bob issueshttps://gitlab.idiap.ch/groups/bob/-/issues2020-04-09T17:03:15Zhttps://gitlab.idiap.ch/bob/bob.db.meds/-/issues/4Add Metadata into the samples2020-04-09T17:03:15ZTiago de Freitas PereiraAdd Metadata into the samplesHey @ydayer
Is it possible to add all the possible metadata in the samples?
For instance, here
https://gitlab.idiap.ch/bob/bob.db.meds/blob/master/bob/db/meds/database.py#L351
You could have amended the metadata from here direct in t...Hey @ydayer
Is it possible to add all the possible metadata in the samples?
For instance, here
https://gitlab.idiap.ch/bob/bob.db.meds/blob/master/bob/db/meds/database.py#L351
You could have amended the metadata from here direct in the samples: https://gitlab.idiap.ch/bob/bob.db.meds/blob/master/bob/db/meds/subject_metadata.csv
Like this:
```python
sets[subject].insert(
index=-1, # Insert at last position
item=DelayedSample(
load=functools.partial(
bob.io.image.load,
os.path.join(self.directory, path),
),
key=path,
subject=subject,
annotations=self._annotations(filename),
gender=GENDER,
ethnicity=ETHNICITY,
height=HEIGHT,
weight=WEIGHT,
pode=POSE,
```
This can be useful in the future.
For instance, we could craft a script that given a score file and a database,
we could do all the analysis we want without having to parse the score file.....
Can you add these metadata in the database if you have the time?
ThanksYannick DAYERYannick DAYERhttps://gitlab.idiap.ch/bob/bob.db.meds/-/issues/3Annotations2020-04-09T06:42:26ZTiago de Freitas PereiraAnnotationsHi @ydayer,
Why the annotations are shipped like this (https://gitlab.idiap.ch/bob/bob.db.meds/blob/master/bob/db/meds/database.py#L349):
```python
sets[subject].insert(
index=-1, # Insert at last position
...Hi @ydayer,
Why the annotations are shipped like this (https://gitlab.idiap.ch/bob/bob.db.meds/blob/master/bob/db/meds/database.py#L349):
```python
sets[subject].insert(
index=-1, # Insert at last position
item=DelayedSample(
load=functools.partial(
bob.io.image.load,
os.path.join(self.directory, path),
),
key=path,
subject=subject,
eyes=self.eyes_position(filename),
)
)
```
This could be done like this and avoid you to create the `Annotator` in the config file
```python
sets[subject].insert(
index=-1, # Insert at last position
item=DelayedSample(
load=functools.partial(
bob.io.image.load,
os.path.join(self.directory, path),
),
key=path,
subject=subject,
annotations={'reye':(r_y, r_x), 'leye':(l_y, l_x)}
)
)
```
Cheershttps://gitlab.idiap.ch/bob/bob.pipelines/-/issues/9SampleSet.insert not accepting DelayedSample objects as item2020-04-06T06:25:29ZYannick DAYERSampleSet.insert not accepting DelayedSample objects as itemIn [`bob/pipelines/sample.py`](https://gitlab.idiap.ch/bob/bob.pipelines/blob/master/bob/pipelines/sample.py#L78), in the `SampleSet` class, the `insert(self, index, item)` does not accept `DelayedSample` objects.
(Because of the test: ...In [`bob/pipelines/sample.py`](https://gitlab.idiap.ch/bob/bob.pipelines/blob/master/bob/pipelines/sample.py#L78), in the `SampleSet` class, the `insert(self, index, item)` does not accept `DelayedSample` objects.
(Because of the test: `if not isinstance(item, Sample):`.)
To solve:
- either make `DelayedSample` and `Sample` inherit from a `SampleBase` class,
- change the tests in `SampleSet.insert` to accept the base class an thus all Sample-like classes;
or:
- change the tests in `SampleSet.insert` to accept both `Sample` and `DelayedSample`.
