diff --git a/.ipynb_checkpoints/movie_writer-checkpoint.ipynb b/.ipynb_checkpoints/movie_writer-checkpoint.ipynb
old mode 100755
new mode 100644
diff --git a/Experiments/experiment_04_07_2018___13.46.49.495901/experiment_04_07_2018___13.46.49.495901.log b/Experiments/experiment_04_07_2018___13.46.49.495901/experiment_04_07_2018___13.46.49.495901.log
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/Experiments/experiment_27_06_2018___12.13.14.428842/experiment_27_06_2018___12.13.14.428842.log b/Experiments/experiment_27_06_2018___12.13.14.428842/experiment_27_06_2018___12.13.14.428842.log
deleted file mode 100644
index be1e4c34121b3ffa3b8e3617527946d3412aa9c9..0000000000000000000000000000000000000000
--- a/Experiments/experiment_27_06_2018___12.13.14.428842/experiment_27_06_2018___12.13.14.428842.log
+++ /dev/null
@@ -1,438 +0,0 @@
-INFO:root:sending command to stage:SAS 50 ....................27_06_2018___12.13.17.314775
-INFO:root:response received from stage:0 .....................27_06_2018___12.13.17.328241
-INFO:root:sending command to stage:BLSH 0 ....................27_06_2018___12.13.17.329090
-INFO:root:response received from stage:0 .....................27_06_2018___12.13.17.342783
-INFO:root:sending command to attenuator:;AT:TF 0.6 ...........27_06_2018___12.13.17.567204
-INFO:root:sending command to laser:M .........................27_06_2018___12.13.18.004452
-INFO:root:sending command to laser:W 200 .....................27_06_2018___12.13.18.005272
-WARNING:tensorflow:Variable *= will be deprecated. Use variable.assign_mul if you want assignment to the variable value or 'x = x * y' if you want a new python Tensor object.
-INFO:root:video properties: ..................................27_06_2018___12.13.24.851858
-INFO:root:finished gui init ..................................27_06_2018___12.13.24.852354
-INFO:root:property 0, value: -1.0 ............................27_06_2018___12.13.24.852354
-INFO:root:property 1, value: -1.0 ............................27_06_2018___12.13.24.852849
-INFO:root:property 2, value: -1.0 ............................27_06_2018___12.13.24.852849
-INFO:root:property 3, value: 1024.0 ..........................27_06_2018___12.13.24.853345
-INFO:root:property 4, value: 822.0 ...........................27_06_2018___12.13.24.853345
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-INFO:root:property 12, value: 128.0 ..........................27_06_2018___12.13.24.995169
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-INFO:root:property 14, value: 100.0 ..........................27_06_2018___12.13.25.101642
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-INFO:root:property 16, value: -1.0 ...........................27_06_2018___12.13.25.143777
-INFO:root:property 17, value: 6503.0 .........................27_06_2018___12.13.25.183803
-INFO:root:property 18, value: -1.0 ...........................27_06_2018___12.13.25.184317
-INFO:root:click move vector: [ 40 -99] .......................27_06_2018___12.13.52.125994
-INFO:root:sending command to stage:GR,40,-99 .................27_06_2018___12.13.52.126485
-INFO:root:response received from stage:R .....................27_06_2018___12.13.52.253902
-INFO:root:magnification changed to: 100 ......................27_06_2018___12.14.21.107310
-INFO:root:objective offset correction: [ -79. -139.] .........27_06_2018___12.14.21.108303
-INFO:root:sending command to stage:GR,-79.0,-139.0 ...........27_06_2018___12.14.21.109295
-INFO:root:response received from stage:R .....................27_06_2018___12.14.21.243973
-INFO:root:click move vector: [-34 -5] ........................27_06_2018___12.14.22.436236
-INFO:root:sending command to stage:GR,-34,-5 .................27_06_2018___12.14.22.436730
-INFO:root:response received from stage:R .....................27_06_2018___12.14.22.532673
-INFO:root:click move vector: [-26 -6] ........................27_06_2018___12.14.23.124873
-INFO:root:sending command to stage:GR,-26,-6 .................27_06_2018___12.14.23.125398
-INFO:root:response received from stage:R .....................27_06_2018___12.14.23.198030
-INFO:root:click move vector: [ -5 -18] .......................27_06_2018___12.14.23.588604
-INFO:root:sending command to stage:GR,-5,-18 .................27_06_2018___12.14.23.589102
-INFO:root:response received from stage:R .....................27_06_2018___12.14.23.656350
-INFO:root:click move vector: [22 -1] .........................27_06_2018___12.14.24.269828
-INFO:root:sending command to stage:GR,22,-1 ..................27_06_2018___12.14.24.270820
-INFO:root:response received from stage:R .....................27_06_2018___12.14.24.352837
-INFO:root:click move vector: [22 -1] .........................27_06_2018___12.14.24.881415
-INFO:root:sending command to stage:GR,22,-1 ..................27_06_2018___12.14.24.882070
-INFO:root:response received from stage:R .....................27_06_2018___12.14.24.949596
-INFO:root:click move vector: [-15 -19] .......................27_06_2018___12.14.25.443985
-INFO:root:sending command to stage:GR,-15,-19 ................27_06_2018___12.14.25.444477
-INFO:root:response received from stage:R .....................27_06_2018___12.14.25.511759
-INFO:root:click move vector: [-14 -4] ........................27_06_2018___12.14.27.045108
-INFO:root:sending command to stage:GR,-14,-4 .................27_06_2018___12.14.27.045422
-INFO:root:response received from stage:R .....................27_06_2018___12.14.27.107032
-INFO:root:click move vector: [1 6] ...........................27_06_2018___12.14.28.103608
-INFO:root:sending command to stage:GR,1,6 ....................27_06_2018___12.14.28.104066
-INFO:root:response received from stage:R .....................27_06_2018___12.14.28.155465
-INFO:root:click move vector: [ 8 12] .........................27_06_2018___12.14.28.527240
-INFO:root:sending command to stage:GR,8,12 ...................27_06_2018___12.14.28.528060
-INFO:root:response received from stage:R .....................27_06_2018___12.14.28.583907
-INFO:root:click move vector: [ 8 12] .........................27_06_2018___12.14.28.956142
-INFO:root:sending command to stage:GR,8,12 ...................27_06_2018___12.14.28.956673
-INFO:root:response received from stage:R .....................27_06_2018___12.14.29.013909
-INFO:root:click move vector: [-4 -7] .........................27_06_2018___12.15.14.223982
-INFO:root:sending command to stage:GR,-4,-7 ..................27_06_2018___12.15.14.224946
-INFO:root:response received from stage:R .....................27_06_2018___12.15.14.278074
-INFO:root:click move vector: [-4 -7] .........................27_06_2018___12.15.14.659518
-INFO:root:sending command to stage:GR,-4,-7 ..................27_06_2018___12.15.14.659867
-INFO:root:response received from stage:R .....................27_06_2018___12.15.14.711119
-INFO:root:click move vector: [-7 -5] .........................27_06_2018___12.15.14.893244
-INFO:root:sending command to stage:GR,-7,-5 ..................27_06_2018___12.15.14.893752
-INFO:root:response received from stage:R .....................27_06_2018___12.15.14.943971
-INFO:root:click move vector: [-16 0] .........................27_06_2018___12.15.20.586843
-INFO:root:sending command to stage:GR,-16,0 ..................27_06_2018___12.15.20.586843
-INFO:root:response received from stage:R .....................27_06_2018___12.15.20.647356
-INFO:root:click move vector: [-24 -21] .......................27_06_2018___12.15.25.526555
-INFO:root:sending command to stage:GR,-24,-21 ................27_06_2018___12.15.25.527006
-INFO:root:response received from stage:R .....................27_06_2018___12.15.25.599497
-INFO:root:click move vector: [-10 -29] .......................27_06_2018___12.15.26.240201
-INFO:root:sending command to stage:GR,-10,-29 ................27_06_2018___12.15.26.240201
-INFO:root:response received from stage:R .....................27_06_2018___12.15.26.318740
-INFO:root:click move vector: [ -7 -31] .......................27_06_2018___12.15.26.578290
-INFO:root:sending command to stage:GR,-7,-31 .................27_06_2018___12.15.26.578780
-INFO:root:response received from stage:R .....................27_06_2018___12.15.26.659339
-INFO:root:click move vector: [ 2 -24] ........................27_06_2018___12.15.27.005714
-INFO:root:sending command to stage:GR,2,-24 ..................27_06_2018___12.15.27.006210
-INFO:root:response received from stage:R .....................27_06_2018___12.15.27.085595
-INFO:root:click move vector: [-24 -20] .......................27_06_2018___12.15.27.573010
-INFO:root:sending command to stage:GR,-24,-20 ................27_06_2018___12.15.27.573541
-INFO:root:response received from stage:R .....................27_06_2018___12.15.27.646869
-INFO:root:click move vector: [-35 -8] ........................27_06_2018___12.15.28.028584
-INFO:root:sending command to stage:GR,-35,-8 .................27_06_2018___12.15.28.029167
-INFO:root:response received from stage:R .....................27_06_2018___12.15.28.113508
-INFO:root:click move vector: [-32 0] .........................27_06_2018___12.15.28.543788
-INFO:root:sending command to stage:GR,-32,0 ..................27_06_2018___12.15.28.544278
-INFO:root:response received from stage:R .....................27_06_2018___12.15.28.619112
-INFO:root:click move vector: [9 6] ...........................27_06_2018___12.15.29.610143
-INFO:root:sending command to stage:GR,9,6 ....................27_06_2018___12.15.29.610667
-INFO:root:response received from stage:R .....................27_06_2018___12.15.29.663260
-INFO:root:click move vector: [24 0] ..........................27_06_2018___12.15.30.829451
-INFO:root:sending command to stage:GR,24,0 ...................27_06_2018___12.15.30.829948
-INFO:root:response received from stage:R .....................27_06_2018___12.15.30.895556
-INFO:root:click move vector: [24 0] ..........................27_06_2018___12.15.31.133589
-INFO:root:sending command to stage:GR,24,0 ...................27_06_2018___12.15.31.134083
-INFO:root:response received from stage:R .....................27_06_2018___12.15.31.200910
-INFO:root:click move vector: [24 0] ..........................27_06_2018___12.15.31.404435
-INFO:root:sending command to stage:GR,24,0 ...................27_06_2018___12.15.31.405426
