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, roi.getClass()
newcal = imp.getCalibration().copy(
) # make a copy of current calibration object
if MC_DEBUG: print("Assume calibration is a custom function.")
# call the class' `classObj.cal( ImagePlusObject )` function to get the scale value:
try:
calObject = sets.autoupdatecal_name
calName = calObject.name
newPixelPerUnit = calObject.cal(imp)
except AttributeError:
raise ValueError(
'This calibration Name value is invalid, please check your Settings.py file!/n/tFor Calibration Number %i, got: `'
% (CalIdx) + str(cal.names[CalIdx]) +
'`. Expected a String or a Class instance with ".cal()" method, but got type '
+ str(type(cal.names[CalIdx])) + ' with no ".cal()" method.')
#end try
newUnit = calObject.unit
newAspect = calObject.aspect_ratio
newPixelWidth = 1. / newPixelPerUnit
newPixelHeight = newPixelWidth * newAspect
# the following translated from "Microscope_Scale.java":
newcal.setUnit(newUnit)
newcal.pixelWidth = newPixelWidth
newcal.pixelHeight = newPixelHeight
imp.setGlobalCalibration(None)
imp.setCalibration(newcal) # set the new calibration
imp.getWindow().repaint() # refresh the image?
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, 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()+")" )
p1 = [int(roi.x1d), int(roi.y1d)] # point 1 (x,y)
p2 = [int(roi.x2d), int(roi.y2d)] # point 2
print "DrawMeas(): Line Points: p1=", p1, " & p2=", p2
pm = midpoint(p1, p2) # get midpoint coord
# set ROI params from settings:
''' Using new method - used ip.drawLine instead of roi.draw, since roi.draw didn't always apply the line thickness. Would be best to use the ROI method, in case other types of ROI's could be annotated.
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
'''
ip.setLineWidth(int(sets.linethickness))
ip.setColor(
jColor(float(sets.linecolor[0]), float(sets.linecolor[1]),
float(sets.linecolor[2]), float(sets.linecolor[3])))
#ip.draw(roi) # changed to ip.drawLine()
ip.drawLine(int(roi.x1d), int(roi.y1d), int(roi.x2d), int(roi.y2d))
'''Draw text annotation'''
unit = imp.getCalibration().getUnit().encode(
'utf8') # get the unit as UTF-8 (for \mu)
print "Draw_Meas(): Unit (raw) = `", unit, "`", type(unit),
if unit[0] == u'\xc2': unit = unit[1:] # strip weird char at start of \mu
# format of measurement text (eg. 3 decimal points):
lenstr = "%0.3f" % roi.getLength() + " %s" % (
unit) # string to print as length
print "DrawMeas(): Line length= %s" % lenstr
#print "x,y=", p2[0], p2[1]
'''determine position of text from line coords, eg "bottom right" or "top left" etc. '''
# y-coord:
if p2[1] > p1[1]:
posstr = 'bottom'
else:
posstr = 'top'
# x-coord:
if p2[0] > p1[0]:
posstr += ' right'
else:
posstr += ' left'
drawText(lenstr, p2[0], p2[1], position=posstr)
imp.updateAndDraw() #update the image
## to be representative of the likely seams, but the program offers the opportunity to set the
## width of the seams manually should this automated part fail. 100X images are not currently
## supported.
## Again, the program works best when pixel resolution was carried over in microns. If not,
## the estimation of the seams will be totally off.
## Good luck and happy stitching!
import ij.plugin as plugin
import ij.gui as gui
import ij.process
from ij import ImageStack
from ij import IJ
import ij.io.FileInfo as fileInfo
imp = IJ.getImage()
impProcessor = IJ.getProcessor()
impProcessor.setLineWidth(1)
impProcessor.setColor(25)
imp.setOverlay(gui.Overlay())
pixelHeight = round(imp.getLocalCalibration().pixelHeight, 4)
name = imp.getShortTitle().upper()
magnification = ''
if [x in name for x in ['5X', '10X', '20X', '40X', '63X']].count(True) == 1:
window = gui.NonBlockingGenericDialog("Specify Tile Scan Properties")
window.addMessage("What are the tile scan dimensions?")
window.addNumericField('Height: ', 2.0, 1)
window.addNumericField('Width: ', 3.0, 1)
window.addCheckbox('Set seam sizes manually? ', False)
window.addCheckbox('Approve seams first? ', True)
window.showDialog()
def drawText(text, x, y, position='bottom right'):
'''Draw a text string at the specified coordinates & relative position, ensuring text doesn't go over the edge of the image.
