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d2::align: Fix display of pre-following alignment.
2007-05-07
D
a
vid Hilvert
d2::align:
F
ix di
s
play
of pre-
f
ollowing alignment
.
commit
|
commitdiff
|
tree
2007-05-07
David Hilver
t
Add information r
e
garding following t
o
logging u
i
output
.
commit
|
commitdiff
|
tree
2007-05-07
D
avid Hilvert
Allow --
f
o
l
low
to act in cases w
h
ere tr
a
nsformations
.
.
.
commit
|
commitdiff
|
tree
2007-05-07
Davi
d
Hi
l
vert
D
is
a
ble --follow when
p
ertu
r
b is
n
ot
greater than
z
ero
.
commit
|
commitdiff
|
tree
2007-05-07
David Hilvert
Modif
y
i
t
e
r
a
tion
bou
n
ds to allow for floating point
.
.
.
commit
|
commitdiff
|
tree
2007-05-07
Da
v
i
d
H
ilvert
ui: Add no
t
i
ce
f
or global alignment
.
commit
|
commitdiff
|
tree
2007-05-06
D
avid Hil
v
e
r
t
Increase
t
olerance
for tran
s
formation
compariso
n
operat
i
ons
.
commit
|
commitdiff
|
tree
2007-05-06
David
Hilvert
d2::trans_single::snap(): S
n
ap the
rotational parameter
.
commit
|
commitdiff
|
tree
2007-05-05
D
avid Hi
l
vert
Refi
n
e various assignment, c
o
mparison, and const
r
uctor
.
.
.
commit
|
commitdiff
|
tree
2007-05-05
Da
v
i
d
Hilvert
Increas
e
default --cache to
2
56
M
B
.
commit
|
commitdiff
|
tree
2007-05-05
David Hilvert
d2::re
n
der::ipc:
Ad
d
ext
e
nts calculatio
n
to limit pixels
.
.
.
commit
|
commitdiff
|
tree
2007-05-05
David Hil
v
ert
Mo
d
if
y
-
-cache
h
e
lp text
to be
more
easily human-re
a
dab
l
e
.
commit
|
commitdiff
|
tree
2007-05-04
David
H
ilvert
Add
caching i
n
formati
o
n to UI
.
commit
|
commitdiff
|
tree
2007-05-04
D
a
vid Hilve
r
t
ui_log: Add log_message() method
.
commit
|
commitdiff
|
tree
2007-05-04
David Hilvert
ui_
l
og:
A
dd
c
ache usage infor
m
a
tion
.
commit
|
commitdiff
|
tree
2007-05-04
David Hil
v
e
r
t
A
d
d
a --c
a
c
h
e
o
p
t
i
on
f
o
r ca
c
h
ing imag
e
s
.
commit
|
commitdiff
|
tree
2007-05-03
D
a
vid
H
ilvert
M
a
ke --16bpc default
.
commit
|
commitdiff
|
tree
2007-05-03
David Hilve
r
t
d2::al
i
gn::_
a
lign(): Increase stabl
e
_count l
i
mit to 5
.
commit
|
commitdiff
|
tree
2007-05-03
David Hilvert
Add pertu
r
bation snap-to-grid, move pertur
b
atio
n
mult
i
pliers
.
.
.
commit
|
commitdiff
|
tree
2007-05-02
Da
v
id Hilvert
All
o
w non-fini
t
e m
u
ltipliers
i
n perturb
_
t
e
st(); remove
.
.
.
commit
|
commitdiff
|
tree
2007-05-02
David Hilvert
Resolve rota
t
iona
l
al
i
g
nment
b
u
g;
add rotati
o
n
a
l and
.
.
.
commit
|
commitdiff
|
tree
2007-05-02
David Hilve
r
t
Add d2::
a
lig
n
::diff_s
t
at_t::o
l
d_runs, to store
old
.
.
