latest demo changes

FocusCorrectionPlaneWindow.py

@@ -201,5 +201,5 @@ def handle_open_dialog(self):
     win = FocusCorrectionPlaneWindow(plist,imgSrc)
     win.show()
     app.exec_()
-    imgSrc.mmc.reset()
+    imgSrc.shutdown()
     sys.exit()

LiveMode.py

@@ -7,7 +7,6 @@
 import pyqtgraph.ptime as ptime
 import time
 from skimage import img_as_ubyte,exposure
-import MMCorePy
 import cv2
 from pyqtgraph.widgets.RawImageWidget import RawImageWidget
 import functools
@@ -21,13 +20,12 @@ def __init__(self,imgSrc,exposure_times=dict([]),channelGroup="Channels"):
         self.channelGroup=channelGroup
         self.exposure_times=exposure_times
         #self.setContentsMargins(0,0,0,0)
-        self.mmc = imgSrc.mmc
+
         self.imgSrc = imgSrc
-        self.channels=self.mmc.getAvailableConfigs(self.channelGroup)
+        self.channels=self.imgSrc.get_channels()
         self.init_mmc()
         self.initUI()
 
-
         self.i = 0
         self.updateTime = ptime.time()
         self.fps = 0
@@ -36,23 +34,18 @@ def __init__(self,imgSrc,exposure_times=dict([]),channelGroup="Channels"):
 
     def init_mmc(self):   
         #filename="C:\Users\Smithlab\Documents\ASI_LUM_RETIGA_CRISP.cfg"
-        #self.mmc.loadSystemConfiguration(filename)
-        #self.mmc.enableStderrLog(False)
-        #self.mmc.enableDebugLog(False)
-        # # mmc.setCircularBufferMemoryFootprint(100)
-        self.cam=self.mmc.getCameraDevice()
-        self.mmc.setExposure(50)
-        #self.mmc.setProperty(self.cam, 'Gain', 1)
+
+
+        self.imgSrc.set_exposure(50)
+
         Nch=len(self.channels)
         startChan=self.channels[Nch-1]
         for ch in self.channels:
             if 'dapi' in ch.lower():
-                self.mmc.setConfig(self.channelGroup,ch)
-                self.mmc.waitForConfig(self.channelGroup,ch)
-        camera = self.mmc.getCameraDevice()
-        self.mmc.setProperty(camera,'Binning','1x1')
-        print 'Binning is:', self.mmc.getProperty(camera,'Binning')
-        self.mmc.startContinuousSequenceAcquisition(1)
+                self.imgSrc.set_channel(ch)
+        self.imgSrc.set_binning(1)
+        print 'Binning is:', self.imgSrc.get_binning()
+        self.startContinuousSequenceAcquisition(1)
 
     def initUI(self):
 
@@ -103,7 +96,7 @@ def initUI(self):
             if ch in keys:
                 spnBox.setValue(self.exposure_times[ch])
             else:
-                spnBox.setValue(self.mmc.getExposure())
+                spnBox.setValue(self.imgSrc.get_exposure())
             spnBox.setSuffix(" ms")
             btn.clicked.connect(self.make_channelButtonClicked(ch,spnBox))
             self.expSpnBoxes.append(spnBox)
@@ -145,23 +138,22 @@ def getExposureTimes(self):
         return exposure_times
 
     def setExposureAuto(self,evt):
-
-        self.mmc.stopSequenceAcquisition() 
+        
+        self.imgSrc.stopSequenceAcquisition() 
         perc=95; #the goal is to make the X percentile value equal to Y percent of the maximum value
         #perc is X
         desired_frac=.7 #desired_frac is Y
         max_exposure = 3000 #exposure times shall not end up more than this
         close_frac = .2 #fractional change in exposure for which we will just trust the math
-        bit_depth=self.mmc.getImageBitDepth()
-        max_val=np.power(2,bit_depth)
+        max_val=self.imgSrc.get_max_pixel_value()
+
         #loop over the channels
         for i,ch in enumerate(self.channels):
             img_counter =0 #counter to count how many snaps it takes us
             if 'Dark' not in ch: #don't set the 'Dark' channel for obvious reasons
                 print ch
                 #setup to use the channel
-                self.mmc.setConfig(self.channelGroup,ch)
-                self.mmc.waitForConfig(self.channelGroup,ch)
+                self.imgSrc.set_channel(ch)
 
