Merge branch 'develop' of https://github.com/ofloveandhate/bertini_real…

… into develop

m4/ax_boost_timer.m4

@@ -66,9 +66,9 @@ AC_DEFUN([AX_BOOST_TIMER],
 		AC_CACHE_CHECK(whether the Boost::Timer library is available,
 			ax_cv_boost_timer,
 			[AC_LANG_PUSH([C++])
-			AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[@%:@include <boost/timer.hpp>
+			AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[@%:@include <boost/timer/timer.hpp>
 			]],
-			[[boost::timer r(); return 0;]])],
+			[[boost::timer::auto_cpu_timer r(); return 0;]])],
 			ax_cv_boost_timer=yes, ax_cv_boost_timer=no)
 			AC_LANG_POP([C++])
 		])

python/example/plot_surface_colored_by_piece.py

@@ -0,0 +1,36 @@
+# an example of splitting an algebraic surface into pieces separated by singularities, 
+# and plotting each with a solid color
+
+import bertini_real as br
+import matplotlib.pyplot as plt
+
+import pathlib
+
+pkl_files = list(pathlib.Path('.').glob('*.pkl'))
+
+if not pkl_files:
+	print('found no pickled data, so trying to gather_and_save')
+	br.data.gather_and_save()
+
+
+decomposition = br.data.read_most_recent()
+print(f'done reading data')
+
+
+pieces = decomposition.separate_into_nonsingular_pieces()
+print(f'separated into {len(pieces)} pieces')
+
+
+# make a plotter object
+plotter = br.plot.Plotter()
+
+# set some options
+plotter.options.render.vertices = False
+plotter.options.render.surface_raw = False
+
+plotter.options.style.colormap = plt.cm.viridis
+
+# plot it!
+plotter.plot(pieces)
+
+

python/example/surface_separate_and_save_raw_and_smooth.py

@@ -0,0 +1,29 @@
+import bertini_real as br
+import matplotlib.pyplot as plt
+
+import pathlib
+
+pkl_files = list(pathlib.Path('.').glob('*.pkl'))
+
+if not pkl_files:
+	print('found no pickled data, so trying to gather_and_save')
+	br.data.gather_and_save()
+
+
+
+thickness = 0.01 # this is in object dimensions.  
+
+decomposition = br.data.read_most_recent()
+
+print(f'done reading data')
+
+pieces = decomposition.separate_into_nonsingular_pieces()
+print(f'separated into {len(pieces)} pieces')
+
+
+
+
+
+for p in pieces:
+	p.solidify_smooth(distance=thickness)
+	p.solidify_raw(distance=thickness)

test/surface/dingdong/demo.py

@@ -0,0 +1,15 @@
+import bertini_real as br
+
+surface = br.data.read_most_recent()
+
+pieces = surface.separate_into_nonsingular_pieces()
+
+surface.write_piece_data()
+
+br.surface.copy_all_scad_files_here()
+
+for p in pieces:
+	p.export_smooth()
+
+
+br.plot.plot(pieces)

test/surface/nordstrands_weird/assemble.py

@@ -0,0 +1,43 @@
+import bertini_real as br
+import matplotlib.pyplot as plt
+import dill
+# br.data.gather_and_save()
+
+surf = br.data.read_most_recent()
+
+# fileObject = open('BRdata3.pkl', 'rb')
+# surf = dill.load(fileObject)
+# fileObject.close()
+
+surf.write_piece_data()
+
+pieces = surf.separate_into_nonsingular_pieces()
+
+
+br.surface.copy_all_scad_files_here()
+# 
+# plotter = br.plot.plot(pieces)
+
+# plotter = br.plot.plot(pieces[0])
+
+# surf.export_raw()
+# surf.export_smooth()
+
+for p in pieces:
+	# p.export_smooth()
+	p.solidify_smooth(0.02)
+
+	print(p.point_singularities() )
+# 	p.solidify_raw(0.02)
+
+
+
+plotter = br.plot.Plotter()
+plotter.options.render.vertices = False
+plotter.options.render.surface_raw = False
+
+plotter.options.style.colormap = plt.cm.nipy_spectral
+
+# plotter.plot(decomposition)
+plotter.plot(pieces)
+

test/surface/octdong/assemble.py

@@ -0,0 +1,26 @@
+import bertini_real as br
+import matplotlib.pyplot as plt
+import dill
+
+def plot_pieces(pieces):
+	plotter = br.plot.Plotter()
+	plotter.options.render.vertices = False
+	plotter.options.render.surface_raw = False
+
+	plotter.options.style.colormap = plt.cm.nipy_spectral
+
+	plotter.plot(pieces)
+
+
+br.data.gather_and_save()
+
+surf = br.data.read_most_recent()
+surf.write_piece_data()
+pieces = surf.separate_into_nonsingular_pieces()
+br.surface.copy_all_scad_files_here()
+
+for p in pieces:
+	p.export_smooth()
+
+plot_pieces(pieces)
+