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Diffstat (limited to '.venv/lib/python3.12/site-packages/PIL/SpiderImagePlugin.py')
| -rw-r--r-- | .venv/lib/python3.12/site-packages/PIL/SpiderImagePlugin.py | 326 |
1 files changed, 326 insertions, 0 deletions
diff --git a/.venv/lib/python3.12/site-packages/PIL/SpiderImagePlugin.py b/.venv/lib/python3.12/site-packages/PIL/SpiderImagePlugin.py new file mode 100644 index 00000000..3a87d009 --- /dev/null +++ b/.venv/lib/python3.12/site-packages/PIL/SpiderImagePlugin.py @@ -0,0 +1,326 @@ +# +# 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, 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 = [ImageFile._Tile("raw", (0, 0) + self.size, offset, self.rawmode)] + 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[Image.Image] | 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 + + byte_imgs = [] + for img in filelist: + if not os.path.exists(img): + print(f"unable to find {img}") + continue + try: + with Image.open(img) as im: + assert isinstance(im, SpiderImageFile) + byte_im = im.convert2byte() + except Exception: + if not isSpiderImage(img): + print(f"{img} is not a Spider image file") + continue + byte_im.info["filename"] = img + byte_imgs.append(byte_im) + return byte_imgs + + +# -------------------------------------------------------------------- +# 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, [ImageFile._Tile("raw", (0, 0) + im.size, 0, rawmode)]) + + +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) |