def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params["input"].get()
res = validateSet(objs)
if res is not 1:
return HttpResponse(res)
else:
volumes = self._getVols(objs)
if len(volumes) == 0:
return HttpResponse("errorIterate")
params["value"] = proccessModeFilter(params["mode"], params["value"])
params["label"] = params["label"]
params["samplingRate"] = objs.getSamplingRate()
itemDim, _, _ = objs.getDim()
if params["unit"] == UNIT_ANGSTROM:
params["min"] = 2.0 * params["samplingRate"]
params["max"] = 2.0 * itemDim * params["samplingRate"]
else:
params["min"] = 0.01
params["max"] = 0.5
params["value"] = setValueOnRange(params["value"], params["min"], params["max"])
context = {"objects": volumes, "params": params}
context = base_wiz(request, context)
return render_to_response("wizards/wiz_filter_volumes.html", context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params['input'].get()
res = validateParticles(objs)
if res is not 1:
return HttpResponse(res)
else:
particles = self._getParticles(objs)
if len(particles) == 0:
return HttpResponse("errorIterate")
# getting dimension in Pixels
xdim = getImageXdim(request, particles[0].text)
# Multiply by sampling rate to convert to angstroms
xdim *= objs.getSamplingRate()
params['value'] = validateMaskRadius(params['value'], xdim, radius=1)
context = {'objects': particles,
'xdim': int(xdim/2),
'params': params}
context = base_wiz(request, context)
return render_to_response('wizards/wiz_particle_mask_radius.html', context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params['input'].get()
res = validateSet(objs)
if res is not 1:
return HttpResponse(res)
else:
vols = self._getVols(objs)
if len(vols) == 0:
return HttpResponse("errorIterate")
xdim = getImageXdim(request, vols[0].getFileName())
# Multiply by sampling rate to convert to angstroms
xdim *= objs.getSamplingRate()
params['value'] = validateMaskRadius(params['value'], xdim, radius=2)
context = {'objects': vols,
'xdim': int(xdim/2),
'params': params}
context = base_wiz(request, context)
return render_to_response('wizards/wiz_volumes_mask_radii.html', context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params['input'].get()
res = validateParticles(objs)
if res is not 1:
return HttpResponse(res)
else:
particles = self._getParticles(objs)
if len(particles) == 0:
return HttpResponse("errorIterate")
params['value'] = proccessModeFilter(params['mode'], params['value'])
params['samplingRate'] = particles[1].getSamplingRate()
itemDim,_,_ = particles[1].getDim()
if params['unit'] == UNIT_ANGSTROM:
params['min'] = 2.*params['samplingRate']
params['max'] = 2.*itemDim*params['samplingRate']
else:
params['min'] = 0.01
params['max'] = 0.5
params['value'] = setValueOnRange(params['value'], params['min'], params['max'])
context = {'objects': particles,
'params':params}
context = base_wiz(request, context)
return render_to_response('wizards/wiz_filter_particles.html', context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params['input'].get()
res = validateParticles(objs)
if res is not 1:
return HttpResponse(res)
else:
particles = self._getParticles(objs)
if len(particles) == 0:
return HttpResponse("errorIterate")
print "params mode", params['mode']
params['value'] = proccessModeFilter(params['mode'],
params['value'])
params['value'] = setValueOnRange(params['value'], 0, 0.5)
context = {'objects': particles, 'params': params}
context = base_wiz(request, context)
return render_to_response('wizards/wiz_filter_spider.html',
context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params['input'].get()
res = validateParticles(objs)
if res is not 1:
return HttpResponse(res)
else:
particles = self._getParticles(objs)
if len(particles) == 0:
return HttpResponse("errorIterate")
print "params mode", params['mode']
params['value'] = proccessModeFilter(params['mode'], params['value'])
params['value'] = setValueOnRange(params['value'], 0, 0.5)
