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A Capsule Network-based framework for identification of COVID-19 cases from chest X-ray Images

Python 100.00%

capsule-networks chest-xray-images covid-19 covid-detection covid-xray medical-image-processing

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When I try to run the code with a different dataset I get unwanted results.

Using TensorFlow backend.
/usr/local/lib/python3.6/dist-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)])
/usr/local/lib/python3.6/dist-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)])
/usr/local/lib/python3.6/dist-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)])
/usr/local/lib/python3.6/dist-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)])
/usr/local/lib/python3.6/dist-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)])
/usr/local/lib/python3.6/dist-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)])
/usr/local/lib/python3.6/dist-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)])
/usr/local/lib/python3.6/dist-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)])
/usr/local/lib/python3.6/dist-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)])
/usr/local/lib/python3.6/dist-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)])
/usr/local/lib/python3.6/dist-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)])
/usr/local/lib/python3.6/dist-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)])
tcmalloc: large alloc 1204224000 bytes == 0x57dc000 @  0x7fcf4464c1e7 0x7fcf421725e1 0x7fcf421db90d 0x7fcf421dc522 0x7fcf42273bce 0x50a7f5 0x50cfd6 0x507f24 0x509c50 0x50a64d 0x50cfd6 0x507f24 0x509c50 0x50a64d 0x50c1f4 0x507f24 0x50b053 0x634dd2 0x634e87 0x63863f 0x6391e1 0x4b0dc0 0x7fcf44249b97 0x5b26fa
WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:74: The name tf.get_default_graph is deprecated. Please use tf.compat.v1.get_default_graph instead.

WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:517: The name tf.placeholder is deprecated. Please use tf.compat.v1.placeholder instead.

WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:4138: The name tf.random_uniform is deprecated. Please use tf.random.uniform instead.

WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:174: The name tf.get_default_session is deprecated. Please use tf.compat.v1.get_default_session instead.

WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:181: The name tf.ConfigProto is deprecated. Please use tf.compat.v1.ConfigProto instead.

2020-08-08 22:27:04.973016: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2020-08-08 22:27:04.975812: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2200000000 Hz
2020-08-08 22:27:04.975982: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x2594a00 executing computations on platform Host. Devices:
2020-08-08 22:27:04.976009: I tensorflow/compiler/xla/service/service.cc:175]   StreamExecutor device (0): <undefined>, <undefined>
2020-08-08 22:27:04.993713: W tensorflow/compiler/jit/mark_for_compilation_pass.cc:1412] (One-time warning): Not using XLA:CPU for cluster because envvar TF_XLA_FLAGS=--tf_xla_cpu_global_jit was not set.  If you want XLA:CPU, either set that envvar, or use experimental_jit_scope to enable XLA:CPU.  To confirm that XLA is active, pass --vmodule=xla_compilation_cache=1 (as a proper command-line flag, not via TF_XLA_FLAGS) or set the envvar XLA_FLAGS=--xla_hlo_profile.
WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:1834: The name tf.nn.fused_batch_norm is deprecated. Please use tf.compat.v1.nn.fused_batch_norm instead.

WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:3980: The name tf.nn.avg_pool is deprecated. Please use tf.nn.avg_pool2d instead.

WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/keras/optimizers.py:790: The name tf.train.Optimizer is deprecated. Please use tf.compat.v1.train.Optimizer instead.

