def extractCoordinates(self, partsIds=None):
inPart = self.getInputParticles()
inMics = self.getInputMicrographs()
scale = inPart.getSamplingRate() / inMics.getSamplingRate()
print("Scaling coordinates by a factor *%0.2f*" % scale)
alignType = inPart.getAlignment()
suffix = self.getSuffix(partsIds[0]) if partsIds is not None else ''
outputCoords = self._createSetOfCoordinates(inMics, suffix=suffix)
# Prepare a double key dictionary to do the match: micname and micId
micDict = dict()
for mic in inMics.iterItems():
# Clone the mics! otherwise we will get pointers and
# will end up with the same mic in the dictionary.
clonedMic = mic.clone()
micDict[clonedMic.getObjId()] = clonedMic
micDict[clonedMic.getMicName()] = clonedMic
def appendCoordFromParticle(part):
coord = part.getCoordinate()
# Try micname
micName = coord.getMicName()
mic = micDict.get(micName, None)
# Try micid
if mic is None:
micKey = coord.getMicId()
mic = micDict.get(micKey, None)
if mic is None:
print("Skipping particle, %s or id %s not found" %
(micName, micKey))
else:
newCoord.copyObjId(part)
x, y = coord.getPosition()
if self.applyShifts:
shifts = self.getShifts(part.getTransform(), alignType)
xCoor, yCoor = x - int(shifts[0]), y - int(shifts[1])
newCoord.setPosition(xCoor * scale, yCoor * scale)
else:
newCoord.setPosition(x * scale, y * scale)
newCoord.setMicrograph(mic)
outputCoords.append(newCoord)
newCoord = emobj.Coordinate()
if self.streamingModeOn:
for partId in partsIds:
particle = inPart[partId]
appendCoordFromParticle(particle)
else:
for particle in inPart:
appendCoordFromParticle(particle)
boxSize = inPart.getXDim() * scale
outputCoords.setBoxSize(boxSize)
return outputCoords
def testWriteSetOfCoordinatesWithoutFlip(self):
from collections import OrderedDict
# Define a temporary sqlite file for micrographs
fn = self.getOutputPath('convert_mics.sqlite')
mics = emobj.SetOfMicrographs(filename=fn)
# Create SetOfCoordinates data
# Define a temporary sqlite file for coordinates
fn = self.getOutputPath('convert_coordinates.sqlite')
coordSet = emobj.SetOfCoordinates(filename=fn)
coordSet.setBoxSize(60)
coordSet.setMicrographs(mics)
data = OrderedDict()
data['006'] = [(30, 30)]
data['016'] = [(40, 40)]
micList = []
for key, coords in data.items():
mic = emobj.Micrograph(self.ds.getFile('micrographs/%s.mrc' % key))
mics.append(mic)
micList.append(mic)
print("Adding mic: %s, id: %s" % (key, mic.getObjId()))
for x, y in coords:
coord = emobj.Coordinate(x=x, y=y)
coord.setMicrograph(mic)
coordSet.append(coord)
# Get boxDirectory
boxFolder = self.getOutputPath('boxFolder')
os.mkdir(boxFolder)
micFolder = self.getOutputPath('micFolder')
pwutils.makePath(micFolder)
# Invoke the write set of coordinates method
convert.writeSetOfCoordinates(boxFolder, coordSet)
convert.convertMicrographs(micList, micFolder)
# Assert output of writesetofcoordinates
for mic in micList:
boxFile = os.path.join(boxFolder,
convert.getMicIdName(mic, '.box'))
self.assertTrue(os.path.exists(boxFile),
'Missing box file: %s' % boxFile)
micFile = os.path.join(micFolder,
convert.getMicIdName(mic, '.mrc'))
self.assertTrue(os.path.exists(micFile),
'Missing box file: %s' % micFile)
# Assert coordinates in box files
fh = open(os.path.join(boxFolder, 'mic00001.box'))
box1 = fh.readline()
fh.close()
box1 = box1.split('\t')
self.assertEquals(box1[0], '0')
self.assertEquals(box1[1], '964')
def _convert(coordsIn, yFlipHeight=None):
tmpFile = os.path.join(boxDir, 'tmp.cbox')
# Write input coordinates
writer = convert.CoordBoxWriter(boxSize, yFlipHeight=yFlipHeight)
writer.open(tmpFile)
for x, y, _ in coordsIn:
writer.writeCoord(emobj.Coordinate(x=x, y=y))
writer.close()
reader = convert.CoordBoxReader(boxSize, yFlipHeight=yFlipHeight)
reader.open(tmpFile)
coordsOut = [c for c in reader.iterCoords()]
reader.close()
return coordsOut
def readMicrographCoords(mic,
coordSet,
coordsFile,
boxSize,
yFlipHeight=None,
boxSizeEstimated=False):
reader = CoordBoxReader(boxSize,
yFlipHeight=yFlipHeight,
boxSizeEstimated=boxSizeEstimated)
reader.open(coordsFile)
coord = emobj.Coordinate()
