[Avida-SVN] r1061 - in development/source: actions cpu targets/avida-viewer tools utils/process_map
ofria at myxo.css.msu.edu
ofria at myxo.css.msu.edu
Wed Oct 25 12:28:18 PDT 2006
Author: ofria
Date: 2006-10-25 15:28:17 -0400 (Wed, 25 Oct 2006)
New Revision: 1061
Added:
development/source/utils/process_map/Makefile
development/source/utils/process_map/process_map.cc
Modified:
development/source/actions/PrintActions.cc
development/source/cpu/cHardwareCPU.cc
development/source/targets/avida-viewer/cView.cc
development/source/targets/avida-viewer/cZoomScreen.cc
development/source/tools/cProbSchedule.cc
development/source/tools/cStringUtil.cc
development/source/tools/tDictionary.h
development/source/tools/tList.h
Log:
Added in source/utils/process_map/ with a new tool to help generate movies of
an Avida grid over time. To compile, simply run 'make' in the directory (we
should eventually tie this into our regular build system). More directions
forthcoming.
Fixed a bug in the Probabilistic scheduler where it crashed if all of the
organisms in the population die out.
Fixed a bug in the DumpGenotypeIDGrid where it was swapping the rows and
columns in the grid (this is hard to notice with square grids...)
Fixed a bug in the zoom mode of the text viewer where Avida would crash if
zoomed into an empty cell.
Fixed a bug in cView in the text viewer where Avida would sometime crash
when unpausing.
Modified: development/source/actions/PrintActions.cc
===================================================================
--- development/source/actions/PrintActions.cc 2006-10-24 16:45:50 UTC (rev 1060)
+++ development/source/actions/PrintActions.cc 2006-10-25 19:28:17 UTC (rev 1061)
@@ -1245,8 +1245,8 @@
if (filename == "") filename.Set("grid_genotype_id.%d.dat", m_world->GetStats().GetUpdate());
ofstream& fp = m_world->GetDataFileOFStream(filename);
- for (int i = 0; i < m_world->GetPopulation().GetWorldX(); i++) {
- for (int j = 0; j < m_world->GetPopulation().GetWorldY(); j++) {
+ for (int j = 0; j < m_world->GetPopulation().GetWorldY(); j++) {
+ for (int i = 0; i < m_world->GetPopulation().GetWorldX(); i++) {
cPopulationCell& cell = m_world->GetPopulation().GetCell(j * m_world->GetPopulation().GetWorldX() + i);
int id = (cell.IsOccupied()) ? cell.GetOrganism()->GetGenotype()->GetID() : -1;
fp << id << " ";
Modified: development/source/cpu/cHardwareCPU.cc
===================================================================
--- development/source/cpu/cHardwareCPU.cc 2006-10-24 16:45:50 UTC (rev 1060)
+++ development/source/cpu/cHardwareCPU.cc 2006-10-25 19:28:17 UTC (rev 1061)
@@ -1229,9 +1229,10 @@
m_advance_ip = false;
}
- // Activate the child, and do more work if the parent lives through the
- // birth.
+ // Activate the child
bool parent_alive = organism->ActivateDivide(ctx);
+
+ // Do more work if the parent lives through the birth of the offspring
if (parent_alive) {
if (m_world->GetConfig().DIVIDE_METHOD.Get() == DIVIDE_METHOD_SPLIT) Reset();
}
Modified: development/source/targets/avida-viewer/cView.cc
===================================================================
--- development/source/targets/avida-viewer/cView.cc 2006-10-24 16:45:50 UTC (rev 1060)
+++ development/source/targets/avida-viewer/cView.cc 2006-10-25 19:28:17 UTC (rev 1061)
@@ -282,7 +282,9 @@
if (info.GetPauseLevel() != PAUSE_OFF) {
info.DisEngageStepMode();
info.SetPauseLevel(PAUSE_OFF);
- info.GetActiveCell()->GetOrganism()->GetPhenotype().SetFault("");
+ if (info.GetActiveCell()->IsOccupied()) {
+ info.GetActiveCell()->GetOrganism()->GetPhenotype().SetFault("");
+ }
}
// Otherwise, turn on the pause.
