def map_name_to_coordinate(name):
'''Maps identifier string representation to coordinate.
Parameters
----------
name: str
well name
Returns
-------
Tuple[int]
zero-based row, column position of a given well within the plate
Examples
--------
>>> Well.map_name_to_coordinate("A02")
(0, 1)
'''
row_name, col_name = re.match(r'([A-Z])(\d+)', name).group(1, 2)
row_index = utils.map_letter_to_number(row_name) - 1
col_index = int(col_name) - 1
return (row_index, col_index)
def map_name_to_coordinate(name):
'''Maps identifier string representation to coordinate.
Parameters
----------
name: str
well name
Returns
-------
Tuple[int]
zero-based row, column position of a given well within the plate
Examples
--------
>>> Well.map_name_to_coordinate("A02")
(0, 1)
'''
row_name, col_name = re.match(r'([A-Z])(\d+)', name).group(1, 2)
row_index = utils.map_letter_to_number(row_name) - 1
col_index = int(col_name) - 1
return (row_index, col_index)
def read(self, microscope_metadata_files, microscope_image_filenames):
'''Reads metadata from "mlf" and "mrf" metadata files in case they
are provided.
Parameters
----------
microscope_metadata_files: List[str]
absolute path to microscope metadata files
microscope_image_filenames: List[str]
names of the corresponding microscope image files
Returns
-------
bioformats.omexml.OMEXML
OMEXML image metadata
'''
microscope_image_filenames = natsorted(microscope_image_filenames)
metadata = bioformats.OMEXML(XML_DECLARATION)
if len(microscope_metadata_files) == 0:
logger.warn('no microscope metadata files found')
return None
elif len(microscope_metadata_files) != 2:
logger.warn('expected two microscope metadata files')
return None
for f in microscope_metadata_files:
if f.endswith('mlf'):
mlf_filename = f
elif f.endswith('mrf'):
mrf_filename = f
mrf_tree = etree.parse(mrf_filename)
mrf_root = mrf_tree.getroot()
mrf_ns = mrf_root.nsmap['bts']
# Obtain the positional information for each image acquisition site
# from the ".mlf" file:
mlf_tree = etree.parse(mlf_filename)
mlf_root = mlf_tree.getroot()
record_elements = mlf_root.xpath('.//bts:MeasurementRecord',
namespaces=mlf_root.nsmap)
mlf_ns = mlf_root.nsmap['bts']
metadata.image_count = len([
e for e in record_elements
if e.attrib['{%s}Type' % mlf_ns] != 'ERR'
])
lookup = defaultdict(list)
for e in record_elements:
# Translate positional information into well identifier string
well_row = utils.map_number_to_letter(
int(e.attrib['{%s}Row' % mlf_ns]))
well_col = int(e.attrib['{%s}Column' % mlf_ns])
well_id = '%s%.2d' % (well_row, well_col)
if e.attrib['{%s}Type' % mlf_ns] == 'ERR':
field_index = int(e.attrib['{%s}FieldIndex' % mlf_ns])
logger.error(
'erroneous acquisition - no channel and z-position '
'information available at well %s field %d' %
(well_id, field_index))
continue
# This microscope stores each plane in a separate file. Therefore,
# we can use the filename to match images.
name = e.text
index = microscope_image_filenames.index(name)
img = metadata.image(index)
img.AcquisitionDate = e.attrib['{%s}Time' % mlf_ns]
