def create_movie_params(self, prot, updateIds):
for movie in self.iter_updated_set(prot.outputMovies):
movieId = movie.getObjId()
if movieId in self.movies: # this movie has been processed, skip
continue
movieFn = movie.getFileName()
if self.numberOfFrames is None:
self.numberOfFrames = movie.getNumberOfFrames()
images_path = self.find_ispyb_path(movieFn)
self.imageGenerator = ImageGenerator(self.project.path,
images_path,
bigThumb=True,
smallThumb=512)
acquisition = movie.getAcquisition()
self.movies[movieId] = {
'experimenttype': 'single particle',
'run_status': 'DataCollection Successful',
'imgdir': abspath(dirname(movieFn)),
'imgsuffix': pwutils.getExt(movieFn),
'file_template': pwutils.removeBaseExt(movieFn) + '#####' + pwutils.getExt(movieFn),
'file_location': abspath(dirname(movieFn)),
'filename': movieFn,
'n_passes': self.numberOfFrames,
'magnification': acquisition.getMagnification(),
'total_absorbed_dose': acquisition.getDoseInitial() + (acquisition.getDosePerFrame() * self.numberOfFrames),
'wavelength': self.convert_volts_to_debroglie_wavelength(acquisition.getVoltage())
}
self.dataCollection.update(self.movies[movieId])
self.update_from_metadata(Path(movieFn), self.movies[movieId])
updateIds.append(movieId)
def _doShowDeformedOrigRef(self, param=None):
scriptFile = self.protocol._getPath('morph_deformed_ref_chimera.cxc')
fhCmd = open(scriptFile, 'w')
fnbase = removeExt(self.protocol._getFileName('fnOutVol'))
ext = getExt(self.protocol._getFileName('fnOutVol'))
fninput = abspath(fnbase + ext[0:4])
smprt = self.protocol.outputVolume.getSamplingRate()
fnbase2 = removeExt(self.protocol._getFileName('fnRefVol'))
ext2 = getExt(self.protocol._getFileName('fnRefVol'))
fnref = abspath(fnbase2 + ext2[0:4])
fhCmd.write(self.OPEN_FILE % fninput)
fhCmd.write(self.OPEN_FILE % fnref)
counter = 1
fhCmd.write(self.VOXEL_SIZE % (counter, str(smprt)))
fhCmd.write(self.VOL_HIDE % counter)
counter += 1
fhCmd.write(self.VOXEL_SIZE % (counter, str(smprt)))
# fhCmd.write("focus\n")
fhCmd.write(self.VOL_HIDE % counter)
fhCmd.write("volume morph #%d,%d frames 500\n" %
(counter - 1, counter))
fhCmd.write(self.VIEW)
fhCmd.close()
view = ChimeraView(scriptFile)
return [view]
def convertInputStep(self):
""" Read the input volume.
"""
self.vol1Fn = self.half1.get().getFileName()
self.vol2Fn = self.half2.get().getFileName()
extVol1 = getExt(self.vol1Fn)
extVol2 = getExt(self.vol2Fn)
if (extVol1 == '.mrc') or (extVol1 == '.map'):
self.vol1Fn = self.vol1Fn + ':mrc'
if (extVol2 == '.mrc') or (extVol2 == '.map'):
self.vol2Fn = self.vol2Fn + ':mrc'
if self.useMask.get():
if (not self.Mask.hasValue()):
self.ifNomask(self.vol1Fn)
else:
self.maskFn = self.Mask.get().getFileName()
extMask = getExt(self.maskFn)
if (extMask == '.mrc') or (extMask == '.map'):
self.maskFn = self.maskFn + ':mrc'
if self.Mask.hasValue():
params = ' -i %s' % self.maskFn
params += ' -o %s' % self._getFileName(BINARY_MASK)
params += ' --select below %f' % 0.5 # Mask threshold = 0.5 self.maskthreshold.get()
params += ' --substitute binarize'
self.runJob('xmipp_transform_threshold', params)
def createChimeraScript(self):
fnRoot = "extra/"
scriptFile = self.protocol._getPath('Chimera_resolution.cmd')
fhCmd = open(scriptFile, 'w')
imageFile = self.protocol._getExtraPath(OUTPUT_RESOLUTION_FILE_CHIMERA)
img = ImageHandler().read(imageFile)
imgData = img.getData()
min_Res = round(np.amin(imgData) * 100) / 100
max_Res = round(np.amax(imgData) * 100) / 100
numberOfColors = 21
colors_labels = self.numberOfColors(min_Res, max_Res, numberOfColors)
colorList = self.colorMapToColorList(colors_labels, self.getColorMap())
if self.protocol.halfVolumes.get() is True:
#fhCmd.write("open %s\n" % (fnRoot+FN_MEAN_VOL)) #Perhaps to check the use of mean volume is useful
fnbase = removeExt(self.protocol.inputVolume.get().getFileName())
ext = getExt(self.protocol.inputVolume.get().getFileName())
fninput = abspath(fnbase + ext[0:4])
fhCmd.write("open %s\n" % fninput)
else:
fnbase = removeExt(self.protocol.inputVolumes.get().getFileName())
ext = getExt(self.protocol.inputVolumes.get().getFileName())
fninput = abspath(fnbase + ext[0:4])
fhCmd.write("open %s\n" % fninput)
fhCmd.write("open %s\n" % (fnRoot + OUTPUT_RESOLUTION_FILE_CHIMERA))
if self.protocol.halfVolumes.get() is True:
smprt = self.protocol.inputVolume.get().getSamplingRate()
else:
smprt = self.protocol.inputVolumes.get().getSamplingRate()
fhCmd.write("volume #0 voxelSize %s\n" % (str(smprt)))
fhCmd.write("volume #1 voxelSize %s\n" % (str(smprt)))
