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This script will convert tiff stacks to CCP4 maps for reading in PyMOL. | This script will convert tiff stacks to CCP4 maps for reading in PyMOL. | ||
| + | |||
| + | ''See also the [[load_img_stack]] script for loading image stacks directly into PyMOL''. | ||
If someone knows how to determine the file's dimensions from the file itself (not the image size, but the physical dimension size) please let me know. | If someone knows how to determine the file's dimensions from the file itself (not the image size, but the physical dimension size) please let me know. | ||
Latest revision as of 02:06, 22 August 2016
Overview
This script will convert tiff stacks to CCP4 maps for reading in PyMOL.
See also the load_img_stack script for loading image stacks directly into PyMOL.
If someone knows how to determine the file's dimensions from the file itself (not the image size, but the physical dimension size) please let me know.
Note: requires Python 2.7 or later (for argparse).
Usage
#
# convert input.tiff to output.ccp4 which has cell dimensions
# x=40 A, y=80.5 A, Z=125.2 A
#
python tiff2ccp4.py input.tiff output.ccp4 -x 40 -y 80.5 -z 125.2
#
# print help
#
python tiff2ccp4.py -h
The Code
#
# tiff2ccp4.py -- convert a TIFF stack to a CCP4 map
#
# Author: Jason Vertrees
# Date : 2011-09-16
#
# Notes : To get help, type "python tiff2ccp4.py -h"
#
import struct
import sys
import string
# key = field_type
# value = # bytes for that field
field_types = {
1 : 1,
2 : 1,
3 : 2,
4 : 4,
5 : 8,
6 : 1,
7 : 1,
8 : 2,
9 : 4,
10: 8,
11: 4,
12: 8 }
field_fmt = {
1 : "B",
2 : "c",
3 : "H",
4 : "I",
5 : "II",
6 : "i",
7 : "B",
8 : "h",
9 : "i",
10: "ii",
11: "f",
12: "d" }
tag_types = {
"NewSubfileType" : 254,
"ImageWidth" : 256, # # cols (number of pixels per scanline)
"ImageLength" : 257, # # rows (number of scanlines)
"BitsPerSample" : 258,
"PhotometricInterpretation" : 262,
"ImageDescription" : 270,
"StripOffsets" : 273,
"SamplesPerPixel" : 277,
"RowsPerStrip" : 278,
"StripByteCounts" : 279,
"XResolution" : 282,
"YResolution" : 283,
"ZResolution" : 284,
"ResolutionUnit" : 296,
}
class TIFFStack:
def __init__(self,filename):
self._filename = filename
self._f = open(self._filename, 'rb')
self._file_size = self.get_file_size()
# read and store the file header
self._header = self.get_header()
# read all IFDs and store
self._IFDs = self.get_IFDs()
def __str__(self):
s = ""
s += "[TIFFStack]\n"
s += "Filename : %s\n" % self._filename
s += "File size : %s\n" % self._file_size
s += "Header : %s\n" % self._header
s += "IFDs : %s\n" % self._IFDs
return s
def get_file_size(self):
"""
file size in bytes
"""
if not self._f:
print "Invalid: Must have open file handle."
