def test_rgb_channel(self, tmpdir):
f = str(tmpdir.join('rgb.companion.ome'))
i = Image("test", 256, 512, 1, 3, 1)
i.add_channel(samplesPerPixel=3)
create_companion(images=[i], out=f)
root = ElementTree.parse(f).getroot()
images = root.findall('OME:Image', namespaces=NS)
assert len(images) == 1
assert images[0].attrib['Name'] == 'test'
pixels = images[0].findall('OME:Pixels', namespaces=NS)
assert len(pixels) == 1
assert pixels[0].attrib['SizeX'] == '256'
assert pixels[0].attrib['SizeY'] == '512'
assert pixels[0].attrib['SizeZ'] == '1'
assert pixels[0].attrib['SizeC'] == '3'
assert pixels[0].attrib['SizeT'] == '1'
assert pixels[0].attrib['DimensionOrder'] == 'XYZTC'
assert pixels[0].attrib['Type'] == 'uint16'
channels = pixels[0].findall('OME:Channel', namespaces=NS)
assert len(channels) == 1
assert 'Name' not in channels[0].attrib
assert 'Color' not in channels[0].attrib
assert channels[0].attrib['SamplesPerPixel'] == '3'
def test_too_many_channel_samples(self, tmpdir):
f = str(tmpdir.join('invalid.companion.ome'))
i = Image("test", 512, 512, 1, 2, 1)
i.add_channel(samplesPerPixel=3)
with pytest.raises(AssertionError):
create_companion(images=[i], out=f)
def test_channel(self, tmpdir, name, color):
f = str(tmpdir.join('3channels.companion.ome'))
i = Image("test", 256, 512, 3, 4, 5)
i.add_channel()
i.add_channel(name="Blue", color="65535", samplesPerPixel=1)
i.add_channel(name=name, color=color)
create_companion(images=[i], out=f)
root = ElementTree.parse(f).getroot()
images = root.findall('OME:Image', namespaces=NS)
assert len(images) == 1
assert images[0].attrib['Name'] == 'test'
pixels = images[0].findall('OME:Pixels', namespaces=NS)
assert len(pixels) == 1
assert pixels[0].attrib['SizeX'] == '256'
assert pixels[0].attrib['SizeY'] == '512'
assert pixels[0].attrib['SizeZ'] == '3'
assert pixels[0].attrib['SizeC'] == '4'
assert pixels[0].attrib['SizeT'] == '5'
assert pixels[0].attrib['DimensionOrder'] == 'XYZTC'
assert pixels[0].attrib['Type'] == 'uint16'
channels = pixels[0].findall('OME:Channel', namespaces=NS)
assert len(channels) == 3
assert 'Name' not in channels[0].attrib
assert 'Color' not in channels[0].attrib
assert channels[0].attrib['SamplesPerPixel'] == '1'
assert channels[1].attrib['Name'] == 'Blue'
assert channels[1].attrib['Color'] == '65535'
assert channels[1].attrib['SamplesPerPixel'] == '1'
if name:
assert channels[2].attrib['Name'] == name
else:
assert 'Name' not in channels[2].attrib
if color:
assert channels[2].attrib['Color'] == color
else:
assert 'Color' not in channels[2].attrib
assert channels[2].attrib['SamplesPerPixel'] == '1'
def create_genotypic_companions(slides):
GENO_CYCLES = 11
logging.info("Generating genotypic metadata files")
filePaths = []
for slide in slides:
for i in range(GENO_CYCLES):
images = []
index = i + 1
logging.debug("Processing %s" % slide)
# Genotypic metadata generation
for position in sorted(slides[slide]):
logging.debug(" Creating image for %s" % position)
image = Image(position,
2048,
879,
1,
5,
1,
order="XYZCT",
type="uint16")
image.add_channel("Cy5", -16776961)
image.add_channel("Cy3", 16711935)
image.add_channel("TxR", 65535)
image.add_channel("Fam", -65281)
image.add_channel("Phase", -1)
image.add_tiff(get_genotypic_filename(position, "1_cy5_fluor",
index),
c=0,
z=0,
t=0)
image.add_tiff(get_genotypic_filename(position, "2_cy3_fluor",
index),
c=1,
z=0,
t=0)
image.add_tiff(get_genotypic_filename(position, "3_TxR_fluor",
index),
c=2,
z=0,
t=0)
image.add_tiff(get_genotypic_filename(position, "4_fam_flour",
index),
c=3,
z=0,
t=0)
image.add_tiff(get_genotypic_filename(position, "phase",
index),
c=4,
z=0,
t=0)
images.append(image)
position_dir = join(EXPERIMENTB_DIRECTORY, 'companions', slide,
'geno', position)
if not os.path.lexists(position_dir):
os.symlink(join(DATA_DIRECTORY, slide, "geno", position),
position_dir)
companion_file = join(
EXPERIMENTB_DIRECTORY, 'companions', slide, "geno",
'%s_round-%02g.companion.ome' % (slide, index))
write_companion(images, companion_file)
filePaths.append(
"Project:name:idr0065-camsund-crispri/experimentB/"
"Dataset:name:%s_round-%02g\t"
"%s\t%s\n" % (slide, index, companion_file, slide))
