mikhailmashukov / particles_nsu

Public repository with core code for counting particles by means of neural networks

particles_nsu

Public repository with core code for counting particles by means of neural networks.

Requirements

(determined by used mmdetection)

• Linux or macOS (Windows is not currently officially supported)
• Python 3.6+
• PyTorch 1.3+
• CUDA 9.2+ (If you build PyTorch from source, CUDA 9.0 is also compatible)
• GCC 5+
• mmcv 0.2.14+
• mmdetection 1.0rc (we used commit d0c0418763 that is in between 1.0rc0 and 1.0rc1, the config file and weights are incompatible with some other versions).

You also need to download epoch_500_3x.pth from http://particlesnn.nsu.ru/data/static/weights/epoch_500_3x.pth before start. And to put it into a "weights" subfolder.

The code that works at http://particlesnn.nsu.ru/, MMDetection NanoPart v. 3.0 model is at the nano_predict.py, processFileForSite3_0 procedure. It runs pre-trained neural model, calculates and saves particles statistics. The model initialization code itself is at the getModel3_0 function.

particles_nsu's Issues

I got a bug below, Can I know the version of mmcv and mmdet you use? Thanks

Processing sample/Pt-HOPG-01-0041.bmp
building model (config cascade_mask_rcnn_x101_64x4d_fpn_1x_nanopart_3_0.py, weights weights/epoch_500_3x.pth)
/home/iot/anaconda3/envs/torchreid/lib/python3.7/site-packages/mmdet/models/builder.py:53: UserWarning: train_cfg and test_cfg is deprecated, please specify them in model
'please specify them in model', UserWarning)
Traceback (most recent call last):
File "/home/iot/anaconda3/envs/torchreid/lib/python3.7/site-packages/mmcv/utils/registry.py", line 52, in build_from_cfg
return obj_cls(**args)
TypeError: init() got an unexpected keyword argument 'num_stages'

Errors from nano_predict.py implementation

I am trying to reproduce the code on your data provided and my custom data by running the nano_predict.py file but I am getting different errors.

The first (shown below) was a type error which I resolved using a new config according to this solution

After resolving it, I then got an Index Error from line 70 of nano_predict.py (as seen in the screenshot below) that I am yet to rectify and would need help with as I still get the same error even when I use my own data.

It seems the error is coming from the the content of segms[inst_cls][i] which was passed inside maskUtils.decode(). When I print out the segms[inst_cls][i], it shows the screenshot below.

I would appreciate any help in rectifying this error. Thanks.

Link for downloading epoch_500_3x.pth errors

Many thanks to all the contributors for this project
Link for downloading epoch_500_3x.pth http://particlesnn.nsu.ru/data/static/weights/epoch_500_3x.pth errors.
Can you update the link?