Source code for pwem.emlib.image.image_handler

# **************************************************************************
# *
# * Authors:     J.M. de la Rosa Trevin ( [1]
# *
# * [1] SciLifeLab, Stockholm University
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 3 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307  USA
# *
# *  All comments concerning this program package may be sent to the
# *  e-mail address ''
# *
# **************************************************************************

import os

import numpy

import pyworkflow.utils as pwutils
import pwem.objects as emobj
import pwem.constants as emcts
from .. import lib
import logging
logger = logging.getLogger(__name__)

    from .image_readers import ImageReadersRegistry
except Exception as e:
    logger.warning("Are you missing mrcfile ? Are you in devel mode ?. "
                   "So, please run: scipion3 pip install mrcfile")

[docs]class ImageHandler(object): """ Class to provide several Image manipulation utilities. """ # TODO: remove dependency from Xmipp def __init__(self): # Now it will use Xmipp image library # to read and write most of formats, in the future # if we want to be independent of Xmipp, we should have # our own image library self._img = lib.Image() self._imgClass = lib.Image
[docs] @classmethod def fixXmippVolumeFileName(cls, image): """ This method will add :mrc to .mrc volumes because for mrc format is not possible to distinguish between 3D volumes and 2D stacks. """ # We can not import Volume from top level since # data depends on this module fn = image.getFileName() if isinstance(image, emobj.Volume): if fn.endswith('.mrc') or fn.endswith('.map'): fn += ':mrc' elif isinstance(image, emobj.Movie): if fn.endswith('.mrc'): fn += ':mrcs' elif fn.endswith('.em'): fn += ':ems' return fn
[docs] @classmethod def locationToXmipp(cls, location): """ Convert an index and filename location to a string with @ as expected in Xmipp. """ index, filename = cls._convertToLocation(location) if index != emcts.NO_INDEX: return "%06d@%s" % (index, filename) return filename
@classmethod def _convertToLocation(cls, location): """ Get a location in a tuple format (index, filename). location could be: tuple -> (index, filename) string -> (NO_INDEX, filename) image -> (image.getIndex(), image.getFileName()) """ if isinstance(location, tuple): outLocation = location elif isinstance(location, str): outLocation = (emcts.NO_INDEX, location) elif hasattr(location, 'getLocation'): # This case includes Image and its subclasses outLocation = (location.getIndex(), cls.fixXmippVolumeFileName(location)) else: raise Exception('Can not convert object %s to (index, location)' % type(location)) return outLocation
[docs] @classmethod def existsLocation(cls, locationObj): """ Return True if a given location exists. Location have the same meaning than in _convertToLocation. """ if locationObj is None: fn = None elif isinstance(locationObj, tuple): fn = locationObj[1] elif isinstance(locationObj, str): fn = locationObj elif hasattr(locationObj, 'getLocation'): # This case includes Image and its subclasses fn = locationObj.getLocation()[1] else: raise Exception('Can not match object %s to ' '(index, location)' % type(locationObj)) # If either the location is None or location if fn is None: return False # Remove filename format specification such as :mrc, :mrcs or :ems if ':' in fn: fn = fn.split(':')[0] return os.path.exists(fn)
[docs] @classmethod def getSupportedDataType(cls, inDataType, outputFilename): """ Returns the most similar data type supported by the output format""" outDataType = inDataType if outputFilename.endswith(".mrc") or outputFilename.endswith(".mrcs"): if inDataType == lib.DT_SCHAR: outDataType = lib.DT_USHORT return outDataType
