bob issueshttps://gitlab.idiap.ch/groups/bob/-/issues2021-03-26T09:48:58Zhttps://gitlab.idiap.ch/bob/bob.pad.base/-/issues/27Problem importing `evaluate.py`2021-03-26T09:48:58ZManuel Günthersiebenkopf@googlemail.comProblem importing `evaluate.py`I am not sure if this is a real bug or if I do not understand some implicitly happening things with the new way of handling the evaluation via `bob pad ...`.
As reported in https://groups.google.com/d/msg/bob-devel/5KpSh0SId34/wGa6MEwoA...I am not sure if this is a real bug or if I do not understand some implicitly happening things with the new way of handling the evaluation via `bob pad ...`.
As reported in https://groups.google.com/d/msg/bob-devel/5KpSh0SId34/wGa6MEwoAQAJ
there seems to be an issue with importing things in: https://gitlab.idiap.ch/bob/bob.pad.base/blob/f322e5d09d4844a0abf2ebb7acf24f06ea31eb68/bob/pad/base/script/evaluate.py#L8
I cannot see any of these imports being in the same directory as the `evaluate.py`, so I don't think that importing `evaluate.py` would work in any circumstance.Bob 9.0.0Yannick DAYERYannick DAYERhttps://gitlab.idiap.ch/bob/bob.extension/-/issues/66verbose not picked-up from configuration file?2020-02-14T16:15:22ZAndré Anjosverbose not picked-up from configuration file?I'm trying to get the ball rolling (dump config, use it to run program). It all works wonders, except for the `verbose` option. It is not correctly picked-up from the configuration file.
If I pass `-vv` to the program, then it starts sp...I'm trying to get the ball rolling (dump config, use it to run program). It all works wonders, except for the `verbose` option. It is not correctly picked-up from the configuration file.
If I pass `-vv` to the program, then it starts spitting out log messages, but `verbose=2` on my configuration file does not.
@theophile.gentilhomme: could you please check if you test for this?
For reference, my implementation is here:
https://gitlab.idiap.ch/bob/bob.ip.hed/blob/master/bob/ip/hed/script/hed.py
The configuration file I use is here:
https://gitlab.idiap.ch/bob/bob.ip.hed/blob/master/bob/ip/hed/configurations/bsds500.pyAmir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.learn.em/-/issues/28Add adaptive S-norm as a score normalization method2020-11-05T09:37:01ZSaeed SARFJOOAdd adaptive S-norm as a score normalization methodIn adaptive S-norm, only part of the cohort is selected to compute the mean and variance for normalization which is target specific. For more information see "Analysis of Score Normalization in Multilingual Speaker Recognition" paper fro...In adaptive S-norm, only part of the cohort is selected to compute the mean and variance for normalization which is target specific. For more information see "Analysis of Score Normalization in Multilingual Speaker Recognition" paper from the following link:
https://www.isca-speech.org/archive/Interspeech_2017/pdfs/0803.PDFSaeed SARFJOOSaeed SARFJOOhttps://gitlab.idiap.ch/bob/bob.io.base/-/issues/21HDF5File cannot read files written by keras/tensorflow2022-05-13T13:25:29ZManuel Günthersiebenkopf@googlemail.comHDF5File cannot read files written by keras/tensorflowI have just tried to train a model with keras/tensorflow, where I wanted to add some information to the HDF5 file. Unfortunately, an exception is raised when I try to open the file [model.hdf5](/uploads/699cb6d243d8f94472b09905df8f3ab0/m...I have just tried to train a model with keras/tensorflow, where I wanted to add some information to the HDF5 file. Unfortunately, an exception is raised when I try to open the file [model.hdf5](/uploads/699cb6d243d8f94472b09905df8f3ab0/model.hdf5):
```
>>> import bob.io.base
>>> h = bob.io.base.HDF5File("model.hdf5")
RuntimeError: HDF5File - hdf5 constructor: C++ exception caught: 'empty HDF5 dataset'
```
In some cases (which I cannot reproduce here), I even get a `Segmentation fault` crashing the Python console.
Note that the file is perfectly valid, you can open it with `hdfview` and `h5py`:
```
>>> import h5py
>>> h = h5py.File("model.hdf5")
>>> list(h.keys())
['model_weights', 'optimizer_weights']
```
I am not sure, what causes this issue. I haven't dug deeper into the code.https://gitlab.idiap.ch/bob/bob.extension/-/issues/65bob config fixes2019-09-18T15:03:11ZAndré Anjosbob config fixesThe current incarnation of `bob config` does not allow one to remove variables from the configuration file.
