def parse_array_definition(self):
"""Reads and returns the element type and length of the array.
The position in the file must be just after the
array encoded dtype.
"""
self.skipif4()
enc_eltype = iou.read_long(self.f, "big")
self.skipif4()
length = iou.read_long(self.f, "big")
return length, enc_eltype
def parse_array_definition(self):
"""Reads and returns the element type and length of the array.
The position in the file must be just after the
array encoded dtype.
"""
self.skipif4()
enc_eltype = iou.read_long(self.f, "big")
self.skipif4()
length = iou.read_long(self.f, "big")
return length, enc_eltype
def parse_struct_definition(self):
"""Reads and returns the struct definition tuple.
The position in the file must be just after the
struct encoded dtype.
"""
self.f.seek(4, 1) # Skip the name length
self.skipif4(2)
nfields = iou.read_long(self.f, "big")
definition = ()
for ifield in range(nfields):
self.f.seek(4, 1)
self.skipif4(2)
definition += (iou.read_long(self.f, "big"),)
return definition
def parse_string_definition(self):
"""Reads and returns the length of the string.
The position in the file must be just after the
string encoded dtype.
"""
self.skipif4()
return iou.read_long(self.f, "big")
def parse_header(self):
self.dm_version = iou.read_long(self.f, "big")
if self.dm_version not in (3, 4):
raise NotImplementedError(
"Currently we only support reading DM versions 3 and 4 but "
"this file "
"seems to be version %s " % self.dm_version)
filesizeB = self.read_l_or_q(self.f, "big")
is_little_endian = iou.read_long(self.f, "big")
_logger.info('DM version: %i', self.dm_version)
_logger.info('size %i B', filesizeB)
_logger.info('Is file Little endian? %s', bool(is_little_endian))
if bool(is_little_endian):
self.endian = 'little'
else:
self.endian = 'big'
def parse_struct_definition(self):
"""Reads and returns the struct definition tuple.
The position in the file must be just after the
struct encoded dtype.
"""
self.f.seek(4, 1) # Skip the name length
self.skipif4(2)
nfields = iou.read_long(self.f, "big")
definition = ()
for ifield in range(nfields):
self.f.seek(4, 1)
self.skipif4(2)
definition += (iou.read_long(self.f, "big"), )
return definition
def parse_string_definition(self):
"""Reads and returns the length of the string.
The position in the file must be just after the
string encoded dtype.
"""
self.skipif4()
return iou.read_long(self.f, "big")
def parse_header(self):
self.dm_version = iou.read_long(self.f, "big")
if self.dm_version not in (3, 4):
raise NotImplementedError(
"Currently we only support reading DM versions 3 and 4 but "
"this file "
"seems to be version %s " % self.dm_version)
filesizeB = self.read_l_or_q(self.f, "big")
is_little_endian = iou.read_long(self.f, "big")
_logger.info('DM version: %i', self.dm_version)
_logger.info('size %i B', filesizeB)
_logger.info('Is file Little endian? %s', bool(is_little_endian))
if bool(is_little_endian):
self.endian = 'little'
else:
self.endian = 'big'
def parse_tag_group(self, skip4=1):
"""Parse the root TagGroup of the given DM3 file f.
Returns the tuple (is_sorted, is_open, n_tags).
endian can be either 'big' or 'little'.
"""
is_sorted = iou.read_byte(self.f, "big")
is_open = iou.read_byte(self.f, "big")
self.skipif4(n=skip4)
n_tags = iou.read_long(self.f, "big")
return bool(is_sorted), bool(is_open), n_tags
def parse_tag_group(self, skip4=1):
"""Parse the root TagGroup of the given DM3 file f.
Returns the tuple (is_sorted, is_open, n_tags).
endian can be either 'big' or 'little'.
"""
is_sorted = iou.read_byte(self.f, "big")
is_open = iou.read_byte(self.f, "big")
self.skipif4(n=skip4)
n_tags = iou.read_long(self.f, "big")
return bool(is_sorted), bool(is_open), n_tags
def parse_tags(self, ntags, group_name='root', group_dict={}):
"""Parse the DM file into a dictionary.
