TMVA, preparations for multiclass handling in DNN

.gitignore

@@ -26,6 +26,12 @@ etc/allDict.h
 xcuserdata
 project.xcworkspace
 
+# Visual Code
+.vscode/*
+
+# Vim
+*.swp
+
 # Other Stuff
 *.d
 

Makefile

@@ -609,6 +609,12 @@ CXXFLAGS += $(ROOT_CXXMODULES_CXXFLAGS)
 CFLAGS   += $(ROOT_CXXMODULES_CFLAGS)
 endif
 
+ifneq ($(GCCTOOLCHAIN),)
+CXXFLAGS += --gcc-toolchain=$(GCCTOOLCHAIN)
+CFLAGS   += --gcc-toolchain=$(GCCTOOLCHAIN)
+LDFLAGS  += --gcc-toolchain=$(GCCTOOLCHAIN)
+endif
+
 
 ALLLIBS      := $(CORELIB)
 ALLMAPS      := $(COREMAP)
@@ -1075,7 +1081,6 @@ endif
 	-@(mv -f tutorials/tmva/data/toy_sigbkg_categ_varoff.root tutorials/tmva/data/toy_sigbkg_categ_varoff.root- >/dev/null 2>&1;true)
 	-@(mv -f tutorials/tmva/tmva_logo.gif tutorials/tmva/tmva_logo.gif- >/dev/null 2>&1;true)
 	-@(mv -f tutorials/spectrum/TSpectrum.root tutorials/spectrum/TSpectrum.root- >/dev/null 2>&1;true)
-	-@(mv -f test/stressRooFit_ref.root test/stressRooFit_ref.root- >/dev/null 2>&1;true)
 	@(find tutorials -name "files" -exec rm -rf {} \; >/dev/null 2>&1;true)
 	@(find tutorials -name "*.root" -exec rm -rf {} \; >/dev/null 2>&1;true)
 	@(find tutorials -name "*.ps" -exec rm -rf {} \; >/dev/null 2>&1;true)
@@ -1094,7 +1099,6 @@ endif
 	-@(mv -f tutorials/tmva/data/toy_sigbkg_categ_varoff.root- tutorials/tmva/data/toy_sigbkg_categ_varoff.root >/dev/null 2>&1;true)
 	-@(mv -f tutorials/tmva/tmva_logo.gif- tutorials/tmva/tmva_logo.gif >/dev/null 2>&1;true)
 	-@(mv -f tutorials/spectrum/TSpectrum.root- tutorials/spectrum/TSpectrum.root >/dev/null 2>&1;true)
-	-@(mv -f test/stressRooFit_ref.root- test/stressRooFit_ref.root >/dev/null 2>&1;true)
 	@rm -f $(ROOTA) $(PROOFSERVA) $(ROOTALIB)
 	@rm -f README/ChangeLog build/dummy.d
 	@rm -f etc/gitinfo.txt

README/INSTALL

@@ -33,32 +33,19 @@ Contents:
 
 To install ROOT from source you first have to get the tar file
 containing the source. This tar file can be found in the usual
-ROOT download area (ftp://root.cern.ch/root). The files are named
+ROOT download page http://root.cern.ch/downloading-root. The files are named
 root-<version>.source.tar.gz.
 
 Here's a short summary:
 
-1) Get access to the FTP area (substitute any FTP client and appropriate
-   email address below):
 
-     prompt% ftp root.cern.ch
-     User: anonymous
-     Password: <your-email-address>
+1) Get the sources
 
-2) Go to the directory, and prepare for binary transfer of files:
+     wget https://root.cern.ch/download/root_<version>.source.tar.gz
 
-     ftp> cd /root
-     ftp> bin
+2) Unpack the distribution:
 
-3) Get the sources tar-ball (substitute the appropriate version
-   number), and exit FTP client:
-
-     ftp> get root-<version>.source.tar.gz
-     ftp> bye
-
-4) Unpack the distribution:
-
-     prompt% gzip -dc root-<version>.source.tar.gz | tar -xf -
+     tar -zxf root_<version>.source.tar.gz
 
 An alternative approach is to use our public GIT repository to get
 the latest version.
@@ -81,7 +68,7 @@ You may want to compile features into ROOT, which depends on third
 party libraries. Make sure you meet all demands for additional
 features before trying to enable them (see below).
 
