def run(self):
IJ.resetEscape()
IJ.setTool("point")
listener = ML()
self.imp.show()
canvas = self.imp.getWindow().getCanvas()
canvas.addMouseListener(listener)
# wait for mouse click
while (not listener.mouseWasPressed) and (not IJ.escapePressed()):
Thread.sleep(200) # todo: how to make this better?
canvas.removeMouseListener(listener)
if IJ.escapePressed():
IJ.log("command has been aborted")
else:
print listener.x, listener.y
self.pos = [listener.x, listener.y]
"Cross-Correlation": 2,
"Normalised cross-correlation": 3,
"0-mean cross-correlation": 4,
"Normalised 0-mean cross-correlation": 5
}
Method = Dico_Method[method]
# Loop over the images in the stack (or directly process if unique)
ImageStack = image.getStack()
nSlice = image.getStackSize()
imageBis = image.duplicate(
) # duplicate full stack to be sure to not mess around with ROI display
for i in xrange(1, nSlice + 1):
if IJ.escapePressed():
IJ.resetEscape() # for next call
raise KeyboardInterrupt("Escape was pressed")
imageBis.setSlice(
i
) # for stacks (important for both with/without searchRoi) for single image no adversial effect
if Bool_SearchRoi:
imageBis.setRoi(searchRoi)
searchedImage = imageBis.crop(
) # Single image -> crop to ROI - Stack -> crop the slice to the ROI (in this case)
elif nSlice > 1: # no SearchRoi, but with Stack still crop to isolate the slice
# Remove any ROI and crop
def main():
try:
# Retrieve valid data
rt = Utils.getTable();
start = time.time()
# Retrive x,y,t positions (all in unc. units)
x = getColumn(rt, X_POS_HEADING)
y = getColumn(rt, Y_POS_HEADING)
t = getColumn(rt, T_POS_HEADING)
# Retrieve the total n. of tracks
track_ids = getColumn(rt, ID_HEADING)
track_ids = [int(i) for i in track_ids]
n_tracks = track_ids[-1]
log("Tracks to be analyzed: ", n_tracks)
except:
IJ.error("Invalid Results Table")
return
# Create "nan"-padded tables to hold results
detail_rt = new_Table()
# Extract individual tracks and determine the track with the
# largest data (i.e., the one with the highest number of rows)
track_row = 0
max_track_row = 0
for i in range(0, rt.getCounter()-1):
track_label = str(track_ids[i])
if (track_ids[i]==track_ids[i+1]):
dx = (x[i+1]-x[i])**2
dy = (y[i+1]-y[1])**2
dt = t[i+1]-t[i]
dis = math.sqrt(dx+dy)
vel = dis/dt
if (track_row>max_track_row):
max_track_row = track_row
# Log to "detailed" table
if (i<=max_track_row):
detail_rt.incrementCounter()
detail_rt.setValue("Dis_" + track_label, track_row, dis)
detail_rt.setValue("Vel_" + track_label, track_row, vel)
detail_rt.setValue("Dur_" + track_label, track_row, dt)
detail_rt.setValue("Flag_" + track_label, track_row,
RESTING_FLAG if vel < restingVelocity else MOVING_FLAG)
track_row += 1
else:
# Analyzed track just ended: Reset loop variables and create column
# to hold bout flags
track_row = 0
detail_rt.setValue("BoutFlag_" + track_label, 0, float("nan"))
detail_rt.setValue("Mov_Dur_" + track_label, 0, float("nan"))
detail_rt.setValue("Rest_Dur_" + track_label, 0, float("nan"))
log("Extracting track ", track_label)
listOfRasterPaths = [] # List holding raster tracks
# Loop through individual tracks and tag each datapoint (i.e., each row)
for track in range(0, n_tracks):
durHeading = "Dur_" + str(track)
fFlagHeading = "Flag_" + str(track)
bFlagHeading = "BoutFlag_" + str(track)
mDurHeading = "Mov_Dur_" + str(track)
rDurHeading = "Rest_Dur_" + str(track)
durations = getColumn(detail_rt, durHeading)
fFlags = getColumn(detail_rt, fFlagHeading)
bFlags = getColumn(detail_rt, bFlagHeading)
nDataPoints = findLastNonNumberIdx(durations) + 1
log("Tagging track ", track, ": ", nDataPoints , " positions")
for row in range(0, nDataPoints):
