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_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_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_ome(self, tmpdir):
f = str(tmpdir.join('root.companion.ome'))
create_companion(out=f)
root = ElementTree.parse(f).getroot()
assert root.tag == '{%s}OME' % NS['OME']
assert root.attrib['Creator'] == 'ome_model %s' % __version__
def write_companion(images, file_path):
# Generate companion OME-XML file
if not os.path.exists(dirname(file_path)):
os.makedirs(dirname(file_path))
logging.info("Created %s" % dirname(file_path))
create_companion(images=images, out=file_path)
# Indent XML for readability
proc = subprocess.Popen(
['xmllint', '--format', '-o', file_path, file_path],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE)
(output, error_output) = proc.communicate()
logging.info("Created %s" % file_path)
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 create_companion(file_template, name, outdir, maxindex):
os.makedirs(outdir, exist_ok=True)
outpath = f'{outdir}/{name}.companion.ome'
if os.path.isfile(outpath):
print(f'{outpath} already exists, not overwriting')
return
for index in range(maxindex + 1):
tif = file_template.format(index=index)
if os.path.exists(tif):
with tifffile.TiffFile(tif) as t:
assert len(t.series) == 1
s = t.series[0]
assert s.axes == 'ZYX'
t = index
if index == 0:
z, y, x = s.shape
dt = str(s.dtype)
companion = ome.Image(
os.path.basename(name), x, y, z, 1, sizeT=(maxindex + 1),
order='XYZCT', type=dt)
companion.add_channel(samplesPerPixel=1)
else:
assert s.shape == (z, y, x)
#assert str(s.dtype) == dt, (tif, index, dt)
companion.add_tiff(os.path.basename(tif), t=t, planeCount=z)
else:
no_tif = tif
tif = file_template.format(index=(index-1))
if not os.path.exists(tif):
tif = file_template.format(index=(index+2))
if not os.path.exists(tif):
print("{} doesn't exit, not substitute found.".format(no_tif))
exit(1)
print("{} doesn't exit, using {}".format(no_tif, tif))
companion.add_tiff(os.path.basename(tif), t=t, planeCount=z)
tifbase = os.path.basename(tif)
tiflink = f'{outdir}/{tifbase}'
if not os.path.islink(tiflink):
os.symlink(tif, tiflink)
with open(outpath, 'wb') as o:
ome.create_companion(images=[companion], out=o)
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_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_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_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 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
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'
],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE)
(output, error_output) = proc.communicate()
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.")
