def run(imagefile, verbose=False):
# open image file and get a specific series
log.log(LogLevel.INFO, 'Opening Image: ' + imagefile)
imp, MetaInfo = ImportTools.openfile(imagefile)
# output of image metadata in log window
if verbose:
for k, v in MetaInfo.items():
log.log(LogLevel.INFO, str(k) + ' : ' + str(v))
log.log(LogLevel.INFO, 'File Extension : ' + MetaInfo['Extension'])
if 'ResolutionCount' in MetaInfo:
log.log(LogLevel.INFO,
'Resolution Count : ' + str(MetaInfo['ResolutionCount']))
if 'SeriesCount' in MetaInfo:
log.log(LogLevel.INFO,
'SeriesCount : ' + str(MetaInfo['SeriesCount']))
if 'SizeC' in MetaInfo:
log.log(LogLevel.INFO, 'Channel Count : ' + str(MetaInfo['SizeC']))
# do the processing
log.log(LogLevel.INFO, 'Start Processing ...')
# create empty image list
imglist = []
numch = imp.getNChannels()
# do the processing
for ch in range(numch):
# get a channel
imp_c = MiscTools.splitchannel(imp, ch)
name = os.path.basename(imagefile) + '_CH=' + str(ch)
sp, fv, fv_max, fv_max_index = calc_focus(imp_c, name)
log.log(LogLevel.INFO, 'Processing Channel : ' + str(ch))
log.log(LogLevel.INFO, 'Max. Value : ' + str(fv_max))
log.log(LogLevel.INFO, 'Max. Value Slice : ' + str(fv_max_index))
# set correct image properties
sp = MiscTools.setproperties(sp,
scaleX=MetaInfo['ScaleX'],
scaleY=MetaInfo['ScaleY'],
scaleZ=MetaInfo['ScaleZ'],
unit='micron',
sizeC=1,
sizeZ=1,
sizeT=1)
imglist.append(sp)
# in case of more than one channel use an jarray
if numch > 1:
# create an array
imgarray = jarray.array(imglist, ImagePlus)
# create an ImageStack from the array
imgstack = ImageStack.create(imgarray)
# create an ImagePlus object from the jarray
new_name = os.path.splitext(os.path.basename(imagefile))[0]
imp_sp = ImagePlus(new_name + '_SHARPEST', imgstack)
# ic case of exactly one channel directly use the ImgPlus
if numch == 1:
imp_sp = imglist[0]
# set correct image properties for the final image
imp_sp = MiscTools.setproperties(imp_sp,
scaleX=MetaInfo['ScaleX'],
scaleY=MetaInfo['ScaleY'],
scaleZ=MetaInfo['ScaleZ'],
unit='micron',
sizeC=numch,
sizeZ=1,
sizeT=1)
return imp_sp
def run(imagefile, verbose=False):
# open image file and get a specific series
log.log(LogLevel.INFO, 'Opening Image: ' + imagefile)
imp, MetaInfo = ImportTools.openfile(imagefile)
# output of image metadata in log window
if verbose:
for k, v in MetaInfo.items():
log.log(LogLevel.INFO, str(k) + ' : ' + str(v))
log.log(LogLevel.INFO, 'File Extension : ' + MetaInfo['Extension'])
if 'ResolutionCount' in MetaInfo:
log.log(LogLevel.INFO,
'Resolution Count : ' + str(MetaInfo['ResolutionCount']))
if 'SeriesCount' in MetaInfo:
log.log(LogLevel.INFO,
'SeriesCount : ' + str(MetaInfo['SeriesCount']))
if 'SizeC' in MetaInfo:
log.log(LogLevel.INFO, 'Channel Count : ' + str(MetaInfo['SizeC']))
# do the processing
log.log(LogLevel.INFO, 'Start Processing ...')