# Define the boundaries of the moving window. "Stopping flags"
# within this window will be monitoried to define a motionless bout
# NB: Boundaries are defined from the rows of the input table. This
# works only when the time elapsed betwen two rows is a single frame.
# So we'll have to monitor the actual time that has elapsed within the
# bounderies of the window
lower_bound = max(0, row - neighborhood + 1)
upper_bound = min(nDataPoints, row+neighborhood)
sum_of_flags = 0
sum_of_frames = 0
neighborhood_sum = upper_bound - lower_bound
for i in xrange(lower_bound, upper_bound):
if isNumber(durations[i]) and isNumber(fFlags[i]):
sum_of_flags += (fFlags[i] * durations[i])
sum_of_frames += durations[i]
if sum_of_frames >= neighborhood_sum:
break
# Assign this tracked point to its bout
moving_bout_duration = float("nan")
resting_bout_duration = float("nan")
bout_flag = float("nan")
if sum_of_flags >= neighborhood_sum:
bout_flag = MOVING_FLAG
moving_bout_duration = durations[row]
else:
bout_flag = RESTING_FLAG
resting_bout_duration = durations[row]
detail_rt.setValue(bFlagHeading, row, bout_flag)
detail_rt.setValue(mDurHeading, row, moving_bout_duration)
detail_rt.setValue(rDurHeading, row, resting_bout_duration)
if generateRasterTracks:
# Generate raster column if path is long enough
if nDataPoints > shortestRasterTrack:
# Retrieve updated column of bout flags
bFlags = getColumn(detail_rt, bFlagHeading)
# Generate raster column (motion-flags temporally aligned, all 1
# frame apart) until the path duration reaches the maximum limit
keepGrowingRasterPath = True
for idx, duration in enumerate(durations):
if (keepGrowingRasterPath):
flag = bFlags[idx]
for insertIdx in range(1, int(duration)):
if (len(bFlags)==longestRasterTrack):
keepGrowingRasterPath = False
break
bFlags.insert(idx+insertIdx, flag)
# Store only lists without NaN values
listOfRasterPaths.append(bFlags[:findLastNonNumberIdx(bFlags)])
# Allow analysis to be interrupted
if IJ.escapePressed():
break
# Display table. Displaying it now may ensure all tracks are padded with "NaN"
if (displayDetailedTable):
detail_rt.show("Track_Details["+ str(restingVelocity) +"-"+ str(neighborhood) +"]")
# Now that all paths are contained in listOfRasterPaths. Sort them by length of track
listOfRasterPaths = sorted(listOfRasterPaths, key = len)
# Create Image of analysis. We'll create it from a ResultsTable. It would be much
# more efficient to generate a text image directly, but this allows the table to be
# processed elsewhere if needed. In IJ1, column headings of a ResultsTable must be
# unique, so we will use distinct identifiers
if generateRasterTracks:
raster_rt = new_Table()
log('Tracks to be rendered:', len(listOfRasterPaths))
for rasterPath in xrange(len(listOfRasterPaths)):
log("Rendering track ", rasterPath)
for row, raster_flag in enumerate(listOfRasterPaths[rasterPath]):
if not isNumber(raster_flag):
break
if (row>raster_rt.getCounter()-1):
raster_rt.incrementCounter()
# Create upper border: 1 px-wide
bColor = borderColor if isNumber(raster_flag) else backgroundColor
raster_rt.setValue("Delim1_" + str(rasterPath), row, bColor)
# Create raster path: 18 px wide
raster_flag_color = colorizeFlag(raster_flag)
for i in 'abcdefghijklmnopq':
raster_rt.setValue("Raster_" + str(rasterPath) + str(i), row, raster_flag_color)
# Create lower border: 1 px-wide
raster_rt.setValue("Delim2_" + str(rasterPath), row, bColor)
# Append padding space between tracks: 10px wide
for j in 'abcdefghij':
raster_rt.setValue("Space_" + str(rasterPath) + str(j), row, backgroundColor)
# Allow analysis to be interrupted
if IJ.escapePressed():
break
# Display table of rasterized tracks
if displayRasterTable:
raster_rt.show("RasterTracks["+ str(restingVelocity) +"-"+ str(neighborhood ) +"]")
# Display image of rasterized tracks
ip = raster_rt.getTableAsImage().rotateLeft()
paintNaNpixels(ip, backgroundColor)
ip = ip.convertToByte(False)
imp = ImagePlus("RasterTracks["+ str(restingVelocity) +"-"+ str(neighborhood ) +"]", ip)
imp.show()
## Add scale-bar for time
IJ.run(imp, "Set Scale...", "distance=1 known="+ str(frameCal[0]) +" unit="+ frameCal[1]);
IJ.run(imp, "Scale Bar...", "width=10 color=Black location=[Lower Right] overlay");
# Loop through individual tracks and extract some basic statistics. Most of these parameters
# are already retrieved by Trackmate. We calculate them here just for convenience
track_ids = [] # List holding the track identifier
sum_distances = [] # List holding the track's total distance
sum_durations = [] # List holding the track's total duration
max_speeds = [] # List holding the track's Max speed
min_speeds = [] # List holding the track's Min speed
sum_n_rests = [] # List holding the number of resting bouts in each track
sum_n_moves = [] # List holding the number of moving bouts in each track
sum_dur_rests = [] # List holding the total resting time of each tracked object
sum_dur_moves = [] # List holding the total moving time of each tracked object
log("Logging Summaries...")
