Merge branch 'dev-large-stage-logging'

mesoSPIM · Aug 19, 2019 · 270842c · 270842c
2 parents ed31e90 + 03a6d1e
commit 270842c
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diff --git a/.gitignore b/.gitignore
@@ -1,20 +1,19 @@
-__pycache__
-/**/__pycache__
-.ipynb_checkpoints
-/**/.ipynb_checkpoints
-**/*.ipynb_checkpoints/
-log/*
-mesoSPIM/legacy/*
-/log/*
-tmp/*
-/tmp/*
-mesoSPIM/src/devices/zoom/dynamixel/*
-mesoSPIM/PI_GCS2_DLL_x64.dll
-.idea
-prototypes/orcas/*.tif
-*.bin
-
-prototypes/python-essentials/temp\.tif
+__pycache__
+/**/__pycache__
+.ipynb_checkpoints
+/**/.ipynb_checkpoints
+**/*.ipynb_checkpoints/
+mesoSPIM/legacy/*
+tmp/*
+/tmp/*
+*.log
+mesoSPIM/src/devices/zoom/dynamixel/*
+mesoSPIM/PI_GCS2_DLL_x64.dll
+.idea
+prototypes/orcas/*.tif
+*.bin
+
+prototypes/python-essentials/temp\.tif
 
 mesoSPIM/src/devices/stages/galil/gclib/gclib\.py
 
@@ -24,6 +23,26 @@ mesoSPIM/src/devices/stages/galil/gclib/__init__\.py
 
 mesoSPIM/config/etl_parameters/ETL-parameters - Fabian - DBE - H45\.csv
 
-*.log
+mesoSPIM/src/devices/stages/galil/gclib/gclib\.py
+
+mesoSPIM/src/devices/stages/galil/gclib\.py
+
+mesoSPIM/src/devices/stages/galil/gclib/__init__\.py
+
+mesoSPIM/config/etl_parameters/ETL-parameters - Fabian - DBE - H45\.csv
+
+
+mesoSPIM/src/mesoSPIM_DemoSerial\.py
 
-mesoSPIM/src/devices/zoom/dynamixel\.zip
+
+mesoSPIM/src/devices/stages/galil/gclib/gclib\.py
+
+mesoSPIM/src/devices/stages/galil/gclib\.py
+
+mesoSPIM/src/devices/stages/galil/gclib/__init__\.py
+
+mesoSPIM/config/etl_parameters/ETL-parameters - Fabian - DBE - H45\.csv
+
+*.log
+
+mesoSPIM/src/devices/zoom/dynamixel\.zip

diff --git a/mesoSPIM/config/config_H45.py b/mesoSPIM/config/config_H45.py
@@ -72,6 +72,7 @@
                      'y_pixels' : 2048,
                      'x_pixel_size_in_microns' : 6.5,
                      'y_pixel_size_in_microns' : 6.5,
+                     'subsampling' : [1,2,4],
                      'camera_id' : 0,
                      'sensor_mode' : 12,    # 12 for progressive
                      'defect_correct_mode': 2,
@@ -86,35 +87,49 @@
 '''
 Stage configuration
 '''
-stage_parameters = {'stage_type' : 'PI_f_rot_and_Galil_xyz', # 'PI' or 'Debug'
-                    'startfocus' : 95000,
-                    'y_load_position': -40000,
-                    'y_unload_position': -90000,
+stage_parameters = {'stage_type' : 'PI_rotz_and_Galil_xyf', # 'PI' or 'Debug'
+                    'startfocus' : -10000,
+                    'y_load_position': -86000,
+                    'y_unload_position': -120000,
                     'x_max' : 51000,
                     'x_min' : -46000,
                     'y_max' : 0,
                     'y_min' : -160000,
-                    'z_max' : -2000,
-                    'z_min' : -97000,
+                    'z_max' : 99000,
+                    'z_min' : -99000,
                     'f_max' : 99000,
-                    'f_min' : 0,
+                    'f_min' : -99000,
                     'theta_max' : 999,
                     'theta_min' : -999,
                     'x_rot_position': 0,
-                    'y_rot_position': -58000,
-                    'z_rot_position': -35000,
+                    'y_rot_position': -121000,
+                    'z_rot_position': 66000,
                     }
 
-xyz_galil_parameters = {'COMport' : 'COM48',
-                    'x_encodercounts_per_um' : 2,
-                    'y_encodercounts_per_um' : 2,
-                    'z_encodercounts_per_um' : 2}
+'''Sample XYZ controller'''                    
+xyf_galil_parameters = {'port' : '192.168.1.43',#'or COM48'
+                        'x_encodercounts_per_um' : 2,
+                        'y_encodercounts_per_um' : 2,
+                        'f_encodercounts_per_um' : 2
+                        }
 