fhCmd.write("vol #1 hide\n")
scolorStr = '%s,%s:' * numberOfColors
scolorStr = scolorStr[:-1]
line = ("scolor #0 volume #1 perPixel false cmap " + scolorStr +
"\n") % colorList
fhCmd.write(line)
scolorStr = '%s %s ' * numberOfColors
str_colors = ()
for idx, elem in enumerate(colorList):
if (idx % 2 == 0):
if ((idx % 8) == 0):
str_colors += str(elem),
else:
str_colors += '" "',
else:
str_colors += elem,
line = ("colorkey 0.01,0.05 0.02,0.95 " + scolorStr +
"\n") % str_colors
fhCmd.write(line)
fhCmd.close()
def createChimeraScript(self):
fnRoot = "extra/"
scriptFile = self.protocol._getPath('Chimera_resolution.cmd')
fhCmd = open(scriptFile, 'w')
imageFile = self.protocol._getExtraPath(OUTPUT_RESOLUTION_FILE_CHIMERA)
img = ImageHandler().read(imageFile)
imgData = img.getData()
min_Res = round(np.amin(imgData)*100)/100
max_Res = round(np.amax(imgData)*100)/100
numberOfColors = 21
colors_labels = self.numberOfColors(min_Res, max_Res, numberOfColors)
colorList = self.colorMapToColorList(colors_labels, self.getColorMap())
if self.protocol.halfVolumes.get() is True:
#fhCmd.write("open %s\n" % (fnRoot+FN_MEAN_VOL)) #Perhaps to check the use of mean volume is useful
fnbase = removeExt(self.protocol.inputVolume.get().getFileName())
ext = getExt(self.protocol.inputVolume.get().getFileName())
fninput = abspath(fnbase + ext[0:4])
fhCmd.write("open %s\n" % fninput)
else:
fnbase = removeExt(self.protocol.inputVolumes.get().getFileName())
ext = getExt(self.protocol.inputVolumes.get().getFileName())
fninput = abspath(fnbase + ext[0:4])
fhCmd.write("open %s\n" % fninput)
fhCmd.write("open %s\n" % (fnRoot + OUTPUT_RESOLUTION_FILE_CHIMERA))
if self.protocol.halfVolumes.get() is True:
smprt = self.protocol.inputVolume.get().getSamplingRate()
else:
smprt = self.protocol.inputVolumes.get().getSamplingRate()
fhCmd.write("volume #0 voxelSize %s\n" % (str(smprt)))
fhCmd.write("volume #1 voxelSize %s\n" % (str(smprt)))
fhCmd.write("vol #1 hide\n")
scolorStr = '%s,%s:' * numberOfColors
scolorStr = scolorStr[:-1]
line = ("scolor #0 volume #1 perPixel false cmap " + scolorStr + "\n") % colorList
fhCmd.write(line)
scolorStr = '%s %s ' * numberOfColors
str_colors = ()
for idx, elem in enumerate(colorList):
if (idx % 2 == 0):
if ((idx % 8) == 0):
str_colors += str(elem),
else:
str_colors += '" "',
else:
str_colors += elem,
line = ("colorkey 0.01,0.05 0.02,0.95 " + scolorStr + "\n") % str_colors
fhCmd.write(line)
fhCmd.close()
def convertInputStep(self):
""" Read the input volume.
"""
self.volFn = self.inputVolume.get().getFileName()
self.resFn = self.resolutionVolume.get().getFileName()
extVol = getExt(self.volFn)
extRes = getExt(self.resFn)
if (extVol == '.mrc') or (extVol == '.map'):
self.volFn = self.volFn + ':mrc'
if (extRes == '.mrc') or (extRes == '.map'):
self.resFn = self.resFn + ':mrc'
def convertInputStep(self):
""" Read the input volume.
"""
self.volFn = self.inputVolume.get().getFileName()
self.resFn = self.resolutionVolume.get().getFileName()
extVol = getExt(self.volFn)
extRes = getExt(self.resFn)
if (extVol == '.mrc') or (extVol == '.map'):
self.volFn = self.volFn + ':mrc'
if (extRes == '.mrc') or (extRes == '.map'):
self.resFn = self.resFn + ':mrc'
def convertInputStep(self):
""" Read the input volume.
"""
self.micsFn = self._getPath()
if self.halfVolumes:
self.vol1Fn = self.inputVolume.get().getFileName()
self.vol2Fn = self.inputVolume2.get().getFileName()
extVol1 = getExt(self.vol1Fn)
extVol2 = getExt(self.vol2Fn)
if (extVol1 == '.mrc') or (extVol1 == '.map'):
self.vol1Fn = self.vol1Fn + ':mrc'
if (extVol2 == '.mrc') or (extVol2 == '.map'):
self.vol2Fn = self.vol2Fn + ':mrc'
if not self.Mask.hasValue():
self.ifNomask(self.vol1Fn)
else:
self.maskFn = self.Mask.get().getFileName()
self.inputVolumes.set(None)
else:
self.vol0Fn = self.inputVolumes.get().getFileName()
extVol0 = getExt(self.vol0Fn)
if (extVol0 == '.mrc') or (extVol0 == '.map'):
self.vol0Fn = self.vol0Fn + ':mrc'
if not self.Mask.hasValue():
self.ifNomask(self.vol0Fn)
else:
self.maskFn = self.Mask.get().getFileName()
print self.maskFn
self.inputVolume.set(None)
self.inputVolume2.set(None)
extMask = getExt(self.maskFn)
if (extMask == '.mrc') or (extMask == '.map'):
self.maskFn = self.maskFn + ':mrc'
if self.Mask.hasValue():
params = ' -i %s' % self.maskFn
params += ' -o %s' % self._getFileName(BINARY_MASK)
params += ' --select below %f' % self.maskthreshold.get()
params += ' --substitute binarize'
self.runJob('xmipp_transform_threshold', params)
def convertInputStep(self):
""" Read the input volume.
