def importCoordinates(self, fileName, addCoordinate):
if exists(fileName):
ext = getExt(fileName)
if ext == ".json":
print "importando un json"
jsonPosDict = loadJson(fileName)
if jsonPosDict.has_key("boxes"):
boxes = jsonPosDict["boxes"]
for box in boxes:
x, y = box[:2]
coord = Coordinate()
coord.setPosition(x, y)
addCoordinate(coord)
elif ext == ".box":
md = MetaData()
md.readPlain(fileName, 'xcoor ycoor xSize ySize')
for objId in md:
x = md.getValue(MDL_XCOOR, objId)
y = md.getValue(MDL_YCOOR, objId)
coord = Coordinate()
coord.setPosition(x, y)
addCoordinate(coord)
else:
print "importando un queseyo"
def _plotHistogram(self, param=None):
md = MetaData()
md.read(self.protocol._getPath('extra/hist.xmd'))
x_axis = []
y_axis = []
i = 0
for idx in md:
x_axis_ = md.getValue(MDL_X, idx)
if i==0:
x0 = x_axis_
elif i==1:
x1 = x_axis_
y_axis_ = md.getValue(MDL_COUNT, idx)
i+=1
x_axis.append(x_axis_)
y_axis.append(y_axis_)
delta = x1-x0
plt.figure()
plt.bar(x_axis, y_axis, width = delta)
plt.title("Resolutions Histogram")
plt.xlabel("Resolution (A)")
plt.ylabel("Counts")
return plt.show()
def readCoordinates(mic, fileName, coordsSet):
if exists(fileName):
md = MetaData()
md.readPlain(fileName, 'xcoor ycoor')
for objId in md:
x = md.getValue(MDL_XCOOR, objId)
y = md.getValue(MDL_YCOOR, objId)
coord = Coordinate()
coord.setPosition(x, y)
coord.setMicrograph(mic)
coordsSet.append(coord)
def importCoordinates(self, fileName, addCoordinate):
print "In importCoordinates Appion with filename=%s" % fileName
if exists(fileName):
md = MetaData()
md.readPlain(fileName, 'xcoor ycoor')
for objId in md:
x = md.getValue(MDL_XCOOR, objId)
y = md.getValue(MDL_YCOOR, objId)
coord = Coordinate()
coord.setPosition(x, y)
addCoordinate(coord)
def _computeCTFDiscrepancy(self, method1, method2):
#TODO must be same micrographs
#move to a single step, each step takes 5 sec while the function takes 0.03 sec
#convert to md
md1 = MetaData()
md2 = MetaData()
for ctf1 in method1: #reference CTF
ctfId = ctf1.getObjId()
self._ctfToMd(ctf1, md1)
ctf2 = method2[ctfId] #.target
self._ctfToMd(ctf2, md2)
key = ctfId
self._freqResol[key] = xmipp.errorMaxFreqCTFs2D(md1, md2)
def importCoordinates(self, fileName, addCoordinate):
if exists(fileName):
ext = getExt(fileName)
if ext == ".json":
jsonPosDict = loadJson(fileName)
if jsonPosDict.has_key("boxes"):
boxes = jsonPosDict["boxes"]
for box in boxes:
x, y = box[:2]
coord = Coordinate()
coord.setPosition(x, y)
addCoordinate(coord)
elif ext == ".box":
md = MetaData()
md.readPlain(fileName, "xcoor ycoor particleSize")
size = md.getValue(MDL_PICKING_PARTICLE_SIZE, md.firstObject())
if size is None:
print ">>> WARNING: Error parsing coordinate file: %s" % fileName
print " Skipping this file."
else:
half = size / 2
for objId in md:
x = md.getValue(MDL_XCOOR, objId)
y = md.getValue(MDL_YCOOR, objId)
coord = Coordinate()
coord.setPosition(x+half, y+half)
addCoordinate(coord)
else:
raise Exception('Unknown extension "%s" to import Eman coordinates' % ext)
def _computeCTFDiscrepancyStep(self, ctfId, method1, method2):
#TODO must be same micrographs
#convert to md
mdList = [MetaData(), MetaData()]
ctfList = [
self.inputCTFs[method1].get()[ctfId],
self.inputCTFs[method2].get()[ctfId]
]
ctfRow = Row()
for md, ctf in izip(mdList, ctfList):
objId = md.addObject()
convert.ctfModelToRow(ctf, ctfRow)
convert.micrographToRow(ctf.getMicrograph(),
ctfRow,
alignType=convert.ALIGN_NONE)
ctfRow.writeToMd(md, objId)
self._freqResol[(method1, method2,
ctfId)] = xmipp.errorMaxFreqCTFs2D(*mdList)
def _computeCTFDiscrepancy(self, method1, method2):
# TODO must be same micrographs
# move to a single step, each step takes 5 sec while the function
# takes 0.03 sec
# convert to md
md1 = MetaData()
md2 = MetaData()
for ctf1 in method1: # reference CTF
ctfId = ctf1.getObjId()
if ctfId in self.processedDict:
continue
for ctf2 in method2:
ctfId2 = ctf2.getObjId()
if ctfId2 != ctfId:
continue
self.processedDict.append(ctfId)
self._ctfToMd(ctf1, md1)
self._ctfToMd(ctf2, md2)
self._freqResol[ctfId] = xmippLib.errorMaxFreqCTFs2D(md1, md2)
def getBoxSize(self, coordFile):
""" Try to infer the box size from the given coordinate file.