-INFO:root:response received from stage:R .....................27_06_2018___12.15.31.470292
-INFO:root:click move vector: [24 0] ..........................27_06_2018___12.15.31.598350
-INFO:root:sending command to stage:GR,24,0 ...................27_06_2018___12.15.31.599066
-INFO:root:response received from stage:R .....................27_06_2018___12.15.31.673272
-INFO:root:click move vector: [24 0] ..........................27_06_2018___12.15.31.783945
-INFO:root:sending command to stage:GR,24,0 ...................27_06_2018___12.15.31.783945
-INFO:root:response received from stage:R .....................27_06_2018___12.15.31.849298
-INFO:root:click move vector: [24 0] ..........................27_06_2018___12.15.32.025523
-INFO:root:sending command to stage:GR,24,0 ...................27_06_2018___12.15.32.025942
-INFO:root:response received from stage:R .....................27_06_2018___12.15.32.098577
-INFO:root:click move vector: [24 0] ..........................27_06_2018___12.15.32.325782
-INFO:root:sending command to stage:GR,24,0 ...................27_06_2018___12.15.32.326310
-INFO:root:response received from stage:R .....................27_06_2018___12.15.32.392057
-INFO:root:click move vector: [-13 -31] .......................27_06_2018___12.15.33.355223
-INFO:root:sending command to stage:GR,-13,-31 ................27_06_2018___12.15.33.355717
-INFO:root:response received from stage:R .....................27_06_2018___12.15.33.434239
-INFO:root:click move vector: [-13 -31] .......................27_06_2018___12.15.33.636161
-INFO:root:sending command to stage:GR,-13,-31 ................27_06_2018___12.15.33.636703
-INFO:root:response received from stage:R .....................27_06_2018___12.15.33.718043
-INFO:root:click move vector: [ 8 -28] ........................27_06_2018___12.15.34.432100
-INFO:root:sending command to stage:GR,8,-28 ..................27_06_2018___12.15.34.432812
-INFO:root:response received from stage:R .....................27_06_2018___12.15.34.505257
-INFO:root:click move vector: [33 -8] .........................27_06_2018___12.15.35.246545
-INFO:root:sending command to stage:GR,33,-8 ..................27_06_2018___12.15.35.247107
-INFO:root:response received from stage:R .....................27_06_2018___12.15.35.330270
-INFO:root:click move vector: [-22 -23] .......................27_06_2018___12.15.38.157588
-INFO:root:sending command to stage:GR,-22,-23 ................27_06_2018___12.15.38.158307
-INFO:root:response received from stage:R .....................27_06_2018___12.15.38.230960
-INFO:root:click move vector: [-27 1] .........................27_06_2018___12.15.38.962912
-INFO:root:sending command to stage:GR,-27,1 ..................27_06_2018___12.15.38.963439
-INFO:root:response received from stage:R .....................27_06_2018___12.15.39.034735
-INFO:root:click move vector: [ -5 -44] .......................27_06_2018___12.15.39.757539
-INFO:root:sending command to stage:GR,-5,-44 .................27_06_2018___12.15.39.758244
-INFO:root:response received from stage:R .....................27_06_2018___12.15.39.852293
-INFO:root:click move vector: [ -5 -44] .......................27_06_2018___12.15.40.068521
-INFO:root:sending command to stage:GR,-5,-44 .................27_06_2018___12.15.40.068521
-INFO:root:response received from stage:R .....................27_06_2018___12.15.40.163965
-INFO:root:click move vector: [-15 4] .........................27_06_2018___12.15.40.815541
-INFO:root:sending command to stage:GR,-15,4 ..................27_06_2018___12.15.40.816132
-INFO:root:response received from stage:R .....................27_06_2018___12.15.40.877317
-INFO:root:click move vector: [21 7] ..........................27_06_2018___12.15.41.669952
-INFO:root:sending command to stage:GR,21,7 ...................27_06_2018___12.15.41.670489
-INFO:root:response received from stage:R .....................27_06_2018___12.15.41.737052
-INFO:root:click move vector: [21 7] ..........................27_06_2018___12.15.41.922200
-INFO:root:sending command to stage:GR,21,7 ...................27_06_2018___12.15.41.922682
-INFO:root:response received from stage:R .....................27_06_2018___12.15.41.988822
-INFO:root:click move vector: [21 7] ..........................27_06_2018___12.15.42.145492
-INFO:root:sending command to stage:GR,21,7 ...................27_06_2018___12.15.42.146484
-INFO:root:response received from stage:R .....................27_06_2018___12.15.42.214561
-INFO:root:click move vector: [21 7] ..........................27_06_2018___12.15.42.406919
-INFO:root:sending command to stage:GR,21,7 ...................27_06_2018___12.15.42.407613
-INFO:root:response received from stage:R .....................27_06_2018___12.15.42.474596
-INFO:root:click move vector: [21 7] ..........................27_06_2018___12.15.42.679658
-INFO:root:sending command to stage:GR,21,7 ...................27_06_2018___12.15.42.680399
-INFO:root:response received from stage:R .....................27_06_2018___12.15.42.747563
-INFO:root:click move vector: [21 7] ..........................27_06_2018___12.15.42.881423
-INFO:root:sending command to stage:GR,21,7 ...................27_06_2018___12.15.42.881917
-INFO:root:response received from stage:R .....................27_06_2018___12.15.42.961291
-INFO:root:click move vector: [21 7] ..........................27_06_2018___12.15.42.969210
-INFO:root:sending command to stage:GR,21,7 ...................27_06_2018___12.15.42.970200
-INFO:root:response received from stage:R .....................27_06_2018___12.15.43.036722
-INFO:root:click move vector: [21 7] ..........................27_06_2018___12.15.43.124696
-INFO:root:sending command to stage:GR,21,7 ...................27_06_2018___12.15.43.125225
-INFO:root:response received from stage:R .....................27_06_2018___12.15.43.192274
-INFO:root:click move vector: [21 7] ..........................27_06_2018___12.15.43.322553
-INFO:root:sending command to stage:GR,21,7 ...................27_06_2018___12.15.43.323249
-INFO:root:response received from stage:R .....................27_06_2018___12.15.43.388127
-INFO:root:click move vector: [18 10] .........................27_06_2018___12.15.43.872039
-INFO:root:sending command to stage:GR,18,10 ..................27_06_2018___12.15.43.872570
-INFO:root:response received from stage:R .....................27_06_2018___12.15.43.936957
-INFO:root:click move vector: [18 10] .........................27_06_2018___12.15.44.124491
-INFO:root:sending command to stage:GR,18,10 ..................27_06_2018___12.15.44.124999
-INFO:root:response received from stage:R .....................27_06_2018___12.15.44.189190
-INFO:root:click move vector: [18 10] .........................27_06_2018___12.15.44.356327
-INFO:root:sending command to stage:GR,18,10 ..................27_06_2018___12.15.44.356327
-INFO:root:response received from stage:R .....................27_06_2018___12.15.44.422413
-INFO:root:click move vector: [18 10] .........................27_06_2018___12.15.44.521918
-INFO:root:sending command to stage:GR,18,10 ..................27_06_2018___12.15.44.522607
-INFO:root:response received from stage:R .....................27_06_2018___12.15.44.597884
-INFO:root:click move vector: [18 10] .........................27_06_2018___12.15.44.754065
-INFO:root:sending command to stage:GR,18,10 ..................27_06_2018___12.15.44.754558
-INFO:root:response received from stage:R .....................27_06_2018___12.15.44.819108
-INFO:root:click move vector: [18 10] .........................27_06_2018___12.15.45.036426
-INFO:root:sending command to stage:GR,18,10 ..................27_06_2018___12.15.45.036426
-INFO:root:response received from stage:R .....................27_06_2018___12.15.45.106284
-INFO:root:click move vector: [18 10] .........................27_06_2018___12.15.45.278347
-INFO:root:sending command to stage:GR,18,10 ..................27_06_2018___12.15.45.278842
-INFO:root:response received from stage:R .....................27_06_2018___12.15.45.342742
-INFO:root:click move vector: [32 9] ..........................27_06_2018___12.15.45.621527
-INFO:root:sending command to stage:GR,32,9 ...................27_06_2018___12.15.45.621883
-INFO:root:response received from stage:R .....................27_06_2018___12.15.45.698881
-INFO:root:click move vector: [-13 15] ........................27_06_2018___12.15.46.326169
-INFO:root:sending command to stage:GR,-13,15 .................27_06_2018___12.15.46.326836
-INFO:root:response received from stage:R .....................27_06_2018___12.15.46.389244
-INFO:root:click move vector: [-13 15] ........................27_06_2018___12.15.46.685520
-INFO:root:sending command to stage:GR,-13,15 .................27_06_2018___12.15.46.686133
-INFO:root:response received from stage:R .....................27_06_2018___12.15.46.747979
-INFO:root:click move vector: [ 17 -16] .......................27_06_2018___12.15.55.077651
-INFO:root:sending command to stage:GR,17,-16 .................27_06_2018___12.15.55.078375
-INFO:root:response received from stage:R .....................27_06_2018___12.15.55.144214
-INFO:root:click move vector: [ 19 -11] .......................27_06_2018___12.15.55.552071
-INFO:root:sending command to stage:GR,19,-11 .................27_06_2018___12.15.55.553066
-INFO:root:response received from stage:R .....................27_06_2018___12.15.55.619435
-INFO:root:click move vector: [ 19 -11] .......................27_06_2018___12.15.55.776498
-INFO:root:sending command to stage:GR,19,-11 .................27_06_2018___12.15.55.777049
-INFO:root:response received from stage:R .....................27_06_2018___12.15.55.844548
-INFO:root:click move vector: [ 15 -18] .......................27_06_2018___12.15.56.193778
-INFO:root:sending command to stage:GR,15,-18 .................27_06_2018___12.15.56.194110
-INFO:root:response received from stage:R .....................27_06_2018___12.15.56.258650
-INFO:root:click move vector: [21 -1] .........................27_06_2018___12.15.56.688280
-INFO:root:sending command to stage:GR,21,-1 ..................27_06_2018___12.15.56.688280
-INFO:root:response received from stage:R .....................27_06_2018___12.15.56.754034
-INFO:root:click move vector: [21 -1] .........................27_06_2018___12.15.56.959935