"""
self.micsFn = self._getPath()
if self.halfVolumes:
self.vol1Fn = self.inputVolume.get().getFileName()
self.vol2Fn = self.inputVolume2.get().getFileName()
extVol1 = getExt(self.vol1Fn)
extVol2 = getExt(self.vol2Fn)
if (extVol1 == '.mrc') or (extVol1 == '.map'):
self.vol1Fn = self.vol1Fn + ':mrc'
if (extVol2 == '.mrc') or (extVol2 == '.map'):
self.vol2Fn = self.vol2Fn + ':mrc'
if not self.Mask.hasValue():
self.ifNomask(self.vol1Fn)
else:
self.maskFn = self.Mask.get().getFileName()
self.inputVolumes.set(None)
else:
self.vol0Fn = self.inputVolumes.get().getFileName()
extVol0 = getExt(self.vol0Fn)
if (extVol0 == '.mrc') or (extVol0 == '.map'):
self.vol0Fn = self.vol0Fn + ':mrc'
if not self.Mask.hasValue():
self.ifNomask(self.vol0Fn)
else:
self.maskFn = self.Mask.get().getFileName()
print self.maskFn
self.inputVolume.set(None)
self.inputVolume2.set(None)
extMask = getExt(self.maskFn)
if (extMask == '.mrc') or (extMask == '.map'):
self.maskFn = self.maskFn + ':mrc'
if self.Mask.hasValue():
params = ' -i %s' % self.maskFn
params += ' -o %s' % self._getFileName(BINARY_MASK)
params += ' --select below %f' % self.maskthreshold.get()
params += ' --substitute binarize'
self.runJob('xmipp_transform_threshold', params)
def convertInputStep(self):
""" Read the input volume.
"""
self.micsFn = self._getPath()
self.volFn = self.inputVolume.get().getFileName()
self.maskFn = self.Mask.get().getFileName()
extVol = getExt(self.volFn)
if (extVol == '.mrc') or (extVol == '.map'):
self.volFn = self.volFn + ':mrc'
extMask = getExt(self.maskFn)
if (extMask == '.mrc') or (extMask == '.map'):
self.maskFn = self.maskFn + ':mrc'
def getEmpiarFormat(self, imagePath):
ext = pwutils.getExt(imagePath).lower().strip('.')
imgFormat = self._imageSetFormats.get(ext, None)
if imgFormat is None:
raise EmpiarMappingError('Image format not recognized: %s' % ext)
else:
return imgFormat, ''
def _pickMicrograph(self, mic, args):
# Prepare mic folder and convert if needed
micName = mic.getFileName()
micDir = self._getTmpPath(pwutils.removeBaseExt(micName))
pwutils.makePath(micDir)
ih = ImageHandler()
# If needed convert micrograph to mrc format, otherwise link it
if pwutils.getExt(micName) != ".mrc":
fnMicBase = pwutils.replaceBaseExt(micName, 'mrc')
inputMic = os.path.join(micDir, fnMicBase)
ih.convert(mic.getLocation(), inputMic)
else:
inputMic = os.path.join(micDir, os.path.basename(micName))
pwutils.createLink(micName, inputMic)
# Prepare environment
from appion import Plugin
Plugin.getEnviron()
# Program to execute and it arguments
program = "python2"
outputFile = self._getExtraPath(pwutils.replaceBaseExt(
inputMic, "txt"))
args += " --image=%s --outfile=%s" % (inputMic, outputFile)
dogpicker = Plugin.getHome("ApDogPicker.py")
args = dogpicker + " " + args
self.runJob(program, args)
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()
if ext == '.png' or ext == '.jpg':
im = PIL.Image.open(fn)
x, y = im.size # (width,height) tuple
return x, y, 1, 1
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 .img files
from pyworkflow.em.packages.eman2.convert import getImageDimensions
return getImageDimensions(fn) # we are ignoring index here
else:
self._img.read(location, xmipp.HEADER)
return self._img.getDimensions()
else:
return None, None, None, None
def getFinalGainPath(self, tifFlipped=False):
fnBest = self.getOrientedGainPath()
if os.path.exists(fnBest):
# If the best orientatin has been calculated, take it
finalGainFn = fnBest
elif self.getInputGain() != None:
# Elif, take the input gain provided
finalGainFn = self.getInputGain()
else:
# Elif, take the estimated gain
finalGainFn = self.searchEstimatedGainPath()
if finalGainFn == None:
# If no gains have been estimated, estimate one and use that
firstMovie = self.inputMovies.get().getFirstItem()
movieId = firstMovie.getObjId()
if not movieId in self.estimatedIds:
self.estimatedIds.append(movieId)
self.estimateGainFun(firstMovie)
finalGainFn = self.getEstimatedGainPath(movieId)
ext = pwutils.getExt(
