def readImageVolume(request, path, convert, dataType, reslice, axis, getStats):
#_newPath = path
_stats = None
img = xmipp.Image()
imgFn = os.path.join(request.session['projectPath'], path)
if not convert and not reslice and not getStats:
# img.read(str(imgFn), xmipp.HEADER)
pass
else:
img.read(str(imgFn))
if getStats:
_stats = img.computeStats()
if convert:
img.convert2DataType(dataType, xmipp.CW_ADJUST)
if reslice:
if axis != xmipp.VIEW_Z_NEG:
img.reslice(axis)
_newPath = getTmpVolumePath(imgFn.replace(':mrc', ''))
if (convert and not os.path.exists(_newPath)) or reslice:
img.write(_newPath)
return _newPath, _stats
def normalize(self, what):
# Get overall minimum and maximum
V = xmipp.Image()
minAll = 1e38
maxAll = -1e38
for prot in self.inputRuns:
protId = prot.get().getObjId()
protDir = prot.get()._getPath('')
fnVol = os.path.join(protDir, "extra", "result_%s.vol" % what)
V.read(fnVol)
_, _, minVal, maxVal = V.computeStats()
minAll = min(minAll, minVal)
maxAll = max(maxAll, maxVal)
# Write the Chimera file
for prot in self.inputRuns:
protId = prot.get().getObjId()
protDir = prot.get()._getPath('')
fnRoot = os.path.relpath(os.path.join(protDir, "extra", "result"),
self._getPath(''))
scriptFile = self._getPath('%d_result_%s_chimera.cmd' %
(protId, what))
fhCmd = open(scriptFile, 'w')
fhCmd.write("open %s\n" % (fnRoot + "_final.vol"))
fhCmd.write("open %s\n" % (fnRoot + "_%s.vol" % what))
fhCmd.write("vol #1 hide\n")
fhCmd.write(
"scolor #0 volume #1 cmap rainbow cmapRange %f,%f reverseColors True\n"
% (minAll, maxAll))
fhCmd.close()
def getImageFromPath(imagePath):
""" Read an image using Xmipp, convert to PIL
and then return as expected by Tk.
"""
import xmipp
img = xmipp.Image(imagePath)
imgPIL = getPILImage(img)
from PIL import ImageTk
imgTk = ImageTk.PhotoImage(imgPIL)
return imgTk
def convertVolume(request, path):
imgFn = os.path.join(request.session['projectPath'], path)
imgConvertedFn = getTmpVolumePath(imgFn.replace(':mrc', ''))
# For rendering volume slices over the web, PIL need that
# the volume is stored with a specific datatype
# So, we write a temporarly volume the first time
if not os.path.exists(imgConvertedFn):
img = xmipp.Image()
img.read(str(imgFn))
img.convert2DataType(xmipp.DT_UCHAR, xmipp.CW_ADJUST)
img.write(imgConvertedFn)
return imgConvertedFn
def createRandomMicAtep(self, mic):
from pyworkflow.em.packages.xmipp3 import getEnviron
# create image
img = xmipp.Image()
img.setDataType(xmipp.DT_FLOAT)
img.resize(self.xDim, self.yDim)
img.initRandom(0., 1., xmipp.XMIPP_RND_UNIFORM)
baseFn = self._getExtraPath(self._singleImageFn)
img.write(baseFn)
md1 = xmipp.MetaData()
md1.setColumnFormat(False)
idctf = md1.addObject()
baseFnCtf = self._getTmpPath("ctf_%d.param" % mic)
baseFnImageCTF = self._getExtraPath("imageCTF_%d.xmp" % mic)
md1.setValue(xmipp.MDL_CTF_SAMPLING_RATE, 1., idctf)
md1.setValue(xmipp.MDL_CTF_VOLTAGE, 200., idctf)
defocus = 20000 + 10000 * random.random()
udefocus = defocus + 1000 * random.random()
vdefocus = defocus + 1000 * random.random()
if udefocus < vdefocus:
aux = vdefocus
vdefocus = udefocus
udefocus = aux
md1.setValue(xmipp.MDL_CTF_DEFOCUSU, udefocus, idctf)
md1.setValue(xmipp.MDL_CTF_DEFOCUSV, vdefocus, idctf)
md1.setValue(xmipp.MDL_CTF_DEFOCUS_ANGLE, 180.0 * random.random(),
idctf)
md1.setValue(xmipp.MDL_CTF_CS, 2., idctf)
md1.setValue(xmipp.MDL_CTF_Q0, 0.07, idctf)
md1.setValue(xmipp.MDL_CTF_K, 1., idctf)
md1.write(baseFnCtf)
