Merge branch 'developRR'

GUI/Android/UC2-TheBox/app/src/main/java/de/nanoimaging/uc2controler/MainActivity.java

@@ -48,22 +48,23 @@ public class MainActivity extends AppCompatActivity implements SeekBar.OnSeekBar
     String serverUri = "0.0.0.0";
 
 
+
     // Assign Random ID for the Client
     Random rand = new Random();
     String rand_id = String.format("%04d", rand.nextInt(1000));
     final String clientId = "AND123"+rand_id;
 
     boolean is_vibration = false;
     // TAG
-    String TAG = "UC2 Controler";
+    String TAG = "UC2 Controller";
 
     // Save settings for later
     private final String PREFERENCE_FILE_KEY = "myAppPreference";
 
     // MQTT Topics
     // environment variables
-    public static String experiment_id = "1";
-    public static String topic_prefix_setup = "/S004/";
+    public static String experiment_id = "5";
+    public static String topic_prefix_setup = "/S005/";
     public static final String topic_prefix_dev1 = "MOT01/";
     public static final String topic_prefix_dev2 = "MOT02/";
     public static final String topic_prefix_dev3 = "LAR01/";
@@ -139,7 +140,7 @@ protected void onCreate(Bundle savedInstanceState) {
         // Manage the Actionbar settings
         ActionBar actionBar = getSupportActionBar();
         actionBar.setLogo(R.mipmap.ic_launcher);
-        actionBar.setTitle("UC2 Controler");
+        actionBar.setTitle("UC2 Controller");
         actionBar.setDisplayUseLogoEnabled(true);
         actionBar.setDisplayShowHomeEnabled(true);
 
@@ -258,7 +259,7 @@ public void run() {
                     } else if (tap_counter_ipadress_button == 2) {
                         //Double click
                         tap_counter_ipadress_button = 0;
-                        serverUri = "192.168.43.88";
+                        serverUri = "21.3.2.103";
                         EditTextIPAddress.setText(serverUri);
                         Toast.makeText(MainActivity.this, "IP-Address set to default: " + serverUri, Toast.LENGTH_SHORT).show();
                         stopConnection();

GUI/RASPBERRY_PI/RASPIapp_py3/SCRIPTS/MQTT_fluo.py

@@ -0,0 +1,22 @@
+# %% imports
+import sys
+import os
+import subprocess
+
+# %% parameters
+msetup = 8
+mdev = "MOT01"
+mtopic = "/S00" + str(msetup) + "/" + mdev + "/RECM"
+mcmd = "FLUO+"
+
+# %% scripts
+while True:
+    in_val = int(input(
+        "Please input an integer between 0 (=off) and 100 (=max). Anything else ends the program."))
+    if in_val >= 0 and in_val < 101:
+        mcmdsend = ["mosquitto_pub", "-h", "localhost",
+                    "-t", mtopic, "-m", mcmd + str(in_val)]
+        subprocess.run(mcmdsend)
+        print("Changed to {} ".format(" ".join(mcmdsend)))
+    else:
+        break

GUI/RASPBERRY_PI/RASPIapp_py3/config/backup/camera_properties.bak

@@ -1,7 +1,7 @@
 awbGain:
 - 1.5
 - 1.5
-awbMode: 'off'
+awbMode: 'auto'
 brightness: 50
 colorEffects: null
 contrast: 0
@@ -18,11 +18,12 @@ iso: 100
 meterMode: average
 previewLength: 3
 resolution:
-- 2592
-- 1944
+- 3280
+- 2464
 rotation: 0
 saturation: 0
 sharpness: 0
-shutterSpeed: 0
+shutterSpeed: 1000000
+sensor_mode: 4
 vflip: false
 videoStabilization: false