context = {'objects': particles,
'params':params }
context = base_wiz(request, context)
return render_to_response('wizards/wiz_filter_spider.html', context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params['input'].get()
res = validateSet(objs)
if res is not 1:
return HttpResponse(res)
else:
vols = self._getVols(objs)
if len(vols) == 0:
return HttpResponse("errorIterate")
xdim = getImageXdim(request, vols[0].getFileName())
params['value'] = validateMaskRadius(params['value'],
xdim,
radius=2)
context = {'objects': vols, 'xdim': xdim / 2, 'params': params}
context = base_wiz(request, context)
return render_to_response('wizards/wiz_volumes_mask_radii.html',
context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params['input'].get()
res = validateParticles(objs)
if res is not 1:
return HttpResponse(res)
else:
particles = self._getParticles(objs)
if len(particles) == 0:
return HttpResponse("errorIterate")
xdim = getImageXdim(request, particles[0].text)
params['value'] = validateMaskRadius(params['value'],
xdim,
radius=1)
context = {
'objects': particles,
'xdim': int(xdim / 2),
'params': params
}
context = base_wiz(request, context)
return render_to_response('wizards/wiz_particle_mask_radius.html',
context)
def _run(self, protocol, request):
if not protocol.useSplitVolume:
emptyInput = protocol.inputVolume.pointsNone()
else:
emptyInput = (protocol.volumeHalf1.pointsNone()
or protocol.volumeHalf2.pointsNone())
if emptyInput:
return HttpResponse("Error: select the input volume(s) first.")
else:
plotUrl, min_ang = getPlotResMap(request, protocol)
ang = protocol.prewhitenAng.get()
if ang < min_ang:
ang = min_ang
context = {
# Params
'ang': round(ang, 2),
'ramp': protocol.prewhitenRamp.get(),
# Extra Params
'pValue': protocol.pVal.get(),
'minRes': protocol.minRes.get(),
'maxRes': protocol.maxRes.get(),
'stepRes': protocol.stepRes.get(),
# Others
'plot': plotUrl,
'min_ang': round(min_ang, 2),
'messi_js': getResourceJs('messi'),
'messi_css': getResourceCss('messi'),
}
if protocol.useSplitVolume:
context.update({
'useSplit': 1,
'inputId': protocol.volumeHalf1.getUniqueId(),
'splitId': protocol.volumeHalf2.getUniqueId()
})
else:
context.update({'inputId': protocol.inputVolume.getUniqueId()})
if protocol.applyMask:
if protocol.maskVolume.pointsNone():
return HttpResponse("Error: select the input mask first.")
context.update({
'useMask': 1,
'maskId': protocol.maskVolume.getUniqueId()
})
context = base_wiz(request, context)
return render_to_response('wizards/wiz_resmap.html', context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params['input'].get()
res = validateSet(objs)
if res is not 1:
return HttpResponse(res)
else:
context = {'objects': self._getMics(objs), 'params': params}
context = base_wiz(request, context)
return render_to_response('wizards/wiz_downsampling.html', context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params["input"].get()
res = validateSet(objs)
if res is not 1:
return HttpResponse(res)
else:
context = {"objects": self._getMics(objs), "params": params}
context = base_wiz(request, context)
return render_to_response("wizards/wiz_ctf_downsampling.html", context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params['input'].get()
res = validateSet(objs)
if res is not 1:
return HttpResponse(res)
else:
context = {'objects': self._getMics(objs),
'params': params}
context = base_wiz(request, context)
return render_to_response('wizards/wiz_downsampling.html', context)
def _run(self, protocol, request):
if not protocol.inputVolume.get().hasValue():
return HttpResponse("errorInput")
elif protocol.useSplitVolume == True:
if not protocol.splitVolume.get().hasValue():
return HttpResponse("errorInput")
else:
plotUrl, min_ang = getPlotResMap(request, protocol)
ang = protocol.prewhitenAng.get()
if ang < min_ang:
ang = min_ang
context = {
# Params
'inputId': protocol.inputVolume.get().getObjId(),
'ang': round(ang, 2),
'ramp': protocol.prewhitenRamp.get(),
