/usr/share/pyshared/fabio/dm3image.py is in python-fabio 0.0.8-1.
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 | """
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 numpy
from fabioimage import fabioimage
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 _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):
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]
#print 'TagGroup is sorted? ',self.grouptag_is_sorted
#print 'TagGroup is open? ',self.grouptag_is_open
#print 'no of tags in TagGroup', 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]
#print 'does Tag have data ?' , self.tag_is_data, ' - 20 = Tag group , 21 = data '
#print '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()
#print 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]
#print 'data is of type :', self.tag_data_type , ' - 1 = simple, 2= string, 3 = array, >3 structs'
self.tag_encoded_type = self.readbytes(4, numpy.uint32)[0]
# print 'encode type: ', 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:
#print 'skip bytes', self.no_data_elements
dump = self.infile.read(self.no_data_elements)
return None
# print 'Data are stored as a simple a array -'
# print '%i data elemets stored as ' %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]
#print 'found array - new tag_encoded_type', 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]]
#print 'skip bytes', 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()
|