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Pillow/PIL/SpiderImagePlugin.py
Andrew Murray ee34d6843b Further health fixes
2015-04-24 18:24:52 +10:00

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#
# The Python Imaging Library.
#
# SPIDER image file handling
#
# History:
# 2004-08-02 Created BB
# 2006-03-02 added save method
# 2006-03-13 added support for stack images
#
# Copyright (c) 2004 by Health Research Inc. (HRI) RENSSELAER, NY 12144.
# Copyright (c) 2004 by William Baxter.
# Copyright (c) 2004 by Secret Labs AB.
# Copyright (c) 2004 by Fredrik Lundh.
#
##
# Image plugin for the Spider image format. This format is is used
# by the SPIDER software, in processing image data from electron
# microscopy and tomography.
##
#
# SpiderImagePlugin.py
#
# The Spider image format is used by SPIDER software, in processing
# image data from electron microscopy and tomography.
#
# Spider home page:
# http://www.wadsworth.org/spider_doc/spider/docs/spider.html
#
# Details about the Spider image format:
# http://www.wadsworth.org/spider_doc/spider/docs/image_doc.html
#
from __future__ import print_function
from PIL import Image, ImageFile
import os
import struct
import sys
def isInt(f):
try:
i = int(f)
if f-i == 0:
return 1
else:
return 0
except ValueError:
return 0
iforms = [1, 3, -11, -12, -21, -22]
# There is no magic number to identify Spider files, so just check a
# series of header locations to see if they have reasonable values.
# Returns no.of bytes in the header, if it is a valid Spider header,
# otherwise returns 0
def isSpiderHeader(t):
h = (99,) + t # add 1 value so can use spider header index start=1
# header values 1,2,5,12,13,22,23 should be integers
for i in [1, 2, 5, 12, 13, 22, 23]:
if not isInt(h[i]):
return 0
# check iform
iform = int(h[5])
if iform not in iforms:
return 0
# check other header values
labrec = int(h[13]) # no. records in file header
labbyt = int(h[22]) # total no. of bytes in header
lenbyt = int(h[23]) # record length in bytes
# print "labrec = %d, labbyt = %d, lenbyt = %d" % (labrec,labbyt,lenbyt)
if labbyt != (labrec * lenbyt):
return 0
# looks like a valid header
return labbyt
def isSpiderImage(filename):
fp = open(filename, 'rb')
f = fp.read(92) # read 23 * 4 bytes
fp.close()
t = struct.unpack('>23f', f) # try big-endian first
hdrlen = isSpiderHeader(t)
if hdrlen == 0:
t = struct.unpack('<23f', f) # little-endian
hdrlen = isSpiderHeader(t)
return hdrlen
class SpiderImageFile(ImageFile.ImageFile):
format = "SPIDER"
format_description = "Spider 2D image"
def _open(self):
# check header
n = 27 * 4 # read 27 float values
f = self.fp.read(n)
try:
self.bigendian = 1
t = struct.unpack('>27f', f) # try big-endian first
hdrlen = isSpiderHeader(t)
if hdrlen == 0:
self.bigendian = 0
t = struct.unpack('<27f', f) # little-endian
hdrlen = isSpiderHeader(t)
if hdrlen == 0:
raise SyntaxError("not a valid Spider file")
except struct.error:
raise SyntaxError("not a valid Spider file")
h = (99,) + t # add 1 value : spider header index starts at 1
iform = int(h[5])
if iform != 1:
raise SyntaxError("not a Spider 2D image")
self.size = int(h[12]), int(h[2]) # size in pixels (width, height)
self.istack = int(h[24])
self.imgnumber = int(h[27])
if self.istack == 0 and self.imgnumber == 0:
# stk=0, img=0: a regular 2D image
offset = hdrlen
self.nimages = 1
elif self.istack > 0 and self.imgnumber == 0:
# stk>0, img=0: Opening the stack for the first time
self.imgbytes = int(h[12]) * int(h[2]) * 4
self.hdrlen = hdrlen
self.nimages = int(h[26])
# Point to the first image in the stack
offset = hdrlen * 2
self.imgnumber = 1
elif self.istack == 0 and self.imgnumber > 0:
# stk=0, img>0: an image within the stack
offset = hdrlen + self.stkoffset
self.istack = 2 # So Image knows it's still a stack
else:
raise SyntaxError("inconsistent stack header values")
if self.bigendian:
self.rawmode = "F;32BF"
else:
self.rawmode = "F;32F"
self.mode = "F"
self.tile = [
("raw", (0, 0) + self.size, offset,
