def main(*R):
""" Main function
"""
# Show intial progress bar
IJ.showProgress(0, 50)
IJ.showStatus("Heterogeneous Z Correction")
# Retrieve the values R (with default values) from previous attempts
Rstr = "[(-0.05977, 83.3, 78.73),(-0.05976, 41.65, 39.36)]"
R = eval(Prefs.get("HetZCorr.R", Rstr))
# Load current image and get infos
imp = IJ.getImage()
stk = imp.getStack()
(sx, sy, sz) = stackSize(stk)
cal = imp.getCalibration()
# Get unique values
val = getUniqueValues(stk)
# Get R from dialog
R = showDialogR(R, val)
# Generate optical model
correction = generateModel(stk, R, val)
imp.setCalibration(cal)
#Show model image
correction.show()
correction.setSlice(sz)
IJ.run(correction, "Enhance Contrast", "saturated=0.35")
IJ.run(correction, "Fire", "")
def downsample_for_isotropy(imp, extra_downsample_factor=2.0, info=None):
"""downsample x, y pixel directions to get ~cubic voxels"""
title = imp.getTitle();
cal = imp.getCalibration();
if info is None:
pix_w = cal.pixelWidth;
pix_h = cal.pixelHeight;
pix_d = cal.pixelDepth;
else:
pix_w = info.get_xy_pixel_size_um();
pix_h = pix_w;
pix_d = info.get_z_plane_spacing_um();
im_w = imp.getWidth();
im_h = imp.getHeight();
im_d = imp.getNSlices();
print("original pixel whd = ({}, {}, {})".format(pix_w, pix_h, pix_d));
print("original image whd = ({}, {}, {})".format(im_w, im_h, im_d));
im_nch = imp.getNChannels();
if im_nch > 1:
split_ch = ChannelSplitter().split(imp);
else:
split_ch = [imp];
print("downsampling {} and making isotropic...".format(title));
IJ.showStatus("Downsampling and making ~isotropic...");
xy_scale = pix_h / (pix_d * extra_downsample_factor);
xy_scaled_h = int(xy_scale * im_h);
xy_scaled_w = int(xy_scale * im_w);
z_scale = 1/ extra_downsample_factor;
z_scaled_h = int(z_scale * im_d);
out_imps = [];
for ch_imp in split_ch:
print(ch_imp.getTitle());
sp = StackProcessor(ch_imp.getStack());
print((xy_scaled_w, xy_scaled_h));
stack = sp.resize(xy_scaled_w, xy_scaled_h, True);
xz_stack = rot_around_x(stack);
xz_sp = StackProcessor(xz_stack);
xz_stack = xz_sp.resize(xy_scaled_w, z_scaled_h, True);
out_stack = rot_around_x(xz_stack);
out_imps.append(ImagePlus("Isotropic downsampled {}".format(title), out_stack));
cal.setUnit('um');
cal.pixelWidth = im_w/xy_scaled_w * pix_w;
cal.pixelHeight = im_h/xy_scaled_h * pix_h;
cal.pixelDepth = im_d/z_scaled_h * pix_d;
print("new pixel whd = ({}, {}, {})".format(cal.pixelWidth, cal.pixelHeight, cal.pixelDepth));
imp.changes = False;
imp.close();
for ch_imp in split_ch:
ch_imp.close();
if len(out_imps) > 1:
out_imp = RGBStackMerge().mergeChannels(out_imps, False);
else:
out_imp = out_imps[0];
out_imp.setCalibration(cal);
print("new image whd = ({}, {}, {})".format(out_imp.getWidth(), out_imp.getHeight(), out_imp.getNSlices()));
print("...done downsampling {} and making isotropic. ".format(title));
IJ.showStatus("...done downsampling and making ~isotropic. ");
return out_imp;
def download_from_url(download_url,
target_dir,
download_file=None,
download_msg=None):
'''
download file in temporary location
move to target_dir
clean up download
'''
from ij import IJ
print(download_url)
# open url and set up using header information
u = urllib2.urlopen(download_url)
headers = u.info()
download_size = int(headers['Content-Length'])
print(u)
print(headers)
if download_file == None:
if headers.has_key('Content-Disposition'):
download_file = re.sub(".*filename=", "",
headers['Content-Disposition'])
else:
IJ.error(
"No filename specified for download and none in http header!")
if download_msg == None:
download_msg = 'Downloading: %s' % (download_file)
tf = tempfile.NamedTemporaryFile(suffix=download_file, delete=False)
print 'Downloading ' + download_url + ' to ' + tf.name
print "Download size should be %d" % (download_size)
dest_file = os.path.join(target_dir, download_file)
print 'Destination location %s' % (dest_file)
# Now for the download
block_size = 100000
if download_size > block_size:
bytes_read = 0
while bytes_read < download_size:
IJ.showStatus("%s (%.1f/%.1f Mb)" % (download_msg,
(bytes_read / 1000000.0),
(download_size / 1000000.0)))
IJ.showProgress(bytes_read, download_size)
tf.file.write(u.read(block_size))
bytes_read += block_size
IJ.showProgress(1.0)
else:
tf.file.write(u.read())
u.close()
tf.file.close()
print('Downloaded file has size %d') % (os.path.getsize(tf.name))
tf.close()
shutil.move(tf.name, dest_file)
IJ.showStatus('Cleaning up!')
def __init__(self, download = True):
'''
Display the list of project descriptions in a non-modal dialog.
'''
super(ProjectDialog, self).__init__(self)
self.biaflows = ConnectionWindow.getInstance().getBiaflows()
IJ.showStatus('Connecting to: ' + self.biaflows.getHost() + " - please stand by...")
self.download = download
self.eventHandler = ProjectDialogEventHandler('BIAFlows', self.getHTML(), False)
def run(title):
gd = GenericDialog('Record Desktop')
gd.addNumericField('Max. frames:', 50, 0)
gd.addNumericField('Milisecond interval:', 300, 0)
gd.addSlider('Start in (seconds):', 0, 20, 5)
gd.showDialog()
if gd.wasCanceled():
return
n_frames = int(gd.getNextNumber())
interval = gd.getNextNumber() / 1000.0 # in seconds
delay = int(gd.getNextNumber())
snaps = []
try:
while delay > 0:
IJ.showStatus('Starting in ' + str(delay) + 's.')
time.sleep(1) # one second
delay -= 1
IJ.showStatus('')
System.out.println("Starting...")
# start capturing
robot = Robot()
box = Rectangle(IJ.getScreenSize())
start = System.currentTimeMillis() / 1000.0 # in seconds
last = start
intervals = []
real_interval = 0
# Initial shot
snaps.append(robot.createScreenCapture(box))
while len(snaps) < n_frames and last - start < n_frames * interval:
now = System.currentTimeMillis() / 1000.0 # in seconds
real_interval = now - last
if real_interval >= interval:
last = now
snaps.append(robot.createScreenCapture(box))
intervals.append(real_interval)
else:
time.sleep(interval / 5) # time in seconds
# Create stack
System.out.println("End")
awt = snaps[0]
stack = ImageStack(awt.getWidth(None), awt.getHeight(None), None)
t = 0
for snap, real_interval in zip(snaps, intervals):
stack.addSlice(str(IJ.d2s(t, 3)),
ImagePlus('', snap).getProcessor())
snap.flush()
t += real_interval
ImagePlus("Desktop recording", stack).show()
except Exception, e:
print "Some error ocurred:"
print e
for snap in snaps:
snap.flush()
def run(title):
gd = GenericDialog("Record Desktop")
gd.addNumericField("Max. frames:", 50, 0)
gd.addNumericField("Milisecond interval:", 300, 0)
gd.addSlider("Start in (seconds):", 0, 20, 5)
gd.showDialog()
if gd.wasCanceled():
return
n_frames = int(gd.getNextNumber())
interval = gd.getNextNumber() / 1000.0 # in seconds
delay = int(gd.getNextNumber())
snaps = []
try:
while delay > 0:
IJ.showStatus("Starting in " + str(delay) + "s.")
time.sleep(1) # one second
delay -= 1
IJ.showStatus("")
System.out.println("Starting...")
