Nikon take 2

ImageCollection.py

@@ -194,7 +194,7 @@ def add_image_at(self,x,y):
             (thedata,bbox)=self.imageSource.take_image(x,y)
             if thedata.dtype == np.uint16:
                 print "converting"
-                maxval=self.imageSource.get_max_pixel_value()
+                maxval=thedata.max()#self.imageSource.get_max_pixel_value()
                 thedata=self.lut_convert16as8bit(thedata,0,maxval)
 
         except:
@@ -340,4 +340,4 @@ def loadImageCollection(self):
 
 # plt.show()
 
-
+

LiveMode.py

@@ -87,7 +87,7 @@ def initUI(self):
 
         keys = self.exposure_times.keys()
 
-        gridlay=QtGui.QGridLayout(margin=0,spacing=-1)
+        gridlay=QtGui.QGridLayout(spacing=-1)
         for i,ch in enumerate(self.channels):
             btn=QtGui.QPushButton(ch,self)
             self.chnButtons.append(btn)

MosaicImage.py

@@ -23,6 +23,7 @@
 import numpy as np
 import threading
 import os
+import sys
 import Queue
 from CenterRectangle import CenterRectangle
 from matplotlib.lines import Line2D
@@ -32,11 +33,10 @@
 import cv2 
 import ransac
 from scipy.signal import correlate2d
-from skimage.measure import block_reduce
+#from skimage.measure import block_reduce
 import norm_xcorr
 #implicity this relies upon matplotlib.axis matplotlib.AxisImage matplotlib.bar 
 
-
 #my custom 2d correlation function for numpy 2d matrices.. 
 def mycorrelate2d(fixed,moved,skip=1):
     """a 2d correlation function for numpy 2d matrices
@@ -57,7 +57,7 @@ def mycorrelate2d(fixed,moved,skip=1):
     if the variance in the subsampled region of fixed is lower than the variance of the entire matrix
 
     """
-    if skip>1:
+    if skip>1 and 'block_reduce' in sys.modules:
         fixed = block_reduce(fixed,block_size = (int(skip),int(skip)),func = np.mean,cval=np.mean(fixed))
         moved = block_reduce(moved,block_size = (int(skip),int(skip)),func = np.mean,cval=np.mean(moved))
 
@@ -668,4 +668,4 @@ def make_preview_stack(self,xpos,ypos,width,height,directory):
             (cx_pix,cy_pix)=self.convert_pos_to_ind(xpos[i],ypos[i])
             rect=[cx_pix-hw_pix,cy_pix-hh_pix,cx_pix+hw_pix,cy_pix+hh_pix]
             queue.put((self.imagefile,rect,i))
-        queue.join()
+        queue.join()

MosaicPlanner.py

@@ -1214,10 +1214,10 @@ def OnClose(self,event):
 
 #dirname=sys.argv[1]
 #print dirname
-faulthandler.enable()
+#faulthandler.enable()
 app = wx.App(False)  
 # Create a new app, don't redirect stdout/stderr to a window.
 frame = ZVISelectFrame(None,"Mosaic Planner") 
 # A Frame is a top-level window.
 app.MainLoop()
-QtGui.QApplication.quit()
+QtGui.QApplication.quit()