Imitial Commit - v1.1 + instructions

Analyze/Microscope Measurement Tools/Choose_Microscope_Calibration.py

@@ -0,0 +1,173 @@
+''' Choose_Microscope_Calibration.py
+Plugin for FIJI, to enable custom scaling for various microscope objectives.
+
+Reads user settings from `Microscope_Calibrations_user_settings.py` 
+including user-calibrations and names for various microscope objectives.
+This function will popup a menu of all available microscope cals listed in the settings file, and then apply that scaling (and unit) to the image.
+User can optionally apply the scaling to all open images, and/or run the "Scale Bar..." command afterwards.
+
+Based off Microscope_Scale.java & Correct_3d_drift.py
+
+
+v1.1
+Demis D. John, Praevium Research Inc., 2015-05-29
+'''
+
+#print "hello outside!"
+
+## Import some modules:
+from ij import IJ, ImagePlus, WindowManager
+from ij.gui import GenericDialog, YesNoCancelDialog
+
+import sys, os
+
+
+
+
+# add the path to this script, so we can find the user-settings
+libpth = os.path.split(  os.path.split( sys.path[0] )[0]  )[0]  # path to Fiji folder
+#print  libpth
+libpth = os.path.join(libpth, 'plugins', 'Scripts', 'Analyze', 'Microscope Measurement Tools')
+
+
+try:
+    sys.path.index( libpth )    # see if search-path is already added
+except ValueError:
+    # path wasn't included yet, so add it:
+    sys.path.append( libpth )
+#sys.path.append('/Applications/Fiji.app/plugins/Scripts/Plugins/Demis/')
+#print sys.path
+
+# microscope settings should be in the file `Microscope_Calibrations_user_settings.py`:
+import Microscope_Calibrations_user_settings as cal      # imports `names`, `cals`, `units` under namespace `cal.names` etc.
+
+
+
+
+# the run() function is called at the end of this script:
+def run():
+    '''This is the main function run when the plugin is called.'''
+
+    #print "hello in run()"
+
+
+
+    #print cal.names, cal.cals, cal.units
+
+
+    imp = IJ.getImage()     # get the current Image as ImagePlus object?
+    #print "imp=", imp
+
+
+    CalIdx, SetGlobalScale, AddScaleBar = uScopeCalDialog(cal)    # show Calibrations dialog
+
+    if CalIdx == None: return       # User cancelled - exit
+
+    # the following translated from "Microscope_Scale.java":
+    newcal = imp.getCalibration().copy()   # make a copy of calibration object
+    newcal.setUnit(  cal.units[CalIdx]  )
+    print "Chosen Cal=", cal.cals[CalIdx], " px/unit"
+    newcal.pixelWidth =  1./cal.cals[CalIdx]  
+    newcal.pixelHeight = newcal.pixelWidth * cal.aspect_ratio[CalIdx]
+
+    if SetGlobalScale:
+        '''Apply to all images'''
+        imp.setGlobalCalibration(newcal)
+        winlist = WindowManager.getIDList();
+        #print "winlist=", winlist
+        if (winlist==None):  return # exit if no images open
+        for win in winlist:
+            #(int i=0; i<list.length; i++) {
+            nextimp = WindowManager.getImage(win);
+            #print 'win=', win, '\tnextimp=', nextimp
+            if (nextimp != None):   nextimp.getWindow().repaint()
+    else:
+        imp.setGlobalCalibration(None)
+        imp.setCalibration( newcal )    # set the new calibration
+        imp.getWindow().repaint()     # refresh the image?
+
+    if AddScaleBar:
+        IJ.run("Scale Bar...")  # run Scale Bar plugin
+#end run()
+
+
+
+
+def uScopeCalDialog(cal):
+    '''
+    
+    CalIdx, SetGlobalScale, AddScaleBar = uScopeCalDialog(cal)
+    
+    `cal` should be the object containing `names`, `cals`, `units` attributes
+    as set in the "user_settings.py" file.
+    
+    `CalIdx` is the list index to the chosen calibration.  
+    Eg., if the options were 
+        ['5x', '10x', '20x']
+    and the user chose '10x', then 
+        CalIdx = 1
+    `SetGlobalScale` is a boolean from a checkbox option, if the user wants this calibration set 'globally'.
+    `AddScaleBar` is also a boolean, for a checkbox option, if user would like to run "Scale Bar..." afterwards.