for x, y, score in reader.iterCoords():
# Clean up objId to add as a new coordinate
coord.setObjId(None)
coord.setPosition(x, y)
coord.setMicrograph(mic)
coord._cryoloScore = emobj.Float(score)
# Add it to the set
coordSet.append(coord)
reader.close()
def rowToCoordinate(coordRow):
""" Create a Coordinate from a row of a meta """
# Check that all required labels are present in the row
if coordRow.containsAll(COOR_DICT):
coord = pwobj.Coordinate()
rowToObject(coordRow, coord, COOR_DICT, extraLabels=COOR_EXTRA_LABELS)
micName = None
if coordRow.hasLabel(md.RLN_MICROGRAPH_ID):
micId = int(coordRow.get(md.RLN_MICROGRAPH_ID))
coord.setMicId(micId)
# If RLN_MICROGRAPH_NAME is not present, use the id as a name
micName = micId
if coordRow.hasLabel(md.RLN_MICROGRAPH_NAME):
micName = coordRow.get(md.RLN_MICROGRAPH_NAME)
coord.setMicName(micName)
else:
coord = None
return coord
def extractCoordinates(self, partsIds=None):
inPart = self.getInputParticles()
inMics = self.getInputMicrographs()
scale = inPart.getSamplingRate() / inMics.getSamplingRate()
print("Scaling coordinates by a factor *%0.2f*" % scale)
alignType = inPart.getAlignment()
suffix = self.getSuffix(partsIds[0]) if partsIds is not None else ''
outputCoords = self._createSetOfCoordinates(inMics, suffix=suffix)
# Prepare a double key dictionary to do the match: micname and micId
micDict = dict()
for mic in inMics.iterItems():
# Clone the mics! otherwise we will get pointers and
# will end up with the same mic in the dictionary.
clonedMic = mic.clone()
micDict[clonedMic.getObjId()] = clonedMic
micDict[clonedMic.getMicName()] = clonedMic
def appendCoordFromParticle(part):
coord = part.getCoordinate()
# Try micname
micName = coord.getMicName()
mic = micDict.get(micName, None)
# Try micid
if mic is None:
micKey = coord.getMicId()
mic = micDict.get(micKey, None)
if mic is None:
print("Skipping particle, %s or id %s not found" %
(micName, micKey))
else:
newCoord.copyObjId(part)
x, y = coord.getPosition()
if self.applyShifts:
# Get the shifts, they are returned with the sign reverted
shifts = self.getShifts(part.getTransform(), alignType)
# Add the shifts (values are inverted so subtract)
x -= shifts[0]
y -= shifts[1]
# Apply the scale
x *= scale
y *= scale
# Round coordinates to closer integer 39.9 --> 40 and not 39
finalX = round(x)
finalY = round(y)
# Annotate fractions if shifts applied
if self.applyShifts:
newCoord.xFrac = Float(finalX - x)
newCoord.yFrac = Float(finalY - y)
newCoord.setPosition(finalX, finalY)
newCoord.setMicrograph(mic)
outputCoords.append(newCoord)
newCoord = emobj.Coordinate()
if self.streamingModeOn:
for partId in partsIds:
particle = inPart[partId]
appendCoordFromParticle(particle)
else:
for particle in inPart:
appendCoordFromParticle(particle)
boxSize = inPart.getXDim() * scale
outputCoords.setBoxSize(boxSize)
return outputCoords
def createCoorSetProtocol(self):
MICNUMBER = 2
MICSIZE = 1000
# create dummy protocol
dummyProt = self.newProtocol(EMProtocol)
dummyProt.setObjLabel('dummy protocol')
self.launchProtocol(dummyProt)
# create set of micrographs
# create two tif image
matrix = np.zeros((MICSIZE, MICSIZE), np.uint8)
R = np.linspace(0, MICSIZE // 2 - 2, 20)
# note we have 0 and 2*pi for each radius
THETA = np.linspace(0, 2 * np.pi, 30)
radii, thetas = np.meshgrid(R, THETA)
X = (R * np.cos(thetas)).astype(int) + MICSIZE // 2
Y = (R * np.sin(thetas)).astype(int) + MICSIZE // 2
# TODO: next double loop should be equivalen to
# the more elegant solution
# pairlist = np.vstack(list(map(np.ravel, (X,Y)))).T
# matrix[pairList] = 255 but it is not
for xx, yy in zip(X, Y):
for x, y in zip(xx, yy):
matrix[y][x] = 255
fn = dummyProt._getExtraPath('mic_000001.tif')
Image.fromarray(matrix).save(fn)
fn = dummyProt._getExtraPath('mic_000002.tif')
Image.fromarray(matrix).save(fn)
micSet = dummyProt._createSetOfMicrographs()
mic = emobj.Micrograph()
for i in range(MICNUMBER):
mic.setFileName\
(dummyProt._getExtraPath("mic_%06d.tif" % (i%2 + 1 )))
mic.setMicName("mic_%06d.tif" % (i % 2 + 1))
mic.setSamplingRate(1.)
