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Merge remote-tracking branch 'origin/master'
2014-12-12
Stephan S
a
a
l
f
e
l
d
Merge remo
t
e-track
i
n
g
branch 'o
r
i
gin/master'
commit
|
commitdiff
|
tree
2014-12-12
Stephan Saalfeld
bump
to
new develo
p
m
e
nt c
y
cle
commit
|
commitdiff
|
tree
2014-12-12
Stephan
S
aalfeld
reproducible build pom-trakem2
-
1
.
1
.
0
commit
|
commitdiff
|
tree
2014-12-12
Stephan Saal
f
e
ld
Merge bran
c
h
'
ma
s
t
e
r' of
g
i
thub
.
com:trakem2/
T
ra
k
E
M
2
commit
|
commitdiff
|
tree
2014-11-12
St
e
phan Sa
a
lfeld
U
pd
a
te README
commit
|
commitdiff
|
tree
2014-11-12
S
tepha
n
Saalfeld
Update R
E
A
DME
commit
|
commitdiff
|
tree
2014-11-07
Stephan
S
aalfeld
Merge br
a
n
ch 'master' into
c
o
o
rdXfmFix
commit
|
commitdiff
|
tree
2014-11-07
Stephan
S
aa
l
fe
l
d
Merge remote-tra
c
king b
r
anch 'origin/intensity-
t
ransform'
commit
|
commitdiff
|
tree
2014-10-04
Stepha
n
Saalfeld
added R
o
bustNormalizedLocalContrastFilter
,
fast and
.
.
.
commit
|
commitdiff
|
tree
2014-10-04
S
tephan
S
aalfel
d
Changed default block radius
in
Normalize
L
ocalContrast
.
.
.
commit
|
commitdiff
|
tree
2014-10-02
Stephan Saal
f
eld
auto-removed
some
training w
h
itespa
c
es
commit
|
commitdiff
|
tree
2014-10-02
Step
h
an Saalfeld
a
dded run me
t
h
o
d that does no
t
need a worker for e
a
s
ie
r
.
.
.
commit
|
commitdiff
|
tree
2014-10-02
Ste
p
h
a
n
S
a
alfeld
a
u
to-remo
v
ed some tra
i
ling whit
e
spaces
commit
|
commitdiff
|
tree
2014-10-02
Stephan Saa
l
f
eld
parallel
i
z
e
d intersect
i
on tests for
p
airOverlappingTiles
commit
|
commitdiff
|
tree
2014-10-02
Stephan Saalfeld
a
u
to-
f
inalize
c
onstant propert
i
es and
p
aramete
r
s in
.
.
.
commit
|
commitdiff
|
tree
2014-10-02
Steph
a
n Saalfeld
threadsafe Utils
.
ensure(File)
commit
|
commitdiff
|
tree
2014-06-06
Stephan Saalfeld
f
ixed bug i
n
gen
e
ration
of alpham
a
sks
commit
|
commitdiff
|
tree
2014-06-05
S
t
epha
n
S
a
a
l
fel
d
external
i
zed
Distor
t
ionC
o
rrecti
o
n
.
run to enab
l
e calling
.
.
.
commit
|
commitdiff
|
tree
2014-06-05
St
e
p
han Saalfe
l
d
Eclipse autu-cosmet
i
cs
i
n D
i
stort
i
onCor
r
ection
commit
|
commitdiff
|
tree
2014-05-19
Stephan Saal
f
eld
M
e
r
g
e
branch 'master' into intensity
-
trans
f
orm
commit
|
commitdiff
|
tree
2014-05-19
Stephan Saal
f
eld
u
se
standard writer for coordinat
e
transforms
commit
|
commitdiff
|
tree
2014-05-19
Stephan Saa
l
feld
d
e
pend on javax
.
medi
a
for jai
commit
|
commitdiff
|
tree
2014-05-19
S
t
ep
h
an Saalfeld
add
e
d meth
o
d
s
f
or
downsam
p
li
n
g more than one
l
evel
commit
|
commitdiff
|
tree
2013-10-10
S
teph
a
n Saalfeld
replaced plugins
.
config with the Fiji
version
commit
|
commitdiff
|
tree
2013-09-20
St
e
pha
n
Saalfe
l
d
Me
r
ge branch
'
m
a
ster' o
f
ssh://rep
o
.
or
.
cz/s
r
v
/git/trakem2
commit
|
commitdiff
|
tree
2013-09-19
Stephan Saalfeld
M
erge branch 'master' of ssh://repo
.
or
.
cz/srv/git/
t
rakem2
commit
|
commitdiff
|
tree
2013-09-19
S
tephan Saalfeld
Para
l
lel pair
O
verl
a
ppingTiles did not work
a
nd reported
.
