def setup(self, path,
extensions=None, ignore_prefixes=None, multi_image=None):
self.path = os.path.normpath(path)
self.extensions = self.EXTENSIONS if extensions is None \
else extensions
self.ignore_prefixes = self.IGNORE_PREFIXES if ignore_prefixes is None \
else ignore_prefixes
self.multi_image = self.MULTIIMAGE_USE_ZSLICE if multi_image is None \
else multi_image
self.has_multi_images = False
self.timestamps_from_file = None
self.use_frame_indices = False
self.dimension_lookup = {}
self.meta_data = MetaData()
def setup(self, path, extensions=None, ignore_prefixes=None, multi_image=None):
self.path = os.path.normpath(path)
self.extensions = self.EXTENSIONS if extensions is None else extensions
self.ignore_prefixes = self.IGNORE_PREFIXES if ignore_prefixes is None else ignore_prefixes
self.multi_image = self.MULTIIMAGE_USE_ZSLICE if multi_image is None else multi_image
self.has_multi_images = False
self.timestamps_from_file = None
self.use_frame_indices = False
self.dimension_lookup = {}
self.meta_data = MetaData()
class AbstractImporter(XmlSerializer):
EXTENSIONS = [".tif", ".png", ".png"]
IGNORE_PREFIXES = ["."]
MULTIIMAGE_IGNORE = "ignore"
MULTIIMAGE_USE_ZSLICE = "zslice"
def __init__(self):
super(AbstractImporter, self).__init__()
def setup(self, path, extensions=None, ignore_prefixes=None, multi_image=None):
self.path = os.path.normpath(path)
self.extensions = self.EXTENSIONS if extensions is None else extensions
self.ignore_prefixes = self.IGNORE_PREFIXES if ignore_prefixes is None else ignore_prefixes
self.multi_image = self.MULTIIMAGE_USE_ZSLICE if multi_image is None else multi_image
self.has_multi_images = False
self.timestamps_from_file = None
self.use_frame_indices = False
self.dimension_lookup = {}
self.meta_data = MetaData()
def __setstate__(self, state):
for k, v in state.iteritems():
self.__dict__[k] = v
def scan(self):
self.dimension_lookup = self._build_dimension_lookup()
self.meta_data.setup()
@property
def is_valid(self):
"""
Return the import success. For now only the number of identified files
is checked.
"""
return self.meta_data.image_files > 0
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 _build_dimension_lookup(self):
s = StopWatch(start=True)
lookup = {}
has_xy = False
positions = []
times = []
channels = []
zslices = []
dimension_items = self._get_dimension_items()
print("Get dimensions: %s" % s.interim())
s.reset(start=True)
# if use_frame_indices is set in the ini file,
# we make a first scan of the items and determine for each position
# the list of timepoints.
# Then, we can assign to each position a dictionary that assigns to each timepoint
# its index (after ordering).
if self.use_frame_indices:
# all_times = list(set([int(item[Dimensions.Time]) if Dimensions.Time in item else 0
# for item in dimension_items]))
# all_times.sort()
first_pass = {}
for item in dimension_items:
position = item[Dimensions.Position]
if not position in first_pass:
first_pass[position] = []
if Dimensions.Time in item:
time_val = int(item[Dimensions.Time])
else:
time_val = 0
first_pass[position].append(time_val)
time_index_correspondence = {}
for pos in first_pass.keys():
first_pass[position].sort()
time_index_correspondence[pos] = dict(zip(first_pass[position], range(len(first_pass[position]))))
for item in dimension_items:
# import image info only once
if not has_xy:
has_xy = True
info = ccore.ImageImportInfo(os.path.join(self.path, item["filename"]))
self.meta_data.set_image_info(info)
self.has_multi_images = False # info.images > 1
# position
position = item[Dimensions.Position]
if not position in lookup:
lookup[position] = {}
# time
if Dimensions.Time in item:
time_from_filename = int(item[Dimensions.Time])
else:
time_from_filename = 0
item[Dimensions.Time] = str(time_from_filename)
if self.use_frame_indices:
time = time_index_correspondence[position][time_from_filename]
else:
time = time_from_filename
if not time in lookup[position]:
lookup[position][time] = {}
# channels
if Dimensions.Channel in item:
channel = item[Dimensions.Channel]
else:
channel = "1"
item[Dimensions.Channel] = channel
if not channel in lookup[position][time]:
