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_invalid_plane_option(self, tmpdir):
f = str(tmpdir.join('invalid_plane_options.companion.ome'))
i = Image("test", 512, 512, 1, 1, 1)
options = {
'EmissionWavelength': '512.0',
'EmissionWavelengthUnit': 'nm',
}
i.add_plane(z=0, c=0, t=0, options=options)
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'] == '512'
assert pixels[0].attrib['SizeY'] == '512'
assert pixels[0].attrib['SizeZ'] == '1'
assert pixels[0].attrib['SizeC'] == '1'
assert pixels[0].attrib['SizeT'] == '1'
assert pixels[0].attrib['DimensionOrder'] == 'XYZTC'
assert pixels[0].attrib['Type'] == 'uint16'
planes = pixels[0].findall('OME:Plane', namespaces=NS)
assert len(planes) == 1
assert planes[0].attrib['TheZ'] == '0'
assert planes[0].attrib['TheC'] == '0'
assert planes[0].attrib['TheT'] == '0'
assert 'EmissionWavelength' not in planes[0].attrib
assert 'EmissionWavelengthUnit' not in planes[0].attrib
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_pixelzies(self, tmpdir, pixel_size_x, pixel_size_y, pixel_size_z,
pixel_size_x_unit, pixel_size_y_unit,
pixel_size_z_unit):
f = str(tmpdir.join('image.companion.ome'))
i = Image("test",
256,
512,
3,
4,
5,
physSizeX=pixel_size_x,
physSizeY=pixel_size_y,
physSizeZ=pixel_size_z,
physSizeXUnit=pixel_size_x_unit,
physSizeYUnit=pixel_size_y_unit,
physSizeZUnit=pixel_size_z_unit,
type="unit8")
create_companion(images=[i], out=f)
root = ElementTree.parse(f).getroot()
images = root.findall('OME:Image', namespaces=NS)
pixels = images[0].findall('OME:Pixels', namespaces=NS)[0]
if pixel_size_x:
assert pixels.attrib['PhysicalSizeX'] == pixel_size_x
if pixel_size_x_unit:
assert pixels.attrib['PhysicalSizeXUnit'] == pixel_size_x_unit
if pixel_size_y:
assert pixels.attrib['PhysicalSizeY'] == pixel_size_y
if pixel_size_y_unit:
assert pixels.attrib['PhysicalSizeYUnit'] == pixel_size_y_unit
if pixel_size_z:
assert pixels.attrib['PhysicalSizeZ'] == pixel_size_z
if pixel_size_z_unit:
assert pixels.attrib['PhysicalSizeZUnit'] == pixel_size_z_unit
def test_multiple_rows_columns_wellsamples(self, tmpdir):
f = str(tmpdir.join('plate.companion.ome'))
p = Plate("test", 4, 5)
for row in range(4):
for column in range(5):
well = p.add_well(row, column)
for field in range(6):
i = Image("test", 256, 512, 3, 4, 5)
well.add_wellsample(field, i)
create_companion(plates=[p], out=f)
root = ElementTree.parse(f).getroot()
plates = root.findall('OME:Plate', namespaces=NS)
assert len(plates) == 1
assert plates[0].attrib['Name'] == 'test'
wells = plates[0].findall('OME:Well', namespaces=NS)
assert len(wells) == 20
imageids = []
for i in range(20):
wellsamples = wells[i].findall('OME:WellSample', namespaces=NS)
assert len(wellsamples) == 6
for ws in wellsamples:
imagerefs = ws.findall('OME:ImageRef', namespaces=NS)
assert len(imagerefs) == 1
imageids.append(imagerefs[0].attrib['ID'])
assert len(imageids) == 120
images = root.findall('OME:Image', namespaces=NS)
assert len(images) == 120
assert [x.attrib['ID'] for x in images] == imageids
def test_invalid_plane_index(self, tmpdir, invalidindex):
i = Image("test", 512, 512, 1, 1, 1)
with pytest.raises(AssertionError):
i.add_plane(z=invalidindex, c=0, t=0)
with pytest.raises(AssertionError):
i.add_plane(z=0, c=invalidindex, t=0)
with pytest.raises(AssertionError):
i.add_plane(z=0, c=0, t=invalidindex)
def test_plane_options(self, tmpdir):
f = str(tmpdir.join('plane_options.companion.ome'))
i = Image("test", 512, 512, 1, 1, 1)
options = {
'DeltaT': '0.0',
'DeltaTUnit': 's',
'ExposureTime': '100',
'ExposureTimeUnit': 'ms',
'PositionX': '0.0',
'PositionXUnit': 'reference frame',
'PositionY': '0.0',
'PositionYUnit': 'reference frame',
'PositionZ': '0.0',
'PositionZUnit': 'reference frame',
}
i.add_plane(z=0, c=0, t=0, options=options)
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'] == '512'
assert pixels[0].attrib['SizeY'] == '512'
assert pixels[0].attrib['SizeZ'] == '1'
assert pixels[0].attrib['SizeC'] == '1'
assert pixels[0].attrib['SizeT'] == '1'
assert pixels[0].attrib['DimensionOrder'] == 'XYZTC'
assert pixels[0].attrib['Type'] == 'uint16'
planes = pixels[0].findall('OME:Plane', namespaces=NS)
assert len(planes) == 1
assert planes[0].attrib['TheZ'] == '0'
assert planes[0].attrib['TheC'] == '0'
assert planes[0].attrib['TheT'] == '0'
assert planes[0].attrib['DeltaT'] == '0.0'
