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Merge branch 'master' into spring-mesh2
2013-03-05
Stephan Saal
f
eld
Me
r
ge branc
h
'mast
e
r
' into sp
r
ing-
m
esh2
commit
|
commitdiff
|
tree
2013-01-18
Stephan Saalfel
d
use arraylist whe
r
e arr
a
y
list
s
are r
e
tu
r
ned
commit
|
commitdiff
|
tree
2013-01-16
St
e
phan Saalfeld
adjust mpicbg s
p
r
i
ng-mesh2 which n
e
eds
l
es
s
d
amping
commit
|
commitdiff
|
tree
2013-01-11
Stephan
S
aalfel
d
F
i
xed
bug in P
a
t
ch
.
getFullC
o
ordinateTra
n
sform that
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
St
e
pha
n
Saalfeld
Changed
fixed
P
atc
h
es
/
Til
e
s in
p
ut collection to S
e
t
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Stephan S
a
al
f
el
d
P
a
ir constructor has t
o
b
e
public
commit
|
commitdiff
|
tree
2013-01-10
St
e
phan Saalfeld
forgot to set isAligne
d
f
l
ag in ela
s
tic laye
r
alignme
n
t
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
S
tepha
n
Sa
a
lfeld
elastic montage param
m
u
st be pu
b
lic
commit
|
commitdiff
|
tree
2013-01-07
Ste
p
h
a
n Saalfeld
added Patch
.
ge
t
FullCordinat
e
Transform() which ge
n
erates a
commit
|
commitdiff
|
tree
2013-01-07
Stepha
n
Saal
f
eld
* removed isAligned
f
ro
m
Abstrac
t
Param class
commit
|
commitdiff
|
tree
2013-01-05
Step
h
an Saalfeld
877:
i
t
is leg
a
l f
o
r
la
y
erThing to
be null
commit
|
commitdiff
|
tree
2012-12-21
S
tephan Saalfeld
C
o
rrected seve
r
al l
o
ng-standing
iss
u
e
s
with
S
I
F
T-l
i
near
and
commit
|
commitdiff
|
tree
2012-12-19
S
te
p
han Saalfeld
Regulariz
e
dLayerAlignme
n
t go
t
more flex
i
ble API methods and
commit
|
commitdiff
|
tree
2012-12-19
Stephan Saalfeld
c
lea
r
i
ng cache in layer alignment must be
d
efault true
commit
|
commitdiff
|
tree
2012-12-19
Stephan
Sa
a
lf
e
ld
print o
p
timizer res
u
lt
s
and do not print
"matching
.
.
.
commit
|
commitdiff
|
tree
2012-12-19
Stephan Saalfeld
do not
r
emove empty layers
i
n
lay
e
r alignment
commit
|
commitdiff
|
tree
2012-11-07
Stephan Saal
f
eld
fixed
v
e
r
s
ion number of mpicbg
d
epen
d
en
c
y
commit
|
commitdiff
|
tree
2012-11-07
Stephan Sa
a
lfeld
f
i
xed merge e
r
ror: moved Robust
N
ormal
i
zeLocal
C
ontrast
.
.
.
commit
|
commitdiff
|
tree
2012-09-01
S
tephan Saalfeld
multi-threa
d
e
d
Robu
s
tNo
r
malizeLoca
l
Contrast
main body
commit
|
commitdiff
|
tree
2012-09-01
Stephan Saalfeld
Removed
D
isplayCa
n
v
as
.
s
etDr
a
win
g
Color(i
n
t,
i
nt
,
boolean
.
.
.
commit
|
commitdiff
|
tree
2012-08-31
S
t
ephan Saalfeld
Merge branch 'mast
e
r'
o
f
s
sh://repo
.
o
r
.
cz/srv/
g
it/trakem2
commit
|
commitdiff
|
tree
2012-08-31
Stephan S
a
alfeld
added exp
e
ri
m
ent
a
l loc
a
l contrast enhancer R
o
bust
N
ormalizeLo
.
.
.
commit
|
commitdiff
|
tree
2012-06-29
S
t
ephan Saalfeld
removed obsolet
e
c
hoice from align
l
aye
r
s dialog
commit
|
commitdiff
|
tree
2012-06-26
Stephan Saalfeld
spl
i
t elas
t
ic montag
e
di
a
log for bl
o
ck matching and use
commit
|
commitdiff
|
tree
2012-06-26
Stephan
Saa
l
f
el
d
Merge bran
c
h
'
master' of ssh://repo
.
o
r
.
cz
/
s
rv/git/trak
e
m2
commit
|
commitdiff
|
tree
2012-06-26
Stephan Saalfel
d
use
and do not ignore alpha
i
n
h
elper
m
e
t
hod
commit
|
commitdiff
|
tree
2012-06-21
Stepha
n
Saalfeld
us
e
the new sequential dial
o
g
s
in "montage" f
o
r a selection
.