# create empty image list
imglist_t_c = []
imglist_t = []
numch = imp.getNChannels()
# do the processing
for t in range(MetaInfo['SizeT']):
# get the timepoint
imp_t = getstackfrom5d(imp,
MetaInfo,
firstC=1,
lastC=MetaInfo['SizeC'],
firstZ=1,
lastZ=MetaInfo['SizeZ'],
firstT=t + 1,
lastT=t + 1)
# calc the focus values for the different channels
for ch in range(numch):
# get a stack for a channel
imp_t_c = getstackfrom5d(imp_t,
MetaInfo,
firstC=ch + 1,
lastC=ch + 1,
firstZ=1,
lastZ=MetaInfo['SizeZ'],
firstT=1,
lastT=1)
# create a name for the plane
#name = os.path.basename(imagefile) + 'T=' + str(t+1) + '_CH=' + str(ch+1)
name = 'T=' + str(t + 1) + '_CH=' + str(ch + 1)
# get the plane with the bst focus to the current timepoint and current channel
sp_c, fv, fv_max, fv_max_index = calc_focus(imp_t_c, name)
log.log(LogLevel.INFO, 'Processing TimePoint : ' + str(t + 1))
log.log(LogLevel.INFO, 'Processing Channel : ' + str(ch + 1))
log.log(LogLevel.INFO, 'Max. Value : ' + str(fv_max))
log.log(LogLevel.INFO,
'Max. Value Slice : ' + str(fv_max_index))
# set correct image properties
sp_c = MiscTools.setproperties(sp_c,
scaleX=MetaInfo['ScaleX'],
scaleY=MetaInfo['ScaleY'],
scaleZ=MetaInfo['ScaleZ'],
unit='micron',
sizeC=1,
sizeZ=1,
sizeT=1)
imglist_t_c.append(sp_c)
print 'List CH Stacks :', len(imglist_t_c)
for i in range(len(imglist_t_c)):
print str(i) + ' : ', type(imglist_t_c[i])
# in case of more than one channel use an jarray
if numch > 1:
# create an array
imgarray_c = jarray.array(imglist_t_c, ImagePlus)
# create an ImageStack from the array
print 'Type imgarray_c : ', type(imgarray_c)
for i in range(numch):
print type(imgarray_c[i])
imgstack_c = ImageStack.create(imgarray_c)
# create an ImagePlus object from the jarray
new_name = os.path.splitext(os.path.basename(imagefile))[0]
imp_sp_c = ImagePlus(new_name + '_SHARPEST_C', imgstack_c)
# in case of exactly one channel directly use the ImgPlus
if numch == 1:
imp_sp_c = imglist_t_c[0]
# set correct image properties for the final image
imp_sp_c = MiscTools.setproperties(imp_sp_c,
scaleX=MetaInfo['ScaleX'],
scaleY=MetaInfo['ScaleY'],
scaleZ=MetaInfo['ScaleZ'],
unit='micron',
sizeC=numch,
sizeZ=1,
sizeT=1)
# concatenate the timepoints
imglist_t.append(imp_sp_c)
if numch > 1:
# create an array
imgarray = jarray.array(imglist_t, ImagePlus)
# create an ImageStack from the array
imgstack = ImageStack.create(imgarray)
# create an ImagePlus object from the jarray
new_name = os.path.splitext(os.path.basename(imagefile))[0]
imp_sp_t = ImagePlus(new_name + '_SHARPEST_CT', imgstack)
# in case of exactly one channel directly use the ImgPlus
if numch == 1:
imp_sp_t = imglist_t[0]
return imp_sp_t
namepattern = os.path.splitext(os.path.basename(imagefile))[0]
stack = MiscTools.import_sequence(targetdir,
number=MetaInfo['SizeZ'],
start=1,
increment=1,
filepattern=namepattern,
sort=True,
use_virtualstack=False)
# set properties for new stack
stack = MiscTools.setproperties(stack,
scaleX=MetaInfo['ScaleX'],
scaleY=MetaInfo['ScaleY'],
scaleZ=MetaInfo['ScaleZ'],
unit="micron",
sizeC=MetaInfo['SizeC'],
sizeZ=MetaInfo['SizeZ'],
sizeT=MetaInfo['SizeT'])
# save the registered stack
savepath_stack = ExportTools.savedata(stack,
outputimagepath,
extension=saveformat,
replace=True)
stack.close()
log.info('SavePath Registered Stack : ' + savepath_stack)
# read the registered stack