 
                 #get current exposure
@@ -172,10 +164,10 @@ def setExposureAuto(self,evt):
                 #follow loop till we get it right
                 while 1:
 
-                    self.mmc.setExposure(curr_exposure)
-                    self.mmc.snapImage()
+                    self.imgSrc.set_exposure(curr_exposure)
+                    img=self.imgSrc.snap_image()
                     img_counter+=1
-                    img=self.mmc.getImage()
+
                     vec=img.flatten()
 
                     #the value which is at the perc percentile
@@ -234,20 +226,17 @@ def make_channelButtonClicked(self,ch,spnBox):
         def channelButtonClicked():
             #print ch
             #print spnBox.value()
-            self.mmc.stopSequenceAcquisition() 
-            self.mmc.clearCircularBuffer() 
-            self.mmc.setConfig(self.channelGroup,ch)
+            self.imgSrc.stopSequenceAcquisition() 
+            self.imgSrc.set_channel(ch)
             expTime=spnBox.value()
-            self.mmc.setExposure(expTime)
-            self.mmc.waitForConfig(self.channelGroup,ch)
-            self.mmc.startContinuousSequenceAcquisition(expTime)
+            self.imgSrc.set_exposure(expTime)
+            self.imgSrc.startContinuousSequenceAcquisition(expTime)
         return channelButtonClicked
 
     def closeEvent(self,evt):
-        self.mmc.stopSequenceAcquisition()
-        camera = self.mmc.getCameraDevice()
-        self.mmc.setProperty(camera,'Binning','2x2')
-        print 'Binning is:', self.mmc.getProperty(camera,'Binning')
+        self.imgSrc.stopSequenceAcquisition()
+        self.imgSrc.set_binning(2)
+        print 'Binning is:', self.get_binning()
         print "stopped acquisition"
         #if self.timer is not None:
         #    print "cancelling timer if it exists"
@@ -276,59 +265,25 @@ def lut_convert16as8bit(self,image, display_min, display_max) :
 
     def updateData(self):
 
-        remcount = self.mmc.getRemainingImageCount()
-        #print 'remcount',remcount
-        #remcount=0
-        if remcount > 0:
-            #rgb32 = self.mmc.popNextImage()
-            data =  self.mmc.getLastImage()
-
-
-            if data.dtype == np.uint16:
-                maxval=self.imgSrc.get_max_pixel_value()
-                #print "max val is",maxval
-                #print 'max_before',np.max(data)
-                #data = exposure.rescale_intensity(data,in_range=(0,maxval))
-                #print 'max after rescale',np.max(data)
-                #data = img_as_ubyte(data)
-                #data=self.lut_convert16as8bit(data,0,5000)
+
+        data =  self.imgSrc.get_image()
+        maxval=self.imgSrc.get_max_pixel_value()
+        self.img.setImage(data,autoLevels=True)
 
-                # "maxval",maxval,np.max(data),data.dtype
-
-            flipx,flipy,trans = self.imgSrc.get_image_flip()
-            if trans:
-                data = np.transpose(data)
-            if flipx:
-                data = np.fliplr(data)
-            if flipy:
-                data = np.flipud(data)
-            data = np.rot90(data,k=3)
-            #gray=cv2.equalizeHist(gray)
-            self.img.setImage(data,autoLevels=True)
-            #cv2.imshow('Video', gray)
-        #else:
-            #print('No frame')
-
         if not self.ended:
-            self.timer = QtCore.QTimer.singleShot(self.mmc.getExposure(), self.updateData)
+            self.timer = QtCore.QTimer.singleShot(self.imgSrc.get_exposure(), self.updateData)
         now = ptime.time()
         fps1 = 1.0 / (now-self.updateTime)
         self.updateTime = now
         self.fps = self.fps * 0.6 + fps1 * 0.4
         if self.i == 0:
             print "%0.1f fps" % self.fps
 
-
-#def myExitHandler(mmc): 
-
-    #mmc.stopSequenceAcquisition()
-    #QtGui.QApplication.quit()
-    #mmc.reset()
 
-def launchLive(mmc,exposure_times):  
+def launchLive(imgSrc,exposure_times):  
     import sys  
 
-    vidview = VideoView(mmc,exposure_times)
+    vidview = VideoView(imgSrc,exposure_times)
     vidview.setGeometry(250,50,1100,1000)
     vidview.show()
 