"""
unnammed_data_tags = 0
unnammed_group_tags = 0
for tag in range(ntags):
_logger.debug('Reading tag name at address: %s', self.f.tell())
tag_header = self.parse_tag_header()
tag_name = tag_header['tag_name']
skip = True if (group_name == "ImageData" and
tag_name == "Data") else False
_logger.debug('Tag name: %s', tag_name[:20])
_logger.debug('Tag ID: %s', tag_header['tag_id'])
if tag_header['tag_id'] == 21: # it's a TagType (DATA)
if not tag_name:
tag_name = 'Data%i' % unnammed_data_tags
unnammed_data_tags += 1
_logger.debug('Reading data tag at address: %s', self.f.tell())
# Start reading the data
# Raises IOError if it is wrong
self.check_data_tag_delimiter()
self.skipif4()
infoarray_size = iou.read_long(self.f, 'big')
_logger.debug("Infoarray size: %s", infoarray_size)
self.skipif4()
if infoarray_size == 1: # Simple type
_logger.debug("Reading simple data")
etype = iou.read_long(self.f, "big")
data = self.read_simple_data(etype)
elif infoarray_size == 2: # String
_logger.debug("Reading string")
enctype = iou.read_long(self.f, "big")
if enctype != 18:
raise IOError("Expected 18 (string), got %i" % enctype)
string_length = self.parse_string_definition()
data = self.read_string(string_length, skip=skip)
elif infoarray_size == 3: # Array of simple type
_logger.debug("Reading simple array")
# Read array header
enctype = iou.read_long(self.f, "big")
if enctype != 20: # Should be 20 if it is an array
raise IOError("Expected 20 (string), got %i" % enctype)
size, enc_eltype = self.parse_array_definition()
data = self.read_array(size, enc_eltype, skip=skip)
elif infoarray_size > 3:
enctype = iou.read_long(self.f, "big")
if enctype == 15: # It is a struct
_logger.debug("Reading struct")
definition = self.parse_struct_definition()
_logger.debug("Struct definition %s", definition)
data = self.read_struct(definition, skip=skip)
elif enctype == 20: # It is an array of complex type
# Read complex array info
# The structure is
# 20 <4>, ? <4>, enc_dtype <4>, definition <?>,
# size <4>
self.skipif4()
enc_eltype = iou.read_long(self.f, "big")
if enc_eltype == 15: # Array of structs
_logger.debug("Reading array of structs")
definition = self.parse_struct_definition()
self.skipif4() # Padding?
size = iou.read_long(self.f, "big")
_logger.debug("Struct definition: %s", definition)
_logger.debug("Array size: %s", size)
data = self.read_array(
size=size,
enc_eltype=enc_eltype,
extra={"definition": definition},
skip=skip)
elif enc_eltype == 18: # Array of strings
_logger.debug("Reading array of strings")
string_length = \
self.parse_string_definition()
size = iou.read_long(self.f, "big")
data = self.read_array(
size=size,
enc_eltype=enc_eltype,
extra={"length": string_length},
skip=skip)
elif enc_eltype == 20: # Array of arrays
_logger.debug("Reading array of arrays")
el_length, enc_eltype = \
self.parse_array_definition()
size = iou.read_long(self.f, "big")
data = self.read_array(
size=size,
enc_eltype=enc_eltype,
extra={"size": el_length},
skip=skip)
else: # Infoarray_size < 1
raise IOError("Invalided infoarray size ", infoarray_size)
group_dict[tag_name] = data
elif tag_header['tag_id'] == 20: # it's a TagGroup (GROUP)
if not tag_name:
tag_name = 'TagGroup%i' % unnammed_group_tags
unnammed_group_tags += 1
_logger.debug(
'Reading Tag group at address: %s',
self.f.tell())
ntags = self.parse_tag_group(skip4=3)[2]
group_dict[tag_name] = {}
self.parse_tags(
ntags=ntags,
group_name=tag_name,
group_dict=group_dict[tag_name])
else:
_logger.debug('File address:', self.f.tell())
raise DM3TagIDError(tag_header['tag_id'])
def parse_tags(self, ntags, group_name='root', group_dict={}):
"""Parse the DM file into a dictionary.