+    '''
+
+    # The following copied from Correct_3D_drift.py:
+
+    #print "uScopeCalDialog():"
+    #print cal.names, [str(x) for x in cal.cals]
+
+    gd = GenericDialog("Microscope Calibrations")
+    gd.addMessage("Choose the calibration to load:")
+
+
+    # generate text to display in list:
+    # Radio Buttons:
+    CalStr = []
+    for ii, name in enumerate(cal.names):
+        CalStr.append(  name + "      (%s"%cal.cals[ii] + " %s/pixel)"%cal.units[ii]  )
+
+    '''if > 20 cals, use dropdown list, otherwise use radio buttons'''
+    if len(cal.names) > 20:
+        Radio=False
+        # Drop-Down list:
+        gd.addChoice("     Calibration:", CalStr, CalStr[0]   )   # default = 1st
+
+    else:
+        Radio=True
+        gd.addRadioButtonGroup("     Calibration:", CalStr, len(CalStr), 1, CalStr[0])
+        #addRadioButtonGroup(label, [String items],  rows,  columns,  String:defaultItem)
+    #end if(cal>20)
+
+    gd.addCheckbox("Apply Scale to all open images?", False)
+    gd.addCheckbox("Add Scale Bar to this image?", False)
+    gd.addMessage("These calibrations can be altered by editing the file: \nFiji.app/plugins/Scripts/Plugins/Analyze/...\n\tMicroscope Measurement Tools/...\n\tMicroscope_Calibrations_user_settings.py")
+
+    gd.showDialog()
+
+
+    if gd.wasCanceled():
+        return  None, None, None  # return None's if user cancels
+
+    if Radio:
+        ChosenCal = gd.getNextRadioButton()
+        # Find the index to the chosen radio button w/ [list].index():
+        CalIdx = CalStr.index(  ChosenCal )
+    else:
+        ChosenCal = gd.getNextChoiceIndex()
+        CalIdx = ChosenCal  # the index to the choice
+
+    SetGlobalScale = gd.getNextBoolean()
+    AddScaleBar = gd.getNextBoolean()
+
+
+
+    #print ChosenRadio,CalIdx, SetGlobalScale
+    #print "end uScopeCalDialog()."
+    return CalIdx, SetGlobalScale, AddScaleBar
+#end uScopeCalDialog()
+
+
+
+
+run()       # Run the script function!
+
+

Analyze/Microscope Measurement Tools/Draw_Measurement_-_Line.py

@@ -0,0 +1,163 @@
+'''Draw Measurement - Line.py
+Part of the "Microscope Measurement Tools" scripts
+by Demis D. John, Praevium Research Inc., 2015-05-25
+
+Draw a Line & Length of the Line along the currently selected Line ROI.
+
+'''
+
+#print "hello outside!"
+
+## Import some modules:
+from ij import IJ, ImagePlus, WindowManager #, gui
+from ij.gui import GenericDialog, YesNoCancelDialog
+
+from java.awt import Color as jColor    # for setting color
+from java.awt import Font as jFont      # for setting text font
+
+import sys, os
+
+
+
+
+# add the path to this script, so we can find the user-settings
+libpth = os.path.split(  os.path.split( sys.path[0] )[0]  )[0]  # split-off the "/jars/lib" part
+#print  libpth
+libpth = os.path.join(libpth, 'plugins', 'Scripts', 'Analyze', 'Microscope Measurement Tools')
+# hard-coded path, underneath the Fiji directory.
+
+try:
+    sys.path.index( libpth )    # see if search-path is already added
+except ValueError:
+    # path wasn't included yet, so add it:
+    sys.path.append( libpth )
+#sys.path.append('/Applications/Fiji.app/plugins/Scripts/Plugins/uScopeMeas/')
+#print sys.path
+
+# microscope settings should be in the file `Microscope_Calibrations_user_settings.py`:
+import Microscope_Calibrations_user_settings as sets      # imports settings under `sets.linecolor`, `sets.linethickness` etc.
+
+#print os.path.abspath(sets.__file__)
+#print dir(sets)
+#print sets.cals
+
+
+# the run() function is called at the end of this script:
+def run():
+    '''This is the main function run when the plugin is called.'''
