@@ -1,7 +1,7 @@

 Package: CytoML

 Type: Package

 Title: A GatingML Interface for Cross Platform Cytometry Data Sharing

-Version: 2.3.4

+Version: 2.3.5

 Date: 2016-04-15

 Author: Mike Jiang, Jake Wagner

 Maintainer: Mike Jiang <wjiang2@fhcrc.org>

@@ -11,7 +11,7 @@ License: file LICENSE

 License_restricts_use: yes

 LazyData: TRUE

 Imports:

-    cytolib(>= 2.3.9),

+    cytolib(>= 2.3.10),

     flowCore (>= 1.99.10),

     flowWorkspace (>= 4.1.8),

     openCyto (>= 1.99.2),

@@ -442,26 +442,33 @@ public:

 				gh->transform_gate();

-				// add the scaleTrans for the implicit time transformation based on $TIMESTEP in FCS

-				// This reproduces some of the logic of cytolib::CytoFrame::scale_time_channel

 				string time_channel = "time";

-				auto idx = frptr->get_col_idx(time_channel, ColType::channel);

-				if(idx >= 0){

-					EVENT_DATA_TYPE timestep = frptr->get_time_step(time_channel);

-					if(g_loglevel>=GATING_HIERARCHY_LEVEL)

-					PRINT("Adding transformation to multiply "+time_channel+" by :"+ to_string(timestep) + "\n");

-

-					shared_ptr<scaleTrans> timeTrans(new scaleTrans(timestep));

-

-					timeTrans->setGateOnlyFlag(false);

-					timeTrans->setName(time_channel);

-					timeTrans->setChannel(time_channel);

-					timeTrans->setType(SCALE);

-

-					trans_local lTrans = gh->getLocalTrans();

-					lTrans.addTrans(time_channel, timeTrans);

-					gh->addTransMap(lTrans.getTransMap());

+				if (!gh->getLocalTrans().getTran(

+				    time_channel))  // only use timestep when time transform is not

+				  // present

+				{

+				  // add the cytolib::scaleTrans for the implicit time transformation

+				  // based on $TIMESTEP in FCS This reproduces some of the logic of

+				  // cytolib::CytoFrame::scale_time_channel

+				  auto idx = frptr->get_col_idx(time_channel, ColType::channel);

+  				if(idx >= 0){

+  					EVENT_DATA_TYPE timestep = frptr->get_time_step(time_channel);

+  					if(g_loglevel>=GATING_HIERARCHY_LEVEL)

+  					PRINT("Adding transformation to multiply "+time_channel+" by :"+ to_string(timestep) + "\n");

+  

+  					shared_ptr<scaleTrans> timeTrans(new scaleTrans(timestep));

+  

+  					timeTrans->setGateOnlyFlag(false);

+  					timeTrans->setName(time_channel);

+  					timeTrans->setChannel(time_channel);

+  					timeTrans->setType(SCALE);

+  

+  					trans_local lTrans = gh->getLocalTrans();

+  					lTrans.addTrans(time_channel, timeTrans);

+  					gh->addTransMap(lTrans.getTransMap());

+  				}

 				}

+				

 				gh->shift_gate();

 				gh->transform_data(fr);

 				gh->extendGate(fr, config_const.gate_extend_trigger_value);

@@ -849,18 +849,40 @@ public:

 				//only meaningful for scaling ellipsoidGate from 256 back to raw

 				if(g_loglevel>=GATING_SET_LEVEL)

 					COUT<<"flin func:"<<pname<<endl;

-//				double minRange=atof(transNode.getProperty("minRange").c_str());

-				double maxRange=atof(transNode.getProperty("maxRange").c_str());

-				if(maxRange==0)

-					maxRange = 1;

-

-				shared_ptr<scaleTrans> curTran(new scaleTrans(maxRange,maxRange));

-

-				curTran->setName("");

-				curTran->setChannel(pname);

-

-				curTp[curTran->getChannel()]=curTran;

-

+				auto gain = transNode.getProperty("gain");

+				

+				if (boost::to_lower_copy(pname) == "time") {

+				  if (gain !=

+          "1") {  // cytolib::EVENT_DATA_TYPEmust skip adding it when gain == 1 since $TIMESTEP should

+				    // be used for scaling time channel in that case

+				    

+				    auto scale_factor = stof(gain);

+				    

+				    std::shared_ptr<cytolib::scaleTrans> curTran(

+				        new cytolib::scaleTrans(scale_factor));

+				    curTran->setName("");

+				    curTran->setChannel(pname);

+				    curTran->setGateOnlyFlag(false);

+				    curTran->setDataOnlyFlag(true);

+				    curTp[pname] = curTran;

+				  }

+				} else {  // need it for ellipsoid gate rescaling

+				  // and only meaningful for scaling cytolib::ellipsoidGate from 256 back

+				  // minRange=atof(transNode.getProperty("minRange").c_str());to raw

+				  cytolib::EVENT_DATA_TYPE maxRange =

+				    atof(transNode.getProperty("transforms:maxRange").c_str());

+				  if (maxRange == 0) maxRange = 1;

+				  

+				  std::shared_ptr<cytolib::scaleTrans> curTran(

+				      new cytolib::scaleTrans(maxRange, maxRange));

+				  

+				  curTran->setName("");

+				  curTran->setChannel(pname);

+				  curTran->setGateOnlyFlag(true);

+				  curTran->setDataOnlyFlag(false);

+				  curTp[pname] = curTran;

+				}

+				

 			}else if(transType.compare("log")==0){

 				if(g_loglevel>=GATING_SET_LEVEL)

 					COUT<<"flog func:"<<pname<<endl;