-INFO:root:sending command to stage:GR,21,-1 ..................27_06_2018___12.15.56.960232
-INFO:root:response received from stage:R .....................27_06_2018___12.15.57.026133
-INFO:root:click move vector: [21 -1] .........................27_06_2018___12.15.57.192760
-INFO:root:sending command to stage:GR,21,-1 ..................27_06_2018___12.15.57.193525
-INFO:root:response received from stage:R .....................27_06_2018___12.15.57.263991
-INFO:root:click move vector: [ 5 13] .........................27_06_2018___12.15.57.589754
-INFO:root:sending command to stage:GR,5,13 ...................27_06_2018___12.15.57.590251
-INFO:root:response received from stage:R .....................27_06_2018___12.15.57.647522
-INFO:root:click move vector: [ 5 13] .........................27_06_2018___12.15.57.958899
-INFO:root:sending command to stage:GR,5,13 ...................27_06_2018___12.15.57.959440
-INFO:root:response received from stage:R .....................27_06_2018___12.15.58.026696
-INFO:root:click move vector: [ 5 13] .........................27_06_2018___12.15.58.143731
-INFO:root:sending command to stage:GR,5,13 ...................27_06_2018___12.15.58.143731
-INFO:root:response received from stage:R .....................27_06_2018___12.15.58.200430
-INFO:root:click move vector: [ 5 13] .........................27_06_2018___12.15.58.337437
-INFO:root:sending command to stage:GR,5,13 ...................27_06_2018___12.15.58.337437
-INFO:root:response received from stage:R .....................27_06_2018___12.15.58.394084
-INFO:root:click move vector: [ 5 13] .........................27_06_2018___12.15.58.512228
-INFO:root:sending command to stage:GR,5,13 ...................27_06_2018___12.15.58.512681
-INFO:root:response received from stage:R .....................27_06_2018___12.15.58.569777
-INFO:root:click move vector: [ 5 13] .........................27_06_2018___12.15.58.712363
-INFO:root:sending command to stage:GR,5,13 ...................27_06_2018___12.15.58.712363
-INFO:root:response received from stage:R .....................27_06_2018___12.15.58.769342
-INFO:root:click move vector: [ 5 13] .........................27_06_2018___12.15.58.910287
-INFO:root:sending command to stage:GR,5,13 ...................27_06_2018___12.15.58.910287
-INFO:root:response received from stage:R .....................27_06_2018___12.15.58.966805
-INFO:root:click move vector: [ 5 13] .........................27_06_2018___12.15.59.142933
-INFO:root:sending command to stage:GR,5,13 ...................27_06_2018___12.15.59.143593
-INFO:root:response received from stage:R .....................27_06_2018___12.15.59.199125
-INFO:root:click move vector: [ 5 13] .........................27_06_2018___12.15.59.452295
-INFO:root:sending command to stage:GR,5,13 ...................27_06_2018___12.15.59.452792
-INFO:root:response received from stage:R .....................27_06_2018___12.15.59.510495
-INFO:root:click move vector: [ 5 13] .........................27_06_2018___12.15.59.667153
-INFO:root:sending command to stage:GR,5,13 ...................27_06_2018___12.15.59.667685
-INFO:root:response received from stage:R .....................27_06_2018___12.15.59.725477
-INFO:root:click move vector: [ 5 13] .........................27_06_2018___12.15.59.792279
-INFO:root:sending command to stage:GR,5,13 ...................27_06_2018___12.15.59.792772
-INFO:root:response received from stage:R .....................27_06_2018___12.15.59.849450
-INFO:root:click move vector: [ 5 13] .........................27_06_2018___12.15.59.948248
-INFO:root:sending command to stage:GR,5,13 ...................27_06_2018___12.15.59.948752
-INFO:root:response received from stage:R .....................27_06_2018___12.16.00.005324
-INFO:root:click move vector: [ 5 13] .........................27_06_2018___12.16.00.122577
-INFO:root:sending command to stage:GR,5,13 ...................27_06_2018___12.16.00.123067
-INFO:root:response received from stage:R .....................27_06_2018___12.16.00.178990
-INFO:root:click move vector: [-7 14] .........................27_06_2018___12.16.00.540382
-INFO:root:sending command to stage:GR,-7,14 ..................27_06_2018___12.16.00.540382
-INFO:root:response received from stage:R .....................27_06_2018___12.16.00.600809
-INFO:root:click move vector: [-7 14] .........................27_06_2018___12.16.00.849541
-INFO:root:sending command to stage:GR,-7,14 ..................27_06_2018___12.16.00.850070
-INFO:root:response received from stage:R .....................27_06_2018___12.16.00.919941
-INFO:root:click move vector: [-7 14] .........................27_06_2018___12.16.01.034024
-INFO:root:sending command to stage:GR,-7,14 ..................27_06_2018___12.16.01.034555
-INFO:root:response received from stage:R .....................27_06_2018___12.16.01.093421
-INFO:root:click move vector: [-7 14] .........................27_06_2018___12.16.01.219168
-INFO:root:sending command to stage:GR,-7,14 ..................27_06_2018___12.16.01.219663
-INFO:root:response received from stage:R .....................27_06_2018___12.16.01.278478
-INFO:root:click move vector: [-7 14] .........................27_06_2018___12.16.01.411715
-INFO:root:sending command to stage:GR,-7,14 ..................27_06_2018___12.16.01.412214
-INFO:root:response received from stage:R .....................27_06_2018___12.16.01.472783
-INFO:root:click move vector: [-7 14] .........................27_06_2018___12.16.01.635148
-INFO:root:sending command to stage:GR,-7,14 ..................27_06_2018___12.16.01.635680
-INFO:root:response received from stage:R .....................27_06_2018___12.16.01.695452
-INFO:root:click move vector: [-7 14] .........................27_06_2018___12.16.01.878687
-INFO:root:sending command to stage:GR,-7,14 ..................27_06_2018___12.16.01.878982
-INFO:root:response received from stage:R .....................27_06_2018___12.16.01.938792
-INFO:root:click move vector: [10 10] .........................27_06_2018___12.16.03.149143
-INFO:root:sending command to stage:GR,10,10 ..................27_06_2018___12.16.03.149676
-INFO:root:response received from stage:R .....................27_06_2018___12.16.03.208786
-INFO:root:click move vector: [10 10] .........................27_06_2018___12.16.03.352786
-INFO:root:sending command to stage:GR,10,10 ..................27_06_2018___12.16.03.353311
-INFO:root:response received from stage:R .....................27_06_2018___12.16.03.408225
-INFO:root:click move vector: [13 10] .........................27_06_2018___12.16.03.672812
-INFO:root:sending command to stage:GR,13,10 ..................27_06_2018___12.16.03.673810
-INFO:root:response received from stage:R .....................27_06_2018___12.16.03.732439
-INFO:root:click move vector: [13 10] .........................27_06_2018___12.16.03.924931
-INFO:root:sending command to stage:GR,13,10 ..................27_06_2018___12.16.03.925462
-INFO:root:response received from stage:R .....................27_06_2018___12.16.03.985029
-INFO:root:click move vector: [19 12] .........................27_06_2018___12.16.06.267689
-INFO:root:sending command to stage:GR,19,12 ..................27_06_2018___12.16.06.268189
-INFO:root:response received from stage:R .....................27_06_2018___12.16.06.335217
-INFO:root:click move vector: [19 12] .........................27_06_2018___12.16.06.621852
-INFO:root:sending command to stage:GR,19,12 ..................27_06_2018___12.16.06.622388
-INFO:root:response received from stage:R .....................27_06_2018___12.16.06.695529
-INFO:root:click move vector: [-10 13] ........................27_06_2018___12.16.07.805148
-INFO:root:sending command to stage:GR,-10,13 .................27_06_2018___12.16.07.805644
-INFO:root:response received from stage:R .....................27_06_2018___12.16.07.864367
-INFO:root:taking target picture ..............................27_06_2018___12.16.46.077286
-INFO:root:sending command to stage:GR,4400,0 .................27_06_2018___12.17.19.503316
-INFO:root:response received from stage:R .....................27_06_2018___12.17.20.096747
-INFO:root:sending command to stage:GR,-4400,0 ................27_06_2018___12.17.21.463224
-INFO:root:response received from stage:R .....................27_06_2018___12.17.22.057779
-INFO:root:sending command to stage:GR,4400,0 .................27_06_2018___12.17.22.694540
-INFO:root:response received from stage:R .....................27_06_2018___12.17.23.289180
-INFO:root:click move vector: [33 -1] .........................27_06_2018___12.17.33.432366
-INFO:root:sending command to stage:GR,33,-1 ..................27_06_2018___12.17.33.432986
-INFO:root:response received from stage:R .....................27_06_2018___12.17.33.509512
-INFO:root:click move vector: [33 -1] .........................27_06_2018___12.17.34.004869
-INFO:root:sending command to stage:GR,33,-1 ..................27_06_2018___12.17.34.005375
-INFO:root:response received from stage:R .....................27_06_2018___12.17.34.082207
-INFO:root:sending command to stage:GR,-4400,0 ................27_06_2018___12.17.44.688376
-INFO:root:response received from stage:R .....................27_06_2018___12.17.45.284596
-INFO:root:click move vector: [ -4 -27] .......................27_06_2018___12.17.47.607100
-INFO:root:sending command to stage:GR,-4,-27 .................27_06_2018___12.17.47.607100
-INFO:root:response received from stage:R .....................27_06_2018___12.17.47.696062
-INFO:root:click move vector: [-16 0] .........................27_06_2018___12.17.48.101767
-INFO:root:sending command to stage:GR,-16,0 ..................27_06_2018___12.17.48.102230
-INFO:root:response received from stage:R .....................27_06_2018___12.17.48.162147
-INFO:root:click move vector: [-18 1] .........................27_06_2018___12.17.48.480650
-INFO:root:sending command to stage:GR,-18,1 ..................27_06_2018___12.17.48.481146
-INFO:root:response received from stage:R .....................27_06_2018___12.17.48.544964
-INFO:root:click move vector: [-5 4] ..........................27_06_2018___12.17.48.985200
-INFO:root:sending command to stage:GR,-5,4 ...................27_06_2018___12.17.48.985692
-INFO:root:response received from stage:R .....................27_06_2018___12.17.49.035709