.
commit
|
commitdiff
|
tree
2007-04-30
David Hi
l
vert
Add a structur
e
f
o
r ru
n
-specific data to
d
i
ff_sta
t
_t
.
commit
|
commitdiff
|
tree
2007-04-27
Da
v
id
H
il
v
e
r
t
R
emo
v
e d2::
t
rans_mu
l
ti::operato
r
= and instrument
a
t
i
on
.
commit
|
commitdiff
|
tree
2007-04-26
Davi
d
Hi
l
vert
d2
:
:
align: Minor
bugf
i
xes and debugging instrumenta
t
ion
.
commit
|
commitdiff
|
tree
2007-04-26
Dav
i
d Hilvert
Add code
t
o
use
e
rror m
u
ltipliers an
d
centroids
.
commit
|
commitdiff
|
tree
2007-04-25
David H
i
lve
r
t
d2::ali
g
n:
Initial, broken
i
mplem
e
ntatio
n
of align
m
ent
.
.
.
commit
|
commitdiff
|
tree
2007-04-25
D
a
vid
Hilvert
d2::ali
g
n
::d
i
ff_sta
t
_t::
s
ample():
Fix
i
ncorrect
use
.
.
.
commit
|
commitdiff
|
tree
2007-04-25
David
Hilv
e
r
t
d
2:
:
align: Update diff and sample c
o
d
e to
o
perate on
.
.
.
commit
|
commitdiff
|
tree
2007-04-25
David
H
i
lvert
d2::align: Add code to calculate a
v
er
a
ge pi
x
el displ
a
c
ement
.
.
.
commit
|
commitdiff
|
tree
2007-04-24
David Hilvert
ui/input
.
h: Rep
o
r
t an error when --ui
i
s
use
d
with
.
.
.
commit
|
commitdiff
|
tree
2007-04-24
D
avid Hilve
r
t
Change u
i
_log logging to stdout and r
e
v
i
s
e dyn
a
mic
.
.
.
commit
|
commitdiff
|
tree
2007-04-23
David Hi
l
vert
d2::
a
li
g
n: A
d
d method is_better(), whi
c
h could be used
.
.
.
commit
|
commitdiff
|
tree
2007-04-22
David Hilver
t
ui/he
l
p
.
h
:
Change hel
p
t
ex
t
f
o
r
-
-
mc
d
-removal to reflect
.
.
.
commit
|
commitdiff
|
tree
2007-04-22
Dav
i
d Hi
l
ve
r
t
Match parent
h
eses
.
commit
|
commitdiff
|
tree
2007-04-22
D
av
i
d Hilvert
d
2/a
l
ign
.
h: E
n
caps
u
late reliability ch
e
ck within is_relia
b
le
.
.
.
commit
|
commitdiff
|
tree
2007-04-22
David Hil
v
ert
Change
-
-mc
d
-
r
emov
a
l de
f
ault
to 1
.
commit
|
commitdiff
|
tree
2007-04-22
David
Hilvert
Va
r
ious changes and bugfixes for dyna
m
ic monte carlo
.
.
.
commit
|
commitdiff
|
tree
2007-04-22
D
avid Hilvert
d2/align
.
h
:
prior
t
o
changing pert
u
rb
a
t
i
o
n ste
p
size
.
.
.
commit
|
commitdiff
|
tree
2007-04-21
D
avid Hilvert
Upd
a
t
e
changel
o
g
commit
|
commitdiff
|
tree
2007-04-21
David H
i
lvert
Upda
t
e cha
n
gelog
commit
|
commitdiff
|
tree
2007-04-21
David Hilvert
Set --no-
i
nc to default
.
commit
|
commitdiff
|
tree
2007-04-21
David
H
ilver
t
Add
co
m
men
t
regarding removal met
h
o
d
s i
n
d2/align
.
h
.
commit
|
commitdiff
|
tree
2007-04-20
Da
v
id Hilvert
ui_tty: Add
m
o
re updates; revise
Irani-Peleg output
.
commit
|
commitdiff
|
tree
2007-04-20
D
a
vid
H
ilvert
d2::alig
n
: Select best er
r
o
r
from each c
o
n
s
ecuti
v
e
.
.