Modified: development/source/targets/avida-viewer/cZoomScreen.cc
===================================================================
--- development/source/targets/avida-viewer/cZoomScreen.cc 2006-10-24 16:45:50 UTC (rev 1060)
+++ development/source/targets/avida-viewer/cZoomScreen.cc 2006-10-25 19:28:17 UTC (rev 1061)
@@ -1474,7 +1474,10 @@
void cZoomScreen::DoInput(int in_char)
{
- cHardwareBase& hardware = info.GetActiveCell()->GetOrganism()->GetHardware();
+ cHardwareBase * hardware = NULL;
+ if (info.GetActiveCell()->IsOccupied()) {
+ hardware = &(info.GetActiveCell()->GetOrganism()->GetHardware());
+ }
// First do the Mode specific io...
@@ -1483,19 +1486,16 @@
if (mode == ZOOM_MODE_GENOTYPE && DoInputGenotype(in_char)) return;
int num_threads = 0;
- if (info.GetActiveCell()->GetOrganism() != NULL) {
- num_threads = hardware.GetNumThreads();
- }
+ if (hardware != NULL) num_threads = hardware->GetNumThreads();
+
switch(in_char) {
case 't':
case 'T':
- if(num_threads>1)
- {
+ if (num_threads > 1) {
memory_offset=0;
++cur_view_thread%=num_threads;
- if(info.GetConfig().HARDWARE_TYPE.Get() != HARDWARE_TYPE_CPU_ORIGINAL)
- {
- cur_mem_space = hardware.IP(cur_view_thread).GetMemSpace();
+ if(info.GetConfig().HARDWARE_TYPE.Get() != HARDWARE_TYPE_CPU_ORIGINAL){
+ cur_mem_space = hardware->IP(cur_view_thread).GetMemSpace();
}
Update();
}
@@ -1576,8 +1576,7 @@
}
}
else if (active_section == ZOOM_SECTION_MEMORY) {
- if(info.GetConfig().HARDWARE_TYPE.Get() != HARDWARE_TYPE_CPU_ORIGINAL)
- {
+ if(info.GetConfig().HARDWARE_TYPE.Get() != HARDWARE_TYPE_CPU_ORIGINAL){
cur_mem_space++;
// @DMB - Should handle the extensibility of SMT Memory Spaces
cur_mem_space %= 1;
@@ -1596,7 +1595,7 @@
}
}
else if (active_section == ZOOM_SECTION_MEMORY) {
- if(info.GetConfig().HARDWARE_TYPE.Get() != HARDWARE_TYPE_CPU_ORIGINAL) {
+ if(info.GetConfig().HARDWARE_TYPE.Get() != HARDWARE_TYPE_CPU_ORIGINAL){
cur_mem_space--;
// @DMB - Should handle the extensibility of SMT Memory Spaces
if (cur_mem_space < 0) cur_mem_space = 0;
Modified: development/source/tools/cProbSchedule.cc
===================================================================
--- development/source/tools/cProbSchedule.cc 2006-10-24 16:45:50 UTC (rev 1060)
+++ development/source/tools/cProbSchedule.cc 2006-10-25 19:28:17 UTC (rev 1061)
@@ -17,7 +17,7 @@
int cProbSchedule::GetNextID()
{
- assert(chart.GetTotalWeight() > 0);
+ if (chart.GetTotalWeight() == 0) return -1;
const double position = m_rng.GetDouble(chart.GetTotalWeight());
return chart.FindPosition(position);
}
Modified: development/source/tools/cStringUtil.cc
===================================================================
--- development/source/tools/cStringUtil.cc 2006-10-24 16:45:50 UTC (rev 1060)
+++ development/source/tools/cStringUtil.cc 2006-10-25 19:28:17 UTC (rev 1061)
@@ -267,28 +267,28 @@
return (int) dist_matrix(size2, size1);
}
-const cString & cStringUtil::Convert(const cString & in_string,
- const cString & out_string)
+const cString & cStringUtil::Convert(const cString& in_string,
+ const cString& out_string)
{
return in_string;
}
-bool cStringUtil::Convert(const cString & in_string, bool type_bool)
+bool cStringUtil::Convert(const cString& in_string, bool type_bool)
{
return (in_string.AsInt() != 0);
}
-int cStringUtil::Convert(const cString & in_string, int type_int)
+int cStringUtil::Convert(const cString& in_string, int type_int)