-The prerequisites neded for the different platforms are documented at 
+The prerequisites needed for the different platforms are documented at 
 
   https://root.cern.ch/build-prerequisites
 
@@ -97,7 +84,7 @@ Both require to set the CMAKE_INSTALL_PREFIX variable at configuration time.
 The 'fix location' requires in addition to set the 'gnuinstall' option at configuration. 
 
 
-3.1. Environment driven build:
+3.1. Location independent build:
 ------------------------------
 
 You want to install in a generic directory, depending on environment
@@ -109,7 +96,7 @@ variables ROOTSYS, LD_LIBRARY_PATH, and PATH.
         mkdir <builddir>
         cd <builddir>
         cmake ../root
-        cmake --build .  [ or simply "make -j<N>" on Unix systems ] 
+        cmake --build . [ -- -j<N> ] [ or simply "make -j<N>" on Unix systems ] 
 
    3) Add bin/ to PATH and lib/ to LD_LIBRARY_PATH. For the sh shell family do:
         . bin/thisroot.sh
@@ -120,7 +107,7 @@ variables ROOTSYS, LD_LIBRARY_PATH, and PATH.
    4) try running root:
         root
 
-3.2. Fixed locations build:
+3.2. Fixed location build:
 ---------------------------
 
 You want to install ROOT in a fixed location, not depending on
@@ -231,7 +218,7 @@ Here's the complete list:
 5. Makefile targets:
 ====================
 
-The availble Makefile top level targets are shown by doing 
+The available Makefile top level targets are shown by doing 
 
     make help
 
@@ -267,7 +254,7 @@ On how to get an open source version of OpenGL see:
 
    http://www.mesa3d.org
 
-For prebuilt versions see:
+For pre-built versions see:
 
    ftp://root.cern.ch/root/opengl/
 
@@ -403,7 +390,7 @@ containing Globus lib, include and bin. For compilation purposes
 you can pass this directory to the configure script with the option
 --with-globus-dir=<globus_dir>. An experimental path is available
 for versions 2.2.3 and 2.2.4 of the Globus Tool Kit to fix a small
-bug preventing full functionallity of the root implementation; this
+bug preventing full functionality of the root implementation; this
 is activated by setting --with-globus-patch-dir=<globus_src_dir>
 where <globus_src_dir> is the globus tool kit source,
 

README/ReleaseNotes/v608/index.md

@@ -129,6 +129,12 @@ Add a new mode for `TClass::SetCanSplit` (2) which indicates that this class and
 * Added support for AWS temporary security credentials to TS3WebFile by allowing the security token to be given.
 * Resolve an issue when space is freed in a large `ROOT` file and a TDirectory is updated and stored the lower (less than 2GB) freed portion of the file [ROOT-8055].
 
+- ##### TBufferJSON:
+   - support data members with //[fN] comment
+   - preliminary support of STL containers
+   - JSON data can be produced with TObject::SaveAs() method
+
+
 ## TTree Libraries
 
 * TChains can now be histogrammed without any C++ code, using the command line tool `rootdrawtree`. It is based on the new class `TSimpleAnalysis`.
@@ -399,6 +405,34 @@ We added a cache specifically for the fast option of the TTreeCloner to signific
 
