added chart of nuclides example

Makefile

@@ -4,8 +4,8 @@ LDLIBS = $$(root-config --glibs)
 
 DATATABLES = ame16/mass16.txt ame16/rct1-16.txt ame16/rct2-16.txt nubase16/nubase2016.txt
 EXAMPLE_DIR = examples
-EXAMPLE_FIGURES = qec-all.pdf qec-no-estimates.pdf
-EXAMPLE_DATAFILES = qec.dat
+EXAMPLE_FIGURES = qec-all.pdf qec-no-estimates.pdf beta-delayed.pdf
+EXAMPLE_DATAFILES = qec.dat beta-delayed.dat
 EXPANSION_DIR = expansion
 EXPANSION_EXS = expand-nuchart-QEC expand-nuchart-QECp expand-nuchart-QEC2p expand-nuchart-QECa expand-nuchart-QB2n expand-nuchart-QBa
 EXS = dataprinter
@@ -16,7 +16,7 @@ EXS = dataprinter
 
 default: nuchart.root dataprinter
 
-all: default example1
+all: default example1 example2
 
 nuchart.root: treemaker.py $(addprefix $(EXPANSION_DIR)/, $(EXPANSION_EXS))
 ifeq ($(ROOTSYS), ) # source thisroot.sh if ROOTSYS is not defined
@@ -25,7 +25,6 @@ else
 	python3 treemaker.py
 endif
 	$(foreach exec, $(addprefix $(EXPANSION_DIR)/, $(EXPANSION_EXS)), ./$(exec); )
-	$(RM) -r __pycache__
 
 example1: $(EXAMPLE_DIR)/graph-example-qec.py # PHONEY target avoids multiple executions with two real targets ('qec-all.pdf', 'qec-no-estimates.pdf'), but results in 'example1' always being executed if make is run on 'all' or 'example1'
 	python3 $<
@@ -33,7 +32,15 @@ example1: $(EXAMPLE_DIR)/graph-example-qec.py # PHONEY target avoids multiple ex
 $(EXAMPLE_DIR)/graph-example-qec.py: $(EXAMPLE_DIR)/qec.dat
 
 $(EXAMPLE_DIR)/qec.dat: dataprinter nuchart.root Makefile
-	./$< nuchart.root a A Z QEC QEC_est "A <= 70" "QEC >= 0" > $@
+	./$< nuchart.root a A Z QEC QEC_est "A <= 70" "QEC > 0" > $@
+
+example2: $(EXAMPLE_DIR)/graph-example-beta-delayed.py
+	python3 $<
+
+$(EXAMPLE_DIR)/graph-example-beta-delayed.py: $(EXAMPLE_DIR)/beta-delayed.dat
+
+$(EXAMPLE_DIR)/beta-delayed.dat: dataprinter nuchart.root Makefile
+	./$< nuchart.root a Z N QECp QBn QEC2p QB2n QECa QBa QECp_est QBn_est QEC2p_est QB2n_est QECa_est QBa_est half_life_stbl "Z <= 50" "N <= 50" > $@
 
 dataprinter: dataprinter.cxx
 	$(CXX) $(CXXFLAGS) -o $@ $< $(LDLIBS)

README.md

-# TODO
+# Nuchart
+This project extracts mass excesses, various Q-values and separation energies, 
+half-lives, spins and parities of all nuclides documented in the *AME* and *NUBASE* 
+data tables of 2016.
+The extracted values are stored in a *ROOT* tree called ***nuchart.root***.
 
-* Make example with N:Z:E colour plot (see Uffe Bergmann) using matshow or pcolor or something else in matplotlib
-* Make QBa:A figure
-* Do TODO in top of *datagetter.py*
+It is possible to expand the tree with more values derived from the values already 
+present in the tree.
+For example, one could calculate Q-values of beta-delayed two-neutron emission by 
+using the Q-values of beta decay and subsequent two-neutron separation energies 
+stored in the tree.
+This specific expansion, among others, is carried out in the C++ files in the 
+***expansion*** directory.
+Those files serve as general templates for doing further user-specified expansions.
 
+As an added bonus, so to say, the ***dataprinter*** executable made in this project 
+can take any ROOT file containing a tree, and, given various parameters and 
+conditions on the parameters, produce output in easily human- and machine-interpretable 
+ASCII format containing just the parameters fulfilling the given conditions.
+This enables further manipulation/analysis of the data outside of ROOT.
 
