326 lines
9.8 KiB
Python
326 lines
9.8 KiB
Python
|
#
|
||
|
|
# 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
|
||
|
|
#
|
||
|
|
from __future__ import annotations
|
||
|
|
|
||
|
|
import os
|
||
|
|
import struct
|
||
|
|
import sys
|
||
|
|
from typing import IO, TYPE_CHECKING, Any, Tuple, cast
|
||
|
|
|
||
|
|
from . import Image, ImageFile
|
||
|
|
|
||
|
|
|
||
|
|
def isInt(f: Any) -> int:
|
||
|
|
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: tuple[float, ...]) -> int:
|
||
|
|
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: str) -> int:
|
||
|
|
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) -> None:
|
||
|
|
# 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) -> int:
|
||
|
|
return self._nimages
|
||
|
|
|
||
|
|
@property
|
||
|
|
def is_animated(self) -> bool:
|
||
|
|
return self._nimages > 1
|
||
|
|
|
||
|
|
# 1st image index is zero (although SPIDER imgnumber starts at 1)
|
||
|
|
def tell(self) -> int:
|
||
|
|
if self.imgnumber < 1:
|
||
|
|
return 0
|
||
|
|
else:
|
||
|
|
return self.imgnumber - 1
|
||
|
|
|
||
|
|
def seek(self, frame: int) -> None:
|
||
|
|
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
|
||
|
|
def convert2byte(self, depth: int = 255) -> Image.Image:
|
||
|
|
extrema = self.getextrema()
|
||
|
|
assert isinstance(extrema[0], float)
|
||
|
|
minimum, maximum = cast(Tuple[float, float], extrema)
|
||
|
|
m: float = 1
|
||
|
|
if maximum != minimum:
|
||
|
|
m = depth / (maximum - minimum)
|
||
|
|
b = -m * minimum
|
||
|
|
return self.point(lambda i: i * m + b).convert("L")
|
||
|
|
|
||
|
|
if TYPE_CHECKING:
|
||
|
|
from . import ImageTk
|
||
|
|
|
||
|
|
# returns a ImageTk.PhotoImage object, after rescaling to 0..255
|
||
|
|
def tkPhotoImage(self) -> ImageTk.PhotoImage:
|
||
|
|
from . import ImageTk
|
||
|
|
|
||
|
|
return ImageTk.PhotoImage(self.convert2byte(), palette=256)
|
||
|
|
|
||
|
|
|
||
|
|
# --------------------------------------------------------------------
|
||
|
|
# Image series
|
||
|
|
|
||
|
|
|
||
|
|
# given a list of filenames, return a list of images
|
||
|
|
def loadImageSeries(filelist: list[str] | None = None) -> list[SpiderImageFile] | 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 None
|
||
|
|
|
||
|
|
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(f"{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: Image.Image) -> list[bytes]:
|
||
|
|
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 = [0.0] * nvalues
|
||
|
|
|
||
|
|
# 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: Image.Image, fp: IO[bytes], filename: str | bytes) -> None:
|
||
|
|
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: Image.Image, fp: IO[bytes], filename: str | bytes) -> None:
|
||
|
|
# get the filename extension and register it with Image
|
||
|
|
filename_ext = os.path.splitext(filename)[1]
|
||
|
|
ext = filename_ext.decode() if isinstance(filename_ext, bytes) else filename_ext
|
||
|
|
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(f"image: {im}")
|
||
|
|
print(f"format: {im.format}")
|
||
|
|
print(f"size: {im.size}")
|
||
|
|
print(f"mode: {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)
|