From af6122e85770636a30943f6ebcbc7d6c62e7f877 Mon Sep 17 00:00:00 2001
From: Forrest Collman <forrest.collman@gmail.com>
Date: Wed, 4 Nov 2015 12:59:23 -0800
Subject: [PATCH] fixed stage flip error, added timing debug statements.

---
 ImageCollection.py |  2 +-
 MosaicImage.py     |  2 +-
 MosaicPlanner.py   | 15 ++++++++++-----
 imageSourceMM.py   | 32 ++++++++++++++++----------------
 4 files changed, 28 insertions(+), 23 deletions(-)

diff --git a/ImageCollection.py b/ImageCollection.py
index 9a37e60..3dc40f7 100644
--- a/ImageCollection.py
+++ b/ImageCollection.py
@@ -131,7 +131,7 @@ def display8bit(self,image, display_min, display_max):
         image = np.array(image, copy=True)
         image.clip(display_min, display_max, out=image)
         image -= display_min
-        image //= (display_max - display_min + 1) / 256.
+        image = image / ((display_max - display_min + 1) / 256.)
         return image.astype(np.uint8)
 
     def lut_convert16as8bit(self,image, display_min, display_max) :
diff --git a/MosaicImage.py b/MosaicImage.py
index 3cf4115..e3fa6a7 100644
--- a/MosaicImage.py
+++ b/MosaicImage.py
@@ -432,7 +432,7 @@ def align_by_correlation(self,xy1,xy2,CorrSettings = CorrSettings()):
         
 
         print "one_cut,two_cut.shape",one_cut.shape,two_cut.shape
-        pix_shift, error, diffphase=register_translation(one_cut,two_cut,upsample_factor=20)
+        pix_shift, error, diffphase = register_translation(one_cut,two_cut,upsample_factor=20)
         
         dy_pix,dx_pix = pix_shift
 
diff --git a/MosaicPlanner.py b/MosaicPlanner.py
index 9298860..f5a7174 100644
--- a/MosaicPlanner.py
+++ b/MosaicPlanner.py
@@ -44,6 +44,8 @@
 from FocusCorrectionPlaneWindow import FocusCorrectionPlaneWindow
 import pickle
 import faulthandler
+import datetime
+
 
 
 class MosaicToolbar(NavBarImproved):
@@ -395,20 +397,22 @@ def write_session_metadata(self,outdir):
                 f.write(self.channel_settings.prot_names[ch] + "\t" + "%f\t%s\n" % (self.channel_settings.exposure_times[ch],ch))
               
     def MultiDAcq(self,outdir,x,y,slice_index,frame_index=0):
-    
+
+        print datetime.datetime.now().time()," starting multiDAcq, autofocus on"
         self.imgSrc.set_hardware_autofocus_state(True)
+        print datetime.datetime.now().time()," starting stage move"
         self.imgSrc.move_stage(x,y)
         attempts=0
-        
+        print datetime.datetime.now().time()," starting autofocus"
         if self.imgSrc.has_hardware_autofocus():
             #wait till autofocus settles
             while not self.imgSrc.is_hardware_autofocus_done():
-                time.sleep(.1)
+                time.sleep(.05)
                 attempts+=1
                 if attempts>100:
                     print "not auto-focusing correctly.. giving up after 10 seconds"
                     break
-            time.sleep(.1) #wait an extra 100 ms for settle
+
             
             self.imgSrc.set_hardware_autofocus_state(False) #turn off autofocus
         
@@ -416,9 +420,10 @@ def MultiDAcq(self,outdir,x,y,slice_index,frame_index=0):
             score=self.imgSrc.image_based_autofocus(chan=self.channel_settings.map_chan)
             print score
 
-        time.sleep(.05)
+        print datetime.datetime.now().time()," starting multichannel acq"
         currZ=self.imgSrc.get_z()
         for k,ch in enumerate(self.channel_settings.channels):
+            print datetime.datetime.now().time()," start channel",ch
             prot_name=self.channel_settings.prot_names[ch]
             path=os.path.join(outdir,prot_name)
             if self.channel_settings.usechannels[ch]:
diff --git a/imageSourceMM.py b/imageSourceMM.py
index ef559d6..0634d0e 100644
--- a/imageSourceMM.py
+++ b/imageSourceMM.py
@@ -176,10 +176,10 @@ def set_xy(self,x,y,use_focus_plane=False):
         if use_focus_plane:
             z  = self.get_focal_z(x,y)
             self.set_z(z)
-        if flipx==1:
-            x = -x
-        if flipy == 1:
-            y = -y
+        #if flipx==1:
+        #    x = -x
+        #if flipy == 1:
+        #    y = -y
         
         stg=self.mmc.getXYStageDevice()
         self.mmc.setXYPosition(stg,x,y)
@@ -203,10 +203,10 @@ def get_xy(self):
         x=self.mmc.getXPosition(xystg)
         y=self.mmc.getYPosition(xystg)
         
-        if flipx:
-            x = -x
-        if flipy:
-            y = -y
+        #if flipx:
+        #    x = -x
+        #if flipy:
+        #    y = -y
 
         return (x,y)
     def get_z(self):
@@ -255,14 +255,14 @@ def snap_image(self):
         #snap a picture, and return the data as a numpy 2d array
         self.mmc.snapImage()
         data = self.mmc.getImage()
-        (flipx,flipy,trans) = self.get_image_flip()
-        print "flx,y,trans",flipx,flipy,trans
-        if trans:
-            data = np.transpose(data)    
-        if flipx:
-            data=np.fliplr(data)
-        if flipy:
-            data=np.flipud(data)
+
+        #(flipx,flipy,trans) = self.get_image_flip()
+        #if trans:
+        #    data = np.transpose(data)
+        #if flipx:
+        #    data=np.fliplr(data)
+        #if flipy:
+        #    data=np.flipud(data)
         return data