-INFO:root:click move vector: [ 0 11] .........................27_06_2018___12.17.49.266307
-INFO:root:sending command to stage:GR,0,11 ...................27_06_2018___12.17.49.266770
-INFO:root:response received from stage:R .....................27_06_2018___12.17.49.319538
-INFO:root:click move vector: [ 0 11] .........................27_06_2018___12.17.49.546216
-INFO:root:sending command to stage:GR,0,11 ...................27_06_2018___12.17.49.546754
-INFO:root:response received from stage:R .....................27_06_2018___12.17.49.599577
-INFO:root:click move vector: [23 12] .........................27_06_2018___12.18.10.389330
-INFO:root:sending command to stage:GR,23,12 ..................27_06_2018___12.18.10.389827
-INFO:root:response received from stage:R .....................27_06_2018___12.18.10.458793
-INFO:root:click move vector: [28 15] .........................27_06_2018___12.18.10.802497
-INFO:root:sending command to stage:GR,28,15 ..................27_06_2018___12.18.10.802994
-INFO:root:response received from stage:R .....................27_06_2018___12.18.10.879377
-INFO:root:click move vector: [-20 0] .........................27_06_2018___12.18.12.310623
-INFO:root:sending command to stage:GR,-20,0 ..................27_06_2018___12.18.12.311118
-INFO:root:response received from stage:R .....................27_06_2018___12.18.12.375889
-INFO:root:sending command to stage:GR,-5,0 ...................27_06_2018___12.18.14.014688
-INFO:root:response received from stage:R .....................27_06_2018___12.18.14.059306
-INFO:root:sending command to stage:GR,-5,0 ...................27_06_2018___12.18.14.178246
-INFO:root:response received from stage:R .....................27_06_2018___12.18.14.222777
-INFO:root:sending command to stage:GR,-5,0 ...................27_06_2018___12.18.14.550432
-INFO:root:response received from stage:R .....................27_06_2018___12.18.14.593492
-INFO:root:sending command to stage:GR,-5,0 ...................27_06_2018___12.18.14.738313
-INFO:root:response received from stage:R .....................27_06_2018___12.18.14.793171
-INFO:root:sending command to stage:GR,-5,0 ...................27_06_2018___12.18.14.966127
-INFO:root:response received from stage:R .....................27_06_2018___12.18.15.008759
-INFO:root:sending command to stage:GR,-5,0 ...................27_06_2018___12.18.15.107169
-INFO:root:response received from stage:R .....................27_06_2018___12.18.15.151402
-INFO:root:sending command to stage:GR,-5,0 ...................27_06_2018___12.18.15.267470
-INFO:root:response received from stage:R .....................27_06_2018___12.18.15.315016
-INFO:root:sending command to stage:GR,-5,0 ...................27_06_2018___12.18.15.417078
-INFO:root:response received from stage:R .....................27_06_2018___12.18.15.469107
-INFO:root:sending command to stage:GR,-5,0 ...................27_06_2018___12.18.15.582690
-INFO:root:response received from stage:R .....................27_06_2018___12.18.15.627123
-INFO:root:sending command to stage:GR,-5,0 ...................27_06_2018___12.18.15.760857
-INFO:root:response received from stage:R .....................27_06_2018___12.18.15.808706
-INFO:root:sending command to stage:GR,-5,0 ...................27_06_2018___12.18.16.100153
-INFO:root:response received from stage:R .....................27_06_2018___12.18.16.143136
-INFO:root:sending command to stage:GR,-5,0 ...................27_06_2018___12.18.16.292211
-INFO:root:response received from stage:R .....................27_06_2018___12.18.16.335468
-INFO:root:sending command to stage:GR,-5,0 ...................27_06_2018___12.18.16.466358
-INFO:root:response received from stage:R .....................27_06_2018___12.18.16.509124
-INFO:root:step size changed to: 10.0 .........................27_06_2018___12.18.18.414401
-INFO:root:step size changed to: 15.0 .........................27_06_2018___12.18.18.714054
-INFO:root:sending command to stage:GR,-15.0,0 ................27_06_2018___12.18.23.253414
-INFO:root:response received from stage:R .....................27_06_2018___12.18.23.314605
-INFO:root:sending command to stage:GR,-15.0,0 ................27_06_2018___12.18.23.804114
-INFO:root:response received from stage:R .....................27_06_2018___12.18.23.864373
-INFO:root:sending command to stage:GR,-15.0,0 ................27_06_2018___12.18.23.974638
-INFO:root:response received from stage:R .....................27_06_2018___12.18.24.035373
-INFO:root:sending command to stage:GR,-15.0,0 ................27_06_2018___12.18.24.216500
-INFO:root:response received from stage:R .....................27_06_2018___12.18.24.293291
-INFO:root:step size changed to: 20.0 .........................27_06_2018___12.18.27.717896
-INFO:root:step size changed to: 25.0 .........................27_06_2018___12.18.27.997369
-INFO:root:step size changed to: 30.0 .........................27_06_2018___12.18.28.217978
-INFO:root:step size changed to: 35.0 .........................27_06_2018___12.18.28.443461
-INFO:root:step size changed to: 40.0 .........................27_06_2018___12.18.28.617939
-INFO:root:sending command to stage:GR,-40.0,0 ................27_06_2018___12.18.30.153711
-INFO:root:response received from stage:R .....................27_06_2018___12.18.30.235136
-INFO:root:sending command to stage:GR,-40.0,0 ................27_06_2018___12.18.30.743718
-INFO:root:response received from stage:R .....................27_06_2018___12.18.30.824684
-INFO:root:sending command to stage:GR,-40.0,0 ................27_06_2018___12.18.31.034365
-INFO:root:response received from stage:R .....................27_06_2018___12.18.31.115888
-INFO:root:sending command to stage:GR,-40.0,0 ................27_06_2018___12.18.31.205633
-INFO:root:response received from stage:R .....................27_06_2018___12.18.31.287715
-INFO:root:sending command to stage:GR,-40.0,0 ................27_06_2018___12.18.31.829922
-INFO:root:response received from stage:R .....................27_06_2018___12.18.31.910745
-INFO:root:sending command to stage:GR,-40.0,0 ................27_06_2018___12.18.32.049278
-INFO:root:response received from stage:R .....................27_06_2018___12.18.32.142724
-INFO:root:sending command to stage:GR,-40.0,0 ................27_06_2018___12.18.32.333993
-INFO:root:response received from stage:R .....................27_06_2018___12.18.32.414427
-INFO:root:sending command to stage:GR,-40.0,0 ................27_06_2018___12.18.32.647532
-INFO:root:response received from stage:R .....................27_06_2018___12.18.32.734280
-INFO:root:sending command to stage:GR,-40.0,0 ................27_06_2018___12.18.32.928156
-INFO:root:response received from stage:R .....................27_06_2018___12.18.33.009448
-INFO:root:sending command to stage:GR,-40.0,0 ................27_06_2018___12.18.33.219727
-INFO:root:response received from stage:R .....................27_06_2018___12.18.33.301414
-INFO:root:sending command to stage:GR,-40.0,0 ................27_06_2018___12.18.33.533717
-INFO:root:response received from stage:R .....................27_06_2018___12.18.33.615462
-INFO:root:sending command to stage:GR,-40.0,0 ................27_06_2018___12.18.33.680296
-INFO:root:response received from stage:R .....................27_06_2018___12.18.33.760871
-INFO:root:sending command to stage:GR,-40.0,0 ................27_06_2018___12.18.33.951034
-INFO:root:response received from stage:R .....................27_06_2018___12.18.34.033333
-INFO:root:sending command to stage:GR,-40.0,0 ................27_06_2018___12.18.34.349566
-INFO:root:response received from stage:R .....................27_06_2018___12.18.34.431256
-INFO:root:sending command to stage:GR,40.0,0 .................27_06_2018___12.18.34.843500
-INFO:root:response received from stage:R .....................27_06_2018___12.18.34.924883
-INFO:root:sending command to stage:GR,40.0,0 .................27_06_2018___12.18.35.058936
-INFO:root:response received from stage:R .....................27_06_2018___12.18.35.138460
-INFO:root:sending command to stage:GR,40.0,0 .................27_06_2018___12.18.35.235628
-INFO:root:response received from stage:R .....................27_06_2018___12.18.35.316732
-INFO:root:sending command to stage:GR,40.0,0 .................27_06_2018___12.18.35.423001
-INFO:root:response received from stage:R .....................27_06_2018___12.18.35.502422
-INFO:root:sending command to stage:GR,40.0,0 .................27_06_2018___12.18.35.624780
-INFO:root:response received from stage:R .....................27_06_2018___12.18.35.705269
-INFO:root:sending command to stage:GR,40.0,0 .................27_06_2018___12.18.35.791167
-INFO:root:response received from stage:R .....................27_06_2018___12.18.35.873447
-INFO:root:sending command to stage:GR,40.0,0 .................27_06_2018___12.18.36.049573
-INFO:root:response received from stage:R .....................27_06_2018___12.18.36.134388
-INFO:root:sending command to stage:GR,40.0,0 .................27_06_2018___12.18.36.215286
-INFO:root:response received from stage:R .....................27_06_2018___12.18.36.299906
-INFO:root:sending command to stage:GR,40.0,0 .................27_06_2018___12.18.36.503534
-INFO:root:response received from stage:R .....................27_06_2018___12.18.36.584556
diff --git a/Experiments/experiment_27_06_2018___12.13.14.428842/target___27_06_2018___12.16.46.121489.tif b/Experiments/experiment_27_06_2018___12.13.14.428842/target___27_06_2018___12.16.46.121489.tif
deleted file mode 100644
index c30b1cc2602ba1bc905b498fdbe0969f8a36c008..0000000000000000000000000000000000000000
Binary files a/Experiments/experiment_27_06_2018___12.13.14.428842/target___27_06_2018___12.16.46.121489.tif and /dev/null differ
diff --git a/LCL.ui b/LCL.ui
old mode 100755
new mode 100644
diff --git a/LCL_run.py b/LCL_run.py
old mode 100755
new mode 100644
index 7285843ced0ee5681267f3485e88502f5226ab21..ab6c7fb1f7b87cac921026820f47b2f7ed6efc7a
--- a/LCL_run.py
+++ b/LCL_run.py
@@ -129,7 +129,7 @@ class main_window(QMainWindow):
 		self.vid = ShowVideo(self.ui.verticalLayoutWidget.size())
 		self.screen_shooter = screen_shooter()
 		self.image_viewer = ImageViewer()
-		self.autofocuser = autofocuser()
+		# self.autofocuser = autofocuser()
 		self.localizer = Localizer()		
 
