def run_straighten(roiWindowsize = 4):
""" Original straightening function based on Nick's macro. Used in final version.
Returns coordinate string used to make centerline. """
IJ.run("Set Measurements...", "mean min center redirect=None decimal=3")
IJ.runMacro("//setTool(\"freeline\");")
IJ.run("Line Width...", "line=80");
numPoints = 512/roiWindowsize
xvals = []
yvals = []
maxvals = []
counter = 0
for i in range(0, 512, roiWindowsize):
IJ.run("Clear Results")
IJ.makeRectangle(i, 0, roiWindowsize, 512)
IJ.run("Measure")
table = RT.getResultsTable()
xvals.append(i + roiWindowsize/2)
yvals.append(RT.getValue(table, "YM", 0))
maxvals.append((RT.getValue(table, "Max", 0)))
if maxvals[counter] == 0 and counter > 0:
yvals[counter] = yvals[counter - 1]
counter += 1
coords = ""
for i in range(numPoints - 1):
coords += str(xvals[i]) + ", " + str(yvals[i]) +", "
coords += str(xvals[numPoints-1]) + ", " + str(yvals[numPoints-1])
IJ.runMacro("makeLine("+coords+")")
IJ.run("Straighten...", "line = 80")
return coords
def run_straighten(roiWindowsize=4):
""" Original straightening function based on Nick's macro. Used in final version.
Returns coordinate string used to make centerline. """
IJ.run("Set Measurements...", "mean min center redirect=None decimal=3")
IJ.runMacro("//setTool(\"freeline\");")
IJ.run("Line Width...", "line=80")
numPoints = 512 / roiWindowsize
xvals = []
yvals = []
maxvals = []
counter = 0
for i in range(0, 512, roiWindowsize):
IJ.run("Clear Results")
IJ.makeRectangle(i, 0, roiWindowsize, 512)
IJ.run("Measure")
table = RT.getResultsTable()
xvals.append(i + roiWindowsize / 2)
yvals.append(RT.getValue(table, "YM", 0))
maxvals.append((RT.getValue(table, "Max", 0)))
if maxvals[counter] == 0 and counter > 0:
yvals[counter] = yvals[counter - 1]
counter += 1
coords = ""
for i in range(numPoints - 1):
coords += str(xvals[i]) + ", " + str(yvals[i]) + ", "
coords += str(xvals[numPoints - 1]) + ", " + str(yvals[numPoints - 1])
IJ.runMacro("makeLine(" + coords + ")")
IJ.run("Straighten...", "line = 80")
return coords
def measure_growth(imgDir, filename = "Fiji_Growth.txt"):
""" Collects measurement data in pixels and writes to a file. Uses straightened binary images"""
f = open(imgDir + filename, 'w')
f.write("Img number\tEnd point (pixels)\n")
IJ.run("Set Measurements...", "area mean min center redirect=None decimal=3")
index = "000000000"
filename = imgDir + "/binary" + "/img_" + index + "__000-padded.tif"
while path.exists(filename):
imp = IJ.openImage(filename)
imp.show()
IJ.run("Clear Results")
for i in xrange(800): #hard coded to target length for now
IJ.makeRectangle(i, 0, 1, 80)
IJ.run("Measure")
table = RT.getResultsTable()
#print "i:", i, "counter:", table.getCounter()
maxi = RT.getValue(table, "Max", i)
if maxi == 0:
f.write(str(int(index)) + "\t" + str(i) + "\n")
break
IJ.runMacro("while (nImages>0) {selectImage(nImages);close();}")
index = to_9_Digits(str(int(index)+1))
filename = imgDir + "/padded" + "/img_" + index + "__000-padded.tif"
f.close()
def main_noninteractive():
"""The main routine for running non-interactively."""
global imcftpl
args = parse_arguments()
set_loglevel(args.verbose)
log.info('Running in non-interactive mode.')
