bob.bio.vein issueshttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues2023-02-13T13:04:35Zhttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/28Switch to new CI/CD configuration2023-02-13T13:04:35ZYannick DAYERSwitch to new CI/CD configurationWe need to adapt this package to the new CI/CD and package format using citools:
- [x] Modify `pyproject.toml`:
- [x] Add information from `setup.py`,
- [x] Add version from `version.txt`,
- [x] Add requirements from `requir...We need to adapt this package to the new CI/CD and package format using citools:
- [x] Modify `pyproject.toml`:
- [x] Add information from `setup.py`,
- [x] Add version from `version.txt`,
- [x] Add requirements from `requirements.txt` and `conda/meta.yaml`,
- [x] Empty `setup.py`:
- Leave the call to `setup()` for compatibility,
- [x] Remove `version.txt`,
- [x] Remove `requirements.txt`,
- [x] Modify `conda/meta.yaml`,
- [x] Import data from `pyproject.toml` (`name`, `version`, ...),
- [x] Add the `source.path` field with value `..`,
- [x] Add the `build.noarch` field with value `python`,
- [x] Edit the `build.script` to only contain `"{{ PYTHON }} -m pip install {{ SRC_DIR }} -vv"`,
- [x] Remove test and documentation commands and comments,
- [x] Modify `.gitlab-ci.yml` to point to citools' `python.yml`,
- Use the fields format instead of the URL,
- [x] Move files to follow the `src` layout:
- [x] the whole `bob` folder to `src/bob/`,
- [x] all the tests in `tests/`,
- [x] the test data files in `tests/data`,
- [x] Edit the tests to load the data correctly, either with `os.path.join(os.path.basename(__file__), "data/xxx.txt")` or `pkg_resources.resource_filename(__name__, "data/xxx.txt")`,
- [x] Activate the `packages` option in `settings -> general -> visibility` in the Gitlab project,
- [x] Edit the latest doc badges to point to the `sphinx` directory in `doc/[...]/master`:
- [x] in README.md,
- [x] in the GitLab project settings,
- [x] Edit the coverage badges to point to the doc's coverage directory:
- [x] in README.md,
- [x] in the GitLab project settings,
- [x] Ensure the CI pipeline passes.
You can look at [bob.learn.em](https://gitlab.idiap.ch/bob/bob.learn.em) for an example of a ported package.Roadmap to the major version of Bob 12https://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/27`all_samples` in `full` protocol of utfvp dataset2022-08-10T08:28:12ZHatef OTROSHI`all_samples` in `full` protocol of utfvp datasetHi,
It seems that `all_samples` in `full` protocol of the utfvp dataset has a problem and raises an issue.
Here is a sample code:
```
from bob.bio.vein.database.utfvp import UtfvpDatabase
database = UtfvpDatabase(protocol="full")
datab...Hi,
It seems that `all_samples` in `full` protocol of the utfvp dataset has a problem and raises an issue.
Here is a sample code:
```
from bob.bio.vein.database.utfvp import UtfvpDatabase
database = UtfvpDatabase(protocol="full")
database.all_samples()
```
and here is the error:
```
packages/bob/bio/base/database/csv_dataset.py", line 494, in all_samples
samples = samples + self.background_model_samples()
File "..../lib/python3.9/site-packages/bob/bio/base/database/csv_dataset.py", line 381, in background_model_samples
self.csv_to_sample_loader.transform(self.train_csv)
File "..../lib/python3.9/site-packages/sklearn/pipeline.py", line 635, in transform
Xt = transform.transform(Xt)
File "..../lib/python3.9/site-packages/bob/pipelines/sample_loaders.py", line 84, in transform
X.seek(0)
AttributeError: 'NoneType' object has no attribute 'seek'
```https://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/26Fails on MacOS Arm with AttributeError: module 'numpy' has no attribute 'floa...2022-03-03T14:22:23ZAmir MOHAMMADIFails on MacOS Arm with AttributeError: module 'numpy' has no attribute 'float128'Job [#256859](https://gitlab.idiap.ch/bob/bob.bio.vein/-/jobs/256859) failed for 34ddbc6fb35136fcd3cdf7ad6b87296c023b2c64:
```
======================================================================
ERROR: bob.bio.vein.tests.test.test_mas...Job [#256859](https://gitlab.idiap.ch/bob/bob.bio.vein/-/jobs/256859) failed for 34ddbc6fb35136fcd3cdf7ad6b87296c023b2c64:
```
======================================================================
ERROR: bob.bio.vein.tests.test.test_mask_to_image