 		# add the viewer to our ui
@@ -140,9 +140,9 @@ class main_window(QMainWindow):
 		self.screenshooter_thread.start()
 		self.screen_shooter.moveToThread(self.screenshooter_thread)		
 
-		self.autofocuser_thread = QThread()
-		self.autofocuser_thread.start()
-		self.autofocuser.moveToThread(self.autofocuser_thread)		
+		# self.autofocuser_thread = QThread()
+		# self.autofocuser_thread.start()
+		# self.autofocuser.moveToThread(self.autofocuser_thread)		
 
 		self.localizer_thread = QThread()
 		self.localizer_thread.start()
@@ -155,13 +155,13 @@ class main_window(QMainWindow):
 		# connect the outputs to our signals
 		self.vid.VideoSignal.connect(self.image_viewer.setImage)		
 		self.vid.vid_process_signal.connect(self.screen_shooter.screenshot_slot)		
-		self.vid.vid_process_signal.connect(self.autofocuser.vid_process_slot)
+		# self.vid.vid_process_signal.connect(self.autofocuser.vid_process_slot)
 		self.vid.vid_process_signal.connect(self.localizer.vid_process_slot)
 		self.qswitch_screenshot_signal.connect(self.screen_shooter.save_qswitch_fire_slot)
 		self.localizer.qswitch_screenshot_signal.connect(self.screen_shooter.save_qswitch_fire_slot)
-		self.start_focus_signal.connect(self.autofocuser.autofocus)
+		# self.start_focus_signal.connect(self.autofocuser.autofocus)
 		self.start_localization_signal.connect(self.localizer.localize)
-		self.autofocuser.position_and_variance_signal.connect(self.plot_variance_and_position)
+		# self.autofocuser.position_and_variance_signal.connect(self.plot_variance_and_position)
 		self.image_viewer.click_move_signal.connect(stage.click_move_slot)
 		self.localizer.localizer_move_signal.connect(stage.localizer_move_slot)
 		self.localizer.ai_fire_qswitch_signal.connect(self.ai_fire_qswitch_slot)
@@ -290,9 +290,9 @@ class main_window(QMainWindow):
 			16777249:laser.fire_auto,
 			70:self.qswitch_screenshot_slot,
 			81:laser.qswitch_auto,
-			73:self.autofocuser.roll_forward,
-			75:self.autofocuser.roll_backward,
-			79:self.start_autofocus,
+			# 73:self.autofocuser.roll_forward,
+			# 75:self.autofocuser.roll_backward,
+			# 79:self.start_autofocus,
 			# 71:self.toggle_dmf_or_lysis,
 			84:stage.move_left_one_well_slot,
 			89:stage.move_right_one_well_slot,
@@ -307,8 +307,8 @@ class main_window(QMainWindow):
 			# print('key released: {}'.format(event.key()))
 			key_control_dict = {
 			16777249:laser.stop_flash,
-			73:self.autofocuser.stop_roll,
-			75:self.autofocuser.stop_roll
+			# 73:self.autofocuser.stop_roll,
+			# 75:self.autofocuser.stop_roll
 			}
 			if event.key() in key_control_dict.keys():
 				key_control_dict[event.key()]()
diff --git a/LCL_ui.py b/LCL_ui.py
old mode 100755
new mode 100644
diff --git a/LCL_ui.pyc b/LCL_ui.pyc
old mode 100755
new mode 100644
diff --git a/__pycache__/LCL.cpython-36.pyc b/__pycache__/LCL.cpython-36.pyc
old mode 100755
new mode 100644
diff --git a/__pycache__/LCL_ui.cpython-36.pyc b/__pycache__/LCL_ui.cpython-36.pyc
old mode 100755
new mode 100644
diff --git a/__pycache__/autofocus.cpython-36.pyc b/__pycache__/autofocus.cpython-36.pyc
old mode 100755
new mode 100644
diff --git a/__pycache__/image_movement_controller.cpython-36.pyc b/__pycache__/image_movement_controller.cpython-36.pyc
old mode 100755
new mode 100644
diff --git a/__pycache__/image_window_ui.cpython-36.pyc b/__pycache__/image_window_ui.cpython-36.pyc
old mode 100755
new mode 100644
diff --git a/__pycache__/laser_controller.cpython-36.pyc b/__pycache__/laser_controller.cpython-36.pyc
old mode 100755
new mode 100644
diff --git a/__pycache__/localizer.cpython-36.pyc b/__pycache__/localizer.cpython-36.pyc
old mode 100755
new mode 100644
index 14f3529b29e51701748e8410b3fa0ba409fae41d..fa3672df5dc27d1bab5033c9b02494603dfd2c5d
Binary files a/__pycache__/localizer.cpython-36.pyc and b/__pycache__/localizer.cpython-36.pyc differ
diff --git a/__pycache__/picture_handler.cpython-36.pyc b/__pycache__/picture_handler.cpython-36.pyc
old mode 100755
new mode 100644
diff --git a/__pycache__/stage_controller.cpython-36.pyc b/__pycache__/stage_controller.cpython-36.pyc
old mode 100755
new mode 100644
index 9d0f81fbe4d76e71c9a83aac39dd4da997b53d09..af5eaf805acca1759f4c85c90db71a0db87968da
Binary files a/__pycache__/stage_controller.cpython-36.pyc and b/__pycache__/stage_controller.cpython-36.pyc differ
diff --git a/__pycache__/test.cpython-36.pyc b/__pycache__/test.cpython-36.pyc
old mode 100755
new mode 100644
diff --git a/__pycache__/utils.cpython-36.pyc b/__pycache__/utils.cpython-36.pyc
old mode 100755
new mode 100644
diff --git a/__pycache__/zoom_gui_test.cpython-36.pyc b/__pycache__/zoom_gui_test.cpython-36.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..0d57365be1d542870fa623b616e5e7df3f372966
Binary files /dev/null and b/__pycache__/zoom_gui_test.cpython-36.pyc differ
diff --git a/autofocus.py b/autofocus.py
old mode 100755
new mode 100644
diff --git a/autofocus.pyc b/autofocus.pyc
old mode 100755
new mode 100644
diff --git a/denoising_test.py b/denoising_test.py
old mode 100755
new mode 100644
diff --git a/directory_organizer.py b/directory_organizer.py
old mode 100755
new mode 100644
diff --git a/image_annotator_adam_may29.py b/image_annotator_adam_may29.py
old mode 100755
new mode 100644
diff --git a/image_processing.py b/image_processing.py
old mode 100755
new mode 100644
diff --git a/laser_controller.py b/laser_controller.py
old mode 100755
new mode 100644
diff --git a/laser_controller.pyc b/laser_controller.pyc
old mode 100755
new mode 100644
diff --git a/localizer.py b/localizer.py
old mode 100755
new mode 100644
index ac578097e6d8263119b71235b0b6e115ef3bc9ad..88916bfa29a3e2a190e3046c2ef47eaa9f9c3c9a
--- a/localizer.py
+++ b/localizer.py
@@ -13,6 +13,7 @@ from sklearn.preprocessing import StandardScaler
 from utils import MeanIoU
 from keras import backend as K
 graph = tf.get_default_graph()
+import skimage.transform as transform
 
