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 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
#
import os
import struct
import sys

from PIL import Image, ImageFile


[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: msg = "not a valid Spider file" raise SyntaxError(msg) except struct.error as e: msg = "not a valid Spider file" raise SyntaxError(msg) from e h = (99,) + t # add 1 value : spider header index starts at 1 iform = int(h[5]) if iform != 1: msg = "not a Spider 2D image" raise SyntaxError(msg) 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: msg = "inconsistent stack header values" raise SyntaxError(msg) 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: msg = "attempt to seek in a non-stack file" raise EOFError(msg) 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 :py:class:`~PIL.Image.Image` objects for use in a montage""" if filelist is None or len(filelist) < 1: return imglist = [] for img in filelist: if not os.path.exists(img): print(f"unable to find {img}") continue try: with Image.open(img) as im: im = im.convert2byte() except Exception: 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 = int(1024 / lenbyt) if 1024 % lenbyt != 0: labrec += 1 labbyt = labrec * lenbyt nvalues = int(labbyt / 4) if nvalues < 23: return [] hdr = [] for i in range(nvalues): hdr.append(0.0) # NB these are Fortran indices hdr[1] = 1.0 # nslice (=1 for an image) hdr[2] = float(nrow) # number of rows per slice hdr[3] = float(nrow) # number of records in the image 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 return [struct.pack("f", v) for v in hdr]
def _save(im, fp, filename): if im.mode[0] != "F": im = im.convert("F") hdr = makeSpiderHeader(im) if len(hdr) < 256: msg = "Error creating Spider header" raise OSError(msg) # 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: python3 SpiderImagePlugin.py [infile] [outfile]") sys.exit() filename = sys.argv[1] if not isSpiderImage(filename): print("input image must be in Spider format") sys.exit() with Image.open(filename) as im: 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.Transpose.FLIP_LEFT_RIGHT) print( f"saving a flipped version of {os.path.basename(filename)} " f"as {outfile} " ) im.save(outfile, SpiderImageFile.format)