def __init__(self, mapper, images):
super(ImageProcessor, self).__init__()
self.mapper = mapper
self._channels = OrderedDict()
self.metaimages = dict()
for name, image in images.iteritems():
metaimage = MetaImage()
metaimage.set_image(ccore.readImage(image))
self.metaimages[name] = [metaimage]
self.mapper.setImageSize(metaimage.width, metaimage.height)
self._setupChannels(images)
def __init__(self, mapper, images):
super(ImageProcessor, self).__init__()
self.mapper = mapper
self._channels = OrderedDict()
self.metaimages = dict()
for name, image in images.iteritems():
metaimage = MetaImage()
metaimage.set_image(ccore.readImage(image))
self.metaimages[name] = [metaimage]
self.mapper.setImageSize(metaimage.width, metaimage.height)
self._setupChannels(images)
def _run(self, meta_image):
image = meta_image.image
coords = dict(
plate=meta_image.image_container.current_plate,
pos=meta_image.coordinate.position,
time=meta_image.coordinate.time,
zslice=meta_image.coordinate.zslice,
channel=meta_image.coordinate.channel,
)
main_folder = self.params['segmentation_folder']
#FIXME: This is useful enought to put into an reusable function, maybe in utils?
locator = self.params["loader_regex"] % coords
locator_split = locator.split('/')
locator_match = '/'
for loc in locator_split[:-1]:
try:
match_candidates = os.listdir(main_folder + locator_match)
if len(match_candidates) == 0:
raise RuntimeError
except:
raise RuntimeError('No files found in ' + main_folder +
locator_match)
match_results = [
m.group() for l in match_candidates
for m in [re.search(loc, l)] if m
]
if len(match_results) != 1:
raise RuntimeError('Could not match ' + match_candidates[0] +
' with ' + loc)
locator_match += match_results[0] + '/'
match_candidates = os.listdir(main_folder + locator_match)
match_results = [
m.group() for l in match_candidates
for m in [re.search(locator_split[-1], l)] if m
]
if len(match_results) == 0:
raise RuntimeError('Could not match ', match_candidates[0], 'with',
locator_split[-1])
match_result = match_results[0]
img = ccore.readImage(main_folder + locator_match + match_result)
# img_pre = SegmentationPluginPrimary.prefilter(self, img, 2)
# img_bin = SegmentationPluginPrimary.threshold(self, img_pre, 20, 3)
container = ccore.ImageMaskContainer(image, img, False)
return container
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 _run(self, meta_image):
image = meta_image.image
coords = dict(
plate = meta_image.image_container.current_plate,
pos = meta_image.coordinate.position,
time = meta_image.coordinate.time,
zslice = meta_image.coordinate.zslice,
channel = meta_image.coordinate.channel,
)
main_folder = self.params['segmentation_folder']
#FIXME: This is useful enought to put into an reusable function, maybe in utils?
locator = self.params["loader_regex"] % coords
locator_split = locator.split('/')
locator_match = '/'
for loc in locator_split[:-1]:
try:
match_candidates = os.listdir(main_folder + locator_match)
if len(match_candidates) == 0:
raise RuntimeError
except:
raise RuntimeError('No files found in ' + main_folder + locator_match)
match_results = [m.group() for l in match_candidates for m in [re.search(loc, l)] if m]
if len(match_results) != 1:
raise RuntimeError('Could not match ' + match_candidates[0] + ' with ' + loc)
locator_match += match_results[0] + '/'
match_candidates = os.listdir(main_folder + locator_match)
match_results = [m.group() for l in match_candidates for m in [re.search(locator_split[-1], l)] if m]
if len(match_results) == 0:
raise RuntimeError('Could not match ', match_candidates[0], 'with', locator_split[-1])
match_result = match_results[0]
img = ccore.readImage(main_folder + locator_match + match_result)
# img_pre = SegmentationPluginPrimary.prefilter(self, img, 2)
# img_bin = SegmentationPluginPrimary.threshold(self, img_pre, 20, 3)
container = ccore.ImageMaskContainer(image, img, False)
return container
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