minor removals of comments and old code

Analyze/Microscope Measurement Tools/Choose_Microscope_Calibration.py

@@ -13,7 +13,7 @@
 Demis D. John, Univ. of California Santa Barbara, 2019-03-27
 '''
 
-mc_DEBUG = False     # Send debugging info to the log file?
+mc_DEBUG = False     # Print debugging info to the log file?
 
 ## Import some modules:
 from ij import IJ, ImagePlus, WindowManager
@@ -52,12 +52,7 @@ def run():
 
 
     imp = IJ.getImage()     # get the current Image as ImagePlus object
-    #ImagePath = imp.getOriginalFileInfo().directory + os.path.sep + imp.getOriginalFileInfo().fileName
-    #if mc_DEBUG: 
-    #    print( "imp=", imp )
-    #    print( "ImagePath=", ImagePath )
-
-
+
 
     CalIdx, SetGlobalScale, AddScaleBar = uScopeCalDialog(cal)    # show Calibrations dialog
 
@@ -73,7 +68,7 @@ def run():
 
         newPixelWidth = 1. / newPixelPerUnit
         newPixelHeight = newcal.pixelWidth * newAspect
-        print( "Chosen Cal=", cal.cals[CalIdx], " px/unit" )
+        print "Chose `", cal.names[CalIdx], "` : ", newPixelPerUnit, " px/", newUnit
     else:
         ''' Assume we'll be loading a custom function/class '''
         # call the class' `classObj.cal( ImagePlusObject )` function to get the scale value:
@@ -83,8 +78,8 @@ def run():
 
         newPixelWidth = 1. / newPixelPerUnit
         newPixelHeight = newPixelWidth * newAspect
-        if mc_DEBUG: print( "newPixelWidth, newUnit = ", newPixelWidth, newUnit )
-    #end if(cal.name is a string)
+        print "Chose `", cal.names[CalIdx].name, "` : ", newPixelPerUnit, " px/", newUnit
+    #end if(cal.name is a string or function)
 
 
     #end if CalIdx
@@ -119,7 +114,7 @@ def run():
 
 
 def uScopeCalDialog(cal):
-    '''
+    ''' Pop up a dialog asking user to choose from the calibration names etc.
     
     CalIdx, SetGlobalScale, AddScaleBar = uScopeCalDialog(cal)
     
@@ -152,8 +147,6 @@ def uScopeCalDialog(cal):
     CalStr = []
     CalType_IsFunc = []
 
-    # add option for JEOL SEM  (CalIdx = 0)
-    #CalStr.append( "JEOL SEM - auto cal from .txt")
 
     for ii, name in enumerate(cal.names):
         if mc_DEBUG: print( "item #%i: name=" % (ii), name, "\n\t type=", type(name)  )
@@ -202,70 +195,12 @@ def uScopeCalDialog(cal):
 
 
 
-    #print ChosenRadio,CalIdx, SetGlobalScale
-    #print "end uScopeCalDialog()."
+    if mc_DEBUG: print( ChosenRadio,CalIdx, SetGlobalScale )
+    #if mc_DEBUG: print( "end uScopeCalDialog()." )
     return CalIdx, SetGlobalScale, AddScaleBar
 #end uScopeCalDialog()
 
 
-def getJEOLSEMCal( filepath ):
-    '''Find accompying *.txt file that contains pixel-to-unitlength info, and apply the scale automatically.
-    Designed against a JEOL 7600F SEM.  Expects the *.xtx files to be next to the accompying image files of same name.'''
-    import re   # RegEx matching
-
-
-    txtpath = os.path.splitext( filepath )[0] + ".txt"
-    if mc_DEBUG: print "txtpath = ", txtpath
-    if not os.path.isfile(txtpath): raise IOError("Text File not found at: \n\t" + txtpath)
-
-    # set up regex matching:
-    re_bar = re.compile( r'\$\$SM_MICRON_BAR (\d*)'  ) # groups the digits in "$$SM_MICRON_BAR 90"
-    re_barmark = re.compile( r'\$\$SM_MICRON_MARKER (\d*)([a-zA-Z]*)')  # groups the decimals and units in "$$SM_MICRON_MARKER 100nm"
-
-
-    # try to load the .txt file:
-    BarLength_px = None
-    BarLength_dist = None
-    BarLength_unit = None
-
-    txtfile = open(txtpath, 'r')
-    try:
-        while True:
-            txtline = txtfile.readline()
-            if len(txtline) == 0:
-                # end of file, exit the loop
-                break
-            #end(if end-of-file)
-
-            # search for strings/values:
-            match1 = re_bar.search( txtline )
-            if match1:
-                BarLength_px = float( match1.group(1)  )  # this is pixel width of the scale bar
-                if mc_DEBUG: print 'Scale Bar Pixel Length found:', match1.groups(), ' --> ', BarLength_px    
-            #end if(match1)
-
-            match2 = re_barmark.search( txtline )
-            if match2:
-                BarLength_dist = float( match2.group(1)  )  # this is physical width of the scale bar
-                BarLength_unit = str( match2.group(2)  )
-                if mc_DEBUG: print 'Scale Bar Distance Length found:', match2.groups(), ' --> ', BarLength_dist, BarLength_unit
-            #end if(match2)
-
-        #end while(file-reading)
-
-    except IOError:
-        raise IOError("Could not load text file that accompanies this image file.  Expected the text file to have the same filename as the image, except with '.txt' extension.  Expected file to be here:\n\t" + txtpath )
-
-    finally:
-        # make sure python closes the file no matter what
-        txtfile.close()
-    #end try(txtfile)
-
-    # return pixel-per-unit & units
-    return (BarLength_px/BarLength_dist), BarLength_unit
-#end getJEOLSEMCal()
-
-
 run()       # Run the script function!