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Diffstat (limited to 'env/lib/python3.10/site-packages/PIL/SpiderImagePlugin.py')
| -rw-r--r-- | env/lib/python3.10/site-packages/PIL/SpiderImagePlugin.py | 313 |
1 files changed, 0 insertions, 313 deletions
diff --git a/env/lib/python3.10/site-packages/PIL/SpiderImagePlugin.py b/env/lib/python3.10/site-packages/PIL/SpiderImagePlugin.py deleted file mode 100644 index acafc32..0000000 --- a/env/lib/python3.10/site-packages/PIL/SpiderImagePlugin.py +++ /dev/null @@ -1,313 +0,0 @@ -# -# 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) |