def visualize(self):
from protlib_gui_figure import XmippArrayPlotter1D, XmippArrayPlotter2D, XmippArrayPlotter3D
components = self.DisplayRawDeformation.split()
dim = len(components)
if dim > 0:
modeList = []
modeNameList = []
# Get modes
MD = MetaData(self.Modesfile)
MD.removeDisabled()
for modeComponent in components:
mode = int(modeComponent)
if mode > MD.size():
from protlib_gui_ext import showWarning
showWarning("Warning", "You don't have so many modes", parent=self.master)
else:
mode -= 1
currentMode = 0
modeName = ""
for id in MD:
modeName = MD.getValue(MDL_NMA_MODEFILE, id)
currentMode += 1
if currentMode > mode:
break
modeNameList.append(modeName)
modeList.append(mode)
# Actually plot
if dim == 1:
XmippArrayPlotter1D(
self.extraPath("deformations.txt"),
modeList[0],
"Histogram for mode %s" % modeNameList[0],
"Deformation value",
"Number of images",
)
elif dim == 2:
XmippArrayPlotter2D(
self.extraPath("deformations.txt"), modeList[0], modeList[1], "", modeNameList[0], modeNameList[1]
)
elif dim == 3:
XmippArrayPlotter3D(
self.extraPath("deformations.txt"),
modeList[0],
modeList[1],
modeList[2],
"",
modeNameList[0],
modeNameList[1],
modeNameList[2],
)
def readPosCoordinates(posFile):
""" Read the coordinates in .pos file and return corresponding metadata.
There are two possible blocks with particles:
particles: with manual/supervised particles
particles_auto: with automatically picked particles.
If posFile doesn't exist, the metadata will be empty
"""
md = MetaData()
if exists(posFile):
blocks = getBlocksInMetaDataFile(posFile)
for b in ['particles', 'particles_auto']:
if b in blocks:
mdAux = MetaData('%(b)s@%(posFile)s' % locals())
md.unionAll(mdAux)
md.removeDisabled()
return md
def getMdSizeEnabled(filename):
""" Return the metadata size containing only ''enabled'' lines """
md = MetaData(filename)
md.removeDisabled()
return md.size()