Chenhao 180504 (#5)

* put training and validation loss in the same graph

* Renamed file and changed read in details.

* Changed read in details and pickle filename.

* Fixed hardcoded data dir.

* Change no. classes.

* Change to see if it fixes something

* removed log files from git

* Added method for predictions.

* Added printed messages to predict.

* Fixed print

* Fixed format string statements.

* Changed resize to True for predict.

* Fixed filename for saving

* Added forgotten squeeze on pred in predict code.

* Create predictions folder if it doesn't exist.

* Slight updates to dropout and BatchDatsetReader

* Added image augmentation.

* Fixed usage of wrong name of FLAGS.dropout_keep_prob.

* Fixed BatchDatasetReader and changed dropout_keep_value to dropout in FLAGS.

* Fixed bug in BatchDatasetReader

* Added back in an accidentally deleted line.

* Fixed empty list/None check which is incompatible with Numpy.

* Fixed call of np.concatenate

* removed expand_dims for annotations.

* Properly check if annotation_file is not None.

* Mostly implemented new data pipeline.

* Changed DatasetReader record holding structure slightly.

* Fixed using wrong value for iteration.

* Some possibly working changes to reader.

* May have fixed input problem.

* Actually made the change intended in last commit.

* Fixed minor bugs.

* Fixed bug with annotation checking.

* Removed static.

* Fixed map bug.

* Reverted lambda in TFRreader after discovering cause of bug.

* Check for no annotation.

* Might have fixed bug.

* Fixed references to dataset.

* Fixed self.self

* Readded code accidentally removed previously, changed dimension to axi in annotation_pred = tf.argmax(...) because the dimension argument will be depricated in the future.

* Changed call to next to call to sess.run.

* Added resizing.

* Fixed decoding based on tf bug tensorflow/tensorflow#9356.

* Changed iteration getting method.

* Fixed not reading in annotations and other minor fixes.

* Actually fixed iterator getting in FCN.py

* Train ops now set to work with tensors rather than placeholders.

* Added trainable_var above saver.

* Revert "Added trainable_var above saver."

This reverts commit 6011e0b.

* Revert "Train ops now set to work with tensors rather than placeholders."

This reverts commit 6f12d7d.

* Should work now using placeholders.

* Might have fixed annotation shape.

* Fixed _augment_image where annotation image was set to the same as image.

* Added extra dimension to annotation.

* Some minor changes to TFReader.

* Fixed predict with new dataset workflow.

* Slight change to TFRreader.

* Fixed problem with SingleDataset.

* Fixed referencing dataset rather than DatasetReader.

* Changed Dataset Reader to also output filename.

* Fixed multiple runs of predict_names.

* Added Jupyter Notebook for viewing results

* Update current FCN code