New: Histology-to-histology configuration file

src/tirl/scripts/mnd/config/histology_to_histology.json

+{
+    "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
+        }
+    }
+}