# Extra Params
'pValue': protocol.pVal.get(),
'minRes': protocol.minRes.get(),
'maxRes': protocol.maxRes.get(),
'stepRes': protocol.stepRes.get(),
# Others
'plot': plotUrl,
'min_ang': round(min_ang, 2),
'messi_js': getResourceJs('messi'),
'messi_css': getResourceCss('messi'),
}
if protocol.useSplitVolume == True and protocol.splitVolume.get().hasValue():
context.update({'useSplit' : 1,
'splitId' : protocol.splitVolume.getObjId(),
})
if protocol.applyMask == True and protocol.maskVolume.get().hasValue():
context.update({'useMask' : 1,
'maskId' : protocol.maskVolume.getObjId(),
})
context = base_wiz(request, context)
return render_to_response('wizards/wiz_resmap.html', context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params["input"].get()
res = validateSet(objs)
if res is not 1:
return HttpResponse(res)
else:
volumes = self._getVols(objs)
if len(volumes) == 0:
return HttpResponse("errorIterate")
context = {"objects": volumes, "params": params}
context = base_wiz(request, context)
return render_to_response("wizards/wiz_gaussian_vol.html", context)
def _run(self, protocol, request):
if not protocol.inputVolume.get().hasValue():
return HttpResponse("errorInput")
elif protocol.useSplitVolume == True:
if not protocol.splitVolume.get().hasValue():
return HttpResponse("errorInput")
else:
plotUrl, min_ang = getPlotResMap(request, protocol)
ang = protocol.prewhitenAng.get()
if ang < min_ang:
ang = min_ang
context = {
# Params
'inputId': protocol.inputVolume.get().getObjId(),
'ang': round(ang, 2),
'ramp': protocol.prewhitenRamp.get(),
# Extra Params
'pValue': protocol.pVal.get(),
'minRes': protocol.minRes.get(),
'maxRes': protocol.maxRes.get(),
'stepRes': protocol.stepRes.get(),
# Others
'plot': plotUrl,
'min_ang': round(min_ang, 2),
'messi_js': getResourceJs('messi'),
'messi_css': getResourceCss('messi'),
}
if protocol.useSplitVolume == True and protocol.splitVolume.get().hasValue():
context.update({'useSplit' : 1,
'splitId' : protocol.splitVolume.getObjId(),
})
if protocol.applyMask == True and protocol.maskVolume.get().hasValue():
context.update({'useMask' : 1,
'maskId' : protocol.maskVolume.getObjId(),
})
context = base_wiz(request, context)
return render_to_response('wizards/wiz_resmap.html', context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params['input'].get()
res = validateSet(objs)
if res is not 1:
return HttpResponse(res)
else:
volumes = self._getVols(objs)
if len(volumes) == 0:
return HttpResponse("errorIterate")
context = {'objects': volumes, 'params': params}
context = base_wiz(request, context)
return render_to_response('wizards/wiz_gaussian_vol.html', context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params['input'].get()
res = validateParticles(objs)
if res is not 1:
return HttpResponse(res)
else:
particles = self._getParticles(objs)
if len(particles) == 0:
return HttpResponse("errorIterate")
context = {'objects': particles,
'params':params}
context = base_wiz(request, context)
return render_to_response('wizards/wiz_gaussian_particle.html', context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
obj = params['input'].get()
if obj is None:
return HttpResponse("errorInput")
else:
# Single particle
particle = obj.clone()
particle.text = particle.getFileName()
particle.basename = basename(particle.text)
xdim = getImageXdim(request, particle.text)
context = {'obj': particle, 'xdim': xdim, 'params': params}
context = base_wiz(request, context)
return render_to_response('wizards/wiz_custom_mask_spider.html',
context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
obj = params['input'].get()
if obj is None:
return HttpResponse("errorInput")
else:
# Single particle
particle = obj.clone()
particle.text = particle.getFileName()
particle.basename = basename(particle.text)
xdim = getImageXdim(request, particle.text)
context = {'obj': particle,
'xdim':xdim,
'params': params }
context = base_wiz(request, context)
