- Author:
- Randall Britten <r.britten@auckland.ac.nz>
- Date:
- 2010-08-17 19:14:11+12:00
- Desc:
- Replaced use of MathML "rem" (i.e. remainder / modulus) for repeated pacing with 10 explicit pacing "pieces".
Only paces 10 times though, at spacings of 1 second, duration of 5 milliseconds, as per original MATLAB.
This commit has pacing switched off (protocol set to 0).
Have tried with pacing on (protocol set to 1), and do get sort of action potentials, but shape and sign seems wrong.
If the problem with remainder/modulus is sorted out, just revert this commit out.
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/saucerman_brunton_michailova_mcculloch_2003/rawfile/fb6bde2fe936787b55de310e9b774314098f73d2/plots.rb
# plots.rb
require 'rubygems'
require 'Tioga/FigureMaker'
require 'plot_styles.rb'
class MyPlots
include Math
include Tioga
include FigureConstants
include MyPlotStyles
def t
@figure_maker
end
def initialize
@figure_maker = FigureMaker.default
t.def_eval_function { |str| eval(str) }
t.save_dir = 'generated'
@opacity_data = nil
@image_right_margin = 0.07
@margin = 0.3
tmp = File.new('matlab_data_full.sv')
@table1_headers = tmp.readline.chomp.split(",")
#print @table1_headers
#print "\n"
@table1_length = 0
tmp.each {|x| @table1_length = @table1_length + 1; }
tmp.close
tmp = File.new('cellml_data_full.sv')
@table2_headers = tmp.readline.chomp.split(",")
#print @table2_headers
#print "\n"
@table2_length = 0
tmp.each {|x| @table2_length = @table2_length + 1; }
tmp.close
@table1 = Dtable.new(@table1_headers.length, @table1_length) #matlab
@table1.read('matlab_data_full.sv', 1)
@table2 = Dtable.new(@table2_headers.length, @table2_length) #cellml
@table2.read('cellml_data_full.sv', 1)
@names_to_compare = {
'y' => 'y', 'w' => 'w', 'x' => 'x', 'z' => 'z', 'v' => 'v', 'Cai' => 'Ca_i', 'Nai' => 'Na_i', 'Vm' => 'V_m', 'time' => 'time',
#'PKACI' => 'PKAC_I',
#'PKACII' => 'PKAC_II',
'cAMPtot' => 'cAMP_tot', 'm' => 'm'
}
@names_to_compare.each {|matlab, cellml|
t.def_figure(matlab + ' vs ' + cellml) { compare_plot(matlab, cellml, @table1, @table2) }
}
end
def compare_plot(name, n_t_c, d1, d2)
#t.landscape
t.do_box_labels("Comparison view", 'Time', nil)
#t.subplot { t.yaxis_loc = t.ylabel_side = LEFT;
# t.right_edge_type = AXIS_HIDDEN;
#print @table1_headers.index(name)
#print "\n"
#print @table2_headers.index(n_t_c)
#print "\n"
part_plot(d1.column(@table1_headers.index(name)), d1.column(@table1_headers.index('time')), name, d2.column(@table2_headers.index(n_t_c)), d2.column(@table2_headers.index('time')), n_t_c) # }
end
def part_plot(ys1, xs1, name1, ys2, xs2, name2)
t.do_box_labels(name1, 'time', '\textcolor{Black}{Values}')
t.show_plot_with_legend('legend_scale' => 1.3) {
t.show_plot('boundaries' => plot_boundaries(xs1,ys1,xs2,ys2,@margin)) {
t.line_width = t.line_width + 3
t.show_polyline(xs2, ys2, Blue, "CellML: " + name2)
t.line_width = t.line_width - 3
t.show_polyline(xs1, ys1, Red, "Matlab: " + name1);
}
}
end
def plot_boundaries(xs1,ys1,xs2,ys2,margin,ymin=nil,ymax=nil,reverse_xaxis=false,reverse_yaxis=false)
xmin = (xs1.min < xs2.min)? xs1.min: xs2.min
xmax = (xs1.max > xs2.max)? xs1.max: xs2.max
ymin = ((ys1.min < ys2.min)? ys1.min: ys2.min) if ymin == nil
ymax = ((ys1.max > ys2.max)? ys1.max: ys2.max) if ymax == nil
width = (xmax != xmin)? 1 : xmax - xmin
height = (ymax != ymin)? 1 : ymax - ymin
left_boundary = xmin - margin * width
right_boundary = xmax + margin * width
top_boundary = ymax + margin * height
bottom_boundary = ymin - margin * height
if reverse_xaxis
tmp = left_boundary; left_boundary = right_boundary; right_boundary = tmp
end
if reverse_yaxis
tmp = top_boundary; top_boundary = bottom_boundary; bottom_boundary = tmp
end
return [ left_boundary, right_boundary, top_boundary, bottom_boundary ]
end
end
MyPlots.new