log.debug('Python FluoView package file: %s' % fv.__file__)
base = dirname(args.mosaiclog)
fname = basename(args.mosaiclog)
mosaics = fv.FluoViewMosaic(join(base, fname))
log.warn(gen_mosaic_details(mosaics))
if args.templates is not None:
imcftpl = args.templates
code = imagej.gen_stitching_macro_code(mosaics, 'templates/stitching',
path=base, tplpath=imcftpl)
if not args.dryrun:
log.info('Writing stitching macro.')
imagej.write_stitching_macro(code, fname='stitch_all.ijm', dname=base)
log.info('Writing tile configuration files.')
imagej.write_all_tile_configs(mosaics, fixsep=True)
log.info('Launching stitching macro.')
IJ.runMacro(flatten(code))
else:
log.info('Dry-run was selected. Printing generated macro:')
log.warn(flatten(code))
def makeSpline(*points):
macrocode = 'makeLine('
for x, y in points:
macrocode += str(int(x)) + ", " + str(int(y)) + ", "
macrocode = macrocode[:-2] + ');'
#print macrocode
IJ.runMacro(macrocode)
def measure_growth(imgDir, filename="Fiji_Growth.txt"):
""" Collects measurement data in pixels and writes to a file. Uses straightened binary images"""
f = open(imgDir + filename, 'w')
f.write("Img number\tEnd point (pixels)\n")
IJ.run("Set Measurements...",
"area mean min center redirect=None decimal=3")
index = "000000000"
filename = imgDir + "/binary" + "/img_" + index + "__000-padded.tif"
while path.exists(filename):
imp = IJ.openImage(filename)
imp.show()
IJ.run("Clear Results")
for i in xrange(800): #hard coded to target length for now
IJ.makeRectangle(i, 0, 1, 80)
IJ.run("Measure")
table = RT.getResultsTable()
#print "i:", i, "counter:", table.getCounter()
maxi = RT.getValue(table, "Max", i)
if maxi == 0:
f.write(str(int(index)) + "\t" + str(i) + "\n")
break
IJ.runMacro("while (nImages>0) {selectImage(nImages);close();}")
index = to_9_Digits(str(int(index) + 1))
filename = imgDir + "/padded" + "/img_" + index + "__000-padded.tif"
f.close()
def path(i, j, array):
macro = "makePolygon("
for k in range(0, len(array), 2):
if k > 0:
macro = macro + ", "
macro = macro + str(i * w + array[k]) + ", " + str(j * h + array[k + 1])
macro += ");"
IJ.runMacro(macro)
def straighten_roi_rotation(roiWindowsize = 8):
""" Root straightening function that rotates ROI to follow root slope.
Does not work properly.
"""
IJ.run("Set Measurements...", "mean standard min center redirect=None decimal=3")
IJ.runMacro("//setTool(\"freeline\");")
IJ.run("Line Width...", "line=80");
#numPoints = 512/roiWindowsize
xvals = []
yvals = []
maxvals = []
counter = 0
maxIters = 800/roiWindowsize
minIters = 10
imp = IJ.getImage().getProcessor()
rm = RoiManager()
if find_first_pixel(0,imp) == None or find_last_pixel(0,imp)[1] == None:
return
y = (find_first_pixel(0,imp)[1]+find_last_pixel(0,imp)[1])/2
roi = roiWindow_(imp, center = (roiWindowsize/2,y), width = roiWindowsize, height = 512)
xvals.append(roiWindowsize/2)
yvals.append(y)
maxvals.append(0)
roi.findTilt_()
i = 0
while i < maxIters and roi.containsRoot_():
roi.advance_(roiWindowsize)
IJ.run("Clear Results")
IJ.run("Measure")
table = RT.getResultsTable()
x = RT.getValue(table, "XM", 0)
y = RT.getValue(table, "YM", 0)
if imp.getPixel(int(x),int(y)) != 0:
