yaml bugfix

slider/resources/default.json

-{
-    "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

@@ -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: