def _showVolumesSlices(self):
# Write an sqlite with all volumes selected for visualization.
sampling, setOfVolumes = self._createSetOfVolumes()
# setOfVolumes.setSamplingRate(sampling)
if len(setOfVolumes) == 1:
if self.protocol.outputVolume.getHalfMaps():
setOfVolumes = self.protocol._createSetOfVolumes(suffix='tmp')
vol = emobj.Volume()
vol.setFileName(self.protocol.outputVolume.getFileName())
vol.setSamplingRate(sampling)
setOfVolumes.append(vol)
for halfMap in self.protocol.outputVolume.getHalfMaps().split(
','):
volHalf = emobj.Volume()
volHalf.setSamplingRate(sampling)
if not halfMap.endswith(".mrc"):
volHalf.setFileName(halfMap.split(".")[0] + ".mrc")
else:
volHalf.setFileName(halfMap)
setOfVolumes.append(volHalf)
setOfVolumes.write()
return [self.objectView(setOfVolumes)]
else:
return [self.objectView(self.protocol.outputVolume)]
return [self.objectView(setOfVolumes)]
def assignStep(self):
# Create a Volume object
self.inVol = self.inVolume.get()
self.outVol = emobj.Volume()
self.outVol.copy(self.inVol)
# Set sampling Rate (or copy from input)
if self.setSampling.get():
samplingRate = self.samplingRate
else:
samplingRate = self.inVol.getSamplingRate()
self.outVol.setSamplingRate(samplingRate)
# set Origin
if self.setOrigCoord.get():
origin = emobj.Transform()
origin.setShifts(self.x, self.y, self.z)
else:
origin = self.inVol.getOrigin()
self.outVol.setOrigin(origin)
# copy or link
copyOrLink = self.getCopyOrLink()
fileName = self.inVol.getFileName()
fileName = fileName.replace(':mrc', '')
imgBase = basename(fileName)
imgDst = self._getExtraPath(imgBase)
copyOrLink(os.path.abspath(fileName), imgDst)
self.outVol.setLocation(imgDst)
# save
self._defineOutputs(outputVolume=self.outVol)
self._defineSourceRelation(self.inVol, self.outVol)
def assignStep(self):
# Create a Volume object
self.inVol = self.inVolume.get()
self.outVol = emobj.Volume()
self.outVol.copy(self.inVol)
# Set sampling Rate (or copy from input)
if self.setSampling.get():
samplingRate = self.samplingRate.get()
else:
samplingRate = self.inVol.getSamplingRate()
self.outVol.setSamplingRate(samplingRate)
# set Origin
if self.setOrigCoord.get():
origin = emobj.Transform()
origin.setShifts(self.x.get(), self.y.get(), self.z.get())
else:
origin = self.inVol.getOrigin()
self.outVol.setOrigin(origin)
# Files system stuff
fileName = os.path.abspath(self.inVol.getFileName())
fileName = fileName.replace(':mrc', '')
# copy or link
if self.copyFiles:
imgBase = pwutils.replaceBaseExt(fileName, "mrc")
imgDst = self._getExtraPath(imgBase)
Ccp4Header.fixFile(fileName,
imgDst,
origin.getShifts(),
sampling=samplingRate)
else:
imgBase = basename(fileName)
imgDst = self._getExtraPath(imgBase)
pwutils.createAbsLink(fileName, imgDst)
self.outVol.setLocation(imgDst)
# save
self._defineOutputs(outputVolume=self.outVol)
self._defineSourceRelation(self.inVol, self.outVol)
def testLocation(self):
fn = self.mic1
mic = emobj.Micrograph()
mic.setFileName(fn)
# Check that setFileName-getFileName is working properly
self.assertEqual(fn, mic.getFileName())
# Check the location is accepted from constructor
mic2 = emobj.Micrograph(fn)
self.assertEqual(fn, mic2.getFileName())
volStk = '/data/current/volumes/all_volumes.stk'
vol1 = emobj.Volume((1, volStk))
self.assertEqual(1, vol1.getIndex())
self.assertEqual(volStk, vol1.getFileName())
self.assertEqual('all_volumes.stk', vol1.getBaseName())
def createVolumesSqlite(self,
files,
path,
samplingRate,
updateItemCallback=None):
pwutils.cleanPath(path)
volSet = emobj.SetOfVolumes(filename=path)
volSet.setSamplingRate(samplingRate)
for volFn in files:
vol = emobj.Volume()
vol.setFileName(volFn)
if updateItemCallback:
updateItemCallback(vol)
volSet.append(vol)
volSet.write()
volSet.close()
return volSet
def show(self, form, *params):
protocol = form.protocol
filesPath = protocol.filesPath.get()
filesPattern = protocol.filesPattern.get()
if filesPattern:
fullPattern = os.path.join(filesPath, filesPattern)
else:
fullPattern = filesPath
sampling = protocol.samplingRate.get()
for fileName, fileId in protocol.iterFiles():
inputVol = emobj.Volume()
inputVol.setFileName(fileName)
if ((str(fullPattern)).endswith('mrc')
or (str(fullPattern)).endswith('map')):
ccp4header = emconv.Ccp4Header(fileName, readHeader=True)
x, y, z = ccp4header.getOrigin(changeSign=True) # In Angstroms
else:
x, y, z = self._halfOriginCoordinates(inputVol, sampling)
form.setVar('x', x)
form.setVar('y', y)
form.setVar('z', z)
def importVolumesStep(self, pattern, samplingRate, setOrigCoord=False):
""" Copy images matching the filename pattern
Register other parameters.
"""
volSet = self._createSetOfVolumes()
vol = emobj.Volume()
if self.importFrom == self.IMPORT_FROM_FILES:
self.info("Using pattern: '%s'" % pattern)
# Create a Volume template object
vol.setSamplingRate(samplingRate)
imgh = emlib.image.ImageHandler()
volSet.setSamplingRate(samplingRate)
for fileName, fileId in self.iterFiles():
x, y, z, n = imgh.getDimensions(fileName)
if fileName.endswith('.mrc') or fileName.endswith('.map'):
fileName += ':mrc'
if z == 1 and n != 1:
zDim = n
n = 1
else:
zDim = z
else:
zDim = z
origin = emobj.Transform()
if setOrigCoord:
origin.setShiftsTuple(self._getOrigCoord())
else:
origin.setShifts(x / -2. * samplingRate,
y / -2. * samplingRate,
zDim / -2. * samplingRate)
vol.setOrigin(origin) # read origin from form
if self.copyFiles or setOrigCoord:
newFileName = abspath(
self._getVolumeFileName(fileName, "mrc"))
emconv.Ccp4Header.fixFile(fileName, newFileName,
origin.getShifts(), samplingRate,
emconv.Ccp4Header.ORIGIN)
if self.setHalfMaps.get():
newFileName1 = abspath(
self._getVolumeFileName(self.half1map.get(),
"mrc"))
emconv.Ccp4Header.fixFile(self.half1map.get(),
newFileName1,
origin.getShifts(),
samplingRate,
emconv.Ccp4Header.ORIGIN)
newFileName2 = abspath(
self._getVolumeFileName(self.half2map.get(),
"mrc"))
emconv.Ccp4Header.fixFile(self.half2map.get(),
newFileName2,
origin.getShifts(),
samplingRate,
emconv.Ccp4Header.ORIGIN)
vol.setHalfMaps(
[relpath(newFileName1),
relpath(newFileName2)])
else:
newFileName = abspath(self._getVolumeFileName(fileName))
if fileName.endswith(':mrc'):
fileName = fileName[:-4]
pwutils.createAbsLink(fileName, newFileName)
if self.setHalfMaps.get():
pwutils.createAbsLink(
self.half1map.get(),
abspath(
self._getVolumeFileName(self.half1map.get())))
pwutils.createAbsLink(
self.half2map.get(),
abspath(
self._getVolumeFileName(self.half2map.get())))
vol.setHalfMaps([
relpath(
self._getVolumeFileName(self.half1map.get())),
relpath(
self._getVolumeFileName(self.half2map.get()))
])
# Make newFileName relative
# https://github.com/I2PC/scipion/issues/1935
newFileName = relpath(newFileName)
if n == 1:
vol.cleanObjId()
vol.setFileName(newFileName)
volSet.append(vol)
else:
for index in range(1, n + 1):
vol.cleanObjId()
vol.setLocation(index, newFileName)
volSet.append(vol)
else: # import from EMDB
self.info("Downloading map with ID = %s" % self.emdbId)
try:
localFileName, sampling, origin = \
fetch_emdb_map(self.emdbId,
self._getExtraPath(),
self._getTmpPath())
except Exception as e:
print(e)
return
# open volume and fill sampling and origin
vol.setSamplingRate(sampling)
vol.setFileName(localFileName)
from pwem.objects.data import Transform
originMat = Transform()
originMat.setShifts(origin[0], origin[1], origin[2])
vol.setOrigin(originMat)
if volSet.getSize() > 1:
self._defineOutputs(outputVolumes=volSet)
else:
self._defineOutputs(outputVolume=vol)
def assignStep(self):
# Create a Volume object
self.inVol = self.inVolume.get()
self.outVol = emobj.Volume()
self.outVol.copy(self.inVol)
# Set sampling Rate (or copy from input)
if self.setSampling.get():
samplingRate = self.samplingRate
else:
samplingRate = self.inVol.getSamplingRate()
self.outVol.setSamplingRate(samplingRate)
# set Origin
# get location of the subparticles (px)
# this is a string with 3 coor
inputProtocol = self.inputProtocol.get()
if inputProtocol.defineVector == CMM:
cmmFn = inputProtocol.vectorFile.get()
vector = " "
else:
cmmFn = ""
vector = inputProtocol.vector.get()
length = inputProtocol.length.get()
pxSize = inputProtocol.inputParticles.get().getSamplingRate()
subpartVectorList = load_vectors(cmmFn, vector, length, pxSize)
vector = subpartVectorList[0]
# coordinates with origin as defined in localrec
# convert from string to array
length = vector.get_length()
x = vector.vector[0] * length
y = vector.vector[1] * length
z = vector.vector[2] * length
# 0.0 107.3775 281.1066 pixel
# get subvolume
vol = self.inVolume.get()
shifts = vol.getOrigin(force=True).getShifts()
sampling = vol.getSamplingRate()
# 100 100 100
x += shifts[0] / sampling
y += shifts[1] / sampling
z += shifts[2] / sampling
self.origin = emobj.Transform()
samplingRate = samplingRate.get()
self.origin.setShifts(x * samplingRate, y * samplingRate,
z * samplingRate)
self.outVol.setOrigin(self.origin)
# copy or link
copyOrLink = self.getCopyOrLink()
fileName = self.inVol.getFileName()
fileName = fileName.replace(':mrc', '')
imgBase = basename(fileName)
imgDst = self._getExtraPath(imgBase)
copyOrLink(os.path.abspath(fileName), imgDst)
self.outVol.setLocation(imgDst)
# save
self._defineOutputs(outputVolume=self.outVol)
self._defineSourceRelation(self.inVol, self.outVol)
