Source code for PIL.SpiderImagePlugin

#
# 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:
# https://spider.wadsworth.org/spider_doc/spider/docs/spider.html
#
# Details about the Spider image format:
# https://spider.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


[docs]def isInt(f): try: i = int(f) if f-i == 0: return 1 else: return 0 except (ValueError, OverflowError): 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
[docs]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 if labbyt != (labrec * lenbyt): return 0 # looks like a valid header return labbyt
[docs]def isSpiderImage(filename): with open(filename, 'rb') as fp: f = fp.read(92) # read 23 * 4 bytes 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
[docs]class SpiderImageFile(ImageFile.ImageFile): format = "SPIDER" format_description = "Spider 2D image" _close_exclusive_fp_after_loading = False 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 @property def n_frames(self): return self._nimages @property def is_animated(self): return self._nimages > 1 # 1st image index is zero (although SPIDER imgnumber starts at 1)
[docs] def tell(self): if self.imgnumber < 1: return 0 else: return self.imgnumber - 1
[docs] def seek(self, frame): if self.istack == 0: raise EOFError("attempt to seek in a non-stack file") if not self._seek_check(frame): return 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
[docs] 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
[docs] 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
[docs]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
[docs]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 fp.writelines(hdr) rawmode = "F;32NF" # 32-bit native floating point ImageFile._save(im, fp, [("raw", (0, 0)+im.size, 0, (rawmode, 0, 1))]) def _save_spider(im, fp, filename): # get the filename extension and register it with Image ext = os.path.splitext(filename)[1] Image.register_extension(SpiderImageFile.format, ext) _save(im, fp, filename) # -------------------------------------------------------------------- Image.register_open(SpiderImageFile.format, SpiderImageFile) Image.register_save(SpiderImageFile.format, _save_spider) if __name__ == "__main__": if len(sys.argv) < 2: print("Syntax: python SpiderImagePlugin.py [infile] [outfile]") sys.exit() filename = sys.argv[1] if not isSpiderImage(filename): print("input image must be in Spider format") sys.exit() 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 len(sys.argv) > 2: outfile = sys.argv[2] # 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, SpiderImageFile.format)