# start capturing
robot = Robot()
box = Rectangle(IJ.getScreenSize())
start = System.currentTimeMillis() / 1000.0 # in seconds
last = start
intervals = []
real_interval = 0
# Initial shot
snaps.append(robot.createScreenCapture(box))
while len(snaps) < n_frames and last - start < n_frames * interval:
now = System.currentTimeMillis() / 1000.0 # in seconds
real_interval = now - last
if real_interval >= interval:
last = now
snaps.append(robot.createScreenCapture(box))
intervals.append(real_interval)
else:
time.sleep(interval / 5) # time in seconds
# Create stack
System.out.println("End")
awt = snaps[0]
stack = ImageStack(awt.getWidth(None), awt.getHeight(None), None)
t = 0
for snap, real_interval in zip(snaps, intervals):
stack.addSlice(str(IJ.d2s(t, 3)), ImagePlus("", snap).getProcessor())
snap.flush()
t += real_interval
ImagePlus("Desktop recording", stack).show()
except Exception, e:
print "Some error ocurred:"
print e
for snap in snaps:
snap.flush()
def rot3d(imp, axis='x'):
"""pare back Slicer to implement whole-image, +90* rotations that return ImagePlus"""
if imp.getType()==ImagePlus.COLOR_256 or imp.getType()==ImagePlus.COLOR_RGB:
raise NotImplementedError("Handling of colour images isn't implemented yet");
IJ.showStatus("Rotating around {}-axis...".format(axis))
title = imp.getTitle();
original_cal = imp.getCalibration();
new_cal = original_cal;
if imp.getNChannels > 1:
split_ch = ChannelSplitter().split(imp);
else:
split_ch = [imp];
out_imps = [];
if axis=='x':
for ch_imp in split_ch:
input_stack = ch_imp.getStack();
output_stack = rot_around_x(input_stack);
out_imps.append(ImagePlus(title, output_stack));
new_cal.pixelHeight = original_cal.pixelDepth;
new_cal.pixelDepth = original_cal.pixelHeight;
elif axis=='y' or axis=='-y':
for ch_imp in split_ch:
if axis[0]=='-':
input_stack = StackProcessor(ch_imp.getStack()).rotateLeft();
else:
input_stack = StackProcessor(ch_imp.getStack()).rotateRight();
output_stack = rot_around_x(input_stack);
if axis[0]=='-':
final_stack = StackProcessor(output_stack).rotateLeft();
else:
final_stack = StackProcessor(output_stack).rotateRight();
out_imps.append(ImagePlus(title, final_stack));
new_cal.pixelWidth = original_cal.pixelDepth;
new_cal.pixelDepth = original_cal.pixelWidth;
elif axis=='z' or axis=='-z':
for ch_imp in split_ch:
if axis[0]=='-':
output_stack = StackProcessor(ch_imp.getStack()).rotateLeft();
else:
output_stack = StackProcessor(ch_imp.getStack()).rotateRight();
out_imps.append(ImagePlus(title, output_stack));
new_cal.pixelWidth = original_cal.pixelHeight;
new_cal.pixelHeight = original_cal.pixelWidth;
else:
raise NotImplementedError("Please check which axis you've chosen - if not (x, +/-y, +/-z) then it's not implemented...");
imp.changes = False;
imp.close();
if len(out_imps) > 1:
out_imp = RGBStackMerge().mergeChannels(out_imps, False);
else:
out_imp = out_imps[0];
out_imp.setCalibration(new_cal);
return out_imp;
def concatenateImagePlus(files, outfile):
"""Concatenate images contained in files and save in outfile"""
options = ImporterOptions()
options.setId(files[0])
options.setVirtual(1)
options.setOpenAllSeries(1)
options.setQuiet(1)
images = BF.openImagePlus(options)
imageG = images[0]
nrPositions = len(images)
options.setOpenAllSeries(0)
nslices = imageG.getNSlices()
nframes = len(files)
nchannels = imageG.getNChannels()
luts = imageG.getLuts()
for i in range(0, nrPositions):
concatImgPlus = IJ.createHyperStack(
"ConcatFile", imageG.getWidth(), imageG.getHeight(),
imageG.getNChannels(), imageG.getNSlices(),
len(files), imageG.getBitDepth())
concatStack = ImageStack(imageG.getWidth(), imageG.getHeight())
IJ.showStatus("Concatenating files")
for file_ in files:
try:
print '...', basename(file_)
options.setSeriesOn(i, 1)
options.setId(file_)
image = BF.openImagePlus(options)[0]
imageStack = image.getImageStack()
sliceNr = imageStack.getSize()
for j in range(1, sliceNr+1):
concatStack.addSlice(imageStack.getProcessor(j))
image.close()
options.setSeriesOn(i, 0)
except Exception, e:
IJ.log("ERROR")
IJ.log(file_ + str(e))
raise
IJ.showProgress(files.index(file_), len(files))
concatImgPlus.setStack(concatStack, nchannels, nslices, nframes)
concatImgPlus.setCalibration(image.getCalibration())
concatImgPlus.setOpenAsHyperStack(True)
concatImgPlus.setLuts(luts)
concatImgPlus.close()
IJ.saveAs(concatImgPlus, "Tiff", outfile)
def itemStateChanged(self,e):
theRoi = self.theImage.getRoi()
if (theRoi is not None):
if (e.getStateChange() == ItemEvent.SELECTED):
self.theImage.deleteRoi()
backupImage = self.theImage.duplicate()
self.theImage.setRoi(theRoi)
outputImage = self.theImage.duplicate()
for i in range(1,self.theImage.getNSlices()):
self.theImage.setSliceWithoutUpdate(i)
ip = self.theImage.getProcessor()
ip.setValue(0)
ip.fillOutside(theRoi)
self.theImage.updateAndDraw()
params = ("volume surface nb_of_obj._voxels " +
"nb_of_surf._voxels integrated_density mean_gray_value " +
"std_dev_gray_value median_gray_value minimum_gray_value " +
"maximum_gray_value centroid mean_distance_to_surface " +
"std_dev_distance_to_surface median_distance_to_surface centre_of_mass " +
"bounding_box dots_size=5 font_size=10 show_numbers white_numbers " +
"redirect_to=none")
IJ.run("3D OC Options", params)
params = ("threshold=" + str(self.thresholdSlider.getValue()) +
" slice=1 min.=" + self.sizeText.getText() + " max.=24903680 surfaces statistics")
print params
self.theImage.resetDisplayRange()
self.theImage.updateAndDraw()
IJ.run(self.theImage, "3D Objects Counter", params)
self.theImage.setImage(backupImage)
self.theImage.updateAndRepaintWindow()
surfacesImage = WindowManager.getImage("Surface map of " + self.theImage.getTitle())
surfacesImage.setRoi(theRoi)
surfacesImageCut = surfacesImage.duplicate()
IJ.run(surfacesImageCut,"8-bit","")
surfacesImageCut = make_image_binary(surfacesImageCut)
surfacesImageCut.show()
outputImage.show()
surfacesImage.close()
self.theImage.setSlice(self.theImage.getNSlices()/2)
IJ.run("Merge Channels...", "c2=[" + outputImage.getTitle() + "] c6=[" + surfacesImageCut.getTitle() + "] create ignore")
self.workRoiCheckbox.setState(False)
else:
IJ.showStatus("Select freeform ROI to operate on, or delete to operate on whole image")
else:
IJ.showStatus("Need to pick an ROI first before running this option")
self.workRoiCheckbox.setState(False)
def concatenateImagePlus(files, outfile):
"""concatenate images contained in files and save in outfile"""
'''
if len(files) == 1:
IJ.log(files[0] + " has only one time point! Nothing to concatenate!")
return
'''
options = ImporterOptions()
options.setId(files[0])
options.setVirtual(1)
options.setOpenAllSeries(1)
options.setQuiet(1)
images = BF.openImagePlus(options)
imageG = images[0]
nrPositions = len(images)
options.setOpenAllSeries(0)
for i in range(0, nrPositions):
concatImgPlus = IJ.createHyperStack("ConcatFile", imageG.getWidth(), imageG.getHeight(), imageG.getNChannels(), imageG.getNSlices(), len(files), imageG.getBitDepth())
concatStack = ImageStack(imageG.getWidth(), imageG.getHeight())
IJ.showStatus("Concatenating files")
for file in files:
try:
IJ.log(" Add file " + file)
options.setSeriesOn(i,1)
options.setId(file)
image = BF.openImagePlus(options)[0]
imageStack = image.getImageStack()
sliceNr = imageStack.getSize()
for j in range(1, sliceNr+1):
concatStack.addSlice(imageStack.getProcessor(j))
image.close()
options.setSeriesOn(i,0)
except:
traceback.print_exc()
IJ.log(file + " failed to concatenate!")