(Could be the same with `__setitem__`.)Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.ip.tensorflow_extractor/-/issues/10Nightlies failing because of this package2020-04-03T12:20:20ZTiago de Freitas PereiraNightlies failing because of this packageLinux py36/py37
https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/194059/raw
https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/194059
Master branch
https://gitlab.idiap.ch/bob/bob.ip.tensorflow_extractor/pipelines/38691
Some weird conflic...Linux py36/py37
https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/194059/raw
https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/194059
Master branch
https://gitlab.idiap.ch/bob/bob.ip.tensorflow_extractor/pipelines/38691
Some weird conflicts that are very tricky to figure it out.
Installing all the dependencies in my miniconda (beta channel first) .... works
```
conda install python==3.7 setuptools bob.io.base bob.io.image bob.db.mnist bob.ip.color six numpy tensorflow==1.15 --dry-run
```https://gitlab.idiap.ch/bob/bob.devtools/-/issues/52Can't find this package on the beta channel2020-04-02T16:10:53ZTiago de Freitas PereiraCan't find this package on the beta channelHi guys,
This might be a stupid question, but I can't find this package on our beta channel via conda search.
```sh
$ conda search bob.devtools -c http://www.idiap.ch/software/bob/conda/label/beta
Loading channels: done
# Name ...Hi guys,
This might be a stupid question, but I can't find this package on our beta channel via conda search.
```sh
$ conda search bob.devtools -c http://www.idiap.ch/software/bob/conda/label/beta
Loading channels: done
# Name Version Build Channel
bob.devtools 0.1.2 py36h6b6bea4_0 software/bob/conda
bob.devtools 0.1.3 py36h6b6bea4_0 software/bob/conda
bob.devtools 0.1.4 py36h6b6bea4_0 software/bob/conda
bob.devtools 0.1.4 py37h6b6bea4_0 software/bob/conda
bob.devtools 0.1.5 py36h6b6bea4_0 software/bob/conda
bob.devtools 0.1.5 py37h6b6bea4_0 software/bob/conda
bob.devtools 0.1.6 py36h6b6bea4_0 software/bob/conda
bob.devtools 0.1.6 py37h6b6bea4_0 software/bob/conda
bob.devtools 1.0.0 py36ha12d1ad_0 software/bob/conda
bob.devtools 1.0.0 py37ha12d1ad_0 software/bob/conda
bob.devtools 1.0.1 py36h88c16f1_0 software/bob/conda
bob.devtools 1.0.1 py37h88c16f1_0 software/bob/conda
bob.devtools 1.0.2 py36h88c16f1_0 software/bob/conda
bob.devtools 1.0.2 py37h88c16f1_0 software/bob/conda
bob.devtools 1.0.3 py36h88c16f1_0 software/bob/conda
bob.devtools 1.0.3 py37h88c16f1_0 software/bob/conda
bob.devtools 1.0.4 py36h88c16f1_0 software/bob/conda
bob.devtools 1.0.4 py37h88c16f1_0 software/bob/conda
bob.devtools 1.0.5 py36h88c16f1_0 software/bob/conda
bob.devtools 1.0.5 py37h88c16f1_0 software/bob/conda
bob.devtools 2.0.0 py36h661208a_0 software/bob/conda
bob.devtools 2.0.0 py37h661208a_0 software/bob/conda
bob.devtools 2.0.1 py36h661208a_0 software/bob/conda
bob.devtools 2.0.1 py37h661208a_0 software/bob/conda
```
I even added on my `~/.condarc` just to test.
Didn't work
thanks for any insighthttps://gitlab.idiap.ch/bob/bob.pad.base/-/issues/33ERROR: Failure: TypeError (Can't instantiate abstract class TestDatabase with...2020-04-02T15:33:52ZAndré AnjosERROR: Failure: TypeError (Can't instantiate abstract class TestDatabase with abstract methods annotations)```
======================================================================
ERROR: Failure: TypeError (Can't instantiate abstract class TestDatabase with abstract methods annotations)
-----------------------------------------------------...```
======================================================================
ERROR: Failure: TypeError (Can't instantiate abstract class TestDatabase with abstract methods annotations)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/scratch/builds/bob/bob.nightlies/miniconda/conda-bld/bob.pad.base_1585423863782/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.6/site-packages/nose/failure.py", line 39, in runTest
raise self.exc_val.with_traceback(self.tb)
File "/scratch/builds/bob/bob.nightlies/miniconda/conda-bld/bob.pad.base_1585423863782/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.6/site-packages/nose/loader.py", line 522, in makeTest
return self._makeTest(obj, parent)
File "/scratch/builds/bob/bob.nightlies/miniconda/conda-bld/bob.pad.base_1585423863782/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.6/site-packages/nose/loader.py", line 581, in _makeTest
return MethodTestCase(obj)
File "/scratch/builds/bob/bob.nightlies/miniconda/conda-bld/bob.pad.base_1585423863782/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.6/site-packages/nose/case.py", line 345, in __init__
self.inst = self.cls()
TypeError: Can't instantiate abstract class TestDatabase with abstract methods annotations
```Amir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.db.meds/-/issues/2Create protocols2020-04-07T12:14:19ZTiago de Freitas PereiraCreate protocolsHey @ydayer,
As discussed previously, we need some verification protocols for this dataset.
