class ImageGenerator:
def __init__(self, project_path, images_path,
bigThumb=None, smallThumb=None):
self.project_path = project_path
self.images_path = images_path
self.ih = ImageHandler()
self.img = self.ih.createImage()
self.bigThumb = bigThumb
self.smallThumb = smallThumb
def generate_image(self, input_file, outputName=None):
output_root = join(self.images_path, basename(outputName))
output_file = output_root + '.jpg'
print "Generating image: ", output_file
if not exists(output_file):
from PIL import Image
self.img.read(join(self.project_path, input_file))
pimg = getPILImage(self.img)
pwutils.makeFilePath(output_file)
if self.bigThumb:
pimg.save(output_file, "JPEG")
if self.smallThumb:
pimg.thumbnail((self.smallThumb, self.smallThumb), Image.ANTIALIAS)
pimg.save(output_root + 't.jpg', "JPEG")
return output_file
class ImageGenerator:
def __init__(self, project_path, images_path,
bigThumb=None, smallThumb=None):
self.project_path = project_path
self.images_path = images_path
self.ih = ImageHandler()
self.img = self.ih.createImage()
self.bigThumb = bigThumb
self.smallThumb = smallThumb
def generate_image(self, input_file, outputName=None):
output_root = join(self.images_path, basename(outputName))
output_file = output_root + '.png'
print "Generating image: ", output_file
if not exists(output_file):
from PIL import Image
self.img.read(join(self.project_path, input_file))
pimg = getPILImage(self.img)
pwutils.makeFilePath(output_file)
if self.bigThumb:
pimg.save(output_file, "PNG")
if self.smallThumb:
pimg.thumbnail((self.smallThumb, self.smallThumb), Image.ANTIALIAS)
pimg.save(output_root + 't.png', "PNG")
return output_file
def _compareMovies(self, micSet1, micSet2):
print "Comparing micrographs (binary images) from results. "
ih = ImageHandler()
img1 = ih.createImage()
img2 = ih.createImage()
for mic1, mic2 in izip(micSet1, micSet2):
img1.read(mic1.getFileName())
img2.read(mic2.getFileName())
print("Comparing %s vs %s" %
(mic1.getFileName(), mic2.getFileName()))
self.assertTrue(img1.equal(img2, 20))
def createOutputStep(self, particlesId, coordsId, boxSize):
""" Create the input file in STAR format as expected by Relion.
Params:
particlesId: use this parameters just to force redo of convert if
the input particles are changed.
"""
ih = ImageHandler()
outputStack = self._getPath('particles.mrcs')
outputImg = ih.createImage()
inputParticles = self._getInputParticles()
inputCoords = self.inputCoordinates.get()
outputSet = self._createSetOfParticles()
outputSet.copyInfo(inputParticles)
boxSize = self.boxSize.get()
b2 = int(round(boxSize / 2))
center = np.zeros((boxSize, boxSize))
ih = ImageHandler()
i = 0
outliers = 0
partIdExcluded = []
lastPartId = None
for coord in inputCoords.iterItems(
orderBy=['_subparticle._micId', '_micId', 'id']):
# The original particle id is stored in the sub-particle as micId
partId = coord._micId.get()
# Load the particle if it has changed from the last sub-particle
if partId != lastPartId:
particle = inputParticles[partId]
if particle is None:
partIdExcluded.append(partId)
self.info("WARNING: Missing particle with id %s from "
"input particles set" % partId)
else:
# Now load the particle image to extract later sub-particles
img = ih.read(particle)
x, y, _, _ = img.getDimensions()
data = img.getData()
lastPartId = partId
# If particle is not in inputParticles, subparticles will not be
# generated. Now, subtract from a subset of original particles is
# supported.
if not partId in partIdExcluded:
xpos = coord.getX()
ypos = coord.getY()
# Check that the sub-particle will not lay out of the particle
if (ypos - b2 < 0 or ypos + b2 > y or xpos - b2 < 0
or xpos + b2 > x):
outliers += 1
continue
# Crop the sub-particle data from the whole particle image
center[:, :] = data[ypos - b2:ypos + b2, xpos - b2:xpos + b2]
outputImg.setData(center)
i += 1
outputImg.write((i, outputStack))
subpart = coord._subparticle
subpart.setLocation(
(i, outputStack)) # Change path to new stack
subpart.setObjId(None) # Force to insert as a new item
outputSet.append(subpart)
if outliers:
self.info(
"WARNING: Discarded %s particles because laid out of the "
"particle (for a box size of %d" % (outliers, boxSize))
self._defineOutputs(outputParticles=outputSet)
self._defineSourceRelation(self.inputParticles, outputSet)
def createOutputStep(self, particlesId, coordsId, boxSize):
""" Create the input file in STAR format as expected by Relion.
Params:
particlesId: use this parameters just to force redo of convert if
the input particles are changed.
"""
ih = ImageHandler()
outputStack = self._getPath('particles.mrcs')
outputImg = ih.createImage()
inputParticles = self._getInputParticles()
inputCoords = self.inputCoordinates.get()
outputSet = self._createSetOfParticles()
outputSet.copyInfo(inputParticles)
boxSize = self.boxSize.get()
b2 = int(round(boxSize / 2))
center = np.zeros((boxSize, boxSize))
ih = ImageHandler()
i = 0
outliers = 0
partIdExcluded = []
lastPartId = None
for coord in inputCoords.iterItems(orderBy=['_subparticle._micId',
'_micId', 'id']):
# The original particle id is stored in the sub-particle as micId
partId = coord._micId.get()
# Load the particle if it has changed from the last sub-particle
if partId != lastPartId:
particle = inputParticles[partId]
if particle is None:
partIdExcluded.append(partId)
self.info("WARNING: Missing particle with id %s from "
"input particles set" % partId)
else:
# Now load the particle image to extract later sub-particles
img = ih.read(particle)
x, y, _, _ = img.getDimensions()
data = img.getData()
lastPartId = partId
# If particle is not in inputParticles, subparticles will not be
# generated. Now, subtract from a subset of original particles is
# supported.
if not partId in partIdExcluded:
xpos = coord.getX()
ypos = coord.getY()
# Check that the sub-particle will not lay out of the particle
if (ypos - b2 < 0 or ypos + b2 > y or
xpos - b2 < 0 or xpos + b2 > x):
outliers += 1
continue
# Crop the sub-particle data from the whole particle image
center[:, :] = data[ypos-b2:ypos+b2, xpos-b2:xpos+b2]
outputImg.setData(center)
i += 1
outputImg.write((i, outputStack))
subpart = coord._subparticle
subpart.setLocation((i, outputStack)) # Change path to new stack
subpart.setObjId(None) # Force to insert as a new item
outputSet.append(subpart)
if outliers:
self.info("WARNING: Discarded %s particles because laid out of the "
"particle (for a box size of %d" % (outliers, boxSize))
self._defineOutputs(outputParticles=outputSet)
self._defineSourceRelation(self.inputParticles, outputSet)
