def group_metadata_per_zstack(self):
'''Group all focal planes belonging to one z-stack (i.e. acquired
at different z resolutions but at the same microscope stage position,
time point and channel) together.
Returns
-------
pandas.DataFrame
metadata for each 2D *Plane* element
'''
md = self.metadata
logger.info('group metadata per z-stack')
zstacks = md.groupby([
'well_name', 'well_position_x', 'well_position_y', 'channel_name',
'tpoint'
])
logger.debug('identified %d z-stacks', zstacks.ngroups)
# Map the locations of each plane with the original image files
# in order to be able to perform the intensity projection later on
grouped_file_mapper_list = list()
grouped_file_mapper_lut = collections.defaultdict(list)
rows_to_drop = list()
for key, indices in zstacks.groups.iteritems():
fm = ImageFileMapping()
fm.files = list()
fm.series = list()
fm.planes = list()
fm.ref_index = indices[0]
for index in indices:
fm.files.extend(self._file_mapper_list[index].files)
fm.series.extend(self._file_mapper_list[index].series)
fm.planes.extend(self._file_mapper_list[index].planes)
grouped_file_mapper_list.append(fm)
grouped_file_mapper_lut[tuple(fm.files)].append(fm)
# Keep only the first record
rows_to_drop.extend(indices[1:])
# Update metadata and file mapper objects
self.metadata.drop(self.metadata.index[rows_to_drop], inplace=True)
del self.metadata['zplane']
self._file_mapper_list = grouped_file_mapper_list
self._file_mapper_lut = grouped_file_mapper_lut
return self.metadata
def _combine_omexml_elements(self, omexml_images, omexml_metadata):
logger.info('combine OMEXML elements')
# We assume here that each image files contains the same number images.
n_images = omexml_images.values()[0].image_count * len(omexml_images)
if omexml_metadata is not None:
extra_omexml_available = True
if not isinstance(omexml_metadata, bioformats.omexml.OMEXML):
raise TypeError('Argument "omexml_metadata" must have type '
'bioformats.omexml.OMEXML.')
if omexml_metadata.image_count != n_images:
raise MetadataError(
'Number of images in "omexml_metadata" must match '
'the total number of Image elements in "omexml_images".')
else:
extra_omexml_available = False
omexml_metadata = bioformats.OMEXML(XML_DECLARATION)
omexml_metadata.image_count = n_images
image_element_attributes = {'AcquisitionDate', 'Name'}
channel_element_attributes = {'Name'}
pixel_element_attributes = {
'PixelType', 'SizeC', 'SizeT', 'SizeX', 'SizeY', 'SizeZ'
}
plane_element_attributes = {
'PositionX', 'PositionY', 'PositionZ', 'TheC', 'TheT', 'TheZ'
}
filenames = natsorted(omexml_images)
count = 0
for i, f in enumerate(filenames):
omexml_img = omexml_images[f]
n_series = omexml_img.image_count
for s in xrange(n_series):
extracted_image = omexml_img.image(s)
md_image = omexml_metadata.image(count)
for attr in image_element_attributes:
extracted_value = getattr(extracted_image, attr)
if extracted_value is not None:
setattr(md_image, attr, extracted_value)
extracted_pixels = extracted_image.Pixels
n_planes = extracted_pixels.plane_count
if n_planes == 0:
# Sometimes an image doesn't have any plane elements.
# Let's create them for consistency.
extracted_pixels = self._create_channel_planes(
extracted_pixels)
n_planes = extracted_pixels.plane_count
md_pixels = md_image.Pixels
md_pixels.plane_count = n_planes
if extra_omexml_available and (md_pixels.plane_count !=
n_planes):
raise MetadataError(
'Image element #%d in OMEXML obtained from additional '
'metdata files must have the same number of Plane '
'elements as the corresponding Image elements in the '
'OMEXML element obtained from image file "%s".' %
(i, f))
for attr in pixel_element_attributes:
extracted_value = getattr(extracted_pixels, attr)
if extracted_value is not None:
# This is python-bioformats being stupid by setting
# random default values.
setattr(md_pixels, attr, extracted_value)
for p in xrange(n_planes):
extracted_plane = extracted_pixels.Plane(p)
md_plane = md_pixels.Plane(p)
for attr in plane_element_attributes:
extracted_value = getattr(extracted_plane, attr)
md_value = getattr(md_plane, attr)
if md_value is None and extracted_value is not None:
setattr(md_plane, attr, extracted_value)
fm = ImageFileMapping()
fm.ref_index = count + p
fm.files = [f]
fm.series = [s]
fm.planes = [p]
self._file_mapper_list.append(fm)
self._file_mapper_lut[f].append(fm)
n_channels = extracted_pixels.channel_count
md_image.channel_count = n_channels
for c in xrange(n_channels):
extracted_channel = extracted_pixels.Channel(c)
md_channel = md_pixels.Channel(c)
for attr in channel_element_attributes:
extracted_value = getattr(extracted_channel, attr)
if extracted_value is not None:
setattr(md_channel, attr, extracted_value)
count += 1
return omexml_metadata