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/gitlab/builds/sAZPGTqW/0/bob/bob.bio.vein/miniconda/conda-bld/bob.bio.vein_1644593419589//lib/python3.9/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Users/gitlab/builds/sAZPGTqW/0/bob/bob.bio.vein/miniconda/conda-bld/bob.bio.vein_1644593419589//lib/python3.9/site-packages/bob/bio/vein/tests/test.py", line 474, in test_mask_to_image
_check_float(32)
File "/Users/gitlab/builds/sAZPGTqW/0/bob/bob.bio.vein/miniconda/conda-bld/bob.bio.vein_1644593419589//lib/python3.9/site-packages/bob/bio/vein/tests/test.py", line 470, in _check_float
conv = preprocessor_utils.mask_to_image(sample, 'float%d' % n)
File "/Users/gitlab/builds/sAZPGTqW/0/bob/bob.bio.vein/miniconda/conda-bld/bob.bio.vein_1644593419589//lib/python3.9/site-packages/bob/bio/vein/preprocessor/utils.py", line 158, in mask_to_image
elif dtype in (numpy.float32, numpy.float64, numpy.float128):
File "/Users/gitlab/builds/sAZPGTqW/0/bob/bob.bio.vein/miniconda/conda-bld/bob.bio.vein_1644593419589//lib/python3.9/site-packages/numpy/__init__.py", line 313, in __getattr__
raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'float128'
```https://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/25Nightlies failing because of this2021-10-29T15:34:57ZTiago de Freitas PereiraNightlies failing because of thishttps://gitlab.idiap.ch/bob/nightlies/-/jobs/235895
It seems a simple sphinx issue.
Anyone willing to look at it?https://gitlab.idiap.ch/bob/nightlies/-/jobs/235895
It seems a simple sphinx issue.
Anyone willing to look at it?Amir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/24MaximumCurvature Config file2020-12-03T08:36:47ZHatef OTROSHIMaximumCurvature Config fileI was looking at the MaximumCurvature config file and I noticed that at
[#L41](https://gitlab.idiap.ch/bob/bob.bio.vein/-/blob/master/bob/bio/vein/config/maximum_curvature.py#L41) the subdirectory is defined `rlt`. I think it should be...I was looking at the MaximumCurvature config file and I noticed that at
[#L41](https://gitlab.idiap.ch/bob/bob.bio.vein/-/blob/master/bob/bio/vein/config/maximum_curvature.py#L41) the subdirectory is defined `rlt`. I think it should be `mc`, because it is for Maximum Curvature (MC) method.https://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/23Drop dependency on bob.io.matlab2020-11-03T08:31:33ZAmir MOHAMMADIDrop dependency on bob.io.matlabLooks like bob.io.matlab is listed here but not used:
```
bob.bio.vein/requirements.txt
12:bob.io.matlab
bob.bio.vein/bob/bio/vein/tests/test.py
22:import bob.io.matlab
bob.bio.vein/develop.cfg
22: src/bob.io.matlab
52:bob.io....Looks like bob.io.matlab is listed here but not used:
```
bob.bio.vein/requirements.txt
12:bob.io.matlab
bob.bio.vein/bob/bio/vein/tests/test.py
22:import bob.io.matlab
bob.bio.vein/develop.cfg
22: src/bob.io.matlab
52:bob.io.matlab = git git@gitlab.idiap.ch:bob/bob.io.matlab
bob.bio.vein/matlab/compare.py
9:import bob.io.matlab
bob.bio.vein/conda/meta.yaml
39: - bob.io.matlab
```
bob.io.matlab is deprecated https://gitlab.idiap.ch/bob/bob.io.matlab/-/issues/5Bob 9.0.0https://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/22PC feature extractor2020-11-03T16:03:18ZHatef OTROSHIPC feature extractorHi there,
I tried to use PC feature extractor, but the code is not working for me. In particular, there is a function `ut_gauss()` which is used but it seems it is not been defined or imported. See for example [L46](https://gitlab.idiap...Hi there,
I tried to use PC feature extractor, but the code is not working for me. In particular, there is a function `ut_gauss()` which is used but it seems it is not been defined or imported. See for example [L46](https://gitlab.idiap.ch/bob/bob.bio.vein/-/blob/master/bob/bio/vein/extractor/PrincipalCurvature.py#L46) or [L47](https://gitlab.idiap.ch/bob/bob.bio.vein/-/blob/master/bob/bio/vein/extractor/PrincipalCurvature.py#L47) . I was wondering if anyone can has any experience with it and can help.
Best,
Hatefhttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/21Dask Pipelines2020-12-03T08:37:30ZTiago de Freitas PereiraDask PipelinesThis package needs to be ported to the new API (https://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/180).
The job is extremely easy, though.
I short we need to:
- [x] Wrap all the preprocessors and extractors from here (https://...This package needs to be ported to the new API (https://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/180).