assert planes[0].attrib['DeltaTUnit'] == 's'
assert planes[0].attrib['ExposureTime'] == '100'
assert planes[0].attrib['ExposureTimeUnit'] == 'ms'
assert planes[0].attrib['PositionX'] == '0.0'
assert planes[0].attrib['PositionXUnit'] == 'reference frame'
assert planes[0].attrib['PositionY'] == '0.0'
assert planes[0].attrib['PositionYUnit'] == 'reference frame'
assert planes[0].attrib['PositionZ'] == '0.0'
assert planes[0].attrib['PositionZUnit'] == 'reference frame'
def test_minimal_plate(self, tmpdir, rc):
f = str(tmpdir.join('plate.companion.ome'))
if rc:
p = Plate("test", 1, 2)
else:
p = Plate("test")
well = p.add_well(0, 0)
i = Image("test", 256, 512, 3, 4, 5)
well.add_wellsample(0, i)
create_companion(plates=[p], out=f)
root = ElementTree.parse(f).getroot()
plates = root.findall('OME:Plate', namespaces=NS)
assert len(plates) == 1
assert plates[0].attrib['Name'] == 'test'
if rc:
assert plates[0].attrib['Rows'] == '1'
assert plates[0].attrib['Columns'] == '2'
wells = plates[0].findall('OME:Well', namespaces=NS)
assert len(wells) == 1
assert wells[0].attrib['Row'] == '0'
assert wells[0].attrib['Column'] == '0'
wellsamples = wells[0].findall('OME:WellSample', namespaces=NS)
assert len(wellsamples) == 1
imagerefs = wellsamples[0].findall('OME:ImageRef', namespaces=NS)
assert len(imagerefs) == 1
imageid = imagerefs[0].attrib['ID']
images = root.findall('OME:Image', namespaces=NS)
assert len(images) == 1
assert images[0].attrib['Name'] == 'test'
assert images[0].attrib['ID'] == imageid
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) == 0
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 test_pixeltypes(self, tmpdir, pixel_type):
f = str(tmpdir.join('image.companion.ome'))
i = Image("test", 256, 512, 3, 4, 5, type=pixel_type)
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'] == pixel_type
channels = pixels[0].findall('OME:Channel', namespaces=NS)
assert len(channels) == 0
def test_multiple_plates_one_per_file(self, tmpdir):
files = [str(tmpdir.join('%s.companion.ome' % i)) for i in range(4)]
for i in range(4):
p = Plate("test %s" % i, 1, 1)
well = p.add_well(0, 0)
img = Image("test %s" % i, 256, 512, 3, 4, 5)
well.add_wellsample(0, img)
create_companion(plates=[p], out=files[i])
for i in range(4):
root = ElementTree.parse(files[i]).getroot()
plates = root.findall('OME:Plate', namespaces=NS)
assert len(plates) == 1
assert plates[0].attrib['Name'] == 'test %s' % i
wells = plates[0].findall('OME:Well', namespaces=NS)
assert len(wells) == 1
wellsamples = wells[0].findall('OME:WellSample', namespaces=NS)
assert len(wellsamples) == 1
imagerefs = wellsamples[0].findall('OME:ImageRef', namespaces=NS)
assert len(imagerefs) == 1
images = root.findall('OME:Image', namespaces=NS)
assert len(images) == 1
assert images[0].attrib['Name'] == 'test %s' % i
def test_planes(self, tmpdir):
f = str(tmpdir.join('planes.companion.ome'))
i = Image("test", 256, 512, 1, 2, 2)
i.add_plane(c=0, z=0, t=0)
i.add_plane(c=0, z=0, t=1)
i.add_plane(c=1, z=0, t=0)
i.add_plane(c=1, z=0, t=1)
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'] == '2'
assert pixels[0].attrib['SizeT'] == '2'
assert pixels[0].attrib['DimensionOrder'] == 'XYZTC'
assert pixels[0].attrib['Type'] == 'uint16'
planes = pixels[0].findall('OME:Plane', namespaces=NS)
assert len(planes) == 4
assert planes[0].attrib['TheZ'] == '0'
assert planes[0].attrib['TheC'] == '0'
assert planes[0].attrib['TheT'] == '0'
assert planes[1].attrib['TheZ'] == '0'
assert planes[1].attrib['TheC'] == '0'
assert planes[1].attrib['TheT'] == '1'
assert planes[2].attrib['TheZ'] == '0'
assert planes[2].attrib['TheC'] == '1'
assert planes[2].attrib['TheT'] == '0'
assert planes[3].attrib['TheZ'] == '0'
assert planes[3].attrib['TheC'] == '1'
assert planes[3].attrib['TheT'] == '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
# Image Dimensions
img = PIL_Image.open(join(cell, rawtiffs[1]))
(size_x, size_y) = img.size
size_z = 0
while True:
try:
img.seek(size_z)
except EOFError:
break
size_z += 1
# 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,
columns = ['01', '02', '03', '04', '05', '06']
rows = ['A', 'B', 'C', 'D']
timepoints = ['0h', '24h', '48h', '72h', '96h']
print("Creating {}.companion.ome ...".format(plate_name))
plate = Plate(plate_name, len(rows), len(columns))
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)