xvals.append(x)
yvals.append(y)
maxvals.append((RT.getValue(table, "Max", 0)))
#roi.advance_(roiWindowsize)
print "here"
roi.unrotateRoot_()
IJ.run("Clear Results")
IJ.run("Measure")
roi.restoreCenter_(RT.getValue(table, "XM", 0), RT.getValue(table, "YM", 0))
#exit(1)
sleep(.5)
roi.findTilt_()
i += 1
coords = ""
for i in range(len(xvals)-1):
coords += str(xvals[i]) + ", " + str(yvals[i]) +", "
coords += str(xvals[len(xvals)-1]) + ", " + str(yvals[len(xvals)-1])
IJ.runMacro("makeLine("+coords+")")
IJ.run("Straighten...", "line = 80")
def path(i, j, array):
macro = 'makePolygon('
for k in range(0, len(array), 2):
if k > 0:
macro = macro + ', '
macro = macro + str(i * w + array[k]) + ', ' + str(j * h +
array[k + 1])
macro += ');'
IJ.runMacro(macro)
def square(i, j, currentX, currentY):
IJ.runMacro("makeRectangle(" + str(w * i) + ", " + str(h * j) + ", " + str(w) + ", " + str(h) + ");")
if i == currentX and j == currentY:
color = "orange"
elif (i + j) & 1 == 1:
color = "black"
else:
color = "white"
setColor(color)
IJ.run("Fill")
def preProcess_(imp):
""" Noise filtering step. Removes particles other than the root after segmentation.
Takes a pointer to an ImagePlus, returns pointer to new ImagePlus. """
IJ.runMacro("//setThreshold(1, 255);")
IJ.runMacro("run(\"Convert to Mask\");")
IJ.run("Analyze Particles...", "size=400-Infinity show=Masks")
filteredImp = IJ.getImage()
#imp.close()
#IJ.run("Invert")
IJ.run("Invert LUT")
return filteredImp
def preProcess_(imp):
""" Noise filtering step. Removes particles other than the root after segmentation.
Takes a pointer to an ImagePlus, returns pointer to new ImagePlus. """
IJ.runMacro("//setThreshold(1, 255);")
IJ.runMacro("run(\"Convert to Mask\");")
IJ.run("Analyze Particles...", "size=400-Infinity show=Masks")
filteredImp = IJ.getImage()
#imp.close()
#IJ.run("Invert")
IJ.run("Invert LUT")
return filteredImp
def square(i, j, currentX, currentY):
IJ.runMacro('makeRectangle(' + str(w * i) + ', ' + str(h * j) + ', ' +
str(w) + ', ' + str(h) + ');')
if i == currentX and j == currentY:
color = 'orange'
elif (i + j) & 1 == 1:
color = 'black'
else:
color = 'white'
setColor(color)
IJ.run('Fill')
def straighten_with_centerpoints(roiWindowsize = 4):
""" Failed straightening method utilizing ROI rotation. """
IJ.run("Set Measurements...", "mean min center redirect=None decimal=3")
IJ.runMacro("//setTool(\"freeline\");")
IJ.run("Line Width...", "line=80");
numPoints = 512/(roiWindowsize)
xvals = []
yvals = []
maxvals = []
imp = IJ.getImage().getProcessor()
for i in range(0, 512, roiWindowsize):
topLeft = find_first_pixel(i, imp)
bottomLeft = find_last_pixel(i, imp)
#print "topLeft:", topLeft, "bottomLeft:", bottomLeft
#sleep(.2)
if not topLeft == None and not bottomLeft == None:
xvals.append(i)
yvals.append((topLeft[1] + bottomLeft[1])/2)
topRight = find_first_pixel(i + roiWindowsize, imp)
bottomRight = find_last_pixel(i + roiWindowsize, imp)
if not topRight == None and not bottomRight == None:
xvals.append(i + roiWindowsize)
yvals.append((topRight[1] + bottomRight[1])/2)
coords = ""
#print "xvals:", xvals
#print "yvals:", yvals
for i in range(len(xvals)-1):
