added config with masking

slider/resources/slide_with_mask.yaml

+header:
+  author: Istvan N Huszar - adapted by Istvan & Amy Howard Mar 2021 - Adapted by Sean Fitz 2021
+  description: ''
+  title: TIRL MBP-to-NeuN image registration routine - adapted for histology-to-histology registration
+
+# general settings
+general:
+  isotropic: true
+  logfile: ./logfile.log
+  loglevel: debug
+  name: slice-to-slice
+  outputdir: ./reg
+  paramlogfile: ./paramlog.log
+  stages:
+  - rotation
+  - rigid
+  - affine
+  - nonlinear
+  system: linux
+  verbose: false
+  warnings: true
+
+# moving image settings
+moving:
+  dtype: f4
+  export: true
+  file: ''
+  mask:
+    automask:
+      thr: 0.0
+      uthr: 1
+    file: null
+    # function: null
+    function: gmm_mask
+    normalise: true
+  preview: false
+  resolution_level: 4
+  snapshot: true
+  storage: mem
+
+# fixed image settings
+fixed:
+  dtype: f4
+  export: false
+  file: ''
+  mask:
+    automask:
+      thr: 0
+      uthr: 1
+    file: null
+    function: gmm_mask
+    # function: null
+    normalise: true
+  preview: false
+  resolution_level: 4
+  snapshot: true
+  storage: mem
+
+# preprocessing settings
+preprocessing:
+  fixed: ["fixed_preprocessing"]
+  moving: ["moving_preprocessing", "match_fixed_resolution"]
+  # fixed: null
+  # moving: ["match_fixed_resolution"]
+
+# registration settings
+regparams:
+
+  init:
+      scale:
+        lb: 0.95
+        ub: 1.05
+        x0: 1.0
+      rotation:
+        lb: -10
+        mode: deg
+        ub: 10
+        x0: 0.0
+      translation:
+        x0: [0.0, 0.0]
+        lb: [-5.0, -5.0]
+        ub: [5.0, 5.0]
+        # restrict lower and upper bound
+        # lb: [-1.0, -1.0]
+        # ub: [1.0, 1.0]
+      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:
+        lb: null
+        ub: null
+        x0: 0.0
+
+  rotsearch:
+    coarse: 1
+    opt_step: 0.5
+    scale: 0.125
+    visualise: false
+    xtol_abs: [0.001, 0.001, 0.001, 0.001]
+    xtol_rel: 0.01
+    export: false
+    snapshot: true
+
+  rigid:
+    opt_step: 0.1
+    scaling: [160, 80, 40, 20, 10, 5]
+    smoothing: [0, 0, 0, 0, 0]
+    visualise: false
+    xtol_abs: [0.001, 0.001, 0.001, 0.001]
+    xtol_rel: 0.01
+    export: false
+    snapshot: true
+
+  affine:
+    opt_step: 0.1
+    scaling: [160, 80, 40, 20, 10, 5]
+    smoothing: [0, 0, 0, 0, 0, 0, 0]
+    visualise: false
+    xtol_abs: [0.001, 0.001, 0.001, 0.001, 0.001, 0.001]
+    xtol_rel: 0.01
+    export: false
+    snapshot: true
+
+  nonlinear:
+    maxiter: [20, 20, 20, 20, 10, 10]
+    # more regularised
+    regweight: 0.4
+    # regweight: 0.6
+    scaling: [160, 80, 40, 20, 10, 5]
+    # scaling: [80, 60, 40, 20, 10, 5]
+    # can try increasing (1.5, 2, ) number of pixels
+    # radius of smoothing kernel (number of pixels)
+    sigma: 1
+    smoothing: [0, 0, 0, 0, 0, 0]
+    truncate: 1.5
+    visualise: false
+    # lower will lead to longer registration, might not converge if too small
+    xtol_abs: 0.1
+    xtol_rel: 0.01 #mm median magnitude
+    kernel: MK_FULL
+    export: true
+    snapshot: true
+    maskmode: or
+
+  
+
+