return -1
# less typing
f = self._f
# get file size
curP = f.tell()
f.seek(0,2)
sz = f.tell()
# return to previous location
f.seek(curP)
return sz
def get_header(self):
return TIFFHeader(self._f)
def get_IFDs(self):
return IFD_Store(self._f, self._header)
def get_data(self):
f = self._f
# bits per sample
bps = 258
# StripOffsets
offset = 273
# byte counts per strip
byte_count = 279
sample_format = 339
data = []
ifds = self._IFDs._store
for curIFD in ifds:
curOffset = curIFD[offset]._val
curLength = curIFD[byte_count]._val
curBPS = curIFD[bps]._val
bytesPerSample = curBPS / 8.0
fld = self.get_field_fmt(curIFD)
# use "B" for now; support 16-bit later using tag 339 (SampleFormat)
unpackStr = self._header._e_flg + fld * int(curLength/bytesPerSample)
f.seek(curOffset)
data.extend(struct.unpack(unpackStr, f.read(curLength)))
return data
def get_field_fmt(self,ifd):
"""
Determines the Python struct code given
BitsPerSample and SampleFormat from the IFD
"""
bits_per_sample, sample_fmt = 258, 339
bps = ifd[bits_per_sample]._val
fmt = None
if sample_fmt in ifd.keys():
fmt = ifd[sample_fmt]._val
else:
fmt = 1
if bps==8:
# 1-byte unsigned int
if fmt==1:
return "B"
# 1-byte signed
elif fmt==2:
return "b"
elif bps==16:
# 2-byte unsigned
if fmt==1:
return "H"
elif fmt==2:
return "h"
def get_size(self):
fX, fY = 256, 257
x = self._IFDs._store[0][fX]._val
y = self._IFDs._store[0][fY]._val
z = len(self._IFDs._store)
return x, y, z
def get_axes_scale(self):
# for now
return 1,1,1
def asCCP4(self,filename,dimX=-1,dimY=-1,dimZ=-1):
data = self.get_data()
# pixels size x,y,z
nX, nY, nZ = self.get_size()
# dimension scaling
if -1 in (dimX,dimY,dimZ):
dimX, dimY, dimZ = self.get_axes_scale()
dimX *= nX
dimY *= nY
dimZ *= nZ
m, avg, M = min(data), sum(data)/len(data), max(data)
outFile = open(filename, 'wb')
outFile.write(struct.pack('i',nX)) # col
outFile.write(struct.pack('i',nY)) # row
outFile.write(struct.pack('i',nZ)) # section
outFile.write(struct.pack('i',2)) # mode = 2
outFile.write(struct.pack('i',1)) # number of first col
outFile.write(struct.pack('i',1)) # '' row
outFile.write(struct.pack('i',1)) # '' section
outFile.write(struct.pack('i',nX)) # nIntervals
outFile.write(struct.pack('i',nY)) #
outFile.write(struct.pack('i',nZ)) #
outFile.write(struct.pack('f',dimX)) # length in X
outFile.write(struct.pack('f',dimY)) # length in Y
outFile.write(struct.pack('f',dimZ)) # length in Z
outFile.write(struct.pack('f',90.)) # alpha
outFile.write(struct.pack('f',90.)) # beta
outFile.write(struct.pack('f',90.)) # gamma
outFile.write(struct.pack('i',1)) # axis cols
outFile.write(struct.pack('i',2)) # axis rows
outFile.write(struct.pack('i',3)) # axis section
outFile.write(struct.pack('f', m)) # min density
outFile.write(struct.pack('f', avg)) # max density
outFile.write(struct.pack('f', M)) # mean density
outFile.write(struct.pack('i',0)) # space gp ?
# header info; blank for us
for x in range(24,257): outFile.write(struct.pack('i',0))
# assume constant data in file
norm = 255.
bps = tag_types["BitsPerSample"]
max_bits = self._IFDs._store[0][bps]._val
norm = float(2**max_bits-1.)
# read/write data
for x in data:
outFile.write(struct.pack('f', x/norm))
outFile.close()
class TIFFHeader:
def __init__(self,fileHandle):
self._endian, self._e_flg = self.get_endian(fileHandle)
self._magic_number = self.get_magic_number(fileHandle)
self._first_IFD = self.get_first_IFDOffset(fileHandle)
def __str__(self):
s = "\n"
s += " [TIFF Header]\n"
s += " Endian : %s\n" % self._endian
s += " Endian Flag : %s\n" % self._e_flg
s += " Magic Number : %s\n" % self._magic_number
s += " IFD[0] Offset : %s" % self._first_IFD
return s
# for struct.unpackx
def _1byte(self,n=1):
return self._e_flg + "C"*n
def _2byte(self,n=1):
return self._e_flg + "H"*n
def _4byte(self,n=1):
return self._e_flg + "I"*n
def _IFDbyte(self,n=1):
return self._e_flg + "HHII"*n
def get_endian(self,fileHandle):
f = fileHandle
f.seek(0)
code = struct.unpack("cc", f.read(2))
code = "".join(code)
flg = ""
if code=="II":
flg = "<"
elif code=="MM":
flg = ">"
else:
print "This file is not a valid TIFF (bad endian tag)."