In the case of .box files, the size is the 3rd column
In the case of .json files, we will look for file e2boxercache/base.json
"""
if coordFile.endswith('.box'):
md = MetaData()
md.readPlain(coordFile, "xcoor ycoor particleSize")
return md.getValue(MDL_PICKING_PARTICLE_SIZE, md.firstObject())
elif coordFile.endswith('.json'):
infoDir = dirname(coordFile)
# Still go one level up of info dir
jsonBase = join(dirname(infoDir), 'e2boxercache', 'base.json')
if exists(jsonBase):
jsonDict = loadJson(jsonBase)
if jsonDict.has_key('box_size'):
return int(jsonDict["box_size"])
return None
def _plotHistogram(self, param=None):
md = MetaData()
md.read(self.protocol._getFileName(FN_METADATA_HISTOGRAM))
x_axis = []
y_axis = []
i = 0
for idx in md:
x_axis_ = md.getValue(MDL_X, idx)
if i == 0:
x0 = x_axis_
elif i == 1:
x1 = x_axis_
y_axis_ = md.getValue(MDL_COUNT, idx)
i += 1
x_axis.append(x_axis_)
y_axis.append(y_axis_)
delta = x1 - x0
fig = plt.figure()
plt.bar(x_axis, y_axis, width=delta)
plt.title("Resolutions Histogram")
plt.xlabel("Resolution (A)")
plt.ylabel("Counts")
return [Plotter(figure2=fig)]
def _plotHistogram(self, fnhist, titlename, xname):
md = MetaData()
md.read(self.protocol._getPath('extra/' + fnhist))
x_axis = []
y_axis = []
i = 0
for idx in md:
x_axis_ = md.getValue(MDL_X, idx)
if i == 0:
x0 = x_axis_
elif i == 1:
x1 = x_axis_
y_axis_ = md.getValue(MDL_COUNT, idx)
i += 1
x_axis.append(x_axis_)
y_axis.append(y_axis_)
delta = x1 - x0
plt.figure()
plt.bar(x_axis, y_axis, width=delta)
plt.title(titlename + "Histogram")
plt.xlabel(xname + "(a.u.)")
plt.ylabel("Counts")
return plt.show()
def _plotHistogram(self, param=None):
md = MetaData()
md.read(self.protocol._getPath('extra/hist.xmd'))
x_axis = []
y_axis = []
i = 0
for idx in md:
x_axis_ = md.getValue(MDL_X, idx)
if i == 0:
x0 = x_axis_
elif i == 1:
x1 = x_axis_
y_axis_ = md.getValue(MDL_COUNT, idx)
i += 1
x_axis.append(x_axis_)
y_axis.append(y_axis_)
delta = x1 - x0
plt.figure()
plt.bar(x_axis, y_axis, width=delta)
plt.title("Resolutions Histogram")
plt.xlabel("Resolution (A)")
plt.ylabel("Counts")
return plt.show()
def getBoxSize(self, coordFile):
""" Try to infer the box size from the given coordinate file.
In the case of .box files, the size is the 3rd column
In the case of .json files, we will look for file
e2boxercache/base.json
"""
if coordFile.endswith('.box'):
md = MetaData()
md.readPlain(coordFile, "xcoor ycoor particleSize")
return md.getValue(MDL_PICKING_PARTICLE_SIZE, md.firstObject())
elif coordFile.endswith('.json'):
infoDir = pwutils.dirname(coordFile)
# Still go one level up of info dir
jsonBase = pwutils.join(pwutils.dirname(infoDir), 'e2boxercache',
'base.json')
jsonBase2 = pwutils.join(infoDir, 'project.json')
if pwutils.exists(jsonBase):
jsonDict = loadJson(jsonBase)
if jsonDict.has_key('box_size'):
return int(jsonDict["box_size"])
elif pwutils.exists(jsonBase2):
jsonDict = loadJson(jsonBase2)
if jsonDict.has_key('global.boxsize'):
return int(jsonDict["global.boxsize"])
return None
def _plotHistogram(self, param=None):
md = MetaData()
md.read(self.protocol._getFileName(FN_METADATA_HISTOGRAM))
x_axis = []
y_axis = []
for idx in md:
x_axis_ = md.getValue(MDL_X, idx)
y_axis_ = md.getValue(MDL_COUNT, idx)
x_axis.append(x_axis_)
y_axis.append(y_axis_)
plotter = EmPlotter()
plotter.createSubPlot("Resolutions Histogram", "Resolution (A)",
"# of Counts")
barwidth = (x_axis[-1] - x_axis[0]) / len(x_axis)
plotter.plotDataBar(x_axis, y_axis, barwidth)
return [plotter]
def _showColorSlices(self, fileName, setrangelimits, titleFigure, lowlim,
highlim):
imageFile = self.protocol._getExtraPath(fileName)
img = ImageHandler().read(imageFile)
imgData = img.getData()
imgData2 = np.ma.masked_where(imgData < 0.001, imgData, copy=True)
if setrangelimits is True:
fig, im = self._plotVolumeSlices(titleFigure,
imgData2,
lowlim,
highlim,
self.getColorMap(),
dataAxis=self._getAxis())
else:
md = MetaData()
md.read(self.protocol._getExtraPath(OUTPUT_THRESHOLDS_FILE))
idx = 1
val1 = md.getValue(MDL_RESOLUTION_FREQ, idx)
val2 = md.getValue(MDL_RESOLUTION_FREQ2, idx)
if val1 >= val2:
max_Res = val1 + 0.01
else:
max_Res = val2
# max_Res = np.nanmax(imgData2)
min_Res = np.nanmin(imgData2)
fig, im = self._plotVolumeSlices(titleFigure,
imgData2,
min_Res,
max_Res,
self.getColorMap(),
dataAxis=self._getAxis())
cax = fig.add_axes([0.9, 0.1, 0.03, 0.8])
cbar = fig.colorbar(im, cax=cax)
cbar.ax.invert_yaxis()
return plt.show(fig)