@@ -347,18 +302,18 @@ def launchLive(mmc,exposure_times):
     app = QtGui.QApplication(sys.argv)
     faulthandler.enable()
 
-    #mmc = MMCorePy.CMMCore()
+
     defaultMMpath = "C:\Program Files\Micro-Manager-1.4"
     configFile = QtGui.QFileDialog.getOpenFileName(
         None, "pick a uManager cfg file", defaultMMpath, "*.cfg")
     configFile = str(configFile.replace("/", "\\"))
     print configFile
     imgSrc = imageSource(configFile)
-    #mmc.loadSystemConfiguration(configFile)
+
     print "loaded configuration file"
     launchLive(imgSrc,dict([]))
     #app.exec_()
     print "got out of the event loop"
-    imgSrc.mmc.reset()
+    imgSrc.shutdown()
     print "reset micromanager core"
     sys.exit()

MMArduino.py

@@ -12,6 +12,11 @@ def __init__(self,port = 'COM8',baudrate = '57600'):
         self.ser.timeout =.5
         self.ser.open()
         time.sleep(2)
+        self.ser.readlines()
+        self.sendCmd(chr(27))
+        self.sendCmd(chr(27))
+        self.sendCmd(chr(27))
+        self.sendCmd(chr(27))
     def sendMessage(self,message,debug=False):
         cmd = bytearray(message)
         answer = self.sendDirect(message,len(message))
@@ -88,7 +93,7 @@ def setTriggerPolarity(self,triggerHigh = True):
             return self.sendMessage([23,0])
         else:
             return self.sendMessage([23,1])
-
+    
     def setupExposure(self,exposures,interframe=10,exp_pattern=[0,0,0,0,0,0,0,1]):
         i =0
         for exp in exposures:

MosaicPlanner.py

@@ -38,7 +38,7 @@
 from MyLasso import MyLasso
 from MosaicImage import MosaicImage
 from Transform import Transform,ChangeTransform
-from imageSourceMM import imageSource
+from imageSourceDemo import imageSource
 from MMPropertyBrowser import MMPropertyBrowser
 from ASI_Control import ASI_AutoFocus
 from FocusCorrectionPlaneWindow import FocusCorrectionPlaneWindow
@@ -510,7 +510,7 @@ def handle_close(self,evt=None):
         print "handling close"
         #if not self.mosaicImage == None:
         #    self.mosaicImage.cursor_timer.cancel()
-        self.imgSrc.mmc.unloadAllDevices()
+        self.imgSrc.shutdown()
 
     def on_load(self,rootPath):
         self.rootPath = rootPath
@@ -675,29 +675,8 @@ def ResetPiezo(self):
 
         do_stage_reset=self.cfg['StageResetSettings']['enableStageReset']
         if do_stage_reset:
-            z_label = self.cfg['StageResetSettings']['compensationStage']
-            piezo_label = self.cfg['StageResetSettings']['resetStage']
-            min_threshold = self.cfg['StageResetSettings']['minThreshold']
-            max_threshold = self.cfg['StageResetSettings']['maxThreshold']
-            reset_position = self.cfg['StageResetSettings']['resetPosition']
-            invert_compensation = self.cfg['StageResetSettings']['invertCompensation']
-
-            piezo = self.imgSrc.mmc.getPosition(piezo_label)
-            if (piezo<min_threshold) or (piezo>max_threshold):
-                z = self.imgSrc.mmc.getPosition(z_label)
-                islocked = self.imgSrc.mmc.isContinuousFocusEnabled()
-
-                if islocked:
-                    self.imgSrc.mmc.enableContinuousFocus(False)
-
-                if invert_compensation:
-                    self.imgSrc.mmc.setPosition(z_label,z+(piezo-reset_position))
-                else:
-                    self.imgSrc.mmc.setPosition(z_label,z-(piezo-reset_position))
-                self.imgSrc.mmc.setPosition(piezo_label,reset_position)
-
-                if islocked:
-                    self.imgSrc.mmc.enableContinuousFocus(True)
+            self.imgSrc.reset_piezo(self.cfg['StageResetSettings'])
+
 