micSet.append(mic)
mic.cleanObjId()
micSet.setSamplingRate(1.)
micSet.write()
coordSet = dummyProt._createSetOfCoordinates(micSet)
coordSet.setBoxSize(10)
coord = emobj.Coordinate()
for xx, yy in zip(X, Y):
for x, y in zip(xx, yy):
for mic in range(1, MICNUMBER + 1):
coord.setX(x)
coord.setY(y)
coord.setMicId(mic)
coord.setMicName("mic_%06d.tif" % (mic))
coordSet.append(coord)
coord.cleanObjId()
coordSet.write()
outputArgs = {OUTPUT_COORDINATES: coordSet, 'outputMic': micSet}
dummyProt._defineOutputs(**outputArgs)
dummyProt._store()
return dummyProt
def test_mapper(self):
""" test that indexes are created when a
setOfCoordinates is created """
PARTNUMBER = 10
MICNUMBER = 600
NUMBERCOORDINATES = PARTNUMBER * MICNUMBER
indexesNames = ['_micId']
prot = createDummyProtocol("dummy_protocol")
# create set of micrographs
micSet = emobj.SetOfMicrographs(filename=":memory:")
mic = emobj.Micrograph()
for i in range(NUMBERCOORDINATES):
mic.setLocation(i, "mic_%06d.mrc" % i)
micSet.append(mic)
mic.cleanObjId()
micSet.write()
# create a set of particles
coordSet = prot._createSetOfCoordinates(micSet)
coord = emobj.Coordinate()
for i in range(NUMBERCOORDINATES):
coordSet.append(coord)
coord.cleanObjId()
coordSet.write()
# check defined indexes
setOfCoordinatesFileName = \
prot._getPath("coordinates.sqlite")
print(os.path.abspath(setOfCoordinatesFileName))
indexes = sorted(
[index[1] for index in getIndex(setOfCoordinatesFileName)])
for index, indexName in zip(indexes, indexesNames):
self.assertEqual(index, 'index_' + indexName)
# Test speed: based on loop in file protocol_extractparticles.py
# for 600 mic and 100 part the values for the first
# second and third case where:
# Loop with index: 5 sec
# Loop no index: 8:01 min
# Loop optimized code: 4 sec
# for 6000 mic and 200 part the values for the first
# Loop with index: 1:47 min
# optimized Loop with index: 1:20 min
# Loop no index: after several hours I stopped the process
SPEEDTEST = True
if SPEEDTEST: # code from protocol_particles. line 415
testTimer = pwutils.Timer()
testTimer.tic()
for mic in micSet:
micId = mic.getObjId()
coordList = []
for coord in coordSet.iterItems(where='_micId=%s' % micId):
coordList.append(coord.clone())
testTimer.toc("Loop with INDEX took:")
lastMicId = None
testTimer.tic()
for coord in coordSet.iterItems(orderBy='_micId', direction='ASC'):
micId = coord.getMicId()
if micId != lastMicId:
lastMicId = micId
coordList = []
coordList.append(coord.clone())
testTimer.toc("Loop with INDEX and proper code, took:")
# delete INDEX, this will not work
# if database is not sqlite
conn = sqlite3.connect(setOfCoordinatesFileName)
cur = conn.cursor()
for index in indexesNames:
cur.execute("DROP INDEX index_%s" % index)
cur.close()
conn.close()
testTimer.tic()
for mic in micSet:
micId = mic.getObjId()
coordList = []
for coord in coordSet.iterItems(where='_micId=%s' % micId):
coordList.append(coord.clone())
testTimer.toc("Loop with NO INDEX took:")
lastMicId = None
testTimer.tic()
for coord in coordSet.iterItems(orderBy='_micId', direction='ASC'):
micId = coord.getMicId()
if micId != lastMicId:
lastMicId = micId
coordList = []
coordList.append(coord.clone())
testTimer.toc("Loop with NO INDEX but proper code, took:")
