Update README and docs - Githubissues

bw4sz commented 3 years ago

The README from DeepForest needs to be updated to represent any changes in the API.

Key steps

[x] Copy docs from DeepForest
[x] Look for changes in names, predict_generator -> predict_file, check color ordering from tensorflow to pytorch
[x] A tutorial, preferably written in google collab and/or ipython is needed on model training.
[ ] Once a pretrained model is recreated, a collab tutorial for prediction is needed.

@dingyif, feel free to ignore any of these contributions, but i'll always add you if interested. My lab has a strong focus on inclusivity and making tools available to a wide audience. I speak English and Spanish, and so did a brief summary of the package at the top. Do you want/is it useful to add a mandarin explanation?

dingyif commented 3 years ago

I think I can add a mandarin explanation for the summary part.

bw4sz commented 3 years ago

if its not useful, don't worry about it. We always try to make these things are available as possible.

On Sat, Feb 6, 2021 at 8:39 AM Dingyi Fang notifications@github.com wrote:

I think I can add a mandarin explanation for the summary part.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/weecology/DeepForest-pytorch/issues/8#issuecomment-774504359, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJHBLARFRAELNUAWLTUFUTS5VWDFANCNFSM4XGLY2ZQ .

-- Ben Weinstein, Ph.D. Postdoctoral Fellow University of Florida http://benweinstein.weebly.com/

bw4sz commented 3 years ago

Docs were regenerated and being built https://deepforest-pytorch.readthedocs.io/en/latest/

dingyif commented 3 years ago

If it will help this to reach more audience, of course. Not a huge issue for me, I can write it up really quick.

bw4sz commented 3 years ago

first set of docs pass, need to be update for the port

https://deepforest-pytorch.readthedocs.io/en/latest/

bw4sz commented 3 years ago

Updated getting started page.

dingyif commented 3 years ago

Did you start to write the Google Colab tutorial yet? I can work on that one if you haven't started it.

bw4sz commented 3 years ago

nope go for it. Wait like twenty minutes to get the release model. I just finished it. It is virtually identical to the tensorflow. about 80% recall, 64% on the NeonTreeEvaluation benchmark we are publishing https://github.com/weecology/NeonTreeEvaluation [image: image.png]

There is very little left to do in terms of code before 0.2.0 milestone. Need to write a multi-class tutorial and make sure the labels aren't hard-coded in the dataloader. Also need to write a test to make sure the order of labels is the same on save and reload.

On Sun, Mar 14, 2021 at 1:59 PM Dingyi Fang @.***> wrote:

Did you start to write the Google Colab tutorial yet? I can work on that one if you haven't started it.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/weecology/DeepForest-pytorch/issues/8#issuecomment-798978671, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJHBLCU3VHKUJT2GSYTEATTDUPSNANCNFSM4XGLY2ZQ .

-- Ben Weinstein, Ph.D. Postdoctoral Fellow University of Florida http://benweinstein.weebly.com/

dingyif commented 3 years ago

Great! Glad to hear that!! Can't wait to try it on my dataset.

bw4sz commented 3 years ago

I see some very small extra boxes that need to be filtered. Probably the anchor box generator default sizes are too small. Very minor.

On Sun, Mar 14, 2021 at 2:17 PM Dingyi Fang @.***> wrote:

Great! Glad to hear that!! Can't wait to try it on my dataset.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/weecology/DeepForest-pytorch/issues/8#issuecomment-798981473, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJHBLFH7T2ZAKNYJRF2NWTTDURXJANCNFSM4XGLY2ZQ .

-- Ben Weinstein, Ph.D. Postdoctoral Fellow University of Florida http://benweinstein.weebly.com/

dwaipayan05 commented 3 years ago

Hello @dingyif @bw4sz If the work of making a Google Colab Tutorial for Training a Model DeepForest-Pytorch requires some contribution. I would like to help in this context. Please point me towards what has to be included in the tutorial, I'll send a PR for the same.

I have gone through the Training Model of DeepForest (keras-retinanet) implementation. They have the following modules -> Design Evaluation Data -> Gather Annotations -> Training Accuracy -> View the Training Plots

Should I make similar modules for the above issue based on the pytorch implementation ?

