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Diffstat (limited to 'PIL/SpiderImagePlugin.py')
| -rw-r--r-- | PIL/SpiderImagePlugin.py | 294 |
1 files changed, 0 insertions, 294 deletions
diff --git a/PIL/SpiderImagePlugin.py b/PIL/SpiderImagePlugin.py deleted file mode 100644 index e0fd045..0000000 --- a/PIL/SpiderImagePlugin.py +++ /dev/null @@ -1,294 +0,0 @@ -# -# 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") |