     def summarize_stage_settings(self):
         do_stage_reset = self.cfg['StageResetSettings']['enableStageReset']
@@ -829,7 +808,7 @@ def execute_imaging(self,pos_list,numFrames,numSections,channel_settings,chrome_
             if pos.activated:
                 if not goahead:
                     break
-                if not self.imgSrc.mmc.isContinuousFocusEnabled():
+                if not self.imgSrc.get_hardware_autofocus_state():
                     print "autofocus not enabled when moving between sections.. "
                     goahead=False
                     break
@@ -844,7 +823,7 @@ def execute_imaging(self,pos_list,numFrames,numSections,channel_settings,chrome_
                         if not goahead:
                             print "breaking out!"
                             break
-                        if not self.imgSrc.mmc.isContinuousFocusEnabled():
+                        if not self.imgSrc.get_hardware_autofocus_state():
                             print "autofocus no longer enabled while moving between frames.. quiting"
                             goahead = False
                             break
@@ -966,7 +945,8 @@ def on_run_acq(self,event="none"):
 
 
         goahead = True
-        if not self.imgSrc.mmc.isContinuousFocusEnabled():
+
+        if not self.imgSrc.get_hardware_autofocus_state():
             self.slack_notify('HELP! lost autofocus on way to first position',notify=True)
             print 'HELP! lost autofocus on way to first position'
             goahead=False
@@ -979,7 +959,7 @@ def on_run_acq(self,event="none"):
             if pos.activated:
                 if not goahead:
                     break
-                if not self.imgSrc.mmc.isContinuousFocusEnabled():
+                if not self.imgSrc.get_hardware_autofocus_state():
                     self.slack_notify('HELP! lost autofocus between sections',notify=True)
                     goahead=False
                     break
@@ -999,7 +979,7 @@ def on_run_acq(self,event="none"):
                         if not goahead:
                             print "breaking out!"
                             break
-                        if not self.imgSrc.mmc.isContinuousFocusEnabled():
+                        if not self.imgSrc.get_hardware_autofocus_state():
                             self.slack_notify('HELP! lost autofocus between frames',notify=True)
                             print "autofocus no longer enabled while moving between frames.. quiting"
                             goahead = False
@@ -1132,6 +1112,10 @@ def launch_MManager_browser(self, event=None):
         win = MMPropertyBrowser(self.imgSrc.mmc)
         win.show()
 
+    def launch_retake(self,event=None):
+        if self.retakeView is NOne:
+            self.retakeView = Retake(self)
+
     def launch_snap(self, event=None):
         if self.snapView is None:
             self.imgSrc.set_binning(1)
@@ -1663,7 +1647,7 @@ def on_run_multi_acq(self,event="none"): #MultiRibbons
                     if pos.activated:
                         if not goahead:
                             break
-                        if not self.imgSrc.mmc.isContinuousFocusEnabled():
+                        if not self.imgSrc.get_hardware_autofocus_state():
                             self.slack_notify('HELP! lost autofocus between frames',notify=True)
                             print "autofocus not enabled when moving between sections.. "
                             goahead=False
@@ -1682,7 +1666,7 @@ def on_run_multi_acq(self,event="none"): #MultiRibbons
                                 if not goahead:
                                     print "breaking out!"
                                     break
-                                if not self.imgSrc.mmc.isContinuousFocusEnabled():
+                                if not self.imgSrc.get_hardware_autofocus_state():
                                     self.slack_notify('HELP! lost autofocus between frames',notify=True)
                                     print "autofocus no longer enabled while moving between frames.. quiting"
                                     goahead = False

PositionList.py

@@ -53,7 +53,7 @@ class posListSchema(mm.Schema):
     camera_settings = mm.Nested(CameraSettingsSchema,required=True)
     slicePositions = mm.List(slicePositionSchema)
     dosort = mm.fields.Bool(required=False,default=True)
-    numberDisplaySettings = mm.Nested(NumberDisplaySettings)
+    numberDisplaySettings = mm.Nested(NumberDisplaySettingsSchema)
 
 class posList():
     """class for holding, altering, and plotting the position list"""
@@ -968,7 +968,7 @@ class slicePositionSchema(mm.Schema):
     activated = mm.fields.Bool(required=False,default=True)
     withpoint = mm.fields.Bool(required=False,default=True)
     number = mm.fields.Int(required=True)
-    numberDisplaySettings = mm.Nested(NumberDisplaySettings)
+    numberDisplaySettings = mm.Nested(NumberDisplaySettingsSchema)
     self.frameList = mm.Nested(posListSchema)