self.inputMovies.get().getFirstItem().getFileName()).lower()
if ext in ['.tif', '.tiff'] and tifFlipped:
finalGainFn = xmutils.flipYImage(finalGainFn,
outDir=self._getExtraPath())
return finalGainFn
def convertStep(self, volFn, volDim, volSr, minDim, maxSr, nVoli):
Xdim = volDim
Ts = volSr
newTs = self.targetResolution.get() * 1.0 / 3.0
newTs = max(maxSr, newTs)
newXdim = Xdim * Ts / newTs
newRmax = self.Rmax.get() * Ts / newTs
self.newRmax = min(newRmax, self.Rmax.get())
fnOut = os.path.splitext(volFn)[0]
fnOut = self._getExtraPath(
os.path.basename(fnOut + self.OUTPUT_SUFFIX % nVoli))
ih = ImageHandler()
volFn = volFn if getExt(volFn) == '.vol' else volFn + ':mrc'
if Xdim != newXdim:
self.runJob("xmipp_image_resize",
"-i %s -o %s --dim %d" % (volFn, fnOut, newXdim))
else:
ih.convert(volFn, fnOut)
if newXdim > minDim:
self.runJob(
"xmipp_transform_window",
" -i %s -o %s --crop %d" % (fnOut, fnOut, (newXdim - minDim)))
def convertPdbStep(self):
vol1 = self.vol1.get()
pdbFn = self._getPdbFileName()
self.outFile = self._getVolName()
if getExt(pdbFn) == ".cif":
pdbFn2 = replaceBaseExt(pdbFn, 'pdb')
cifToPdb(pdbFn, pdbFn2)
pdbFn = pdbFn2
samplingR = vol1.getSamplingRate()
size = vol1.getDim()
ccp4header = headers.Ccp4Header(vol1.getFileName(), readHeader=True)
self.shifts = ccp4header.getOrigin()
# convert pdb to volume with the size and origin of the input volume
args = ' -i %s --sampling %f -o %s --size %d %d %d --orig %d %d %d' % \
(pdbFn, samplingR, removeExt(self.outFile), size[2], size[1], size[0], self.shifts[0]/samplingR,
self.shifts[1]/samplingR, self.shifts[2]/samplingR)
program = "xmipp_volume_from_pdb"
self.runJob(program, args)
volpdbmrc = "%s.mrc" % removeExt(self.outFile)
# convert volume from pdb to .mrc in order to store the origin in the mrc header
args2 = ' -i %s -o %s -t vol' % (self.outFile, volpdbmrc)
program2 = "xmipp_image_convert"
self.runJob(program2, args2)
# write origin in mrc header of volume from pdb
ccp4headerOut = headers.Ccp4Header(volpdbmrc, readHeader=True)
ccp4headerOut.setOrigin(self.shifts)
def getFilePreview(self, objFile):
self._imgPreview = None
self._imgInfo = None
filename = objFile.getPath()
ext = getExt(filename)
if ext == '.xmd' or ext == '.ctfparam' or ext == '.pos' or ext == '.doc':
msg = "*Metadata File* "
blocks = xmipp.getBlocksInMetaDataFile(filename)
nblocks = len(blocks)
if nblocks <= 1:
mdStr = self._getMdString(filename)
msg += " (single block)\n"
if self._imgInfo:
msg += "\nFirst item: \n" + self._imgInfo
msg += '\n' + mdStr
else:
mdStr = self._getMdString(filename, blocks[0])
msg += " (%d blocks) " % nblocks
if self._imgInfo:
msg += "\nFirst item: \n" + self._imgInfo
msg += "\nFirst block: \n" + mdStr
msg += "\nAll blocks:" + ''.join(["\n - %s" % b for b in blocks])
elif ext == '.star':
msg = "*Relion STAR file* \n"
msg += self._getMdString(filename)
return self._imgPreview, msg
def _convert(self, image):
imageFn = image.getFileName()
if self.outputDir is None:
return imageFn
ext = pwutils.getExt(imageFn)[1:]
if ext in self.extensions:
finalExt = ext
convertFunc = pwutils.createAbsLink
else:
finalExt = self.extensions[0]
convertFunc = self._ih.convert
if self.useBaseName:
newName = pwutils.replaceBaseExt(image.getFileName(), finalExt)
else:
newName = "%s_%06d.%s" % (self._prefix, image.getObjId(), finalExt)
newPath = os.path.join(self.outputDir, newName)
convertFunc(os.path.abspath(imageFn), newPath)
# If there is a rootDir defined, we should return the path relative
# to that location, probably to be used from the star file
if self.rootDir is not None:
newPath = os.path.relpath(newPath, self.rootDir)
return newPath
def getEmpiarFormat(self, imagePath):
ext = pwutils.getExt(imagePath).lower().strip('.')
imgFormat = self._imageSetFormats.get(ext, 'OT')
if imgFormat == 'OT':
return 'OT', ext
else:
return imgFormat, ''
def convertPdbStep(self):
""" Although is not mandatory, usually is used by the protocol to
register the resulting outputs in the database.
