Merge branch 'apply-pointcloud' of github.com:WireCell/wire-cell-tool…

…kit into apply-pointcloud
WireCell · Jan 6, 2025 · 67250d4 · 67250d4
2 parents 5f859f1 + 426271c
commit 67250d4
Show file tree

Hide file tree

Showing 3 changed files with 216 additions and 0 deletions.
diff --git a/patrec/docs/QLBundles/Bundle.md b/patrec/docs/QLBundles/Bundle.md
@@ -0,0 +1,123 @@
+## Describe FlashTPCBundle in WCP
+
+For more detailed information, please refer to the [OpFlash documentation](https://github.com/BNLIF/wire-cell-data/blob/master/docs/FlashTPCBundle.md).
+
+## Example prototype jobs or files ...
+
+A WCP rootfile can be found @ [this link](https://www.phy.bnl.gov/xqian/talks/wire-cell-porting/nuselEval_5384_137_6852.root)
+
+Bundle information are saved in 
+```cpp
+  TTree *T_match1 = new TTree("T_match","T_match");
+  T_match1->SetDirectory(file1);
+  Int_t ncluster;
+  T_match1->Branch("tpc_cluster_id",&ncluster,"tpc_cluster_id/I");  // TPC parent cluster id (see TC tree for more explainations)
+  T_match1->Branch("flash_id",&flash_id,"flash_id/I"); // PMT Flash ID, see flash_id for more information
+  T_match1->Branch("event_type",&event_type,"event_type/I"); // this is to save the event tagger information (saved as bits in WCP)
+  Double_t flash_time;
+  T_match1->Branch("flash_time",&flash_time,"flash_time/D"); // Flash time 
+  cluster_length = 0;
+  T_match1->Branch("cluster_length",&cluster_length,"cluster_length/D"); // cluster length for main cluster
+```
+
+
+TPC Blob information are saved in 
+```cpp
+
+  // load mcell
+  TTree *TC = (TTree*)file->Get("TC");
+  std::vector<int> *cluster_id_vec = new std::vector<int>;
+  std::vector<int> *parent_cluster_id = new std::vector<int>;
+  std::vector<int> *time_slice_vec = new std::vector<int>;
+  std::vector<double> *q_vec = new std::vector<double>;
+  std::vector<double> *uq_vec = new std::vector<double>;
+  std::vector<double> *vq_vec = new std::vector<double>;
+  std::vector<double> *wq_vec = new std::vector<double>;
+  std::vector<double> *udq_vec = new std::vector<double>;
+  std::vector<double> *vdq_vec = new std::vector<double>;
+  std::vector<double> *wdq_vec = new std::vector<double>;
+
+  std::vector<int> *nwire_u_vec = new  std::vector<int>;
+  std::vector<int> *nwire_v_vec = new  std::vector<int>;
+  std::vector<int> *nwire_w_vec = new  std::vector<int>;
+  std::vector<int> *flag_u_vec = new  std::vector<int>;
+  std::vector<int> *flag_v_vec = new  std::vector<int>;
+  std::vector<int> *flag_w_vec = new  std::vector<int>;
+
+  std::vector<std::vector<int>> *wire_index_u_vec = new std::vector<std::vector<int>>;
+  std::vector<std::vector<int>> *wire_index_v_vec = new std::vector<std::vector<int>>;
+  std::vector<std::vector<int>> *wire_index_w_vec = new std::vector<std::vector<int>>;
+  std::vector<std::vector<double>> *wire_charge_u_vec = new std::vector<std::vector<double>>;
+  std::vector<std::vector<double>> *wire_charge_v_vec = new std::vector<std::vector<double>>;
+  std::vector<std::vector<double>> *wire_charge_w_vec = new std::vector<std::vector<double>>;
+  std::vector<std::vector<double>> *wire_charge_err_u_vec = new std::vector<std::vector<double>>;
+  std::vector<std::vector<double>> *wire_charge_err_v_vec = new std::vector<std::vector<double>>;
+  std::vector<std::vector<double>> *wire_charge_err_w_vec = new std::vector<std::vector<double>>;
+  
