Gecko [ biogenelab.eu ]

Name	Size	Permission
BdfFontFile.py	3.28 KB	-rw-r--r--
BdfFontFile.pyc	2.83 KB	-rw-r--r--
BmpImagePlugin.py	7.26 KB	-rw-r--r--
BmpImagePlugin.pyc	6.13 KB	-rw-r--r--
BufrStubImagePlugin.py	1.47 KB	-rw-r--r--
BufrStubImagePlugin.pyc	1.99 KB	-rw-r--r--
ContainerIO.py	2.54 KB	-rw-r--r--
ContainerIO.pyc	2.07 KB	-rw-r--r--
CurImagePlugin.py	1.9 KB	-rw-r--r--
CurImagePlugin.pyc	1.63 KB	-rw-r--r--
DcxImagePlugin.py	1.76 KB	-rw-r--r--
DcxImagePlugin.pyc	1.89 KB	-rw-r--r--
EpsImagePlugin.py	12.11 KB	-rw-r--r--
EpsImagePlugin.pyc	9.92 KB	-rw-r--r--
ExifTags.py	4.97 KB	-rw-r--r--
ExifTags.pyc	5.27 KB	-rw-r--r--
FitsStubImagePlugin.py	1.61 KB	-rw-r--r--
FitsStubImagePlugin.pyc	2 KB	-rw-r--r--
FliImagePlugin.py	3.38 KB	-rw-r--r--
FliImagePlugin.pyc	3.49 KB	-rw-r--r--
FontFile.py	2.76 KB	-rw-r--r--
FontFile.pyc	2.87 KB	-rw-r--r--
FpxImagePlugin.py	6.21 KB	-rw-r--r--
FpxImagePlugin.pyc	4.62 KB	-rw-r--r--
GbrImagePlugin.py	1.54 KB	-rw-r--r--
GbrImagePlugin.pyc	1.8 KB	-rw-r--r--
GdImageFile.py	2.13 KB	-rw-r--r--
GdImageFile.pyc	1.7 KB	-rw-r--r--
GifImagePlugin.py	16.47 KB	-rw-r--r--
GifImagePlugin.pyc	10.32 KB	-rw-r--r--
GimpGradientFile.py	3.26 KB	-rw-r--r--
GimpGradientFile.pyc	3.68 KB	-rw-r--r--
GimpPaletteFile.py	1.3 KB	-rw-r--r--
GimpPaletteFile.pyc	1.47 KB	-rw-r--r--
GribStubImagePlugin.py	1.47 KB	-rw-r--r--
GribStubImagePlugin.pyc	2 KB	-rw-r--r--
Hdf5StubImagePlugin.py	1.51 KB	-rw-r--r--
Hdf5StubImagePlugin.pyc	2 KB	-rw-r--r--
IcnsImagePlugin.py	8.99 KB	-rw-r--r--
IcnsImagePlugin.pyc	8.71 KB	-rw-r--r--
IcoImagePlugin.py	7.56 KB	-rw-r--r--
IcoImagePlugin.pyc	6.07 KB	-rw-r--r--
ImImagePlugin.py	9.87 KB	-rw-r--r--
ImImagePlugin.pyc	8.01 KB	-rw-r--r--
Image.py	78.54 KB	-rw-r--r--
Image.pyc	73.54 KB	-rw-r--r--
ImageChops.py	6.04 KB	-rw-r--r--
ImageChops.pyc	7.68 KB	-rw-r--r--
ImageCms.py	36.25 KB	-rw-r--r--
ImageCms.pyc	33.86 KB	-rw-r--r--
ImageColor.py	7.79 KB	-rw-r--r--
ImageColor.pyc	7.79 KB	-rw-r--r--
ImageDraw.py	11.39 KB	-rw-r--r--
ImageDraw.pyc	8.63 KB	-rw-r--r--
ImageDraw2.py	3.12 KB	-rw-r--r--
ImageDraw2.pyc	5.06 KB	-rw-r--r--
ImageEnhance.py	3.1 KB	-rw-r--r--
ImageEnhance.pyc	4.11 KB	-rw-r--r--
ImageFile.py	15.65 KB	-rw-r--r--
ImageFile.pyc	11.4 KB	-rw-r--r--
ImageFileIO.py	1022 B	-rw-r--r--
ImageFileIO.pyc	1.22 KB	-rw-r--r--
ImageFilter.py	6.29 KB	-rw-r--r--
ImageFilter.pyc	10.83 KB	-rw-r--r--
ImageFont.py	17.19 KB	-rw-r--r--
ImageFont.pyc	17.14 KB	-rw-r--r--
ImageGrab.py	1.19 KB	-rw-r--r--
ImageGrab.pyc	1.18 KB	-rw-r--r--
ImageMath.py	7.28 KB	-rw-r--r--
ImageMath.pyc	10.63 KB	-rw-r--r--
ImageMode.py	1.27 KB	-rw-r--r--
ImageMode.pyc	1.33 KB	-rw-r--r--
ImageMorph.py	7.78 KB	-rw-r--r--
ImageMorph.pyc	7.99 KB	-rw-r--r--
ImageOps.py	12.92 KB	-rw-r--r--
ImageOps.pyc	12.26 KB	-rw-r--r--
ImagePalette.py	6.25 KB	-rw-r--r--
ImagePalette.pyc	6.76 KB	-rw-r--r--
ImagePath.py	1.2 KB	-rw-r--r--
ImagePath.pyc	1.35 KB	-rw-r--r--
ImageQt.py	2.61 KB	-rw-r--r--
ImageQt.pyc	2.02 KB	-rw-r--r--
ImageSequence.py	939 B	-rw-r--r--
ImageSequence.pyc	1.19 KB	-rw-r--r--
ImageShow.py	4.67 KB	-rw-r--r--
ImageShow.pyc	5.36 KB	-rw-r--r--
ImageStat.py	3.74 KB	-rw-r--r--
ImageStat.pyc	4.53 KB	-rw-r--r--
ImageTransform.py	2.81 KB	-rw-r--r--
ImageTransform.pyc	1.85 KB	-rw-r--r--