.
.
commit
|
commitdiff
|
tree
2013-09-16
Stephan Saalfeld
Merge
b
r
a
n
ch 'ma
s
ter'
of
s
sh:
/
/repo
.
or
.
cz/srv/git/t
r
ake
m
2
commit
|
commitdiff
|
tree
2013-09-16
Stephan
S
a
alfeld
r
e-ad
d
ed legacy optimize
r
for sprin
g
meshes, this
w
ould
.
.
.
commit
|
commitdiff
|
tree
2013-09-16
Stephan Saal
f
e
ld
T2-NIT/pom
.
xm
l
can
i
nhe
r
it v
e
rsi
o
n n
u
mber
f
rom parent
commit
|
commitdiff
|
tree
2013-08-14
Stephan Saalfe
l
d
a
d
ded missing dep
e
ndenc
i
es to java3d core-utils
and
.
.
.
commit
|
commitdiff
|
tree
2013-08-14
Stephan Saa
l
feld
s
et
parent pom
o
f
po
m
-
t
r
akem2 to
pom-fiji
.
2
.
0
.
0-
S
N
A
PSHOT
commit
|
commitdiff
|
tree
2013-08-12
Ste
p
han Saalfeld
Merge
br
a
n
ch
'
s
p
ring-mesh2' of ssh:/
/
repo
.
or
.
cz/srv
.
.
.
commit
|
commitdiff
|
tree
2013-08-12
Stephan Saalfeld
Me
r
ge branch 'master' into
spring-mes
h
2
commit
|
commitdiff
|
tree
2013-08-12
Stepha
n
S
a
alfeld
raised
m
picbg
d
ep
e
ndency
v
ersio
n
t
o
0
.
6
.
1
-SNAPSHOT
commit
|
commitdiff
|
tree
2013-08-12
S
tephan Saa
l
feld
raised dependenc
y
to Simp
l
e
_Neurite_Tracer
to 2
.
0
.
2
commit
|
commitdiff
|
tree
2013-08-12
Stephan Saalfe
l
d
Merge bra
n
ch 'master' int
o
sprin
g
-mesh2
commit
|
commitdiff
|
tree
2013-08-12
Stephan
Sa
a
lfeld
added comments a
n
d auto-fin
a
lize in Disto
r
tionCorrection/NLT
commit
|
commitdiff
|
tree
2013-08-12
Stephan Saalfeld
added mpic
b
g
.
version as maven
propert
y
,
commit
|
commitdiff
|
tree
2013-05-06
S
t
e
p
han S
a
alfeld
tra
c
k m
o
ve o
f
the
i
mglib1 d
e
pendency
commit
|
commitdiff
|
tree
2013-04-22
Stephan S
a
alfe
l
d
Merge branch 'master' in
t
o spri
n
g-mesh2
commit
|
commitdiff
|
tree
2013-03-05
S
tephan Saalfe
l
d
Merge branch '
m
a
s
ter' into sprin
g
-
m
esh2
commit
|
commitdiff
|
tree
2013-01-18
Stephan Saalfeld
use arraylist where
a
rraylists are returned
commit
|
commitdiff
|
tree
2013-01-16
Stephan Sa
a
lfeld
adjust mpicbg
s
p
r
i
n
g-mesh2 whi
c
h
n
e
e
ds less
damp
i
ng
commit
|
commitdiff
|
tree
2013-01-11
St
e
phan Saalfeld
Fixed bug
i
n Patc
h
.
g
etFu
l
lCoor
d
inateTransform
that
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
St
e
p
han
S
aalfeld
Changed fixedPatches/Tile
s
i
nput collection to
S
et
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
S
t
epha
n
Saalf
e
ld
Pair constructor has to be publ
i
c
commit
|
commitdiff
|
tree
2013-01-10
St
e
phan Saalfeld
forgot
t
o
set
isA
l
igned flag in elastic layer alignm
e
nt
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
Stephan
S
aalfeld
elastic montage param must be publi
c
commit
|
commitdiff
|
tree
2013-01-07
Step
h
a
n
Saalfeld
added Pat
c
h
.