{
return in_string.AsInt();
}
-double cStringUtil::Convert(const cString & in_string, double type_double)
+double cStringUtil::Convert(const cString& in_string, double type_double)
{
return in_string.AsDouble();
}
-cString cStringUtil::Convert(const cString & in_string)
+cString cStringUtil::Convert(const cString& in_string)
{
return in_string;
}
Modified: development/source/tools/tDictionary.h
===================================================================
--- development/source/tools/tDictionary.h 2006-10-24 16:45:50 UTC (rev 1060)
+++ development/source/tools/tDictionary.h 2006-10-25 19:28:17 UTC (rev 1061)
@@ -57,10 +57,22 @@
bool Find(const cString& name, T& out_data) const { return m_hash.Find(name, out_data); }
T Remove(const cString& name) { return m_hash.Remove(name); }
void SetHash(int _hash) { m_hash.SetTableSize(_hash); }
- void AsLists(tList<cString>& name_list, tList<T>& value_list) const
- {
+ void AsLists(tList<cString>& name_list, tList<T>& value_list) const {
m_hash.AsLists(name_list, value_list);
}
+
+ // This function will take an input string and load its value into the
+ // dictionary; it will only work for types that cStringUtil can convert to.
+ void Load(cString load_string, char assign='=') {
+ // Break the string into two based on the assignment character.
+ cString key(load_string.Pop(assign));
+
+ // Convert the value to the correct type.
+ T value;
+ value = cStringUtil::Convert(load_string, value);
+
+ SetValue(key, value);
+ }
// This function has no direct implementation in tHashTable
// Grabs key/value lists, and processes the keys.
Modified: development/source/tools/tList.h
===================================================================
--- development/source/tools/tList.h 2006-10-24 16:45:50 UTC (rev 1060)
+++ development/source/tools/tList.h 2006-10-25 19:28:17 UTC (rev 1061)
@@ -226,7 +226,7 @@
}
public:
- T * Pop() { return RemoveNode(root.next); }
+ T * Pop() { return RemoveNode(root.next); }
T * PopRear() { return RemoveNode(root.prev); }
void Clear() { while (size > 0) Pop(); }
Added: development/source/utils/process_map/Makefile
===================================================================
--- development/source/utils/process_map/Makefile 2006-10-24 16:45:50 UTC (rev 1060)
+++ development/source/utils/process_map/Makefile 2006-10-25 19:28:17 UTC (rev 1061)
@@ -0,0 +1,74 @@
+### Compile and Link Command & Options #######################################
+
+CXX = g++
+FLAGS = -Wall -pedantic -g -ffast-math -DNDEBUG #-Winline
+
+# Include directories [May need to adjust. See your system administrator]
+#INCDIR = -I/usr/include/g++/
+INCDIR =
+
+# Libraries to link
+LDLIBS =
+
+### Shouldn't need to change below ###########################################
+
+# Compile flags
+CXXFLAGS= $(FLAGS)
+
+# Flags durring linking
+LDFLAGS = $(CXXFLAGS)
+
+
+### Different Builds #########################################################
+
+# executable make
+TARGET = process_map
+
+default: $(TARGET)
+
+### List Source Files in the Project #########################################
+SRC = process_map.cc ../../tools/cFile.cc \
+ ../../tools/cInitFile.cc ../../tools/cString.cc \
+ ../../tools/cStringList.cc ../../tools/cStringIterator.cc \
+ ../../tools/cRandom.cc
+
+### List Object Files (for each source file there is a object file) ###########
+OBJ = $(SRC:.cc=.o)
+
+
