def test_10_07_iter_wells(self):
o = O.OMEXML(self.GROUPFILES_XML)
for i, name in enumerate(o.plates[0].Well):
row = int(i / 12)
column = i % 12
self.assertEqual(name, "ABCDEFGH"[row] + "%02d" % (column + 1))
self.assertEqual(name, "H12")
def test_08_03_plate_iter(self):
o = O.OMEXML(self.GROUPFILES_XML)
nplates = 5
for i in range(1, nplates):
o.plates.newPlate("MyPlate%d" % i, "Plate:%d" % i)
for i, plate in enumerate(o.plates):
self.assertEqual(plate.ID, "Plate:%d" % i)
def test_05_18_pixels_set_channel_count(self):
o = O.OMEXML(TIFF_XML)
o.image(0).Pixels.channel_count = 2
self.assertEqual(
len(
o.image(0).Pixels.node.findall(O.qn(o.get_ns("ome"),
"Channel"))), 2)
def test_14_14_set_delta_t(self):
o = O.OMEXML(TIFF_XML)
pixels = o.image(0).Pixels
self.assertTrue(isinstance(pixels, O.OMEXML.Pixels))
plane = pixels.Plane(0)
plane.DeltaT = 1.25
self.assertEqual(float(plane.node.get("DeltaT")), 1.25)
def test_14_17_set_position_z(self):
o = O.OMEXML(TIFF_XML)
pixels = o.image(0).Pixels
self.assertTrue(isinstance(pixels, O.OMEXML.Pixels))
plane = pixels.Plane(0)
plane.PositionZ = 7.5
self.assertEqual(float(plane.node.get("PositionZ")), 7.5)
def test_14_02_set_plane_count(self):
o = O.OMEXML()
pixels = o.image(0).Pixels
self.assertTrue(isinstance(pixels, O.OMEXML.Pixels))
pixels.plane_count = 2
self.assertEqual(
len(pixels.node.findall(O.qn(o.get_ns('ome'), "Plane"))), 2)
def test_13_11_get_image_ref(self):
o = O.OMEXML(self.GROUPFILES_XML)
ws = o.plates[0].Well['A02'].Sample[3]
self.assertEqual(ws.ImageRef, "Image:9")
ref = ws.node.find(O.qn(O.NS_SPW, "ImageRef"))
ws.node.remove(ref)
self.assertTrue(ws.ImageRef is None)
def test_14_08_set_the_t(self):
o = O.OMEXML(TIFF_XML)
pixels = o.image(0).Pixels
self.assertTrue(isinstance(pixels, O.OMEXML.Pixels))
plane = pixels.Plane(0)
plane.TheC = 7
self.assertEqual(int(plane.node.get("TheC")), 7)
def test_14_05_get_the_t(self):
o = O.OMEXML(TIFF_XML)
pixels = o.image(0).Pixels
self.assertTrue(isinstance(pixels, O.OMEXML.Pixels))
plane = pixels.Plane(0)
self.assertTrue(isinstance(plane, O.OMEXML.Plane))
plane.node.set("TheT", "9")
self.assertEqual(plane.TheT, 9)
def test_10_08_new_well(self):
o = O.OMEXML()
plate = o.plates.newPlate("Foo", "Bar")
plate.Well.new(4, 5, "xyz")
w = plate.Well[0]
self.assertEqual(w.node.get("Row"), "4")
self.assertEqual(w.node.get("Column"), "5")
self.assertEqual(w.node.get("ID"), "xyz")
def test_02_04_set_text(self):
o = O.OMEXML(TIFF_XML)
ad = o.root_node.find("/".join(
[O.qnome(x) for x in ("Image", "AcquiredDate")]))
im = o.root_node.find(O.qnome("Image"))
O.set_text(im, "Foo")
self.assertEqual(O.get_text(im), "Foo")
O.set_text(ad, "Bar")
self.assertEqual(O.get_text(ad), "Bar")
def test_13_08_set_timepoint(self):
o = O.OMEXML(self.GROUPFILES_XML)
ws = o.plates[0].Well['A02'].Sample[3]
now = datetime.datetime.now()
now_string = now.isoformat()
ws.Timepoint = now
