OwlCyberSecurity - MANAGER

Edit File: SpiderImagePlugin.py

#
# 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
#
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:
            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)
    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)

def _close__fp(self):
        try:
            if self.__fp != self.fp:
                self.__fp.close()
        except AttributeError:
            pass
        finally:
            self.__fp = None

# --------------------------------------------------------------------
# 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("unable to find %s" % 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
    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 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: 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)