+### General Make Commands #####################################################
+
+CCC = $(CXX) # Compatibility
+
+$(TARGET): $(OBJ)
+ ### LINKING ###
+ $(CXX) $(LDFLAGS) $(INCDIR) $(OBJ) $(LDLIBS) -o $(TARGET)
+ ### FINISHED MAKING "$(TARGET)" ###
+
+.cc.o:
+ $(CXX) $(CXXFLAGS) $(INCDIR) -c $< -o $*.o
+
+clean:
+ ### REMOVING OBJECT FILES AND EXECUTEABLE ###
+ rm -f core $(TARGET) $(OBJ)
+
+new: clean $(TARGET)
+
+install:
+ configure
+ $(MAKE) new
+
+
+### Dependency Generation #####################################################
+
+#depend: $(SRC)
+# makedepend -- $(CXXFLAGS) -- $(INCDIR) $(SRC)
+
+depend: local_depend
+
+local_depend: $(SRC)
+ makedepend -Y -- $(CXXFLAGS) -- $(INCDIR) $(SRC)
+
+### Release Packageing ########################################################
+# DO NOT DELETE
+
Added: development/source/utils/process_map/process_map.cc
===================================================================
--- development/source/utils/process_map/process_map.cc 2006-10-24 16:45:50 UTC (rev 1060)
+++ development/source/utils/process_map/process_map.cc 2006-10-25 19:28:17 UTC (rev 1061)
@@ -0,0 +1,350 @@
+// This program take in a series of map dumps and reprocesses them into a
+// simpler format where colors get pre-chosen.
+
+#include <iostream>
+#include <fstream>
+
+#include "../../tools/tMatrix.h"
+#include "../../tools/tDictionary.h"
+
+
+#include "../../tools/cString.h"
+#include "../../tools/cFile.h"
+#include "../../tools/cInitFile.h"
+#include "../../tools/cRandom.h"
+
+using namespace std;
+
+// A dictionary of input settings.
+tDictionary<int> value_dict;
+tDictionary<cString> desc_dict;
+
+void AddSetting(const cString & key, int value, const cString & desc) {
+ value_dict.Add(key, value);
+ desc_dict.Add(key, desc);
+}
+
+int main(int argc, char * argv[])
+{
+ // Setup the default settings...
+ AddSetting("start", 0, "Start of frame window (exclusive; start is skipped)");
+ AddSetting("step", 100, "Number of updates to skip between frames.");
+ AddSetting("stop", 10000, "Last update to frame (inclusive)");
+ AddSetting("seed", 1, "Random number seed");
+ AddSetting("num_demes", 0, "How many demes in the population (0=none)");
+ AddSetting("num_colors", 65, "Number of colors in map (Use 43 for bright colors)");
+ AddSetting("threshold1", 10, "Abundance threshold for color shift.");
+ AddSetting("threshold2", 100, "Abundance threshold for assigning unique color");
+
+ if (argc == 1) {
+ cerr << endl;
+ cerr << "This program will load in Avida-generated files with the naming scheme" << endl;
+ cerr << "grid_genotype_id.####.dat (where #### = update output)." << endl;
+ cerr << endl;
+ cerr << "Format: " << argv[0] << " {settings...}" << endl;
+ cerr << "Example: " << argv[0] << " start=1000 step=100 stop=2000" << endl;
+ cerr << endl;
+ cerr << "Available settings: " << endl;
+
+ tList<cString> setting_list;
+ tList<int> value_list;
+ value_dict.AsLists(setting_list, value_list);
+
+ while(setting_list.GetSize()) {
+ cString setting = *(setting_list.Pop());
+ int value = *(value_list.Pop());
+ cString desc;
+ desc_dict.Find(setting, desc);
+ cerr << " " << setting << " (default = " << value << ") : "
+ << desc << endl;
+ }
+
+ cerr << endl;
+ cerr << "To run with all defaults, type: " << argv[0] << " go" << endl;
+ cerr << endl;
+ return 1;
+ }
+
+ cerr << "Initializing..." << endl;
+
+ // Load in the command line arguments.