return render_to_response('wizards/wiz_custom_mask_spider.html', context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params["input"].get()
res = validateSet(objs)
if res is not 1:
return HttpResponse(res)
else:
vols = self._getVols(objs)
if len(vols) == 0:
return HttpResponse("errorIterate")
xdim = getImageXdim(request, vols[0].getFileName())
params["value"] = validateMaskRadius(params["value"], xdim, radius=1)
context = {"objects": vols, "xdim": int(xdim / 2), "params": params}
context = base_wiz(request, context)
return render_to_response("wizards/wiz_volume_mask_radius.html", context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params['input'].get()
res = validateSet(objs)
if res is not 1:
return HttpResponse(res)
else:
volumes = self._getVols(objs)
if len(volumes) == 0:
return HttpResponse("errorIterate")
params['value'] = proccessModeFilter(params['mode'],
params['value'])
params['label'] = ['', params['label'], '']
params['samplingRate'] = objs.getSamplingRate()
params['unit'] = UNIT_ANGSTROM
# Correct default values to angstroms
params['value'][0] = params['samplingRate'] / params['value'][0]
params['value'][2] = params['samplingRate'] / params['value'][2]
itemDim, _, _ = objs.getDim()
params['min'] = 2. * params['samplingRate']
params['max'] = 2. * itemDim * params['samplingRate']
params['value'] = setValueOnRange(params['value'], params['min'],
params['max'])
context = {'objects': volumes, 'params': params}
context = base_wiz(request, context)
return render_to_response('wizards/wiz_filter_volumes.html',
context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params['input'].get()
res = validateSet(objs)
if res is not 1:
return HttpResponse(res)
else:
volumes = self._getVols(objs)
if len(volumes) == 0:
return HttpResponse("errorIterate")
params['value'] = proccessModeFilter(params['mode'], params['value'])
params['label'] = ['',params['label'],'']
params['samplingRate'] = objs.getSamplingRate()
params['unit'] = UNIT_ANGSTROM
# Correct default values to angstroms
params['value'][0] = params['samplingRate'] / params['value'][0]
params['value'][2] = params['samplingRate'] / params['value'][2]
itemDim,_,_ = objs.getDim()
params['min'] = 2.*params['samplingRate']
params['max'] = 2.*itemDim*params['samplingRate']
params['value'] = setValueOnRange(params['value'], params['min'], params['max'])
context = {'objects': volumes,
'params':params}
context = base_wiz(request, context)
return render_to_response('wizards/wiz_filter_volumes.html', context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params['input'].get()
res = validateParticles(objs)
if res is not 1:
return HttpResponse(res)
else:
particles = self._getParticles(objs)
if len(particles) == 0:
return HttpResponse("errorIterate")
params['value'] = proccessModeFilter(params['mode'],
params['value'])
params['samplingRate'] = particles[1].getSamplingRate()
itemDim, _, _ = particles[1].getDim()
if params['unit'] == UNIT_ANGSTROM:
params['min'] = 2. * params['samplingRate']
params['max'] = 2. * itemDim * params['samplingRate']
else:
params['min'] = 0.01
params['max'] = 0.5
params['value'] = setValueOnRange(params['value'], params['min'],
params['max'])
context = {'objects': particles, 'params': params}
context = base_wiz(request, context)
return render_to_response('wizards/wiz_filter_particles.html',
context)
def _run(self, protocol, request):
params = self._getParameters(protocol)
objs = params['input'].get()
res = validateParticles(objs)
if res is not 1:
return HttpResponse(res)
else:
particles = self._getParticles(objs)
if len(particles) == 0:
return HttpResponse("errorIterate")
xdim = getImageXdim(request, particles[0].text)
params['value'] = validateMaskRadius(params['value'], xdim, radius=1)
context = {'objects': particles,
'xdim': int(xdim/2),
'params': params}
context = base_wiz(request, context)
return render_to_response('wizards/wiz_particle_mask_radius.html', context)