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Sean Fitzgibbon
SlideR 🍔
Commits
5f10c7f7
Commit
5f10c7f7
authored
Jun 22, 2021
by
Sean Fitzgibbon
Browse files
yaml bugfix
parent
61b73395
Changes
2
Hide whitespace changes
Inline
Side-by-side
slider/resources/default.json
deleted
100644 → 0
View file @
61b73395
{
"header"
:
{
"title"
:
"TIRL MBP-to-NeuN image registration routine - adapted for histology-to-histology registration"
,
"description"
:
""
,
"author"
:
"Istvan N Huszar - adapted by Istvan & Amy Howard Mar 2021 - Adapted by Sean Fitz 2021"
},
"general"
:
{
"name"
:
"slice-to-slice"
,
"system"
:
"linux"
,
"loglevel"
:
"debug"
,
"logfile"
:
"./logfile.log"
,
"paramlogfile"
:
"./paramlog.log"
,
"verbose"
:
false
,
"outputdir"
:
"./reg"
,
"stages"
:
[
"rotation"
,
"rigid"
,
"affine"
,
"nonlinear"
],
"warnings"
:
true
,
"isotropic"
:
true
},
"moving"
:
{
"file"
:
""
,
"storage"
:
"mem"
,
"dtype"
:
"f4"
,
"resolution_level"
:
4
,
"mask"
:
{
"file"
:
null
,
"normalise"
:
true
,
"function"
:
null
,
"automask"
:
{
"thr"
:
0.00
,
"uthr"
:
1.0
}
},
"preview"
:
false
,
"export"
:
true
,
"snapshot"
:
true
},
"fixed"
:
{
"file"
:
""
,
"storage"
:
"mem"
,
"dtype"
:
"f4"
,
"resolution_level"
:
4
,
"mask"
:
{
"file"
:
null
,
"normalise"
:
true
,
"function"
:
null
,
"automask"
:
{
"thr"
:
0.0
,
"uthr"
:
1.0
}
},
"preview"
:
false
,
"export"
:
false
,
"snapshot"
:
true
},
"preprocessing"
:
{
"moving"
:
[
"moving_preprocessing"
,
"match_fixed_resolution"
],
"fixed"
:
[
"fixed_preprocessing"
]
},
"regparams"
:
{
"init"
:
{
"scale"
:
{
"x0"
:
1.0
,
"lb"
:
0.95
,
"ub"
:
1.05
},
"rotation"
:
{
"x0"
:
0.0
,
"mode"
:
"deg"
,
"lb"
:
-10
,
"ub"
:
10
},
"translation"
:
{
"x0"
:
[
0.0
,
0.0
],
"lb"
:
[
-5.0
,
-5.0
],
"ub"
:
[
5.0
,
5.0
]
},
"affine"
:
{
"x0"
:
[
1.0
,
0.0
,
0.0
,
0.0
,
1.0
,
0.0
],
"lb"
:
[
0.95
,
-0.2
,
-1.0
,
-0.2
,
0.95
,
-1.0
],
"ub"
:
[
1.05
,
0.2
,
1.0
,
0.2
,
1.05
,
1.0
]
},
"nonlinear"
:
{
"x0"
:
0.0
,
"lb"
:
null
,
"ub"
:
null
}
},
"rotsearch"
:
{
"coarse"
:
1
,
"scale"
:
0.125
,
"visualise"
:
false
,
"xtol_rel"
:
0.01
,
"xtol_abs"
:
[
0.001
,
0.001
,
0.001
,
0.001
],
"opt_step"
:
0.5
},
"rigid"
:
{
"scaling"
:
[
160
,
80
,
40
,
20
,
10
,
5
],
"smoothing"
:
[
0
,
0
,
0
,
0
,
0
],
"xtol_rel"
:
0.01
,
"xtol_abs"
:
[
0.001
,
0.001
,
0.001
,
0.001
],
"opt_step"
:
0.1
,
"visualise"
:
false
},
"affine"
:
{
"scaling"
:
[
160
,
80
,
40
,
20
,
10
,
5
],
"smoothing"
:
[
0
,
0
,
0
],
"xtol_rel"
:
0.01
,
"xtol_abs"
:
[
0.001
,
0.001
,
0.001
,
0.001
,
0.001
,
0.001
],
"opt_step"
:
0.1
,
"visualise"
:
false
},
"nonlinear"
:
{
"scaling1"
:
[
8
,
4
,
2
,
1
],
"scaling"
:
[
160
,
80
,
40
,
20
,
10
,
5
],
"smoothing"
:
[
0
,
0
,
0
,
0
,
0
,
0
],
"sigma"
:
1
,
"truncate"
:
1.5
,
"regweight"
:
0.4
,
"regweight1"
:
0.6
,
"maxiter"
:
[
20
,
20
,
20
,
20
,
10
,
5
],
"xtol_abs"
:
0.1
,
"xtol_rel"
:
0.01
,
"visualise"
:
false
}
}
}
slider/resources/slide.yaml
View file @
5f10c7f7
...
...
@@ -106,7 +106,7 @@ regparams:
scaling
:
[
160
,
80
,
40
,
20
,
10
,
5
]
smoothing
:
[
0
,
0
,
0
]
visualise
:
false
xtol_abs
:
[
0.001
,
0.001
,
0.001
,
0.001
]
xtol_abs
:
[
0.001
,
0.001
,
0.001
,
0.001
,
0.001
,
0.001
]
xtol_rel
:
0.01
nonlinear
:
...
...
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