self.assertEqual(ws.node.get("Timepoint"), now_string)
ws = o.plates[0].Well['A03'].Sample[4]
ws.Timepoint = now_string
self.assertEqual(ws.node.get("Timepoint"), now_string)
def test_04_07_image_1_acquisition_date(self):
# regression test of #38
o = O.OMEXML()
o.set_image_count(2)
date_1 = "2011-12-21T11:04:14.903000"
date_2 = "2015-10-13T09:57:00.000000"
o.image(0).AcquisitionDate = date_1
o.image(1).AcquisitionDate = date_2
self.assertEqual(o.image(0).AcquisitionDate, date_1)
self.assertEqual(o.image(1).AcquisitionDate, date_2)
def test_12_05_new_sample_item(self):
o = O.OMEXML()
plate = o.plates.newPlate("foo", "bar")
w = plate.Well.new(4, 5, "xyz")
w.Sample.new("ooo")
w.Sample.new("ppp")
sample_nodes = w.node.findall(O.qn(O.NS_SPW, "WellSample"))
self.assertEqual(len(sample_nodes), 2)
self.assertEqual(sample_nodes[0].get("ID"), "ooo")
self.assertEqual(sample_nodes[1].get("ID"), "ppp")
self.assertEqual(sample_nodes[0].get("Index"), "0")
self.assertEqual(sample_nodes[1].get("Index"), "1")
def test_07_01_sa_get_item(self):
o = O.OMEXML(TIFF_XML)
a = o.structured_annotations["Annotation:4"]
self.assertEqual(a.tag, O.qn(O.NS_SA, "XMLAnnotation"))
values = a.findall(O.qn(O.NS_SA, "Value"))
self.assertEqual(len(values), 1)
oms = values[0].findall(
O.qn(O.NS_ORIGINAL_METADATA, "OriginalMetadata"))
self.assertEqual(len(oms), 1)
keys = oms[0].findall(O.qn(O.NS_ORIGINAL_METADATA, "Key"))
self.assertEqual(len(keys), 1)
self.assertEqual(O.get_text(keys[0]), "XResolution")
values = oms[0].findall(O.qn(O.NS_ORIGINAL_METADATA, "Value"))
self.assertEqual(len(values), 1)
self.assertEqual(O.get_text(values[0]), "72")
def test_07_05_om_setitem(self):
o = O.OMEXML()
o.structured_annotations.OriginalMetadata["Foo"] = "Bar"
sa = o.structured_annotations.node
a = sa.findall(O.qn(O.NS_SA, "XMLAnnotation"))
self.assertEqual(len(a), 1)
vs = a[0].findall(O.qn(O.NS_SA, "Value"))
self.assertEqual(len(vs), 1)
om = vs[0].findall(O.qn(O.NS_ORIGINAL_METADATA, "OriginalMetadata"))
self.assertEqual(len(om), 1)
k = om[0].findall(O.qn(O.NS_ORIGINAL_METADATA, "Key"))
self.assertEqual(len(k), 1)
self.assertEqual(O.get_text(k[0]), "Foo")
v = om[0].findall(O.qn(O.NS_ORIGINAL_METADATA, "Value"))
self.assertEqual(len(v), 1)
self.assertEqual(O.get_text(v[0]), "Bar")
def test_08_04_plate_slice(self):
o = O.OMEXML(self.GROUPFILES_XML)
for i in range(1, 5):
o.plates.newPlate("MyPlate%d" % i, "Plate:%d" % i)
plates = o.plates[2:-1]
self.assertEqual(len(plates), 2)
self.assertTrue(
all([
plate.ID == "Plate:%d" % (i + 2)
for i, plate in enumerate(plates)
]))
plates = o.plates[-4:4]
self.assertEqual(len(plates), 3)
self.assertTrue(
all([
plate.ID == "Plate:%d" % (i + 1)
for i, plate in enumerate(plates)
]))
def test_04_03_image_get_name(self):
o = O.OMEXML(TIFF_XML)
self.assertEquals(o.image(0).Name, "Channel1-01-A-01.tif")
def test_04_02_image_set_id(self):
o = O.OMEXML(TIFF_XML)
o.image(0).ID = "Foo"
