#
# 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
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
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
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
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 as e:
raise SyntaxError("not a valid Spider file") from e
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)
def tell(self):
if self.imgnumber < 1:
return 0
else:
return self.imgnumber - 1
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
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
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 :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
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:
raise OSError("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: 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)