IJ.showProgress(files.index(file), len(files))
concatImgPlus.setStack(concatStack)
concatImgPlus.setCalibration(image.getCalibration())
if len(images) > 1:
outfileP = addPositionName(i+1,outfile)
IJ.saveAs(concatImgPlus, "Tiff", outfileP)
else:
IJ.saveAs(concatImgPlus, "Tiff", outfile)
concatImgPlus.close()
def itemStateChanged(self,e):
imgList = []
imgList.append(virginImage)
for i in range(len(checkboxObjects)):
if checkboxObjects[i].getState() == True:
imgList.append(self.boxImages[i])
titles = WindowManager.getImageTitles()
p = re.compile(r'^Result')
for title in titles:
m = p.search(title)
if m is not None:
computedImage = WindowManager.getImage(title)
computedImage.close()
IJ.showStatus("Computing...")
computedImage = reduce(self.addImages,imgList)
computedImage.show()
IJ.showStatus("Ready")
def download_and_untar_url(download_url,target_dir,untarfun,download_file=None,
download_msg=None):
'''
download file in temporary location
untar to target_dir using untarfun
clean up download
'''
# open url and set up using header information
u = urllib2.urlopen(download_url)
headers = u.info()
download_size = int(headers['Content-Length'])
if download_file == None:
if headers.has_key('Content-Disposition'):
download_file = re.sub(".*filename=","",headers['Content-Disposition'])
else:
myErr("No filename specified for download and none in http header!")
if download_msg==None:
download_msg='Downloading: %s' % (download_file)
tf=tempfile.NamedTemporaryFile(suffix=download_file)
print 'Downloading '+download_url+' to '+ tf.name
print "Download size should be %d" % (download_size)
from ij import IJ
# Now for the download
block_size=100000
if download_size>block_size:
bytes_read=0
while bytes_read<download_size:
IJ.showStatus("%s (%.1f/%.1f Mb)" %
(download_msg,(bytes_read/1000000.0),(download_size/1000000.0)))
IJ.showProgress(bytes_read,download_size)
tf.file.write(u.read(block_size))
bytes_read+=block_size
IJ.showProgress(1.0)
else:
tf.file.write(u.read())
u.close()
tf.file.close()
print ('Downloaded file has size %d')%(os.path.getsize(tf.name))
untarfun(tf.name,target_dir)
IJ.showStatus('Cleaning up!')
tf.close()
def stack_median_filter(imp, radius_um=5.0):
"""perform 2D median filtering slicewise on a stack"""
t1 = datetime.now();
stack = imp.getStack();
title = imp.getTitle();
n_z = imp.getNSlices();
progress_inc = 1 if n_z/20 < 1 else n_z/20;
filt = RankFilters();
for idx in range(n_z):
#print("Median filtering stack, {} % complete...".format(100 * round(float(zidx)/n_z, 3)));
ip = stack.getProcessor(idx+1);
filt.rank(ip, radius_um, RankFilters.MEDIAN);
IJ.showProgress(float(idx)/n_z);
if idx%progress_inc==0:
IJ.showStatus("Median filtering stack in 2D: {}/{}".format(idx, n_z));
imp.updateAndDraw();
imp.setTitle("Median filtered (r={}) {}".format(radius_um, imp.getTitle()).replace(".tif", ""));
t2 = datetime.now();
IJ.showProgress(1.0);
print("Median filtering took {} s".format((t2-t1).total_seconds()));
return imp;
def keyPressed(self, event):
try:
dx, dy, dz = self.delta.get(event.getKeyCode(), (0, 0, 0))
if dx + dy + dz == 0:
return
syncPrintQ("Translating source")
if event.isShiftDown():
dx *= self.shift
dy *= self.shift
dz *= self.shift
if event.isAltDown():
dx *= self.alt
dy *= self.alt
dz *= self.alt
syncPrintQ("... by x=%i, y=%i, z=%i" % (dx, dy, dz))
x, y, z = self.translatable.translate(dx, dy, dz)
IJ.showStatus("[x=%i y=%i z=%i]" %
(x, y, z + 1)) # 1-based stack index
self.imp.updateAndDraw()
event.consume()
except:
printException()
def getProjectData(self):
'''
Retrieve the project data of all available projects from the BIAFLOWS server.
'''
projects = ProjectCollection().fetch()
projectData = []
for i in range(0, projects.size()):
if (i%2):
IJ.showStatus('Connecting to: ' + self.biaflows.getHost() + " - please stand by.../")
else:
IJ.showStatus('Connecting to: ' + self.biaflows.getHost() + " - please stand by...\\")
project = projects.get(i)
name = project.get("name")
pId = project.get('id')
try:
text = Description().fetch(project).get('data')
text = self.downloadThumbnailsAndReplaceLinks(text)
message = '\n' + '<h1>' + name + '</h1>'
message = message + '\n' + text
projectData.append({'id': pId, 'name': name, 'message': message})
except CytomineException, e:
print(e.getMessage())
continue
def robust_convertStackToGrayXbit(imp, x=8, normalise=False):
"""simplified from https://github.com/imagej/imagej1/blob/master/ij/process/StackConverter.java,
avoiding complications of scaling based on LUT taken from the current frame. Assumes conversion
from grayscale image"""
if x!=8 and x!=16 and x!=32:
raise NotImplementedError("can't convert to the specified bit depth");
if imp.getBitDepth()==x:
return imp;
if normalise:
stats = StackStatistics(imp);
offset = stats.min;
maxtomin = stats.max - stats.min;
IJ.run(imp, "Subtract...", "value={} stack".format(offset));
IJ.run(imp, "Multiply...", "value={} stack".format(float(2**x - 1)/maxtomin));
current_slice = imp.getCurrentSlice();
stack = imp.getStack();
out_stack = ImageStack(imp.getWidth(), imp.getHeight());
n_z = imp.getNSlices();
progress_inc = 1 if n_z/20 < 1 else n_z/20;
for idx in range(n_z):
# always use 1 as old stack index since we remove a slice at each iteration
label = stack.getSliceLabel(1);
ip = stack.getProcessor(1);
stack.deleteSlice(1);
if x==8:
out_stack.addSlice(label, ip.convertToByte(False));
elif x==16:
out_stack.addSlice(label, ip.convertToShort(False));
elif x==32:
out_stack.addSlice(label, ip.convertToFloat());
IJ.showProgress(float(idx)/n_z);
if idx%progress_inc==0:
IJ.showStatus("Converting stack to {}-bits: {}/{}".format(x, idx, n_z));
imp.setStack(out_stack);
IJ.showProgress(1.0);
imp.setSlice(current_slice);
return imp;
def regBf(fn=None, imp=None, refId=None):
"""
Register a time series stack to a specified reference slice,
from a file (imported by BioFormat) or a stack ImagePlus.
Returns a registered ImagePlus.
The stack must have only 1 z layer.
refId is in the format of [int channel, int slice, int frame]
If no refId is supplied, will use the first slice [1,1,1]
Note: since TurboReg is used for registeration, there will be
temporary opened image windows.
