def scaleImageUI():
gd = GenericDialog("Scale")
gd.addSlider("Scale", 1, 200, 100)
gd.addCheckbox("Preview", True)
# The UI elements for the above two inputs
slider = gd.getSliders().get(0) # the only one
checkbox = gd.getCheckboxes().get(0) # the only one
imp = WM.getCurrentImage()
if not imp:
print "Open an image first!"
return
previewer = ScalingPreviewer(imp, slider, checkbox)
slider.addAdjustmentListener(previewer)
checkbox.addItemListener(previewer)
gd.showDialog()
if gd.wasCanceled():
previewer.reset()
print "User canceled dialog!"
else:
previewer.scale()
previewer.destroy()
def getOptions(imp):
gd = GenericDialog("Correct 3D Drift Options")
channels = []
for ch in range(1, imp.getNChannels()+1 ):
channels.append(str(ch))
methods = ["phase_correlation","center_of_mass"]
gd.addChoice("Channel for registration:", channels, channels[0])
gd.addChoice("Method for registration:", methods, methods[1])
gd.addNumericField("Background value:", 0, 0)
gd.addCheckbox("Multi_time_scale computation for enhanced detection of slow drifts?", False)
gd.addCheckbox("Sub_pixel drift correction (possibly needed for slow drifts)?", False)
gd.addCheckbox("Edge_enhance images for possibly improved drift detection?", False)
gd.addCheckbox("Use virtualstack for saving the results to disk to save RAM?", False)
gd.addCheckbox("Drift correct only data inside ROI?", False)
gd.addCheckbox("Only compute drift vectors?", False)
gd.addMessage("If you put a ROI, drift will only be computed in this region;\n the ROI will be moved along with the drift to follow your structure of interest.")
gd.addSlider("z_min of ROI", 1, imp.getNSlices(), 1)
gd.addSlider("z_max of ROI", 1, imp.getNSlices(), imp.getNSlices())
gd.showDialog()
if gd.wasCanceled():
return
channel = gd.getNextChoiceIndex() + 1 # zero-based
method = gd.getNextChoiceIndex() + 1 # zero-based
bg_value = gd.getNextNumber()
multi_time_scale = gd.getNextBoolean()
subpixel = gd.getNextBoolean()
process = gd.getNextBoolean()
virtual = gd.getNextBoolean()
only_roi = gd.getNextBoolean()
only_compute = gd.getNextBoolean()
roi_z_min = int(gd.getNextNumber())
roi_z_max = int(gd.getNextNumber())
return channel, method, bg_value, virtual, multi_time_scale, subpixel, process, only_roi, only_compute, roi_z_min, roi_z_max
def get_opts():
gd = GenericDialog("setup plugin")
#channels = map(lambda x: str(x), range(1,imp.getNChannels()+1))
channels = ['1','2','3'];
modes = ['batch mode', 'manual']
gd.addChoice("processing mode",modes,modes[1])
gd.addChoice("choose channel for pre-registration: ", channels, channels[0])
gd.addChoice("choose channel for registration: ", channels, channels[2])
gd.addChoice("channel for cell detection: ", channels, channels[1])
gd.addChoice("channel for osteoblast detection: ", channels, channels[2])
gd.addChoice("channel for vasculature detection: ", channels, channels[0])
# gd.addNumericField("quantile for cell segmentation", 0.9995, 36)
gd.addNumericField("rough cell size in microns", 15., 2)
# gd.addSlider("minimal z depth (voxels) for detected cells", 1, imp.getNSlices()+1, 8)
gd.addSlider("minimal z depth (voxels) for detected cells", 1,36, 5)
gd.addSlider("minimal z depth (voxels) for detected cells", 1,36, 25)
gd.addCheckbox("delete black frames (recommended)", True)
gd.addChoice("channel to estimate black frames: ", channels, channels[2])
gd.addCheckbox("rough registration of time series", True)
gd.addCheckbox("descriptor-based registration of time series", True)
gd.addCheckbox("detect cells", False)
gd.addCheckbox("export osteoblast structures", False)
gd.addCheckbox("export vasculature structures", False)
gd.addCheckbox("save registered movie", True)
gd.addCheckbox("delete temporary files", True)
#gd.addCheckbox("show 3d vis", False)
gd.showDialog()
proc_mode = gd.getNextChoice()
ch_pre = gd.getNextChoice()
reg = gd.getNextChoice()
cc = gd.getNextChoice()
ost_ch = gd.getNextChoice()
vasc_ch = gd.getNextChoice()
#quantile = gd.getNextNumber()
size = gd.getNextNumber()
minz = gd.getNextNumber()
zmax = gd.getNextNumber()
del_black = gd.getNextBoolean();
black_ch = gd.getNextChoice()
preregflag = gd.getNextBoolean();
regflag = gd.getNextBoolean()
detect_cells = gd.getNextBoolean()
struct_exp = gd.getNextBoolean()
vasc_exp = gd.getNextBoolean()
save_res = gd.getNextBoolean()
del_tmp = gd.getNextBoolean()
#vis = gd.getNextBoolean()
return proc_mode, ch_pre, reg, cc, ost_ch, vasc_ch, size, minz, zmax, del_black, black_ch, preregflag, regflag, detect_cells, struct_exp, vasc_exp, save_res, del_tmp
def getOptions():
gd = GenericDialog("Options")
gd.addStringField("name", "Untitled")
gd.addNumericField("alpha", 0.25, 2) # show 2 decimals
gd.addCheckbox("optimize", True)
types = ["8-bit", "16-bit", "32-bit"]
gd.addChoice("output as", types, types[2])
gd.addSlider("scale", 1, 100, 100)
gd.showDialog()
#
if gd.wasCanceled():
print "User canceled dialog!"