ImageWin.py	7.49 KB	-rw-r--r--
ImageWin.pyc	9.69 KB	-rw-r--r--
ImtImagePlugin.py	2.17 KB	-rw-r--r--
ImtImagePlugin.pyc	1.56 KB	-rw-r--r--
IptcImagePlugin.py	6.8 KB	-rw-r--r--
IptcImagePlugin.pyc	5.76 KB	-rw-r--r--
Jpeg2KImagePlugin.py	7.57 KB	-rw-r--r--
Jpeg2KImagePlugin.pyc	6.49 KB	-rw-r--r--
JpegImagePlugin.py	24.43 KB	-rw-r--r--
JpegImagePlugin.pyc	19.47 KB	-rw-r--r--
JpegPresets.py	12.05 KB	-rw-r--r--
JpegPresets.pyc	6.3 KB	-rw-r--r--
McIdasImagePlugin.py	1.71 KB	-rw-r--r--
McIdasImagePlugin.pyc	1.66 KB	-rw-r--r--
MicImagePlugin.py	2.12 KB	-rw-r--r--
MicImagePlugin.pyc	2.08 KB	-rw-r--r--
MpegImagePlugin.py	1.77 KB	-rw-r--r--
MpegImagePlugin.pyc	2.47 KB	-rw-r--r--
MpoImagePlugin.py	2.73 KB	-rw-r--r--
MpoImagePlugin.pyc	2.48 KB	-rw-r--r--
MspImagePlugin.py	2.13 KB	-rw-r--r--
MspImagePlugin.pyc	2.38 KB	-rw-r--r--
OleFileIO-README.md	17.38 KB	-rw-r--r--
OleFileIO.py	87.39 KB	-rwxr-xr-x
OleFileIO.pyc	47.97 KB	-rw-r--r--
PSDraw.py	6.71 KB	-rw-r--r--
PSDraw.pyc	6.55 KB	-rw-r--r--
PaletteFile.py	1.08 KB	-rw-r--r--
PaletteFile.pyc	1.31 KB	-rw-r--r--
PalmImagePlugin.py	9.02 KB	-rw-r--r--
PalmImagePlugin.pyc	9.41 KB	-rw-r--r--
PcdImagePlugin.py	1.77 KB	-rw-r--r--
PcdImagePlugin.pyc	1.72 KB	-rw-r--r--
PcfFontFile.py	6.05 KB	-rw-r--r--
PcfFontFile.pyc	6.18 KB	-rw-r--r--
PcxImagePlugin.py	5.16 KB	-rw-r--r--
PcxImagePlugin.pyc	4.15 KB	-rw-r--r--
PdfImagePlugin.py	5.67 KB	-rw-r--r--
PdfImagePlugin.pyc	5.02 KB	-rw-r--r--
PixarImagePlugin.py	1.58 KB	-rw-r--r--
PixarImagePlugin.pyc	1.24 KB	-rw-r--r--
PngImagePlugin.py	22.14 KB	-rw-r--r--
PngImagePlugin.pyc	20.66 KB	-rw-r--r--
PpmImagePlugin.py	4.47 KB	-rw-r--r--
PpmImagePlugin.pyc	3.84 KB	-rw-r--r--
PsdImagePlugin.py	7.25 KB	-rw-r--r--
PsdImagePlugin.pyc	6.13 KB	-rw-r--r--
PyAccess.py	8.33 KB	-rw-r--r--
PyAccess.pyc	12.66 KB	-rw-r--r--
SgiImagePlugin.py	2.06 KB	-rw-r--r--
SgiImagePlugin.pyc	1.97 KB	-rw-r--r--
SpiderImagePlugin.py	8.99 KB	-rw-r--r--
SpiderImagePlugin.pyc	7.58 KB	-rw-r--r--
SunImagePlugin.py	1.9 KB	-rw-r--r--
SunImagePlugin.pyc	1.98 KB	-rw-r--r--
TarIO.py	1.19 KB	-rw-r--r--
TarIO.pyc	1.07 KB	-rw-r--r--
TgaImagePlugin.py	4.85 KB	-rw-r--r--
TgaImagePlugin.pyc	3.99 KB	-rw-r--r--
TiffImagePlugin.py	41.83 KB	-rw-r--r--
TiffImagePlugin.pyc	30.04 KB	-rw-r--r--
TiffTags.py	7.28 KB	-rw-r--r--
TiffTags.pyc	7.88 KB	-rw-r--r--
WalImageFile.py	5.41 KB	-rw-r--r--
WalImageFile.pyc	2.12 KB	-rw-r--r--
WebPImagePlugin.py	1.92 KB	-rw-r--r--
WebPImagePlugin.pyc	2.69 KB	-rw-r--r--
WmfImagePlugin.py	4.04 KB	-rw-r--r--
WmfImagePlugin.pyc	3.95 KB	-rw-r--r--
XVThumbImagePlugin.py	1.8 KB	-rw-r--r--
XVThumbImagePlugin.pyc	1.59 KB	-rw-r--r--
XbmImagePlugin.py	2.4 KB	-rw-r--r--
XbmImagePlugin.pyc	2.51 KB	-rw-r--r--
XpmImagePlugin.py	3.02 KB	-rw-r--r--
XpmImagePlugin.pyc	2.79 KB	-rw-r--r--
__init__.py	1.52 KB	-rw-r--r--
__init__.pyc	1.24 KB	-rw-r--r--
_binary.py	1.54 KB	-rw-r--r--
_binary.pyc	2.79 KB	-rw-r--r--
_imaging.x86_64-linux-gnu.so	308.97 KB	-rw-r--r--
_imagingcms.x86_64-linux-gnu.s...	16.02 KB	-rw-r--r--
_imagingft.x86_64-linux-gnu.so	20.64 KB	-rw-r--r--
_imagingmath.x86_64-linux-gnu....	18.17 KB	-rw-r--r--
_imagingmorph.x86_64-linux-gnu...	10.27 KB	-rw-r--r--
_util.py	553 B	-rw-r--r--
_util.pyc	1.58 KB	-rw-r--r--
_webp.x86_64-linux-gnu.so	10.35 KB	-rw-r--r--

