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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:
+ 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):
+ (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):
+ 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
+ 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: ", 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")