"""
pdbFn = self._getPdbFileName()
outFile = removeExt(self._getVolName())
if getExt(pdbFn) == ".cif":
pdbFn2 = replaceBaseExt(pdbFn, 'pdb')
cifToPdb(pdbFn, pdbFn2)
pdbFn = pdbFn2
args = '-i %s --sampling %f -o %s' % (pdbFn, self.sampling.get(),
outFile)
if self.centerPdb:
args += ' --centerPDB'
if self.setSize:
args += ' --size'
if self.size.hasValue():
args += ' %d' % self.size.get()
self.info("Input file: " + pdbFn)
self.info("Output file: " + outFile)
program = "xmipp_volume_from_pdb"
self.runJob(program, args)
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 = getExt(fn).lower()
if ext == '.png' or ext == '.jpg':
im = PIL.Image.open(fn)
x, y = im.size # (width,height) tuple
return x, y, 1, 1
else:
self._img.read(location, xmipp.HEADER)
x, y, z, n = self._img.getDimensions()
return x, y, z, n
else:
return None, None, None, None
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()
if ext == '.png' or ext == '.jpg':
im = PIL.Image.open(fn)
x, y = im.size # (width,height) tuple
return x, y, 1, 1
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 .img files
from pyworkflow.em.packages.eman2.convert import getImageDimensions
return getImageDimensions(fn) # we are ignoring index here
else:
self._img.read(location, xmipp.HEADER)
return self._img.getDimensions()
else:
return None, None, None, None
def _doShowStrain(self, param=None):
scriptFile = self.protocol._getPath('strain_chimera.cxc')
fhCmd = open(scriptFile, 'w')
fnbase = removeExt(self.protocol._getFileName('fnInputVol'))
ext = getExt(self.protocol._getFileName('fnInputVol'))
fninput = abspath(fnbase + ext[0:4])
smprt = self.protocol.outputVolume.getSamplingRate()
fnbase2 = removeExt(self.protocol._getFileName('fnOutVol'))
fnStrain = abspath(fnbase2)
fhCmd.write(self.OPEN_FILE % fninput)
fhCmd.write(self.OPEN_FILE % (fnStrain + "_strain.mrc"))
counter = 1
fhCmd.write(self.VOXEL_SIZE % (counter, str(smprt)))
counter += 1
fhCmd.write(self.VOXEL_SIZE % (counter, str(smprt)))
fhCmd.write(self.VOL_HIDE % counter)
fhCmd.write('color sample #%d map #%d palette rainbow\n' %
(counter - 1, counter))
fhCmd.write(self.VIEW)
fhCmd.close()
view = ChimeraView(scriptFile)
return [view]
def getFilePreview(self, objFile):
self._imgPreview = None
self._imgInfo = None
filename = objFile.getPath()
ext = getExt(filename)
if ext == '.xmd' or ext == '.ctfparam' or ext == '.pos' or ext == '.doc':
msg = "*Metadata File* "
blocks = xmippLib.getBlocksInMetaDataFile(filename)
nblocks = len(blocks)
if nblocks <= 1:
mdStr = self._getMdString(filename)
msg += " (single block)\n"
if self._imgInfo:
msg += "\nFirst item: \n" + self._imgInfo
msg += '\n' + mdStr
else:
mdStr = self._getMdString(filename, blocks[0])
msg += " (%d blocks) " % nblocks
if self._imgInfo:
msg += "\nFirst item: \n" + self._imgInfo
msg += "\nFirst block: \n" + mdStr
msg += "\nAll blocks:" + ''.join(
["\n - %s" % b for b in blocks])
elif ext == '.star':
msg = "*Relion STAR file* \n"
msg += self._getMdString(filename)
return self._imgPreview, msg
def needToFlipOnY(filename):
""" Returns true if need to flip coordinates on Y"""
ext = pwutils.getExt(filename)
if ext in ".mrc":
header = Ccp4Header(filename, readHeader=True)
return header.getISPG() != 0 # ISPG 1, cryolo will not flip the image
return ext in constants.CRYOLO_SUPPORTED_FORMATS
def getFileFormat(cls, fileName):
ext = getExt(fileName)
if (ext == '.mrc') or (ext == '.map'):
return cls.MRC
elif (ext == '.spi') or (ext == '.vol'):
return cls.SPIDER
else:
return cls.UNKNOWNFORMAT
def getTypeFromFile(self, fileName):
'''Returns the expected BioPython file type according to the filename'''
ext = getExt(fileName)
if ext == '.fasta':
type = 'fasta'
elif ext == '.genbank' or ext == '.gb':
type = 'genbank'
else:
type = 'fasta'
return type
def getFileFormat(fileName):
ext = getExt(fileName)
if ext in [
'.mrc', '.map', '.mrcs', '.mrc:mrc', '.mrc:mrcs', '.st', '.rec'
]:
return MRC
elif ext == '.spi' or ext == '.vol':
return SPIDER
else:
return UNKNOWNFORMAT
def _getOutputMicrograph(self, mic):
""" Return the name of the output micrograph, given
the input Micrograph object.
"""
fn = mic.getFileName()
extFn = getExt(fn)
if extFn != ".mrc":
fn = replaceExt(fn, "mrc")
fnOut = self._getExtraPath(basename(fn))
return fnOut
def convertInputStep(self):
""" Read the input volume.