return
# Read out the options
name = gd.getNextString()
alpha = gd.getNextNumber()
optimize = gd.getNextBoolean()
output = gd.getNextChoice()
scale = gd.getNextNumber()
return name, alpha, optimize, output, scale
def setupDialog(imp):
gd = GenericDialog("Collective migration buddy options")
gd.addMessage("Collective migration buddy 2.0, you are analyzing: " +
imp.getTitle())
calibration = imp.getCalibration()
if (calibration.frameInterval > 0):
default_interval = calibration.frameInterval
default_timeunit = calibration.getTimeUnit()
else:
default_interval = 8
default_timeunit = "min"
gd.addNumericField("Frame interval:", default_interval,
2) # show 2 decimals
gd.addCheckbox("Do you want to use a gliding window?", True)
gd.addCheckbox(
"Project hyperStack? (defaluts to projecting current channel only)",
False)
gd.addStringField("time unit", default_timeunit, 3)
gd.addSlider("Start compacting at frame:", 1, imp.getNFrames(), 1)
gd.addSlider("Stop compacting at frame:", 1, imp.getNFrames(),
imp.getNFrames())
gd.addNumericField("Number of frames to project in to one:", 3,
0) # show 0 decimals
gd.addChoice('Method to use for frame projection:', methods_as_strings,
methods_as_strings[5])
gd.showDialog()
if gd.wasCanceled():
IJ.log("User canceled dialog!")
return
return gd
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 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()
# Take a snapshot after a delay specified in a dialog
#
# The plugin has to fork, which is done by:
# 1 - declaring a function to do the work, 'snasphot'
# 2 - invoking the function via thread.start_new_thread,
# which runs it in a separate thread.
from ij import IJ
from ij.gui import GenericDialog
import thread
import time
def snapshot(delay):
time.sleep(delay)
IJ.doCommand('Capture Screen')
gd = GenericDialog('Delay')
gd.addSlider('Delay (secs.): ', 0, 20, 5)
gd.showDialog()
if not gd.wasCanceled():
# the 'extra' comma signals tuple, a kind of list in python.
thread.start_new_thread(snapshot, (int(gd.getNextNumber()),))
from java.lang import Math, System
image = WindowManager.getCurrentImage()
ip = image.getProcessor()
pixelsCopy = ip.getPixelsCopy()
pixels = ip.getPixels()
width = ip.getWidth()
height = ip.getHeight()
minWidth = int(Math.sqrt(len(pixels) / 16))
maxWidth = minWidth * 16
class Listener(AdjustmentListener):
def adjustmentValueChanged(self, event):
value = event.getSource().getValue()
rowstride = min(width, value)
for j in range(0, min(height, int(width * height / value))):
System.arraycopy(pixelsCopy, j * value, pixels, j * width,
rowstride)
image.updateAndDraw()
gd = GenericDialog("Width")
gd.addSlider("width", minWidth, maxWidth, ip.getHeight())
gd.getSliders().get(0).addAdjustmentListener(Listener())
gd.showDialog()
if gd.wasCanceled():
pixels[0:width * height] = pixelsCopy
image.updateAndDraw()
from java.awt.event import AdjustmentListener
from java.lang import Math, System
image = WindowManager.getCurrentImage()
ip = image.getProcessor()
pixelsCopy = ip.getPixelsCopy()
pixels = ip.getPixels()
width = ip.getWidth()
height = ip.getHeight()
minWidth = int(Math.sqrt(len(pixels) / 16))
maxWidth = minWidth * 16
class Listener(AdjustmentListener):
def adjustmentValueChanged(self, event):
value = event.getSource().getValue()
rowstride = min(width, value)
for j in range(0, min(height, int(width * height / value))):
System.arraycopy(pixelsCopy, j * value,
pixels, j * width, rowstride)
image.updateAndDraw()
gd = GenericDialog("Width")
gd.addSlider("width", minWidth, maxWidth, ip.getHeight())
gd.getSliders().get(0).addAdjustmentListener(Listener())
gd.showDialog()
if gd.wasCanceled():
pixels[0:width * height] = pixelsCopy
image.updateAndDraw()
# Take a snapshot after a delay specified in a dialog
#
# The plugin has to fork, which is done by:
# 1 - declaring a function to do the work, 'snasphot'
# 2 - invoking the function via thread.start_new_thread,
# which runs it in a separate thread.
from ij import IJ
from ij.gui import GenericDialog
import thread
import time
def snapshot(delay):
time.sleep(delay)
IJ.doCommand('Capture Screen')
gd = GenericDialog('Delay')
gd.addSlider('Delay (secs.): ', 0, 20, 5)
gd.showDialog()
if not gd.wasCanceled():
# the 'extra' comma signals tuple, a kind of list in python.
thread.start_new_thread(snapshot, (int(gd.getNextNumber()), ))