The job is extremely easy, though.
I short we need to:
- [x] Wrap all the preprocessors and extractors from here (https://gitlab.idiap.ch/bob/bob.bio.vein/-/tree/master/bob/bio/vein/configurations) to their corresponding transformers https://gitlab.idiap.ch/bob/bob.bio.base/-/tree/dask-pipelines/bob/bio/base/transformers
- [x] Wrap all the algorithms from here https://gitlab.idiap.ch/bob/bob.bio.vein/-/tree/master/bob/bio/vein/configurations using this
https://gitlab.idiap.ch/bob/bob.bio.base/-/blob/dask-pipelines/bob/bio/base/pipelines/vanilla_biometrics/legacy.py#L183
- [ ] Wrap all the databases from here https://gitlab.idiap.ch/bob/bob.bio.vein/-/tree/master/bob/bio/vein/configurations using this https://gitlab.idiap.ch/bob/bob.bio.base/-/blob/dask-pipelines/bob/bio/base/pipelines/vanilla_biometrics/legacy.py#L39
This will get 95% of the task done.
The other 5% are minor adjustments with documentation, extra test cases, and possible bugs that might be risen
Is anyone willing to help?
THanksBob 9.0.0Yannick DAYERYannick DAYERhttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/20UTFVP database2020-07-16T09:39:19ZHatef OTROSHIUTFVP databaseHi there,
I want to make some experiments using `utfvp` database which is available in `bob.bio.vein` by using the following script:
```
from bob.bio.vein.configurations.utfvp import database
```
However, I can not use `eval` and `world`...Hi there,
I want to make some experiments using `utfvp` database which is available in `bob.bio.vein` by using the following script:
```
from bob.bio.vein.configurations.utfvp import database
```
However, I can not use `eval` and `world` groups for evaluation using `verify.py`.
- when using `eval` group, it can not be found
- when using `world` group, it can calculate the scores but `scores-world` file is empty.
Does anyone have any idea how I should fix these issues?https://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/19DEPRECATION. Question2020-10-07T14:33:40ZTiago de Freitas PereiraDEPRECATION. QuestionHi @bob,
Shall we keep this vein recognition stuff for the next generation?
ThanksHi @bob,
Shall we keep this vein recognition stuff for the next generation?
Thankshttps://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.vein/-/issues/17[sphinx] Replace evaluation scripts and other tasks2018-06-05T07:41:38ZTiago de Freitas Pereira[sphinx] Replace evaluation scripts and other tasksWe need to update the documentation of this package w.r.t the new evaluation scripts implemented in `bob.measure`.
For instance, there are some references that points to `bob_eval_threshold.py` and such metric was replaced by `bob bio .....We need to update the documentation of this package w.r.t the new evaluation scripts implemented in `bob.measure`.
For instance, there are some references that points to `bob_eval_threshold.py` and such metric was replaced by `bob bio ....`.
There are other things that should be updated in this package and they are listed below:
- [x] replace `bob_eval_threshold.py` to the correspondent evaluation script in `bob bio`
- [x] There are references to `./bin/` in the documentation and this should be removed
- [x] The entry_point console scripts of this package should have some prefix. This is something that we are doing in `bob.bio` and in bob in general. For instance the scripts:
* compare_rois.py should be bob_bio_vein_compare_rois.py
* view_sample.py should be bob_bio_vein_view_sample.py
* blame.py should be bob_bio_vein_view_blame.py
* markdet.py should be bob_bio_vein_markdet.py
* watershed_mask.py should be bob_bio_vein_watershed_mask.py
ping @andre.anjoshttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/16Not ported to the new CI2018-02-22T11:21:29ZTiago de Freitas PereiraNot ported to the new CIConda-based CIAndré AnjosAndré Anjoshttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/15Match scores not split up into "genuine" and "impostor" categories correctly ...2017-08-24T14:23:05ZVedrana KRIVOKUCAMatch scores not split up into "genuine" and "impostor" categories correctly for 1vsall UTFVP database protocolThe 1vsall UTFVP database protocol is supposed to compare every fingervein sample to every other sample. The following is an excerpt from the score file:
10_1_1 59_4 0059/0059_4_1_120511-152502 0.23330404
As can be seen in the line ab...The 1vsall UTFVP database protocol is supposed to compare every fingervein sample to every other sample. The following is an excerpt from the score file:
10_1_1 59_4 0059/0059_4_1_120511-152502 0.23330404
As can be seen in the line above, the first two items (10_1_1 and 59_4) are not in the same format. In particular, the first item is supposed to be the client ID corresponding to the model and the second item is supposed to be the client ID corresponding to the probe. While the client ID for the probe (59_4) is correct, it seems that the model ID (10_1_1) instead of the client ID (10_1) is written to the score file for the model. This is a problem, because during matching the model and probe IDs will never match, so all the resulting match scores will be placed into the "impostor" category and we will end up with no "genuine" scores. Of course, if we then try to do any evaluation/plotting, the result will be wrong.