+
+    #print dir(IJ)
+    ip = IJ.getProcessor()
+
+    imp = IJ.getImage()     # get the current Image, which is an ImagePlus object
+    #print "imp=", type(imp), imp
+    #print dir(imp)
+
+    roi = imp.getRoi()  # get the drawn ROI
+    #print "roi=", roi
+
+    #print roi.getClass()
+
+
+    # check ROI type
+    if roi==None:
+        gd = GenericDialog("Draw Measurement - Line")
+        gd.addMessage("Please draw a straight-line first!")
+        gd.showDialog()
+        return
+        #raise Exception(  "Please draw a line ROI first!" )
+    if roi.getTypeAsString()  != "Straight Line":
+        gd = GenericDialog("Draw Measurement - Line")
+        gd.addMessage("Please draw a straight-line first!")
+        gd.showDialog()
+        return
+        #raise Exception(  "Not a Line ROI!  (type="+roi.getTypeAsString()+")"  )
+
+
+
+    # set ROI params from settings:
+    roi.setStrokeWidth( sets.linethickness )
+    roi.setStrokeColor(  jColor(float(sets.linecolor[0]), float(sets.linecolor[1]), float(sets.linecolor[2]), float(sets.linecolor[3]))  )
+
+    #roi.drawPixels( ip )   # draw along the ROI - only draws outline unfortunately
+    ip.drawRoi(roi)     # draw the ROI on the image
+
+
+    #imp.updateAndDraw()     #update the image
+
+    p1 = [  int(roi.x1d),  int(roi.y1d)  ]    # point 1 (x,y)
+    p2 = [  int(roi.x2d),  int(roi.y2d)  ]    # point 2
+    print "Line Points: p1=", p1, " & p2=", p2
+    pm = midpoint(p1, p2)   # get midpoint coord
+
+    unit = imp.getCalibration().getUnit().encode('utf8')    # get the unit as UTF-8 (for \mu)
+    if unit != 'pixel': unit=unit[1:]  # strip weird char at start
+
+
+    # format of measurement text (eg. 3 decimal points):
+    lenstr = "%0.3f" % roi.getLength() + " %s" % (unit)  # string to print as length
+    print "Line length= %s" % lenstr
+    print "x,y=", p2[0], p2[1]
+
+    #ip.moveTo(p2[0]-ip.getStringWidth(lenstr), p2[1]);  # move the drawing 'pen'
+    if sets.texttoleft:
+        x=p2[0]-ip.getStringWidth(lenstr)
+    else:
+        x = p2[0]
+    y=p2[1]
+
+
+    # set font
+    ip.setFont(   jFont('SansSerif', 0, sets.textsize)   )
+    ip.setColor(    jColor(  float(sets.textcolor[0]), float(sets.textcolor[1]), float(sets.textcolor[2]), float(sets.textcolor[3])  )   )
+
+
+    if sets.textbackgroundcolor:
+        ip.drawString( lenstr, x, y, jColor(  float(sets.textbackgroundcolor[0]), float(sets.textbackgroundcolor[1]), float(sets.textbackgroundcolor[2]), float(sets.textbackgroundcolor[3])  ) )     # write the text w/ BG color
+    else:
+        ip.drawString( lenstr, x, y )     # write the text
+
+
+    imp.updateAndDraw()     #update the image
+
+    # to do:
+    #   Add dialogue for user to alter draw options?  Or just from settings file?
+
+
+
+#end run()
+""" java.awt.Font: Font(String name, int style (0=plain?), int size)    """
+"""
+class ImageProcessor:
+    drawString(java.lang.String s, int x, int y)
+        Draws a string at the specified location using the current fill/draw value.
+    drawString(java.lang.String s, int x, int y, java.awt.Color background)
+        Draws a string at the specified location with a filled background.
+"""
+'''ImageProcessor:
+    drawRoi(Roi roi):  Draws the specified ROI on this image using the stroke width, stroke color and fill color defined by roi.setStrokeWidth, roi.setStrokeColor() and roi.setFillColor().
+'''
+
+
+
+def midpoint( p1, p2 ):
+    ''' return the midpoint as [x,y] list.
+    Takes two points, also as a pair of [x,y] lists.
+    '''
+
+    x1 = min( p1[0], p2[0] )
+    y1 = min( p1[1], p2[1] )
+    x2 = max( p1[0], p2[0] )
+    y2 = max( p1[1], p2[1] )
+
+    xm = (x2-x1)/2. + x1
+    ym = (y2-y1)/2. + y1
+
+    return [int(xm), int(ym)]
+#end midpoint()
+
+
+
+
+run()       # Run the script function!
+