tsv = join(EXPERIMENTB_DIRECTORY, 'idr0065-experimentB-filePaths.tsv')
with open(tsv, 'w') as f:
for p in filePaths:
f.write(p)
def create_phenotypic_companions():
"""Phenotypic metadata files"""
logging.info("Generating phenotypic metadata files")
time_indexes = read_phenotypic_time_indexes()
timestamps = read_phenotypic_timestamps()
slides = parse_phenotypic_filenames(timestamps)
filePaths = []
for slide in slides:
images = []
logging.debug("Processing phenotypic %s" % slide)
# Genotypic metadata generation
for position in sorted(slides[slide]):
logging.debug(" Creating image for %s" % position)
image = Image(position,
2048,
879,
1,
2,
481,
order="XYZCT",
type="uint16")
image.add_channel("Phase", -1)
image.add_channel("Fluorescence", 16711935)
# Phase images
for t in range(481):
relative_path = get_phenotypic_filename(position, "phase", t)
full_path = get_phenotypic_filename(position,
"phase",
t,
slide=slide)
image.add_tiff(relative_path, c=0, z=0, t=t, planeCount=1)
plane_options = {
"DeltaT": timestamps[full_path],
"DeltaTUnit": "s",
"ExposureTime": "20",
"ExposureTimeUnit": "ms",
}
image.add_plane(c=0, z=0, t=t, options=plane_options)
# Fluorescence images
for i in range(241):
relative_path = get_phenotypic_filename(position, "fluor", i)
full_path = get_phenotypic_filename(position,
"fluor",
i,
slide=slide)
t = time_indexes[full_path]
plane_options = {
"DeltaT": timestamps[full_path],
"DeltaTUnit": "s",
"ExposureTime": "300",
"ExposureTimeUnit": "ms",
}
if t == 2 * i:
image.add_tiff(relative_path, c=1, z=0, t=t, planeCount=1)
if i != 240:
image.add_tiff(None, c=1, z=0, t=(2 * i) + 1)
elif t == (2 * i) + 1:
image.add_tiff(None, c=1, z=0, t=2 * i)
if t != 481:
image.add_tiff(relative_path,
c=1,
z=0,
t=t,
planeCount=1)
else:
raise Exception("Invalid mapping")
image.add_plane(c=1, z=0, t=t, options=plane_options)
images.append(image)
position_dir = join(EXPERIMENTA_DIRECTORY, 'companions', slide,
"pheno", position)
if not os.path.lexists(position_dir):
os.symlink(join(DATA_DIRECTORY, slide, "pheno", position),
position_dir)
companion_file = join(EXPERIMENTA_DIRECTORY, 'companions', slide,
"pheno", slide + '.companion.ome')
write_companion(images, companion_file)
filePaths.append("Project:name:idr0065-camsund-crispri/experimentA/"
"Dataset:name:%s\t"
"%s\t%s\n" % (slide, companion_file, slide))
tsv = join(EXPERIMENTA_DIRECTORY, 'idr0065-experimentA-filePaths.tsv')
with open(tsv, 'w') as f:
for p in filePaths:
f.write(p)
return slides
# Create 2-channel image
image = Image(os.path.basename(cell),
size_x,
size_y,
size_z,
2,
1,
order="XYZCT",
type="uint16")
image.data['Pixels']['PhysicalSizeX'] = '20'
image.data['Pixels']['PhysicalSizeXUnit'] = 'nm'
image.data['Pixels']['PhysicalSizeY'] = '20'
image.data['Pixels']['PhysicalSizeYUnit'] = 'nm'
(n1, c1, n2, c2) = CHANNEL_MAPPING[os.path.basename(folder)]
image.add_channel(n1, c1)
image.add_channel(n2, c2)
for i in range(len(rawtiffs)):
image.add_tiff("%s/%s" % (os.path.basename(cell), rawtiffs[i]),
c=i,
z=0,
t=0,
ifd=0,
planeCount=size_z)
create_companion(images=[image], out=cell + '.companion.ome')
# Generate indented XML for readability
proc = subprocess.Popen([
'xmllint', '--format', '-o', cell + '.companion.ome',
cell + '.companion.ome'
well_index = 0
for row_index, row in enumerate(rows):
for column_index, column in enumerate(columns):
well = plate.add_well(row_index, column_index)
test = "{}_{}{}_0h.tiff".format(plate_name, row, column)
if test in filenames:
basename = "{}{}".format(row, column)
image = Image(basename,
2080,
1552,
25,
3,
len(timepoints),
order="XYZTC",
type="uint8")
image.add_channel(samplesPerPixel=3)
for i, timepoint in enumerate(timepoints):
filename = "{}_{}{}_{}.tiff".format(plate_name, row, column,
timepoint)
image.add_tiff(filename, c=0, z=0, t=i, planeCount=25)
options = {
'DeltaT': timepoint[:-1],
'DeltaTUnit': 'h',
}
for z in range(25):
image.add_plane(c=0, z=z, t=i, options=options)
well.add_wellsample(well_index, image)
well_index += 1
companion_file = "../companions/{}.companion.ome".format(plate_name)
create_companion(plates=[plate], out=companion_file)