self.assertEquals(o.image(0).node.get("ID"), "Foo")
def test_04_01_image_get_id(self):
o = O.OMEXML(TIFF_XML)
self.assertEquals(o.image(0).ID, "Image:0")
def test_03_04_structured_annotations(self):
o = O.OMEXML(TIFF_XML)
self.assertEqual(o.structured_annotations.node.tag,
O.qn(O.NS_SA, "StructuredAnnotations"))
def test_03_03_image(self):
o = O.OMEXML(self.GROUPFILES_XML)
self.assertEquals(o.image_count, 576)
for i in range(576):
im = o.image(i)
self.assertEqual(im.node.get("ID"), "Image:%d" % i)
def test_14_13_get_position_z(self):
o = O.OMEXML(TIFF_XML)
pixels = o.image(0).Pixels
self.assertTrue(isinstance(pixels, O.OMEXML.Pixels))
plane = pixels.Plane(0)
self.assertEqual(plane.PositionZ, 2.25)
def test_14_10_get_exposure_time(self):
o = O.OMEXML(TIFF_XML)
pixels = o.image(0).Pixels
self.assertTrue(isinstance(pixels, O.OMEXML.Pixels))
plane = pixels.Plane(0)
self.assertEqual(plane.ExposureTime, 0.25)
def test_14_09_get_delta_t(self):
o = O.OMEXML(TIFF_XML)
pixels = o.image(0).Pixels
self.assertTrue(isinstance(pixels, O.OMEXML.Pixels))
plane = pixels.Plane(0)
self.assertEqual(plane.DeltaT, 1.25)
def test_03_01_get_image_count(self):
for xml, count in ((self.GROUPFILES_XML, 576), (TIFF_XML, 1)):
o = O.OMEXML(xml)
self.assertEqual(o.image_count, count)
def write(img, path, dtype='uint16', verbose=True):
"""
Write img as TIF on disk
:param img: Numpy ZYX stack
:param path: Full path (with filename) to save
:param type: byte type to save
:param verbose: Print process
:return: Nothing, saves file to disk
"""
import bioformats.omexml as ome
import javabridge as jutil
import bioformats
import numpy as np
import os
import sys
# Memotrack works on TZYX, swaps to XYZT, for the standard.
# memotrack numpy sequence T[0]Z[1]Y[2]X[3]
img_swap = np.swapaxes(img, 0, 3) # Here swapping T and X: TZYX -> XZYT
img_swap = np.swapaxes(img_swap, 1, 2) # Now on Z and Y: XZYT -> XYZT
# Inserting the C dimension (to get the XYCZT)
img_XYCZT = np.expand_dims(img_swap, 2)
if verbose:
print('Dimensions (XYCZT): ' + str(np.shape(img_XYCZT)))
sys.stdout.flush()
# Get the new dimensions
SizeX = np.shape(img_XYCZT)[0]
SizeY = np.shape(img_XYCZT)[1]
SizeC = np.shape(img_XYCZT)[2]
SizeZ = np.shape(img_XYCZT)[3]
SizeT = np.shape(img_XYCZT)[4]
# Start JVM for bioformats
jutil.start_vm(class_path=bioformats.JARS)
# Getting metadata info
omexml = ome.OMEXML()
omexml.image(0).Name = os.path.split(path)[1]
p = omexml.image(0).Pixels
assert isinstance(p, ome.OMEXML.Pixels)
p.SizeX = SizeX
p.SizeY = SizeY
p.SizeC = SizeC
p.SizeT = SizeT
p.SizeZ = SizeZ
p.DimensionOrder = ome.DO_XYCZT
p.PixelType = dtype
p.channel_count = SizeC
p.plane_count = SizeZ
p.Channel(0).SamplesPerPixel = SizeC
omexml.structured_annotations.add_original_metadata(
ome.OM_SAMPLES_PER_PIXEL, str(SizeC))
# Converting to omexml
xml = omexml.to_xml()
# Write file using Bioformats
if verbose:
print('Writing frames:'),
