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use arraylist where arraylists are returned
2013-01-18
Stephan Sa
a
lfeld
use arraylist where arraylists are
ret
u
rned
commit
|
commitdiff
|
tree
2013-01-16
S
t
ephan
Saalfeld
adjust
mpic
b
g spring-mesh2 which nee
d
s less damping
commit
|
commitdiff
|
tree
2013-01-11
Step
h
an Saalfel
d
F
i
xed bug
in Patch
.
getFullC
o
ordinat
e
T
ransfor
m
tha
t
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Stephan S
a
alfeld
Cha
n
ged fi
x
edPatc
h
es/Ti
l
es input
c
ollection to Set
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Stepha
n
Saalfeld
Pair
c
on
s
tructo
r
ha
s
to be
p
ubli
c
commit
|
commitdiff
|
tree
2013-01-10
Stephan Saalfeld
f
orgot
to set is
A
ligned
flag
i
n
elastic
la
y
er alignment
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
Stephan Saalfeld
e
la
s
t
i
c
monta
g
e param must be pu
b
lic
commit
|
commitdiff
|
tree
2013-01-07
Stephan Saalfeld
added Patch
.
getFullCordina
t
eTransfo
r
m()
w
h
i
c
h generate
s
a
commit
|
commitdiff
|
tree
2013-01-07
S
t
ephan
S
a
a
lfeld
* removed isAligned fro
m
Abstract
Param class
commit
|
commitdiff
|
tree
2013-01-05
Stephan Saalf
e
ld
877: it
i
s
l
e
gal for
layerT
h
ing to be
null
commit
|
commitdiff
|
tree
2012-12-21
Steph
a
n Saalfeld
Corrected sever
a
l long-standing issues
w
i
t
h
S
I
FT-line
a
r and
commit
|
commitdiff
|
tree
2012-12-19
Ste
p
han Saalfeld
RegularizedLayer
A
lignment got more flexible AP
I
methods
a
n
d
commit
|
commitdiff
|
tree
2012-12-19
Ste
p
han
Saalfeld
clearing cache in l
a
yer alignment must
be default true
commit
|
commitdiff
|
tree
2012-12-19
S
tepha
n
Saalfel
d
print optim
i
zer
r
e
s
ul
t
s
a
nd do
n
ot print "mat
c
hing
.
.
.
commit
|
commitdiff
|
tree
2012-12-19
Stephan
S
aalfeld
do no
t
remove
e
m
pty lay
e
rs
in la
y
e
r alignment
commit
|
commitdiff
|
tree
2012-11-07
Stephan
S
a
alfeld
fix
e
d versi
o
n nu
m
ber of mpicbg depen
d
ency
commit
|
commitdiff
|
tree
2012-11-07
S
tephan Saalfeld
f
ixed merg
e
e
r
ror: moved R
o
bustNormalizeLocalCon
t
rast
.
.
.
commit
|
commitdiff
|
tree
2012-09-01
Stephan
S
aalfeld
multi-threaded R
o
bustNorm
a
lizeL
o
c
a
lContrast mai
n
body
commit
|
commitdiff
|
tree
2012-09-01
Ste
p
h
a
n
Saalfeld
Rem
o
ved
Display
C
anvas
.
setDrawi
n
gCo
l
or(int,int,b
o
olean
.
.
.
commit
|
commitdiff
|
tree
2012-08-31
S
tephan
S
aalfeld
Merge branch 'master' of ssh:
/
/repo
.
or
.
cz
/
srv/
g
it/trak
e
m2
commit
|
commitdiff
|
tree
2012-08-31
Stephan Saalfeld
added
e
xp
e
rimental local
con
t
r
ast enhance
r
Robu
s
tNormalize
L
o
.
.
.
commit
|
commitdiff
|
tree
2012-06-29
Steph
a
n Saalfeld
re
m
oved obsol
e
t
e c
h
oice from
align laye
r
s dialog
commit
|
commitdiff
|
tree
2012-06-26
S
t
eph
a
n
Sa
a
l
feld
s
p
l
i
t
elastic
m
ontage
d
i
alo
g
for block matching and use
commit
|
commitdiff
|
tree
2012-06-26
Stephan
Sa
a
l
f
eld
Merge bra
n
ch 'master' of ssh://repo
.
or
.
cz/srv/git/t
r
a
kem2
commit
|
commitdiff
|
tree
2012-06-26
Stepha
n
Saalfeld
us
e
and do
n
ot ignore alpha
i
n h
e
l
per method
commit
|
commitdiff
|
tree
2012-06-21
S
tepha
n
S
a
alfeld
use th
e
new sequential
d
ialogs
in "montage" f
o
r
a
selection
.
.