Parameters:
-----------
text : string
The text string to write on the image.
x, y : int
The coordinates at which to draw the text.
position : { 'bottom right', 'top right', 'top left', 'bottom left' }, case-insensitive, optional
Where to draw the text, with respect to the coordinates given.
Synonyms for 'bottom right' are 'br'. This is the default.
Synonyms for 'top right' are 'tr'.
Synonyms for 'bottom left' are 'bl'.
Synonyms for 'top left' are 'tl'.
'''
print "drawText(): original (x,y)=(%i,%i)" % (x, y)
# 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.
ip = IJ.getProcessor() # Image Processor
imp = IJ.getImage() # get the current Image, which is an ImagePlus object
'''Acquire arguments'''
position = position.strip().lower()
if position == 'bottom right' or position == 'br':
pos = 'br'
elif position == 'bottom left' or position == 'bl':
pos = 'bl'
elif position == 'top left' or position == 'tl':
pos = 'tl'
elif position == 'top right' or position == 'tr':
pos = 'tr'
else:
raise ValueError('drawText(): Invalid `position` argument: "%s".' %
(position))
'''Setup text annotation'''
# 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])))
'''determine text position'''
margin = 6 # space in pixels away from edge of image
spacer = 4 # space in pixels to add between point & text
strw = ip.getStringWidth(text)
strh = ip.getFontMetrics().getHeight()
imgw = ip.getWidth()
imgh = ip.getHeight()
'''
print "strw =", strw
print "strh =", strh
print "imgw =", imgw
print "imgh =", imgh
'''
# set coords (x,y) based on `position` argument
''' By default, text is horizontally centered at point (x), and vertically above the point (y). We then modify these default coords. '''
if pos[0] == 'b':
y = y + spacer + strh # moves down
elif pos[0] == 't':
y = y - spacer
if pos[1] == 'r':
x = x + spacer # moves right
elif pos[1] == 'l':
x = x - spacer - int(strw)
print "drawText(): %s " % (pos) + "(x,y)=(%i,%i)" % (x, y)
'''Correct for edge of image'''
if y - strh < 0:
y = 0 + strh + margin
elif y > imgh:
y = imgh - margin
if (x) < 0:
x = 0 + margin
elif (x + strw) > imgw:
x = imgw - strw - margin
print "drawText(): final (x,y)=(%i,%i)" % (x, y)
if sets.textbackgroundcolor:
ip.drawString(text, 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(text, x, y) # write the text alone
imp.updateAndDraw() #update the image
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, 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()+")" )
p1 = [ int(roi.x1d), int(roi.y1d) ] # point 1 (x,y)
p2 = [ int(roi.x2d), int(roi.y2d) ] # point 2
print "DrawMeas(): Line Points: p1=", p1, " & p2=", p2
pm = midpoint(p1, p2) # get midpoint coord
# set ROI params from settings:
''' Using new method - used ip.drawLine instead of roi.draw, since roi.draw didn't always apply the line thickness. Would be best to use the ROI method, in case other types of ROI's could be annotated.