# apply ctf
args = " -i %s" % baseFn
args += " -o %s" % baseFnImageCTF
args += " -f ctf %s" % baseFnCtf
args += " --sampling %f" % self.samplingRate
self.runJob("xmipp_transform_filter", args, env=getEnviron())
self.dictObj[baseFnImageCTF] = True
time.sleep(self.creationInterval.get())
def get_slice(request):
sliceNo = None
imagePath = request.GET.get('image')
imageDim = request.GET.get('dim', 150)
mirrorY = 'mirrorY' in request.GET
# applyTransformMatrix = 'applyTransformMatrix' in request.GET
# onlyApplyShifts = request.GET.get('onlyApplyShifts',False)
# wrap = request.GET.get('wrap',False)
# transformMatrix = request.GET.get('transformMatrix',None)
# This validations not works for volumes into a stack
if '__slice__' in imagePath:
parts = imagePath.split('__slice__', 1)
sliceNo = int(parts[0])
imagePath = parts[1]
# if '@' in imagePath:
# parts = imagePath.split('@')
# imageNo = parts[0]
# imagePath = parts[1]
imagePath = convertVolume(request, imagePath)
imgXmipp = xmipp.Image()
if sliceNo is None:
imgXmipp.readPreview(imagePath, int(imageDim))
else:
imgXmipp.readPreview(imagePath, int(imageDim), sliceNo)
# if applyTransformMatrix and transformMatrix != None:
# imgXmipp.applyTransforMatScipion(transformMatrix, onlyApplyShifts, wrap)
#
if mirrorY:
imgXmipp.mirrorY()
# from PIL import Image
# img = getPILImage(imgXmipp, None, False)
img = getPILImage(imgXmipp, normalize=False)
response = HttpResponse(mimetype="image/png")
if img.mode != 'RGB':
img = img.convert('RGB')
img.save(response, "PNG")
return response
def __init__(self, filename=None, dim=256, dpi=96, image=None, label=None):
pwgui.Window.__init__(self, minsize=None)
if image is None:
image = xmipp.Image()
if dim is None:
image.read(filename)
dim, _, _, _ = image.getDimensions()
else:
image.readPreview(filename, dim)
dpi = min(dpi, dim)
self.imagePreview = ImagePreview(self.root, dim, dpi, label, 0)
if image is None and filename is None:
raise Exception(
"ImageWindow: image or filename should be provided.")
if filename is None:
filename = "No filename"
self.updateImage(image)
self.imagePreview.grid(row=0, column=0)
def get_image(request):
imageNo = None
# TO DO: Change the way to obtain the separate string of the imagePath
imagePath = request.GET.get('image')
imageDim = request.GET.get('dim', 150)
# This prefix can be passed to avoid that image is not refresh when cached by browser (name does not change)
prefix = request.GET.get('prefix', "")
mirrorY = 'mirrorY' in request.GET
applyTransformMatrix = 'applyTransformMatrix' in request.GET
onlyShifts = 'onlyShifts' in request.GET
wrap = 'wrap' in request.GET
matrix = request.GET.get('matrix', None)
try:
# PAJM: Como vamos a gestionar lsa imagen
if imagePath.endswith('png') or imagePath.endswith('gif'):
imagePathTmp = os.path.join(request.session['projectPath'],
prefix + imagePath)
img = getImage(imagePathTmp, tkImage=False)
else:
if '@' in imagePath:
parts = imagePath.split('@')
imageNo = parts[0]
imagePath = parts[1]
if 'projectPath' in request.session:
imagePathTmp = os.path.join(request.session['projectPath'],
imagePath)
if not os.path.isfile(imagePathTmp):
raise Exception('should not use getInputPath')
#imagePath = getInputPath('showj', imagePath)
if imageNo:
imagePath = '%s@%s' % (imageNo, imagePath)
imgXmipp = xmipp.Image()
imgXmipp.readPreview(imagePath, int(imageDim))
#===================================================================