+ for (int arg_num = 1; arg_num < argc; arg_num++) {
+ cString cur_arg(argv[arg_num]);
+
+ // Ignore a "go" argument...
+ if (cur_arg == "go") continue;
+
+ // Otherwise, process the argument.
+ cString key(cur_arg.Pop('='));
+
+ if (value_dict.HasEntry(key) == false) {
+ cerr << "ERROR: Unknown keyword '" << key << "'." << endl;
+ exit(1);
+ }
+
+ if (cur_arg.GetSize() == 0 || cur_arg.IsNumeric() == false) {
+ cerr << "ERROR: Keyword '" << key << "' must be set to numeric value."
+ << endl;
+ exit(1);
+ }
+
+ int value = cur_arg.AsInt();
+ value_dict.SetValue(key, value);
+ cerr << "Setting '" << key << "' to " << value << "." << endl;
+ }
+
+ // Load in the status of all arguments.
+ int UD_start, UD_step, UD_stop, seed, num_demes;
+ int num_colors, threshold1, threshold2;
+
+ value_dict.Find("start", UD_start);
+ value_dict.Find("step", UD_step);
+ value_dict.Find("stop", UD_stop);
+ value_dict.Find("seed", seed);
+ value_dict.Find("num_demes", num_demes);
+ value_dict.Find("num_colors", num_colors);
+ value_dict.Find("threshold1", threshold1);
+ value_dict.Find("threshold2", threshold2);
+
+ // Setup variables based on command-line arguments.
+ cRandom random(seed);
+ const int num_files = (UD_stop - UD_start)/ UD_step;
+
+ cerr << "A total of " << num_files << " files needed." << endl;
+
+ // Load in the first file to get some basic information about the grids.
+ cString filename;
+ filename.Set("grid_genotype_id.%d.dat", (UD_step + UD_start));
+ cInitFile file1(filename);
+ file1.Load();
+ file1.Close();
+
+ const int height = file1.GetNumLines();
+ const int width = file1.GetLine(0).CountNumWords();
+ const int num_cells = height * width;
+
+ const int deme_height = (num_demes > 1) ? (height / num_demes) : height;
+ const int deme_size = deme_height * width;
+
+ // Do a brute-force square root.
+ int num_deme_cols = 1;
+ if (num_demes > 1) {
+ while (num_deme_cols * num_deme_cols < num_demes) num_deme_cols++;
+ }
+ int num_deme_rows = num_demes / num_deme_cols;
+
+ // Print out some basic info...
+ cerr << "World size = " << width << " x " << height << endl;
+ if (num_demes > 1) {
+ cerr << "Planning on " << num_demes << " demes, organized in a "
+ << num_deme_cols << "x" << num_deme_rows << " grid."
+ << endl;
+ }
+
+ // Build a matrix that can hold all of the information from all of the files.
+ tMatrix<int> grid_matrix(num_files, num_cells);
+
+ // Loop through all files, loading them in.
+ int update = UD_start;
+ int max_id = -1;
+ const int file_step = num_files / 50;
+ cerr << "LOADING FILES....................................." << endl;
+ for (int file_id = 0; file_id < num_files; file_id++) {
+ // Keep a status bar printing on the screen.
+ if (file_id % file_step == 0) {
+ cerr << '#';
+ cerr.flush();
+ }
+
+ // Generate the filename...
+ update += UD_step;
+ filename.Set("grid_genotype_id.%d.dat", update);
+
+ cInitFile file(filename);
+ file.Load();
+
+ // Load in this file...