 num_classes = 3
 miou_metric = MeanIoU(num_classes)
@@ -66,7 +67,8 @@ class Localizer(QtCore.QObject):
 
 	def __init__(self, parent = None):
 		super(Localizer, self).__init__(parent)		
-		self.localizer_model = load_model(os.path.join(experiment_folder_location,'multiclass_localizer18_2.hdf5'),custom_objects={'mean_iou': mean_iou})
+		# self.localizer_model = load_model(os.path.join(experiment_folder_location,'multiclass_localizer18_2.hdf5'),custom_objects={'mean_iou': mean_iou})
+		self.localizer_model = load_model(os.path.join(experiment_folder_location,'model2018-10-18_08_47'),custom_objects={'mean_iou': mean_iou})
 		self.norm = StandardScaler()		
 		self.localizer_model._make_predict_function()
 		self.position = np.zeros((1,2))
@@ -89,8 +91,10 @@ class Localizer(QtCore.QObject):
 
 	def change_type_to_lyse(self,index):
 		map_dict = {
-		0:('red','multiclass_localizer18_2.hdf5'),
-		1:('green','multiclass_localizer18_2.hdf5'),
+		# 0:('red','multiclass_localizer18_2.hdf5'),
+		# 1:('green','multiclass_localizer18_2.hdf5'),
+		0:('red','model2018-10-18_08_47'),
+		1:('green','model2018-10-18_08_47'),
 		2:('green hope','second_binary_green_hope_localizer_16_0.28892_1_54_7_12.hdf5')
 		}
 		self.cell_type_to_lyse = map_dict[index][0]
@@ -123,7 +127,7 @@ class Localizer(QtCore.QObject):
 		
 	def get_network_output(self,img,mode):
 		img = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)		
-		img = cv2.resize(img, (125, 125))
+		img = transform.resize(img, (128, 128), anti_aliasing=False)
 		img = self.norm.fit_transform(img)
 		img = np.expand_dims(img,axis = 4) 
 		img = np.expand_dims(img,axis = 0) 
@@ -131,13 +135,14 @@ class Localizer(QtCore.QObject):
 			segmented_image = self.localizer_model.predict(img,batch_size = 1)	
 		if mode == 'multi':
 			# print(segmented_image.shape)
-			return_img = np.zeros((125,125,3))
+			return_img = np.zeros((128,128,3))
 			#red cell
-			return_img[:,:,2] = segmented_image[0,:,:,1]			
+			return_img[:,:,2] = segmented_image[0,:,:,2]			
 			#green cell
-			return_img[:,:,1] = segmented_image[0,:,:,2]			
+			return_img[:,:,1] = segmented_image[0,:,:,1]			
 		elif mode == 'binary':
 			return_img = segmented_image[0,:,:,0]
+		return_img = transform.resize(return_img, (125, 125), anti_aliasing=False)
 		return return_img
 
 	@QtCore.pyqtSlot('PyQt_PyObject')
@@ -196,9 +201,9 @@ class Localizer(QtCore.QObject):
 		self.auto_lysis = True
 		self.well_center = self.get_stage_position()		
 		# now start moving and lysing all in view
-		# self.lyse_all_in_view()
+		self.lyse_all_in_view()
 		box_size = 5
-		stitcher = wellStitcher(box_size,self.image)		
+		# stitcher = wellStitcher(box_size,self.image)		
 		directions = self.get_spiral_directions(box_size)		
 		self.get_well_center = False
 		for num,let in directions:
@@ -216,11 +221,11 @@ class Localizer(QtCore.QObject):
 				QApplication.processEvents()
 				self.delay()
 				QApplication.processEvents()
-				stitcher.add_img(let,self.image)
-				# self.lyse_all_in_view()
+				# stitcher.add_img(let,self.image)
+				self.lyse_all_in_view()
 		comment('lysis completed!')
-		stitcher.write_well_img()
-		# self.return_to_original_position(self.well_center)
+		# stitcher.write_well_img()
+		self.return_to_original_position(self.well_center)
 
 
 	def get_spiral_directions(self,box_size):
@@ -293,7 +298,7 @@ class Localizer(QtCore.QObject):
 	def excision_lysis(self,cell_contours):
 		# for each contour we want to trace it
 		window_center = np.array([125./2,125./2])
-		if len(cell_contours) >0:
+		if len(cell_contours) > 0:
 			for i in range(len(cell_contours)):			
 				contour = cell_contours[i]
 				point_number = contour.shape[0] 
@@ -339,6 +344,9 @@ class Localizer(QtCore.QObject):
 
 	def direct_lysis(self,cell_centers):
 		window_center = np.array([125./2,125./2])
+		if len(cell_centers) < 2: return
+		cell_centers = cell_centers[1:]
+
 		print('centers:',cell_centers)
 		old_center = cell_centers[0]
 		self.move_to_target(old_center-window_center,True)
@@ -392,9 +400,9 @@ class Localizer(QtCore.QObject):
 