summary_rt = new_Table()
for track in range(0, n_tracks):
# Retrieve and store the track identifier
track_id = str(track)
track_ids.insert(track, "Track_"+track_id)
# Retrive tracking data
distances = getColumn(detail_rt, "Dis_" + track_id)
durations = getColumn(detail_rt, "Dur_" + track_id)
velocities = getColumn(detail_rt, "Vel_" + track_id)
mov_durations = getColumn(detail_rt, "Mov_Dur_" + track_id)
rest_durations = getColumn(detail_rt, "Rest_Dur_" + track_id)
# Reset stats for this track
track_sum_dis = 0
track_sum_dur = 0
track_max_vel = 0
track_min_vel = sys.maxint
track_sum_move = 0
track_sum_rest = 0
track_n_moves = 0
track_n_rests = 0
# Compute basic stats and store them in dedicated lists
nDataPoints = findLastNonNumberIdx(distances) + 1
for row in xrange(nDataPoints):
track_sum_dis += distances[row]
track_sum_dur += durations[row]
if (velocities[row]>track_max_vel):
track_max_vel = velocities[row]
if (velocities[row]<track_min_vel):
track_min_vel = velocities[row]
if isNumber(mov_durations[row]):
track_sum_move += mov_durations[row]
if isNumber(rest_durations[row]):
track_sum_rest += rest_durations[row]
sum_distances.insert(track, track_sum_dis)
sum_durations.insert(track, track_sum_dur)
max_speeds.insert(track, track_max_vel)
min_speeds.insert(track, track_min_vel)
sum_dur_moves.insert(track, track_sum_move)
sum_dur_rests.insert(track, track_sum_rest)
# Assess the number of moving/resting bouts in this track
for row in xrange(nDataPoints-1):
if isNumber(mov_durations[row]) and not isNumber(mov_durations[row+1]):
track_n_moves += 1
if isNumber(rest_durations[row]) and not isNumber(rest_durations[row+1]):
track_n_rests += 1
# Predict cases in which bouts lasted entire track duration
if track_n_moves==0 and track_sum_dur==track_sum_move:
track_n_moves += 1
if track_n_rests==0 and track_sum_dur==track_sum_rest:
track_n_rests += 1
sum_n_moves.insert(track, track_n_moves)
sum_n_rests.insert(track, track_n_rests)
# Log summary data
for i in range(0, n_tracks):
# Ignore tracks shorter than neighborhood
if hideShortTracks and sum_durations[i]<neighborhood:
continue
row = summary_rt.getCounter()
summary_rt.incrementCounter()
summary_rt.setLabel(track_ids[i], row)
summary_rt.setValue("Total dx", row, sum_distances[i])
summary_rt.setValue("Duration", row, sum_durations[i])
summary_rt.setValue("Max speed", row, max_speeds[i])
summary_rt.setValue("Min speed", row, min_speeds[i])
summary_rt.setValue("Moving dur", row, sum_dur_moves[i])
summary_rt.setValue("Resting dur", row, sum_dur_rests[i])
summary_rt.setValue("Resting %", row, 100 * sum_dur_rests[i] / sum_durations[i])
summary_rt.setValue("Moving bouts", row, sum_n_moves[i])
summary_rt.setValue("Resting bouts", row, sum_n_rests[i])
if sum_n_moves[i]!=0:
summary_rt.setValue("Avg moving bout dur", row, sum_dur_moves[i] / sum_n_moves[i])
if sum_n_rests[i]!=0:
summary_rt.setValue("Avg resting bout dur", row, sum_dur_rests[i] / sum_n_rests[i])
summary_rt.show("Track_Summaries["+ str(restingVelocity) +"-"+ str(neighborhood) +"]")
log("Finished: ", time.time()-start, " seconds")
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()