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._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, 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 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 _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 _plotCurve(self, a, fnDir, labelmd):
print labelmd
md = MetaData(fnDir)
resolution = []
radius = []
for objId in md:
resolution.append(md.getValue(labelmd, objId))
radius.append(md.getValue(MDL_IDX, objId))
# resolution_inv = [md.getValue(labelmd, objId) for objId in md]
# frc = [md.getValue(MDL_IDX, objId) for objId in md]
self.maxFrc = max(radius)
self.minInv = min(resolution)
self.maxInv = max(resolution)
a.plot(radius, resolution, 'x')
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 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 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 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 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 _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)
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