lookup[position][time][channel] = {}
# leave zslice optional.
# in case of multi-images it must not be defined
if Dimensions.ZSlice in item:
zslice = item[Dimensions.ZSlice]
else:
zslice = 0
item[Dimensions.ZSlice] = zslice
if zslice == "":
zslice = None
if not zslice is None:
zslice = int(zslice)
if not zslice in lookup[position][time][channel]:
lookup[position][time][channel][zslice] = item["filename"]
# allow to read timestamps from file if not present
if MetaInfo.Timestamp in item:
timestamp = float(item[MetaInfo.Timestamp])
self.meta_data.append_absolute_time(position, time, timestamp)
elif self.timestamps_from_file in ["mtime", "ctime"]:
filename_full = os.path.join(self.path, item["filename"])
if self.timestamps_from_file == "mtime":
timestamp = os.path.getmtime(filename_full)
else:
timestamp = os.path.getctime(filename_full)
item[MetaInfo.Timestamp] = timestamp
self.meta_data.append_absolute_time(position, time, timestamp)
if MetaInfo.Well in item:
well = item[MetaInfo.Well]
subwell = item.get(MetaInfo.Subwell, None)
self.meta_data.append_well_subwell_info(position, well, subwell)
if self.has_multi_images and self.multi_image == self.MULTIIMAGE_USE_ZSLICE:
if not zslice is None:
raise ValueError("Multi-image assigned for zslice conflicts" " with zslice token in filename!")
zslices.extend(range(1, info.images + 1))
else:
zslices.append(zslice)
positions.append(position)
times.append(time)
channels.append(channel)
self.meta_data.positions = tuple(sorted(set(positions)))
# assure that all items of one dimension are of same length
times = set(times)
channels = set(channels)
zslices = set(zslices)
# find overall valid number of frames
for p in lookup:
times = times.intersection(lookup[p].keys())
# find overall valid channels/zslices based on overall valid frames
for p in lookup:
for t in times:
channels = channels.intersection(lookup[p][t].keys())
for c in channels:
zslices = zslices.intersection(lookup[p][t][c].keys())
self.meta_data.times = sorted(times)
self.meta_data.channels = sorted(channels)
self.meta_data.zslices = sorted(zslices)
self.meta_data.image_files = len(dimension_items)
print("Build time: %s" % s.stop())
return lookup
def _get_dimension_items(self):
raise NotImplementedError()
class AbstractImporter(XmlSerializer):
EXTENSIONS = ['.tif', '.png', '.png']
IGNORE_PREFIXES = ['.']
MULTIIMAGE_IGNORE = 'ignore'
MULTIIMAGE_USE_ZSLICE = 'zslice'
def __init__(self):
super(AbstractImporter, self).__init__()
def setup(self,
path,
extensions=None,
ignore_prefixes=None,
multi_image=None):
self.path = os.path.normpath(path)
self.extensions = self.EXTENSIONS if extensions is None \
else extensions
self.ignore_prefixes = self.IGNORE_PREFIXES if ignore_prefixes is None \
else ignore_prefixes
self.multi_image = self.MULTIIMAGE_USE_ZSLICE if multi_image is None \
else multi_image
self.has_multi_images = False
self.timestamps_from_file = None
self.use_frame_indices = False
self.dimension_lookup = {}
self.meta_data = MetaData()
def __setstate__(self, state):
for k, v in state.iteritems():
self.__dict__[k] = v
def scan(self):
self.dimension_lookup = self._build_dimension_lookup()
self.meta_data.setup()
@property
def is_valid(self):
"""
Return the import success. For now only the number of identified files
is checked.