+ cString cur_line;
+ for (int pos = 0; pos < num_cells; pos++) {
+ if (cur_line.GetSize() == 0) cur_line = file.GetNextLine();
+ const int cur_id = cur_line.PopWord().AsInt();
+ if (cur_id > max_id) max_id = cur_id;
+ grid_matrix(file_id, pos) = cur_id;
+ }
+
+ file.Close();
+ }
+ cerr << endl << "LOADING COMPLETE" << endl;
+ cerr << "Max ID = " << max_id << endl;
+
+ // Do a second pass and collect some extra statistics.
+ tArray<int> org_count(max_id+1);
+ org_count.SetAll(0);
+ cerr << "PROCESSING COUNTS................................." << endl;
+ for (int frame_id = 0; frame_id < num_files; frame_id++) {
+ // Keep a status bar printing on the screen.
+ if (frame_id % file_step == 0) {
+ cerr << '#';
+ cerr.flush();
+ }
+ for (int pos = 0; pos < num_cells; pos++) {
+ const int gen_id = grid_matrix(frame_id, pos);
+ if (gen_id >= 0) org_count[gen_id]++;
+ }
+ }
+ cerr << endl;
+
+ // Choose colors for each genotype.
+ // Color 0 -> No orgs or dead cell. (Black)
+ // Color 1 -> One organism ever; probably lethal mutation (Dark Gray)
+ // Color 2 -> 2-T1 organisms ever; unsuccessful genotrype (Light Gray)
+ // Color 3 -> T1+1-T2 organisms ever; margenally successful genotype (White)
+ // Colors 4+ -> T2+1+ orgs in genotypes; ideally unique color (num_colors)
+ //
+ // Where T1 = threshold1 and T2 = threshold2
+
+ cerr << "CHOOSING COLORS..................................." << endl;
+ tArray<int> color_array(max_id+1);
+ for (int i = 0; i < color_array.GetSize(); i++) {
+ int cur_count = org_count[i];
+ if (cur_count == 0) color_array[i] = 0;
+ else if (cur_count == 1) color_array[i] = 1;
+ else if (cur_count <= threshold1) color_array[i] = 2;
+ else if (cur_count <= threshold2) color_array[i] = 3;
+ else {
+ int color_choice = random.GetUInt(num_colors - 4) + 4;
+ color_array[i] = color_choice;
+ }
+ }
+
+ cerr << "OUTPUTING RESULTS................................." << endl;
+ ofstream fp("avida_movie.m");
+ fp << "'Data Loaded from File...'" << endl;
+
+ for (int frame_id = 0; frame_id < num_files; frame_id++) {
+ // Keep a status bar printing on the screen.
+ if (frame_id % file_step == 0) {
+ cerr << '#';
+ cerr.flush();
+ }
+
+ // NORMAL MAPS: Print the full matrix.
+ if (num_demes <= 1) {
+ fp << "frame" << frame_id << " = [ ";
+ for (int pos = 0; pos < num_cells; pos++) {
+ if (pos > 0 && pos % width == 0) fp << "; ";
+ const int gen_id = grid_matrix(frame_id, pos);
+ if (gen_id == -1) fp << "0 ";
+ else fp << color_array[gen_id] << " ";
+ }
+ fp << "];" << endl;
+ }
+
+ // DEME MAPS: A bit more complex to keep the demes orderly.
+ else {
+ fp << "frame" << frame_id << " = [ ";
+
+ // Loop through each row of demes.
+ for (int deme_row = 0; deme_row < num_deme_rows; deme_row++) {
+ // Now loop through each row of cells within this row of demes...
+ for (int cell_row = 0; cell_row < deme_height; cell_row++) {
+ // Within this row, loop through all columns of demes...
+ for (int deme_col = 0; deme_col < num_deme_cols; deme_col++) {
+ const int deme_id = deme_row * num_deme_cols + deme_col;
+ // Finally, loop through all columns of demes...
+ for (int cell_col = 0; cell_col < width; cell_col++) {
+ // Determine which cell we're working with here.
