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325 lines
9.3 KiB
325 lines
9.3 KiB
2 weeks ago
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#
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# The Python Imaging Library.
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#
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# SPIDER image file handling
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#
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# History:
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# 2004-08-02 Created BB
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# 2006-03-02 added save method
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# 2006-03-13 added support for stack images
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#
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# Copyright (c) 2004 by Health Research Inc. (HRI) RENSSELAER, NY 12144.
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# Copyright (c) 2004 by William Baxter.
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# Copyright (c) 2004 by Secret Labs AB.
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# Copyright (c) 2004 by Fredrik Lundh.
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#
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##
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# Image plugin for the Spider image format. This format is is used
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# by the SPIDER software, in processing image data from electron
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# microscopy and tomography.
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##
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#
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# SpiderImagePlugin.py
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#
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# The Spider image format is used by SPIDER software, in processing
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# image data from electron microscopy and tomography.
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#
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# Spider home page:
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# https://spider.wadsworth.org/spider_doc/spider/docs/spider.html
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#
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# Details about the Spider image format:
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# https://spider.wadsworth.org/spider_doc/spider/docs/image_doc.html
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#
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import os
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import struct
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import sys
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from PIL import Image, ImageFile
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def isInt(f):
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try:
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i = int(f)
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if f - i == 0:
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return 1
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else:
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return 0
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except (ValueError, OverflowError):
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return 0
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iforms = [1, 3, -11, -12, -21, -22]
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# There is no magic number to identify Spider files, so just check a
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# series of header locations to see if they have reasonable values.
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# Returns no. of bytes in the header, if it is a valid Spider header,
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# otherwise returns 0
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def isSpiderHeader(t):
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h = (99,) + t # add 1 value so can use spider header index start=1
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# header values 1,2,5,12,13,22,23 should be integers
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for i in [1, 2, 5, 12, 13, 22, 23]:
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if not isInt(h[i]):
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return 0
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# check iform
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iform = int(h[5])
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if iform not in iforms:
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return 0
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# check other header values
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labrec = int(h[13]) # no. records in file header
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labbyt = int(h[22]) # total no. of bytes in header
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lenbyt = int(h[23]) # record length in bytes
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if labbyt != (labrec * lenbyt):
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return 0
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# looks like a valid header
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return labbyt
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def isSpiderImage(filename):
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with open(filename, "rb") as fp:
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f = fp.read(92) # read 23 * 4 bytes
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t = struct.unpack(">23f", f) # try big-endian first
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hdrlen = isSpiderHeader(t)
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if hdrlen == 0:
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t = struct.unpack("<23f", f) # little-endian
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hdrlen = isSpiderHeader(t)
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return hdrlen
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class SpiderImageFile(ImageFile.ImageFile):
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format = "SPIDER"
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format_description = "Spider 2D image"
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_close_exclusive_fp_after_loading = False
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def _open(self):
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# check header
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n = 27 * 4 # read 27 float values
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f = self.fp.read(n)
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try:
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self.bigendian = 1
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t = struct.unpack(">27f", f) # try big-endian first
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hdrlen = isSpiderHeader(t)
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if hdrlen == 0:
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self.bigendian = 0
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t = struct.unpack("<27f", f) # little-endian
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hdrlen = isSpiderHeader(t)
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if hdrlen == 0:
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raise SyntaxError("not a valid Spider file")
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except struct.error as e:
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raise SyntaxError("not a valid Spider file") from e
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h = (99,) + t # add 1 value : spider header index starts at 1
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iform = int(h[5])
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if iform != 1:
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raise SyntaxError("not a Spider 2D image")
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self._size = int(h[12]), int(h[2]) # size in pixels (width, height)
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self.istack = int(h[24])
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self.imgnumber = int(h[27])
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if self.istack == 0 and self.imgnumber == 0:
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# stk=0, img=0: a regular 2D image
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offset = hdrlen
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self._nimages = 1
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elif self.istack > 0 and self.imgnumber == 0:
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# stk>0, img=0: Opening the stack for the first time
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self.imgbytes = int(h[12]) * int(h[2]) * 4
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self.hdrlen = hdrlen
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self._nimages = int(h[26])
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# Point to the first image in the stack
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offset = hdrlen * 2
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self.imgnumber = 1
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elif self.istack == 0 and self.imgnumber > 0:
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# stk=0, img>0: an image within the stack
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offset = hdrlen + self.stkoffset
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self.istack = 2 # So Image knows it's still a stack
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else:
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raise SyntaxError("inconsistent stack header values")
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if self.bigendian:
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self.rawmode = "F;32BF"
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else:
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self.rawmode = "F;32F"
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self.mode = "F"
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self.tile = [("raw", (0, 0) + self.size, offset, (self.rawmode, 0, 1))]
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self.__fp = self.fp # FIXME: hack
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@property
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def n_frames(self):
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return self._nimages
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@property
