def addMultipleRandomPuffs(self):
nSites = self.getValue('nSites')
if self.currentWin == None:
g.alert('First select window')
return
#select current ROI
self.currentROI = self.currentWin.currentROI
if self.currentWin.currentROI == None:
g.alert('First draw an ROI')
return
bounds = self.currentROI.parentBounds()
topLeft_x = bounds.topLeft().x()
topLeft_y = bounds.topLeft().y()
bottomRight_x = bounds.bottomRight().x()
bottomRight_y = bounds.bottomRight().y()
print('adding puffs to {} sites from {},{} to {},{}'.format(
nSites, topLeft_x, topLeft_y, bottomRight_x, bottomRight_y))
sites = self.getRandomSites(topLeft_x, bottomRight_x, topLeft_y,
bottomRight_y, nSites)
for site in sites:
print("Puff site: ", self.siteNumber)
self.addRandomPuffs(singleSite=False, x=site[0], y=site[1])
self.siteNumber += 1
print('Finished adding sites')
return
def make_cluster_im(self):
print('Generating Cluster Movie')
mt, mx, my=self.movieShape
try:
cluster_im=np.zeros((mt,mx,my,4),dtype=np.float16)
except MemoryError:
g.alert('There is not enough memory to create the image of clusters (error in function clusters.make_cluster_im).')
return None
for i, cluster in enumerate(self.clusters):
color = cmap(int(((i%5)*255./6)+np.random.randint(255./12)))
pos = self.idxs[cluster]
cluster_im[pos[:, 0], pos[:, 1], pos[:, 2], :] = color
return cluster_im
def exportTimes(self):
if self.getValue('active_window') == None:
g.alert('First select window')
return
if self.randomPuffsAdded == False:
g.alert('Add puffs first')
return
#set export path
savePath, _ = QFileDialog.getSaveFileName(None, "Save file", "",
"Text Files (*.csv)")
#write file
self.timesAdded.to_csv(savePath)
print('List of times saved to: {}'.format(savePath))
def exportTimes(self):
if self.randommeppsAdded == False:
g.alert('Add MEPPs first')
return
#set export path
savePath, _ = QFileDialog.getSaveFileName(None, "Save file", "",
"Text Files (*.csv)")
#write file
try:
# opening the csv file in 'w+' mode
file = open(savePath, 'w+', newline='')
# writing the data into the file
with file:
write = csv.writer(file)
write.writerows(map(lambda x: [x], self.timesAdded))
print('List of times saved to: {}'.format(savePath))
except BaseException as e:
print(e)
print('Export of times failed, printing times to console')
print(self.timesAdded)
def addRandomPuffs(self, singleSite=True, x=None, y=None):
if self.getValue('active_window') == None:
g.alert('First select window')
return
mean = self.getValue('meanExp')
#nPuffs = self.getValue('nPuffs')
puffsAdded = 0
puffsOutsideOfRange = 0
# add first puff
try:
if self.randomDuration.isChecked():
startTime = int(
np.random.exponential(scale=mean, size=1) +
self.getValue('startFrame'))
duration = float(
np.random.exponential(scale=self.getValue('meanDuration'),
size=1)[0])
self.addPuff(time=startTime,
singleSite=singleSite,
x=x,
y=y,
duration=duration)
else:
startTime = int(
np.random.exponential(scale=mean, size=1) +
self.getValue('startFrame'))
duration = self.getValue('nFrames')
self.addPuff(time=startTime, singleSite=singleSite, x=x, y=y)
if self.getValue('puffsSequential'):
endTime = startTime + duration
else:
endTime = startTime
except Exception as e:
print(e)
puffsOutsideOfRange += 1
print('{} puffs added, {} puffs out of range'.format(
puffsAdded, puffsOutsideOfRange))
print('1st puff outside of range, aborting')
return
# add puff after each time selection untill end of stack
# rounding the exponential continous value to an int to select frame
while startTime < self.dt - self.getValue('nFrames'):
try:
startTime = int(endTime +
np.random.exponential(scale=mean, size=1))
#if random duration
if self.randomDuration.isChecked():
#print('original time: ', startTime)
duration = np.random.exponential(
scale=self.getValue('meanDuration'), size=1)
startTime = startTime + ceil(duration)
#print('time: ', startTime)
#print('duration: ', duration)
#add puff at time
self.addPuff(time=startTime,
singleSite=singleSite,
x=x,
y=y,
duration=duration)
#if sequental, add puff duration to time
if self.getValue('puffsSequential'):
endTime = startTime + duration
else:
endTime = startTime
#else use duration from GUI
else:
startTime = startTime + self.getValue('nFrames')
duration = self.getValue('nFrames')
#add puff at time
self.addPuff(time=startTime,
singleSite=singleSite,
x=x,
y=y)
#if sequental, add puff duration to time
if self.getValue('puffsSequential'):
endTime = startTime + duration
else:
endTime = startTime
#update puff time log
self.timesAdded = self.timesAdded.append(
{
'time of puff': startTime,
'duration': duration,
'site': int(self.siteNumber)
},
ignore_index=True)
puffsAdded += 1
except:
puffsOutsideOfRange += 1
