#note_32314):
> same here.
- [x] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pad.face/merge_requests/53#note_32315):
> pls remove these comments
- [x] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pad.face/merge_requests/53#note_32316):
> pls pass kwargs to the init method here.
- [x] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pad.face/merge_requests/53#note_32317):
> pls pass kwargs to the init method here.
- [x] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pad.face/merge_requests/53#note_32318): (+1 comment)
> You need to put these classes in the appropriate method below
- [x] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pad.face/merge_requests/53#note_32319):
> Why did you add this file? I think this was moved by @onikisins before.
- [x] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pad.face/merge_requests/53#note_32320):
> Li is not a very descriptive name
- [x] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pad.face/merge_requests/53#note_32321):
> I thought we are going to depend on bob.rppg.base only, no?
- [x] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pad.face/merge_requests/53#note_32322):
> same here not appropiated
- [x] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pad.face/merge_requests/53#note_32323):
> I don't see this script being added in this MR. Why are you adding an entry point here?Guillaume HEUSCHGuillaume HEUSCHhttps://gitlab.idiap.ch/bob/bob.db.maskattack/-/issues/1bob.db.maskattack release2018-07-13T13:43:59ZGuillaume HEUSCHbob.db.maskattack release@amohammadi @andre.anjos @tiago.pereira
Dear Bob Masters,
I revived the old xbob.db.maskattack project (https://gitlab.idiap.ch/bob/xbob.db.maskattack), and it looks like the new version is fine (according to the CI at least). So, I w...@amohammadi @andre.anjos @tiago.pereira
Dear Bob Masters,
I revived the old xbob.db.maskattack project (https://gitlab.idiap.ch/bob/xbob.db.maskattack), and it looks like the new version is fine (according to the CI at least). So, I would like to release it - I'll need that for the package of my chapter in hobpad2.
However, and due to my lack of confidence with these matters, it would be nice if one of you could take a little time to review what I did, point me to potential issues and stuff to correct - and eventually give me a green light to proceed with the release.
Thankshttps://gitlab.idiap.ch/bob/bob.pad.face/-/issues/22docstring harmonization2018-07-02T13:36:26ZGuillaume HEUSCHdocstring harmonizationHi (@onikisins @amohammadi @ageorge),
More a question than an issue actually. I'm currently working on the rppg branch of this package and I followed the latest "standard" we agreed upon for docstrings (i.e. numpy style https://sphinxco...Hi (@onikisins @amohammadi @ageorge),
More a question than an issue actually. I'm currently working on the rppg branch of this package and I followed the latest "standard" we agreed upon for docstrings (i.e. numpy style https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html).
Problem is that most of (if not all) existing code's docstrings does not follow this format. As a consequence, it looks like my numpystyle docstrings are not parsed properly by sphinx.
So my question is: should we stick to the original docstring format for the package, or should we move everything to numpystyle docstrings ?
Thanks !https://gitlab.idiap.ch/bob/nightlies/-/issues/39It's green :-)2018-06-30T10:17:13ZTiago de Freitas PereiraIt's green :-)Yes,
https://gitlab.idiap.ch/bob/bob.nightlies/pipelines/21482
Thanks :-)Yes,
https://gitlab.idiap.ch/bob/bob.nightlies/pipelines/21482
Thanks :-)https://gitlab.idiap.ch/bob/bob.extension/-/issues/61Creating configuration files from scratch2018-07-23T20:40:44ZAndré AnjosCreating configuration files from scratchIt would be awesome if commands that are `@click.command(cls=bob.extension.scripts.click_helper.ConfigCommand)` add an option by default that allows the user to create a new configuration file (python-file) in which the configuration opt...It would be awesome if commands that are `@click.command(cls=bob.extension.scripts.click_helper.ConfigCommand)` add an option by default that allows the user to create a new configuration file (python-file) in which the configuration options, their defaults and documentation is pasted on. Here is an example:
```python
@hed.command(cls=ConfigCommand)
@click.option(
'--output-path',
'-o',
required=True,
default=/my/path/file.txt,
help="Path leading to the local destination of the file to be downloaded",
cls=ResourceOption)
@verbosity_option(cls=ResourceOption)
def download(output_path):
pass
```
Then, using `--dump-config defaults.py` with the command above, the user would get on `defaults.py`:
```python
#!/usr/bin/env python
# This configuration file was generated automatically from
# `bob foo download --dump-config` on <date>
# Path leading to the local destination of the file to be downloaded
# Option: -o, --output-path
output_path = "/my/path/file.txt"
# Increase verbosity leval from 0 (only error messages)...
# Option: -v, --verbose
verbose = 3
```
Running this file through the command should produce the same results as running the command-line w/o any options or arguments. Options that are required should be set to ``None``.Theophile GENTILHOMMETheophile GENTILHOMMEhttps://gitlab.idiap.ch/bob/bob.extension/-/issues/60bob.extension.download should check and be more explicit2020-12-04T22:57:58ZAndré Anjosbob.extension.download should check and be more explicitThis is a set of useful extensions, but:
1. It would be good that the documentation of these functions explicitly state what they are doing: (a) checking the if the directory leading to the destination file exists, otherwise creates it;...This is a set of useful extensions, but:
1. It would be good that the documentation of these functions explicitly state what they are doing: (a) checking the if the directory leading to the destination file exists, otherwise creates it; (b) checks if the file is there - and if so, does **not** redownload the file.
2. There should be an option to pass an sha256 or md5 checksum to check if the downloaded file is not corrupted. Only if that matches, the file is not re-downloaded
3. There should be an option to "force" re-download no matter what
4. The documentation should also say that the function outputs logs in the info channel.Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.measure/-/issues/54Documentation issues2018-07-17T09:11:36ZAndré AnjosDocumentation issuesCurrently, we're using FRR/FAR as information about FNR/FPR, which are the ML de-facto standards.