A subcommand to `unset` a variable would be welcome - the command should also allow for the file to be cleared of all variables ...The current incarnation of `bob config` does not allow one to remove variables from the configuration file.
A subcommand to `unset` a variable would be welcome - the command should also allow for the file to be cleared of all variables starting with a substring. E.g.:
```sh
$ bob config unset bob.db.atnt #removes everything concerning bob.db.atnt
```
Other than that, it would be beneficial if the documentation of this command followed the changes in #61 (i.e., documenting options and arguments via the epilog and `help` entries, followed by examples.Guillaume HEUSCHGuillaume HEUSCHhttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues/129Add protocol input argument to probe_file_sets function2018-07-23T15:57:26ZSaeed SARFJOOAdd protocol input argument to probe_file_sets functionThis is better to add `protocol` as an input argument to `probe_file_sets` function. Something like:
``` python
def probe_file_sets(self, model_id=None, group='dev', protocol=None):
"""probe_file_sets(model_id = None, group ...This is better to add `protocol` as an input argument to `probe_file_sets` function. Something like:
``` python
def probe_file_sets(self, model_id=None, group='dev', protocol=None):
"""probe_file_sets(model_id = None, group = 'dev') -> files
Returns a list of probe FileSet objects, respecting the selected or current protocol.
If a ``model_id`` is specified, only the probe files that should be compared with the given model id are returned (for most databases, these are all probe files of the given group).
Otherwise, all probe files of the given group are returned.
**Parameters:**
model_id : int or str or ``None``
A unique ID that identifies the model.
group : one of ``('dev', 'eval')``
The group to get the probe files for.
protocol : str or ``None``
The protocol to get the probe files for.
**Returns:**
files : [:py:class:`bob.bio.base.database.BioFileSet`] or something similar
The list of file sets used to probe the model with the given model id."""
protocol = protocol or self.protocol
if model_id is not None:
file_sets = self.object_sets(protocol=protocol, groups=group, model_ids=(model_id,), purposes='probe',
**self.all_files_options)
else:
file_sets = self.object_sets(protocol=protocol, groups=group, purposes='probe',
**self.all_files_options)
return self.sort(file_sets)
```https://gitlab.idiap.ch/bob/bob.bio.face/-/issues/32Job Failed #1445052018-07-19T14:45:59ZAmir MOHAMMADIJob Failed #144505Job [#144505](/bob/bob.bio.face/-/jobs/144505) failed for 22da5aff316fe0e388281ddb1b6d2678b641b0d3:Job [#144505](/bob/bob.bio.face/-/jobs/144505) failed for 22da5aff316fe0e388281ddb1b6d2678b641b0d3:Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues/128Fix the order of for_scores.lst file in bob.bio.base documentation2018-07-17T15:26:15ZSaeed SARFJOOFix the order of for_scores.lst file in bob.bio.base documentationIt seems the order of colums in `for_scores.lst` file is `filename claimed_client_id model_id client_id` not `filename model_id claimed_client_id client_id`It seems the order of colums in `for_scores.lst` file is `filename claimed_client_id model_id client_id` not `filename model_id claimed_client_id client_id`https://gitlab.idiap.ch/bob/docs/-/issues/5Fix the order of for_scores.lst file in bob.bio.base documentation2018-07-17T10:22:21ZSaeed SARFJOOFix the order of for_scores.lst file in bob.bio.base documentationIt seems the order of colums in `for_scores.lst` file is `filename claimed_client_id model_id client_id` not `filename model_id claimed_client_id client_id`It seems the order of colums in `for_scores.lst` file is `filename claimed_client_id model_id client_id` not `filename model_id claimed_client_id client_id`https://gitlab.idiap.ch/bob/bob.db.maskattack/-/issues/2Implement rc configuration for global variables2018-07-13T14:26:28ZGuillaume HEUSCHImplement rc configuration for global variableshttps://gitlab.idiap.ch/bob/bob.pad.face/merge_requests/72
https://www.idiap.ch/software/bob/docs/bob/docs/master/bob.extension/doc/rc.html
https://gitlab.idiap.ch/bob/bob.bio.base/issues/107https://gitlab.idiap.ch/bob/bob.pad.face/merge_requests/72
https://www.idiap.ch/software/bob/docs/bob/docs/master/bob.extension/doc/rc.html
https://gitlab.idiap.ch/bob/bob.bio.base/issues/107Guillaume HEUSCHGuillaume HEUSCHhttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues/127WARNING: Downloading the AT&T database2020-11-23T15:21:39ZAmir MOHAMMADIWARNING: Downloading the AT&T database```
bob.bio.base@2016-09-16 15:29:27,200 -- WARNING: Downloading the AT&T database from 'http://www.cl.cam.ac.uk/Research/DTG/attarchive/pub/data/att_faces.zip' to '/tmp/atnt_db_PLmxUp' ...