"""
if (self.halfVolumes.get() is False):
extVol0 = getExt(self.vol0Fn)
if (extVol0 == '.mrc') or (extVol0 == '.map'):
self.vol0Fn = self.vol0Fn + ':mrc'
if self.halfVolumes.get() is True:
extVol1 = getExt(self.vol1Fn)
extVol2 = getExt(self.vol2Fn)
if (extVol1 == '.mrc') or (extVol1 == '.map'):
self.vol1Fn = self.vol1Fn + ':mrc'
if (extVol2 == '.mrc') or (extVol2 == '.map'):
self.vol2Fn = self.vol2Fn + ':mrc'
extMask = getExt(self.maskFn)
if (extMask == '.mrc') or (extMask == '.map'):
self.maskFn = self.maskFn + ':mrc'
def writeSetOfSubtomograms(self, subtomoSet, subtomosStar, isPyseg=False):
currentTomo = ''
MRC = 'mrc'
ih = ImageHandler()
tomoTable = self._createStarTomoTable(isPyseg)
tmpDir = pwutils.getParentFolder(subtomosStar)
for subtomo in subtomoSet:
if pwutils.getExt(subtomo.getFileName().replace(':' + MRC,
'')) != '.' + MRC:
mrcDir = join(tmpDir,
pwutils.removeBaseExt(subtomo.getVolName()))
if currentTomo != subtomo.getVolName():
mkdir(mrcDir)
mrcFile = join(
mrcDir, pwutils.replaceBaseExt(subtomo.getFileName(), MRC))
ih.convert(subtomo.getFileName(), mrcFile)
angles, shifts = self._getTransformInfoFromSubtomo(subtomo)
magn = subtomo.getAcquisition().getMagnification()
rlnMicrographName = subtomo.getVolName()
rlnCoordinateX = subtomo.getCoordinate3D().getX(BOTTOM_LEFT_CORNER)
rlnCoordinateY = subtomo.getCoordinate3D().getY(BOTTOM_LEFT_CORNER)
rlnCoordinateZ = subtomo.getCoordinate3D().getZ(BOTTOM_LEFT_CORNER)
rlnImageName = subtomo.getFileName().replace(':' + MRC, '')
rlnCtfImage = self._getCTFFileFromSubtomo(subtomo)
rlnMagnification = magn if magn else 10000 #64000
rlnDetectorPixelSize = subtomo.getSamplingRate()
rlnAngleRot = angles[0]
rlnAngleTilt = angles[1]
rlnAnglePsi = angles[2]
rlnOriginX = shifts[0]
rlnOriginY = shifts[1]
rlnOriginZ = shifts[2]
rlnTiltPrior = subtomo._tiltPriorAngle.get() if hasattr(
subtomo, '_tiltPriorAngle') else rlnAngleTilt
rlnTiltPsi = subtomo._psiPriorAngle.get() if hasattr(
subtomo, '_psiPriorAngle') else rlnAnglePsi
# Add row to the table which will be used to generate the STAR file
fieldsToAdd = [
rlnMicrographName, rlnCoordinateX, rlnCoordinateY,
rlnCoordinateZ, rlnImageName, rlnCtfImage, rlnMagnification,
rlnDetectorPixelSize, rlnAngleRot, rlnAngleTilt, rlnTiltPrior,
rlnAnglePsi, rlnTiltPsi, rlnOriginX, rlnOriginY, rlnOriginZ
]
if isPyseg:
fieldsToAdd = [
rlnMicrographName, rlnCoordinateX, rlnCoordinateY,
rlnCoordinateZ, rlnImageName, rlnCtfImage, rlnAngleRot,
rlnAngleTilt, rlnAnglePsi, rlnOriginX, rlnOriginY,
rlnOriginZ
]
tomoTable.addRow(*fieldsToAdd)
# Write the STAR file
tomoTable.write(subtomosStar)
def _visualize(self, obj, **args):
cls = type(obj)
if issubclass(cls, Volume) or issubclass(cls, Image):
fn = obj.getFileName()
if pwutils.getExt(fn) in ['.stk', '.vol', '.xmp']:
# eman2 expects spider files with .spi extension only
pwutils.createLink(fn, pwutils.replaceExt(fn, 'spi'))
fn = pwutils.replaceExt(fn, 'spi')
view = CommandView("%s %s &" %
(Plugin.getProgram('e2display.py'), fn),
env=Plugin.getEnviron())
return [view]
elif isinstance(obj, EmanProtBoxing):
coords = obj.getCoords()
if coords:
return DataViewer._visualize(self, obj.outputCoordinates)
elif isinstance(obj, EmanProtInitModel):
obj = obj.outputVolumes
fn = obj.getFileName()
labels = 'id enabled comment _filename '
objCommands = "'%s' '%s' '%s'" % (OBJCMD_CLASSAVG_PROJS,
OBJCMD_PROJS, OBJCMD_INITVOL)
self._views.append(
ObjectView(self._project,
obj.strId(),
fn,
viewParams={
showj.MODE: showj.MODE_MD,
showj.VISIBLE: labels,
showj.RENDER: '_filename',
showj.OBJCMDS: objCommands
}))
return self._views
elif isinstance(obj, EmanProtInitModelSGD):
obj = obj.outputVolumes
fn = obj.getFileName()
labels = 'id enabled comment _filename '
objCommands = "'%s'" % OBJCMD_CLASSAVG_PROJS
self._views.append(
ObjectView(self._project,
obj.strId(),
fn,
viewParams={
showj.MODE: showj.MODE_MD,
showj.VISIBLE: labels,
showj.RENDER: '_filename',
showj.OBJCMDS: objCommands
}))
return self._views
def mrc_convert(self, fileName, outputFileName):
"""Check if the extension is .mrc, if not then uses xmipp to convert it
"""
ext = getExt(fileName)
if (ext != '.mrc') and (ext != '.map'):
params = ' -i "%s"' % fileName
params += ' -o "%s"' % outputFileName
self.runJob('xmipp_image_convert', params)
return outputFileName + ':mrc'
else:
return fileName + ':mrc'
def _getOutputMicrograph(self, mic):
""" Return the name of the output micrograph, given
the input Micrograph object.