coords += str(xvals[i]) + ", " + str(yvals[i]) +", "
coords += str(xvals[len(xvals)-1]) + ", " + str(yvals[len(xvals)-1])
IJ.runMacro("makeLine("+coords+")")
IJ.run("Straighten...", "line = 80")
def straighten_with_centerpoints(roiWindowsize=4):
""" Failed straightening method utilizing ROI rotation. """
IJ.run("Set Measurements...", "mean min center redirect=None decimal=3")
IJ.runMacro("//setTool(\"freeline\");")
IJ.run("Line Width...", "line=80")
numPoints = 512 / (roiWindowsize)
xvals = []
yvals = []
maxvals = []
imp = IJ.getImage().getProcessor()
for i in range(0, 512, roiWindowsize):
topLeft = find_first_pixel(i, imp)
bottomLeft = find_last_pixel(i, imp)
#print "topLeft:", topLeft, "bottomLeft:", bottomLeft
#sleep(.2)
if not topLeft == None and not bottomLeft == None:
xvals.append(i)
yvals.append((topLeft[1] + bottomLeft[1]) / 2)
topRight = find_first_pixel(i + roiWindowsize, imp)
bottomRight = find_last_pixel(i + roiWindowsize, imp)
if not topRight == None and not bottomRight == None:
xvals.append(i + roiWindowsize)
yvals.append((topRight[1] + bottomRight[1]) / 2)
coords = ""
#print "xvals:", xvals
#print "yvals:", yvals
for i in range(len(xvals) - 1):
coords += str(xvals[i]) + ", " + str(yvals[i]) + ", "
coords += str(xvals[len(xvals) - 1]) + ", " + str(yvals[len(xvals) - 1])
IJ.runMacro("makeLine(" + coords + ")")
IJ.run("Straighten...", "line = 80")
def showMessage(mssg):
IJ.runMacro('showMessage("' + mssg + '")')
def wait(msecs):
IJ.runMacro('wait(' + str(msecs) + ')')
def waitForUser(mssg):
IJ.runMacro('waitForUser("' + mssg + '")')
def import_and_straighten(imgDir):
"""
Core function. Opens images in given directory in series and calls a straightening function.
Thresholds using weka if stddev of pixel intensities is too high (bright field), otherwise uses
histogram based segmentation.
"""
targetWidth = 800 #adjustable
make_directory(imgDir)
index = "000000000"
filename = imgDir + "/img_" + index + "__000.tif"
if path.exists(filename):
weka = Weka_segmentor(IJ.openImage(filename))
while path.exists(filename):
IJ.run("Set Measurements...", "mean standard min center redirect=None decimal=3")
IJ.run("Clear Results")
imp = IJ.openImage(filename)
imp.show()
IJ.run("Rotate 90 Degrees Left")
IJ.run("Measure")
table = RT.getResultsTable()
stddev = RT.getValue(table, "StdDev", 0)
if stddev < 20:
segmented = weka.getThreshold(imp)
segmented.show()
IJ.run("8-bit")
IJ.run("Invert")
imp.close()
imp = segmented
else:
IJ.run(imp, "Auto Threshold", "method=Li white") #threshold
imp = preProcess_(imp)
#straighten_roi_rotation()
coords = run_straighten()
newImp = IJ.getImage()
"""
fs = FileSaver(newImp)
fs.saveAsTiff(imgDir + "/straightened" + "/img_" + index + "__000-straight.tif")
"""
IJ.run("Image Padder", "pad_right="+str(targetWidth - newImp.getWidth()))
paddedImp = IJ.getImage()
fs = FileSaver(paddedImp)
fs.saveAsTiff(imgDir + "/binary" + "/img_" + index + "__000-padded.tif")
IJ.runMacro("while (nImages>0) {selectImage(nImages);close();}")
#use same centerline for original greyscale image
imp = IJ.openImage(filename)
imp.show()
IJ.run("Rotate 90 Degrees Left")
IJ.run("8-bit")
IJ.runMacro("makeLine("+coords+")")