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def is_animated(self):
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return self._nimages > 1
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# 1st image index is zero (although SPIDER imgnumber starts at 1)
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def tell(self):
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if self.imgnumber < 1:
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return 0
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else:
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return self.imgnumber - 1
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def seek(self, frame):
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if self.istack == 0:
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raise EOFError("attempt to seek in a non-stack file")
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if not self._seek_check(frame):
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return
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self.stkoffset = self.hdrlen + frame * (self.hdrlen + self.imgbytes)
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self.fp = self.__fp
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self.fp.seek(self.stkoffset)
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self._open()
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# returns a byte image after rescaling to 0..255
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def convert2byte(self, depth=255):
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(minimum, maximum) = self.getextrema()
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m = 1
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if maximum != minimum:
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m = depth / (maximum - minimum)
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b = -m * minimum
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return self.point(lambda i, m=m, b=b: i * m + b).convert("L")
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# returns a ImageTk.PhotoImage object, after rescaling to 0..255
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def tkPhotoImage(self):
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from PIL import ImageTk
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return ImageTk.PhotoImage(self.convert2byte(), palette=256)
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def _close__fp(self):
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try:
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if self.__fp != self.fp:
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self.__fp.close()
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except AttributeError:
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pass
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finally:
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self.__fp = None
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# --------------------------------------------------------------------
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# Image series
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# given a list of filenames, return a list of images
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def loadImageSeries(filelist=None):
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"""create a list of :py:class:`~PIL.Image.Image` objects for use in a montage"""
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if filelist is None or len(filelist) < 1:
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return
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imglist = []
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for img in filelist:
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if not os.path.exists(img):
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print(f"unable to find {img}")
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continue
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try:
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with Image.open(img) as im:
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im = im.convert2byte()
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except Exception:
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if not isSpiderImage(img):
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print(img + " is not a Spider image file")
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continue
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im.info["filename"] = img
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imglist.append(im)
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return imglist
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# --------------------------------------------------------------------
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# For saving images in Spider format
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def makeSpiderHeader(im):
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nsam, nrow = im.size
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lenbyt = nsam * 4 # There are labrec records in the header
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labrec = int(1024 / lenbyt)
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if 1024 % lenbyt != 0:
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labrec += 1
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labbyt = labrec * lenbyt
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hdr = []
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nvalues = int(labbyt / 4)
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for i in range(nvalues):
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hdr.append(0.0)
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if len(hdr) < 23:
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return []
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# NB these are Fortran indices
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hdr[1] = 1.0 # nslice (=1 for an image)
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hdr[2] = float(nrow) # number of rows per slice
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hdr[5] = 1.0 # iform for 2D image
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hdr[12] = float(nsam) # number of pixels per line
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hdr[13] = float(labrec) # number of records in file header
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hdr[22] = float(labbyt) # total number of bytes in header
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hdr[23] = float(lenbyt) # record length in bytes
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# adjust for Fortran indexing
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hdr = hdr[1:]
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hdr.append(0.0)
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# pack binary data into a string
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hdrstr = []
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for v in hdr:
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hdrstr.append(struct.pack("f", v))
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return hdrstr
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def _save(im, fp, filename):
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if im.mode[0] != "F":
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im = im.convert("F")
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hdr = makeSpiderHeader(im)
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if len(hdr) < 256:
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raise OSError("Error creating Spider header")
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# write the SPIDER header
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fp.writelines(hdr)
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rawmode = "F;32NF" # 32-bit native floating point
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ImageFile._save(im, fp, [("raw", (0, 0) + im.size, 0, (rawmode, 0, 1))])
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def _save_spider(im, fp, filename):
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# get the filename extension and register it with Image
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ext = os.path.splitext(filename)[1]
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Image.register_extension(SpiderImageFile.format, ext)
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_save(im, fp, filename)
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# --------------------------------------------------------------------
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Image.register_open(SpiderImageFile.format, SpiderImageFile)
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Image.register_save(SpiderImageFile.format, _save_spider)
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if __name__ == "__main__":
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if len(sys.argv) < 2:
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print("Syntax: python SpiderImagePlugin.py [infile] [outfile]")
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sys.exit()
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filename = sys.argv[1]
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if not isSpiderImage(filename):
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print("input image must be in Spider format")
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sys.exit()
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with Image.open(filename) as im:
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print("image: " + str(im))
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print("format: " + str(im.format))
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print("size: " + str(im.size))
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print("mode: " + str(im.mode))
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print("max, min: ", end=" ")
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print(im.getextrema())
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if len(sys.argv) > 2:
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outfile = sys.argv[2]
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# perform some image operation
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im = im.transpose(Image.FLIP_LEFT_RIGHT)
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print(
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f"saving a flipped version of {os.path.basename(filename)} "
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f"as {outfile} "
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)
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im.save(outfile, SpiderImageFile.format)
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