_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input_1 (InputLayer)         (None, None, None, 3)     0         
_________________________________________________________________
conv2d_1 (Conv2D)            (None, None, None, 64)    1792      
_________________________________________________________________
batch_normalization_1 (Batch (None, None, None, 64)    256       
_________________________________________________________________
conv2d_2 (Conv2D)            (None, None, None, 64)    36928     
_________________________________________________________________
average_pooling2d_1 (Average (None, None, None, 64)    0         
_________________________________________________________________
conv2d_3 (Conv2D)            (None, None, None, 128)   73856     
_________________________________________________________________
conv2d_4 (Conv2D)            (None, None, None, 128)   147584    
_________________________________________________________________
reshape_1 (Reshape)          (None, None, 128)         0         
_________________________________________________________________
capsule_1 (Capsule)          (None, 32, 8)             32768     
_________________________________________________________________
capsule_2 (Capsule)          (None, 32, 8)             2048      
_________________________________________________________________
capsule_3 (Capsule)          (None, 2, 16)             256       
_________________________________________________________________
lambda_1 (Lambda)            (None, 2)                 0         
=================================================================
Total params: 295,488
Trainable params: 295,360
Non-trainable params: 128
_________________________________________________________________
Not using data augmentation.
WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/tensorflow/python/ops/math_grad.py:1250: add_dispatch_support.<locals>.wrapper (from tensorflow.python.ops.array_ops) is deprecated and will be removed in a future version.
Instructions for updating:
Use tf.where in 2.0, which has the same broadcast rule as np.where
Train on 2000 samples, validate on 241 samples
Epoch 1/100
2020-08-08 22:27:07.765238: W tensorflow/core/framework/allocator.cc:107] Allocation of 201867264 exceeds 10% of system memory.
2020-08-08 22:27:07.967568: W tensorflow/core/framework/allocator.cc:107] Allocation of 201867264 exceeds 10% of system memory.
2020-08-08 22:27:07.967568: W tensorflow/core/framework/allocator.cc:107] Allocation of 201867264 exceeds 10% of system memory.
2020-08-08 22:27:08.485600: W tensorflow/core/framework/allocator.cc:107] Allocation of 198246400 exceeds 10% of system memory.
tcmalloc: large alloc 1784520704 bytes == 0x89d4c000 @  0x7fcf4464c1e7 0x7fcf2d855804 0x7fcf2fa61e34 0x7fcf3009ddbb 0x7fcf3009fb9c 0x7fcf300c57d1 0x7fcf300ca212 0x7fcf300cab11 0x7fcf2969ed94 0x7fcf29691050 0x7fcf2973c6d4 0x7fcf2973b544 0x7fcf42f2ea50 0x7fcf440106db 0x7fcf44349a3f
2020-08-08 22:27:10.457322: W tensorflow/core/framework/allocator.cc:107] Allocation of 184090624 exceeds 10% of system memory.
  16/2000 [..............................] - ETA: 25:53 - loss: nan - acc: 1.0000tcmalloc: large alloc 1784520704 bytes == 0x9e30c000 @  0x7fcf4464c1e7 0x7fcf2d855804 0x7fcf2fa61e34 0x7fcf3009ddbb 0x7fcf3009fb9c 0x7fcf300c57d1 0x7fcf300ca212 0x7fcf300cab11 0x7fcf2969ed94 0x7fcf29691050 0x7fcf2973c6d4 0x7fcf2973b544 0x7fcf42f2ea50 0x7fcf440106db 0x7fcf44349a3f
  32/2000 [..............................] - ETA: 23:56 - loss: nan - acc: 1.0000tcmalloc: large alloc 1784520704 bytes == 0x9db26000 @  0x7fcf4464c1e7 0x7fcf2d855804 0x7fcf2fa61e34 0x7fcf3009ddbb 0x7fcf3009fb9c 0x7fcf300c57d1 0x7fcf300ca212 0x7fcf300cab11 0x7fcf2969ed94 0x7fcf29691050 0x7fcf2973c6d4 0x7fcf2973b544 0x7fcf42f2ea50 0x7fcf440106db 0x7fcf44349a3f
  48/2000 [..............................] - ETA: 23:14 - loss: nan - acc: 1.0000tcmalloc: large alloc 1784520704 bytes == 0x97f98000 @  0x7fcf4464c1e7 0x7fcf2d855804 0x7fcf2fa61e34 0x7fcf3009ddbb 0x7fcf3009fb9c 0x7fcf300c57d1 0x7fcf300ca212 0x7fcf300cab11 0x7fcf2969ed94 0x7fcf29691050 0x7fcf2973c6d4 0x7fcf2973b544 0x7fcf42f2ea50 0x7fcf440106db 0x7fcf44349a3f
  64/2000 [..............................] - ETA: 22:48 - loss: nan - acc: 1.0000

Hey, Thank you for the amazing implementation of Capsule Network. I tried using the code with a different dataset containing COVID-19 CT samples. And in the starting only I get acc = 1.0000.

Can you help me up with this?

No source for reproducing x_train.npy,y_train.npy and valid.npy

Hello,

I managed to get pretrained data and use it as described in your repository
I inspected your github repository and process the data according to the source of COVID-NET, but the output is data/test and data/train, however in your code you use
x_train= np.load("x_train.npy")
y_train= np.load("y_train.npy")>=3
x_valid= np.load("x_valid.npy")

I did my best, but couldn't find a way to transform the output of COVID-NET into the npy arrays.
Please help me to clarify it.

Thanks.

Cannot construct pre-training dataset

Hi,

Downloaded the images from https://nihcc.app.box.com/v/ChestXray-NIHCC/folder/37178474737 using batch_download_zips.py
As instructed in https://github.com/ShahinSHH/COVID-CAPS/tree/master/database, extracted each zip archive to its corresponding directory database/images_0**/
Ran xray14_preprocess.py. This created database_preprocessed which contains images.
Ran xray14_selection.py. This created X_image.npy (which I renamed as X_images.npy) and Y_labels.npy.
Ran pre-train.py, which gives the following error:

Traceback (most recent call last):
  File "pre-train.py", line 142, in <module>
    x = Capsule(32, 8, 3, True)(x)  
  File "/home/arda/Programs/py3_envs/tfenv/lib/python3.7/site-packages/tensorflow_core/python/keras/engine/base_layer.py", line 842, in __call__
    outputs = call_fn(cast_inputs, *args, **kwargs)
  File "/home/arda/Programs/py3_envs/tfenv/lib/python3.7/site-packages/tensorflow_core/python/autograph/impl/api.py", line 237, in wrapper
    raise e.ag_error_metadata.to_exception(e)
ValueError: in converted code:

    pre-train.py:109 call  *
        b = keras.backend.batch_dot(o, hat_inputs, [2, 3])
    /home/arda/Programs/py3_envs/tfenv/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:1496 batch_dot  *
        raise ValueError('Can not do batch_dot on inputs with shapes ' +

    ValueError: Can not do batch_dot on inputs with shapes (None, 32, 32, 8) and (None, 32, None, 8) with axes=[2, 3]. x.shape[2] != y.shape[3] (32 != 8).