Warnings when using test data

[Axolotl233]

Hi

I was testing diploSHIC with example data, but I got some warnings when i run "python diploSHIC.py train training/ testing/ fooModel --epochs 10". Our machine is multicore with CentOS7 and packages is python 3.6.9, tensorflow 1.14.0 keras 2.3.1 and pandas 1.0.1.

Although it runs normally after this, I am confused as to whether the result is correct or not. So, please check if this will affect the results

warnings messages:

/data/00/user/user112/.local/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:516: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint8 = np.dtype([("qint8", np.int8, 1)])
/data/00/user/user112/.local/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/data/00/user/user112/.local/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint16 = np.dtype([("qint16", np.int16, 1)])
/data/00/user/user112/.local/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/data/00/user/user112/.local/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint32 = np.dtype([("qint32", np.int32, 1)])
/data/00/user/user112/.local/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  np_resource = np.dtype([("resource", np.ubyte, 1)])
/data/00/user/user112/.local/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:541: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint8 = np.dtype([("qint8", np.int8, 1)])
/data/00/user/user112/.local/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:542: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/data/00/user/user112/.local/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:543: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint16 = np.dtype([("qint16", np.int16, 1)])
/data/00/user/user112/.local/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:544: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/data/00/user/user112/.local/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:545: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint32 = np.dtype([("qint32", np.int32, 1)])
/data/00/user/user112/.local/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:550: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  np_resource = np.dtype([("resource", np.ubyte, 1)])

Tiande

[Axolotl233]

Hi

when I using ‘predict’ submodule, i got some Error

Traceback (most recent call last):  File "diploSHIC.py", line 299, in <module>
    model.load_weights(argsDict['modelWeights'])
  File "/data/00/user/user112/.local/lib/python3.6/site-packages/keras/engine/saving.py", line 492, in load_wrapper                                                        
    return load_function(*args, **kwargs)
  File "/data/00/user/user112/.local/lib/python3.6/site-packages/keras/engine/network.py", line 1230, in load_weights                                                      
    f, self.layers, reshape=reshape)  File "/data/00/user/user112/.local/lib/python3.6/site-packages/keras/engine/saving.py", line 1183, in load_weights_from_hdf5_group                                       
    original_keras_version = f.attrs['keras_version'].decode('utf8')
AttributeError: 'str' object has no attribute 'decode'

i can't fix it by my self because I am newble about python. My command line is

python diploSHIC.py predict fooModel.json fooModel.weights.hdf5 testEmpirical.fvec testEmpirical.preds

please point out what is wrong with it. Thanks Tiande

[andrewkern]

hi there- you first issue above looks like deprecation warnings. nothing to worry about.

the second issue here with the predict mode looks like an issue with your tensorflow / keras install and doesn't appear to have to do with diploSHIC per se. Can you run other things using keras?

[Axolotl233]

Hi~ I have reinstalled tensorflow 1.14.0 and keras 2.3.1 but problem not be solved. I really know little about python, so i don't how to test them whether they work well. If you could kindly provide me some ways or code to test them, I will be appreciate.

Tiande

[andrewkern]

you could try one of these examples to make sure everything is working, but your error above is coming from keras. you might raise an issue on that repo

https://keras.io/examples/vision/image_classification_from_scratch/

[Axolotl233]

hi, Sorry i didn't see your reply, i will test it as soon as possible you can close this question temporary, if i meet any other question of DiploSHIC, i will ask again. Thank you~