# # 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 # import Image, ImageFile import os, string, struct, sys def isInt(f): try: i = int(f) if f-i == 0: return 1 else: return 0 except: 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 not iform 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() bigendian = 1 t = struct.unpack('>23f',f) # try big-endian first hdrlen = isSpiderHeader(t) if hdrlen == 0: bigendian = 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): (min, max) = self.getextrema() m = 1 if max != min: m = depth / (max-min) b = -m * min 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): 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 == 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 = 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 fn, ext = os.path.splitext(filename) 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: ", 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")