"""
## Prepare the right ImagePlus
if imp is None:
if fn is None:
od = OpenDialog("Choose a file", None)
filename = od.getFileName()
if filename is None:
print "User canceled the dialog!"
return
else:
directory = od.getDirectory()
filepath = directory + filename
print "Selected file path:", filepath
else:
if os.path.exists(fn) and os.path.isfile(fn):
filepath = fn
else:
print "File does not exist!"
return
imps = BF.openImagePlus(filepath)
imp = imps[0]
if imp is None:
print "Cannot load file!"
return
else:
if fn is not None:
print "File or ImagePlus? Cannot load both."
return
width = imp.getWidth()
height = imp.getHeight()
# C
nChannels = imp.getNChannels()
# Z
nSlices = imp.getNSlices()
# T
nFrames = imp.getNFrames()
# pixel size
calibration = imp.getCalibration()
# Only supoort one z layer
if nSlices != 1:
print "Only support 1 slice at Z dimension."
return
# set registration reference slice
if refId is None:
refC = 1
refZ = 1
refT = 1
else:
refC = refId[0]
refZ = refId[1]
refT = refId[2]
if (refC not in range(1, nChannels+1) or
refZ not in range(1, nSlices+1) or
refT not in range(1, nFrames+1) ):
print "Invalid reference image!"
return
stack = imp.getImageStack()
registeredStack = ImageStack(width, height, nChannels*nFrames*nSlices)
# setup windows, these are needed by TurboReg
tmpip = FloatProcessor(width, height)
refWin = ImageWindow(ImagePlus("ref", tmpip))
bounds = refWin.getBounds()
# refWin.setVisible(False)
toRegWin = ImageWindow(ImagePlus("toReg", tmpip))
toRegWin.setLocation(bounds.width + bounds.x, bounds.y)
# toRegWin.setVisible(False)
toTransformWin = ImageWindow(ImagePlus("toTransform", tmpip))
toTransformWin.setLocation(2 * bounds.width + bounds.x, bounds.y)
# toTransformWin.setVisible(False)
# get reference image
refImp = ImagePlus("ref", stack.getProcessor(imp.getStackIndex(refC, refZ, refT)))
refWin.setImage(refImp)
tr = TurboReg_()
for t in xrange(1, nFrames+1):
IJ.showProgress(t-1, nFrames)
# print "t ", t
# do TurboReg on reference channel
toRegId = imp.getStackIndex(refC, refZ, t)
toRegImp = ImagePlus("toReg", stack.getProcessor(toRegId))
toRegWin.setImage(toRegImp)
regArg = "-align " +\
"-window " + toRegImp.getTitle() + " " +\
"0 0 " + str(width - 1) + " " + str(height - 1) + " " +\
"-window " + refImp.getTitle() + " " +\
"0 0 " + str(width - 1) + " " + str(height - 1) + " " +\
"-rigidBody " +\
str(width / 2) + " " + str(height / 2) + " " +\
str(width / 2) + " " + str(height / 2) + " " +\
"0 " + str(height / 2) + " " +\
"0 " + str(height / 2) + " " +\
str(width - 1) + " " + str(height / 2) + " " +\
str(width - 1) + " " + str(height / 2) + " " +\
"-hideOutput"
tr = TurboReg_()
tr.run(regArg)
registeredImp = tr.getTransformedImage()
sourcePoints = tr.getSourcePoints()
targetPoints = tr.getTargetPoints()
registeredStack.setProcessor(registeredImp.getProcessor(), toRegId)
# toRegImp.flush()
# apply transformation on other channels
for c in xrange(1, nChannels+1):
# print "c ", c
if c == refC:
continue
toTransformId = imp.getStackIndex(c, 1, t)
toTransformImp = ImagePlus("toTransform", stack.getProcessor(toTransformId))
toTransformWin.setImage(toTransformImp)
transformArg = "-transform " +\
"-window " + toTransformImp.getTitle() + " " +\
str(width) + " " + str(height) + " " +\
"-rigidBody " +\
str(sourcePoints[0][0]) + " " +\
str(sourcePoints[0][1]) + " " +\
str(targetPoints[0][0]) + " " +\
str(targetPoints[0][1]) + " " +\
str(sourcePoints[1][0]) + " " +\
str(sourcePoints[1][1]) + " " +\
str(targetPoints[1][0]) + " " +\
str(targetPoints[1][1]) + " " +\
str(sourcePoints[2][0]) + " " +\
str(sourcePoints[2][1]) + " " +\
str(targetPoints[2][0]) + " " +\
str(targetPoints[2][1]) + " " +\
"-hideOutput"
tr = TurboReg_()
tr.run(transformArg)
registeredStack.setProcessor(tr.getTransformedImage().getProcessor(), toTransformId)
# toTransformImp.flush()
sourcePoints = None
targetPoints = None
IJ.showProgress(t, nFrames)
IJ.showStatus("Frames registered: " + str(t) + "/" + str(nFrames))
refWin.close()
toRegWin.close()
toTransformWin.close()
imp2 = ImagePlus("reg_"+imp.getTitle(), registeredStack)
imp2.setCalibration(imp.getCalibration().copy())
imp2.setDimensions(nChannels, nSlices, nFrames)
# print "type ", imp.getType()
# print "type ", imp2.getType()
# print nChannels, " ", nSlices, " ", nFrames
# print registeredStack.getSize()
for key in imp.getProperties().stringPropertyNames():
imp2.setProperty(key, imp.getProperty(key))
# comp = CompositeImage(imp2, CompositeImage.COLOR)
# comp.show()
# imp2 = imp.clone()
# imp2.setStack(registeredStack)
# imp2.setTitle("reg"+imp.getTitle())
# imp2.show()
# imp.show()
return imp2
try:
download_url='https://github.com/jefferis/fiji-cmtk-gui/tarball/master'
# check date
installed_version='NA'
local_version_info=cmtkgui.gui_local_versioninfo()
if local_version_info.has_key('date'):
installed_version=local_version_info['date']
github_version_info=cmtkgui.gui_github_versioninfo()
update_available=cmtkgui.gui_update_available(github_version_info)
gd = GenericDialogPlus('Update CMTK GUI')
if update_available:
gd.addMessage('CMTK GUI update available')
gd.setOKLabel("Download")
else:
gd.addMessage('CMTK GUI is up to date')
gd.addMessage('Currently installed CMTK GUI version: '+installed_version)
gd.showDialog()
if gd.wasOKed() and update_available:
# nb url has a suffix to indicate that user agreed to license
from ij import IJ
IJ.showStatus('Downloading CMTK GUI')
cmtkgui.download_and_untar_url(download_url,cmtkgui.gui_install_dir(),untar_github_archive)
cmtkgui.gui_write_local_versioninfo(github_version_info)
except SystemExit, e:
from ij import IJ
IJ.showStatus(str(e))
regparams = gd.getNextChoice()
print regparams
regparams = gd.getNextString()
mungeropts = gd.getNextString()
action = gd.getNextChoice()
if action == 'Test': mungeropts += ' -t'
if verbose: mungeropts += ' -v'
mungeropts += ' -T %d' % (int(corestouse))
if not outsuffix == '':
mungeropts += ' -d .' + outsuffix
cmd = '"%s" -b "%s" %s %s %s -s "%s" %s' % (
munger, bindir, munger_actions, regparams, mungeropts, refBrain, image)
print cmd
if action != 'Test':
# make a script
script = makescript(cmd,
rootDir,
outdir=os.path.join(rootDir, 'commands'))
print 'script is %s' % (script)
if action != 'Write Script':
# Actually run the script
subprocess.call(script, shell=False)
except SystemExit, e:
from ij import IJ
IJ.showStatus(str(e))
def run(title):
gd = GenericDialog("Record Window")
gd.addMessage("Maximum number of frames to record.\nZero means infinite, interrupt with ESC key.")
gd.addNumericField("Max. frames:", 50, 0)
gd.addNumericField("Milisecond interval:", 300, 0)
gd.addSlider("Start in (seconds):", 0, 20, 5)
frames = []
titles = []
for f in Frame.getFrames():
if f.isEnabled() and f.isVisible():
frames.append(f)
titles.append(f.getTitle())
gd.addChoice("Window:", titles, titles[0])
gd.addCheckbox("To file", False)
gd.showDialog()
if gd.wasCanceled():
return
n_frames = int(gd.getNextNumber())
interval = gd.getNextNumber() / 1000.0 # in seconds
frame = frames[gd.getNextChoiceIndex()]
delay = int(gd.getNextNumber())
tofile = gd.getNextBoolean()
dir = None
if tofile:
dc = DirectoryChooser("Directory to store image frames")
dir = dc.getDirectory()
if dir is None:
return # dialog canceled
snaps = []
borders = None
executors = Executors.newFixedThreadPool(1)
try:
while delay > 0:
IJ.showStatus("Starting in " + str(delay) + "s.")
