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): 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 = 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)