 ## JavaScript ROOT
 
+- New geometry (TGeo) classes support:
+   - browsing  through volumes hieararchy
+   - changing visibility flags
+   - drawing of selected volumes
+   - support of large (~10M volumes) models, only most significant volumes are shown
+   - one could activate several clip planes (only with WebGL)
+   - interaction with object browser to change visibility flags or focus on selected volume
+   - support of floating browser for TGeo objects
+   - intensive use of HTML Worker to offload computation tasks and keep interactivity   
+   - enable more details when changing camera position/zoom
+- Improvements in histograms 3D drawing
+   - all lego options: lego1..lego4, combined with 'fb', 'bb', '0' or 'z'
+   - support axis labels on lego plots
+   - support lego plots for TH1
+- Significant (up to factor 10) performance improvement in 3D-graphics
+- Implement ROOT6-like color palettes
+- Support non-equidistant bins for TH1/TH2 objects.
+- Improve TF1 drawing - support exp function in TFormula, fix errors with logx scale, enable zoom-in, (re)calculate function points when zooming
+- Introduce many context menus for improving interactivity
+- Implement col0 and col0z draw option for TH2 histograms, similar to ROOT6
+- Implement box and hbox draw options for TH1 class
+- Significant (factor 4) I/O performance improvement
+- New 'flex' layout:
+   - create frames like in Multi Document Interface
+   - one could move/resize/minimize/maximize such frames
+
+For more details, like the complete change log, the documentation, and very detailed examples, see the [JSROOT home page](https://root.cern.ch/js) and the [JSROOT project github page](https://github.com/linev/jsroot) 
+
 
 ## Tutorials
 * New tutorial `treegetval.C` illustrating how to retrieve  `TTree` variables in arrays.

README/ReleaseNotes/v610/index.md

@@ -53,10 +53,29 @@ The following interfaces have been removed, after deprecation in v6.08.
 
 
 ## 2D Graphics Libraries
-
+- If one used "col2" or "colz2", the value of `TH1::fMaximum` got modified.
+  This deviated from the behavior of "col" or "colz". This is now fixed as
+  requested [here](https://sft.its.cern.ch/jira/browse/ROOT-8389).
+- When the option SAME (or "SAMES") is used with the option COL, the boxes' color
+  are computing taking the previous plots into account. The range along the Z axis
+  is imposed by the first plot (the one without option SAME); therefore the order
+  in which the plots are done is relevant.
+- With option BOX on 2D histos with negative content:
+    - do not draw the empty bins as requested [here](https://sft.its.cern.ch/jira/browse/ROOT-8385).
+    - fix the issue mentioned [here](https://sft.its.cern.ch/jira/browse/ROOT-*402).
+- When several histogram were drawn on top of each other with the option
+  `BOX SAME` and if the log scale along Z was on, the plot showed only the
+  first histogram. This can be reproduce by using the documentation example
+  illustrating `BOX SAME`and turning the canvas into log scale along Z.
+- In TLatex: Do not paint the text when the text size is <= 0. This fixes
+  the problem mentioned [here](https://sft.its.cern.ch/jira/browse/ROOT-8305)
+- From: Sergey Linev: In `TPad::SaveAs` method json file extension is now handled
 
 ## 3D Graphics Libraries
-
+- In `TMarker3DBox::PaintH3` the boxes' sizes was not correct.
+- The option `BOX`and `GLBOX` now draw boxes with a volume proportional to the
+  bin content to be conform to the 2D case where the surface of the boxes is
+  proportional to the bin content.
 
 ## Geometry Libraries
 

bindings/pyroot/JsMVA/Factory.py

@@ -14,7 +14,6 @@
 from threading import Thread
 import time
 from string import Template
-import numpy as np
 
 
 # This class contains the necessary HTML, JavaScript, CSS codes (templates)
@@ -762,15 +761,15 @@ def __bookDNN(optString):
 # @param net DNN in JSON format
 # @param selectedLayers the selected layers
 def CreateWeightHist(net, selectedLayers):
-    firstLayer=int(selectedLayers.split("->")[0])
+    firstLayer = int(selectedLayers.split("->")[0])
     weights = net["layers"][firstLayer]["Weights"]
     n1 = int(weights["row"])
     n2 = int(weights["cols"])
-    tmatrix = np.reshape(weights["data"], (n1, n2))
     m = ROOT.TMatrixD(n1, n2+1)
+    vec = weights["data"]
     for i in xrange(n1):
         for j in xrange(n2):
-            m[i][j]  = tmatrix[i][j]
+            m[i][j] = vec[j+n2*i]
     bvec = net["layers"][firstLayer]["Biases"]["data"]
     if n1!=len(bvec):
         print("Something wrong.. Number of bias weights not equal with the neuron number ("+str(n1)+"!="+str(len(bvec))+")")