getFullC
o
rdinateTransform() which generates
a
commit
|
commitdiff
|
tree
2013-01-07
St
e
phan
S
aalfeld
* removed i
s
Aligned
f
rom Abstrac
t
Param class
commit
|
commitdiff
|
tree
2013-01-05
Stephan Saalf
e
ld
877: it
is le
g
al
f
o
r
layerThing to be
n
ull
commit
|
commitdiff
|
tree
2012-12-21
Stephan Saalfeld
C
orrec
t
ed sev
e
r
a
l lo
n
g-
s
t
anding issues
w
ith
S
IFT
-
l
inea
r
and
commit
|
commitdiff
|
tree
2012-12-19
St
e
phan Saa
l
feld
RegularizedLayerAlignment g
o
t more flex
i
ble A
P
I methods and
commit
|
commitdiff
|
tree
2012-12-19
Stephan Sa
a
lfe
l
d
cl
e
aring cac
h
e in
l
ayer alignment must be def
a
ult true
commit
|
commitdiff
|
tree
2012-12-19
Stephan Sa
a
l
f
e
ld
print optim
i
zer
r
e
s
u
lt
s
a
n
d d
o
n
o
t pr
i
nt "matc
h
i
n
g
.
.
.
commit
|
commitdiff
|
tree
2012-12-19
Stephan Saa
l
feld
do no
t
r
e
move
e
mpty layers in layer alignment
commit
|
commitdiff
|
tree
2012-11-07
Stephan Saal
f
eld
f
ixed
version number of mpicbg depe
n
de
n
cy
commit
|
commitdiff
|
tree
2012-11-07
Stephan S
a
alfeld
fixed merge erro
r
: moved RobustNorm
a
lizeLocalContrast
.
.
.
commit
|
commitdiff
|
tree
2012-09-01
Stephan
S
aalfeld
multi
-
t
hreaded RobustNormalizeLocal
C
ontrast
main body
commit
|
commitdiff
|
tree
2012-09-01
S
tephan S
a
alfeld
R
e
mov
e
d
D
i
splayCanvas
.
setDrawin
g
C
o
lor(int,int,boolean
.
.
.
commit
|
commitdiff
|
tree
2012-08-31
Stephan Saal
f
eld
M
er
g
e b
r
anch 'master' of ssh://
r
epo
.
or
.
cz/srv/git/trakem2
commit
|
commitdiff
|
tree
2012-08-31
S
tephan Saalfe
l
d
add
e
d
e
x
per
i
mental
l
ocal
contrast enhancer RobustNormalize
L
o
.
.
.
commit
|
commitdiff
|
tree
2012-06-29
S
tephan Saalfeld
removed obso
l
ete ch
o
i
c
e
from alig
n
l
ayers d
i
alog
commit
|
commitdiff
|
tree
2012-06-26
Stephan Sa
a
lf
e
ld
s
p
lit
e
lastic montage dialog for blo
c
k matching and use
commit
|
commitdiff
|
tree
2012-06-26
Stephan
S
aalfe
l
d
Me
r
ge b
r
anch
'
master' of s
s
h
:
//repo
.
or
.
cz/srv/git
/
trak
e
m
2
commit
|
commitdiff
|
tree
2012-06-26
Step
h
an S
a
alfeld
use a
n
d do n
o
t ignore alpha
i
n helpe
r
method
commit
|
commitdiff
|
tree
2012-06-21
S
t
ephan
Saalfeld
use the new seque
n
tial dialogs in
"
montage" for
a
selecti
o
n
.
.
.
commit
|
commitdiff
|
tree
2012-06-20
S
t
ephan Saalfeld
Me
r
ge bra
n
ch 'mast
e
r' of ssh://re
p
o
.
or
.
cz/srv/git
/
trakem2
commit
|
commitdiff
|
tree
2012-06-20
Stephan Saalfe
l
d
fixed range ch
e
c
k in layer alignm
e
nt
commit
|
commitdiff
|
tree
2012-06-14
Stephan Saal
f
eld
f
i
x
ed con
d
ition check
i
n Al
i
g
n
La
y
ers fo
r
regul
a
rization
.
.
.
commit
|
commitdiff
|
tree
2012-06-14
Stephan Saalfe
l
d
Merge branch 'master' into regul
a
r
ized-aff
i
ne
commit
|
commitdiff
|
tree
2012-06-08
Ste
p
han Saalfel
d
d
o not consider disco
n
nect
e
d
tiles
commit
|
commitdiff
|
tree
2012-06-08
Stephan Saalfeld
Merge bra
n
ch 'regularized-aff
i
n
e' of
ssh
:
//repo
.
o
r
.
.