time.sleep(1) # one second
delay -= 1
IJ.showStatus("Capturing frame borders...")
bounds = frame.getBounds()
robot = Robot()
frame.toFront()
time.sleep(0.5) # half a second
borders = robot.createScreenCapture(bounds)
IJ.showStatus("Recording " + frame.getTitle())
# Set box to the inside borders of the frame
insets = frame.getInsets()
box = bounds.clone()
box.x = insets.left
box.y = insets.top
box.width -= insets.left + insets.right
box.height -= insets.top + insets.bottom
start = System.currentTimeMillis() / 1000.0 # in seconds
last = start
intervals = []
real_interval = 0
i = 1
fus = None
if tofile:
fus = []
# 0 n_frames means continuous acquisition
while 0 == n_frames or (len(snaps) < n_frames and last - start < n_frames * interval):
now = System.currentTimeMillis() / 1000.0 # in seconds
real_interval = now - last
if real_interval >= interval:
last = now
img = snapshot(frame, box)
if tofile:
fus.append(executors.submit(Saver(i, dir, bounds, borders, img, insets))) # will flush img
i += 1
else:
snaps.append(img)
intervals.append(real_interval)
else:
time.sleep(interval / 5)
# interrupt capturing:
if IJ.escapePressed():
IJ.showStatus("Recording user-interrupted")
break
# debug:
# print "insets:", insets
# print "bounds:", bounds
# print "box:", box
# print "snap dimensions:", snaps[0].getWidth(), snaps[0].getHeight()
# Create stack
stack = None
if tofile:
for fu in snaps:
fu.get() # wait on all
stack = VirtualStack(bounds.width, bounds.height, None, dir)
files = File(dir).list(TifFilter())
Arrays.sort(files)
for f in files:
stack.addSlice(f)
else:
stack = ImageStack(bounds.width, bounds.height, None)
t = 0
for snap, real_interval in zip(snaps, intervals):
bi = BufferedImage(bounds.width, bounds.height, BufferedImage.TYPE_INT_RGB)
g = bi.createGraphics()
g.drawImage(borders, 0, 0, None)
g.drawImage(snap, insets.left, insets.top, None)
stack.addSlice(str(IJ.d2s(t, 3)), ImagePlus("", bi).getProcessor())
t += real_interval
snap.flush()
bi.flush()
borders.flush()
ImagePlus(frame.getTitle() + " recording", stack).show()
IJ.showStatus("Done recording " + frame.getTitle())
except Exception, e:
print "Some error ocurred:"
print e.printStackTrace()
IJ.showStatus("")
if borders is not None:
borders.flush()
for snap in snaps:
snap.flush()
# Create a CSV table documenting processed files
csvPath = out_dir + "_ProcessedFileList.csv"
csvExists = os.path.exists(csvPath)
csvFile = open(csvPath, 'a')
csvWriter = csv.writer(csvFile)
# Specify column headings
if not csvExists:
headers = ['Original path','Processed path']
csvWriter.writerow(headers)
# Process list of images
for (counter, f) in enumerate(files):
# Display progress
IJ.showStatus("Processing file "+ str(counter+1) +"/"+ str(len(files)))
# Open each image and process it
imp = IJ.openImage(f)
myRoutines(imp)
# Save processed image in out_dir (enforcing .tif extension)
newpath = os.path.splitext(out_dir + imp.getTitle())[0] +".tif"
IJ.saveAsTiff(imp, newpath)
imp.close()
# Log paths of processed files
csvWriter.writerow([f, newpath])
# Display CSV log
csvFile.close()
ratio_rec_str = "%.3f" % ratio_rec
gd.addMessage(str(i+1)+"-channel: " + str(mem_recs[i]) + "MB; Ratio: " + ratio_rec_str)
gd.showDialog()
ratioRaw = gd.getNextNumber()
ratio = math.sqrt(ratioRaw)
if (gd.wasOKed()):
filecollection = glob.glob(os.path.join(sourceDir, '*.ome.tif'))
numFiles = len(filecollection)
count = 1
for f in filecollection:
bname1 = os.path.basename(f)
bname2 = os.path.splitext(bname1)[0]
bname3 = os.path.splitext(bname2)[0]
print bname3
params = "open=[" + f + "] color_mode=Default view=Hyperstack stack_order=XYCZT"
IJ.run("Bio-Formats Importer",params)
theImage = WindowManager.getCurrentImage()
params2 = "x=" + str(ratio) + " y=" + str(ratio) + " z=1.0 interpolation=Bilinear average process create title=doggie"
IJ.run(theImage,"Scale...",params2)
theImage.close()
saveImage = WindowManager.getImage("doggie")
savePath = sourceDir+"resized/"+bname3+".tif"
IJ.saveAsTiff(saveImage,sourceDir+"resized/"+bname3+".tif")
saveImage.close()
IJ.showStatus("Tile: " + str(count) + "/" + str(numFiles))
count = count + 1
ys = find_tile_range(ymin,ymax,rowStarts)
tiles = make_tile_series(xs,ys,xtiles,ytiles)
print tiles
# Copies tiles for stitching into temp directory and stitches, if necessary
if len(tiles)==1:
params = "open=["+ imgDir +"tile_"+str(tiles[0])+".ome.tif] color_mode=Default view=Hyperstack stack_order=XYCZT"
IJ.run("Bio-Formats Importer", params);
tileImage = WindowManager.getImage("tile_"+str(tiles[0])+".ome.tif")
tileImage.setSlice(int(tileImage.getNSlices()/2))
else:
ind = 1
for t in tiles:
shutil.copyfile(imgDir+"tile_"+str(t)+".ome.tif",imgDir+"temp/tile_"+str(ind)+".ome.tif")
ind = ind + 1
IJ.showStatus("Beginning stitch...")
params = "type=[Grid: row-by-row] order=[Right & Down ] grid_size_x=" + str(xs[2]) + " grid_size_y=" + str(ys[2]) + " tile_overlap=10 first_file_index_i=1 directory=[" + imgDir + "temp] file_names=tile_{i}.ome.tif output_textfile_name=TileConfiguration.txt fusion_method=[Linear Blending] regression_threshold=0.30 max/avg_displacement_threshold=2.50 absolute_displacement_threshold=3.50 compute_overlap ignore_z_stage subpixel_accuracy computation_parameters=[Save memory (but be slower)] image_output=[Fuse and display]"
IJ.run("Grid/Collection stitching", params)
fusedImage = WindowManager.getImage("Fused")
IJ.saveAsTiff(fusedImage,imgDir+"temp/Fused.tif")
fusedImage.close()
IJ.open(imgDir+"temp/Fused.tif")
tileImage = WindowManager.getImage("Fused.tif")
tileImage.setSlice(int(tileImage.getNSlices()/2))
gd = NonBlockingGenericDialog("Explore full resolution...")
gd.addMessage("Select ROI for visualization at full resolution")
gd.showDialog()
doContinue = gd.wasOKed()
##### Removes temporary tile files ######
def run(title):
gd = GenericDialog('Record Window')
gd.addMessage(
"Maximum number of frames to record.\nZero means infinite, interrupt with ESC key."