 	def threshold_based_on_type(self,segmented_image,cell_type):
 		if cell_type == 'green':
-			_,confidence_image = cv2.threshold(segmented_image[:,:,1],.5,1,cv2.THRESH_BINARY)
+			_,confidence_image = cv2.threshold(segmented_image[:,:,1],.9,1,cv2.THRESH_BINARY)
 		elif cell_type == 'red':
-			_,confidence_image = cv2.threshold(segmented_image[:,:,2],.5,1,cv2.THRESH_BINARY)
+			_,confidence_image = cv2.threshold(segmented_image[:,:,2],.9,1,cv2.THRESH_BINARY)
 		elif cell_type == 'green hope':
 			# assumes a binary image!
 			# TODO: find the optimal location on the AUC curve for the threshold
diff --git a/models/VGG_model_5.hdf5 b/models/VGG_model_5.hdf5
old mode 100755
new mode 100644
diff --git a/models/before_qswitch___06_07_2018___11.48.59.274395.tif b/models/before_qswitch___06_07_2018___11.48.59.274395.tif
old mode 100755
new mode 100644
diff --git a/models/binary_green_hope_localizer3.hdf5 b/models/binary_green_hope_localizer3.hdf5
old mode 100755
new mode 100644
diff --git a/models/binary_green_hope_localizer_8_0.001_0.8280362384534469_0.13846914671645638_0.648396880101525_188_9_7.hdf5 b/models/binary_green_hope_localizer_8_0.001_0.8280362384534469_0.13846914671645638_0.648396880101525_188_9_7.hdf5
old mode 100755
new mode 100644
diff --git a/models/feature_extractor3.hdf5 b/models/feature_extractor3.hdf5
deleted file mode 100755
index 9981117d614074f1c0051ab7456828172a31568b..0000000000000000000000000000000000000000
Binary files a/models/feature_extractor3.hdf5 and /dev/null differ
diff --git a/models/localizer_continue_learning.py b/models/localizer_continue_learning.py
old mode 100755
new mode 100644
diff --git a/models/model2018-10-18_08_47 b/models/model2018-10-18_08_47
new file mode 100644
index 0000000000000000000000000000000000000000..1a780acb3aa6877b6ac0f1cc31cb0c36da77ee5d
Binary files /dev/null and b/models/model2018-10-18_08_47 differ
diff --git a/models/multiclass_localizer10.hdf5 b/models/multiclass_localizer10.hdf5
deleted file mode 100755
index 97ae6110dc1687ae8a72a11b1713594190530de5..0000000000000000000000000000000000000000
Binary files a/models/multiclass_localizer10.hdf5 and /dev/null differ
diff --git a/models/multiclass_localizer11.hdf5 b/models/multiclass_localizer11.hdf5
deleted file mode 100755
index 29975c33cf81acffe6108d2469517d3199b2a6a5..0000000000000000000000000000000000000000
Binary files a/models/multiclass_localizer11.hdf5 and /dev/null differ
diff --git a/models/multiclass_localizer14.hdf5 b/models/multiclass_localizer14.hdf5
deleted file mode 100755
index daead7974ddef0113168ba882d8ba99170e6d24a..0000000000000000000000000000000000000000
Binary files a/models/multiclass_localizer14.hdf5 and /dev/null differ
diff --git a/models/multiclass_localizer16.hdf5 b/models/multiclass_localizer16.hdf5
deleted file mode 100755
index d0b3ff670a740d916be2f497b70611b63594e855..0000000000000000000000000000000000000000
Binary files a/models/multiclass_localizer16.hdf5 and /dev/null differ
diff --git a/models/multiclass_localizer18_2.hdf5 b/models/multiclass_localizer18_2.hdf5
old mode 100755
new mode 100644
diff --git a/models/multiclass_localizer5.hdf5 b/models/multiclass_localizer5.hdf5
deleted file mode 100755
index cbc8f8cc99636883a5ed338abf9650bad6b8ca26..0000000000000000000000000000000000000000
Binary files a/models/multiclass_localizer5.hdf5 and /dev/null differ
diff --git a/models/multiclass_localizer6.hdf5 b/models/multiclass_localizer6.hdf5
deleted file mode 100755
index da41c72fbfabbe70ae5eaf4b3d28a698775e4dcf..0000000000000000000000000000000000000000
Binary files a/models/multiclass_localizer6.hdf5 and /dev/null differ
diff --git a/models/second_binary_green_hope_localizer_16_0.28892_1_54_7_12.hdf5 b/models/second_binary_green_hope_localizer_16_0.28892_1_54_7_12.hdf5
old mode 100755
new mode 100644
diff --git a/models/target___28_06_2018___15.16.37.613192.tif b/models/target___28_06_2018___15.16.37.613192.tif
old mode 100755
new mode 100644
diff --git a/movie_writer.ipynb b/movie_writer.ipynb
old mode 100755
new mode 100644
index a4413561a15c2901e7540da1fe46e598397aa1c0..b514dbcdfb0ea26e027df2d1123c11316a5f4b3a
--- a/movie_writer.ipynb
+++ b/movie_writer.ipynb
@@ -23,8 +23,8 @@
    },
    "outputs": [],
    "source": [
-    "in_dir = r'C:\\Users\\Wheeler\\Desktop\\LCL_software\\Experiments\\experiment_20_09_2018___10.08.42.888353'\n",
-    "out_loc = r'C:\\Users\\Wheeler\\Desktop\\LCL_software\\Experiments\\experiment_20_09_2018___10.08.42.avi'\n",
+    "in_dir = r'C:\\Users\\Wheeler\\Desktop\\LCL_software\\Experiments\\experiment_18_10_2018___10.05.26.666558'\n",
+    "out_loc = r'C:\\Users\\Wheeler\\Desktop\\LCL_software\\Experiments\\experiment_18_10_2018___10.05.26.avi'\n",
     "images = []\n",
     "clahe = cv2.createCLAHE(clipLimit=2.0, tileGridSize=(8,8))\n",
     "files = [os.path.join(in_dir, f) for f in os.listdir(in_dir) if '.tif' in f] \n",
@@ -65,7 +65,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "09d2a745ee4b4b68bd1b8fe19bdc89be",
+       "model_id": "a5187b8d345241b6aa300e6ff9241493",
        "version_major": 2,
        "version_minor": 0
       },
diff --git a/position_plotter.py b/position_plotter.py
old mode 100755
new mode 100644
diff --git a/stage_control.py b/stage_control.py
new file mode 100644
index 0000000000000000000000000000000000000000..bec381035208ef4131eb1e8b4f19384a8ba96135
--- /dev/null
+++ b/stage_control.py
@@ -0,0 +1,58 @@
+#just a test for stage_controller
+
+import serial
+from PyQt5 import QtCore
+from utils import comment
+
+class stage_control (QtCore.QObject):
+
+	def __init__(self,parent = None):
+		super(stage_control, self).__init__(parent)
+
+		com = 'COM9'
+		baud = 9600
+		parity = serial.PARITY_NONE
+		self.ser = serial.Serial(com, baud, timeout=.25,
+			parity=parity)
+		self.step_size = 5
+		self.send_receive('SAS 50')
+		self.send_receive('BLSH 0')
+
+		self.magnification = 4
+		self.microns_per_pixel = 100/34
+		self.calibration_factor = 1.20*4
+		
+
+	def issue_command(self,command):
+		'''
+		sends command and handles any errors from stage
+		'''
+		command_string = '{}\r'.format(command)
+		#comment('sending command to stage:{}'.format(command_string))
+		self.ser.write(command_string.encode('utf-8'))
+
+	def get_response(self):
+		response = ''
+		while '\r' not in response:
+			piece = self.ser.read()
+			if piece != b'':
+				response += piece.decode('utf-8')
+		# comment('response received from stage:{}'.format(response))
+		return response
+
+	def send_receive(self,command):
+		self.issue_command(command)
+		response = self.get_response()		
+		return response
+
+
+	def update_mov(self):
+		print("moving")
+		return self.send_receive('GR,-{},0'.format(100*self.step_size))
+
+
+
+
+if __name__ == '__main__':
+	stage = stage_control()
+	stage.update_mov()
\ No newline at end of file
diff --git a/stage_controller.py b/stage_controller.py
old mode 100755
new mode 100644
index af50f3cd489b3fad455249635187b03a24143849..3cda048b8d92470635e6ff0c8deacb39c5ab9987
--- a/stage_controller.py
+++ b/stage_controller.py
@@ -70,12 +70,13 @@ class stage_controller(QtCore.QObject):
 		comment('step size changed to: {}'.format(step_size))
 		self.step_size = step_size
 
-	def issue_command(self,command):
+	def issue_command(self,command, suppress_msg = False):
 		'''
 		sends command and handles any errors from stage
 		'''
 		command_string = '{}\r'.format(command)
-		comment('sending command to stage:{}'.format(command_string))
+		if(not suppress_msg):
+			comment('sending command to stage:{}'.format(command_string))
 		self.ser.write(command_string.encode('utf-8'))
 
 	def get_long_response(self):		
@@ -96,8 +97,8 @@ class stage_controller(QtCore.QObject):
 		comment('response received from stage:{}'.format(response))
 		return response
 
-	def send_receive(self,command):
-		self.issue_command(command)
+	def send_receive(self,command, suppress_msg = False):
+		self.issue_command(command, suppress_msg)
 		response = self.get_response()		
 		return response
 
