/usr/lib/python2.7/dist-packages/fabio/dm3image.py is in python-fabio 0.1.3-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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Authors: Henning O. Sorensen & Erik Knudsen
Center for Fundamental Research: Metal Structures in Four Dimensions
Risoe National Laboratory
Frederiksborgvej 399
DK-4000 Roskilde
email:erik.knudsen@risoe.dk
+ Jon Wright, ESRF
"""
import logging
import numpy
from fabioimage import fabioimage
logger = logging.getLogger("dm3image")
DATA_TYPES = { 2 : numpy.int16,
4 : numpy.uint16,
3 : numpy.int32,
5 : numpy.uint32,
6 : numpy.float32,
7 : numpy.float,
8 : numpy.int8,
9 : None,
10 : None,
15 : 'Struct',
18 : None,
20 : None
}
DATA_BYTES = { 2 : 2,
4 : 2,
3 : 4,
5 : 4,
6 : 4,
7 : 8,
8 : 1,
9 : None,
10 : None,
15 : 'Struct',
18 : None,
20 : None
}
class dm3image(fabioimage):
""" Read and try to write the dm3 data format """
def __init__(self, *args, **kwargs):
fabioimage.__init__(self, *args, **kwargs)
self.encoded_datatype = None
self.no_data_elements = None
self.grouptag_is_sorted = None
self.grouptag_is_open = None
self.tag_encoded_type = None
self.tag_data_type = None
self.tag_is_data = None
self.grouptag_no_tags = None
self.bytes_in_file = None
self.tag_label_length = None
self.go_on = None
def _readheader(self):
self.infile.seek(0)
file_format = self.readbytes(4, numpy.uint32)[0] # should be 3
assert file_format == 3, 'Wrong file type '
self.bytes_in_file = self.readbytes(4, numpy.uint32)[0]
self.byte_order = self.readbytes(4, numpy.uint32)[0] # 0 = big, 1= little
print 'read dm3 file - file format ', file_format
print 'Bytes in file : ' , self.bytes_in_file
print 'Byte order :', self.byte_order, ' - 0 = bigEndian , 1 = littleEndian'
if self.byte_order == 0:
self.swap = True
elif self.byte_order == 1:
self.swap = False
else:
raise ValueError
def read(self, fname, frame=None):
self.header = {}
self.resetvals()
self.infile = self._open(fname, "rb")
self._readheader()
self.go_on = True
print self.go_on
while self.go_on:
self.read_tag_group()
self.read_tag_entry()
if self.infile.tell() > self.bytes_in_file: break
while self.tag_is_data == 21:
self.read_tag_entry()
if self.infile.tell() > self.bytes_in_file:
self.go_on = False
(dim1_raw, dim2_raw) = self.header['Active Size (pixels)'].split()
(dim1_raw, dim2_raw) = (eval(dim1_raw), eval(dim2_raw))
(dim1_binning, dim2_binning) = self.header['Binning'].split()
(dim1_binning, dim2_binning) = (eval(dim1_binning), eval(dim2_binning))
self.dim1 = dim1_raw / dim1_binning
self.dim2 = dim2_raw / dim2_binning
#print dim1,dim2
if self.header.has_key('Data'):
self.data = self.header['Data'].reshape(self.dim1, self.dim2)
def readbytes(self, bytes_to_read, format, swap=True):
raw = self.infile.read(bytes_to_read)
if format != None:
data = numpy.fromstring(raw, format)
else:
data = raw
if swap:
data = data.byteswap()
return data
def read_tag_group(self):
self.grouptag_is_sorted = self.readbytes(1, numpy.uint8)[0]
self.grouptag_is_open = self.readbytes(1, numpy.uint8)[0]
self.grouptag_no_tags = self.readbytes(4, numpy.uint32)[0]
logger.debug('TagGroup is sorted? %s', self.grouptag_is_sorted)
logger.debug('TagGroup is open? %s', self.grouptag_is_open)
logger.debug('no of tags in TagGroup %s', self.grouptag_no_tags)
def read_tag_entry(self):
self.tag_is_data = self.readbytes(1, numpy.uint8)[0]
self.tag_label_length = self.readbytes(2, numpy.uint16)[0]
logger.debug('does Tag have data ? %s - 20 = Tag group , 21 = data ', self.tag_is_data)
logger.debug('length of tag_label ', self.tag_label_length)
if self.tag_label_length != 0:
tag_label = self.infile.read(self.tag_label_length)
else:
tag_label = None
if self.tag_is_data == 21:
# This is data
self.header[tag_label] = self.read_tag_type()
logger.debug("%s: %s", tag_label, self.header[tag_label])
def read_tag_type(self):
if self.infile.read(4) != '%%%%':
raise IOError
self.tag_data_type = self.readbytes(4, numpy.uint32)[0]
logger.debug('data is of type : %s - 1 = simple, 2= string, 3 = array, >3 structs', self.tag_data_type)
self.tag_encoded_type = self.readbytes(4, numpy.uint32)[0]
logger.debug('encode type: %s %s', self.tag_encoded_type, DATA_TYPES[ self.tag_encoded_type])
if self.tag_data_type == 1:
# simple type
return self.readbytes(DATA_BYTES[ self.tag_encoded_type],
DATA_TYPES[ self.tag_encoded_type],
swap=self.swap)[0]