+  TC->SetBranchAddress("cluster_id",&cluster_id_vec);  // actual cluster id where this blob belons
+  TC->SetBranchAddress("parent_cluster_id",&parent_cluster_id);  // main cluster id that is used in T_match bundle
+  TC->SetBranchAddress("time_slice",&time_slice_vec);
+  TC->SetBranchAddress("q",&q_vec);
+  TC->SetBranchAddress("uq",&uq_vec);
+  TC->SetBranchAddress("vq",&vq_vec);
+  TC->SetBranchAddress("wq",&wq_vec);
+  TC->SetBranchAddress("udq",&udq_vec);
+  TC->SetBranchAddress("vdq",&vdq_vec);
+  TC->SetBranchAddress("wdq",&wdq_vec);
+  TC->SetBranchAddress("nwire_u",&nwire_u_vec);
+  TC->SetBranchAddress("nwire_v",&nwire_v_vec);
+  TC->SetBranchAddress("nwire_w",&nwire_w_vec);
+  TC->SetBranchAddress("flag_u",&flag_u_vec);
+  TC->SetBranchAddress("flag_v",&flag_v_vec);
+  TC->SetBranchAddress("flag_w",&flag_w_vec);
+  TC->SetBranchAddress("wire_index_u",&wire_index_u_vec);
+  TC->SetBranchAddress("wire_index_v",&wire_index_v_vec);
+  TC->SetBranchAddress("wire_index_w",&wire_index_w_vec);
+  TC->SetBranchAddress("wire_charge_u",&wire_charge_u_vec);
+  TC->SetBranchAddress("wire_charge_v",&wire_charge_v_vec);
+  TC->SetBranchAddress("wire_charge_w",&wire_charge_w_vec);
+  TC->SetBranchAddress("wire_charge_err_u",&wire_charge_err_u_vec);
+  TC->SetBranchAddress("wire_charge_err_v",&wire_charge_err_v_vec);
+  TC->SetBranchAddress("wire_charge_err_w",&wire_charge_err_w_vec);
+```
+
+
+Opflash are saved in 
+```cpp
+  TTree *T_flash = (TTree*)file->Get("T_flash");
+  Double_t time;
+  Int_t type;
+  Int_t flash_id;
+  Int_t temp_run_no, temp_subrun_no, temp_event_no;
+  T_flash->SetBranchAddress("runNo",&temp_run_no);
+  T_flash->SetBranchAddress("subRunNo",&temp_subrun_no);
+  T_flash->SetBranchAddress("eventNo",&temp_event_no);
+  T_flash->SetBranchAddress("time",&time);
+  T_flash->SetBranchAddress("type",&type);  // flash type, full waveform or Cosmic mode, two different types in MicroBooNE
+  T_flash->SetBranchAddress("flash_id",&flash_id);   // this id is useful for matching with TPC object in bundle
+  Double_t low_time, high_time, total_PE;
+  Double_t temp_PE[32], temp_PE_err[32];
+  std::vector<int> *fired_channels = new std::vector<int>;
+  std::vector<double> *l1_fired_time = new std::vector<double>;
+  std::vector<double> *l1_fired_pe = new std::vector<double>;
+  T_flash->SetBranchAddress("low_time",&low_time);   // start time of flash
+  T_flash->SetBranchAddress("high_time",&high_time);  // end time of flash
+  T_flash->SetBranchAddress("total_PE",&total_PE);   // total PE
+  T_flash->SetBranchAddress("PE",temp_PE);           // PE for each PMT
+  T_flash->SetBranchAddress("PE_err",temp_PE_err);   // PE_err for each PMT
+  T_flash->SetBranchAddress("fired_channels",&fired_channels);    // which channel are included in flash
+  T_flash->SetBranchAddress("l1_fired_time",&l1_fired_time);      // advanced flash info 
+  T_flash->SetBranchAddress("l1_fired_pe",&l1_fired_pe);          // advanced flash info
+```
+
+## Describe WCT version
+
+## Example WCT jobs or files ... 
+
+
+## WCP's requirements 
+
+N/A
+
+## WCT's questions to confirm functionality 
+
diff --git a/patrec/docs/QLBundles/Opflash.md b/patrec/docs/QLBundles/Opflash.md
@@ -0,0 +1,46 @@
+## Describe OpFlash in WCP
+
+For more detailed information, please refer to the [OpFlash documentation](https://github.com/BNLIF/wire-cell-data/blob/master/docs/OpFlash.md).
+
+## Example prototype jobs or files ...
