##turn off afc so that you could do an MDA if you wanted
scope.mmc.enableContinuousFocus(False)
## Take your images
channels=[Illuminations.BF2]
if int(pos_label[3:])< 17:
channels=[Illuminations.BF2,Illuminations.dimGREEN,Illuminations.dimRED]
elif int(pos_label[3:])>17 and int(pos_label[3:])<25:
channels=[Illuminations.BF2,Illuminations.dimRED]
elif int(pos_label[3:])>25:
channels=[Illuminations.BF2,Illuminations.dimGREEN]
images,metadata=scope.complicated_multichannel_zstack(channels,
z_width=3,
z_increments=1,
channels_for_z=channels[:1])
file_name="Timelapse_%s_t%s" % (pos_label,i)
FileOut.mda_save2(out_dir=save_dir,prefix=file_name,
mda=images,md=metadata,channels=channels)
#for channel in channels:
# scope.set_illumination(channel)
# scope.mmc.snapImage()
# img=scope.mmc.getImage()
# md=scope.getFullSystemState()
# # save your images
# file_name="Timelapse_%s_%s_t%s" % (pos_label,channel.name,i)
# save_loc=os.path.join(save_dir,file_name)
# FileOut.tif_writer(numpy_array=img,path=save_loc,md_string=md)
# if pos_label=="Pos4":
# break ## this position will only take the first channel
# record location info
loc_data="%s;%s;%s;%s;%s;%s;%s;%s;%s;%s;%s;%s;%s;%s\n" % (pos_label,
i,
x,
def plateScan(scope,
positions,
scan_illumination,
mda_channels,
prefix="",
blacklist=[],
well_limit=15,
well_count_dict={},
data_dir="",
visible=True,
stack_height=5,
slice_height=.5,
minAreaCOI=100,
maxAreaCOI=1000,
thresholdCOI=1000):
"""
Write the doc string!!
"""
if prefix=="":
prefix=time.asctime().replace(" ","_").replace(":","_")
if data_dir is not "":
if os.path.isdir(data_dir) is False:
os.mkdir(data_dir)
data_dir=os.path.join(data_dir,"Scan_%s" % prefix)
if os.path.isdir(data_dir) is False:
os.mkdir(data_dir)
order=-1
## set up the
rows=string.ascii_uppercase[1:7]
columns=range(2,12)
sites=range(0,225)
well_count_dict={}
for row in rows:
## flip the order that the columns are gone through
order=order*-1
for column in columns[::order]:
well="%s%s" % (row,column)
if well not in well_count_dict: well_count_dict[well]=0
if well not in blacklist:
for site in sites:
try:
#if scope.mmc.isContinuousFocusLocked() is False:
# ## try waiting a few seconds
# time.sleep(10)
# if scope.mmc.isContinuousFocusLocked() is False:
# ## tried waiting, that didnt work, lets exit
# print "Lost focus on %s site %s" % (well, site)
# return well_count_dict
x,y=positions["%s%s-Site_%s" % (row,column,site)].get_xy()
scope.mmc.setXYPosition("XYStage",x,y)
print ">Looking at %s%s-Site_%s" % (row,column,site)
site_name="%s%s-Site_%s" % (row,column,site)
site_imaged,mda,md = plateScanSite(scope,
scan_illumination,
mda_channels,
x,
y,
name=site_name,
visible=visible,
stack_height=stack_height,
slice_height=slice_height,
minAreaCOI=minAreaCOI,
maxAreaCOI=maxAreaCOI,
thresholdCOI=thresholdCOI)
well_count_dict[well]+=site_imaged
if mda:
FileOut.mda_save2(out_dir=data_dir,
prefix="%s%s-Site_%s" % (row,
column,
site),
mda=mda,
md=md,
channels=mda_channels)
del mda
del md
del site_imaged
if well_count_dict[well] >= well_limit:
count = well_count_dict[well]
print "I have found %s cells/stacks in %s" %(count,
well)
break
if scope.mmc.isContinuousFocusLocked() is False:
## try waiting a few seconds
time.sleep(10)
if scope.mmc.isContinuousFocusLocked() is False:
## tried waiting, that didnt work, lets exit
msg="Lost focus on %s site %s" % (well, site)
print msg
return str(well_count_dict)+"\n\n"+msg
except:
tb=StringIO.StringIO()
exc_type, exc_value, exc_traceback = sys.exc_info()
traceback.print_exception(exc_type,
exc_value,
exc_traceback,
file=tb)
message=str(well_count_dict)+"\n\n"+tb.getvalue()
return message
return well_count_dict