.
commit
|
commitdiff
|
tree
2012-06-20
Stephan Saa
l
feld
M
erge b
r
an
c
h 'maste
r
'
of ssh://repo
.
or
.
cz/srv/g
i
t
/
trakem2
commit
|
commitdiff
|
tree
2012-06-20
S
tephan Saalfeld
fixed ra
n
ge c
h
eck in layer alig
n
m
ent
commit
|
commitdiff
|
tree
2012-06-14
S
t
ephan Saalfeld
fi
x
ed c
o
ndition check in Ali
g
n Layers
for
re
g
ularizat
i
on
.
.
.
commit
|
commitdiff
|
tree
2012-06-14
Steph
a
n Saalfel
d
Merge branch 'master' into r
e
gulari
z
ed-a
f
fine
commit
|
commitdiff
|
tree
2012-06-08
Stephan S
a
alfe
l
d
do no
t
conside
r
disco
n
n
ected tiles
commit
|
commitdiff
|
tree
2012-06-08
Stephan Saalfeld
Mer
g
e branch 'reg
u
lari
z
ed-affine' of ssh://r
e
po
.
or
.
.
.
commit
|
commitdiff
|
tree
2012-06-08
Stephan Saalfel
d
pre-
a
lign graphs
a
nd
m
a
t
ch o
n
ly o
v
erlapping tiles
commit
|
commitdiff
|
tree
2012-06-08
S
t
ephan Saalfeld
pre-
a
lign graphs and match only overla
p
p
ing
tiles
commit
|
commitdiff
|
tree
2012-06-08
Stephan Saalfeld
i
nitialize Til
e
models a
n
d
n
ot only patches in
a
lignGraphs
commit
|
commitdiff
|
tree
2012-06-08
Stephan Saalfe
l
d
changed al
i
gnGraphs input c
o
l
l
ections f
r
om
S
et to Iterable
commit
|
commitdiff
|
tree
2012-06-08
Stephan Saalfeld
m
ake su
r
e
th
a
t
stati
c
para
m
e
t
ers do not override each
.
.
.
commit
|
commitdiff
|
tree
2012-06-05
Stephan Saalfeld
r
e
m
ov
e
sp
u
rious import
commit
|
commitdiff
|
tree
2012-06-05
S
tephan Sa
a
lfeld
w
orkaround Oracle javac generics issue
commit
|
commitdiff
|
tree
2012-06-05
S
teph
a
n Saalfeld
m
ul
t
i-laye
r
-mosaic uses Param/
P
aramOptimize
.
set
u
p(Strin
g
.
.
.
commit
|
commitdiff
|
tree
2012-06-05
S
t
e
p
han Sa
a
lf
e
ld
montage la
y
ers uses ParamOpt
i
mize
.
s
e
tup instead of
.
.
.
commit
|
commitdiff
|
tree
2012-06-05
Stephan S
a
alfeld
d
o
not fix a
r
andom tile if none is fixed
commit
|
commitdiff
|
tree
2012-05-29
Stephan S
a
a
lfeld
Co
n
densed
.
mailm
a
p
commit
|
commitdiff
|
tree
2012-05-29
Stephan
Saalfeld
A
dd
e
d
.
mai
l
map
commit
|
commitdiff
|
tree
2012-05-21
Stephan Saalfeld
M
e
rge
branch 'master' i
n
to reg
u
l
a
r
i
z
ed-affine
commit
|
commitdiff
|
tree
2012-05-21
Step
h
an
S
aalfeld
added *None* field to lay
e
r ran
g
e
ref
e
rence select
i
on
commit
|
commitdiff
|
tree
2012-05-21
Stephan Saalf
e
ld
split Align
.
P
a
r
a
mOptimize dialogs in piec
e
s
th
a
t fit
.
.
.
commit
|
commitdiff
|
tree
2012-05-21
Ste
p
han Sa
a
lfeld
add
e
d GenericAffineTi
l
e2D
commit
|
commitdiff
|
tree
2012-05-21
S
tep
h
an Saalfeld
generalized AbstractAf
f
ineTile2D gen
e
r
i
c
parameter
commit
|
commitdiff
|
tree
2012-05-15
St
e
phan
Saalfeld
tra
c
k refactoring in mpicbg
.
commit
|
commitdiff
|
tree
2012-05-09
Stephan S
a
a
lfeld
added r
e
g
ularized affine layer ali
g
nm
e
nt,
commit
|
commitdiff
|
tree
2012-03-28
S
t
ep
h
a
n
S
a
alf
e
ld
fixed createIma
g
e()
:
u
s
e prem
u
lti
p
li
e
d
r
aster
commit
|
commitdiff
|
tree
2012-03-27
Stephan Saalfeld
do no
t
p
rint the mipmap scale
commit
|
commitdiff
|
tree
2012-03-27
Stephan Sa
a
lfeld
for now,
do no
t
us
e
pre-multi
p
li
e
d alpha since
i
t
does
.