+
+A WCP rootfile can be found @ [this link](https://www.phy.bnl.gov/xqian/talks/wire-cell-porting/nuselEval_5384_137_6852.root)
+
+Opflash are saved in 
+```cpp
+  TTree *T_flash = (TTree*)file->Get("T_flash");
+  Double_t time;
+  Int_t type;
+  Int_t flash_id;
+  Int_t temp_run_no, temp_subrun_no, temp_event_no;
+  T_flash->SetBranchAddress("runNo",&temp_run_no);
+  T_flash->SetBranchAddress("subRunNo",&temp_subrun_no);
+  T_flash->SetBranchAddress("eventNo",&temp_event_no);
+  T_flash->SetBranchAddress("time",&time);
+  T_flash->SetBranchAddress("type",&type);  // flash type, full waveform or Cosmic mode, two different types in MicroBooNE
+  T_flash->SetBranchAddress("flash_id",&flash_id);   // this id is useful for matching with TPC object in bundle
+  Double_t low_time, high_time, total_PE;
+  Double_t temp_PE[32], temp_PE_err[32];
+  std::vector<int> *fired_channels = new std::vector<int>;
+  std::vector<double> *l1_fired_time = new std::vector<double>;
+  std::vector<double> *l1_fired_pe = new std::vector<double>;
+  T_flash->SetBranchAddress("low_time",&low_time);   // start time of flash
+  T_flash->SetBranchAddress("high_time",&high_time);  // end time of flash
+  T_flash->SetBranchAddress("total_PE",&total_PE);   // total PE
+  T_flash->SetBranchAddress("PE",temp_PE);           // PE for each PMT
+  T_flash->SetBranchAddress("PE_err",temp_PE_err);   // PE_err for each PMT
+  T_flash->SetBranchAddress("fired_channels",&fired_channels);    // which channel are included in flash
+  T_flash->SetBranchAddress("l1_fired_time",&l1_fired_time);      // advanced flash info 
+  T_flash->SetBranchAddress("l1_fired_pe",&l1_fired_pe);          // advanced flash info
+```
+
+## Describe WCT version
+
+## Example WCT jobs or files ... 
+
+## WCP's requirements 
+
+N/A
+
+## WCT's questions to confirm functionality 
+
diff --git a/patrec/docs/porting_dictionary.md b/patrec/docs/porting_dictionary.md
@@ -0,0 +1,47 @@
+#  Between Clustering and Trajectoryand dQ/dx fitting (Current)
+
+## [Opflash](./QLBundles/Opflash.md) (WCP) vs. <span style="color:red">xxx</span> (WCT)
+
+## [FlashTPCBundle](./QLBundles/Bundle.md) (WCP) vs. <span style="color:red">xxx</span> (WCT)
+
+## [Examine_bundles](https://github.com/BNLIF/wire-cell-2dtoy/blob/master/docs/ExamineBundles.md) is a function that we need to port, [Original ExamineBundles Code](https://github.com/BNLIF/wire-cell-2dtoy/blob/a30305052fc54bbbbbd826b096066d6e8777b54d/src/ExamineBundles.cxx)
+- bundle->get_main_cluster()  (WCP) vs. <span style="color:red">xxx</span> (WCT)
+- bundle->get_other_clusters() (WCP) vs. <span style="color:red">xxx</span> (WCT)
+- bundle->get_main_cluster()->get_mcells() (WCP) vs. [loop blob](https://github.com/WireCell/wire-cell-toolkit/blob/apply-pointcloud/clus/src/clustering_separate.cxx#L1377) (WCT)
+- Create a new temp cluster, PR3DCluster *new_cluster = new PR3DCluster(cluster_id) (WCP) vs.  <span style="color:red">xxx</span> (WCT)
+- Add every blob to this cluster, new_cluster->AddCell(blob, blob->GetTimeSlice())  (WCP) vs. <span style="color:red">xxx</span> (WCT)
+- std::vector<SMGCSelection> sep_mcells = new_cluster->Examine_graph(ct_point_cloud)  [code](https://github.com/BNLIF/wire-cell-data/blob/d5748d87c3113efcb44eed237bb48a10d60002d9/src/PR3DCluster.cxx#L2332) (WCP) vs. similar to [Create_graph](https://github.com/WireCell/wire-cell-toolkit/blob/apply-pointcloud/clus/src/Facade_Cluster.cxx#L1444) (WCT)
+- [Connect_graph_overclustering_protection](https://github.com/BNLIF/wire-cell-data/blob/d5748d87c3113efcb44eed237bb48a10d60002d9/src/PR3DCluster.cxx#L1853) (WCP)  vs. not existing, but example in [connect_graph](https://github.com/WireCell/wire-cell-toolkit/blob/apply-pointcloud/clus/src/Facade_Cluster.cxx#L1444) (WCT)
+- For each sep_mcells, we will form a new set of clusters, we need to find the cluster that overlapped the most with the original main cluster, and assign it as the new MAIN CLUSTER for the new bundle (achieved through compare blobs) (WCP) vs.  <span style="color:red">xxx</span> (WCT)