"""
return self.meta_data.image_files > 0
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 _build_dimension_lookup(self):
s = StopWatch(start=True)
lookup = {}
has_xy = False
positions = []
times = []
channels = []
zslices = []
dimension_items = self._get_dimension_items()
print("Get dimensions: %s" % s.interim())
s.reset(start=True)
# if use_frame_indices is set in the ini file,
# we make a first scan of the items and determine for each position
# the list of timepoints.
# Then, we can assign to each position a dictionary that assigns to each timepoint
# its index (after ordering).
if self.use_frame_indices:
#all_times = list(set([int(item[Dimensions.Time]) if Dimensions.Time in item else 0
# for item in dimension_items]))
#all_times.sort()
first_pass = {}
for item in dimension_items:
position = item[Dimensions.Position]
if not position in first_pass:
first_pass[position] = []
if Dimensions.Time in item:
time_val = int(item[Dimensions.Time])
else:
time_val = 0
first_pass[position].append(time_val)
time_index_correspondence = {}
for pos in first_pass.keys():
first_pass[position].sort()
time_index_correspondence[pos] = dict(
zip(first_pass[position],
range(len(first_pass[position]))))
for item in dimension_items:
# import image info only once
if not has_xy:
has_xy = True
info = ccore.ImageImportInfo(
os.path.join(self.path, item['filename']))
self.meta_data.set_image_info(info)
self.has_multi_images = False #info.images > 1
# position
position = item[Dimensions.Position]
if not position in lookup:
lookup[position] = {}
# time
if Dimensions.Time in item:
time_from_filename = int(item[Dimensions.Time])
else:
time_from_filename = 0
item[Dimensions.Time] = str(time_from_filename)
if self.use_frame_indices:
time = time_index_correspondence[position][time_from_filename]
else:
time = time_from_filename
if not time in lookup[position]:
lookup[position][time] = {}
# channels
if Dimensions.Channel in item:
channel = item[Dimensions.Channel]
else:
channel = '1'
item[Dimensions.Channel] = channel
if not channel in lookup[position][time]:
lookup[position][time][channel] = {}
# leave zslice optional.
# in case of multi-images it must not be defined
if Dimensions.ZSlice in item:
zslice = item[Dimensions.ZSlice]
else:
zslice = 0
item[Dimensions.ZSlice] = zslice
if zslice == '':
zslice = None
if not zslice is None:
zslice = int(zslice)
if not zslice in lookup[position][time][channel]:
lookup[position][time][channel][zslice] = item['filename']
# allow to read timestamps from file if not present
if MetaInfo.Timestamp in item:
timestamp = float(item[MetaInfo.Timestamp])
self.meta_data.append_absolute_time(position, time, timestamp)
elif self.timestamps_from_file in ['mtime', 'ctime']:
filename_full = os.path.join(self.path, item['filename'])
if self.timestamps_from_file == 'mtime':
timestamp = os.path.getmtime(filename_full)
else:
timestamp = os.path.getctime(filename_full)
item[MetaInfo.Timestamp] = timestamp
self.meta_data.append_absolute_time(position, time, timestamp)
if MetaInfo.Well in item:
well = item[MetaInfo.Well]
subwell = item.get(MetaInfo.Subwell, None)
self.meta_data.append_well_subwell_info(
position, well, subwell)
if (self.has_multi_images
and self.multi_image == self.MULTIIMAGE_USE_ZSLICE):
if not zslice is None:
raise ValueError(
'Multi-image assigned for zslice conflicts'
' with zslice token in filename!')
zslices.extend(range(1, info.images + 1))
else:
zslices.append(zslice)
positions.append(position)
times.append(time)
channels.append(channel)
self.meta_data.positions = tuple(sorted(set(positions)))
# assure that all items of one dimension are of same length
times = set(times)
channels = set(channels)
zslices = set(zslices)
# find overall valid number of frames
for p in lookup:
times = times.intersection(lookup[p].keys())
# find overall valid channels/zslices based on overall valid frames
for p in lookup:
for t in times:
channels = channels.intersection(lookup[p][t].keys())
for c in channels:
zslices = zslices.intersection(lookup[p][t][c].keys())
self.meta_data.times = sorted(times)
self.meta_data.channels = sorted(channels)
self.meta_data.zslices = sorted(zslices)
self.meta_data.image_files = len(dimension_items)
print('Build time: %s' % s.stop())
return lookup
def _get_dimension_items(self):
raise NotImplementedError()