mute tf1.15 warnings; resume unet (nonewnet) unit tests

.gitlab-ci.yml

@@ -93,8 +93,8 @@ testjob:
  - coverage run -a --source . net_segment.py inference -c config/vnet_config.ini --batch_size 16 --spatial_window_size 64,64,64 --queue_length 32 --activation_function relu
 
  # need a large GPU to run
-  #- coverage run -a --source . net_segment.py train -c config/unet_config.ini --batch_size 1 --queue_length 5 --num_threads 2
-  #- coverage run -a --source . net_segment.py inference -c config/unet_config.ini --batch_size 1 --spatial_window_size 96,96,96 --queue_length 5
+ - coverage run -a --source . net_segment.py train -c config/unet_config.ini --batch_size 1 --queue_length 5 --num_threads 2
+ - coverage run -a --source . net_segment.py inference -c config/unet_config.ini --batch_size 1 --spatial_window_size 96,96,96 --queue_length 5
 
  #- coverage run -a --source . net_segment.py train -c config/deepmedic_config.ini --batch_size 128 --queue_length 48 --num_threads 4
  #- coverage run -a --source . net_segment.py inference -c config/deepmedic_config.ini --batch_size 12 --spatial_window_size 135,135,135 --queue_length 128

config/unet_config.ini

@@ -11,7 +11,7 @@ interp_order = 3
 path_to_search = ./example_volumes/monomodal_parcellation
 filename_contains = Label
 filename_not_contains =
-spatial_window_size = (8, 8, 8)
+spatial_window_size = (96, 96, 96)
 pixdim = (1.0, 1.0, 1.0)
 axcodes=(A, R, S)
 interp_order = 0
@@ -23,14 +23,14 @@ num_gpus = 1
 model_dir = ./models/model_unet
 
 [NETWORK]
-name = unet
+name = nonewnet
 activation_function = prelu
 batch_size = 1
 decay = 0
 reg_type = L2
 
 # volume level preprocessing
-volume_padding_size = 44
+volume_padding_size = 10
 # histogram normalisation
 histogram_ref_file = ./example_volumes/monomodal_parcellation/standardisation_models.txt
 norm_type = percentile
@@ -56,11 +56,11 @@ max_iter = 10
 max_checkpoints = 20
 
 [INFERENCE]
-border = (24, 24, 24)
-#inference_iter = 10
+# border = (24, 24, 24)
+# inference_iter = 10
 save_seg_dir = ./output/unet
 output_interp_order = 0
-spatial_window_size = (105, 105, 105)
+spatial_window_size = (104, 104, 104)
 
 ############################ custom configuration sections
 [SEGMENTATION]

niftynet/__init__.py

@@ -44,6 +44,17 @@
 
 import os
 
+os.environ['TF_CPP_MIN_LOG_LEVEL'] = '2'
+tf.compat.v1.logging.set_verbosity(tf.compat.v1.logging.ERROR)
+from tensorflow.python.util import deprecation
+deprecation._PRINT_DEPRECATION_WARNINGS = False
+try:
+ from tensorflow.python.util import module_wrapper as deprecation
+except ImportError:
+ from tensorflow.python.util import deprecation_wrapper as deprecation
+deprecation._PER_MODULE_WARNING_LIMIT = 0
+
+
 from niftynet.io.misc_io import set_logger, close_logger
 
 set_logger()