[docs] def convert(self, inputObj, outputObj, dataType=None, transform=None): """ Convert from one image to another. inputObj and outputObj can be: tuple, string, or Image subclass (see self._convertToLocation) transform: if not None, apply this transformation """ inputLoc = self._convertToLocation(inputObj) outputLoc = self._convertToLocation(outputObj) if outputLoc[1].lower().endswith('.img'): # FIXME Since now we can not read dm4 format in Scipion natively # we are opening an Eman2 process to read the dm4 file from pwem import Domain convertImage = Domain.importFromPlugin('eman2.convert', 'convertImage', doRaise=True) convertImage(inputLoc, outputLoc) else: # Read from input if dataType is not None: self._img.convert2DataType(dataType) if transform is not None: self._img.applyTransforMatScipion(transform.getMatrixAsList()) # Write to output self._img.write(outputLoc)
[docs] def convertStack(self, inputFn, outputFn, firstImg=None, lastImg=None, inFormat=None, outFormat=None): """ Convert an input stack file into another. It is possible to only use a subset of frames to be written in the output stack. If outFormat/inFomat=None then there will be inferred from extension.If firstFrame/lastFrame are not None, the output stack will be a subset of input stack. If it are none, the conversion is over the whole stack. If the input format is ".dm4" or ".img" only is allowed the conversion of the whole stack. """ # inputLower = inputFn.lower() outputLower = outputFn.lower() if outputLower.endswith('.img'): if (firstImg and lastImg) is None: # FIXME Since now we can not read dm4 format in Scipion natively # or writing recent .img format # we are opening an Eman2 process to read the dm4 file from pwem import Domain convertImage = Domain.importFromPlugin('eman2.convert', 'convertImage') convertImage(inputFn, outputFn) else: ext = os.path.splitext(outputFn)[1] raise Exception("if convert from %s, firstImg and lastImg " "must be None" % ext) # elif inputLower.endswith('.tif'): # # FIXME: It seems that we have some flip problem with compressed # # tif files, we need to check that # if outputLower.endswith('.mrc'): # self.runJob('tif2mrc', '%s %s' % (inputFn, outputFn)) # else: # raise Exception("Conversion from tif to %s is not " # "implemented yet. " % pwutils.getExt(outputFn)) else: # get input dim (x, y, z, n) = lib.getImageSize(inputFn) location = self._convertToLocation(inputFn), lib.HEADER) dataType = self.getSupportedDataType(self._img.getDataType(), outputLower) if (firstImg and lastImg) is None: n = max(z, n) firstImg = 1 lastImg = n else: n = lastImg - firstImg + 1 # Create empty output stack file to reserve desired space lib.createEmptyFile(outputFn, x, y, 1, n, dataType) for i, j in zip(range(firstImg, lastImg + 1), range(1, n + 1)): self.convert((i, inputFn), (j, outputFn))
[docs] @classmethod def getDimensions(cls, 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 is a stack. """ if cls.existsLocation(locationObj): location = cls._convertToLocation(locationObj) fn = location[1] # Dimensions based on Readers. Registered and defined in the bottom reader = ImageReadersRegistry.getReader(fn) return reader.getDimensions(fn) # 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 = # 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: #, lib.HEADER) # return self._img.getDimensions() else: return None, None, None, None
[docs] def getDataType(self, locationObj): if self.existsLocation(locationObj): location = self._convertToLocation(locationObj), lib.HEADER) return self._img.getDataType() else: return None
[docs] def read(self, inputObj): """ Create a new Image class from inputObj (inputObj can be tuple, str or Image subclass). """ location = self._convertToLocation(inputObj) return self._imgClass(location)
[docs] def createImage(self): return self._imgClass()
[docs] def write(self, image, outputObj): """ Write to disk an image from outputObj (outputObj can be tuple, str or Image subclass). """ location = self._convertToLocation(outputObj) image.write(location)
[docs] def compareData(self, locationObj1, locationObj2, tolerance=0.0001): """ Compare if two locations have the same binary data. """ loc1 = self._convertToLocation(locationObj1) loc2 = self._convertToLocation(locationObj2) return lib.compareTwoImageTolerance(loc1, loc2, tolerance)
