def copy_xml_with_newpath(xml_in,
xml_out,
data_path,
path_type="relative",
data_format=None):
assert path_type in ("absolute", "relative")
if data_format is None:
data_format = get_bdv_format(xml_in)
# get the path node inn the xml tree
root = ET.parse(xml_in).getroot()
seqdesc = root.find("SequenceDescription")
imgload = seqdesc.find("ImageLoader")
imgload.set("format", data_format)
et = imgload.find("hdf5")
if et is None:
et = imgload.find("n5")
if et is None:
raise RuntimeError("Could not find data node")
et.tag = data_format.split(".")[-1]
et.text = data_path
et.set("type", path_type)
indent_xml(root)
tree = ET.ElementTree(root)
tree.write(xml_out)
def add_authentication_field(xml_path, anon):
root = ET.parse(xml_path).getroot()
loader = root.find("SequenceDescription").find("ImageLoader")
auth_text = "Anonymous" if anon else "Protected"
ET.SubElement(loader, "Authentication").text = auth_text
indent_xml(root)
tree = ET.ElementTree(root)
tree.write(xml_path)
def remove_authentication_field(xml):
root = ET.parse(xml).getroot()
# get the image loader node
imgload = root.find("SequenceDescription").find("ImageLoader")
# remove the field
el = imgload.find("Authentication")
imgload.remove(el)
indent_xml(root)
tree = ET.ElementTree(root)
tree.write(xml)
def copy_xml_as_n5_s3(in_xml,
out_xml,
service_endpoint,
bucket_name,
path_in_bucket,
region="us-west-2",
bdv_type="bdv.n5.s3"):
""" Copy a bdv xml file and replace the image data loader with the bdv.n5.s3 format.
Arguments:
in_xml [str] - path to the input xml
out_xml [str] - path to the output xml
service_endpoint [str] - url of the s3 service end-point.
For EMBL: "https://s3.embl.de".
bucket_name [str] - name of the bucket
path_in_bucket [str] - file paths inside of the bucket
region [str] - the region. Only relevant if aws.s3 is used.
Default: "us-west-2"
"""
bdv_types = ("bdv.n5.s3", )
if bdv_type not in bdv_types:
raise ValueError(
f"Invalid bdv type {bdv_type}, expected one of {bdv_types}")
# check if we have an xml already
tree = ET.parse(in_xml)
root = tree.getroot()
# load the sequence description
seqdesc = root.find("SequenceDescription")
# update the image loader
# remove the old image loader
imgload = seqdesc.find("ImageLoader")
seqdesc.remove(imgload)
# write the new image loader
imgload = ET.SubElement(seqdesc, "ImageLoader")
imgload.set("format", bdv_type)
el = ET.SubElement(imgload, "Key")
el.text = path_in_bucket
el = ET.SubElement(imgload, "SigningRegion")
el.text = region
el = ET.SubElement(imgload, "ServiceEndpoint")
el.text = service_endpoint
el = ET.SubElement(imgload, "BucketName")
el.text = bucket_name
indent_xml(root)
tree = ET.ElementTree(root)
tree.write(out_xml)
def write_simple_xml(xml_path, data_path, path_type='absolute'):
# write top-level data
root = ET.Element('SpimData')
root.set('version', '0.2')
bp = ET.SubElement(root, 'BasePath')
bp.set('type', 'relative')
bp.text = '.'
seqdesc = ET.SubElement(root, 'SequenceDescription')
imgload = ET.SubElement(seqdesc, 'ImageLoader')
imgload.set('format', 'bdv.hdf5')
el = ET.SubElement(imgload, 'hdf5')
el.set('type', path_type)
el.text = data_path
indent_xml(root)
tree = ET.ElementTree(root)
tree.write(xml_path)
def copy_xml_with_newpath(xml_in,
xml_out,
data_path,
path_type='relative',
data_format='bdv.hdf5'):
assert path_type in ('absolute', 'relative')
# get the path node inn the xml tree
root = ET.parse(xml_in).getroot()
seqdesc = root.find('SequenceDescription')
imgload = seqdesc.find('ImageLoader')
imgload.set('format', data_format)
et = imgload.find('hdf5')
if et is None:
et = imgload.find('n5')
if et is None:
raise RuntimeError("Could not find data node")
et.tag = data_format.split('.')[-1]
et.text = data_path
et.set('type', path_type)
indent_xml(root)
tree = ET.ElementTree(root)
tree.write(xml_out)
def update_xmls(im_folder, old_name, new_name):
folders = ['local', 'remote']
for folder_name in folders:
folder = os.path.join(im_folder, folder_name)
if not os.path.exists(folder):
continue
xml_pattern = os.path.join(folder, '*.xml')
xmls = glob(xml_pattern)
xmls = [xml for xml in xmls if old_name in xml]
for old_path in xmls:
new_path = old_path.replace(old_name, new_name)
tree = ET.parse(old_path)
root = tree.getroot()
img_loader = root.find('SequenceDescription').find('ImageLoader')
node = img_loader.find('n5')
node.text = node.text.replace(old_name, new_name)
indent_xml(root)
tree = ET.ElementTree(root)
tree.write(new_path)
subprocess.run(['git', 'rm', old_path])
def write_s3_xml(in_xml,
out_xml,
path_in_bucket,
region='us-west-2',
service_endpoint='https://s3.embl.de',
bucket_name='platybrowser',
shape=None,
resolution=None):
nt = 1
# check if we have an xml already
tree = ET.parse(in_xml)
root = tree.getroot()
# load the sequence description
seqdesc = root.find('SequenceDescription')
# update the image loader
# remove the old image loader
imgload = seqdesc.find('ImageLoader')
seqdesc.remove(imgload)
# write the new image loader
imgload = ET.SubElement(seqdesc, 'ImageLoader')
bdv_dtype = 'bdv.n5.s3'
imgload.set('format', bdv_dtype)
el = ET.SubElement(imgload, 'Key')
el.text = path_in_bucket
el = ET.SubElement(imgload, 'SigningRegion')
el.text = region
el = ET.SubElement(imgload, 'ServiceEndpoint')
el.text = service_endpoint
el = ET.SubElement(imgload, 'BucketName')
el.text = bucket_name
# load the view descriptions
viewsets = seqdesc.find('ViewSetups')
vs = viewsets.find('ViewSetup')
oz, oy, ox = 0.0, 0.0, 0.0
# if resolution is not None, write it, otherwise read it
vox = vs.find('voxelSize')
if resolution is None:
resolution = vox.find('size').text
resolution = [float(res) for res in resolution.split()][::-1]
dz, dy, dx = resolution
else:
dz, dy, dx = resolution
voxs = vox.find('size')
voxs.text = '{} {} {}'.format(dx, dy, dz)
# write the shape if it is not None
if shape is not None:
nz, ny, nx = tuple(shape)
vss = vs.find('size')
vss.text = '{} {} {}'.format(nx, ny, nz)
# load the registration description and write the affines
vregs = root.find('ViewRegistrations')
for t in range(nt):
vreg = vregs.find('ViewRegistration')
vt = vreg.find('ViewTransform')
vt.set('type', 'affine')
vta = vt.find('affine')
vta.text = '{} 0.0 0.0 {} 0.0 {} 0.0 {} 0.0 0.0 {} {}'.format(
dx, ox, dy, oy, dz, oz)
indent_xml(root)
tree = ET.ElementTree(root)
tree.write(out_xml)