def isImageFile(cls, imgFn):
""" Check if imgFn has an image extension. The function
is implemented in the Xmipp binding.
"""
# Local import to avoid import loop between ImageHandler and Ccp4Header.
from pwem.convert import headers
return (lib.FileName(imgFn).isImage()
or headers.getFileFormat(imgFn) == headers.MRC)
def getDimensions(self, locationObj):
""" It will return a tuple with the images dimensions.
The tuple will contains:
(x, y, z, n) where x, y, z are image dimensions (z=1 for 2D) and
n is the number of elements if stack.
"""
if self.existsLocation(locationObj):
location = self._convertToLocation(locationObj)
fn = location[1]
ext = pwutils.getExt(fn).lower()
# Local import to avoid import loop between ImageHandler and Ccp4Header.
from pwem.convert import headers
if ext == '.png' or ext == '.jpg':
im = Image.open(fn)
x, y = im.size # (width,height) tuple
return x, y, 1, 1
elif headers.getFileFormat(fn) == headers.MRC:
header = headers.Ccp4Header(fn, readHeader=True)
return header.getXYZN()
elif ext == '.img':
# FIXME Since now we can not read dm4 format in Scipion natively
# or recent .img format
# we are opening an Eman2 process to read the dm4 file
from pwem import Domain
getImageDimensions = Domain.importFromPlugin(
'eman2.convert', 'getImageDimensions', doRaise=True)
return getImageDimensions(fn) # we are ignoring index here
elif ext in ['.eer', '.gain']:
tif = TiffFile(fn)
frames = len(tif.pages) # number of pages in the file
page = tif.pages[
0] # get shape and dtype of the image in the first page
x, y = page.shape
return x, y, frames, 1
else:
self._img.read(location, lib.HEADER)
return self._img.getDimensions()
else:
return None, None, None, None
def _convertInputTi(self, ti, tiFn):
""" This function will convert the input tilt-image
taking into account the downFactor.
It can be overwritten in subclasses if another behaviour is required.
"""
downFactor = self.ctfDownFactor.get()
ih = emlib.image.ImageHandler()
if not ih.existsLocation(ti):
raise Exception("Missing input file: %s" % ti)
tiFName = ti.getFileName()
# Make xmipp considers the input object as TS to work as expected
if getFileFormat(tiFName) == MRC:
tiFName = tiFName.split(':')[0] + ':mrcs'
tiFName = str(ti.getIndex()) + '@' + tiFName
if downFactor != 1:
ih.scaleFourier(tiFName, tiFn, downFactor)
else:
ih.convert(tiFName, tiFn, emlib.DT_FLOAT)