# Transform Matrix
if applyTransformMatrix:
takarras = [
tMatrix[0][0], tMatrix[0][1], tMatrix[0][2],
x if x != None else 0, tMatrix[1][0], tMatrix[1][1],
tMatrix[1][2], y if y != None else 0, tMatrix[2][0],
tMatrix[2][1], tMatrix[2][2], z if z != None else 0
]
# imgXmipp.applyTransforMatScipion(matrix, onlyShifts, wrap)
imgXmipp.applyTransforMatScipion(takarras, onlyShifts, wrap)
#===================================================================
#===================================================================
# Invert Y axis
if mirrorY:
imgXmipp.mirrorY()
#===================================================================
#TO DO: PSD FIX
if imagePath.endswith('.psd'):
imgXmipp.convertPSD()
# from PIL import Image
img = getPILImage(imgXmipp, None)
except Exception:
img = getImage(findResource(getResourceIcon("no_image")),
tkImage=False)
response = HttpResponse(mimetype="image/png")
img.save(response, "PNG")
return response
def testCtfdiscrepancyWorkflow(self):
# create one micrograph set
fnMicSet = self.proj.getTmpPath("mics.sqlite")
fnMic = self.proj.getTmpPath("mic.mrc")
mic = Micrograph()
mic.setFileName(fnMic)
micSet = SetOfMicrographs(filename=fnMicSet)
# create two CTFsets
fnCTF1 = self.proj.getTmpPath("ctf1.sqlite")
fnCTF2 = self.proj.getTmpPath("ctf2.sqlite")
ctfSet1 = SetOfCTF(filename=fnCTF1)
ctfSet2 = SetOfCTF(filename=fnCTF2)
# create one fake micrographs image
projSize = 32
img = xmipp.Image()
img.setDataType(xmipp.DT_FLOAT)
img.resize(projSize, projSize)
img.write(fnMic)
# fill the sets
for i in range(1, 4):
mic = Micrograph()
mic.setFileName(fnMic)
micSet.append(mic)
defocusU = 1000 + 10 * i
defocusV = 1000 + i
defocusAngle = i * 10
psdFile = "psd_1%04d" % i
ctf = self._getCTFModel(defocusU, defocusV, defocusAngle, psdFile)
ctf.setMicrograph(mic)
ctfSet1.append(ctf)
defocusU = 1000 + 20 * i
defocusV = 1000 + i
defocusAngle = i * 20
psdFile = "psd_2%04d" % i
ctf = self._getCTFModel(defocusU, defocusV, defocusAngle, psdFile)
ctf.setMicrograph(mic)
ctfSet2.append(ctf)
ctfSet1.write()
ctfSet2.write()
micSet.write()
# import micrograph set
args = {
'importFrom': ProtImportMicrographs.IMPORT_FROM_SCIPION,
'sqliteFile': fnMicSet,
'amplitudConstrast': 0.1,
'sphericalAberration': 2.,
'voltage': 100,
'samplingRate': 2.1
}
protMicImport = self.newProtocol(ProtImportMicrographs, **args)
protMicImport.setObjLabel('import micrographs from sqlite ')
self.launchProtocol(protMicImport)
# import ctfsets
protCTF1 = \
self.newProtocol(ProtImportCTF,
importFrom=ProtImportCTF.IMPORT_FROM_SCIPION,
filesPath=fnCTF1)
protCTF2 = \
self.newProtocol(ProtImportCTF,
importFrom=ProtImportCTF.IMPORT_FROM_SCIPION,
filesPath=fnCTF2)
protCTF1.inputMicrographs.set(protMicImport.outputMicrographs)
protCTF2.inputMicrographs.set(protMicImport.outputMicrographs)
protCTF1.setObjLabel('import ctfs from scipion_1 ')
protCTF2.setObjLabel('import ctfs from scipion_2 ')
self.launchProtocol(protCTF1)
self.launchProtocol(protCTF2)
# launch CTF discrepancy protocol
protCtfDiscrepancy = self.newProtocol(XmippProtCTFDiscrepancy)
protCtfDiscrepancy.inputCTF1.set(protCTF1.outputCTF)
protCtfDiscrepancy.inputCTF2.set(protCTF2.outputCTF)
protCtfDiscrepancy.setObjLabel('ctf discrepancy')
self.launchProtocol(protCtfDiscrepancy)
ctf0 = protCtfDiscrepancy.outputCTF.getFirstItem()
resolution = int(ctf0.getResolution())
defocusU = int(ctf0.getDefocusU())
self.assertEqual(resolution, 2)
self.assertEqual(defocusU, 1010)