)
gd.addNumericField('Max. frames:', 50, 0)
gd.addNumericField('Milisecond interval:', 300, 0)
gd.addSlider('Start in (seconds):', 0, 20, 5)
frames = []
titles = []
for f in Frame.getFrames():
if f.isEnabled() and f.isVisible():
frames.append(f)
titles.append(f.getTitle())
gd.addChoice('Window:', titles, titles[0])
gd.addCheckbox("To file", False)
gd.showDialog()
if gd.wasCanceled():
return
n_frames = int(gd.getNextNumber())
interval = gd.getNextNumber() / 1000.0 # in seconds
frame = frames[gd.getNextChoiceIndex()]
delay = int(gd.getNextNumber())
tofile = gd.getNextBoolean()
dir = None
if tofile:
dc = DirectoryChooser("Directory to store image frames")
dir = dc.getDirectory()
if dir is None:
return # dialog canceled
snaps = []
borders = None
executors = Executors.newFixedThreadPool(1)
try:
while delay > 0:
IJ.showStatus('Starting in ' + str(delay) + 's.')
time.sleep(1) # one second
delay -= 1
IJ.showStatus('Capturing frame borders...')
bounds = frame.getBounds()
robot = Robot()
frame.toFront()
time.sleep(0.5) # half a second
borders = robot.createScreenCapture(bounds)
IJ.showStatus("Recording " + frame.getTitle())
# Set box to the inside borders of the frame
insets = frame.getInsets()
box = bounds.clone()
box.x = insets.left
box.y = insets.top
box.width -= insets.left + insets.right
box.height -= insets.top + insets.bottom
start = System.currentTimeMillis() / 1000.0 # in seconds
last = start
intervals = []
real_interval = 0
i = 1
fus = None
if tofile:
fus = []
# 0 n_frames means continuous acquisition
while 0 == n_frames or (len(snaps) < n_frames
and last - start < n_frames * interval):
now = System.currentTimeMillis() / 1000.0 # in seconds
real_interval = now - last
if real_interval >= interval:
last = now
img = snapshot(frame, box)
if tofile:
fus.append(
executors.submit(
Saver(i, dir, bounds, borders, img,
insets))) # will flush img
i += 1
else:
snaps.append(img)
intervals.append(real_interval)
else:
time.sleep(interval / 5)
# interrupt capturing:
if IJ.escapePressed():
IJ.showStatus("Recording user-interrupted")
break
# debug:
#print "insets:", insets
#print "bounds:", bounds
#print "box:", box
#print "snap dimensions:", snaps[0].getWidth(), snaps[0].getHeight()
# Create stack
stack = None
if tofile:
for fu in snaps:
fu.get() # wait on all
stack = VirtualStack(bounds.width, bounds.height, None, dir)
files = File(dir).list(TifFilter())
Arrays.sort(files)
for f in files:
stack.addSlice(f)
else:
stack = ImageStack(bounds.width, bounds.height, None)
t = 0
for snap, real_interval in zip(snaps, intervals):
bi = BufferedImage(bounds.width, bounds.height,
BufferedImage.TYPE_INT_RGB)
g = bi.createGraphics()
g.drawImage(borders, 0, 0, None)
g.drawImage(snap, insets.left, insets.top, None)
stack.addSlice(str(IJ.d2s(t, 3)),
ImagePlus('', bi).getProcessor())
t += real_interval
snap.flush()
bi.flush()
borders.flush()
ImagePlus(frame.getTitle() + " recording", stack).show()
IJ.showStatus('Done recording ' + frame.getTitle())
except Exception, e:
print "Some error ocurred:"
print e.printStackTrace()
IJ.showStatus('')
if borders is not None: borders.flush()
for snap in snaps:
snap.flush()
def regBf(fn=None, imp=None, refId=None):
"""
Register a time series stack to a specified reference slice,
from a file (imported by BioFormat) or a stack ImagePlus.
Returns a registered ImagePlus.
The stack must have only 1 z layer.
refId is in the format of [int channel, int slice, int frame]
If no refId is supplied, will use the first slice [1,1,1]
Note: since TurboReg is used for registeration, there will be
temporary opened image windows.
"""
## Prepare the right ImagePlus
if imp is None:
if fn is None:
od = OpenDialog("Choose a file", None)
filename = od.getFileName()
if filename is None:
print "User canceled the dialog!"
return
else:
directory = od.getDirectory()
filepath = directory + filename
print "Selected file path:", filepath
else:
if os.path.exists(fn) and os.path.isfile(fn):
filepath = fn
else:
print "File does not exist!"
return
imps = BF.openImagePlus(filepath)
imp = imps[0]
if imp is None:
print "Cannot load file!"
return
else:
if fn is not None:
print "File or ImagePlus? Cannot load both."
return
width = imp.getWidth()
height = imp.getHeight()
# C
nChannels = imp.getNChannels()
# Z
nSlices = imp.getNSlices()
# T
nFrames = imp.getNFrames()
# pixel size
calibration = imp.getCalibration()
# Only supoort one z layer
if nSlices != 1:
print "Only support 1 slice at Z dimension."
return
# set registration reference slice
if refId is None:
refC = 1
refZ = 1
refT = 1
else:
refC = refId[0]
refZ = refId[1]
refT = refId[2]
if (refC not in range(1, nChannels + 1)
or refZ not in range(1, nSlices + 1)
or refT not in range(1, nFrames + 1)):
print "Invalid reference image!"
return
stack = imp.getImageStack()
registeredStack = ImageStack(width, height, nChannels * nFrames * nSlices)
# setup windows, these are needed by TurboReg
tmpip = FloatProcessor(width, height)
refWin = ImageWindow(ImagePlus("ref", tmpip))
bounds = refWin.getBounds()
# refWin.setVisible(False)
toRegWin = ImageWindow(ImagePlus("toReg", tmpip))
toRegWin.setLocation(bounds.width + bounds.x, bounds.y)
# toRegWin.setVisible(False)
toTransformWin = ImageWindow(ImagePlus("toTransform", tmpip))
toTransformWin.setLocation(2 * bounds.width + bounds.x, bounds.y)
# toTransformWin.setVisible(False)
# get reference image
refImp = ImagePlus("ref",
stack.getProcessor(imp.getStackIndex(refC, refZ, refT)))
refWin.setImage(refImp)
tr = TurboReg_()
for t in xrange(1, nFrames + 1):
IJ.showProgress(t - 1, nFrames)
# print "t ", t
# do TurboReg on reference channel
toRegId = imp.getStackIndex(refC, refZ, t)
toRegImp = ImagePlus("toReg", stack.getProcessor(toRegId))
toRegWin.setImage(toRegImp)
regArg = "-align " +\
"-window " + toRegImp.getTitle() + " " +\
"0 0 " + str(width - 1) + " " + str(height - 1) + " " +\
"-window " + refImp.getTitle() + " " +\
"0 0 " + str(width - 1) + " " + str(height - 1) + " " +\
"-rigidBody " +\
str(width / 2) + " " + str(height / 2) + " " +\
str(width / 2) + " " + str(height / 2) + " " +\
"0 " + str(height / 2) + " " +\
"0 " + str(height / 2) + " " +\
