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 DoRegionScan(x, y, z, position):
global aborted
global output
global cube_data
global action
if aborted:
return
rs_points = []
rs_points.append((x - xoffset, y - yoffset))
rs_points.append((x, y - yoffset))
rs_points.append((x + xoffset, y - yoffset))
rs_points.append((x + xoffset, y))
rs_points.append((x, y))
rs_points.append((x - xoffset, y))
rs_points.append((x - xoffset, y + yoffset))
rs_points.append((x, y + yoffset))
rs_points.append((x + xoffset, y + yoffset))
rs_point_count = 1
# Loop region scan points
for rs_point in rs_points:
if aborted:
return
for cube in cubes:
if aborted:
return
microscope.MoveCubeToPosition(cube)
SetExposureAndGain(cube - 1)
if cube == 1:
Move(rs_point[0], rs_point[1], z, cube - 1)
# We are on the first cube so we do an autofocus
print "Performing AutoFocus"
microscope.PerformSoftwareAutoFocus()
SnapAndSave(cube - 1, rs_point_count)
rs_point_count = rs_point_count + 1
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 OnNewPoint(x, y, z, position):
global core
global output
global cube_data
output_directory = output[0]
filename = output[1]
filename_ext = output[2]
# Move to first cube to perform autofocus.
microscope.MoveCubeToPosition(1)
# AutoFocus Once for each new point (centre point)
print "Performing AutoFocus"
microscope.PerformSoftwareAutoFocus()
for cube in cubes:
if aborted:
return;
print "Setting camera exposure to ", exposures[cube - 1]
microscope.SetExposure(exposures[cube - 1])
print "Setting camera gain to ", gains[cube - 1]
microscope.SetGain(gains[cube - 1])
cube_details = cube_data[cube - 1]
print "Moving to cube position ", cube
microscope.MoveCubeToPosition(cube)
print "Moving to (%d,%d)" % (x, y)
# Apply focus offset
microscope.SetStagePosition(x, y, z + focus_offsets[cube - 1])
# Wait for stage to finish moving (additional delay=0.1 seconds, time out = 1.0 seconds)
microscope.WaitForStage(0.0, 5.0)
filepath = '%s\\%s_Core%d_%s%s' % (output_directory, filename, core, cube_details["Name"], filename_ext)
print "Saving file: ", filepath
microscope.SnapAndSaveImage(filepath)
core = core + 1