+
+## [PRCluster->Create_Graph()](https://github.com/BNLIF/wire-cell/blob/master/uboone_nusel_app/apps/prod-wire-cell-matching-nusel.cxx#L817) (WCP) vs. [Create_graph](https://github.com/WireCell/wire-cell-toolkit/blob/apply-pointcloud/clus/src/Facade_Cluster.cxx#L1444) (WCT)
+
+## [cluster->get_highest_lowest_wcps()](https://github.com/BNLIF/wire-cell/blob/master/uboone_nusel_app/apps/prod-wire-cell-matching-nusel.cxx#L819C103-L819C130) (WCP) vs. [get_ghiehst_lowst_points](https://github.com/WireCell/wire-cell-toolkit/blob/apply-pointcloud/clus/src/Facade_Cluster.cxx#L1241) (WCT)
+
+<span style="color:red">WCT function only returns points, but we need the index to do the shortest path (following two functions), how to get point index from points? </span> 
+
+## [cluster->->dijkstra_shortest_paths(wcps.first)](https://github.com/BNLIF/wire-cell/blob/master/uboone_nusel_app/apps/prod-wire-cell-matching-nusel.cxx#L822C25-L823C58) (WCP) vs. [dijkstra_shortest_paths using point index](https://github.com/WireCell/wire-cell-toolkit/blob/apply-pointcloud/clus/src/Facade_Cluster.cxx#L2631) (WCT)
+
+## [cluster->cal_shortest_path(wcps.second)](https://github.com/BNLIF/wire-cell/blob/master/uboone_nusel_app/apps/prod-wire-cell-matching-nusel.cxx#L823) (WCP) vs. [cal_shortest_path using point index](https://github.com/WireCell/wire-cell-toolkit/blob/apply-pointcloud/clus/src/Facade_Cluster.cxx#L2664) (WCT)
+
+## [Improve_PR3DCluster](https://github.com/BNLIF/wire-cell-2dtoy/blob/master/docs/Improve_PR3DCluster.md) is another function that we need to port. [Original Improve_PR3DCluster Code](https://github.com/BNLIF/wire-cell-2dtoy/blob/master/src/ImprovePR3DCluster.cxx)
+
+- From existing clusters --> blobs --> time, fired channels --> get activities to be used to redo tiling (WCP) vs. <span style="color:red">xxx</span>  (WCT)
+- Access shorest path std::list<WCPointCloud<double>::WCPoint>& wcps = cluster->get_path_wcps() (WCP) vs. [index of points along the path](https://github.com/WireCell/wire-cell-toolkit/blob/apply-pointcloud/clus/src/Facade_Cluster.cxx#L2689) (WCT)
+- for a path point, use ct_point_cloud to convert the point into ch vs. time, and then judge if activities are available (WCP) vs. <span style="color:red">xxx</span>  (WCT)
+- [update the activities according to the path_point's properties](https://github.com/BNLIF/wire-cell-2dtoy/blob/master/src/ImprovePR3DCluster.cxx#L136) (WCP) vs.  <span style="color:red">xxx</span>  (WCT)
+- [redo tiling using the newly created activities](https://github.com/BNLIF/wire-cell-2dtoy/blob/master/src/ImprovePR3DCluster.cxx#L203) (WCP) vs.  <span style="color:red">xxx</span>  (WCT)
+- Compare the newly created blobs vs. the (old) existing blobs using the Overlap_fast function and judge if the blob should be kept or not, then create a new cluster from the remaining blobs (WCP) vs. <span style="color:red">xxx</span>, [overlap_fast](https://github.com/WireCell/wire-cell-toolkit/blob/apply-pointcloud/clus/src/Facade_Cluster.cxx#L513)  (WCT)
+
+## [map from old to new cluster](https://github.com/BNLIF/wire-cell/blob/master/uboone_nusel_app/apps/prod-wire-cell-matching-nusel.cxx#L831) (WCP) vs. <span style="color:red">xxx</span> (WCT)
+
+
+# Include and after Trajectory Fitting (TBD)
+
+## [ProtoSegment](https://github.com/BNLIF/wire-cell-pid/blob/537a3fd17f8a7b3cf5412594267c14c4cc1775cb/docs/protosegment.md) (WCP) vs. <span style="color:red">xxx</span> (WCT)
+
+## [WCShower](https://github.com/BNLIF/wire-cell-pid/blob/537a3fd17f8a7b3cf5412594267c14c4cc1775cb/docs/wcshower.md) (WCP) vs. <span style="color:red">xxx</span> (WCT)
+
+## [ProtoVertex](https://github.com/BNLIF/wire-cell-pid/blob/537a3fd17f8a7b3cf5412594267c14c4cc1775cb/docs/protovertex.md) (WCP) vs. <span style="color:red">xxx</span> (WCT)
+
+## [Steiner Tree](https://github.com/BNLIF/wire-cell-pid/blob/537a3fd17f8a7b3cf5412594267c14c4cc1775cb/docs/PR3DCluster_steiner.md) (WCP) vvs. <span style="color:red">xxx</span> (WCT)