def test_read_chunk_fail_bad_header(self):
with ArtificialND2(self.test_file) as artificial:
fh = artificial.file_handle
chunk_location = artificial.locations['image_attributes'][0]
with self.assertRaises(ValueError) as context:
read_chunk(fh, chunk_location + 1)
self.assertEquals(str(context.exception), "The ND2 file seems to be corrupted.")
def roi_metadata(self):
"""Contains information about the defined ROIs: shape, position and type (reference/background/stimulation).
Returns:
dict: ROI metadata dictionary
"""
return read_metadata(read_chunk(self._fh, self._label_map.roi_metadata), 1)
def image_attributes(self):
"""Image attributes
Returns:
dict: containing the image attributes
"""
return read_metadata(read_chunk(self._fh, self._label_map.image_attributes), 1)
def image_calibration(self):
"""The amount of pixels per micron.
Returns:
dict: pixels per micron
"""
return read_metadata(read_chunk(self._fh, self._label_map.image_calibration), 1)
def app_info(self):
"""NIS elements application info
Returns:
dict: (Version) information of the NIS Elements application
"""
return xmltodict.parse(read_chunk(self._fh, self._label_map.app_info))
def lut_data(self):
"""LUT information
Returns:
dict: LUT information
"""
return xmltodict.parse(read_chunk(self._fh, self._label_map.lut_data))
def custom_data(self):
"""Custom user data
Returns:
dict: custom user data
"""
return xmltodict.parse(read_chunk(self._fh, self._label_map.custom_data))
def grabber_settings(self):
"""Grabber settings
Returns:
dict: Acquisition settings
"""
return xmltodict.parse(read_chunk(self._fh, self._label_map.grabber_settings))
def image_metadata_sequence(self):
"""Image metadata of the sequence
Returns:
dict: containing the metadata
"""
return read_metadata(read_chunk(self._fh, self._label_map.image_metadata_sequence), 1)
def image_text_info(self):
"""Textual image information
Returns:
dict: containing the textual image info
"""
return read_metadata(read_chunk(self._fh, self._label_map.image_text_info), 1)
def image_metadata(self):
"""Image metadata
Returns:
dict: Extra image metadata
"""
if self._label_map.image_metadata:
return read_metadata(read_chunk(self._fh, self._label_map.image_metadata), 1)
def _get_raw_image_data(self, image_group_number, channel_offset, height,
width):
"""Reads the raw bytes and the timestamp of an image.
Args:
image_group_number: the image group number (see _calculate_image_group_number)
channel_offset: the number of the color channel
height: the height of the image
width: the width of the image
Returns:
"""
chunk = self._label_map.get_image_data_location(image_group_number)
data = read_chunk(self._fh, 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.
number_of_true_channels = int(
len(image_group_data[4:]) / (height * width))
try:
image_data = np.reshape(
image_group_data[image_data_start::number_of_true_channels],
(height, width))
except ValueError:
image_data = np.reshape(
image_group_data[image_data_start::number_of_true_channels],
(height,
int(
round(
len(image_group_data[
image_data_start::number_of_true_channels]) /
height))))
# 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_data
# If a blank "gap" image is encountered, generate an array of corresponding height and width to avoid
# errors with ND2-files with missing frames. Array is filled with nan to reflect that data is missing.
else:
empty_frame = np.full((height, width), np.nan)
warnings.warn(
'ND2 file contains gap frames which are represented by np.nan-filled arrays; to convert to zeros use e.g. np.nan_to_num(array)'
)
return timestamp, image_data
def _parse_events(self):
"""Extract events
"""
# list of event names manually extracted from an ND2 file that contains all manually
# insertable events from NIS-Elements software (4.60.00 (Build 1171) Patch 02)
event_names = {
1: 'Autofocus',
7: 'Command Executed',
9: 'Experiment Paused',
10: 'Experiment Resumed',
11: 'Experiment Stopped by User',
13: 'Next Phase Moved by User',
14: 'Experiment Paused for Refocusing',
16: 'External Stimulation',
33: 'User 1',
34: 'User 2',
35: 'User 3',
36: 'User 4',
37: 'User 5',
38: 'User 6',
39: 'User 7',
40: 'User 8',
44: 'No Acquisition Phase Start',
45: 'No Acquisition Phase End',
46: 'Hardware Error',
47: 'N-STORM',
48: 'Incubation Info',
49: 'Incubation Error'
}
self._metadata_parsed['events'] = []
events = read_metadata(
read_chunk(self._fh, self._label_map.image_events), 1)
if events is None or six.b('RLxExperimentRecord') not in events:
return
events = events[six.b('RLxExperimentRecord')][six.b('pEvents')]
if len(events) == 0:
return
for event in events[six.b('')]:
event_info = {
'index': event[six.b('I')],
'time': event[six.b('T')],
'type': event[six.b('M')],
}
if event_info['type'] in event_names.keys():
event_info['name'] = event_names[event_info['type']]
self._metadata_parsed['events'].append(event_info)
def _get_raw_image_data(self,
image_group_number,
channel_offset,
height,
width,
memmap=False):
"""Reads the raw bytes and the timestamp of an image.
Args:
image_group_number: the image group number (see _calculate_image_group_number)
channel_offset: the number of the color channel
height: the height of the image
width: the width of the image
Returns:
"""
chunk = self._label_map.get_image_data_location(image_group_number)
data = read_chunk(self._fh, chunk, memmap=memmap)
# 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]
if memmap:
image_group_data = data[8:].view(np.uint16)
else:
image_group_data = array.array("H", data[8:])
# 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.
number_of_true_channels = int(len(image_group_data) / (height * width))
image_data = np.reshape(
image_group_data[channel_offset::number_of_true_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.
return timestamp, image_data
def test_read_chunk(self):
with ArtificialND2(self.test_file) as artificial:
fh = artificial.file_handle
chunk_location = artificial.locations['image_attributes'][0]
chunk_read = read_chunk(fh, chunk_location)
real_data = six.BytesIO(artificial.raw_text)
real_data.seek(chunk_location)
# The chunk metadata is always 16 bytes long
chunk_metadata = real_data.read(16)
header, relative_offset, data_length = struct.unpack("IIQ", chunk_metadata)
self.assertEquals(header, 0xabeceda)
# We start at the location of the chunk metadata, skip over the metadata, and then proceed to the
# start of the actual data field, which is at some arbitrary place after the metadata.
real_data.seek(chunk_location + 16 + relative_offset)
real_chunk = real_data.read(data_length)
self.assertEqual(real_chunk, chunk_read)