Harsha

`what were you trying to do?` generating a sample brain with synthseg (using default parameters) `what did you expect will happen?` generates a sample without raising any error `what actually...

## Types of changes - [ ] Bug fix (non-breaking change which fixes an issue) - [ ] New feature (non-breaking change which adds functionality) - [ ] Breaking change...

Since the default metric is dice, resuming from a previously trained checkpoint won't pose any issue. However, if the model was initially trained using a different metric or loss. Then,...

https://github.com/neuronets/nobrainer/blob/976691d685824fd4bba836498abea4184cffd798/nobrainer/processing/base.py#L28 `What would you like changed/added and why?` - Similar to `model_args`, I'd like to see `checkpoint_args` passed from outside. `What would be the benefit?` - For example, if I...

Get checkpoint based on create time is probably not a good idea

6

https://github.com/neuronets/nobrainer/blob/976691d685824fd4bba836498abea4184cffd798/nobrainer/processing/checkpoint.py#L57 What am I trying to do? Initialize from a previous checkpoint, to resume training over more epochs. For example, the following snippet ``` try: bem = Segmentation.init_with_checkpoints( "unet", model_args=dict(batchnorm=True),...

refactor code to calculate records per shard using n_volumes and number of shards

2

https://github.com/neuronets/nobrainer/blob/976691d685824fd4bba836498abea4184cffd798/nobrainer/dataset.py#L115-L122 If the number of volumes in the shard is too large, this snippet of code can be time-consuming. Alternatives are - use a combination of `n_volumes` and number of...

Add data count to tfrecords

6

We decided to add an extra feature to each record/example labeled "data_count". While we do this, we also need to add logic to adjust the number of volumes in each...

Refactor code to identify correct steps per epoch

1

Following is an example of how the steps per epoch are incorrect whereas the number of batches is correct. This is because the `get_steps_per_epoch` uses `n_volumes` whereas getting the number...

map_labels fails for n_classes > 1

1

``` File "/net/vast-storage/scratch/vast/gablab/hgazula/nobrainer/nobrainer/dataset.py", line 338, in None * lambda x, y: (x, tf.one_hot(y, self.n_classes)) TypeError: Value passed to parameter 'indices' has DataType float32 not in list of allowed values: uint8,...

suggested refactoring to avoid OOM errors

1

https://github.com/neuronets/nobrainer/blob/cb855feaadd4ac354e1e2d1c760a649df3f61ab4/nobrainer/dataset.py#L249-L250 Suggestion: ``` def scalar_labels(self): temp_ds = self.dataset.map( lambda _, y: tf.experimental.numpy.isscalar(y), deterministic=False, num_parallel_calls=AUTOTUNE, ) return tf.math.reduce_all(list(temp_ds.as_numpy_iterator())).numpy() ``` Notes: 1. The previous snippet collects all label volumes into a list...