print('{} puffs added, {} puffs out of range'.format(
puffsAdded, puffsOutsideOfRange))
if self.plotHistoTimes.isChecked():
plt.hist(self.timesAdded)
plt.xlabel('Time puff added (frames)')
plt.ylabel('Number of puffs added')
plt.show()
self.randomPuffsAdded = True
if singleSite:
self.siteNumber += 1
return
def addPuff(self,
time=False,
singleSite=True,
x=None,
y=None,
duration=False):
'''add synthetic blip to image stack'''
#select window
self.currentWin = self.getValue('active_window')
if self.currentWin == None:
g.alert('First select window')
return
#generate blip
sigma = self.getValue('sigma')
amp = self.getValue('puffAmplitude')
if self.randomDuration.isChecked():
#get random duration
if duration == False:
duration = float(
np.random.exponential(scale=self.getValue('meanDuration'),
size=1)[0])
else:
duration = self.getValue('nFrames')
#scale puff amplitude to account for durations <1 frame
if duration < 1:
amp = amp * duration
duration = ceil(duration)
else:
#round duration to nearest integer number of frames
duration = ceil(duration)
blip = generateBlip(sigma=sigma, amplitude=amp, duration=duration)
blip_time, blip_x_size, blip_y_size = blip.shape
x_size = int(blip_x_size / 2)
y_size = int(blip_y_size / 2)
#add blip to stack
if time == False:
t = self.getValue('startFrame')
else:
t = time
if singleSite:
x = self.getValue('x')
y = self.getValue('y')
tt = np.arange(t, t + duration, dtype=np.int)
xx = np.arange(x - x_size - 1, x + x_size, dtype=np.int)
yy = np.arange(y - y_size - 1, y + y_size, dtype=np.int)
if time == False:
try:
self.data[np.ix_(tt, xx,
yy)] = self.data[np.ix_(tt, xx, yy)] + blip
except:
g.alert(
'Error - Puff might be too large, too long or too close to edge'
)
else:
self.data[np.ix_(tt, xx,
yy)] = self.data[np.ix_(tt, xx, yy)] + blip
frame = self.currentWin.currentIndex
self.currentWin.imageview.setImage(self.data)
self.currentWin.image = self.data
self.currentWin.setIndex(frame)
print(
'Puff added at time: {}, x: {}, y: {} with duration: {}, sigma: {}, amplitude:{}'
.format(t, x, y, duration, sigma, amp))
return
def load_file_gui():
prompt = 'Open file'
filetypes = '*'
filename = open_file_gui(prompt=prompt, filetypes=filetypes)
ext = os.path.splitext(filename)[-1]
print(ext)
if ext == '.flika':
msg = "To open .flika files use puff detector plugin"
g.alert(msg)
if filename in g.settings['recent_files']:
g.settings['recent_files'].remove(filename)
# make_recent_menu()
return
elif ext in ['.tif', '.stk', '.tiff', '.ome']:
open_file(str(filename))
return
elif ext == '.nd2':
g.m.statusBar().showMessage(
'Reading {} using python-bioformats'.format(
os.path.basename(filename)))
A = read_image_series(filename)
g.m.statusBar().showMessage('Array shape {} '.format(A.shape))
print('Array shape {} '.format(A.shape))
mt = A.shape[0]
channels = A.shape[1]
mXX = A.shape[2] #not sure what this dimension is...
mx = A.shape[3]
my = A.shape[4]
if channels > 1 or mXX > 1:
g.alert('Array shape not supported')
return
A = A.reshape(mt, mx, my)
Window(A)
g.m.statusBar().showMessage('Successfully loaded {} '.format(
os.path.basename(filename)))
# elif ext == '.nd2':
# import nd2reader
# nd2 = nd2reader.ND2Reader(str(filename))
# axes = nd2.axes
# print(axes)
# mx = nd2.metadata['width']
# my = nd2.metadata['height']
# mt = nd2.metadata['total_images_per_channel']
# print(nd2.metadata['width'], nd2.metadata['height'], nd2.metadata['total_images_per_channel'])
# A = np.zeros((mt, mx, my))
# percent = 0
# for frame in range(mt):
# A[frame] = nd2[frame].T
# if percent < int(100 * float(frame) / mt):
# percent = int(100 * float(frame) / mt)
# g.m.statusBar().showMessage('Loading file {}%'.format(percent))
# QtWidgets.qApp.processEvents()
# metadata = nd2.metadata
elif ext == '.py':
from ..app.script_editor import ScriptEditor
ScriptEditor.importScript(filename)
return
elif ext == '.whl':
# first, remove trailing (1) or (2)
newfilename = re.sub(r' \([^)]*\)', '', filename)
try:
os.rename(filename, newfilename)
except FileExistsError:
pass
filename = newfilename
result = subprocess.call(
[sys.executable, '-m', 'pip', 'install', '{}'.format(filename)])
if result == 0:
g.alert('Successfully installed {}'.format(filename))
else:
g.alert('Install of {} failed'.format(filename))
return
elif ext == '.jpg' or ext == '.png':
import skimage.io
A = skimage.io.imread(filename)
if len(A.shape) == 3:
perm = get_permutation_tuple(['y', 'x', 'c'], ['x', 'y', 'c'])
A = np.transpose(A, perm)
metadata['is_rgb'] = True
else:
msg = "Could not open. Filetype for '{}' not recognized".format(
filename)
g.alert(msg)
if filename in g.settings['recent_files']:
g.settings['recent_files'].remove(filename)
# make_recent_menu()
return