Code Editor : 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:
# http://www.wadsworth.org/spider_doc/spider/docs/spider.html
#
# Details about the Spider image format:
# http://www.wadsworth.org/spider_doc/spider/docs/image_doc.html
#

from __future__ import print_function

from PIL import Image, ImageFile
import os
import struct
import sys

def isInt(f):
    try:
        i = int(f)
        if f-i == 0:
            return 1
        else:
            return 0
    except:
        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
    # print "labrec = %d, labbyt = %d, lenbyt = %d" % (labrec,labbyt,lenbyt)
    if labbyt != (labrec * lenbyt):
        return 0
    # looks like a valid header
    return labbyt

def isSpiderImage(filename):
    fp = open(filename, 'rb')
    f = fp.read(92)   # read 23 * 4 bytes
    fp.close()
    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"

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

# 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:
            return
        if frame >= self.nimages:
            raise EOFError("attempt to seek past end of file")
        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):
        (min, max) = self.getextrema()
        m = 1
        if max != min:
            m = depth / (max-min)
        b = -m * min
        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 Image.images for use in 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:
            im = Image.open(img).convert2byte()
        except:
            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 = 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 IOError("Error creating Spider header")

# write the SPIDER header
    try:
        fp = open(filename, 'wb')
    except:
        raise IOError("Unable to open %s for writing" % filename)
    fp.writelines(hdr)

rawmode = "F;32NF"  # 32-bit native floating point
    ImageFile._save(im, fp, [("raw", (0, 0)+im.size, 0, (rawmode, 0, 1))])

fp.close()

def _save_spider(im, fp, filename):
    # get the filename extension and register it with Image
    fn, ext = os.path.splitext(filename)
    Image.register_extension("SPIDER", ext)
    _save(im, fp, filename)

# --------------------------------------------------------------------

Image.register_open("SPIDER", SpiderImageFile)
Image.register_save("SPIDER", _save_spider)

if __name__ == "__main__":

if not sys.argv[1:]:
        print("Syntax: python SpiderImagePlugin.py Spiderimage [outfile]")
        sys.exit()

filename = sys.argv[1]
    if not isSpiderImage(filename):
        print("input image must be in Spider format")
        sys.exit()

outfile = ""
    if len(sys.argv[1:]) > 1:
        outfile = sys.argv[2]

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 outfile != "":
        # 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, "SPIDER")

${this.title}

Code Editor : SpiderImagePlugin.py