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import pkg_resources
def register_plugin():
plugin_path = pkg_resources.resource_filename('ont_fast5_api', 'vbz_plugin')
try:
from h5py import h5pl
h5pl.prepend(bytes(plugin_path, 'UTF-8'))
except (ImportError, AttributeError):
# We don't have the plugin library in h5py<2.10 so we fall back on an environment variable
import os
os.environ['HDF5_PLUGIN_PATH'] = plugin_path
return plugin_path
class AbstractCompression:
compression = "AbstractCompression"
compression_opts = ()
shuffle = False
scaleoffset = False
fletcher32 = False
def __repr__(self):
return self.compression
@property
def filter_settings(self):
return {}
class VbzCompression(AbstractCompression):
def __init__(self):
self.compression = 32020 # https://portal.hdfgroup.org/display/support/Registered+Filters
self.compression_opts = (1, 2, 1, 1) # VBZ_VERSION, VBZ_PACKING, VBZ_ZIG_ZAG, VBZ_ZSTD_COMPRESSION
def __repr__(self):
return "vbz"
@property
def filter_settings(self):
return {str(self.compression): self.compression_opts}
class VbzCompressionV0(AbstractCompression):
def __init__(self):
self.compression = 32020 # https://portal.hdfgroup.org/display/support/Registered+Filters
self.compression_opts = (0, 2, 1, 1) # VBZ_VERSION, VBZ_PACKING, VBZ_ZIG_ZAG, VBZ_ZSTD_COMPRESSION
def __repr__(self):
return "vbz_legacy_v0"
@property
def filter_settings(self):
return {str(self.compression): self.compression_opts}
class GzipCompression(AbstractCompression):
def __init__(self):
self.compression = "gzip"
self.compression_opts = 1
@property
def filter_settings(self):
return {str(self.compression): self.compression_opts}
VBZ_ERROR_MESSAGE = "Failed to read compressed raw data. " \
"VBZ compression filter (id=32020) may be missing from expected path: '{}'"
def raise_missing_vbz_error_read(err):
if str(VBZ.compression) in str(err):
raise IOError(VBZ_ERROR_MESSAGE.format(register_plugin())) from err
# If we don't see anything relating to VBZ just raise the existing error without additional info
raise
def raise_missing_vbz_error_write(err):
if type(err) is OSError and "Can't read data" in str(err):
raise IOError(VBZ_ERROR_MESSAGE.format(register_plugin())) from err
# If we don't see anything relating to VBZ just raise the existing error without additional info
raise
VBZ = VbzCompression()
VBZ_V0 = VbzCompressionV0()
GZIP = GzipCompression()
COMPRESSION_MAP = {str(comp): comp for comp in (VBZ, VBZ_V0, GZIP)}
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