Looking at the meds README (/i***p/r******e/database/MEDS/), there are two things that we can analyse in this dataset, the ethnicity aspect (ca...Hey @ydayer,
As discussed previously, we need some verification protocols for this dataset.
Looking at the meds README (/i***p/r******e/database/MEDS/), there are two things that we can analyse in this dataset, the ethnicity aspect (caucasian/black) and age.
Unfortunatelly, we don't have enough data for gender.
Would be nice to have 3 fold verification protocol containing **only men** AND **only black/caucasian** such that:
- [x] the `world` has all the samples that has only one image per identiy
- [x] the `dev` set has 50% of the images with more than one image per identiy
- [x] the `eval` set has 50% of the images with more than one image per identiy
- [x] for each fold you randomize the identities in the dev/eval set
Is it possible to carry this on?
Thanks
Cheershttps://gitlab.idiap.ch/bob/bob.ip.stereo/-/issues/1Pipelines are failing2020-07-21T07:55:13ZAnjith GEORGEanjith.george@idiap.chPipelines are failingVincent POLLETVincent POLLEThttps://gitlab.idiap.ch/bob/bob.db.meds/-/issues/1Access rights2020-03-27T10:30:14ZYannick DAYERAccess rightsHello,
Could you make me a maintainer of the project, so I can push to the master branch?
Thanks ;)Hello,
Could you make me a maintainer of the project, so I can push to the master branch?
Thanks ;)Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues/133remove collect_results.py script2020-07-29T12:02:51ZAmir MOHAMMADIremove collect_results.py scriptSee https://groups.google.com/d/msgid/bob-devel/dc74b86e-5bd0-442b-88fb-654105541487%40googlegroups.com?utm_medium=email&utm_source=footerSee https://groups.google.com/d/msgid/bob-devel/dc74b86e-5bd0-442b-88fb-654105541487%40googlegroups.com?utm_medium=email&utm_source=footerAmir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.pipelines/-/issues/8Follow-up from "WIP: Make scikit operations daskable"2020-05-05T07:39:23ZTiago de Freitas PereiraFollow-up from "WIP: Make scikit operations daskable"The following discussion from !5 should be addressed:
- [ ] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pipelines/merge_requests/5#note_50104): (+3 comments)
> All these dynamic object creation is going to m...The following discussion from !5 should be addressed:
- [ ] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pipelines/merge_requests/5#note_50104): (+3 comments)
> All these dynamic object creation is going to make debugging a hell, wouldn't it? Could you print a traceback here when something fails in sklearn estimator?https://gitlab.idiap.ch/bob/bob.pipelines/-/issues/7Follow-up from "WIP: Make scikit operations daskable"2020-05-05T07:39:10ZTiago de Freitas PereiraFollow-up from "WIP: Make scikit operations daskable"The following discussion from !5 should be addressed:
- [ ] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pipelines/merge_requests/5#note_50099): (+2 comments)
> `features_dir` was optional, please revert this.The following discussion from !5 should be addressed:
- [ ] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pipelines/merge_requests/5#note_50099): (+2 comments)
> `features_dir` was optional, please revert this.Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.pipelines/-/issues/6Follow-up from "WIP: Make scikit operations daskable"2020-05-05T07:38:59ZTiago de Freitas PereiraFollow-up from "WIP: Make scikit operations daskable"The following discussion from !5 should be addressed:
- [ ] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pipelines/merge_requests/5#note_50170): (+2 comments)
> Is it possible to put this inside a scikit.pipe...The following discussion from !5 should be addressed:
- [ ] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.pipelines/merge_requests/5#note_50170): (+2 comments)