flg = "?"
return code,flg
def get_magic_number(self,fileHandle):
f = fileHandle
f.seek(2)
# read the magic number
idx = 0
if self._endian == "II": idx = 1
_42 = struct.unpack(self._2byte(), f.read(2))[0]
if _42!=42:
print "Error: Improperly formatted TIFF file (bad magic number)."
return None
return _42
def get_first_IFDOffset(self,fileHandle):
f=fileHandle
f.seek(4)
off = struct.unpack(self._4byte(), f.read(4))[0]
return off
class IFD_Store:
def __init__(self,fileHandle,fileHeader):
self._f = fileHandle
self._header = fileHeader
self._first_offset = self._header._first_IFD
# array of IFDs
self._store = self.read_ifds()
def __str__(self):
s = "\n"
s += " [IFD_Store]\n"
s += " First Offset : %d\n" % self._first_offset
s += " Store :\n"
for st in self._store:
s += "\n\n IFD Store =>\n"
for k in st:
s += " %s => %s" % (k,st[k])
return s
def read_ifds(self):
f = self._f
pos = self._first_offset
ifds = []
while pos!=0:
ifds.append({})
# get number of IFD_Entries
f.seek(pos)
# read number of IFDs
num_entries = struct.unpack(self._header._2byte(), f.read(2))
num_entries = num_entries[0]
# read all into IFD[x]
for x in range(num_entries):
# pull the current record from file
curParams = struct.unpack(self._header._IFDbyte(), f.read(12))
# format the data if necessary
if (self._header._e_flg==">" and sys.byteorder=="little") and \
curParams[0] not in (270,50838,50839):
scale = 32 - (8 * field_types[curParams[1]])
scaledData = curParams[3] >> scale
else:
scaledData = curParams[3]
ifds[-1][curParams[0]] = IFDEntry(curParams[0], curParams[1], curParams[2], scaledData)
# read next offset
pos = struct.unpack(self._header._4byte(), f.read(4))[0]
return ifds
class IFDEntry:
def __init__(self,theTag=None,theType=None,theCount=None,theValue=None):
self._tag = theTag
self._type = theType
self._count = theCount
self._val = theValue
def __str__(self):
s = "\n"
s += " [IFD_Entry]\n"
s += " Tag : %s\n" % self._tag
s += " Type : %s\n" % self._type
s += " Count : %s\n" % self._count
s += " Val/Off: %s\n" % self._val
return s
if __name__=="__main__":
"""
Running,
python tiff2ccp4.py
will convert all TIFF stacks in the current directory to
CCP4 maps.
"""
import argparse
from string import split
parser = argparse.ArgumentParser(description="Convert a TIFF Stack to a CCP4 Map")
parser.add_argument("input", type=str, help="input file name (usually .tif, .tiff)")
parser.add_argument("output", type=str, help="output file name (usually .ccp4)")
parser.add_argument('-x',"--x", help="length of x-dimension",default=-1.,type=float)
parser.add_argument('-y',"--y", help="length of y-dimension",default=-1.,type=float)
parser.add_argument('-z',"--z", help="length of z-dimension",default=-1.,type=float)
args = parser.parse_args()
s = TIFFStack(args.input)
s.asCCP4(args.output, args.x, args.y, args.z)