def calcFeature(self, imgContainer, pos, t, channels, primary_channel):
primary_filename = os.path.join(
self.inDir, imgContainer[pos][t][primary_channel]['path'],
imgContainer[pos][t][primary_channel]['filename'])
imgMask = self.getBackgroundROI(primary_filename)
res = {}
for channel in channels:
filename = os.path.join(self.inDir,
imgContainer[pos][t][channel]['path'],
imgContainer[pos][t][channel]['filename'])
imgIn = ccore.readImageUInt16(filename)
if self.oSettings.write_images:
plate = os.path.split(os.path.realpath(self.inDir))[-1]
outFilenameBase = os.path.join(
self.oSettings.output_images_dir, plate, pos,
imgContainer[pos][t][channel]['filename'])
else:
outFilenameBase = None
res[channel] = self.getBackgroundForImage(imgIn, imgMask,
outFilenameBase)
return
def getBackgroundROI(self, primary_name):
imgIn = ccore.readImageUInt16(primary_name)
imgConv = ccore.conversionTo8Bit(imgIn, 2**15, 2**15 + 4096, 0, 255)
imgSeg = ccore.window_average_threshold(imgConv, 50, 3)
imgDil = ccore.dilate(imgSeg, 20, 8)
imgMask = ccore.threshold(imgDil, 1, 255, 255, 0)
return imgMask
def get_image(self, coordinate):
index = 0
zslice = coordinate.zslice
if self.has_multi_images and self.multi_image == self.MULTIIMAGE_USE_ZSLICE:
index = zslice - 1
zslice = None
filename_rel = self.dimension_lookup[coordinate.position][coordinate.time][coordinate.channel][zslice]
filename_abs = os.path.join(self.path, filename_rel)
# make sure no back-slashes are left in the path
filename_abs = filename_abs.replace("\\", "/")
if self.meta_data.pixel_type == PixelType.name(PixelType.Uint8):
image = ccore.readImage(filename_abs, index)
elif self.meta_data.pixel_type == PixelType.name(PixelType.Uint16):
image = ccore.readImageUInt16(filename_abs, index)
else:
image = ccore.readImageUInt16(filename_abs, index)
return image
def get_image(self, coordinate):
index = 0
zslice = coordinate.zslice
if (self.has_multi_images
and self.multi_image == self.MULTIIMAGE_USE_ZSLICE):
index = zslice - 1
zslice = None
filename_rel = self.dimension_lookup[coordinate.position] \
[coordinate.time] \
[coordinate.channel] \
[zslice]
filename_abs = os.path.join(self.path, filename_rel)
# make sure no back-slashes are left in the path
filename_abs = filename_abs.replace('\\', '/')
if self.meta_data.pixel_type == UINT8:
image = ccore.readImage(filename_abs, index)
elif self.meta_data.pixel_type == UINT16:
image = ccore.readImageUInt16(filename_abs, index)
else:
image = ccore.readImageUInt16(filename_abs, index)
return image
def calcFeature(self, imgContainer, pos, t, channels, primary_channel):
res = {}
for channel in channels:
filename = os.path.join(self.inDir,
imgContainer[pos][t][channel]['path'],
imgContainer[pos][t][channel]['filename'])
imgIn = ccore.readImageUInt16(filename)
imgConv = ccore.conversionTo8Bit(imgIn, 2**15, 2**15 + 4096, 0,
255)
res[channel] = self.getFocusMeasurementFilterSeries(
imgConv, self.method, self.gauss_sizes)
return res