.
.
commit
|
commitdiff
|
tree
2012-06-20
S
t
epha
n
Saalfel
d
M
e
r
g
e branch '
m
as
t
er' of ssh://
r
epo
.
or
.
cz/srv/git/trakem2
commit
|
commitdiff
|
tree
2012-06-20
S
tephan
Saalfeld
f
i
x
e
d r
a
nge check
i
n layer
a
lig
n
ment
commit
|
commitdiff
|
tree
2012-06-14
Ste
p
han Saalf
e
l
d
fixed co
n
d
i
tion check in Align La
y
ers
f
or regularization
.
.
.
commit
|
commitdiff
|
tree
2012-06-14
S
tep
h
a
n
Saalfeld
Merge b
r
anch '
m
a
s
ter' into
r
egularized-affine
commit
|
commitdiff
|
tree
2012-06-08
Stephan Saalfeld
do not cons
i
der disc
o
n
n
e
c
ted tiles
commit
|
commitdiff
|
tree
2012-06-08
S
t
e
phan Saal
f
eld
Merge branch 'r
e
gularized-
a
f
f
ine
'
of
ssh://repo
.
or
.
.
.
commit
|
commitdiff
|
tree
2012-06-08
S
t
e
phan Saalfe
l
d
pre
-
align
g
r
aphs and matc
h
only overl
a
pping til
e
s
commit
|
commitdiff
|
tree
2012-06-08
Stephan Saalfeld
pre-align grap
h
s and match only over
l
appin
g
tiles
commit
|
commitdiff
|
tree
2012-06-08
S
tephan Sa
a
lfeld
i
n
itialize
Tile models and
n
ot
onl
y
pat
c
h
e
s in
a
lignGraphs
commit
|
commitdiff
|
tree
2012-06-08
Stephan Saalfeld
c
hange
d
alignGraphs input collections from Set to
I
terable
commit
|
commitdiff
|
tree
2012-06-08
Ste
p
han Saa
l
fe
l
d
make sur
e
that s
t
a
tic
par
a
meters do not o
v
e
rr
i
de eac
h
.
.
.
commit
|
commitdiff
|
tree
2012-06-05
Stephan Saalf
e
ld
remove spurio
u
s imp
o
rt
commit
|
commitdiff
|
tree
2012-06-05
Stephan
S
a
alfe
l
d
wo
r
k
a
rou
n
d Oracle j
a
vac generics issue
commit
|
commitdiff
|
tree
2012-06-05
S
t
epha
n
S
a
al
f
eld
multi
-
l
a
yer-mosaic uses Param
/
ParamOptimize
.
setup
(
String
.
.
.
commit
|
commitdiff
|
tree
2012-06-05
Stephan Saalfeld
mont
a
ge
layers uses ParamOpt
i
mize
.
setup instead
o
f
.
.
.
commit
|
commitdiff
|
tree
2012-06-05
Stephan Saalfeld
d
o
not
f
ix a random ti
l
e if none
is fixed
commit
|
commitdiff
|
tree
2012-05-29
Steph
a
n Saalfeld
Condensed
.
mailmap
commit
|
commitdiff
|
tree
2012-05-29
Stephan S
a
alfeld
Ad
d
ed
.
ma
i
lmap
commit
|
commitdiff
|
tree
2012-05-21
Stephan Saalfeld
Merge branc
h
'master
'
i
n
to
r
eg
u
larized
-
affine
commit
|
commitdiff
|
tree
2012-05-21
Steph
a
n Saa
l
feld
added *None* fiel
d
to lay
e
r
ra
n
ge
reference selection
commit
|
commitdiff
|
tree
2012-05-21
Stephan
Saalfeld
split Align
.
P
aramO
p
ti
m
ize dial
o
gs in pi
e
ces that fit
.
.