.
commit
|
commitdiff
|
tree
2012-06-08
S
tephan
S
aalfe
l
d
pre-align graphs and match only ov
e
rlapping t
i
l
e
s
commit
|
commitdiff
|
tree
2012-06-08
Ste
p
han Saalfeld
pr
e
-align graphs and
m
atch o
n
ly overla
p
ping tiles
commit
|
commitdiff
|
tree
2012-06-08
Stephan
S
a
a
lfeld
i
nitialize Tile models
a
nd n
o
t onl
y
patche
s
in alignGrap
h
s
commit
|
commitdiff
|
tree
2012-06-08
St
e
pha
n
Sa
a
lfeld
cha
n
ged
alignGraphs
in
p
ut collections from Set
t
o
I
t
e
rable
commit
|
commitdiff
|
tree
2012-06-08
Stephan S
a
alfeld
make sure t
h
at static parameters d
o
n
ot override ea
c
h
.
.
.
commit
|
commitdiff
|
tree
2012-06-05
Stepha
n
Saalfeld
remove spurious im
p
ort
commit
|
commitdiff
|
tree
2012-06-05
Stephan
Saalfeld
worka
r
ound Or
a
cle javac generics i
s
sue
commit
|
commitdiff
|
tree
2012-06-05
St
e
phan Saalf
e
ld
m
u
l
ti-lay
e
r
-mosaic use
s
P
aram/Par
a
mOptimiz
e
.
setup(Strin
g
.
.
.
commit
|
commitdiff
|
tree
2012-06-05
Stephan
S
aalfeld
monta
g
e layers u
s
es Para
m
Opt
i
mize
.
setup instead of
.
.
.
commit
|
commitdiff
|
tree
2012-06-05
St
e
ph
a
n Saal
f
eld
do not fix
a
ran
d
om
ti
l
e
if
n
one is
f
i
xed
commit
|
commitdiff
|
tree
2012-05-29
Stephan Sa
a
lfeld
Condense
d
.
mailmap
commit
|
commitdiff
|
tree
2012-05-29
Stephan Saalfeld
Adde
d
.
m
a
ilmap
commit
|
commitdiff
|
tree
2012-05-21
Stephan Saalfeld
Merge branch 'm
a
ste
r
' into
r
e
gularized-
a
f
fin
e
commit
|
commitdiff
|
tree
2012-05-21
Stephan
S
aalfeld
a
dded *None*
field
t
o
lay
e
r range refe
r
ence selection
commit
|
commitdiff
|
tree
2012-05-21
Step
h
an
Saalfeld
split
A
li
g
n
.
Param
O
ptimi
z
e dia
l
o
g
s
in pieces that fit
.
.
.
commit
|
commitdiff
|
tree
2012-05-21
Steph
a
n Saalf
e
l
d
added GenericAffineTile2D
commit
|
commitdiff
|
tree
2012-05-21
Stepha
n
Sa
a
lf
e
ld
generalize
d
A
bstr
a
ctAffineTi
l
e2D
generic parameter
commit
|
commitdiff
|
tree
2012-05-15
Stephan Sa
a
lfeld
trac
k
refactoring i
n
mpicbg
.
commit
|
commitdiff
|
tree
2012-05-09
S
tephan Saalfeld
add
e
d
r
egularized affine layer alignment,
commit
|
commitdiff
|
tree
2012-03-28
Stephan S
a
a
l
fel
d
fixe
d
cr
e
ateIma
g
e
(
): use premultiplied raster
commit
|
commitdiff
|
tree
2012-03-27
Stephan
S
aal
f
eld
d
o not
print the
m
ipmap s
c
ale
commit
|
commitdiff
|
tree
2012-03-27
Ste
p
han Saalfeld
for now, do not
u
s
e pr
e
-
m
ultiplie
d
a
lpha since it does
.
.
.
commit
|
commitdiff
|
tree
2012-03-27
Steph
a
n Saalf
e
ld
Fi
x
ed wrong p
a
inting of P
a
tches when using a downsamp
l
er
.
.
.
commit
|
commitdiff
|
tree
2012-03-27
Stephan
S
a
alfeld
D
o
wnsam
p
l
er
M
ipMaps now con
s
isten
t
ly uses combine
d
d
ow
n
sampl
i
.
.
.
commit
|
commitdiff
|
tree
2012-03-27
S
tephan S
a
alf
e
l
d
f
ixed DownsamplerMip
M
ap
s
blendin
g
merg
e
d alpha into
.
.
.
commit
|
commitdiff
|
tree
2012-03-27
Stephan Sa
a
lfeld
Do
w
nsam
p
ler t
e
st
s
till shows
it be
i
ng signi
f
ic
a
ntly
.
.
.
commit
|
commitdiff
|
tree
next