updated tutorial, no pixel size anymore as required input

confidenceMapUtil/FDRutil.py

@@ -63,6 +63,8 @@ def calculateConfidenceMap(em_map, apix, noiseBox, testProc, ecdf, lowPassFilter
 
 	if windowSizeLocScale is not None:
 		wn_locscale = windowSizeLocScale;
+		if window_size is not None:
+			print("Window size for noise estimation is automatically set to the size of LocScale sliding window.");
 	else:
 		wn_locscale = None;
 

confidenceMapUtil/locscaleUtil.py

 import numpy as np
 import FDRutil
 from mapUtil import *
-import mrcfile
 import argparse, math, os, sys
 from argparse import RawTextHelpFormatter
 import time

confidenceMapUtil/mapUtil.py

@@ -144,7 +144,7 @@ def makeDiagnosticPlot(map, windowSize, locscale, boxCoord):
 	if boxCoord != 0 | locscale:
 		singleBox = True;
 	else:
-		locscale = False;
+		singleBox = False;
 	
 	if singleBox == False:
 		visMap[int(center[0]-0.5*sizePatch[0]):(int(center[0]-0.5*sizePatch[0]) + sizePatch[0]),