"""
unnammed_data_tags = 0
unnammed_group_tags = 0
for tag in range(ntags):
_logger.debug('Reading tag name at address: %s', self.f.tell())
tag_header = self.parse_tag_header()
tag_name = tag_header['tag_name']
skip = True if (group_name == "ImageData"
and tag_name == "Data") else False
_logger.debug('Tag name: %s', tag_name[:20])
_logger.debug('Tag ID: %s', tag_header['tag_id'])
if tag_header['tag_id'] == 21: # it's a TagType (DATA)
if not tag_name:
tag_name = 'Data%i' % unnammed_data_tags
unnammed_data_tags += 1
_logger.debug('Reading data tag at address: %s', self.f.tell())
# Start reading the data
# Raises IOError if it is wrong
self.check_data_tag_delimiter()
self.skipif4()
infoarray_size = iou.read_long(self.f, 'big')
_logger.debug("Infoarray size: %s", infoarray_size)
self.skipif4()
if infoarray_size == 1: # Simple type
_logger.debug("Reading simple data")
etype = iou.read_long(self.f, "big")
data = self.read_simple_data(etype)
elif infoarray_size == 2: # String
_logger.debug("Reading string")
enctype = iou.read_long(self.f, "big")
if enctype != 18:
raise IOError("Expected 18 (string), got %i" % enctype)
string_length = self.parse_string_definition()
data = self.read_string(string_length, skip=skip)
elif infoarray_size == 3: # Array of simple type
_logger.debug("Reading simple array")
# Read array header
enctype = iou.read_long(self.f, "big")
if enctype != 20: # Should be 20 if it is an array
raise IOError("Expected 20 (string), got %i" % enctype)
size, enc_eltype = self.parse_array_definition()
data = self.read_array(size, enc_eltype, skip=skip)
elif infoarray_size > 3:
enctype = iou.read_long(self.f, "big")
if enctype == 15: # It is a struct
_logger.debug("Reading struct")
definition = self.parse_struct_definition()
_logger.debug("Struct definition %s", definition)
data = self.read_struct(definition, skip=skip)
elif enctype == 20: # It is an array of complex type
# Read complex array info
# The structure is
# 20 <4>, ? <4>, enc_dtype <4>, definition <?>,
# size <4>
self.skipif4()
enc_eltype = iou.read_long(self.f, "big")
if enc_eltype == 15: # Array of structs
_logger.debug("Reading array of structs")
definition = self.parse_struct_definition()
self.skipif4() # Padding?
size = iou.read_long(self.f, "big")
_logger.debug("Struct definition: %s", definition)
_logger.debug("Array size: %s", size)
data = self.read_array(
size=size,
enc_eltype=enc_eltype,
extra={"definition": definition},
skip=skip)
elif enc_eltype == 18: # Array of strings
_logger.debug("Reading array of strings")
string_length = \
self.parse_string_definition()
size = iou.read_long(self.f, "big")
data = self.read_array(
size=size,
enc_eltype=enc_eltype,
extra={"length": string_length},
skip=skip)
elif enc_eltype == 20: # Array of arrays
_logger.debug("Reading array of arrays")
el_length, enc_eltype = \
self.parse_array_definition()
size = iou.read_long(self.f, "big")
data = self.read_array(size=size,
enc_eltype=enc_eltype,
extra={"size": el_length},
skip=skip)
else: # Infoarray_size < 1
raise IOError("Invalided infoarray size ", infoarray_size)
group_dict[tag_name] = data
elif tag_header['tag_id'] == 20: # it's a TagGroup (GROUP)
if not tag_name:
tag_name = 'TagGroup%i' % unnammed_group_tags
unnammed_group_tags += 1
_logger.debug('Reading Tag group at address: %s',
self.f.tell())
ntags = self.parse_tag_group(skip4=3)[2]
group_dict[tag_name] = {}
self.parse_tags(ntags=ntags,
group_name=tag_name,
group_dict=group_dict[tag_name])
else:
_logger.debug('File address:', self.f.tell())
raise DM3TagIDError(tag_header['tag_id'])