+'''PI Rotation + z controller'''
+pi_parameters = {'controllername' : 'C-884',
+                'stages' : ('M-061.PD','M-406.4PD'),
+                'refmode' : ('FRF',),
+                'serialnum' : ('118015799'), #0185500834
+                'velocity': {0: 22.5, 1: 2}, # in mm/s or °/s
+                }
+
+'''
 pi_parameters = {'controllername' : 'C-884',
                  'stages' : ('M-112K033','L-406.40DG10','M-112K033','M-116.DG','M-406.4PD','M-061.PD'),
                  'refmode' : ('FRF',),
                  'serialnum' : ('118015799'),
                  }
+'''
+
+
 
 '''
 Filterwheel configuration
@@ -225,4 +240,7 @@
 'camera_pulse_%' : 1,
 'camera_exposure_time':0.02,
 'camera_line_interval':0.000075,
+'camera_display_live_subsampling': 1, 
+'camera_display_snap_subsampling': 1, 
+'camera_display_acquisition_subsampling': 2,
 }
diff --git a/mesoSPIM/config/config_H45_demo.py b/mesoSPIM/config/config_H45_demo.py
@@ -72,6 +72,7 @@
                      'y_pixels' : 2048,
                      'x_pixel_size_in_microns' : 6.5,
                      'y_pixel_size_in_microns' : 6.5,
+                     'subsampling' : [1,2,4],
                      'camera_id' : 0,
                      'sensor_mode' : 12,    # 12 for progressive
                      'defect_correct_mode': 2,
@@ -225,4 +226,7 @@
 'camera_pulse_%' : 1,
 'camera_exposure_time':0.02,
 'camera_line_interval':0.000075,
+'camera_display_live_subsampling': 1, 
+'camera_display_snap_subsampling': 1, 
+'camera_display_acquisition_subsampling': 2,
 }
diff --git a/mesoSPIM/config/etl_parameters/ETL-parameters - Fabian - BABB - H45.csv b/mesoSPIM/config/etl_parameters/ETL-parameters - Fabian - BABB - H45.csv
@@ -34,7 +34,7 @@ Objective;Wavelength;Zoom;ETL-Left-Offset;ETL-Left-Amp;ETL-Right-Offset;ETL-Righ
 1x;515 nm;6.3x;2.389000000000008;0.12300000000000003;2.59299999999999;0.09399999999999992
 1x;561 nm;0.63x;2.3609999999999935;1.086;2.51;1.06
 1x;561 nm;0.8x;2.641999999999996;0.6;2.6609999999999983;0.75
-1x;561 nm;1x;2.6339999999999932;0.5820000000000001;2.6609999999999996;0.618
+1x;561 nm;1x;2.22;0.582;2.7249999999999996;0.642
 1x;561 nm;1.25x;2.5940000000000003;0.632;2.691;0.42700000000000005
 1x;561 nm;1.6x;2.5819999999999963;0.47999999999999987;2.6650000000000014;0.3639999999999999
 1x;561 nm;2x;2.5219999999999865;0.388;2.599;0.296