GUI/RASPBERRY_PI/RASPIapp_py3/config/backup/camera_properties_fluo.bak

@@ -1,7 +1,7 @@
 awbGain:
 - 1.5
 - 1.5
-awbMode: 'off'
+awbMode: 'auto'
 brightness: 50
 colorEffects: null
 contrast: 0
@@ -11,18 +11,19 @@ crop:
 - 1.0
 - 1.0
 exposureCompensation: 0
-exposureMode: false
+exposureMode: auto
 hflip: []
 imageEffects: none
 iso: 100
 meterMode: average
 previewLength: 3
 resolution:
-- 2592
-- 1944
+- 3280
+- 2464
 rotation: 0
 saturation: 0
 sharpness: 0
-shutterSpeed: 0
+shutterSpeed: 1000000
+sensor_mode: 4
 vflip: false
 videoStabilization: false

GUI/RASPBERRY_PI/RASPIapp_py3/config/backup/experiment_properties.bak

@@ -26,6 +26,7 @@ snap_num: 0
 success: false
 time_left: 119
 time_passed: 1
+take_raw: 1
 tm_backlash: 10
 tm_endPOS: 200
 tm_motor: Z

GUI/RASPBERRY_PI/RASPIapp_py3/config/backup/imaging_properties.bak

@@ -1,7 +1,7 @@
 alpha: 255
 extension: .jpg
 fullscreen: 0
-speed: 0.1
+speed: 2.0
 window:
 - 2
 - 40

GUI/RASPBERRY_PI/RASPIapp_py3/config/camera_properties.yaml

@@ -1,7 +1,7 @@
 awbGain:
 - 1.5
 - 1.5
-awbMode: 'off'
+awbMode: auto
 brightness: 50
 colorEffects: null
 contrast: 0
@@ -18,8 +18,8 @@ iso: 100
 meterMode: average
 previewLength: 3
 resolution:
-- 2592
-- 1944
+- 3280
+- 2464
 rotation: 0
 saturation: 0
 sharpness: 0

GUI/RASPBERRY_PI/RASPIapp_py3/config/experiment_properties.yaml

@@ -24,9 +24,9 @@ last_expt_num: 1
 path_last_expt: C:\Users\renelachmann\Documents\Programming\UC2_Software-GIT\GUI\RASPBERRY_PI\RASPIapp_py3\data\20191203\expt_001
 snap_num: 0
 success: false
+take_raw: 1
 time_left: 119
 time_passed: 1
-take_raw: 1
 tm_backlash: 10
 tm_endPOS: 200
 tm_motor: Z

GUI/RASPBERRY_PI/RASPIapp_py3/config/imaging_properties.yaml

@@ -1,7 +1,7 @@
 alpha: 255
 extension: .jpg
 fullscreen: 0
-speed: 0.1
+speed: 2.0
 window:
 - 2
 - 40

GUI/RASPBERRY_PI/RASPIapp_py3/config/light_properties.yaml

@@ -7,7 +7,7 @@ color_picked:
 - 255
 - 255
 - 255
-color_picker_counter: 4
+color_picker_counter: 0
 default:
 - - - 0
     - 0

