Case_tube_idx change

[hermands]

Hey Dave, Please test and merge onto master. Thank you! I have handled several downstream issues, but maybe not all...not sure if this error is related:

COMMAND: dev/test_run.sh ~/FCS_2014/ 3

FAILURE is in Extract features --> (I didn't notice this previously)

Extract features ############ │

INFO make_features 51 Creating hdf5 file [db/fcs_features.hdf5] with features extracted by method [Full] │
INFO make_features 54 Loading database input db/fcs.db │
INFO query_database 38 Querying... │
INFO query_database 319 Looking for db creation_date │
INFO query_database 38 Querying... │
INFO query_database 129 Looking for files │
INFO make_features 67 Case: 14-23088, Case_tube_idx: 0, File: 14-23000-23099/14-23088/14-23088_addon.fcs │
INFO make_features 67 Case: 14-23088, Case_tube_idx: 1, File: 14-23000-23099/14-23088/14-23088_Myeloid 4.fcs │
Skipping feature extraction for case: 14-23088 because of 'ValueError The truth value of an array with more than one element is ambiguou│
s. Use a.any() or a.all()' │
INFO make_features 67 Case: 14-23088, Case_tube_idx: 2, File: 14-23000-23099/14-23088/14-23088_Myeloid 2.fcs │
Skipping feature extraction for case: 14-23088 because of 'ValueError The truth value of an array with more than one element is ambiguou│
s. Use a.any() or a.all()' │
INFO make_features 67 Case: 14-23088, Case_tube_idx: 3, File: 14-23000-23099/14-23088/14-23088_Myeloid 1.fcs │
Skipping feature extraction for case: 14-23088 because of 'ValueError The truth value of an array with more than one element is ambiguou│
s. Use a.any() or a.all()' │
INFO make_features 102 Case_tubes that failed feature extraction: [u'14-23088'] │
INFO query_database 38 Querying... │
INFO query_database 382 Flagging case_tube_idxs because of ['feat_extract_failed', 'feat_extract_failed', 'feat_extract_failed']

[hermands]

NOTE: The way this is implemented is such that whenever you instantiate an FCS_object now, it will probably want case_tube_idx to be passed to it.