.
.
commit
|
commitdiff
|
tree
2012-03-27
S
t
e
p
han Saalfeld
Fixed wr
o
ng painting of
P
a
tches when
u
sing a downsampler
.
.
.
commit
|
commitdiff
|
tree
2012-03-27
Stepha
n
Saalfel
d
Downsample
r
MipMaps now
c
onsistent
l
y u
s
es
combined do
w
n
sampli
.
.
.
commit
|
commitdiff
|
tree
2012-03-27
S
tephan Sa
a
l
f
eld
f
i
x
ed DownsamplerMipMap
s
blending merg
e
d
a
lpha into
.
.
.
commit
|
commitdiff
|
tree
2012-03-27
Stepha
n
Saalfel
d
Do
w
nsampler
te
s
t still
shows it be
i
ng si
g
n
i
fica
n
tly
.
.
.
commit
|
commitdiff
|
tree
2012-03-27
Steph
a
n Saal
f
e
ld
Fixed D
o
w
nsampler: rang
e
check in byte conversion was
.
.
.
commit
|
commitdiff
|
tree
2012-03-27
Stephan Saalfeld
Merge branch
'
integra
l
' of ssh://repo
.
or
.
cz/s
r
v
/git
.
.
.
commit
|
commitdiff
|
tree
2012-03-08
Stephan
Saalfel
d
added
m
i
ssin
g
package to Fa
k
efile
commit
|
commitdiff
|
tree
2012-03-08
S
teph
a
n
Saalfel
d
Merge br
a
n
c
h '
m
aster'
of ssh
:
//repo
.
o
r
.
cz/srv/git/trakem2
commit
|
commitdiff
|
tree
2012-03-08
Stephan Saalfeld
fix lo
c
al
s
c
ale estimate
commit
|
commitdiff
|
tree
2012-03-07
Stephan
S
a
a
l
fe
l
d
added getLocalScale(x,y) method to Patch
commit
|
commitdiff
|
tree
2012-03-07
Ste
p
ha
n
Saalfeld
patch doe
s
not prop
a
gate NonIn
v
ertibleModelException
.
.
.
commit
|
commitdiff
|
tree
2012-03-07
Stephan Sa
a
lf
e
ld
Merge bra
n
ch 'master'
of ssh://rep
o
.
o
r
.
c
z
/srv/git/t
r
a
kem2
commit
|
commitdiff
|
tree
2012-03-07
Stephan Saalf
e
ld
a
d
d
ed methods
to
fe
t
ch the cl
o
sest triangl
e
of a tr
a
n
sf
o
rm
.
.
.
commit
|
commitdiff
|
tree
2012-02-27
Stephan
S
a
a
lfeld
in the m
i
ddle of
.
.
.
amend wit
h
final
commit
commit
|
commitdiff
|
tree
2012-02-27
Stepha
n
Saalfeld
demonstrate byte conv
e
rsion in an
e
xtra loop to b
e
.
.
.
commit
|
commitdiff
|
tree
2012-02-25
Stephan
S
a
alfeld
Me
r
ge b
r
anch 'i
n
tegral' of ssh://repo
.
or
.
cz
/
srv/
g
it
.
.
.
commit
|
commitdiff
|
tree
2012-02-25
Ste
p
ha
n
Saalfeld
Downs
a
mpler
finished
.
I hav
e
t
e
s
t
e
d several varia
n
ts
.
.
.
commit
|
commitdiff
|
tree
2012-02-24
Stephan Saalfeld
exp
e
ri
m
antal c
o
mmit:
commit
|
commitdiff
|
tree
2012-02-23
Stephan S
a
alfeld
Merge bra
n
ch 'in
t
egra
l
'
o
f ssh:/
/
repo
.
o
r
.
cz/srv/git
.
.
.
commit
|
commitdiff
|
tree
2012-02-23
S
tephan Saalfe
l
d
Down
s
a
mpler
w
ith
a
lp
h
a-chan
n
els r
e
nderi
n
g int
o
byt
e
.
.