bob.bio.base@2016-09-16 15:29:27,200 -- WARNING...```
bob.bio.base@2016-09-16 15:29:27,200 -- WARNING: Downloading the AT&T database from 'http://www.cl.cam.ac.uk/Research/DTG/attarchive/pub/data/att_faces.zip' to '/tmp/atnt_db_PLmxUp' ...
bob.bio.base@2016-09-16 15:29:27,200 -- WARNING: To avoid this, please download the database manually, extract the data and set the ATNT_DATABASE_DIRECTORY environment variable to this directory.
```Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.fusion.base/-/issues/7Nightlies failing2018-07-12T06:32:27ZTiago de Freitas PereiraNightlies failingLook
https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/142954
I think this is related to the update that you made on click.Look
https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/142954
I think this is related to the update that you made on click.Amir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.extension/-/issues/64ResourceOption cannot load variables from entrypoints.2018-07-16T16:23:18ZAmir MOHAMMADIResourceOption cannot load variables from entrypoints.The problem is when you have entrypoints like:
```
'local-p4 = bob.bio.base.config.grid.local:grid',
'local-p8 = bob.bio.base.config.grid.local:grid_p8',
'local-p16 = bob.bio.base.config....The problem is when you have entrypoints like:
```
'local-p4 = bob.bio.base.config.grid.local:grid',
'local-p8 = bob.bio.base.config.grid.local:grid_p8',
'local-p16 = bob.bio.base.config.grid.local:grid_p16',
```
we usually cannot load them using the ResourceOption class when variable name is something else.
Follow-up from "Created the Baselines Concept" The following discussion from bob.bio.base!151 should be addressed:
- [ ] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.bio.base/merge_requests/151#note_29783): (+10 comments)
> Just give the entry point group name here and it will load the baseline for you. You don't need to load the baseline manually.
Amir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.pad.face/-/issues/24Retrieve colors from all channels for some of pulse-based PAD preprocessors2018-07-10T14:04:04ZGuillaume HEUSCHRetrieve colors from all channels for some of pulse-based PAD preprocessorsrelated to https://gitlab.idiap.ch/bob/bob.rppg.base/issues/15
Looks like only the green color value was returned when computing mean color values in a masked area
This affects both PPGSecure and LiPulseExtraction Preprocessorsrelated to https://gitlab.idiap.ch/bob/bob.rppg.base/issues/15
Looks like only the green color value was returned when computing mean color values in a masked area
This affects both PPGSecure and LiPulseExtraction Preprocessorshttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues/126Nightlies failing2018-07-10T11:17:38ZTiago de Freitas PereiraNightlies failinghttps://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/142724https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/142724Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/nightlies/-/issues/40Nightlies are failing2018-07-12T07:48:38ZTiago de Freitas PereiraNightlies are failingHi guys,
Nightlies are failing, more specifically when testing `bob` package, in 3 points:
- bob.measure
- bob.pad.base
- bob.rppg.base
https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/142546
The problem with `bob.rppg.base` was ea...Hi guys,
Nightlies are failing, more specifically when testing `bob` package, in 3 points:
- bob.measure
- bob.pad.base
- bob.rppg.base
https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/142546
The problem with `bob.rppg.base` was easy to spot and an MR is already opened to fix it (https://gitlab.idiap.ch/bob/bob.rppg.base/merge_requests/7).
The problem with `bob.measure` and `bob.pad.base` I couldn't reproduce it locally.
Everything was fine when I created an env with all the `betas` and run `nosetests`.
Don't know what is going on.https://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.