sys.stdout.flush()
for frame in range(SizeT):
if verbose:
print('[' + str(frame + 1) + ']'),
sys.stdout.flush()
index = frame
pixel_buffer = bioformats.formatwriter.convert_pixels_to_buffer(
img_XYCZT[:, :, :, :, frame], dtype)
script = """
importClass(Packages.loci.formats.services.OMEXMLService,
Packages.loci.common.services.ServiceFactory,
Packages.loci.formats.out.TiffWriter);
var service = new ServiceFactory().getInstance(OMEXMLService);
var metadata = service.createOMEXMLMetadata(xml);
var writer = new TiffWriter();
writer.setBigTiff(true);
writer.setMetadataRetrieve(metadata);
writer.setId(path);
writer.setInterleaved(true);
writer.saveBytes(index, buffer);
writer.close();
"""
jutil.run_script(
script, dict(path=path, xml=xml, index=index, buffer=pixel_buffer))
if verbose:
print('[Done]')
sys.stdout.flush()
if verbose:
print('File saved on ' + str(path))
sys.stdout.flush()
def test_03_02_set_image_count(self):
o = O.OMEXML(TIFF_XML)
o.image_count = 2
self.assertEqual(len(o.root_node.findall(O.qnome("Image"))), 2)
def write_image(pathname,
pixels,
pixel_type,
c=0,
z=0,
t=0,
size_c=1,
size_z=1,
size_t=1,
channel_names=None):
"""Write the image using bioformats.
:param filename: save to this filename
:param pixels: the image to save
:param pixel_type: save using this pixel type
:param c: the image's channel index
:param z: the image's `z` index
:param t: the image's `t` index
:param size_c: # of channels in the stack
:param size_z: # of z stacks
:param size_t: # of timepoints in the stack
:param channel_names: names of the channels (make up names if not present).
"""
omexml = ome.OMEXML()
omexml.image(0).Name = os.path.split(pathname)[1]
p = omexml.image(0).Pixels
assert isinstance(p, ome.OMEXML.Pixels)
p.SizeX = pixels.shape[1]
p.SizeY = pixels.shape[0]
p.SizeC = size_c
p.SizeT = size_t
p.SizeZ = size_z
p.DimensionOrder = ome.DO_XYCZT
p.PixelType = pixel_type
index = c + size_c * z + size_c * size_z * t
if pixels.ndim == 3:
p.SizeC = pixels.shape[2]
p.Channel(0).SamplesPerPixel = pixels.shape[2]
omexml.structured_annotations.add_original_metadata(
ome.OM_SAMPLES_PER_PIXEL, str(pixels.shape[2]))
elif size_c > 1:
p.channel_count = size_c
pixel_buffer = convert_pixels_to_buffer(pixels, pixel_type)
xml = omexml.to_xml()
script = """
importClass(Packages.loci.formats.services.OMEXMLService,
Packages.loci.common.services.ServiceFactory,
Packages.loci.formats.ImageWriter);
var service = new ServiceFactory().getInstance(OMEXMLService);
var metadata = service.createOMEXMLMetadata(xml);
var writer = new ImageWriter();
writer.setMetadataRetrieve(metadata);
writer.setId(path);
writer.setInterleaved(true);
writer.saveBytes(index, buffer);
writer.close();
"""
jutil.run_script(
script, dict(path=pathname, xml=xml, index=index, buffer=pixel_buffer))
def test_14_01_get_plane_count(self):
o = O.OMEXML(TIFF_XML)
self.assertEqual(o.image(0).Pixels.plane_count, 1)