> Is it possible to put this inside a scikit.pipeline?Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.extension/-/issues/74Numpy documentation has moved2020-03-13T07:09:20ZAmir MOHAMMADINumpy documentation has movedStarting from numpy 1.18, the docs are available in https://numpy.org/doc/
the sphinx object links are also changed. For example:
```
# This
https://docs.scipy.org/doc/numpy-1.18.0/objects.inv
# should change to
https://numpy.org/doc/1.1...Starting from numpy 1.18, the docs are available in https://numpy.org/doc/
the sphinx object links are also changed. For example:
```
# This
https://docs.scipy.org/doc/numpy-1.18.0/objects.inv
# should change to
https://numpy.org/doc/1.18/objects.inv
```Amir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.ip.tensorflow_extractor/-/issues/9Tensorflow 2 compatibility2020-03-11T16:11:45ZAmir MOHAMMADITensorflow 2 compatibilityThis package does not work with tensorflow 2!This package does not work with tensorflow 2!Amir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.pipelines/-/issues/5Dask Mixin classes for pipelines2020-03-23T17:21:51ZAmir MOHAMMADIDask Mixin classes for pipelinesIt would be a good idea to have mixin classes to turn transformers dask aware.
This was proposed by @andre.anjos. @tiago.pereira and I have discussed this and see the comments for what we came up with.It would be a good idea to have mixin classes to turn transformers dask aware.
This was proposed by @andre.anjos. @tiago.pereira and I have discussed this and see the comments for what we came up with.Amir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.bio.face/-/issues/34Failure with MTCNN when face is not found2020-03-09T16:16:16ZAnjith GEORGEanjith.george@idiap.chFailure with MTCNN when face is not foundThere is a key error, when face is not detected. The problem is this line
`https://gitlab.idiap.ch/bob/bob.bio.face/blob/master/bob/bio/face/annotator/bobipmtcnn.py#L29`There is a key error, when face is not detected. The problem is this line
`https://gitlab.idiap.ch/bob/bob.bio.face/blob/master/bob/bio/face/annotator/bobipmtcnn.py#L29`Amir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.paper.pad_mccnns_swirdiff/-/issues/2Branches2020-03-09T08:20:30ZAnjith GEORGEanjith.george@idiap.chBranchesNow that the revision is submitted, we can use `bob.db.hqwmca` for all further experiments is it?.
And can you merge the branch to master if the configs are final.Now that the revision is submitted, we can use `bob.db.hqwmca` for all further experiments is it?.
And can you merge the branch to master if the configs are final.Guillaume HEUSCHGuillaume HEUSCHhttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues/132`numpy.testing.decorators.setastest` is no longer available in the latest `nu...2020-03-10T16:10:40ZManuel Günthersiebenkopf@googlemail.com`numpy.testing.decorators.setastest` is no longer available in the latest `numpy 1.18`Updating to `numpy` version 1.18 breaks this package as the import https://gitlab.idiap.ch/bob/bob.bio.base/blob/33b527af1418dff1812e2613d91f55b6e8ee61c8/bob/bio/base/database/database.py#L8 fails.
Workarounds:
1. Use `numpy` version 1....Updating to `numpy` version 1.18 breaks this package as the import https://gitlab.idiap.ch/bob/bob.bio.base/blob/33b527af1418dff1812e2613d91f55b6e8ee61c8/bob/bio/base/database/database.py#L8 fails.
Workarounds:
1. Use `numpy` version 1.17
2. Remove this import and its later use.
I have currently no solution how to replace the functionality of `numpy.testing.decorators.setastest`, though.Amir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.pipelines/-/issues/4Implement checkpointable processors2020-03-09T15:49:22ZAmir MOHAMMADIImplement checkpointable processorsCheckpointable process can be integrated with the Sample class and automaticall cache/save their results.Checkpointable process can be integrated with the Sample class and automaticall cache/save their results.