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
'''
ip.setLineWidth( int(sets.linethickness) )
ip.setColor( jColor(float(sets.linecolor[0]), float(sets.linecolor[1]), float(sets.linecolor[2]), float(sets.linecolor[3])) )
#ip.draw(roi) # changed to ip.drawLine()
ip.drawLine( int(roi.x1d), int(roi.y1d), int(roi.x2d), int(roi.y2d) )
'''Draw text annotation'''
unit = imp.getCalibration().getUnit().encode('utf8') # get the unit as UTF-8 (for \mu)
print "Draw_Meas(): Unit (raw) = `", unit,"`", type(unit),
if unit[0] == u'\xc2': unit=unit[1:] # strip weird char at start of \mu
# format of measurement text (eg. 3 decimal points):
lenstr = "%0.3f" % roi.getLength() + " %s" % (unit) # string to print as length
print "DrawMeas(): Line length= %s" % lenstr
#print "x,y=", p2[0], p2[1]
'''determine position of text from line coords, eg "bottom right" or "top left" etc. '''
# y-coord:
if p2[1] > p1[1]:
posstr = 'bottom'
else:
posstr = 'top'
# x-coord:
if p2[0] > p1[0]:
posstr += ' right'
else:
posstr += ' left'
drawText( lenstr, p2[0], p2[1], position=posstr )
imp.updateAndDraw() #update the image
def drawText( text, x, y, position='bottom right' ):
'''Draw a text string at the specified coordinates & relative position, ensuring text doesn't go over the edge of the image.
Parameters:
-----------
text : string
The text string to write on the image.
x, y : int
The coordinates at which to draw the text.
position : { 'bottom right', 'top right', 'top left', 'bottom left' }, case-insensitive, optional
Where to draw the text, with respect to the coordinates given.
Synonyms for 'bottom right' are 'br'. This is the default.
Synonyms for 'top right' are 'tr'.
Synonyms for 'bottom left' are 'bl'.
Synonyms for 'top left' are 'tl'.
'''
print "drawText(): original (x,y)=(%i,%i)"%( x, y )
# 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.
ip = IJ.getProcessor() # Image Processor
imp = IJ.getImage() # get the current Image, which is an ImagePlus object
'''Acquire arguments'''
position = position.strip().lower()
if position == 'bottom right' or position == 'br':
pos = 'br'
elif position == 'bottom left' or position == 'bl':
pos = 'bl'
elif position == 'top left' or position == 'tl':
pos = 'tl'
elif position == 'top right' or position == 'tr':
pos = 'tr'
else:
raise ValueError( 'drawText(): Invalid `position` argument: "%s".'%(position) )
'''Setup text annotation'''
# 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]) ) )
'''determine text position'''
margin = 6 # space in pixels away from edge of image
spacer = 4 # space in pixels to add between point & text
strw = ip.getStringWidth(text)
strh = ip.getFontMetrics().getHeight()
imgw = ip.getWidth()
imgh = ip.getHeight()
'''
print "strw =", strw
print "strh =", strh
print "imgw =", imgw
print "imgh =", imgh
'''
# set coords (x,y) based on `position` argument
''' By default, text is horizontally centered at point (x), and vertically above the point (y). We then modify these default coords. '''
if pos[0] == 'b':
y = y + spacer + strh # moves down
elif pos[0] == 't':
y = y - spacer
if pos[1] == 'r':
x = x + spacer # moves right
elif pos[1] == 'l':
x = x - spacer - int(strw)
print "drawText(): %s "%(pos) + "(x,y)=(%i,%i)"%( x, y )
'''Correct for edge of image'''
if y - strh < 0:
y = 0 + strh + margin
elif y > imgh :
y = imgh - margin
if (x) < 0:
x = 0 + margin
elif (x + strw) > imgw:
x = imgw - strw - margin
print "drawText(): final (x,y)=(%i,%i)"%( x, y )
if sets.textbackgroundcolor:
ip.drawString( text, 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( text, x, y ) # write the text alone
imp.updateAndDraw() #update the image
''' def getPixelPos(x,y, imp): point = [0,0] point[0] = (x / cal.piXelW) point[1] = (imp.height * (y / 100)) return point ''' rm = RoiManager.getInstance() #get the open ROI manager instance ra = rm.getRoisAsArray() #get all the ROIs in an array #print r1.getPosition() imp = IJ.getImage() #get current image stack = imp.getStack() #get current rm = RoiManager.getInstance() ra = rm.getRoisAsArray() nRois = len(ra) proc = IJ.getProcessor() #get the image processor cal = imp.getCalibration(); #print cal.pixelWidth #print imp.width totSlices = int(stack.getSize()) #print stack.getSize() #print r1.getFloatPolygon().xpoints[0] #get xpoint #first convert our ROIs to something more useful, a tuple containing the point (x,y) and the Z position => (x,y,z) for i in range(0, nRois-1): roi1 = rm.getRoi(i) roi2 = rm.getRoi(i+1) pt1 = (roi1.getFloatPolygon().xpoints[0],roi1.getFloatPolygon().ypoints[0],roi1.getPosition()) pt2 = (roi2.getFloatPolygon().xpoints[0],roi2.getFloatPolygon().ypoints[0],roi2.getPosition()) startSlice = pt1[2] endSlice = pt2[2] nSlices = (endSlice - startSlice)
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, 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()+")" )
# Add auto calibration from text file
if sets.autoupdatecal:
newcal = imp.getCalibration().copy(
) # make a copy of current calibration object
if MC_DEBUG: print("Assume calibration is a custom function.")
