Thanks for this repo. I ran the steps to download and preprocess data. It also starts training, but fails in the last batch of the first epoch. I'm using TF1.14 (not 1.15 as prescribed on the README), however I doubt that has anything to do with this error. Could this be a h5py version issue?
[UPDATE]: Before training, I set USE_KERAS_API to False, hence forcing it to pick tf.keras. Could this be the same issue referred in settings.py?
------------------------------
Fitting model with training data ...
------------------------------
Step 3, training the model started at 2020-06-16 12:51:03.365806
Train on 62930 samples, validate on 4960 samples
Epoch 1/40
62848/62930 [============================>.] - ETA: 1s - loss: 0.7630 - acc: 0.9642 - dice_coef: 0.6290 - soft_dice_coef: 0.2496
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
/scratch/sambhavj/anaconda3/envs/tf1.14/lib/python3.6/site-packages/h5py/_hl/selections.py in select(shape, args, dsid)
84 try:
---> 85 int(a)
86 if isinstance(a, np.ndarray) and a.shape == (1,):
TypeError: int() argument must be a string, a bytes-like object or a number, not 'list'
------------------------------
Fitting model with training data ...
------------------------------
Step 3, training the model started at 2020-06-16 12:51:03.365806
Train on 62930 samples, validate on 4960 samples
Epoch 1/40
62848/62930 [============================>.] - ETA: 1s - loss: 0.7630 - acc: 0.9642 - dice_coef: 0.6290 - soft_dice_coef: 0.2496
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
/scratch/sambhavj/anaconda3/envs/tf1.14/lib/python3.6/site-packages/h5py/_hl/selections.py in select(shape, args, dsid)
84 try:
---> 85 int(a)
86 if isinstance(a, np.ndarray) and a.shape == (1,):
TypeError: int() argument must be a string, a bytes-like object or a number, not 'list'
During handling of the above exception, another exception occurred:
TypeError Traceback (most recent call last)
/scratch/sambhavj/anaconda3/envs/tf1.14/lib/python3.6/site-packages/tensorflow/python/keras/engine/training_arrays.py in model_iteration(model, inputs, targets, sample_weights, batch_size, epochs, verbose, callbacks, val_inputs, val_targets, val_sample_weights, shuffle, initial_epoch, steps_per_epoch, validation_steps, validation_freq, mode, validation_in_fit, prepared_feed_values_from_dataset, steps_name, **kwargs)
345 else:
--> 346 ins_batch = slice_arrays(ins, batch_ids)
347 except TypeError:
/scratch/sambhavj/anaconda3/envs/tf1.14/lib/python3.6/site-packages/tensorflow/python/keras/utils/generic_utils.py in slice_arrays(arrays, start, stop)
530 start = start.tolist()
--> 531 return [None if x is None else x[start] for x in arrays]
532 else:
/scratch/sambhavj/anaconda3/envs/tf1.14/lib/python3.6/site-packages/tensorflow/python/keras/utils/generic_utils.py in <listcomp>(.0)
530 start = start.tolist()
--> 531 return [None if x is None else x[start] for x in arrays]
532 else:
/data/unet-intelai/2D/data.py in __getitem__(self, key)
158 """
--> 159 data = super().__getitem__(key)
160 self.idx += 1
/scratch/sambhavj/anaconda3/envs/tf1.14/lib/python3.6/site-packages/tensorflow/python/keras/utils/io_utils.py in __getitem__(self, key)
113 else:
--> 114 return self.data[idx]
115
h5py/_objects.pyx in h5py._objects.with_phil.wrapper()
h5py/_objects.pyx in h5py._objects.with_phil.wrapper()
/scratch/sambhavj/anaconda3/envs/tf1.14/lib/python3.6/site-packages/h5py/_hl/dataset.py in __getitem__(self, args)
552 # Perform the dataspace selection.
--> 553 selection = sel.select(self.shape, args, dsid=self.id)
554
/scratch/sambhavj/anaconda3/envs/tf1.14/lib/python3.6/site-packages/h5py/_hl/selections.py in select(shape, args, dsid)
89 sel = FancySelection(shape)
---> 90 sel[args]
91 return sel
/scratch/sambhavj/anaconda3/envs/tf1.14/lib/python3.6/site-packages/h5py/_hl/selections.py in __getitem__(self, args)
366 if any(fst >= snd for fst, snd in adjacent):
--> 367 raise TypeError("Indexing elements must be in increasing order")
368
TypeError: Indexing elements must be in increasing order
During handling of the above exception, another exception occurred:
TypeError Traceback (most recent call last)
<ipython-input-24-41921214fca5> in <module>
23 validation_data=(imgs_validation, msks_validation),
24 verbose=1, shuffle="batch",
---> 25 callbacks=model_callbacks)
26
27 print("Total time elapsed for training = {} seconds".format(time.time() - start_time))
/scratch/sambhavj/anaconda3/envs/tf1.14/lib/python3.6/site-packages/tensorflow/python/keras/engine/training.py in fit(self, x, y, batch_size, epochs, verbose, callbacks, validation_split, validation_data, shuffle, class_weight, sample_weight, initial_epoch, steps_per_epoch, validation_steps, validation_freq, max_queue_size, workers, use_multiprocessing, **kwargs)
778 validation_steps=validation_steps,
779 validation_freq=validation_freq,
--> 780 steps_name='steps_per_epoch')
781
782 def evaluate(self,
/scratch/sambhavj/anaconda3/envs/tf1.14/lib/python3.6/site-packages/tensorflow/python/keras/engine/training_arrays.py in model_iteration(model, inputs, targets, sample_weights, batch_size, epochs, verbose, callbacks, val_inputs, val_targets, val_sample_weights, shuffle, initial_epoch, steps_per_epoch, validation_steps, validation_freq, mode, validation_in_fit, prepared_feed_values_from_dataset, steps_name, **kwargs)
407 validation_in_fit=True,
408 prepared_feed_values_from_dataset=(val_iterator is not None),
--> 409 steps_name='validation_steps')
410 if not isinstance(val_results, list):
411 val_results = [val_results]
/scratch/sambhavj/anaconda3/envs/tf1.14/lib/python3.6/site-packages/tensorflow/python/keras/engine/training_arrays.py in model_iteration(model, inputs, targets, sample_weights, batch_size, epochs, verbose, callbacks, val_inputs, val_targets, val_sample_weights, shuffle, initial_epoch, steps_per_epoch, validation_steps, validation_freq, mode, validation_in_fit, prepared_feed_values_from_dataset, steps_name, **kwargs)
346 ins_batch = slice_arrays(ins, batch_ids)
347 except TypeError:
--> 348 raise TypeError('TypeError while preparing batch. '
349 'If using HDF5 input data, '
350 'pass shuffle="batch".')
TypeError: TypeError while preparing batch. If using HDF5 input data, pass shuffle="batch".
. 
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