Upsampling seems to be stuck / going on forever without changes

[Djoels]

Upon trying to upsample using the upsampling.py script, after a while the process just stops changing, and the script seems to be stuck in an eternal loop.

The output of the analyse_classes function looks the same every time and the number of files in the Upsample_Set folder isn't increasing anymore.

Disease_Risk 4384 1.0
DR 752 0.17153284671532848
ARMD 275 0.06272810218978102
MH 500 0.11405109489051095
DN 343 0.07823905109489052
MYA 198 0.045164233576642336
BRVO 219 0.049954379562043794
TSLN 495 0.11291058394160584
ERM 128 0.029197080291970802
LS 139 0.03170620437956204
MS 105 0.023950729927007298
CSR 110 0.02509124087591241
ODC 719 0.16400547445255476
CRVO 100 0.02281021897810219
TV 102 0.023266423357664233
AH 101 0.02303832116788321
ODP 349 0.07960766423357664
ODE 362 0.08257299270072993
ST 101 0.02303832116788321
AION 101 0.02303832116788321
PT 101 0.02303832116788321
RT 104 0.023722627737226276
RS 187 0.042655109489051095
CRS 104 0.023722627737226276
EDN 196 0.04470802919708029
RPEC 102 0.023266423357664233
MHL 115 0.026231751824817517
RP 100 0.02281021897810219
CWS 102 0.023266423357664233
CB 100 0.02281021897810219
ODPM 0 0.0
PRH 100 0.02281021897810219
MNF 101 0.02303832116788321
HR 0 0.0
CRAO 100 0.02281021897810219
TD 102 0.023266423357664233
CME 115 0.026231751824817517
PTCR 101 0.02303832116788321
CF 101 0.02303832116788321
VH 100 0.02281021897810219
MCA 100 0.02281021897810219
VS 100 0.02281021897810219
BRAO 100 0.02281021897810219
PLQ 100 0.02281021897810219
HPED 100 0.02281021897810219
CL 100 0.02281021897810219

I notice a number of disease categories being zero valued...
Could this be the problem?