[docs] def computeAverage(self, inputSet): """ Compute the average image either from filename or set. If inputSet is a filename, we will read the whole stack and compute the average from all images. If inputSet is a SetOfImages subclass, we will iterate and compute the average from all images. """ if isinstance(inputSet, str): _, _, _, n = self.getDimensions(inputSet) if n: avgImage =, inputSet)) for i in range(2, n + 1):, inputSet)) avgImage.inplaceAdd(self._img) avgImage.inplaceDivide(n) return avgImage else: n = inputSet.getSize() if n: imageIter = iter(inputSet) img = next(imageIter) avgImage = for img in imageIter: avgImage.inplaceAdd(self._img) avgImage.inplaceDivide(n) return avgImage return None
[docs] def invertStack(self, inputFn, outputFn): # get input dim (x, y, z, n) = lib.getImageSize(inputFn) # Create empty output stack for efficiency lib.createEmptyFile(outputFn, x, y, z, n) # handle image formats for i in range(1, n + 1): self.invert((i, inputFn), (i, outputFn))
[docs] def invert(self, inputObj, outputObj): """ invert the pixels. inputObj and outputObj can be: tuple, string, or Image subclass (see self._convertToLocation) """ # Read from input self._img.inplaceMultiply(-1) # Write to output self._img.write(self._convertToLocation(outputObj))
@classmethod def __runXmippProgram(cls, program, args): """ Internal shortcut function to launch a Xmipp program. """ from pwem import Domain xmipp3 = Domain.importFromPlugin('xmipp3') xmipp3.Plugin.runXmippProgram(program, args) @classmethod def __runEman2Program(cls, program, args): """ Internal workaround to launch an EMAN2 program. """ from pwem import Domain eman2 = Domain.importFromPlugin('eman2', doRaise=True) from pyworkflow.utils.process import runJob runJob(None, eman2.Plugin.getProgram(program), args, env=eman2.Plugin.getEnviron())
[docs] def createCircularMask(self, radius, refImage, outputFile): """ Create a circular mask with the given radius (pixels) and with the same dimensions of the refImage. The radius should be less or equal dim(refImage)/2 The mask will be stored in 'outputFile' """ inputRef = self.locationToXmipp(refImage) self.__runXmippProgram('xmipp_transform_mask', '-i %s --create_mask %s --mask circular -%d' % (inputRef, outputFile, radius))
[docs] def rotateVolume(self, inputFile, outputFile, transformation): """ Apply geometric transformations to images. You can shift, rotate and scale a group of images/volumes. """ elementList = [str(item) for item in transformation.getRotationMatrix().flatten().tolist()] unrolledMatrix = ' '.join(elementList) self.__runXmippProgram('xmipp_transform_geometry', '-i %s -o %s --rotate_volume matrix %s' % (inputFile, outputFile, unrolledMatrix))
[docs] def addNoise(self, inputFile, outputFile, std=1., avg=0.): """ Add Gaussian noise to an input image (or stack) to produce noisy images. Params: inputFile: the filename of the input images outputFile: the filename of the output noisy images noiseStd: standard deviation for the Gaussian noise. """ self.__runXmippProgram('xmipp_transform_add_noise', '-i %s -o %s --type gaussian %f %f' % (inputFile, outputFile, std, avg))
[docs] def truncateMask(self, inputFile, outputFile, newDim=None): """ Forces the values of a mask to be between 0 and 1. Additionally, the output mask can be scaled to a new dimension. Params: inputFile: the filename of the input either image or volume outputFile: the filename of the output either image or volume newDim: scale the output Mask to a new dimension if not None """ if inputFile.endswith('.mrc'): inputFile += ':mrc' ioStr = '-i %s -o %s' % (inputFile, outputFile) if newDim: self.__runXmippProgram('xmipp_image_resize', '%s --dim %d' % (ioStr, newDim)) ioStr = '-i %s' % outputFile self.__runXmippProgram('xmipp_transform_threshold', '%s --select below 0 --substitute ' 'value 0' % ioStr) self.__runXmippProgram('xmipp_transform_threshold', '-i %s --select above 1 --substitute ' 'value 1' % outputFile)