IJ.run("Straighten...", "line = 80")
newImp = IJ.getImage()
IJ.run("Image Padder", "pad_right="+str(targetWidth - newImp.getWidth()))
paddedImp = IJ.getImage()
IJ.run("8-bit")
fs = FileSaver(paddedImp)
fs.saveAsTiff(imgDir + "/greyscale" + "/img_" + index + "__000-padded.tif")
IJ.runMacro("while (nImages>0) {selectImage(nImages);close();}")
index = to_9_Digits(str(int(index)+1))
filename = filename = imgDir + "/img_" + index + "__000.tif"
The parameters "Seed Dynamics", "Intensity threshold" and "peak flooding" can be made optional
function Signature
resultImage = op.run("H_Watershed", inputImage, hMin, threshold, peakFlooding, outputMask, allowSplitting)
All parameters beyond inputImage are optional. They can be replaced by null or if at the end of the
list they can be remove completely. If the parameter is detected as missing a sensible default is used
hMin = 5(max-min)/100
threshold = min
peakflooding = 100
outputMask = False (default is to output a label image)
allowsplitting = True (default is to allow threshold to create new peaks)
"""
IJ.runMacro("close(\"\\\\Others\")")
hMin = 0
thresh = 100
peakFlooding = 50
result0 = ops.run("H_Watershed", imp)
result1 = ops.run("H_Watershed", imp, hMin)
result2 = ops.run("H_Watershed", imp, hMin, thresh)
outputMask = True
allowSplit = False
result3 = ops.run("H_Watershed", imp, hMin, thresh, peakFlooding, outputMask,
allowSplit)
#imprgb=ImagePlus("rgbStack", rgbstack)
#imprgb.show()
#IJ.selectWindow("rgbStack")
#IJ.run("Hide Overlay", "")
imp.show()
IJ.selectWindow(imp.getTitle())
imp.setOverlay(overlay)
IJ.run("Show Overlay", "")
for i in range(len(cles)) :
pos=dicPos[cles[i]]
command = 'Overlay.drawString("'+cles[i]+'", '+str(pos[0][0])+', '+str(pos[0][1])+')'
IJ.runMacro(command)
f2 = open(rootdir+now+"-R2-MT.txt", "w")
f3 = open(rootdir+now+"-R3-MT.txt", "w")
f4 = open(rootdir+now+"-R4-MT.txt", "w")
tab="\t"
line2 = ["sens"+cle+tab+"speed"+cle+tab+"cumul"+cle+tab+"fluoA"+cle+tab+"fluoB"+cle for cle in cles]
line3 = ["scalA"+cle+tab+"scalB"+cle+tab+"oriX"+cle+tab+"oriY"+cle for cle in cles]
line4 = ["midaxis"+cle+tab+"Feret"+cle+tab+"fluoA"+cle+tab+"fluoB"+cle for cle in cles]
f2.write(tab.join(line2)+"\n")
f3.write(tab.join(line3)+"\n")
f4.write(tab.join(line4)+"\n")
def translate_(self, dx, dy):
IJ.runMacro("roiManager(\"translate\", " + str(dx) + ", " + str(dy) +
")")
self.center = (self.center[0] + dx, self.center[1] + dy)
def selectWindow(name):
IJ.runMacro('selectWindow("' + name + '")')
def close_others():
IJ.runMacro("close(\"\\\\Others\")")
from ij import IJ, ImageJ
ImageJ()
IJ.run("MRI Stack (528K)")
IJ.runMacro("setVoxelSize(1, 1, 4, 'mm')")
IJ.run("3D Viewer",
"display=Volume color=None threshold=0 resampling=1 red green blue")
def close():
IJ.runMacro("close()")
def unrotateRoot_(self): # dTheta):
IJ.runMacro("run(\"Rotate...\",\" angle=" + str((-1) * self.dTheta) +
"\");")
def import_and_straighten(imgDir):
"""
Core function. Opens images in given directory in series and calls a straightening function.
Thresholds using weka if stddev of pixel intensities is too high (bright field), otherwise uses
histogram based segmentation.