It would be good to scan the documentation of this package as well as function/class docs and change occurrences of FRR to FNR and FAR to ...Currently, we're using FRR/FAR as information about FNR/FPR, which are the ML de-facto standards.
It would be good to scan the documentation of this package as well as function/class docs and change occurrences of FRR to FNR and FAR to FPR.Theophile GENTILHOMMETheophile GENTILHOMMEhttps://gitlab.idiap.ch/bob/bob.measure/-/issues/53Logging of score filenames2018-07-09T13:14:44ZAmir MOHAMMADILogging of score filenamesCurrently when you use bash expansion, it is not possible to know if the correct score file goes into the correct place.
For example, with a complicated bash expansion like:
```
bin/bob pad multi -e -pn 10 /idiap/user/amohammadi/swan/swa...Currently when you use bash expansion, it is not possible to know if the correct score file goes into the correct place.
For example, with a complicated bash expansion like:
```
bin/bob pad multi -e -pn 10 /idiap/user/amohammadi/swan/swan_{frame-diff-svm,lbp-svm-160,lbp-svm-64,qm-svm-160,qm-svm-64}/PA.F.1-{0,1,2,3,4,5,6,7,8,9}/scores/scores-{dev,eval} --legends frame-diff-svm,lbp-svm-160,lbp-svm-64,qm-svm-160,qm-svm-64
```
It can become complicated to know which files went where.
The best thing is log these score filenames using the logging module.Theophile GENTILHOMMETheophile GENTILHOMMEhttps://gitlab.idiap.ch/bob/bob.measure/-/issues/52Provide an option to change the precision of floating points when they are pr...2019-01-16T14:45:19ZAmir MOHAMMADIProvide an option to change the precision of floating points when they are printedCurrently floats are rounded to 1 floating point and printed.
It would be best to make this an option on the command lineCurrently floats are rounded to 1 floating point and printed.
It would be best to make this an option on the command lineTheophile GENTILHOMMETheophile GENTILHOMMEhttps://gitlab.idiap.ch/bob/bob.pad.base/-/issues/26Several issues with vuln commands2021-05-26T11:53:07ZAmir MOHAMMADISeveral issues with vuln commands* [ ] vuln must be renamed to vulnerability
* [ ] `bin/bob vuln epsc vuln_scores/{licit,spoof}/scores-{dev,eval}` 's output is just a flat line.
* [ ] `vuln hist` examples are outdated.
* [ ] As requested in bob.measure#38, how can I...* [ ] vuln must be renamed to vulnerability
* [ ] `bin/bob vuln epsc vuln_scores/{licit,spoof}/scores-{dev,eval}` 's output is just a flat line.
* [ ] `vuln hist` examples are outdated.
* [ ] As requested in bob.measure#38, how can I produce the following figures: [EPSC_IAPMR_w-cnn-motion-fusion.pdf](/uploads/d9a883e82a19230704fe8db5926487fc/EPSC_IAPMR_w-cnn-motion-fusion.pdf) [EPSC_HTER_w-cnn-motion-fusion.pdf](/uploads/6c8740aecc1d34aed99e7cf17fa77e2b/EPSC_HTER_w-cnn-motion-fusion.pdf)
* [ ] I don't think it's possible with `bob vuln epsc` command to get fig6 or fig9 of this paper: https://publidiap.idiap.ch/downloads//papers/2014/Chingovska_IEEETIFS_2014.pdfAmir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.pad.base/-/issues/25The option `--preferred-package` does not change the loading behavior of `spo...2020-12-07T18:15:34ZAndré AnjosThe option `--preferred-package` does not change the loading behavior of `spoof.py`I have two resources with the same name:
```sh
./bin/resources.py --types=config | grep verafinger
+ verafinger --> bob.bio.vein.configurations.verafinger
+ verafinger --> bob.pad.vein.configurations.verafinger
`...I have two resources with the same name:
```sh
./bin/resources.py --types=config | grep verafinger
+ verafinger --> bob.bio.vein.configurations.verafinger
+ verafinger --> bob.pad.vein.configurations.verafinger
```
When executing `spoof.py`, I want to use the second one, not the first.
For some reason, if I pass the `--preferred-package=bob.pad.vein` option to `spoof.py`, then it still doesn't respect the preference and continues to load the first configuration resource instead of the second.Pavel KORSHUNOVPavel KORSHUNOVhttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues/123Define the 4 or 5 column score format as the standard format for bob.measure ...2018-06-27T08:13:40ZAmir MOHAMMADIDefine the 4 or 5 column score format as the standard format for bob.measure and document it.Related to bob.measure#25 and bob.measure#37, I think it might be a good idea to define the 4 or 5 column score format as the standard format for bob.measure and document it as opposed to moving it to bob.bio.base. This would allow us to...Related to bob.measure#25 and bob.measure#37, I think it might be a good idea to define the 4 or 5 column score format as the standard format for bob.measure and document it as opposed to moving it to bob.bio.base. This would allow us to have generic evaluation scripts implemented in bob.measure for any machine learning experiment. The score format could be as simple as:
```
claimed_id real_id test_label score
claimed_id model_label real_id test_label score
```
* If `claimed_id` and `real_id` columns are equal, then it's a positive score. Otherwise, it's a negative score.
* The text in columns **should not** contain spaces!
* No need to explain what `claimed_id`, `real_id`, and `model_label` are! We can just mention they are related to biometrics.
* As long as anyone comes up with the scores format above (preferably 4 column format), they can use the scripts in bob.measure.