GUI/RASPBERRY_PI/RASPIapp_py3/fluidiscopeToolbox.py

@@ -22,6 +22,7 @@
     #import usb
     #import cv2 as cv
     from PIL import Image
+    import picamera
 import numpy as np
 from fractions import Fraction
 from kivy.clock import Clock
@@ -565,7 +566,7 @@ def run_measurement(self, instance):
     if instance.uid == self.ids['btn_snap'].uid:
         select_method(self, instance, "take_image")
         activate(instance)
-        take_image(self)
+        take_image_callback(self)
         abort_measurement(self, instance)
     else: 
         # rewrite button-text if necessary
@@ -713,9 +714,23 @@ def take_image_now(self,imaging_cause='MEAS', filename='', method='CUS'):
             return image
         else:
             fg.camera.capture(filename)
-            if 'Fluor' in fg.experiment['experiment']['imaging_method']: 
-                fg.camera.c
-            return True
+            if 'Fluor' in fg.config['experiment']['active_methods']: 
+                logger.debug("RAW: Start acquistion into RAM, extract and concat Green-Channel.")
+                filename[:-4] + '-rawG.npz'
+                stream = picamera.array.PiBayerArray(fg.camera)
+                fg.camera.capture(stream, 'jpeg', bayer=True) #'rgb' -> Error: unable to locate bayer-pattern at end of buffer
+                rawstream = np.transpose(np.dstack((stream.array[1::2,::2,1],stream.array[::2,1::2,1])),[2,0,1])
+                logger.debug("RAW: Save as compressed numpy.")
+                np.savez_compressed(filename, rawstream) # and lossless compressed
+                logger.debug("RAW: done.")
+    return True
+
+def take_image_callback(self, *args):
+    '''
+    Callback function to make sure GUI stays responsive while image is taken. Event is only called once and hence will delete itself.
+    '''
+    fg.EVENT['take_image_callback'] = Clock.schedule_once(partial(take_image, self),0.01)
+    return True
 
 def take_image(self, *args): 
     '''
@@ -790,14 +805,18 @@ def take_image(self, *args):
                             fg.ledarr.send("CLEAR")
                         elif active_method== "FPM":
                             # 1 image per LED
-                            fnwh = file_name_write
+                            fnwh_raw = file_name_write + datetime.strftime(datetime.now(),"%H%M%S" )
+                            logger.debug("Starting FPM.")
                             for myc in range(64): 
-                                fnwh += "-" + str(myc).zfill(2)
+                                fnwh = fnwh_raw + "-" + str(myc).zfill(2)
                                 time.sleep(0.04) # fastened
                                 fg.ledarr.send("PXL", myc, col,col,col)
-                                time.sleep(fg.config['imaging']['speed'])
+                                #time.sleep(fg.config['imaging']['speed'])
+                                time.sleep(1.0) # fastened
                                 tin_returnval = take_image_now(self,fg.config['experiment']['imaging_cause'], fnwh)
+                                logger.debug("Storing LED={} to {}.".format(myc,fnwh))
                                 fg.ledarr.send("CLEAR")
+                                time.sleep(0.04)
                         elif active_method== "RECT":
                             # set now with small NA image
                             file_name_write = uni.Path(fg.expt_path, image_name)
@@ -822,7 +841,6 @@ def take_image(self, *args):
         camera_preview(self,True)
         for x in active_modes:
             buttons_light(self, self.ids[x])
-
     # True -> normal images taken;
     # image -> case of autofocus
     return tin_returnval
@@ -872,25 +890,26 @@ def camera_set_parameter(method='CUS'):
         if method in ['CUS','qDPC','Bright','BG','FG']:
             method_key = 'cam'
             fg.camera.resolution = tuple(fg.config[method_key]['resolution'])
-            fg.camera.contrast = fg.config[method_key]['contrast']
-            fg.camera.sharpness = fg.config[method_key]['sharpness']
-            fg.camera.brightness = fg.config[method_key]['brightness']
-            fg.camera.saturation = fg.config[method_key]['saturation']