"""
targetWidth = 800 #adjustable
make_directory(imgDir)
index = "000000000"
filename = imgDir + "/img_" + index + "__000.tif"
if path.exists(filename):
weka = Weka_segmentor(IJ.openImage(filename))
while path.exists(filename):
IJ.run("Set Measurements...",
"mean standard min center redirect=None decimal=3")
IJ.run("Clear Results")
imp = IJ.openImage(filename)
imp.show()
IJ.run("Rotate 90 Degrees Left")
IJ.run("Measure")
table = RT.getResultsTable()
stddev = RT.getValue(table, "StdDev", 0)
if stddev < 20:
segmented = weka.getThreshold(imp)
segmented.show()
IJ.run("8-bit")
IJ.run("Invert")
imp.close()
imp = segmented
else:
IJ.run(imp, "Auto Threshold", "method=Li white") #threshold
imp = preProcess_(imp)
#straighten_roi_rotation()
coords = run_straighten()
newImp = IJ.getImage()
"""
fs = FileSaver(newImp)
fs.saveAsTiff(imgDir + "/straightened" + "/img_" + index + "__000-straight.tif")
"""
IJ.run("Image Padder",
"pad_right=" + str(targetWidth - newImp.getWidth()))
paddedImp = IJ.getImage()
fs = FileSaver(paddedImp)
fs.saveAsTiff(imgDir + "/binary" + "/img_" + index +
"__000-padded.tif")
IJ.runMacro("while (nImages>0) {selectImage(nImages);close();}")
#use same centerline for original greyscale image
imp = IJ.openImage(filename)
imp.show()
IJ.run("Rotate 90 Degrees Left")
IJ.run("8-bit")
IJ.runMacro("makeLine(" + coords + ")")
IJ.run("Straighten...", "line = 80")
newImp = IJ.getImage()
IJ.run("Image Padder",
"pad_right=" + str(targetWidth - newImp.getWidth()))
paddedImp = IJ.getImage()
IJ.run("8-bit")
fs = FileSaver(paddedImp)
fs.saveAsTiff(imgDir + "/greyscale" + "/img_" + index +
"__000-padded.tif")
IJ.runMacro("while (nImages>0) {selectImage(nImages);close();}")
index = to_9_Digits(str(int(index) + 1))
filename = filename = imgDir + "/img_" + index + "__000.tif"
def straighten_roi_rotation(roiWindowsize=8):
""" Root straightening function that rotates ROI to follow root slope.
Does not work properly.
"""
IJ.run("Set Measurements...",
"mean standard min center redirect=None decimal=3")
IJ.runMacro("//setTool(\"freeline\");")
IJ.run("Line Width...", "line=80")
#numPoints = 512/roiWindowsize
xvals = []
yvals = []
maxvals = []
counter = 0
maxIters = 800 / roiWindowsize
minIters = 10
imp = IJ.getImage().getProcessor()
rm = RoiManager()
if find_first_pixel(0, imp) == None or find_last_pixel(0, imp)[1] == None:
return
y = (find_first_pixel(0, imp)[1] + find_last_pixel(0, imp)[1]) / 2
roi = roiWindow_(imp,
center=(roiWindowsize / 2, y),
width=roiWindowsize,
height=512)
xvals.append(roiWindowsize / 2)
yvals.append(y)
maxvals.append(0)
roi.findTilt_()
i = 0
while i < maxIters and roi.containsRoot_():
roi.advance_(roiWindowsize)
IJ.run("Clear Results")
IJ.run("Measure")
table = RT.getResultsTable()
x = RT.getValue(table, "XM", 0)
y = RT.getValue(table, "YM", 0)
if imp.getPixel(int(x), int(y)) != 0:
xvals.append(x)
yvals.append(y)
maxvals.append((RT.getValue(table, "Max", 0)))
#roi.advance_(roiWindowsize)
print "here"
roi.unrotateRoot_()
IJ.run("Clear Results")
IJ.run("Measure")
roi.restoreCenter_(RT.getValue(table, "XM", 0),
RT.getValue(table, "YM", 0))
#exit(1)
sleep(.5)
roi.findTilt_()
i += 1
coords = ""
for i in range(len(xvals) - 1):
coords += str(xvals[i]) + ", " + str(yvals[i]) + ", "
coords += str(xvals[len(xvals) - 1]) + ", " + str(yvals[len(xvals) - 1])
IJ.runMacro("makeLine(" + coords + ")")
IJ.run("Straighten...", "line = 80")
def main_interactive():
"""The main routine for running interactively."""
log.info('Running in interactive mode.')