(self.rawmode, 0, 1))]
self.__fp = self.fp # FIXME: hack
# 1st image index is zero (although SPIDER imgnumber starts at 1)
def tell(self):
if self.imgnumber < 1:
return 0
else:
return self.imgnumber - 1
def seek(self, frame):
if self.istack == 0:
return
if frame >= self.nimages:
raise EOFError("attempt to seek past end of file")
self.stkoffset = self.hdrlen + frame * (self.hdrlen + self.imgbytes)
self.fp = self.__fp
self.fp.seek(self.stkoffset)
self._open()
# returns a byte image after rescaling to 0..255
def convert2byte(self, depth=255):
(minimum, maximum) = self.getextrema()
m = 1
if maximum != minimum:
m = depth / (maximum-minimum)
b = -m * minimum
return self.point(lambda i, m=m, b=b: i * m + b).convert("L")
# returns a ImageTk.PhotoImage object, after rescaling to 0..255
def tkPhotoImage(self):
from PIL import ImageTk
return ImageTk.PhotoImage(self.convert2byte(), palette=256)
# --------------------------------------------------------------------
# Image series
# given a list of filenames, return a list of images
def loadImageSeries(filelist=None):
" create a list of Image.images for use in montage "
if filelist is None or len(filelist) < 1:
return
imglist = []
for img in filelist:
if not os.path.exists(img):
print("unable to find %s" % img)
continue
try:
im = Image.open(img).convert2byte()
except:
if not isSpiderImage(img):
print(img + " is not a Spider image file")
continue
im.info['filename'] = img
imglist.append(im)
return imglist
# --------------------------------------------------------------------
# For saving images in Spider format
def makeSpiderHeader(im):
nsam, nrow = im.size
lenbyt = nsam * 4 # There are labrec records in the header
labrec = 1024 / lenbyt
if 1024 % lenbyt != 0:
labrec += 1
labbyt = labrec * lenbyt
hdr = []
nvalues = int(labbyt / 4)
for i in range(nvalues):
hdr.append(0.0)
if len(hdr) < 23:
return []
# NB these are Fortran indices
hdr[1] = 1.0 # nslice (=1 for an image)
hdr[2] = float(nrow) # number of rows per slice
hdr[5] = 1.0 # iform for 2D image
hdr[12] = float(nsam) # number of pixels per line
hdr[13] = float(labrec) # number of records in file header
hdr[22] = float(labbyt) # total number of bytes in header
hdr[23] = float(lenbyt) # record length in bytes
# adjust for Fortran indexing
hdr = hdr[1:]
hdr.append(0.0)
# pack binary data into a string
hdrstr = []
for v in hdr:
hdrstr.append(struct.pack('f', v))
return hdrstr
def _save(im, fp, filename):
if im.mode[0] != "F":
im = im.convert('F')
hdr = makeSpiderHeader(im)
if len(hdr) < 256:
raise IOError("Error creating Spider header")
# write the SPIDER header
try:
fp = open(filename, 'wb')
except:
raise IOError("Unable to open %s for writing" % filename)
fp.writelines(hdr)
rawmode = "F;32NF" # 32-bit native floating point
ImageFile._save(im, fp, [("raw", (0, 0)+im.size, 0, (rawmode, 0, 1))])
fp.close()
def _save_spider(im, fp, filename):
# get the filename extension and register it with Image
ext = os.path.splitext(filename)[1]
Image.register_extension("SPIDER", ext)
_save(im, fp, filename)
# --------------------------------------------------------------------
Image.register_open("SPIDER", SpiderImageFile)
Image.register_save("SPIDER", _save_spider)
if __name__ == "__main__":
if not sys.argv[1:]:
print("Syntax: python SpiderImagePlugin.py Spiderimage [outfile]")
sys.exit()
filename = sys.argv[1]
if not isSpiderImage(filename):
print("input image must be in Spider format")
sys.exit()
outfile = ""
if len(sys.argv[1:]) > 1:
outfile = sys.argv[2]
im = Image.open(filename)
print("image: " + str(im))
print("format: " + str(im.format))
print("size: " + str(im.size))
print("mode: " + str(im.mode))
print("max, min: ", end=' ')
print(im.getextrema())
if outfile != "":
# perform some image operation
im = im.transpose(Image.FLIP_LEFT_RIGHT)
print(
"saving a flipped version of %s as %s " %
(os.path.basename(filename), outfile))
im.save(outfile, "SPIDER")
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