str(width - 1) + " " + str(height / 2) + " " +\
str(width - 1) + " " + str(height / 2) + " " +\
"-hideOutput"
tr = TurboReg_()
tr.run(regArg)
registeredImp = tr.getTransformedImage()
sourcePoints = tr.getSourcePoints()
targetPoints = tr.getTargetPoints()
registeredStack.setProcessor(registeredImp.getProcessor(), toRegId)
# toRegImp.flush()
# apply transformation on other channels
for c in xrange(1, nChannels + 1):
# print "c ", c
if c == refC:
continue
toTransformId = imp.getStackIndex(c, 1, t)
toTransformImp = ImagePlus("toTransform",
stack.getProcessor(toTransformId))
toTransformWin.setImage(toTransformImp)
transformArg = "-transform " +\
"-window " + toTransformImp.getTitle() + " " +\
str(width) + " " + str(height) + " " +\
"-rigidBody " +\
str(sourcePoints[0][0]) + " " +\
str(sourcePoints[0][1]) + " " +\
str(targetPoints[0][0]) + " " +\
str(targetPoints[0][1]) + " " +\
str(sourcePoints[1][0]) + " " +\
str(sourcePoints[1][1]) + " " +\
str(targetPoints[1][0]) + " " +\
str(targetPoints[1][1]) + " " +\
str(sourcePoints[2][0]) + " " +\
str(sourcePoints[2][1]) + " " +\
str(targetPoints[2][0]) + " " +\
str(targetPoints[2][1]) + " " +\
"-hideOutput"
tr = TurboReg_()
tr.run(transformArg)
registeredStack.setProcessor(
tr.getTransformedImage().getProcessor(), toTransformId)
# toTransformImp.flush()
sourcePoints = None
targetPoints = None
IJ.showProgress(t, nFrames)
IJ.showStatus("Frames registered: " + str(t) + "/" + str(nFrames))
refWin.close()
toRegWin.close()
toTransformWin.close()
imp2 = ImagePlus("reg_" + imp.getTitle(), registeredStack)
imp2.setCalibration(imp.getCalibration().copy())
imp2.setDimensions(nChannels, nSlices, nFrames)
# print "type ", imp.getType()
# print "type ", imp2.getType()
# print nChannels, " ", nSlices, " ", nFrames
# print registeredStack.getSize()
for key in imp.getProperties().stringPropertyNames():
imp2.setProperty(key, imp.getProperty(key))
# comp = CompositeImage(imp2, CompositeImage.COLOR)
# comp.show()
# imp2 = imp.clone()
# imp2.setStack(registeredStack)
# imp2.setTitle("reg"+imp.getTitle())
# imp2.show()
# imp.show()
return imp2
#for cell in listfilescells :
f1 = open(rootdir+now+"-R1-MT.txt", "w")
tab="\t"
f1.write("cell"+tab+"maxFrames"+tab+"maxcumul"+tab+"nrevs"+"\n")
for cle in listcellname :
rm.runCommand("reset")
#cle = cell.rsplit("/", 1)[1][:-len(".cell")]
#cles.append(cle)
rm.runCommand("Open", dictRois[cle])
rm.runCommand("Show None")
RawroisArray=rm.getRoisAsArray()
if len(RawroisArray)< minLife : continue
roisArray=[RawroisArray[i] for i in range(0,len(RawroisArray), subs)]
IJ.showStatus(cle)
IJ.showProgress(listcellname.index(cle), len(listcellname))
dxA=[]
dyA=[]
dxB=[]
dyB=[]
dA=[]
dB=[]
sensA = 1
sensB = -1
nrev = 0
color=colors.pop(0)
colorA=color.brighter()
verbose=gd.getNextBoolean() corestouse=gd.getNextNumber() outsuffix=gd.getNextString() regparams=gd.getNextChoice() print regparams regparams=gd.getNextString() mungeropts=gd.getNextString() action=gd.getNextChoice() if action == 'Test': mungeropts+=' -t' if verbose: mungeropts+=' -v' mungeropts+=' -T %d' % (int(corestouse)) if not outsuffix == '': mungeropts += ' -d .'+outsuffix cmd='"%s" -b "%s" %s %s %s -s "%s" %s' % (munger,bindir,munger_actions,regparams,mungeropts,refBrain,image) print cmd if action !='Test': # make a script script=makescript(cmd,rootDir,outdir=os.path.join(rootDir,'commands')) print 'script is %s' % (script) if action != 'Write Script': # Actually run the script subprocess.call(script,shell=False) except SystemExit, e: from ij import IJ IJ.showStatus(str(e))
scale_info = estimate_scale_multiplier(parentLSMFilePath+"_tiles/tile_1.ome.tif",parentLSMFilePath+"_tiles/resized/tile_1.tif")
print scale_info
coords_list = read_tileconfig_file(tileConfigFilePath)
coords_normed = normalize_coords_in_list(coords_list)
coords_upscaled = round_coords(upscale_coords(coords_normed,scale_info[0]))
write_tileconfig_file(parentLSMFilePath+"_tiles/v_img/TileConfiguration.fullsize.txt",coords_upscaled,".ome.tif")
max_coords = get_max_coordinates(coords_upscaled)
print max_coords
print basic_info
## Outputs each stitched z plane as a separate file
iReader = ImageReader()
iReader.setId(parentLSMFilePath)
for z in range(max_coords[2]+basic_info[4]):
## for z in range(50,51):
IJ.showStatus("z: "+str(z+1)+" of "+str(max_coords[2]+basic_info[4]))
chIps = []
resImages = []
for ch in range(basic_info[0]):
chIps.append(ByteProcessor(max_coords[0]+scale_info[2],max_coords[1]+scale_info[2]))
for ch in range(basic_info[0]):
resImages.append(ImagePlus("ch"+str(ch+1),chIps[ch]))
for se in range(basic_info[1]):
IJ.showProgress(se,basic_info[1])
if z >= coords_upscaled[se][2] and z <= coords_upscaled[se][2]+basic_info[4]-1:
iReader.setSeries(se)
for ch in range(basic_info[0]):
byteArray = iReader.openBytes((z-coords_upscaled[se][2])*basic_info[0]+ch)
testIp = ByteProcessor(scale_info[2],scale_info[2],byteArray)
testImage = ImagePlus("tester",testIp)
Image_stamper.stampStack(testImage,resImages[ch],coords_upscaled[se][0],coords_upscaled[se][1],0)
def show_status(msg):
"""Wrapper to update the ImageJ status bar and the log simultaneously."""
log.info(msg)
IJ.showStatus(msg)
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))
try:
download_url = 'https://github.com/jefferis/fiji-cmtk-gui/tarball/master'
# check date
installed_version = 'NA'
local_version_info = cmtkgui.gui_local_versioninfo()
if local_version_info.has_key('date'):
installed_version = local_version_info['date']
github_version_info = cmtkgui.gui_github_versioninfo()
update_available = cmtkgui.gui_update_available(github_version_info)
gd = GenericDialogPlus('Update CMTK GUI')
if update_available:
gd.addMessage('CMTK GUI update available')
gd.setOKLabel("Download")
else:
gd.addMessage('CMTK GUI is up to date')
gd.addMessage('Currently installed CMTK GUI version: ' + installed_version)
gd.showDialog()
if gd.wasOKed() and update_available:
# nb url has a suffix to indicate that user agreed to license
from ij import IJ
IJ.showStatus('Downloading CMTK GUI')
cmtkgui.download_and_untar_url(download_url, cmtkgui.gui_install_dir(),
untar_github_archive)
cmtkgui.gui_write_local_versioninfo(github_version_info)