"""
fn = mic.getFileName()
extFn = getExt(fn)
if extFn != ".mrc":
fn = replaceExt(fn, "mrc")
fnOut = self._getExtraPath(basename(fn))
return fnOut
def cleanFileNameAnnotation(self, fileName):
ext = getExt(fileName)
self.isMovie = False
if ext == '.mrcs':
self.isMovie = True
elif ext == '.mrc:mrcs': # Movie --> dims = [X, Y, Z = 1, N]
self.isMovie = True
fileName = fileName.replace(':mrcs', '')
elif ext == '.mrc:mrc': # Volume --> dims = [X, Y, Z, N = 1]
fileName = fileName.replace(':mrc', '')
return fileName
def createChimeraScriptDoA(self, infile, outfile, ellipfile):
fnRoot = "extra/"
scriptFile = self.protocol._getPath(outfile)
fhCmd = open(scriptFile, 'w')
imageFile = self.protocol._getExtraPath(infile)
img = ImageHandler().read(imageFile)
imgData = img.getData()
min_Res = 0.0 #round(np.amin(imgData)*100)/100
max_Res = 1.0 #round(np.amax(imgData)*100)/100
numberOfColors = 21
colors_labels = self.numberOfColors(min_Res, max_Res, numberOfColors)
colorList = self.colorMapToColorList(colors_labels, self.getColorMap())
fnbase = removeExt(self.protocol.inputVolumes.get().getFileName())
ext = getExt(self.protocol.inputVolumes.get().getFileName())
fninput = abspath(fnbase + ext[0:4])
fhCmd.write("open %s\n" % fninput)
fhCmd.write("open %s\n" % (fnRoot + infile))
fhCmd.write("open %s\n" % (fnRoot + ellipfile))
smprt = self.protocol.inputVolumes.get().getSamplingRate()
fhCmd.write("volume #0 voxelSize %s\n" % (str(smprt)))
fhCmd.write("volume #1 voxelSize %s\n" % (str(smprt)))
fhCmd.write("volume #2 voxelSize %s\n" % (str(smprt)))
fhCmd.write("volume #2 style mesh\n")
fhCmd.write("vol #1 hide\n")
scolorStr = '%s,%s:' * numberOfColors
scolorStr = scolorStr[:-1]
line = ("scolor #0 volume #1 perPixel false cmap " + scolorStr +
"\n") % colorList
fhCmd.write(line)
scolorStr = '%s %s ' * numberOfColors
str_colors = ()
for idx, elem in enumerate(colorList):
if (idx % 2 == 0):
if ((idx % 8) == 0):
str_colors += str(elem),
else:
str_colors += '" "',
else:
str_colors += elem,
line = ("colorkey 0.01,0.05 0.02,0.95 " + scolorStr +
"\n") % str_colors
fhCmd.write(line)
fhCmd.close()
def create_movie_params(self, prot, allParams):
for movie in self.iter_updated_set(prot.outputMovies):
movieFn = movie.getFileName()
if self.numberOfFrames is None:
self.numberOfFrames = movie.getNumberOfFrames()
images_path = self.find_ispyb_path(movieFn)
self.imageGenerator = ImageGenerator(self.project.path,
images_path,
smallThumb=512)
movieId = movie.getObjId()
allParams[movieId] = {
'id': self.allIds.get(movieId, None),
'imgdir': dirname(movieFn),
'imgprefix': pwutils.removeBaseExt(movieFn),
'imgsuffix': pwutils.getExt(movieFn),
'file_template': movieFn,
'n_images': self.numberOfFrames
}
def _pickMicrograph(self, mic, args):
# Prepare mic folder and convert if needed
micName = mic.getFileName()
micDir = self._getTmpPath(pwutils.removeBaseExt(micName))
pwutils.makePath(micDir)
ih = ImageHandler()
# If needed convert micrograph to mrc format, otherwise link it
if pwutils.getExt(micName) != ".mrc":
fnMicBase = pwutils.replaceBaseExt(micName, 'mrc')
inputMic = os.path.join(micDir, fnMicBase)
ih.convert(mic.getLocation(), inputMic)
else:
inputMic = os.path.join(micDir, os.path.basename(micName))
pwutils.createLink(micName, inputMic)
# Program to execute and it arguments
program = "ApDogPicker.py"
outputFile = self._getExtraPath(pwutils.replaceBaseExt(inputMic, "txt"))
args += " --image=%s --outfile=%s" % (inputMic, outputFile)
self.runJob(program, args)
def _processMovie(self, movie):
inputMovies = self.inputMovies.get()
movieFolder = self._getOutputMovieFolder(movie)
outputMicFn = self._getRelPath(self._getOutputMicName(movie),
movieFolder)
outputMovieFn = self._getRelPath(self._getOutputMovieName(movie),
movieFolder)
movieBaseName = pwutils.removeExt(movie.getFileName())
aveMicFn = movieBaseName + '_uncorrected_avg.mrc'
logFile = self._getRelPath(self._getMovieLogFile(movie),
movieFolder)
a0, aN = self._getRange(movie, 'align')
if not self.useMotioncor2:
# Get the number of frames and the range to be used
# for alignment and sum
s0, sN = self._getRange(movie, 'sum')
argsDict = {'-crx': self.cropOffsetX.get(),
'-cry': self.cropOffsetY.get(),
'-cdx': self.cropDimX.get(),
'-cdy': self.cropDimY.get(),
'-bin': self.binFactor.get(),
'-nst': '%d' % a0,
'-ned': '%d' % aN,
'-nss': '%d' % s0,
'-nes': '%d' % sN,
'-flg': logFile,
}
args = '"%s" ' % movie.getBaseName()
args += ' '.join(
['%s %s' % (k, v) for k, v in argsDict.iteritems()])
if inputMovies.getGain():
args += ' -fgr "%s"' % inputMovies.getGain()
if inputMovies.getDark():