[docs] @classmethod def createEmptyImage(cls, fnOut, xDim=1, yDim=1, zDim=1, nDim=1, dataType=None): dt = dataType or lib.DT_FLOAT lib.createEmptyFile(fnOut, xDim, yDim, zDim, nDim, dt)
[docs] @classmethod 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)
[docs] def computeThumbnail(self, inputFn, outputFn, scaleFactor=6, flipOnY=False, flipOnX=False): """ Compute a thumbnail of inputFn, save to ouptutFn. Optionally choose a scale factor eg scaleFactor=6 will make a thumbnail 6 times smaller. """ outputFn = outputFn or self.getThumbnailFn(inputFn) args = '"%s" "%s" ' % (inputFn, outputFn) process = "--process normalize" process += '' if not flipOnY else " --process=xform.flip:axis=y" process += '' if not flipOnX else " --process=xform.flip:axis=x" args += "--fouriershrink %s %s" % (scaleFactor, process) self.__runEman2Program('', args) return outputFn
[docs] @staticmethod def getThumbnailFn(inputFn): """Replace the extension in inputFn with thumb.png""" return pwutils.replaceExt(inputFn, "thumb.png")
[docs] @classmethod def getVolFileName(cls, location): if isinstance(location, tuple): fn = location[1] elif isinstance(location, str): fn = location elif hasattr(location, 'getLocation'): fn = location.getLocation()[1] else: raise Exception('Can not match object %s to (index, location)' % type(location)) if fn.endswith('.mrc') or fn.endswith('.map'): fn += ':mrc' return fn
[docs] @classmethod def removeFileType(cls, fileName): # Remove filename format specification such as :mrc, :mrcs or :ems if ':' in fileName: fileName = fileName.split(':')[0] return fileName
[docs] @classmethod def scaleFourier(cls, inputFn, outputFn, scaleFactor): """ Scale an image by cropping in Fourier space. """ # TODO: Avoid using xmipp program for this cls.__runXmippProgram("xmipp_transform_downsample", "-i %s -o %s --step %f --method fourier" % (inputFn, outputFn, scaleFactor))
[docs] @classmethod def scaleSplines(cls, inputFn, outputFn, scaleFactor, finalDimension=None, forceVolume=False): """ Scale an image using splines. """ I = lib.Image() x, y, z, n = I.getDimensions() setDimensions = 0 if forceVolume: z = max(z, n) setDimensions = 1 if finalDimension is not None: x, y, z = int(finalDimension), int(finalDimension), int(finalDimension) else: x, y, z = int(x * scaleFactor), int(y * scaleFactor), int(z * scaleFactor) I.scale(x, y, z, setDimensions) I.write(outputFn)
[docs] @classmethod def scale2DStack(cls, inputFn, outputFn, scaleFactor=None, finalDimension=None): """ Scale a 2D images stack using PIL. """ from PIL import Image if scaleFactor is None and finalDimension is None: raise TypeError("scaleFactor or finalDimension must be passed") I = lib.Image() x, y, z, n = I.getDimensions() if not finalDimension: finalDimension = round(x*scaleFactor) objects = I.getData() newStack = numpy.zeros((n, 1, finalDimension, finalDimension)) count = 0 for object in objects: slice = object[0] image = Image.fromarray(slice) resizedImage = image.resize((finalDimension, finalDimension)) newStack[count] = numpy.array(resizedImage) count += 1 I.setData(newStack) I.write(outputFn)
[docs] @staticmethod def applyTransform(inputFile, outputFile, transformMatrix, shape, fillValue=None, doWrap=False): """Apply the transformation matrix over the input image and return the transformed image in a given shape. Parameters: :param inputFile: path location of the input image :param outputFile: path location of the output image :param transformMatrix: transformation matrix to be applied to the image. It should be a numpy array data type. :param shape: dimensions of the output image given as a tuple (yDim, xDim) :param fillValue: value with which the empty regions due to wrapping will be filled. :param doWrap: if True the empty regions will be filled with the wrapped values of the input image. """ imageObj = lib.Image() if fillValue is None: mean, _, _, _ = imageObj.computeStats() resultImage = imageObj.applyWarpAffine(list(transformMatrix.flatten()), shape, doWrap, mean) else: resultImage = imageObj.applyWarpAffine(list(transformMatrix.flatten()), shape, doWrap, fillValue) resultImage.write(outputFile)