-            fg.camera.ISO = fg.config[method_key]['iso']
-            fg.camera.video_stabilization = fg.config[method_key]['videoStabilization']
-            fg.camera.exposure_compensation = fg.config[method_key]['exposureCompensation']
-            fg.camera.exposure_mode = fg.config[method_key]['exposureMode']
-            fg.camera.meter_mode = fg.config[method_key]['meterMode']
-            fg.camera.awb_mode = fg.config[method_key]['awbMode']
+            #fg.camera.contrast = fg.config[method_key]['contrast']
+            #fg.camera.sharpness = fg.config[method_key]['sharpness']
+            #fg.camera.brightness = fg.config[method_key]['brightness']
+            #fg.camera.saturation = fg.config[method_key]['saturation']
+            #fg.camera.ISO = fg.config[method_key]['iso']
+            #fg.camera.video_stabilization = fg.config[method_key]['videoStabilization']
+            #fg.camera.exposure_compensation = fg.config[method_key]['exposureCompensation']
+            #fg.camera.exposure_mode = fg.config[method_key]['exposureMode']
+            #fg.camera.meter_mode = fg.config[method_key]['meterMode']
+            #fg.camera.awb_mode = fg.config[method_key]['awbMode']
             if fg.config[method_key]['awbMode'] == 'off':
                 fg.camera.awb_gains = (Fraction(200, 128), Fraction(200, 128)) # (red, blue)  [0..8] TODO: Get values from YAML, Only some randomly chosen values!  fg.config[method_key]['awbGain']
-            fg.camera.image_effect = fg.config[method_key]['imageEffects']
-            fg.camera.color_effects = fg.config[method_key]['colorEffects']
-            fg.camera.rotation = fg.config[method_key]['rotation']
-            fg.camera.hflip = fg.config[method_key]['hflip']
-            fg.camera.vflip = fg.config[method_key]['vflip']
-            fg.camera.crop = tuple(fg.config[method_key]['crop'])
+            #fg.camera.image_effect = fg.config[method_key]['imageEffects']
+            #fg.camera.color_effects = fg.config[method_key]['colorEffects']
+            #fg.camera.rotation = fg.config[method_key]['rotation']
+            #fg.camera.hflip = fg.config[method_key]['hflip']
+            #fg.camera.vflip = fg.config[method_key]['vflip']
+            #fg.camera.crop = tuple(fg.config[method_key]['crop'])
             fg.camera.shutter_speed = fg.config[method_key]['shutterSpeed']
+            fg.camera.sensor_mode = fg.config[method_key]['sensor_mode']
         elif method == 'Fluor':
             method_key = 'cam_fluo'
             fg.camera.resolution = tuple(fg.config[method_key]['resolution'])
@@ -913,8 +932,8 @@ def camera_set_parameter(method='CUS'):
             fg.camera.vflip = fg.config[method_key]['vflip']
             fg.camera.crop = tuple(fg.config[method_key]['crop'])
             fg.camera.shutter_speed = fg.config[method_key]['shutterSpeed']
-        logger.debug("Camera shutter_speed={}, exposure_speed={} at ISO=.".format(fg.camera.shutter_speed, fg.camera.exposure_speed, fg.camera.iso))
-        logger.debug("Camera preparation done for method=".format(method))
+        logger.debug("Camera shutter_speed={}, exposure_speed={}, ISO={}, AWB={},AWB_gains={}.".format(fg.camera.shutter_speed, fg.camera.exposure_speed,fg.camera.awb_mode, fg.camera.iso, fg.camera.awb_gains))
+        logger.debug("Camera preparation done for method={}.".format(method))
     return True
 
 def crop_image():
@@ -943,7 +962,7 @@ def imaging_callback(self, instance, *largs):
     if not fg.config['experiment']['is_autofocus_busy']:
         # take image
         fg.config['experiment']['imaging_method']='MEAS'
-        take_image(self)
+        take_image_callback(self)
         deact_me = False
         if (fg.config['experiment']['time_left']-fg.config['experiment']['interval']) >= 0:
             # update config entries

GUI/RASPBERRY_PI/RASPIapp_py3/main.py

@@ -1,9 +1,9 @@
 # I/O
 if (1):
     import os
-    os.environ['KIVY_TEXT'] = 'egl_rpi'
-    os.environ['KIVY_WINDOW'] = 'egl_rpi'  # 'sdl2'
-    os.environ['KIVY_GL_BACKEND'] = 'gl'
+    #os.environ['KIVY_TEXT'] = 'egl_rpi'
+    os.environ['KIVY_WINDOW'] = 'sdl2'  # 'egl_rpi'  # 'sdl2'
+    #os.environ['KIVY_GL_BACKEND'] = 'gl'
     # time.sleep(1)
     pass
     # Fluidiscope