.
commit
|
commitdiff
|
tree
2012-05-21
Ste
p
h
an Saalfeld
ad
d
ed GenericAffineTil
e
2D
commit
|
commitdiff
|
tree
2012-05-21
Stephan
S
aa
l
feld
generalized AbstractAffineTile2D
g
eneric paramet
e
r
commit
|
commitdiff
|
tree
2012-05-15
Stepha
n
Sa
a
lf
e
l
d
t
r
a
c
k refactoring in mpicbg
.
commit
|
commitdiff
|
tree
2012-05-09
S
tephan Saalfel
d
added regularized af
f
ine layer alignment,
commit
|
commitdiff
|
tree
2012-03-28
Stephan Saalf
e
ld
fixe
d
c
re
a
teIma
g
e(): use premultiplied raster
commit
|
commitdiff
|
tree
2012-03-27
Stephan Saalf
e
ld
d
o not print th
e
mipm
a
p s
c
ale
commit
|
commitdiff
|
tree
2012-03-27
Step
h
an Saalfeld
for n
o
w, d
o
not use pre-multi
p
lied
alpha
since it does
.
.
.
commit
|
commitdiff
|
tree
2012-03-27
Stephan Saa
l
feld
Fixed wrong
p
ainting of Patches when
us
i
n
g
a
dow
n
sampler
.
.
.
commit
|
commitdiff
|
tree
2012-03-27
St
e
phan Saalfeld
Downs
a
mp
l
erMipMa
p
s now con
s
iste
n
tly uses combin
e
d downsampli
.
.
.
commit
|
commitdiff
|
tree
2012-03-27
Ste
p
han S
a
alfeld
fi
x
ed Downsampl
e
r
MipMaps bl
e
nding merg
e
d
a
lp
h
a into
.
.
.
commit
|
commitdiff
|
tree
2012-03-27
Steph
a
n Saal
f
el
d
Down
s
ampler t
e
st still
sho
w
s it being
s
ignif
i
cantly
.
.
.
commit
|
commitdiff
|
tree
2012-03-27
S
t
ephan S
a
alfel
d
Fix
e
d Downsam
p
ler: r
a
n
ge check in byte conversion wa
s
.
.
.
commit
|
commitdiff
|
tree
2012-03-27
Stephan S
a
alfeld
Merge bra
n
ch
'
int
e
gra
l
'
o
f
ssh://repo
.
or
.
cz/srv/git
.
.
.
commit
|
commitdiff
|
tree
2012-03-08
Stephan Saalfeld
added missi
n
g p
a
ckage to
F
akefile
commit
|
commitdiff
|
tree
2012-03-08
Stephan Saalfeld
Merge branch
'
master
'
o
f
ssh://rep
o
.
o
r
.
cz/sr
v
/git/trak
e
m2
commit
|
commitdiff
|
tree
2012-03-08
Stephan Saalfeld
fix local scale est
i
mate
commit
|
commitdiff
|
tree
2012-03-07
S
tephan
S
aalfeld
added getLocal
S
ca
l
e(x,y) metho
d
to Patch
commit
|
commitdiff
|
tree
2012-03-07
Stephan Saalfe
l
d
p
atch does not propaga
t
e NonInve
r
tibleM
o
del
E
xceptio
n
.
.
.
commit
|
commitdiff
|
tree
2012-03-07
St
e
phan
S
aalfeld
Merge branch
'
mas
t
e
r
' of ssh://r
e
p
o
.
or
.
cz/sr
v
/git
/
trakem2
commit
|
commitdiff
|
tree
2012-03-07
Steph
a
n
Saalfel
d
add
e
d methods
t
o fetch the closes
t
triangle of a transform
.
.
.
commit
|
commitdiff
|
tree
2012-02-27
S
tephan Sa
a
lf
e
ld
i
n
the m
i
ddle
of
.
.
.
amend wi
t
h fina
l
com
m
it
commit
|
commitdiff
|
tree
2012-02-27
Steph
a
n Saa
l
fel
d
demonstrat
e
byte
con
v
e
rsi
o
n in an extra loop t
o
be
.
.
.
commit
|
commitdiff
|
tree
2012-02-25
Stephan Saalfeld
M
erge branch 'integr
a
l'
of ssh://re
p
o
.
or
.
cz/srv/git
.
.
.
commit
|
commitdiff
|
tree
2012-02-25
Stephan Saal
f
eld
Dow
n
s
a
mpler finis
h
e
d
.
I h
a
ve tested
several variants
.
.
.
commit
|
commitdiff
|
tree
2012-02-24
Stephan Saa
l
feld
experimant
a
l com
m
it:
commit
|
commitdiff
|
tree
2012-02-23
Step
h
an
S
aa
l
feld
Merge b
r
an
c
h
'
i
n
t
eg
r
al' of ssh://repo
.
or
.
cz/srv/g
i
t
.
.
.
commit
|
commitdiff
|
tree
2012-02-23
Step
h
an Saalfeld
D
o
wnsampler
w
ith
alpha-chan
n
els rende
r
ing
into byte
.
.
