/usr/share/pyshared/fabio/dm3image.py is in python-fabio 0.1.4-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 | """
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
"""
# get ready for python3
from __future__ import with_statement, print_function
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
logger.info('read dm3 file - file format %s' % file_format)
logger.info('Bytes in file: %s' % self.bytes_in_file)
logger.info('Byte order: %s - 0 = bigEndian , 1 = littleEndian' % self.byte_order)
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
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()
|