def OnStart():
global output
print "Stage Position, ", microscope.GetStagePosition()
print microscope.GetTimeLapsePoints()
data_dir = microscope.GetUserDataDirectory()
output = microscope.ShowFileSequenceSaveDialog(data_dir)
print "Saving to directory ", output[0]
print "Filename Format ", output[1]
def OnNewPoint(x, y, z, position):
global aborted, point_list
print "Point: ", position
print("input: x %f, y %f, z %f" % (x, y, z))
print "list: ", point_list[position - 1][2]
# Adjust z to last autofocus position, first time round these two will be the same
z = point_list[position - 1][2]
print "Adjust z to last autofocus position: z=", z
if aborted:
pass
microscope.SetStagePosition(x, y, z)
# Wait for stage to finish moving (additional delay seconds, time out seconds)
microscope.WaitForStage(0.0, 1.0)
output_directory = output[0]
filename = output[1]
filename_ext = output[2]
#filename = microscope.ParseSequenceFilename(filename, position)
#filename = microscope.InsertCubeIntoFilename(filename, current_cube_index+1)
#subdir = '%s\\Cube%d\\Region%d\\' % (output_directory, cubes[current_cube_index], position)
#subdir = '%s\\Region%d\\' % (output_directory, position)
subdir = '%s\\Region%d_%s\\' % (output_directory, position,
time.strftime("%d%b%Y_%Hh%Mm%Ss",
time.localtime(time.time())))
try:
os.makedirs(subdir)
except (OSError):
print 'os.makedirs(' + subdir + ') FAILED'
print "Autofocus"
microscope.PerformSoftwareAutoFocus()
autoFocusedZPosition = microscope.GetStagePosition()[2]
point_list[position - 1][2] = autoFocusedZPosition
print "Auto focused position stored:", point_list[position - 1][2]
# get the focal plane options for this region and transfer to the region scan module, correct for the autofocus
rs.SetFocalPlaneOptions(microscope.GetFocalPlaneOptions())
rs.SetFocalPlaneOffsetFromXYZ(x, y, autoFocusedZPosition)
# Set region scan with the region width and height
rs.SetRelativeRoiFromTimelapse(microscope.GetTimeLapseRegion())
rs.Start(action, subdir, filename, filename_ext)
rs.Hide()
def OnNewPoint(x, y, z, position):
# print "Moving Stage ", (x, y, z)
microscope.SetStagePosition(x, y, z)
# wait for stage to finish moving (additional delay=0.1 seconds, time out = 1.0 seconds)
microscope.WaitForStage(0.0, 1.0)
filename = microscope.ParseSequenceFilename(output[1], position)
path = output[0] + filename
microscope.PerformSoftwareAutoFocus(path)
microscope.SnapAndSaveImage(path)
#mrowley - 081209 - recording the software auto focus determined focal point for the given well
xf, yf, zf = microscope.GetStagePosition()
filenameautopts = 'AutoFocusedPlane.pts'
path = output[0] + filenameautopts
fileautopts = open(path, 'a')
fileautopts.write('%.2f' %xf + '\t' + '%.2f' %yf + '\t' + '%.2f' %zf + '\n')
fileautopts.close()
def OnStart():
global cubes
print "Stage Position, ", microscope.GetStagePosition()
print microscope.GetTimeLapsePoints()
try:
# Try to autoexpose within the range of 1 and 60 milli seconds
# Performing AutoExposure
print "Performing autoexposure"
microscope.PerformAutoExposure(1, 60)
except:
print "Could not calculate autoexposure. Is there enough light ?"
try:
print "Retrieving Cubes"
cubes = microscope.GetCubes()
except:
print "Could not get cubes"
def OnStart():
print "Stage Position, ", microscope.GetStagePosition()
print microscope.GetTimeLapsePoints()
def SetRelativeRoiFromTimelapse(self, r):
"""Set the region of interest in microns relative from the current stage position from a width, heigth tuple"""
x, y, z = microscope.GetStagePosition()
half_width = r[0] / 2
half_height = r[1] / 2
self.SetRoi(x - half_width, y - half_height, r[0], r[1])
def SetRelativeRoi(self, width, height):
"""Set the region of interest in microns relative from the current stage position"""
x, y, z = microscope.GetStagePosition()
half_width = width / 2
half_height = height / 2
self.SetRoi(x - half_width, y - half_height, width, height)