(base, fname) = ui_get_input_file()
if (base is None):
return
log.warn("Parsing project file: %s" % (base + fname))
IJ.showStatus("Parsing experiment file...")
mosaics = fv.FluoViewMosaic(join(base, fname), runparser=False)
IJ.showStatus("Parsing mosaics...")
progress = 0.0
count = len(mosaics.mosaictrees)
step = 1.0 / count
for subtree in mosaics.mosaictrees:
IJ.showProgress(progress)
mosaics.add_mosaic(subtree)
progress += step
IJ.showProgress(progress)
IJ.showStatus("Parsed %i mosaics." % len(mosaics))
dialog = GenericDialog('FluoView OIF / OIB Stitcher')
if len(mosaics) == 0:
msg = ("Couldn't find any (valid) mosaics in the project file.\n"
" \n"
"Please make sure to have all files available!\n"
" \n"
"Will stop now.\n")
log.warn(msg)
dialog.addMessage(msg)
dialog.showDialog()
return
msg = "------------------------ EXPORT OPTIONS ------------------------"
dialog.addMessage(msg)
formats = ["OME-TIFF", "ICS/IDS"]
dialog.addChoice("Export Format", formats, formats[0])
dialog.addCheckbox("separate files by Z slices (OME-TIFF only)?", False)
msg = "------------------------ EXPORT OPTIONS ------------------------"
dialog.addMessage(msg)
dialog.addMessage("")
dialog.addMessage("")
msg = gen_mosaic_details(mosaics)
log.warn(msg)
msg += "\n \nPress [OK] to write tile configuration files\n"
msg += "and continue with running the stitcher."
dialog.addMessage(msg)
dialog.showDialog()
opts = {}
if dialog.getNextChoice() == 'ICS/IDS':
opts['export_format'] = '".ids"'
else:
opts['export_format'] = '".ome.tif"'
if dialog.getNextBoolean() == True:
opts['split_z_slices'] = 'true'
code = imagej.gen_stitching_macro_code(mosaics, 'templates/stitching',
path=base, tplpath=imcftpl, opts=opts)
log.warn("============= generated macro code =============")
log.warn(flatten(code))
log.warn("============= end of generated macro code =============")
if dialog.wasOKed():
log.warn('Writing stitching macro.')
imagej.write_stitching_macro(code, fname='stitch_all.ijm', dname=base)
log.warn('Writing tile configuration files.')
imagej.write_all_tile_configs(mosaics, fixsep=True)
log.warn('Launching stitching macro.')