@@ -185,6 +186,17 @@ class stage_controller(QtCore.QObject):
 		elif move_relative == True and scale_vector == False:
 			self.move_relative(move_vector)
 
+	# zoom and recenter gui signals
+	@QtCore.pyqtSlot('PyQt_PyObject')
+	def zoom_and_move_slot(self, move_vector):
+
+		if(move_vector[0] == 0 and  move_vector[1] == 0):
+			return
+					
+		pixel_move_vector = np.array([move_vector[0], move_vector[1]])
+		step_move_vector = self.scale_move_vector(pixel_move_vector)
+		self.move_relative(step_move_vector)
+
 
 	def go_to_dmf_location(self):
 		self.lysing_loc = self.get_position_slot()
diff --git a/stage_controller.pyc b/stage_controller.pyc
old mode 100755
new mode 100644
diff --git a/test.py b/test.py
old mode 100755
new mode 100644
diff --git a/utils.py b/utils.py
old mode 100755
new mode 100644
diff --git a/utils.pyc b/utils.pyc
old mode 100755
new mode 100644
diff --git a/zoom_gui_test.py b/zoom_gui_test.py
old mode 100755
new mode 100644
index 17488a5e2cff63278f252e9a057153cd9486ff74..7d28335f1796aceb04710932e244a39b156ed0da
--- a/zoom_gui_test.py
+++ b/zoom_gui_test.py
@@ -1,53 +1,172 @@
-import numpy
+import numpy as np
 import cv2
+from PyQt5 import QtCore 
 
-img_loc = r'C:\Users\Wheeler\Desktop\LCL_software\well_images\well_image___20_09_2018___12.18.52.033870.tif'
+img_loc = r'C:\Users\Wheeler\Desktop\LCL_software\LCL_zoom_test\well_image___27_09_2018___14.10.52.062012.tif'
 
 
-class Stitcher():
-
-	def __init__(self):
+class Stitcher(QtCore.QObject):
+	#inteface with main program
+	zoom_and_move_signal = QtCore.pyqtSignal('PyQt_PyObject')
+	
+	def __init__(self, parent=None):
+		super(Stitcher, self).__init__(parent)
 		self.img = cv2.imread(img_loc)
+		# self.stage.change_magnification(2)
 
 		# the values we will use to resize the image at the end to fit the screen
 		self.user_view_x = int(1024*.78)
 		self.user_view_y = int(822*.78)
 
-		# the center point of our image (will be updated when we move along the image)
+		# the center point of our image absolute to top left of screen
 		self.x = int(self.img.shape[0]/2)
 		self.y = int(self.img.shape[1]/2)
+		self.prev_x = int(self.img.shape[0]/2)
+		self.prev_y = int(self.img.shape[1]/2)
 
-		# the number of pixels the unaltered image has (will be updated with zoom)
+		# the number of pixels the image has (will be updated with zoom)
 		self.px_x = int(self.img.shape[0])
 		self.px_y = int(self.img.shape[1])
-		
-
 
+		# dimensions of original file in pixels (will not change with zoom)
+		self.px_x_source = int(self.img.shape[0])
+		self.px_y_source = int(self.img.shape[1])
 		self.img_resized = cv2.resize(self.img,(self.user_view_x,self.user_view_y),cv2.INTER_AREA)
+
 		cv2.imshow('Stitch',self.img_resized)
 		cv2.createTrackbar('Zoom','Stitch',0,6,self.manage_zoom)
-		cv2.waitKey(0)
-		cv2.destroyAllWindows()
+		cv2.setMouseCallback('Stitch', self.recenter)
+
+		# cv2.waitKey(0)
+		# cv2.destroyAllWindows()
+
 
 
 	def zoom(self,amt):
-		if amt != 0:
-			self.px_x = int(self.px_x/amt) 
-			self.px_y = int(self.px_y/amt)
-			# now we need to update based on our location and the new unaltered img
-			# values
-			cropped_img = self.img[self.x:self.px_x,self.y:self.px_y]
-			img_resized = cv2.resize(cropped_img,
+		self.prev_x = self.x
+		self.prev_y = self.y
+
+		self.px_x = int(self.px_x_source/(amt+1)) 
+		self.px_y = int(self.px_y_source/(amt+1))
+
+		if(amt == 0):
+			self.x = int(self.px_x_source/2)
+			self.y = int(self.px_y_source/2)
+		# now we need to update based on our location and the new unaltered img
+		# values, centered still at center of image
+		cropped_x_start = self.x-self.px_x//2
+		cropped_x_end   = self.x+self.px_x//2 
+		cropped_y_start = self.y-self.px_y//2
+		cropped_y_end   = self.y+self.px_y//2 
+
+		delta_x = 0
+		delta_y = 0
+		# make the window not leave the source image
+		# important for zooming out, not necessary if amt>previous amt
+		if(cropped_x_start <= 0):
+			delta_x = 0-cropped_x_start
+		elif(cropped_x_end >= self.px_x_source):
+			delta_x = self.px_x_source - cropped_x_end
+		if(cropped_y_start <= 0):
+			delta_y = 0-cropped_y_start
+		elif(cropped_y_end>= self.px_y_source):
+			delta_y = self.px_y_source - cropped_y_end
+
+		cropped_x_start += delta_x
+		cropped_x_end += delta_x
+		self.x += delta_x
+		cropped_y_start += delta_y
+		cropped_y_end += delta_y
+		self.y += delta_y
+
+		cropped_x = cropped_x_start, cropped_x_end
+		cropped_y = cropped_y_start, cropped_y_end
+
+		cropped_img = self.img[cropped_x[0]:cropped_x[1],cropped_y[0]:cropped_y[1]]
+
+		img_resized = cv2.resize(cropped_img,
+			(self.user_view_x,self.user_view_y),
+		 	cv2.INTER_AREA)
+
+		self.move_stage_emit() # move the stage
+		self.draw_center_circle(img_resized)
+		cv2.imshow('Stitch',img_resized)
+
+	#recenter based on the mouse click location
+	def recenter(self,event,x,y,flags,param):
+		if event == cv2.EVENT_LBUTTONUP:
+			self.prev_x = self.x
+			self.prev_y = self.y
+
+			# find x and y coordinates in original picture
+			# might be a few pixels off
+			source_x = self.x-self.px_x//2+int((y/self.user_view_y)*self.px_x)
+			source_y = self.y-self.px_y//2+int((x/self.user_view_x)*self.px_y)
+
+			cropped_x_start = source_x-self.px_x//2
+			cropped_x_end   = source_x+self.px_x//2 
+			cropped_y_start = source_y-self.px_y//2
+			cropped_y_end   = source_y+self.px_y//2 
+
+			delta_x = 0
+			delta_y = 0
+			# make the window not leave the source image
+			if(cropped_x_start <= 0):
+				delta_x = 0-cropped_x_start
+			elif(cropped_x_end >= self.px_x_source):
+				delta_x = self.px_x_source - cropped_x_end
+			if(cropped_y_start <= 0):
+				delta_y = 0-cropped_y_start
+			elif(cropped_y_end>= self.px_y_source):
+				delta_y = self.px_y_source - cropped_y_end
+
+			cropped_x_start += delta_x
+			cropped_x_end += delta_x
+			source_x += delta_x
+			cropped_y_start += delta_y
+			cropped_y_end += delta_y
+			source_y += delta_y
+
+			cropped_x = cropped_x_start, cropped_x_end
+			cropped_y = cropped_y_start, cropped_y_end
+
+			recentered_img = self.img[cropped_x[0]:cropped_x[1],cropped_y[0]:cropped_y[1]]
+			self.x = source_x
+			self.y = source_y
+			img_resized = cv2.resize(recentered_img,
 				(self.user_view_x,self.user_view_y),
-				cv2.INTER_AREA)
+			 	cv2.INTER_AREA)
+
+			#move and update the stage
+			self.move_stage_emit()
+			self.draw_center_circle(img_resized)
 			cv2.imshow('Stitch',img_resized)
+
 	
 	def manage_zoom(self,pos):
-		print('trackbar at',pos)
+		# print('trackbar at',pos)
 		self.zoom(pos)
 
-s = Stitcher()
+	#draw green circle at center of image
+	def draw_center_circle(self, image):
+		cv2.circle(image,(self.user_view_x//2, self.user_view_y//2), 5, (0,255,0), -1)
+
+	@QtCore.pyqtSlot('PyQt_PyObject')
+	def move_stage_emit(self):
+		relative_move = [self.x-self.prev_x, self.y-self.prev_y]
+		self.zoom_and_move_signal.emit(relative_move)
+
+	# def move_stage(self):
+	# 	#Find relative pixels to move stage by
+	# 	relative_x = self.x-self.prev_x
+	# 	relative_y = self.y-self.prev_y
 
+	# 	if(relative_x == 0 and relative_y == 0):
+	# 		return
 
+	# 	pixel_move_vector = np.array([relative_y, relative_x])
+	# 	step_move_vector = self.stage.scale_move_vector(pixel_move_vector)
+	# 	# print(step_move_vector)
+	# 	self.stage.move_relative(step_move_vector)