# Image files always contain only a single plane
img.Pixels.SizeT = 1
img.Pixels.SizeC = 1
img.Pixels.SizeZ = 1
img.Pixels.plane_count = 1
# A name has to be set as a flag for the handler to update
# the metadata
img.Name = name
# Make channel name consistent with how it is encoded in the image
# file name to ensure that the result is the same, independent of
# whether it was obtained from the metadata or the image file name.
img.Pixels.Channel(0).Name = e.attrib['{%s}Ch' % mlf_ns]
img.Pixels.Plane(0).PositionX = float(e.attrib['{%s}X' % mlf_ns])
img.Pixels.Plane(0).PositionY = float(e.attrib['{%s}Y' % mlf_ns])
img.Pixels.Plane(0).PositionZ = float(e.attrib['{%s}Z' % mlf_ns])
img.Pixels.Plane(0).TheZ = int(e.attrib['{%s}ZIndex' % mlf_ns])
img.Pixels.Plane(0).TheT = int(e.attrib['{%s}TimelineIndex' %
mlf_ns])
idx = microscope_image_filenames.index(img.Name)
lookup[well_id].append(idx)
# Obtain the general experiment information and well plate format
# specifications from the ".mrf" file:
name = mrf_root.attrib['{%s}Title' % mrf_ns]
plate = metadata.PlatesDucktype(metadata.root_node).newPlate(name=name)
plate.RowNamingConvention = 'letter'
plate.ColumnNamingConvention = 'number'
plate.Rows = mrf_root.attrib['{%s}RowCount' % mrf_ns]
plate.Columns = mrf_root.attrib['{%s}ColumnCount' % mrf_ns]
wells = lookup.keys()
for w in set(wells):
# Create a *Well* element for each imaged well in the plate
row = utils.map_letter_to_number(w[0]) - 1
col = int(w[1:]) - 1
well = metadata.WellsDucktype(plate).new(row=row, column=col)
well_samples = metadata.WellSampleDucktype(well.node)
for i, ref in enumerate(lookup[w]):
# Create a *WellSample* element for each acquisition site
well_samples.new(index=i)
well_samples[i].ImageRef = ref
return metadata
def read(self, microscope_metadata_files, microscope_image_filenames):
'''Reads metadata from "mlf" and "mrf" metadata files in case they
are provided.
Parameters
----------
microscope_metadata_files: List[str]
absolute path to microscope metadata files
microscope_image_filenames: List[str]
names of the corresponding microscope image files
Returns
-------
bioformats.omexml.OMEXML
OMEXML image metadata
'''
microscope_image_filenames = natsorted(microscope_image_filenames)
metadata = bioformats.OMEXML(XML_DECLARATION)
if len(microscope_metadata_files) == 0:
logger.warn('no microscope metadata files found')
return None
elif len(microscope_metadata_files) != 2:
logger.warn('expected two microscope metadata files')
return None
for f in microscope_metadata_files:
if f.endswith('mlf'):
mlf_filename = f
elif f.endswith('mrf'):
mrf_filename = f
mrf_tree = etree.parse(mrf_filename)
mrf_root = mrf_tree.getroot()
mrf_ns = mrf_root.nsmap['bts']
# Obtain the positional information for each image acquisition site
# from the ".mlf" file:
mlf_tree = etree.parse(mlf_filename)
mlf_root = mlf_tree.getroot()
record_elements = mlf_root.xpath(
'.//bts:MeasurementRecord', namespaces=mlf_root.nsmap
)
mlf_ns = mlf_root.nsmap['bts']
metadata.image_count = len([
e for e in record_elements
if e.attrib['{%s}Type' % mlf_ns] != 'ERR'
])
lookup = defaultdict(list)
for e in record_elements:
# Translate positional information into well identifier string
well_row = utils.map_number_to_letter(
int(e.attrib['{%s}Row' % mlf_ns]))
well_col = int(e.attrib['{%s}Column' % mlf_ns])
well_id = '%s%.2d' % (well_row, well_col)
if e.attrib['{%s}Type' % mlf_ns] == 'ERR':
field_index = int(e.attrib['{%s}FieldIndex' % mlf_ns])
logger.error(
'erroneous acquisition - no channel and z-position '
'information available at well %s field %d'
% (well_id, field_index)
)
continue
# This microscope stores each plane in a separate file. Therefore,
# we can use the filename to match images.
name = e.text
# Check for .tif to .png/.jpg conversion
if microscope_image_filenames[0].endswith('.png'):
name = name.replace('.tif','.png')
elif microscope_image_filenames[0].endswith('.jpg'):
name = name.replace('.tif','.jpg')
index = microscope_image_filenames.index(name)
img = metadata.image(index)
img.AcquisitionDate = e.attrib['{%s}Time' % mlf_ns]