IJ.runMacro(flatten(code))
def rotate_(self): # dTheta):
IJ.runMacro("run(\"Rotate...\",\" angle=" + str(self.dTheta) + "\");")
def selectionType(named=False):
i = int(IJ.runMacro("return toString(selectionType());"))
if not named:
return i
else:
return SELECTION_TYPES[i]
def drawCoord(coord, array, color):
(i, j) = parseCoord(coord)
draw(i, j, array, color)
def erase():
i = WindowManager.getImageCount()
while i > 0:
WindowManager.getImage(WindowManager.getNthImageID(i)).close()
i = i - 1
erase()
IJ.runMacro('newImage("Chess", "RGB", ' + str(w * 8) + ", " + str(h * 8) + ", 1);")
def initial_field():
return [
"Rb",
"Nb",
"Bb",
"Qb",
"Kb",
"Bb",
"Nb",
"Rb",
"Pb",
"Pb",
"Pb",
def rename(newname):
IJ.runMacro('rename("' + newname + '")')
from ij import IJ, Menus
from java.lang import System, Thread
from os import makedirs, rename, stat
from os.path import exists, isdir
from sys import stderr
from time import sleep
import urllib
# force initialization
IJ.runMacro("", "")
menu = User_Plugins.getMenuItem('File>Open Samples')
commands = Menus.getCommands()
plugin = 'ij.plugin.URLOpener("'
samples = System.getProperty('ij.dir') + '/samples'
class FileSizeReporter(Thread):
def __init__(self, name, path):
self.name = name
self.path = path
self.canceled = False
def run(self):
while self.canceled == False:
from ij import IJ, Menus
from java.lang import System, Thread
from os import makedirs, rename, stat
from os.path import exists, isdir
from sys import stderr
from time import sleep
import urllib
# force initialization
IJ.runMacro("", "")
menu = User_Plugins.getMenuItem('File>Open Samples')
commands = Menus.getCommands()
plugin = 'ij.plugin.URLOpener("'
samples = System.getProperty('fiji.dir') + '/samples'
class FileSizeReporter(Thread):
def __init__(self, name, path):
self.name = name
self.path = path
self.canceled = False
def run(self):
while self.canceled == False:
if exists(self.path):
def translate_(self, dx, dy):
IJ.runMacro("roiManager(\"translate\", " +str(dx) + ", " + str(dy) + ")")
self.center = (self.center[0] + dx, self.center[1] +dy)
def drawCoord(coord, array, color):
(i, j) = parseCoord(coord)
draw(i, j, array, color)
def erase():
i = WindowManager.getImageCount()
while i > 0:
WindowManager.getImage(WindowManager.getNthImageID(i)).close()
i = i - 1
erase()
IJ.runMacro('newImage("Chess", "RGB", ' + str(w * 8) + ', ' + str(h * 8) +
', 1);')
def initial_field():
return [
'Rb', 'Nb', 'Bb', 'Qb', 'Kb', 'Bb', 'Nb', 'Rb', 'Pb', 'Pb', 'Pb', 'Pb',
'Pb', 'Pb', 'Pb', 'Pb', '', '', '', '', '', '', '', '', '', '', '', '',
'', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '',
'', '', 'Pw', 'Pw', 'Pw', 'Pw', 'Pw', 'Pw', 'Pw', 'Pw', 'Rw', 'Nw',
'Bw', 'Qw', 'Kw', 'Bw', 'Nw', 'Rw'
]
def get_array(name):
if name == 'P':
return Pawn
def rotate_(self): # dTheta):
IJ.runMacro("run(\"Rotate...\",\" angle=" +str(self.dTheta)+"\");")
print(sys.path)
# extend the search path by $FIJI_ROOT/bin/
path.append('/home/ehrenfeu/.local/lib/python2.7')
path.append('/home/ehrenfeu/.local/lib/python2.7/site-packages/volpy')
# path.append('C:\\Devel\\imcf_toolbox\\lib\\python2.7')
# path.append('C:\\Devel\\imcf_toolbox\\lib\\python2.7\\volpy')
import fluoview as fv
from log import log, set_loglevel
# set_loglevel(1)
infile = OpenDialog("Choose a 'MATL_Mosaic.log' file", '*.log')
print(infile.getDirectory())
print(infile.getFileName())
# dc = DirectoryChooser("Choose a directory with a 'MATL_Mosaic.log' file")
# base = dc.getDirectory()
mf = base + 'MATL_Mosaic.log'
mosaic = fv.FluoViewMosaic(mf)
mosaic.write_all_tile_configs(fixpath=True)
code = mosaic.gen_stitching_macro_code('stitching', base)
flat = ""
for line in code:
flat += line
#print flat
IJ.runMacro(flat)
def unrotateRoot_(self): # dTheta):
IJ.runMacro("run(\"Rotate...\",\" angle=" +str((-1)*self.dTheta)+"\");")
