def _get_raw_image_data(self, image_group_number, channel_offset, height, width):
"""
Reads the raw bytes and the timestamp of an image.
:param image_group_number: groups are made of images with the same time index, field of view and z-level.
:type image_group_number: int
:param channel_offset: the offset in the array where the bytes for this image are found.
:type channel_offset: int
:return: (int, array.array()) or None
"""
chunk = self._label_map[six.b("ImageDataSeq|%d!" % image_group_number)]
data = read_chunk(self._file_handle, chunk)
# All images in the same image group share the same timestamp! So if you have complicated image data,
# your timestamps may not be entirely accurate. Practically speaking though, they'll only be off by a few
# seconds unless you're doing something super weird.
timestamp = struct.unpack("d", data[:8])[0]
image_group_data = array.array("H", data)
image_data_start = 4 + channel_offset
# The images for the various channels are interleaved within the same array. For example, the second image
# of a four image group will be composed of bytes 2, 6, 10, etc. If you understand why someone would design
# a data structure that way, please send the author of this library a message.
image_data = np.reshape(image_group_data[image_data_start::len(self._metadata.channels)], (height, width))
# Skip images that are all zeros! This is important, since NIS Elements creates blank "gap" images if you
# don't have the same number of images each cycle. We discovered this because we only took GFP images every
# other cycle to reduce phototoxicity, but NIS Elements still allocated memory as if we were going to take
# them every cycle.
if np.any(image_data):
return timestamp, Image(image_data)
raise NoImageError
def _parse_metadata(self):
"""
Reads all metadata.
"""
metadata_dict = {}
self._label_map = self._build_label_map()
for label in self._label_map.keys():
if label.endswith(six.b("LV!")) or six.b("LV|") in label:
data = read_chunk(self._fh, self._label_map[label])
stop = label.index(six.b("LV"))
metadata_dict[label[:stop]] = self._read_metadata(data, 1)
height = metadata_dict[six.b('ImageAttributes')][six.b('SLxImageAttributes')][six.b('uiHeight')]
width = metadata_dict[six.b('ImageAttributes')][six.b('SLxImageAttributes')][six.b('uiWidth')]
channels = self._parse_channels(metadata_dict)
date = self._parse_date(metadata_dict)
fields_of_view = self._parse_fields_of_view(metadata_dict)
frames = self._parse_frames(metadata_dict)
z_levels = self._parse_z_levels(metadata_dict)
total_images_per_channel = self._parse_total_images_per_channel(metadata_dict)
self._metadata = Metadata(height, width, channels, date, fields_of_view, frames, z_levels, total_images_per_channel)
def _parse_metadata(self):
"""
Reads all metadata.
"""
metadata_dict = {}
self._label_map = self._build_label_map()
for label in self._label_map.keys():
if label.endswith(six.b("LV!")) or six.b("LV|") in label:
data = read_chunk(self._fh, self._label_map[label])
stop = label.index(six.b("LV"))
metadata_dict[label[:stop]] = self._read_metadata(data, 1)
height = metadata_dict[six.b("ImageAttributes")][six.b("SLxImageAttributes")][six.b("uiHeight")]
width = metadata_dict[six.b("ImageAttributes")][six.b("SLxImageAttributes")][six.b("uiWidth")]
channels = self._parse_channels(metadata_dict)
date = self._parse_date(metadata_dict)
fields_of_view = self._parse_fields_of_view(metadata_dict)
frames = self._parse_frames(metadata_dict)
z_levels = self._parse_z_levels(metadata_dict)
total_images_per_channel = self._parse_total_images_per_channel(metadata_dict)
self._metadata = Metadata(
height, width, channels, date, fields_of_view, frames, z_levels, total_images_per_channel
)
def image_calibration(self):
return read_metadata(read_chunk(self._fh, self._label_map.image_calibration), 1)
def image_metadata_sequence(self):
return read_metadata(read_chunk(self._fh, self._label_map.image_metadata_sequence), 1)
def image_text_info(self):
return read_metadata(read_chunk(self._fh, self._label_map.image_text_info), 1)
def image_metadata(self):
if self._label_map.image_metadata:
return read_metadata(read_chunk(self._fh, self._label_map.image_metadata), 1)
def image_text_info(self):
return read_metadata(read_chunk(self._fh, self._label_map.image_text_info), 1)
def custom_data(self):
return xmltodict.parse(read_chunk(self._fh, self._label_map.custom_data))
def lut_data(self):
return xmltodict.parse(read_chunk(self._fh, self._label_map.lut_data))
def grabber_settings(self):
return xmltodict.parse(read_chunk(self._fh, self._label_map.grabber_settings))
def lut_data(self):
return xmltodict.parse(read_chunk(self._fh, self._label_map.lut_data))
def roi_metadata(self):
return read_metadata(read_chunk(self._fh, self._label_map.roi_metadata), 1)
def image_attributes(self):
return read_metadata(read_chunk(self._fh, self._label_map.image_attributes), 1)
def image_calibration(self):
return read_metadata(read_chunk(self._fh, self._label_map.image_calibration), 1)
def image_metadata_sequence(self):
return read_metadata(read_chunk(self._fh, self._label_map.image_metadata_sequence), 1)
def image_attributes(self):
return read_metadata(read_chunk(self._fh, self._label_map.image_attributes), 1)
def roi_metadata(self):
return read_metadata(read_chunk(self._fh, self._label_map.roi_metadata), 1)
def custom_data(self):
return xmltodict.parse(read_chunk(self._fh, self._label_map.custom_data))
def grabber_settings(self):
return xmltodict.parse(read_chunk(self._fh, self._label_map.grabber_settings))
def app_info(self):
return xmltodict.parse(read_chunk(self._fh, self._label_map.app_info))
def app_info(self):
return xmltodict.parse(read_chunk(self._fh, self._label_map.app_info))
def image_metadata(self):
if self._label_map.image_metadata:
return read_metadata(read_chunk(self._fh, self._label_map.image_metadata), 1)