# are the data stored in a simple array?
if self.tag_encoded_type == 20 and self.tag_data_type == 3 :
self.data_type = self.readbytes(4, numpy.uint32)[0]
self.no_data_elements = self.readbytes(4, numpy.uint32)[0]
if self.data_type == 10:
logger.debug('skip bytes %s', self.no_data_elements)
dump = self.infile.read(self.no_data_elements)
return None
logger.debug('Data are stored as a simple a array -')
logger.debug('%s data elemets stored as %s', self.no_data_elements, self.data_type)
read_no_bytes = DATA_BYTES[self.data_type] * self.no_data_elements
format = DATA_TYPES[self.data_type]
return self.readbytes(read_no_bytes, format, swap=self.swap)
# are the data stored in a complex array ?
# print 'tag_type + data_type', self.tag_encoded_type,self.tag_data_type
#print self.tag_encoded_type , self.tag_data_type
if self.tag_encoded_type == 20 and self.tag_data_type > 3 :
self.tag_encoded_type = self.readbytes(4, numpy.uint32)[0]
logger.debug('found array - new tag_encoded_type %s', self.tag_encoded_type)
if self.tag_encoded_type == 15: # struct type
###type = self.readbytes(4,numpy.int32)
struct_name_length = self.readbytes(4, numpy.int32)[0]
struct_number_fields = self.readbytes(4, numpy.int32)[0]
#print 'struct - name_length, number_field', struct_name_length,struct_number_fields
#print self.infile.read(struct_name_length)
field_info = []
for i in range(struct_number_fields):
field_info.append([self.readbytes(4, numpy.int32)[0], self.readbytes(4, numpy.int32)[0]])
#print field_info
self.no_data_elements = self.readbytes(4, numpy.int32)[0]
#print '%i data elemets stored as ' %self.no_data_elements
bytes_in_struct = 0
for i in range(struct_number_fields):
bytes_in_struct += DATA_BYTES[field_info[i][1]]
logger.debug('skip bytes %s', self.no_data_elements * bytes_in_struct)
dump = self.infile.read(self.no_data_elements * bytes_in_struct)
return None
if self.tag_encoded_type == 15: # struct type
###type = self.readbytes(4,numpy.int32)
struct_name_length = self.readbytes(4, numpy.int32)[0]
struct_number_fields = self.readbytes(4, numpy.int32)[0]
#print 'struct - name_length, number_field', struct_name_length,struct_number_fields
#print self.infile.read(struct_name_length)
field_info = []
for i in range(struct_number_fields):
field_info.append([self.readbytes(4, numpy.int32)[0], self.readbytes(4, numpy.int32)[0]])
#print field_info
field_data = ''
for i in range(struct_number_fields):
#print type(i)
field_data = field_data + self.readbytes(field_info[i][0], None, swap=False) + ' '
field_data = field_data + '%i ' % self.readbytes(DATA_BYTES[field_info[i][1]],
DATA_TYPES[field_info[i][1]],
swap=self.swap)[0]
return field_data
def read_data(self):
self.encoded_datatype = numpy.fromstring(self.infile.read(4), numpy.uint32).byteswap()
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