-# DONE
+***dataprinter*** is utilised in the ***examples*** directory (via the project 
+***Makefile***), in which some figures are produced (outside of ROOT, in python) 
+as examples of the values one can extract from *Nuchart*. 
+Please see ***dataprinter.cxx*** or perhaps the ***Makefile*** for further information 
+on how to use it.
+
+
+### Prerequisites
+The prerequisites for producing ***nuchart.root*** and ***dataprinter*** are 
+
+* GNU Make
+* A fairly recent C++ compiler
+* Python 3.0 or above
+* ROOT with the PyROOT module installed
+
+In order to produce the example figures, the Python libraries NumPy and Matplotlib 
+are also required.
+
+
+### Building 
+In order to build ***nuchart.root*** and ***dataprinter*** run
+
+```shell script
+make
+```
+
+in the project's main directory.
+
+In order to also produce the example figures run
+
+```shell script
+make all
+```
+
+in the project's main directory.
+
+
+### Project status
+While the project is mostly ready to be used, there are still a few details that 
+need fixing or tweaking.
+These are listed below.
+
+#### To do
+* Do todo in top of *datagetter.py* and *graph-example-beta-delayed.py*
+
+#### Done
+* Everything prior
+* Make generic script which writes desired values from root file to a text file
+* Combine subprojects into one big project
+* Make QEC example
+* Tidied root folder up
+* Make chart of nuclides example with beta-delayed particle emission (mostly done)
 
-* Everything prior ✔
-* Make generic script which writes desired values from root file to a text file ✔
-* Combine subprojects into one big project ✔
-* Make QEC example ✔
-* Tidied root folder up ✔ 
\ No newline at end of file

examples/graph-example-beta-delayed.py

+import numpy as np
+import matplotlib.pyplot as plt
+
+# TODO: some points on the final plot are missing, and some should probably be
+#       removed based on beta stability considerations.
+#       this example still serves as a basic draft for making parameter-specific
+#       chart of nuclides figures, however.
+
+n, Z, N, QECp, QBn, QEC2p, QB2n, QECa, QBa, QECp_est, QBn_est, QEC2p_est, \
+QB2n_est, QECa_est, QBa_est, half_life_stbl = np.loadtxt('examples/beta-delayed.dat', unpack=True)
+
+filters = [(half_life_stbl == 1), ((QECp > 0) | (QBn > 0)) & ((QEC2p < 0) | (QB2n < 0)),
+           ((QEC2p > 0) | (QB2n > 0)), ((QECa > 0) | (QBa > 0))]
+labels = ['Stable', '$\mathrm{EC\\alpha \ / \ \\beta^{-}\\alpha}$',
+          '$\mathrm{ECp \ / \ \\beta^{-}n}$',
+          '$\mathrm{EC2p \ / \ \\beta^{-}2n\ (or\ ECp \ / \ \\beta^{-}n)}$']
+rectcenters = [0.5, 0.5, 0.3, 0.3]
+rectsizes = [1.0, 1.0, 0.6, 0.6]
+linewidths = [0.0, 0.0, 0.0, 0.0]
+edgecolors = ['k', 'tomato', 'limegreen', 'dodgerblue', ]
+facecolors = ['k', 'tomato', 'limegreen', 'dodgerblue', ]
+
+xmin = np.min(N)
+xmax = np.max(N)
+ymin = np.min(Z)
+ymax = np.max(Z)
+
+ax = plt.gca()
+ax.set_xticks(np.arange(xmin, xmax + 1, 10))
+ax.set_yticks(np.arange(xmin, xmax + 1, 10))
+ax.set_xticks(np.arange(xmin, xmax + 1, 5), minor=True)
+ax.set_yticks(np.arange(xmin, xmax + 1, 5), minor=True)
+ax.set_axisbelow(True)
+ax.grid(which='both', linestyle='--', alpha=0.5)
+for i in range(len(filters)):
+  plt.plot(-100, -100, marker='s', markeredgecolor=edgecolors[i],
+           markerfacecolor=facecolors[i], linestyle='', linewidth=linewidths[i], label=labels[i])
+  for x, y in zip(N[filters[i]], Z[filters[i]]):
+    ax.add_patch(plt.Rectangle((x - rectcenters[i], y  - rectcenters[i]),
+                               rectsizes[i], rectsizes[i], edgecolor=edgecolors[i],
+                               facecolor=facecolors[i], linewidth=linewidths[i]))
+ax.set_aspect('equal')
+plt.xlim(xmin - 1, xmax + 1)
+plt.ylim(xmin - 1, xmax + 1)
+plt.xlabel('$N$')
+plt.ylabel('$Z$')
+handles, labels = plt.gca().get_legend_handles_labels() # tak til Ian Hincks: https://stackoverflow.com/questions/22263807/how-is-order-of-items-in-matplotlib-legend-determined\
+order = [0, 2, 3, 1]
+plt.title('Note: Incomplete figure. See comment in python code.')
+plt.legend([handles[idx] for idx in order], [labels[idx] for idx in order])
+plt.savefig('examples/beta-delayed.pdf')
+