def mrc2stack(mrc,
out_dir,
indxs=None,
basename="%04d.png",
imfilter=lambda im: im):
"""
Converts an MRC file to an image stack
Arguments:
mrc -- the MRC file (as MRC object) or filepath (as a string)
out_dir -- the directory to save the stack to
Optional Arguments:
indxs -- the indices of slices to save, default is to use all slices
basename -- the template name to use for images, needs to have a %d to be replaced by slice number, default is "%04d.png"
imfilter -- a function/callable that takes and returns an image
"""
from os.path import join
from mrc import MRC
from images import imsave
from utils import make_dir
if isinstance(mrc, basestring): mrc = MRC(mrc)
if not make_dir(out_dir):
raise IOError("Unable to create output directory")
if indxs == None:
for i, sec in enumerate(mrc):
imsave(join(out_dir, basename % i), imfilter(sec))
else:
for i in indxs:
imsave(join(out_dir, basename % i), imfilter(mrc[i]))
def stack2mrc(stack, mrc, imfilter=lambda im: im):
"""
Converts an image stack to an MRC file. Returns the new MRC file object.
Arguments:
stack -- the images to read, an iterable of file names
mrc -- the MRC filename to save to
Optional Arguments:
imfilter -- a function/callable that takes and returns an image
"""
from mrc import MRC
from images import imread
stack = iter(stack)
try:
img = imfilter(imread(stack.next()))
except StopIteration:
raise ValueError("Must provide at least one image")
mrc = MRC(mrc, nx=img.shape[1], ny=img.shape[0], dtype=img.dtype)
mrc.append(img)
mrc.append_all(imfilter(imread(img))
for img in stack) # will skip the first one
mrc.write_header()
return mrc
y = y.split("-")
if len(y) != 2 or not y[0].isdigit() or not y[1].isdigit():
help_msg(2, "Invalid y argument supplied")
y = (int(y[0]), int(y[1]))
else:
imfilters += [imfilter_util.parse_opt(o, a, help_msg)]
# Make sure paths are good
if len(args) != 2:
help_msg(
2,
"You need to provide an MRC and image output directory as arguments"
)
mrc_filename = realpath(args[0])
try:
mrc = MRC(mrc_filename, readonly=True)
except BaseException as e:
help_msg(2, "Failed to open MRC file: " + str(e))
out_dir = realpath(args[1])
if not make_dir(out_dir):
help_msg(
2,
"Output directory already exists as regular file, choose another directory"
)
# Check other arguments, getting values for optional args, etc.
ext = "png" if ext == None else ext.lstrip('.')
if basename == None: basename = "%04d"
if x == None: x = (0, mrc.nx - 1)
elif x[0] < 0 or x[1] < x[0] or x[1] >= mrc.nx:
help_msg(2, "Invalid x argument supplied")