args += ' -fdr "%s"' % inputMovies.getDark()
if self.doSaveAveMic:
args += ' -fcs "%s" ' % outputMicFn
if self.doSaveMovie:
args += ' -fct "%s" -ssc 1' % outputMovieFn
args += ' -gpu %(GPU)s'
args += ' ' + self.extraParams.get()
program = MOTIONCORR_PATH
else:
logFileBase = (logFile.replace('0-Full.log', '').replace(
'0-Patch-Full.log', ''))
# default values for motioncor2 are (1, 1)
cropDimX = self.cropDimX.get() or 1
cropDimY = self.cropDimY.get() or 1
numbOfFrames = self._getNumberOfFrames(movie)
if self.doApplyDoseFilter:
preExp, dose = self._getCorrectedDose(inputMovies)
else:
preExp, dose = 0.0, 0.0
# reset values = 1 to 0 (motioncor2 does it automatically,
# but we need to keep this for consistency)
if self.patchX.get() == 1:
self.patchX.set(0)
if self.patchY.get() == 1:
self.patchY.set(0)
argsDict = {'-OutMrc': '"%s"' % outputMicFn,
'-Patch': '%d %d' % (self.patchX, self.patchY),
'-MaskCent': '%d %d' % (self.cropOffsetX,
self.cropOffsetY),
'-MaskSize': '%d %d' % (cropDimX, cropDimY),
'-FtBin': self.binFactor.get(),
'-Tol': self.tol.get(),
'-Group': self.group.get(),
'-FmDose': dose,
'-Throw': '%d' % a0,
'-Trunc': '%d' % (abs(aN - numbOfFrames + 1)),
'-PixSize': inputMovies.getSamplingRate(),
'-kV': inputMovies.getAcquisition().getVoltage(),
'-LogFile': logFileBase,
}
if getVersion('MOTIONCOR2') != '03162016':
argsDict['-InitDose'] = preExp
argsDict['-OutStack'] = 1 if self.doSaveMovie else 0
if self.isSemVersion():
if self.defectFile.get():
argsDict['-DefectFile'] = self.defectFile.get()
if self.versionGE('1.0.1'): # Patch overlap was introduced in 1.0.1
patchOverlap = self.getAttributeValue('patchOverlap', None)
if patchOverlap: # 0 or None is False
argsDict['-Patch'] += " %d" % patchOverlap
if self._supportsMagCorrection() and self.doMagCor:
if self.useEst:
inputEst = self.inputEst.get().getOutputLog()
if getVersion('MOTIONCOR2') == '01302017':
input_params = parseMagCorrInput(inputEst)
# this version uses stretch parameters as following:
# 1/maj, 1/min, -angle
argsDict['-Mag'] = '%0.3f %0.3f %0.3f' % (
1.0 / input_params[1],
1.0 / input_params[2],
-1 * input_params[0])
else:
# While motioncor2 >=1.0.0 uses estimation params AS IS
input_params = parseMagEstOutput(inputEst)
argsDict['-Mag'] = '%0.3f %0.3f %0.3f' % (
input_params[1],
input_params[2],
input_params[0])
else:
argsDict['-Mag'] = '%0.3f %0.3f %0.3f' % (self.scaleMaj,
self.scaleMin,
self.angDist)
ext = pwutils.getExt(movie.getFileName()).lower()
if ext in ['.mrc', '.mrcs']:
args = ' -InMrc "%s" ' % movie.getBaseName()
elif ext in ['.tif', '.tiff']:
args = ' -InTiff "%s" ' % movie.getBaseName()
else:
raise Exception("Unsupported format: %s" % ext)
args += ' '.join(['%s %s' % (k, v)
for k, v in argsDict.iteritems()])
if inputMovies.getGain():
args += ' -Gain "%s" ' % inputMovies.getGain()
if inputMovies.getDark():
args += ' -Dark "%s"' % inputMovies.getDark()
args += ' -Gpu %(GPU)s'
args += ' ' + self.extraParams2.get()
program = MOTIONCOR2_PATH
try:
self.runJob(program, args, cwd=movieFolder,
env=getEnviron(self.useMotioncor2))
self._fixMovie(movie)
# Compute PSDs
outMicFn = self._getExtraPath(self._getOutputMicName(movie))
if not os.path.exists(outMicFn):
# if only DW mic is saved
outMicFn = self._getExtraPath(self._getOutputMicWtName(movie))
def _extraWork():
if self.doComputePSD:
# Compute uncorrected avg mic
roi = [self.cropOffsetX.get(), self.cropOffsetY.get(),
self.cropDimX.get(), self.cropDimY.get()]
fakeShiftsFn = self.writeZeroShifts(movie)
self.averageMovie(movie, fakeShiftsFn, aveMicFn,
binFactor=self.binFactor.get(),
roi=roi, dark=inputMovies.getDark(),
gain=inputMovies.getGain())
self.computePSDs(movie, aveMicFn, outMicFn,
outputFnCorrected=self._getPsdJpeg(movie))
self._saveAlignmentPlots(movie)
if self._doComputeMicThumbnail():
self.computeThumbnail(outMicFn,
outputFn=self._getOutputMicThumbnail(
movie))
# This protocols takes control of clean up the temporary movie folder
# which is required mainly when using a thread for this extra work
self._cleanMovieFolder(movieFolder)
if self._useWorkerThread():
thread = Thread(target=_extraWork)
thread.start()
else:
_extraWork()
except:
print("ERROR: Movie %s failed\n" % movie.getName())
def getFileHandler(self, obj):
filename = obj.getFileName()
fileExt = getExt(filename)
return self._FILE_HANDLERS.get(fileExt, self._DEFAULT_HANDLER)
def _getConvertExtension(self, filename):
""" Check wether it is needed to convert to .mrc or not """
ext = pwutils.getExt(filename).lower()
return None if ext in ['.mrc', '.mrcs', '.tiff', '.tif'] else 'mrc'