.
commit
|
commitdiff
|
tree
2007-04-20
David H
i
lv
e
rt
Cha
n
gelog updat
e
commit
|
commitdiff
|
tree
2007-04-20
David Hilvert
U
p
d
a
te cha
n
gelog
commit
|
commitdiff
|
tree
2007-04-20
David Hilver
t
Fix calcu
l
ation
o
f global sear
c
h minimum overlap coun
t
.
.
.
commit
|
commitdiff
|
tree
2007-04-19
David
H
ilver
t
u
i
_
l
og
:
F
ix format in set
_
offset()
.
commit
|
commitdiff
|
tree
2007-04-19
D
a
vid H
i
lver
t
Change --g
s
-mo d
e
f
a
ult to 67%
.
commit
|
commitdiff
|
tree
2007-04-19
D
av
i
d Hi
l
v
e
rt
ui: L
o
g output enhancements
.
commit
|
commitdiff
|
tree
2007-04-19
David Hi
l
vert
Allow
-
-gs-mo t
o
be spe
c
ified as a pe
r
centage, m
a
ke
.
.
.
commit
|
commitdiff
|
tree
2007-04-19
Da
v
id Hilvert
d2:
:
align: Modif
y
_align() an
d
make_element_nontrivi
a
l
.
.
.
commit
|
commitdiff
|
tree
2007-04-19
D
a
vid Hilvert
d2::align: Ad
d
m
ethod get_perturb_set()
.
commit
|
commitdiff
|
tree
2007-04-17
Davi
d
Hilve
r
t
Add
file
'V
E
RSION'
f
or
cas
e
s w
h
ere this does not exist
.
commit
|
commitdiff
|
tree
2007-04-17
David Hilvert
d
2
::trans
_
multi::specific_res
c
ale(): Rep
l
a
c
e
a
ssertion
.
.
.
commit
|
commitdiff
|
tree
2007-04-17
D
avid H
i
lvert
C
h
ange
l
og edits
.
commit
|
commitdiff
|
tree
2007-04-17
D
avid Hilv
e
rt
Update changelog
commit
|
commitdiff
|
tree
2007-04-17
Davi
d
H
i
l
ver
t
Add
f
ile ui_qu
i
et
.
h
.
commit
|
commitdiff
|
tree
2007-04-17
David Hilv
e
rt
configure
.
in: U
s
e
co
n
tents of f
i
le VERSION for versi
o
n
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
Da
v
id Hil
v
ert
Modify blac
k
leve
l
implementation t
o
always a
p
p
l
y
t
o
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
David Hilve
r
t
Add 'quiet' user int
e
rface t
y
pe
.
commit
|
commitdiff
|
tree
2007-04-16
Da
v
id
H
i
lvert
Move output
i
den
t
ification details
to
u
se
r
inter
f
ace
.
commit
|
commitdiff
|
tree
2007-04-16
David
H
ilvert
u
i_log::ip_ste
p
_done(): 'Finished frame' -->
'
Finished
.
.
.
commit
|
commitdiff
|
tree
2007-04-16
David Hil
v
er
t
R
efine u
i
_l
o
g:
:
ip_step_done()
.
commit
|
commitdiff
|
tree
2007-04-15
David Hil
v
e
r
t
d
2/ppm
.
h: Don't set g
a
in values if
n
one are
s
pecified
.
.
.
commit
|
commitdiff
|
tree
2007-04-15
David Hilve
r
t
u
i_log:
A
dd separate
output for m
a
tch and mismatch
.
.
.
commit
|
commitdiff
|
tree
2007-04-15
David Hi
l
vert
ui_log: Add mo
r
e logging ou
t
put
.
commit
|
commitdiff
|
tree
2007-04-15
David Hi
l
vert
Add rudimentary logging interfac
e
.
commit
|
commitdiff
|
tree
2007-04-15
David Hilv
e
rt
u
i: Indicate when no local align
m
e
n
t de
t
ail
s
a
r
e availabl
e
.
commit
|
commitdiff
|
tree
2007-04-14
David Hilve
r
t
d
2
::trans_multi::s
p
e
c
ific
_
rescale():
A
dd an a
s
sert
.
.