except SystemExit, e:
from ij import IJ
IJ.showStatus(str(e))
def __fmeasures(self) :
self.__Cutoff = float(self.__display4.text)
nslices = self.__impRes.getImageStackSize()
rt = ResultsTable()
rt.show("RT-"+self.__name)
if self.__maxfinder : twpoints = TextWindow("points-"+self.__name, "index\tlabel\tname\tx\ty\taxis\tcellw\tcellh", "", 200, 450)
twlabels = TextWindow("labels-"+self.__name, "index\tlabel\tname\tnpoints", "", 200, 450)
isres = self.__impRes.getImageStack()
for index in range(1, nslices+1):
pc = (index*100)/nslices
IJ.showStatus("Je suis a "+str(pc)+"%")
self.__impRes.setSlice(index)
self.__impRes.killRoi()
roi = self.__listrois[index-1]
self.__impRes.setRoi(roi)
analyser= Analyzer(self.__impRes, Analyzer.LABELS+Analyzer.CENTER_OF_MASS+Analyzer.CENTROID+Analyzer.INTEGRATED_DENSITY+Analyzer.MEAN+Analyzer.KURTOSIS+Analyzer.SKEWNESS+Analyzer.MIN_MAX+Analyzer.SLICE+Analyzer.STACK_POSITION+Analyzer.STD_DEV, rt)
analyser.measure()
rt.show("RT-"+self.__name)
rect=roi.getBounds()
ip = self.__impRes.getProcessor()
xCoord = []
yCoord = []
currentPixel = []
m00 = 0.00
m10 = 0.00
m01 = 0.00
mc20 = 0.00
mc02 = 0.00
mc11 = 0.00
mc30 = 0.00
mc03 = 0.00
mc21 = 0.00
mc12 = 0.00
mc40 = 0.00
mc04 = 0.00
mc31 = 0.00
mc13 = 0.00
mm20 = 0.00
mm02 = 0.00
mm11 = 0.00
mm30 = 0.00
mm03 = 0.00
mm21 = 0.00
mm12 = 0.00
mm40 = 0.00
mm04 = 0.00
mm31 = 0.00
mm13 = 0.00
#for y in range(rect.y, rect.y+rect.height, 1) :
# for x in range(rect.x, rect.x+rect.width, 1) :
# xCoord.append(x+0.5)
# yCoord.append(y+0.5)
# #pixel=ip.getf(x,y)-self.__Cutoff
# pixel = ip.getPixelValue(x,y)-self.__Cutoff
# if pixel < 0 : pixel = 0
# currentPixel.append(pixel)
# m00 += currentPixel[-1]
# m10 += currentPixel[-1]*xCoord[-1]
# m01 += currentPixel[-1]*yCoord[-1]
#xm = m10/(m00+0.00000001)
#ym = m01/(m00+0.00000001)
#xc = rect.width/2.00
#yc = rect.height/2.00
#for i in range(rect.width*rect.height) :
# xcrel = xCoord[i]-xc
# ycrel = yCoord[i]-yc
# #mc20 += currentPixel[i]*(xCoord[i]-xc)*(xCoord[i]-xc)
# #mc02 += currentPixel[i]*(yCoord[i]-yc)*(yCoord[i]-yc)
# #mc11 += currentPixel[i]*(xCoord[i]-xc)*(yCoord[i]-yc)
# #
# #mc30 += currentPixel[i]*(xCoord[i]-xc)*(xCoord[i]-xc)*(xCoord[i]-xc)
# #mc03 += currentPixel[i]*(yCoord[i]-yc)*(yCoord[i]-yc)*(yCoord[i]-yc)
# #mc21 += currentPixel[i]*(xCoord[i]-xc)*(xCoord[i]-xc)*(yCoord[i]-yc)
# #mc12 += currentPixel[i]*(xCoord[i]-xc)*(yCoord[i]-yc)*(yCoord[i]-yc)
# #
# #mc40 += currentPixel[i]*(xCoord[i]-xc)*(xCoord[i]-xc)*(xCoord[i]-xc)*(xCoord[i]-xc)
# #mc04 += currentPixel[i]*(yCoord[i]-yc)*(yCoord[i]-yc)*(yCoord[i]-yc)*(yCoord[i]-yc)
# #mc31 += currentPixel[i]*(xCoord[i]-xc)*(xCoord[i]-xc)*(xCoord[i]-xc)*(yCoord[i]-yc)
# #mc13 += currentPixel[i]*(xCoord[i]-xc)*(yCoord[i]-yc)*(yCoord[i]-yc)*(yCoord[i]-yc)
# mc20 += currentPixel[i]*xcrel*xcrel
# mc02 += currentPixel[i]*ycrel*ycrel
# mc11 += currentPixel[i]*xcrel*ycrel
# mc30 += currentPixel[i]*xcrel*xcrel*xcrel
# mc03 += currentPixel[i]*ycrel*ycrel*ycrel
# mc21 += currentPixel[i]*xcrel*xcrel*ycrel
# mc12 += currentPixel[i]*xcrel*ycrel*ycrel
# mc40 += currentPixel[i]*xcrel*xcrel*xcrel*xcrel
# mc04 += currentPixel[i]*ycrel*ycrel*ycrel*ycrel
# mc31 += currentPixel[i]*xcrel*xcrel*xcrel*ycrel
# mc13 += currentPixel[i]*xcrel*ycrel*ycrel*ycrel
#for i in range(rect.width*rect.height) :
# mm20 += currentPixel[i]*(xCoord[i]-xm)*(xCoord[i]-xm)
# mm02 += currentPixel[i]*(yCoord[i]-ym)*(yCoord[i]-ym)
# mm11 += currentPixel[i]*(xCoord[i]-xm)*(yCoord[i]-ym)
# mm30 += currentPixel[i]*(xCoord[i]-xm)*(xCoord[i]-xm)*(xCoord[i]-xm)
# mm03 += currentPixel[i]*(yCoord[i]-ym)*(yCoord[i]-ym)*(yCoord[i]-ym)
# mm21 += currentPixel[i]*(xCoord[i]-xm)*(xCoord[i]-xm)*(yCoord[i]-ym)
# mm12 += currentPixel[i]*(xCoord[i]-xm)*(yCoord[i]-ym)*(yCoord[i]-ym)
# mm40 += currentPixel[i]*(xCoord[i]-xm)*(xCoord[i]-xm)*(xCoord[i]-xm)*(xCoord[i]-xm)
# mm04 += currentPixel[i]*(yCoord[i]-ym)*(yCoord[i]-ym)*(yCoord[i]-ym)*(yCoord[i]-ym)
# mm31 += currentPixel[i]*(xCoord[i]-xm)*(xCoord[i]-xm)*(xCoord[i]-xm)*(yCoord[i]-ym)
# mm13 += currentPixel[i]*(xCoord[i]-xm)*(yCoord[i]-ym)*(yCoord[i]-ym)*(yCoord[i]-ym)
#xxcVar = mc20/m00
#yycVar = mc02/m00
#xycVar = mc11/m00
#xcSkew = mc30/(m00 * math.pow(xxcVar,(3.0/2.0)))
#ycSkew = mc03/(m00 * math.pow(yycVar,(3.0/2.0)))
#xcKurt = mc40 / (m00 * math.pow(xxcVar,2.0)) - 3.0
#ycKurt = mc04 / (m00 * math.pow(yycVar,2.0)) - 3.0
#ecc = (math.pow((mc20-mc02),2.0)+(4.0*mc11*mc11))/m00
#xxmVar = mm20/m00
#yymVar = mm02/m00
#xymVar = mm11/m00
#xmSkew = mm30/(m00 * math.pow(xxmVar,(3.0/2.0)))
#ymSkew = mm03/(m00 * math.pow(yymVar,(3.0/2.0)))
#xmKurt = mm40 / (m00 * math.pow(xxmVar,2.0)) - 3.0
#ymKurt = mm04 / (m00 * math.pow(yymVar,2.0)) - 3.0
#ecm = (math.pow((mm20-mm02),2.0)+(4.0*mm11*mm11))/m00
#rt.addValue("xxcVar", xxcVar)
#rt.addValue("yycVar", yycVar)
#rt.addValue("xycVar", xycVar)
#rt.addValue("xcSkew", xcSkew)
#rt.addValue("ycSkew", ycSkew)
#rt.addValue("xcKurt", xcKurt)
#rt.addValue("ycKurt", ycKurt)
#rt.addValue("Ecc", ecc)
#rt.addValue("xxmVar", xxmVar)
#rt.addValue("yymVar", yymVar)
#rt.addValue("xymVar", xymVar)
#rt.addValue("xmSkew", xmSkew)
#rt.addValue("ymSkew", ymSkew)
#rt.addValue("xmKurt", xmKurt)
#rt.addValue("ymKurt", ymKurt)
#rt.addValue("Ecm", ecm)
rt.addValue("roiw", rect.width)
rt.addValue("roih", rect.height)
rt.addValue("cellw", self.__ipw[index-1])
rt.addValue("cellh", self.__iph[index-1])
self.__impRes.killRoi()
xCoord[:] = []
yCoord[:] = []
currentPixel[:] = []
points = []
points[:] = []
npointsmax = 0
#lab = self.__labels[index-1]
nameroi = self.__dictCells[index][0]
lab = self.__dictCells[index][1]
if self.__maxfinder :
self.__impMax.setSlice(index)
ipmax = self.__impMax.getProcessor()
for y in range(ipmax.getHeight()) :
for x in range(ipmax.getWidth()) :
if ipmax.getPixelValue(x,y) > 0 :
twpoints.append(str(index)+"\t"+lab+"\t"+nameroi+"\t"+str(x)+"\t"+str(y)+"\t"+str(self.__cellsrois[index-1][0].getLength())+"\t"+str(self.__ipw[index-1])+"\t"+str(self.__iph[index-1]))
npointsmax+=1
rt.addValue("npoints", npointsmax)
twlabels.append(str(index)+"\t"+lab+"\t"+nameroi+"\t"+str(npointsmax))
rt.show("RT-"+self.__name)
rt.show("RT-"+self.__name)