Thank You !

dingyif commented 3 years ago

I see some very small extra boxes that need to be filtered. Probably the anchor box generator default sizes are too small. Very minor. … On Sun, Mar 14, 2021 at 2:17 PM Dingyi Fang @.***> wrote: Great! Glad to hear that!! Can't wait to try it on my dataset. — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJHBLFH7T2ZAKNYJRF2NWTTDURXJANCNFSM4XGLY2ZQ . -- Ben Weinstein, Ph.D. Postdoctoral Fellow University of Florida http://benweinstein.weebly.com/

While I was testing the pip install deepforest-pytorch, I found out the data folder not contains everything we have in the original Github repo, especially the example.csv and the tif files that used to retrain the model. Is there any way we can fix that?

bw4sz commented 3 years ago

I see those files here: https://github.com/weecology/DeepForest-pytorch/tree/master/deepforest/data

Is this happening only when we pip install?

bw4sz commented 3 years ago

Confirmed. Missing after pip install.

(deepforest_pytorch) benweinstein@Bens-MacBook-Pro deepforest % conda create --name test python=3.7
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# To activate this environment, use
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#     $ conda activate test
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(deepforest_pytorch) benweinstein@Bens-MacBook-Pro deepforest % conda activate test
(test) benweinstein@Bens-MacBook-Pro deepforest % pip install deepforest-pytorch
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(test) benweinstein@Bens-MacBook-Pro deepforest % vf ~
zsh: command not found: vf
(test) benweinstein@Bens-MacBook-Pro deepforest % cd ~
(test) benweinstein@Bens-MacBook-Pro ~ % python
Python 3.8.5 (default, Sep  4 2020, 02:22:02)
[Clang 10.0.0 ] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from deepforest import get_data
>>> get_data("example.csv")
'/Users/benweinstein/opt/miniconda3/lib/python3.8/site-packages/deepforest/data/example.csv'
>>> csv_file = get_data("example.csv")
>>> import pandas as pf

>>>
>>> import pandas as pd
>>> pd.read_csv(csv_file)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/benweinstein/opt/miniconda3/lib/python3.8/site-packages/pandas/io/parsers.py", line 610, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/Users/benweinstein/opt/miniconda3/lib/python3.8/site-packages/pandas/io/parsers.py", line 462, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/Users/benweinstein/opt/miniconda3/lib/python3.8/site-packages/pandas/io/parsers.py", line 819, in __init__
    self._engine = self._make_engine(self.engine)
  File "/Users/benweinstein/opt/miniconda3/lib/python3.8/site-packages/pandas/io/parsers.py", line 1050, in _make_engine
    return mapping[engine](self.f, **self.options)  # type: ignore[call-arg]
  File "/Users/benweinstein/opt/miniconda3/lib/python3.8/site-packages/pandas/io/parsers.py", line 1867, in __init__
    self._open_handles(src, kwds)
  File "/Users/benweinstein/opt/miniconda3/lib/python3.8/site-packages/pandas/io/parsers.py", line 1362, in _open_handles
    self.handles = get_handle(
  File "/Users/benweinstein/opt/miniconda3/lib/python3.8/site-packages/pandas/io/common.py", line 642, in get_handle
    handle = open(
FileNotFoundError: [Errno 2] No such file or directory: '/Users/benweinstein/opt/miniconda3/lib/python3.8/site-packages/deepforest/data/example.csv'
>>> csv_file = get_data("e.csv")

bw4sz commented 3 years ago

Its funny its only example.csv that is missing. Here is the contents of the pip install data folder.

bw4sz commented 3 years ago

@dingyif good catch, this is actually a bug from the original repo, I just fixed it in both. Example.csv was missing from the manifest.in. I pushed a new version to pypi, if all other tests pass it will push. As a workaround till then you can download it from the repo.

dingyif commented 3 years ago

Great! That's what I'm doing right now but I think it will be useful for the users to replicate the tutorial result before implementing their datasets. Thanks for the update!

bw4sz commented 3 years ago

Add colab link to the front readme. I still need to add it to the readthedocs. @henrykironde can you confirm that if you click on this link the permissions are set right for you to see it.

https://colab.research.google.com/drive/1AJUcw5dEpXeDPHd0sotAz5lpWedFYSIL?usp=sharing

Thanks @dingyif! I'll make one for the benchmark score and prediction.

dwaipayan05 commented 3 years ago

Confirmation from @dwaipayan05 Colab Link is Working Permissions are Set Right

henrykironde commented 3 years ago

Looking at this now

henrykironde commented 3 years ago

LGTM, works like a charm .

weecology / DeepForest-pytorch

Update README and docs #8