.
commit
|
commitdiff
|
tree
2012-02-22
Stephan
S
aal
f
eld
Mer
g
e branch 'm
a
ster' of ssh://repo
.
or
.
cz/srv/gi
t
/trakem2
commit
|
commitdiff
|
tree
2012-02-22
S
tephan Saalfeld
set
i
n
terpola
t
io
n
mo
d
e to actual
l
y in
t
erp
o
late masks
commit
|
commitdiff
|
tree
2011-10-01
S
t
e
p
ha
n
S
aalfeld
make IJ
.
log to Utils
.
log in ElasticL
a
yerAlignment
commit
|
commitdiff
|
tree
2011-08-10
Stephan Saalfeld
use Mo
v
ingLeastSquaresTr
a
nsform
2
in
E
lastic
L
ayerAl
i
gn
m
ent
commit
|
commitdiff
|
tree
2011-08-10
Stephan
Saalfeld
us
e
Moving
L
eas
t
SquaresT
r
a
n
sfor
m
2 in E
l
a
sticMontage
commit
|
commitdiff
|
tree
2011-08-10
Stephan Sa
a
lfel
d
use MovingLeastSquaresTra
n
s
f
or
m
2 for warping
in multi
.
.
.
commit
|
commitdiff
|
tree
2011-08-10
Ste
p
han Saalfeld
u
s
e MovingLeastSquare
s
Tra
n
sform2 in
NonLinearT
r
a
n
sformMode
commit
|
commitdiff
|
tree
2011-08-10
Stephan Saalf
e
ld
Add
e
d MovingLeastSquaresTrans
f
orm2 extending
commit
|
commitdiff
|
tree
2011-08-07
St
e
p
h
an
S
aalfeld
E
l
asticLayerAl
i
gnment:
W
hen transferrin
g
layer t
r
an
s
form
a
tio
.
.
.
commit
|
commitdiff
|
tree
2011-08-05
Ste
p
han Saa
l
feld
flush cache betwee
n
laye
r
exp
o
rts (the cache is otherwi
s
e
.
.
.
commit
|
commitdiff
|
tree
2011-08-03
Stephan Saalf
e
ld
free
memory before runn
i
ng
me
m
ory
d
em
a
ndin
g
t
asks in
.
.
.
commit
|
commitdiff
|
tree
2011-08-03
Steph
a
n Saalfeld
fixed bug in linearL
a
yerAl
i
g
n
ment, calc
u
late an
d
apply
.
.
.
commit
|
commitdiff
|
tree
2011-08-02
Steph
a
n Saalfeld
flu
s
h im
a
ge cache memory before doin
g
a montage
commit
|
commitdiff
|
tree
2011-06-29
St
e
phan
Saalfeld
El
a
s
ticM
o
ntage:
commit
|
commitdiff
|
tree
2011-06-29
Stephan Saalfeld
Merge branch 'mas
t
er' int
o
elastic-align
commit
|
commitdiff
|
tree
2011-06-28
Steph
a
n Saalfe
l
d
M
e
rge
br
a
nch 'master' in
t
o
elastic-align
commit
|
commitdiff
|
tree
2011-06-28
Steph
a
n Saalfeld
Added `seem
s
-to-work' el
a
stic
montagin
g
.
Missing
p
art
s
are
commit
|
commitdiff
|
tree
2011-06-28
St
e
phan Saalfeld
* ma
d
e P
a
t
ch
.
Pa
t
c
h
I
m
age a
s
ta
t
i
c
class
(it
h
as no r
e
ferences
.
.
.
commit
|
commitdiff
|
tree
2011-06-24
Stephan Saa
l
feld
added Pair to Abstract
commit
|
commitdiff
|
tree
2011-06-23
Stephan Saal
f
eld
Align
.
ja
v
a: mov
e
d twice
i
m
p
l
emented M
o
del fitting and
.
.
.
commit
|
commitdiff
|
tree
2011-06-23
St
e
phan Saalfeld
E
l
as
t
icAl
i
g
n uses the local s
i
ft
P
aram for ident
i
f
y
i
ng
commit
|
commitdiff
|
tree
2011-06-23
Stephan Saalfeld
Transfor
m
MeshMap
p
ingWit
h
Mask rounds triangel bounding
.
.
.
commit
|
commitdiff
|
tree
2011-06-21
Stepha
n
S
aal
f
eld
att
e
mp
t
to get sha
r
ed
functio
n
for layer al
i
gnment
.
.
.
commit
|
commitdiff
|
tree
2011-06-21
Stephan Saalfeld
ti
t
led mo
n
t
a
ge dialog `
M
ontage
'
con
s
istent
l
y w
i
th the
.
.
.
commit
|
commitdiff
|
tree
2011-06-21
Stephan
S
aalfeld
Fixed Th
r
ead int
e
rrupti
o
n i
n
A
l
ign
.
connectTilePairs
.
.
.
commit
|
commitdiff
|
tree
2011-06-20
Stephan Sa
a
lfeld
`
M
ontage
a
l
l
images in this lay
e
r
':
commit
|
commitdiff
|
tree
next