# call the class' `classObj.cal( ImagePlusObject )` function to get the scale value:
try:
calObject = sets.autoupdatecal_name
calName = calObject.name
newPixelPerUnit = calObject.cal(imp)
except AttributeError:
raise ValueError(
'This calibration Name value is invalid, please check your Settings.py file!/n/tFor Calibration Number %i, got: `'
% (CalIdx) + str(cal.names[CalIdx]) +
'`. Expected a String or a Class instance with ".cal()" method, but got type '
+ str(type(cal.names[CalIdx])) + ' with no ".cal()" method.')
#end try
newUnit = calObject.unit
newAspect = calObject.aspect_ratio
newPixelWidth = 1. / newPixelPerUnit
newPixelHeight = newPixelWidth * newAspect
# the following translated from "Microscope_Scale.java":
newcal.setUnit(newUnit)
newcal.pixelWidth = newPixelWidth
newcal.pixelHeight = newPixelHeight
imp.setGlobalCalibration(None)
imp.setCalibration(newcal) # set the new calibration
imp.getWindow().repaint() # refresh the image?
# Added - add the measurement to the list...
a = Analyzer(imp)
a.measure()
a.displayResults()
# from ij.measure import ResultsTable
# rt = ResultsTable.getResultsTable()
p1 = [int(roi.x1d), int(roi.y1d)] # point 1 (x,y)
p2 = [int(roi.x2d), int(roi.y2d)] # point 2
#print "DrawMeas(): Line Points: p1=", p1, " & p2=", p2
pm = midpoint(p1, p2) # get midpoint coord
# set ROI params from settings:
''' Using new method - used ip.drawLine instead of roi.draw, since roi.draw didn't always apply the line thickness. Would be best to use the ROI method, in case other types of ROI's could be annotated.
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
'''
ip.setLineWidth(int(sets.linethickness))
ip.setColor(
jColor(float(sets.linecolor[0]), float(sets.linecolor[1]),
float(sets.linecolor[2]), float(sets.linecolor[3])))
#ip.draw(roi) # changed to ip.drawLine()
ip.drawLine(int(roi.x1d), int(roi.y1d), int(roi.x2d), int(roi.y2d))
'''Draw text annotation'''
unit = imp.getCalibration().getUnit().encode(
'utf8') # get the unit as UTF-8 (for \mu)
#print "Draw_Meas(): Unit (raw) = `", unit,"`", type(unit),
if unit[0] == u'\xc2': unit = unit[1:] # strip weird char at start of \mu
# format of measurement text (eg. 3 decimal points):
lenstr = "%0.3f" % roi.getLength() + " %s" % (
unit) # string to print as length
print "DrawMeas(): Line length= %s" % lenstr
#print "x,y=", p2[0], p2[1]
'''determine position of text from line coords, eg "bottom right" or "top left" etc. '''
# y-coord:
if p2[1] > p1[1]:
posstr = 'bottom'
else:
posstr = 'top'
# x-coord:
if p2[0] > p1[0]:
posstr += ' right'
else:
posstr += ' left'
drawText(lenstr, p2[0], p2[1], position=posstr)
imp.updateAndDraw() #update the image
