Appion

I have found problems while using myami/trunk the number of particles differ between stacks when changing from invert to no invert. The number of particles decrease by approximately 2%. I have tried this multiple times on different data sets. When switching back to myami/3.2 this problem goes away. When I run the very first stack using myami/3.2 instead of myami/trunk I gain 3,000 particles.
Here are example of two command lines

/opt/applications/myami/trunk/bin/makestack2.py \
--single=start.hed --fromstackid=7 --no-invert --normalize-method=edgenorm \
--boxsize=384 --bin=2 --filetype=imagic --forceInsert --description=stack12 \
--runname=stack12 --rundir=/gpfs/group/em/appion/kubalek/17may30d/stacks/stack12 \
--preset=ed-a-DW --commit --projectid=503 --session=17may30d \
--no-rejects --no-wait --continue --expid=19529 --jobtype=makestack2
[Tue Jun 13 15:39:30 2017]
finished run of makestack2

The number of particles in the above stack =61,018

running the above stack with only the density inverted

[ kubalek@emb0633: Wed Jun 21 14:13:13 2017 ]
/opt/applications/myami/trunk/bin/makestack2.py \
--single=start.hed --fromstackid=13 --invert --normalize-method=edgenorm \
--boxsize=384 --bin=2 --filetype=imagic --forceInsert --description='test redo of stack12' \
--runname=stack21 --rundir=/gpfs/group/em/appion/kubalek/17may30d/stacks/stack21 \
--preset=ed-a-DW --commit --projectid=503 --session=17may30d \
--no-rejects --no-wait --continue --expid=19529 --jobtype=makestack2

the number in this stack now 58,746