script/imaging/fov_arrows.py

@@ -53,7 +53,7 @@ def  update_arrows():
             arrow_a.update(FOV_ARROWS_ORIGIN, Point(xa,ya))
             xa,ya=int(x+FOV_XRAY_LABEL_POS*math.cos(a)),  int(y-FOV_XRAY_LABEL_POS*math.sin(a))
             label_a.update(Point(xa,ya))               
-            angle=angle+azimuth         
+            angle=angle-azimuth         
             a=math.radians(angle)
             xa,ya=int(x+FOV_ARROWS_SIZE*math.cos(a)),  int(y-FOV_ARROWS_SIZE*math.sin(a))
             arrow_x.update(FOV_ARROWS_ORIGIN, Point(xa,ya))

script/imaging/shifts.py

@@ -3,7 +3,9 @@ import java.lang.reflect
 import flanagan.complex.ComplexMatrix as ComplexMatrix
 import flanagan.math.Matrix as Matrix
 import flanagan.complex.Complex as Complex
-import org.jtransforms.fft.DoubleFFT_2D as DoubleFFT_2D
+#import org.jtransforms.fft.DoubleFFT_2D as DoubleFFT_2D
+import edu.emory.mathcs.jtransforms.fft.DoubleFFT_2D 
+
 import math
 from startup import ScriptUtils
 import ij.plugin.filter.PlugInFilterRunner as PlugInFilterRunner
@@ -613,6 +615,7 @@ def calculate_shifts(imp_r, imp_i, roi, upscale_factor=100, reference_slide=1, j
         IJ.showProgress(i + 1, len(ffts))\   
     return shifts  # [ref, drifted, dr, dc, error, diffphase]
 
+#Transforms an array in memory, a BufferedImage, or a file name into a ImagePlus object.
 def to_ip(obj):
     if is_string(obj):
         try: