Commit c562a301 authored by inhuszar's avatar inhuszar
Browse files

New: Histology-to-histology configuration file

parent 7d1adbe1
{
"header": {
"author": "Istvan N Huszar",
"description": "Hand-optimised for testing the reproducibility of SAF measurements on consecutive sections",
"title": "TIRL Stage-1 Registration Routine adapted for histology-to-histology registration"
},
"general": {
"direction": "h2b",
"isotropic": true,
"logfile": "logfile.log",
"loglevel": 10,
"name": "repreg",
"outputdir": "/mnt/elisa/proc/postmort/histology/reproducibility2/CD68/NP123_14",
"paramlogfile": "parameters.log",
"stages": ["rotation", "rigid", "affine", "nonlinear"],
"system": "linux",
"verbose": true,
"warnings": false
},
"histology": {
"dtype": "f4",
"export": true,
"file": "/mnt/elisa/proc/postmort/histology/reproducibility2/CD68/NP123_14_2Lb_1_CD68.svs",
"mask": {
"automask": {
"thr": 0,
"uthr": 1
},
"file": null,
"function": null,
"normalise": true
},
"preview": false,
"resolution": 0.008,
"snapshot": true,
"storage": "mem"
},
"block": {
"dtype": "f4",
"export": false,
"file": "/mnt/elisa/proc/postmort/histology/reproducibility2/CD68/NP123_14_2Lb_3_CD68.svs",
"mask": {
"automask": {
"thr": 0,
"uthr": 1
},
"file": null,
"function": null,
"normalise": true
},
"preview": false,
"resolution": 0.008,
"snapshot": false,
"storage": "mem"
},
"preprocessing": {
"block": ["block_preprocessing"],
"histology": ["histology_preprocessing"]
},
"regparams": {
"init": {
"affine": {
"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],
"x0": [1.0, 0.0, 0.0, 0.0, 1.0, 0.0]
},
"nonlinear": {
"lb": null,
"ub": null,
"x0": 0.0
},
"rotation": {
"lb": -30,
"mode": "deg",
"ub": 30,
"x0": 0.0
},
"scale": {
"lb": 0.98,
"ub": 1.02,
"x0": 1.0
},
"translation": {
"lb": [-5.0, -5.0],
"ub": [5.0, 5.0
],
"x0": [0.0, 0.0]
}
},
"rotsearch": {
"coarse": 5,
"opt_step": 0.5,
"scale": 0.06,
"visualise": false,
"xtol_abs": [
0.001,
0.001,
0.001,
0.001
],
"xtol_rel": 0.01
},
"rigid": {
"opt_step": 0.1,
"scaling": [
16,
8,
4
],
"smoothing": [
0,
0,
0
],
"visualise": false,
"xtol_abs": [
0.001,
0.001,
0.001,
0.001
],
"xtol_rel": 0.01
},
"affine": {
"opt_step": 0.1,
"scaling": [16, 8, 4],
"smoothing": [0, 0, 0],
"visualise": false,
"xtol_abs": 0.001,
"xtol_rel": 0.01
},
"nonlinear": {
"maxiter": [30, 20, 10, 5, 5],
"regweight": 0.4,
"scaling": [50, 25, 12.5, 6.25, 3.125],
"sigma": 1,
"smoothing": [0, 0, 0, 0, 0],
"truncate": 1.5,
"visualise": false,
"xtol_abs": 0.1,
"xtol_rel": 0.01
}
}
}
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