# **************************************************************************
# * Authors: Mohamad Harastani (mohamad.harastani@upmc.fr)
# * Rémi Vuillemot (remi.vuillemot@upmc.fr)
# * IMPMC, UPMC Sorbonne University
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# **************************************************************************
from os.path import basename
from pwem.emlib import MetaData, MDL_ORDER
from pyworkflow.protocol.params import StringParam, LabelParam
from pyworkflow.viewer import (ProtocolViewer, DESKTOP_TKINTER, WEB_DJANGO)
from pyworkflow.utils import replaceBaseExt, replaceExt
from continuousflex.protocols.data import Point, Data
from continuousflex.viewers.nma_plotter import FlexNmaPlotter
from continuousflex.protocols import FlexProtSynthesizeImages
import xmipp3
import pwem.emlib.metadata as md
from pwem.viewers import ObjectView
from continuousflex.protocols.protocol_image_synthesize import NMA_YES
import matplotlib.pyplot as plt
[docs]class FlexProtSynthesizeImageViewer(ProtocolViewer):
""" Visualization of results from synthesized images
"""
_label = 'viewer synthetic images'
_targets = [FlexProtSynthesizeImages]
_environments = [DESKTOP_TKINTER, WEB_DJANGO]
def __init__(self, **kwargs):
ProtocolViewer.__init__(self, **kwargs)
self._data = None
[docs] def getData(self):
if self._data is None:
self._data = self.loadData()
return self._data
def _defineParams(self, form):
form.addSection(label='Visualization')
form.addParam('displayRawDeformation', StringParam, default='7 8',
condition=self.protocol.confVar.get()==NMA_YES,
label='Display the computed normal-mode amplitudes',
help='Type 7 to see the histogram of amplitudes along mode 7; \n'
'type 8 to see the histogram of amplitudes along mode 8, etc.\n'
'Type 7 8 to see the 2D plot of amplitudes along modes 7 and 8.\n'
'Type 7 8 9 to see the 3D plot of amplitudes along modes 7, 8 and 9; etc.'
)
form.addParam('displayHists', LabelParam,
label="Display shift and angle histograms",
help="Display shift and angle histograms")
form.addParam('displayVolumes', LabelParam,
label="Display images",
help="Display the volumes that are generated")
def _getVisualizeDict(self):
return {'displayRawDeformation': self._viewRawDeformation,
'displayHists': self._viewHists,
'displayVolumes': self._viewVolumes,
}
def _viewVolumes(self, paramName):
volumes = self.protocol.outputImages
return [ObjectView(self._project, volumes.strId(), volumes.getFileName())]
def _viewHists(self, paramName):
mdVolumes = md.MetaData(self.protocol._getExtraPath('GroundTruth.xmd'))
X = []
Y = []
Rot = []
Tilt= []
Psi = []
for objId in mdVolumes:
X.append(mdVolumes.getValue(md.MDL_SHIFT_X,objId))
Y.append(mdVolumes.getValue(md.MDL_SHIFT_Y, objId))
Rot.append(mdVolumes.getValue(md.MDL_ANGLE_ROT, objId))
Tilt.append(mdVolumes.getValue(md.MDL_ANGLE_TILT, objId))
Psi.append(mdVolumes.getValue(md.MDL_ANGLE_PSI, objId))
fig, ax = plt.subplots(2, 3)
fig.suptitle('Histogram of generated rigid-body paramerers')
ax[0,0].hist(X, bins=25)
ax[0,0].set_title('Shift X')
ax[0,1].hist(Y, bins=25)
ax[0,1].set_title('Shift Y')
ax[1,0].hist(Rot, bins=25)
ax[1,0].set_title('Rot')
ax[1,1].hist(Tilt, bins=25)
ax[1,1].set_title('Tilt')
ax[1,2].hist(Psi, bins=25)
ax[1,2].set_title('Psi')
plt.show()
def _viewRawDeformation(self, paramName):
components = self.displayRawDeformation.get()
return self._doViewRawDeformation(components)
def _doViewRawDeformation(self, components):
components = list(map(int, components.split()))
dim = len(components)
views = []
if dim > 0:
modeList = []
modeNameList = []
missingList = []
for modeNumber in components:
found = False
modes_md = MetaData(replaceExt(self.protocol.inputModes.get().getFileName(),'xmd'))
for i, objId in enumerate(modes_md):
modeId = modes_md.getValue(MDL_ORDER, objId)
if modeNumber == modeId:
modeNameList.append('Mode %d' % modeNumber)
modeList.append(i)
found = True
break
if not found:
missingList.append(str(modeNumber))
if missingList:
return [self.errorMessage("Invalid mode(s) *%s*\n." % (', '.join(missingList)),
title="Invalid input")]
# Actually plot
plotter = FlexNmaPlotter(data=self.getData())
baseList = [basename(n) for n in modeNameList]
self.getData().XIND = modeList[0]
if dim == 1:
plotter.plotArray1D("Histogram of normal-mode amplitudes: %s" % baseList[0],
"Amplitude", "Number of images")
else:
self.getData().YIND = modeList[1]
if dim == 2:
plotter.plotArray2D_xy("Normal-mode amplitudes: %s vs %s" % tuple(baseList), *baseList)
elif dim == 3:
self.getData().ZIND = modeList[2]
plotter.plotArray3D_xyz("Normal-mode amplitudes: %s %s %s" % tuple(baseList), *baseList)
views.append(plotter)
return views
[docs] def loadData(self):
mdVolumes = md.MetaData(self.protocol._getExtraPath('GroundTruth.xmd'))
data = Data()
for objId in mdVolumes:
# pointData = list(map(float, particle._xmipp_nmaDisplacements))
pointData = list(mdVolumes.getValue(md.MDL_NMA,objId))
# inserting 6 zeros for the first 6 never used modes
for j in range(6):
pointData.insert(0, 0)
# print(pointData)
data.addPoint(Point(pointId=objId,
data=pointData,
weight=0.0))
return data