.
commit
|
commitdiff
|
tree
2012-02-22
Stephan Saalfeld
Merge branc
h
'master' of ssh:
/
/repo
.
or
.
c
z/s
r
v/
g
it/trakem2
commit
|
commitdiff
|
tree
2012-02-22
Step
h
an
Saalfe
l
d
s
e
t interpola
t
ion mode to actually
interpolate ma
s
ks
commit
|
commitdiff
|
tree
2011-10-01
Steph
a
n Saalfeld
make IJ
.
log
to Utils
.
log
in
ElasticLayerA
l
ignment
commit
|
commitdiff
|
tree
2011-08-10
Step
h
an Saalfeld
use MovingLeastSquaresTransform2 in ElasticLayerA
l
ignment
commit
|
commitdiff
|
tree
2011-08-10
Steph
a
n
S
aa
l
feld
use MovingLeastSquaresTransform2 in Ela
s
tic
M
ontage
commit
|
commitdiff
|
tree
2011-08-10
Stephan Saa
l
feld
use
MovingLeastSquaresTransform2
for warpi
n
g in multi
.
.
.
commit
|
commitdiff
|
tree
2011-08-10
Stephan Saa
l
feld
use Movi
n
gLeastSquaresTransform2
i
n NonL
i
n
earTransformMode
commit
|
commitdiff
|
tree
2011-08-10
Stephan Saalfe
l
d
A
d
d
e
d
MovingLeastSquaresTransform2 extending
commit
|
commitdiff
|
tree
2011-08-07
Stephan
S
a
a
lfeld
E
lasticLayerA
l
ignm
e
nt: When transferring layer
t
ransformatio
.
.
.
commit
|
commitdiff
|
tree
2011-08-05
Stephan Saalfel
d
flush cach
e
b
etwee
n
l
ayer
e
xports (t
h
e cach
e
is otherwi
s
e
.
.
.
commit
|
commitdiff
|
tree
2011-08-03
Stephan
S
a
alfeld
free memory before run
n
ing m
e
mory d
e
manding
t
a
sks in
.
.
.
commit
|
commitdiff
|
tree
2011-08-03
Stephan Saalfeld
fixed bug in
linearLayerAl
i
gnment
,
calcul
a
te and
a
pply
.
.
.
commit
|
commitdiff
|
tree
2011-08-02
Step
h
a
n Saalfeld
f
l
ush
i
m
a
ge
ca
c
he
m
emory before doing a montage
commit
|
commitdiff
|
tree
2011-06-29
Steph
a
n Saalfeld
E
lasticM
o
ntage:
commit
|
commitdiff
|
tree
2011-06-29
Ste
p
han
S
aalfeld
Merge branch
'
master'
into elastic-align
commit
|
commitdiff
|
tree
2011-06-28
Stepha
n
Saalf
e
ld
Merge branch 'mas
t
e
r' into elastic-al
i
gn
commit
|
commitdiff
|
tree
2011-06-28
Stephan Saalfe
l
d
A
d
de
d
`se
e
ms
-
to-work' elas
t
ic montaging
.
Missing part
s
are
commit
|
commitdiff
|
tree
2011-06-28
Steph
a
n Saalfe
l
d
* made Patch
.
Pa
t
chImage a static class (it has no re
f
erences
.
.
.
commit
|
commitdiff
|
tree
2011-06-24
Ste
p
han Saal
f
eld
ad
d
ed Pair to Ab
s
tract
commit
|
commitdiff
|
tree
2011-06-23
Ste
p
h
an Saalfeld
Align
.
java: move
d
twic
e
implem
e
nted Model
f
itting and
.
.
.
commit
|
commitdiff
|
tree
2011-06-23
Stephan S
a
alfeld
ElasticAlign uses the local siftPar
a
m for iden
t
ifyin
g
commit
|
commitdiff
|
tree
2011-06-23
Ste
p
ha
n
S
aa
l
feld
Tr
a
ns
f
ormMeshM
a
ppingWithMask
rou
n
ds triangel
b
ound
i
n
g
.
.
.
commit
|
commitdiff
|
tree
2011-06-21
S
tephan
Saalfeld
a
ttempt to get shared
function for layer
alignme
n
t
.
.
.
commit
|
commitdiff
|
tree
2011-06-21
Ste
p
han Saalf
e
ld
titl
e
d
mon
t
ag
e
di
a
log `Monta
g
e' consistently with t
h
e
.
.
.
commit
|
commitdiff
|
tree
2011-06-21
Ste
p
han Saalfel
d
Fixed Thread
i
nt
e
rruption
in
A
lign
.
connectTilePai
r
s
.
.
.
commit
|
commitdiff
|
tree
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