.
commit
|
commitdiff
|
tree
2007-04-13
Da
v
id H
i
lvert
Begin implementing d2:
:
align::c
a
lculate_eleme
n
t
_re
g
ion()
.
commit
|
commitdiff
|
tree
2007-04-13
Da
v
id Hi
l
vert
d
2
:
:
a
lign::_al
i
gn(): Add c
o
de to sto
r
e
t
o
and retrieve
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
David
Hilver
t
Add code to rec
a
lculate
each n
o
n-triv
i
a
l
non-primary
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
Da
v
id Hilvert
Add lo
c
al_ax
_
cou
n
t to the list of parameters taken
.
.
.
commit
|
commitdiff
|
tree
2007-04-09
David
H
ilvert
C
h
ang
e
ba
r
rel distortion m
u
ltiplier and
r
ate of change
.
.
.
commit
|
commitdiff
|
tree
2007-04-08
David Hilvert
Add
methods
d2::align::make_element_nontrivi
a
l(),
d2
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilvert
d
2::align::f
o
llow():
R
evert looping
o
ver
old_* element
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
D
a
vi
d
Hilvert
d2::a
l
ign::follow(): Update
element ind
i
ces o
f
all
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
D
a
vid Hilvert
d2::tfi
l
e: Bugfix in handling of non-pri
m
ar
y
e
l
eme
n
t
s
.
commit
|
commitdiff
|
tree
2007-04-03
D
a
vid Hilvert
C
o
pyright
n
otice updates
.
commit
|
commitdiff
|
tree
2007-04-03
David Hil
v
ert
Add
code for loading and saving non-pr
i
mary al
i
gn
m
ent
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David H
i
lvert
U
pdate
c
hangelog
.
commit
|
commitdiff
|
tree
2007-04-03
David Hilvert
ui:
Modi
f
y m
a
tc
h
f
o
r
m
a
t strings to provide const
a
nt
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
Dav
i
d Hilvert
u
i
_tty: Add fi
e
ld w
i
dth a
n
d
prec
i
s
ion specifiers t
o
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
David
H
ilvert
Swap argumen
t
s to alignment
s
tatus so
that frequent
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
D
a
vid
Hilvert
u
i
_tty:
Change
floating point formats from %f to %g
.
.
.
commit
|
commitdiff
|
tree
2007-04-03
D
avid Hilvert
d2
:
:align: M
o
v
e
following logic from _align
(
) to a
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
David H
i
lvert
Upda
t
e
changelog
commit
|
commitdiff
|
tree
2007-04-02
David Hilvert
R
e
m
ove
f
ile 'sgauss
.
h'
m
issi
n
g from sgau
s
s patch, as
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
D
a
vid Hilvert
A
d
d missing f
i
le f
r
om earlier sg
a
us
s
patch
.
Wil
l
be
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
D
a
vid Hilvert
Update change
l
og
commit
|
commitdiff
|
tree
2007-04-02
David Hilve
r
t
Update chan
g
elog
commit
|
commitdiff
|
tree
2007-04-02
David H
i
lvert
M
o
ve
the multi-transformatio
n
e
l
e
ment switchi
n
g loop
.
.
.
commit
|
commitdiff
|
tree
2007-04-02
D
avid Hi
l
vert
Upda
t
e
C
hangelog
commit
|
commitdiff
|
tree
2007-04-02
D
a
vid Hilvert
d2/a
l
ign
.
h:
Recalculate dif
f
statistics after incr
e
asi
n
g
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
D
a
vid
Hilvert
M
o
dif
y
handling of
-
-identity in d2
:
:a
l
ign so t
h
a
t
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
Da
v
id
Hilvert
Add methods for
e
nabli
n
g
a
nd disabling restricte
d
s
u
p
p
ort
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
Dav
i
d Hi
l
vert
Add
c
h
e
c
k
for transformation suppo
r
t to d2::align:
.
.
.
commit
|
commitdiff
|
tree
2007-04-01
Dav
i
d Hilvert
d2::trans_
m
ulti: Add m
e
thod
supporte
d
() t
o
check for
.
.
.
commit
|
commitdiff
|
tree
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