# Image files always contain only a single plane
img.Pixels.SizeT = 1
img.Pixels.SizeC = 1
img.Pixels.SizeZ = 1
img.Pixels.plane_count = 1
# A name has to be set as a flag for the handler to update
# the metadata
img.Name = name
# Make channel name consistent with how it is encoded in the image
# file name to ensure that the result is the same, independent of
# whether it was obtained from the metadata or the image file name.
img.Pixels.Channel(0).Name = e.attrib['{%s}Ch' % mlf_ns]
img.Pixels.Plane(0).PositionX = float(e.attrib['{%s}X' % mlf_ns])
img.Pixels.Plane(0).PositionY = float(e.attrib['{%s}Y' % mlf_ns])
img.Pixels.Plane(0).PositionZ = float(e.attrib['{%s}Z' % mlf_ns])
img.Pixels.Plane(0).TheZ = int(e.attrib['{%s}ZIndex' % mlf_ns])
img.Pixels.Plane(0).TheT = int(e.attrib['{%s}TimelineIndex' % mlf_ns])
idx = microscope_image_filenames.index(img.Name)
lookup[well_id].append(idx)
# Obtain the general experiment information and well plate format
# specifications from the ".mrf" file:
name = mrf_root.attrib['{%s}Title' % mrf_ns]
plate = metadata.PlatesDucktype(metadata.root_node).newPlate(name=name)
plate.RowNamingConvention = 'letter'
plate.ColumnNamingConvention = 'number'
plate.Rows = mrf_root.attrib['{%s}RowCount' % mrf_ns]
plate.Columns = mrf_root.attrib['{%s}ColumnCount' % mrf_ns]
wells = lookup.keys()
for w in set(wells):
# Create a *Well* element for each imaged well in the plate
row = utils.map_letter_to_number(w[0]) - 1
col = int(w[1:]) - 1
well = metadata.WellsDucktype(plate).new(row=row, column=col)
well_samples = metadata.WellSampleDucktype(well.node)
for i, ref in enumerate(lookup[w]):
# Create a *WellSample* element for each acquisition site
well_samples.new(index=i)
well_samples[i].ImageRef = ref
return metadata
def read(self, microscope_metadata_files, microscope_image_filenames):
'''Read metadata from "nd" metadata file.
Parameters
----------
microscope_metadata_files: List[str]
absolute path to the microscope metadata files
microscope_image_filenames: List[str]
names of the corresponding microscope image files
Returns
-------
bioformats.omexml.OMEXML
OMEXML image metadata
Raises
------
ValueError
when `microscope_metadata_files` doesn't have length one
'''
microscope_image_filenames = natsorted(microscope_image_filenames)
if len(microscope_metadata_files) != 1:
raise ValueError('Expected one microscope metadata file.')
nd_filename = microscope_metadata_files[0]
metadata = bioformats.OMEXML(XML_DECLARATION)
# 1) Obtain the general experiment information and well plate format
# specifications from the ".nd" file:
nd = read_nd_file(nd_filename)
metadata.image_count = nd['NStagePositions']
if nd['DoWave']:
metadata.image_count *= nd['NWavelengths']
if nd['DoTimelapse']:
metadata.image_count *= nd['NTimePoints']
for i in xrange(metadata.image_count):
img = metadata.image(i)
img.Name = ''
# Images files may contain a variable number of z-stacks
# (SizeZ >= 1), but only one time point (SizeT == 1)
# and one channel (SizeC == 1)
img.Pixels.SizeT = 1
img.Pixels.SizeC = 1
img.Pixels.SizeZ = nd['NZSteps']
img.Pixels.plane_count = nd['NZSteps']
# TODO: case when no stage positions are available (manual acquisition)
name = os.path.splitext(os.path.basename(nd_filename))[0]
plate = metadata.PlatesDucktype(metadata.root_node).newPlate(name=name)
plate.RowNamingConvention = 'letter'
plate.ColumnNamingConvention = 'number'
rows = [
nd['Stage%d' % (i+1)]['row']
for i in xrange(nd['NStagePositions'])
]
plate.Rows = len(set(rows))
columns = [
nd['Stage%d' % (i+1)]['column']
for i in xrange(nd['NStagePositions'])
]
plate.Columns = len(set(columns))
# Create a lut table to get all images planes per well
sites = [
nd['Stage%d' % (i+1)]['site']
for i in xrange(nd['NStagePositions'])
]
wells = [
'%s%.2d' % (rows[i], columns[i])
for i in xrange(len(sites))
]
lut = defaultdict(list)
for i, filename in enumerate(natsorted(microscope_image_filenames)):
fields = MetadataHandler.extract_fields_from_filename(
IMAGE_FILE_REGEX_PATTERN, filename, defaults=False
)
# NOTE: We assume that the "site" id is global per plate
field_index = sites.index(int(fields.s))
lut[wells[field_index]].append(i)
for w in set(wells):
# Create a "Well" instance for each imaged well in the plate
row_index = utils.map_letter_to_number(w[0]) - 1
col_index = int(w[1:]) - 1
well = metadata.WellsDucktype(plate).new(
row=row_index, column=col_index
)
well_samples = metadata.WellSampleDucktype(well.node)
for i, ref in enumerate(lut[w]):
# Create a *WellSample* element for each acquisition site
well_samples.new(index=i)
well_samples[i].ImageRef = ref
return metadata