diff --git a/mesoSPIM/config/etl_parameters/ETL-parameters - Fabian.csv b/mesoSPIM/config/etl_parameters/ETL-parameters - Fabian.csv
@@ -10,15 +10,15 @@ Objective;Wavelength;Zoom;ETL-Left-Offset;ETL-Left-Amp;ETL-Right-Offset;ETL-Righ
 1x;405 nm;4x;2.486999999999993;0.197;2.67;0.25
 1x;405 nm;5x;2.486999999999993;0.17800000000000007;2.6850000000000005;0.2
 1x;405 nm;6.3x;2.67;0.25;2.677999999999998;0.058999999999999886
-1x;488 nm;0.63x;2.148;1.146;2.4099999999999997;0.966
-1x;488 nm;0.8x;2.4160000000000004;1.052;2.462;0.868
-1x;488 nm;1x;2.3419999999999996;0.842;2.6120000000000005;0.633
+1x;488 nm;0.63x;2.148;1.146;2.382;1.054
+1x;488 nm;0.8x;2.4160000000000004;1.052;2.4000000000000004;0.846
+1x;488 nm;1x;2.3419999999999996;0.842;2.514;0.597
 1x;488 nm;1.25x;2.3960000000000017;0.692;2.5759999999999974;0.6260000000000001
 1x;488 nm;1.6x;2.4000000000000004;0.422;2.5780000000000003;0.458
 1x;488 nm;2x;2.397000000000001;0.4610000000000001;2.524;0.386
 1x;488 nm;2.5x;2.386999999999998;0.3990000000000001;2.5870000000000006;0.26999999999999996
 1x;488 nm;3.2x;2.389999999999997;0.25700000000000006;2.5910000000000006;0.20499999999999996
-1x;488 nm;4x;2.3420000000000054;0.158;2.622;0.167
+1x;488 nm;4x;2.3420000000000054;0.158;2.426;0.137
 1x;488 nm;5x;2.3949999999999987;0.21100000000000008;2.593000000000001;0.13299999999999998
 1x;488 nm;6.3x;2.3919999999999972;0.14100000000000001;2.590000000000002;0.11099999999999996
 1x;515 nm;0.63x;2.3970000000000007;0.9629999999999999;2.580999999999999;0.9540000000000004
@@ -33,14 +33,14 @@ Objective;Wavelength;Zoom;ETL-Left-Offset;ETL-Left-Amp;ETL-Right-Offset;ETL-Righ
 1x;515 nm;5x;2.3920000000000075;0.16799999999999998;2.59499999999999;0.12599999999999997
 1x;515 nm;6.3x;2.389000000000008;0.12300000000000003;2.59299999999999;0.09399999999999992
 1x;561 nm;0.63x;2.361;1.086;2.579000000000002;1.107999999999997
-1x;561 nm;0.8x;2.4040000000000026;0.9460000000000002;2.580999999999999;0.704
+1x;561 nm;0.8x;2.4040000000000026;0.9460000000000002;2.3899999999999997;0.786
 1x;561 nm;1x;2.399999999999999;0.744;2.586999999999997;0.5939999999999999
 1x;561 nm;1.25x;2.3959999999999995;0.688;2.5409999999999955;0.586
 1x;561 nm;1.6x;2.3320000000000003;0.515;2.5929999999999995;0.472
 1x;561 nm;2x;2.3800000000000012;0.504;2.5990000000000024;0.296
 1x;561 nm;2.5x;2.39;0.37600000000000017;2.593;0.324
 1x;561 nm;3.2x;2.39;0.2760000000000001;2.593;0.26800000000000007
-1x;561 nm;4x;2.389;0.216;2.611999999999997;0.158
+1x;561 nm;4x;2.389;0.216;2.408000000000001;0.126
 1x;561 nm;5x;2.387;0.13599999999999995;2.598;0.18600000000000003
 1x;561 nm;6.3x;2.391;0.10400000000000001;2.5939999999999994;0.12800000000000003
 1x;594 nm;0.63x;2.4080000000000017;1.2600000000000002;2.583999999999999;0.8499999999999996
@@ -55,13 +55,13 @@ Objective;Wavelength;Zoom;ETL-Left-Offset;ETL-Left-Amp;ETL-Right-Offset;ETL-Righ
 1x;594 nm;5x;2.4010000000000065;0.14399999999999996;2.6039999999999934;0.12999999999999998
 1x;594 nm;6.3x;2.401000000000008;0.13800000000000004;2.5999999999999908;0.09199999999999992
 1x;647 nm;0.63x;2.379000000000006;1.344;2.5710000000000024;1.224
-1x;647 nm;0.8x;2.423000000000008;0.9560000000000002;2.6049999999999938;1.018
+1x;647 nm;0.8x;2.423000000000008;0.9560000000000002;2.4;0.78
 1x;647 nm;1x;2.495;0.87;2.602999999999993;0.7479999999999999
 1x;647 nm;1.25x;2.423000000000008;0.6479999999999999;2.6029999999999927;0.582
 1x;647 nm;1.6x;2.4210000000000083;0.5359999999999999;2.6129999999999955;0.4299999999999998
 1x;647 nm;2x;2.3930000000000025;0.432;2.6189999999999993;0.366
 1x;647 nm;2.5x;2.417000000000007;0.3799999999999999;2.606999999999996;0.27999999999999997
 1x;647 nm;3.2x;2.415000000000008;0.23199999999999998;2.608999999999992;0.24199999999999977
-1x;647 nm;4x;2.4190000000000085;0.2;2.6129999999999924;0.20800000000000002
+1x;647 nm;4x;2.4190000000000085;0.2;2.4349999999999996;0.164
 1x;647 nm;5x;2.415000000000002;0.14500000000000002;2.6099999999999923;0.12499999999999994
 1x;647 nm;6.3x;2.495;0.2;2.535;0.19