The root cause of this issue is the fact that the `client_id_from_model_id` function in `bob.bio.base.database` is not being overriden inside `bob.bio.vein.database.utfvp`, the consequence of which is that the client ID is assumed to be the same as the model ID (which is clearly stated in the base class implementation).André AnjosAndré Anjoshttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/14Unused/Maintenance branches2017-06-21T10:14:20ZAndré AnjosUnused/Maintenance branchesWe have a bunch of branches in this project which have not been merged for some time now:
- bh_vein_vein
- biowave
- biowave_temp
- ijcb_stuff
Could you please clean-up/remove unused branches, @onikisins?We have a bunch of branches in this project which have not been merged for some time now:
- bh_vein_vein
- biowave
- biowave_temp
- ijcb_stuff
Could you please clean-up/remove unused branches, @onikisins?Olegs NIKISINSOlegs NIKISINShttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/13C++ exception for bob.core.convert in MaximumCurvature.py and RepeatedLineTra...2018-05-11T07:44:39ZVedrana KRIVOKUCAC++ exception for bob.core.convert in MaximumCurvature.py and RepeatedLineTracking.pyRunning baseline fingervein experiment on Verafinger database using FingerCrop extractor with the Histogram Equalization post-processing option and the Maximum Curvature or Repeated Line Tracking extractor, the following type of error oc...Running baseline fingervein experiment on Verafinger database using FingerCrop extractor with the Histogram Equalization post-processing option and the Maximum Curvature or Repeated Line Tracking extractor, the following type of error occurs:
RuntimeError: convert: C++ exception caught: 'src[13,277] = 63.369219 is above the maximum 1.000000 of input range'
This is a result of the following two lines of code in bob.bio.vein.extractor.MaximumCurvature and bob.bio.vein.extractor.RepeatedLineTracking:
```
if finger_image.dtype != numpy.uint8:
finger_image = bob.core.convert(finger_image,numpy.uint8,(0,255),(0,1))
```
This is, in turn, is due to the new version of the "HE" function in FingerCrop, which rescales the intensities of the histogram equalized preprocessed fingervein images to the range (0, 255):
```
retval = rescale_intensity(equalize_hist(image, mask=mask), out_range = (0, 255))
```
The aforementioned two lines of code in MaximumCurvature.py and RepeatedLineTracking.py are thus not necessary.Vedrana KRIVOKUCAVedrana KRIVOKUCAhttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/12Histogram Equalization in FingerCrop not working properly2018-05-11T07:44:39ZVedrana KRIVOKUCAHistogram Equalization in FingerCrop not working properlyTried to run baseline fingervein experiments with Histogram Equalization post-processing as part of the FingerCrop pre-processor. The arrays in "extracted" directory contain all 0s (but they should be binary) and the score file containo...Tried to run baseline fingervein experiments with Histogram Equalization post-processing as part of the FingerCrop pre-processor. The arrays in "extracted" directory contain all 0s (but they should be binary) and the score file containonly "nan"s. The issue seems to be that the pre-processed data are in the range (0, 1) whereas the binarization threshold is based on the original image range of (0, 255).Vedrana KRIVOKUCAVedrana KRIVOKUCAhttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/11Add tests for extractor Threshold (biowave_test branch)2018-05-11T07:44:39ZTeodors EGLITISAdd tests for extractor Threshold (biowave_test branch)Tests were removed because function ``cv2.adaptiveThreshold`` produces different results with different ``cv2`` versions.
The ``bob-devel-2016-07-14-py27`` has ``cv2`` version ``2.4.12``, but the ``bob-2.5.1-py27_0`` - ``3.1.0``Tests were removed because function ``cv2.adaptiveThreshold`` produces different results with different ``cv2`` versions.
The ``bob-devel-2016-07-14-py27`` has ``cv2`` version ``2.4.12``, but the ``bob-2.5.1-py27_0`` - ``3.1.0``Teodors EGLITISTeodors EGLITIShttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/9Implement PUTvein high-level interface into this package2018-05-11T07:44:39ZAndré AnjosImplement PUTvein high-level interface into this packageTeodors EGLITISTeodors EGLITIShttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/8Change function names in MR !17 to lower-case with underscores2018-05-11T07:44:39ZAndré AnjosChange function names in MR !17 to lower-case with underscoresTeodors EGLITISTeodors EGLITIS