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_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_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_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_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
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)
# Indent XML for readability
proc = subprocess.Popen(
['xmllint', '--format', '-o', companion_file, companion_file],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE)
(output, error_output) = proc.communicate()
print("Done.")