+ const int deme_pos = cell_row * width + cell_col;
+ const int cell_id = deme_id * deme_size + deme_pos;
+
+ // If this is beyond the last cell, just output black.
+ if (cell_id >= num_cells) {
+ fp << "3 ";
+ continue;
+ }
+
+ // If this cell is in the grid, figure out its color.
+ const int gen_id = grid_matrix(frame_id, cell_id);
+ if (gen_id == -1) fp << "0 ";
+ else fp << color_array[gen_id] << " ";
+ } // Cell col
+
+ // At the end of each row of cells in a deme, skip a space w/black.
+ fp << "3 ";
+ } // Deme col
+
+ // At the end of all of the deme columns, mark the end of the row.
+ fp << "; ";
+ } // Cell row
+
+ // After finishing a full row of demes, skip a line.
+ const int matrix_width = num_deme_cols * (width+1);
+ for (int i = 0; i < matrix_width; i++) fp << "3 ";
+ fp << "; ";
+ } // Deme row
+
+ // When we're done with everything, close the bracket.
+ fp << "];" << endl;
+ }
+
+ }
+
+ // fp << endl << "mymapvar = [0 0 0; 0.25 0.25 0.25; 0.5 0.5 0.5; 0.75 0.75 0.75; 0 0 0.5625; 0 0 0.6250; 0 0 0.6875; 0 0 0.7500; 0 0 0.8125; 0 0 0.8750; 0 0 0.9375; 0 0 1.0000; 0 0.0625 1.0000; 0 0.1250 1.0000; 0 0.1875 1.0000; 0 0.2500 1.0000; 0 0.3125 1.0000; 0 0.3750 1.0000; 0 0.4375 1.0000; 0 0.5000 1.0000; 0 0.5625 1.0000; 0 0.6250 1.0000; 0 0.6875 1.0000; 0 0.7500 1.0000; 0 0.8125 1.0000; 0 0.8750 1.0000; 0 0.9375 1.0000; 0 1.0000 1.0000; 0.0625 1.0000 1.0000; 0.1250 1.0000 0.9375; 0.1875 1.0000 0.8750; 0.2500 1.0000 0.8125; 0.3125 1.0000 0.7500; 0.3750 1.0000 0.6875; 0.4375 1.0000 0.6250; 0.5000 1.0000 0.5625; 0.5625 1.0000 0.5000; 0.6250 1.0000 0.4375; 0.6875 1.0000 0.3750; 0.7500 1.0000 0.3125; 0.8125 1.0000 0.2500; 0.8750 1.0000 0.1875; 0.9375 1.0000 0.1250; 1.0000 1.0000 0.0625; 1.0000 1.0000 0; 1.0000 0.9375 0; 1.0000 0.8750 0; 1.0000 0.8125 0; 1.0000 0.7500 0; 1.0000 0.6875 0; 1.0000 0.6250 0; 1.0000 0.5625 0; 1.0000 0.5000 0; 1.0000 0.4375 0; 1.0000 0.37!
50 0; 1.0000 0.3125 0; 1.0000 0.2500 0; 1.0000 0.1875 0; 1.0000 0.1250 0; 1.0000 0.0625 0; 1.0000 0 0; 0.9375 0 0; 0.8750 0 0; 0.8125 0 0; 0.7500 0 0; 0.6875 0 0; 0.6250 0 0; 0.5625 0 0];" << endl;
+
+ fp << endl << "mymapvar = [ 0 0 0; 0.25 0.25 0.25; 0.5 0.5 0.5; 0.75 0.75 0.75; 0.25 0 0; 0.5 0 0; 0.75 0 0; 1 0 0; 1 0.25 0.25; 1 0.5 0.5; 0 0.25 0; 0 0.5 0; 0 0.75 0; 0 1 0; 0.25 1 0.25; 0.5 1 0.5; 0 0 0.25; 0 0 0.5; 0 0 0.75; 0 0 1; 0.25 0.25 1; 0.5 0.5 1; 1 1 0; 1 1 0.5; 1 0 1; 1 0.25 1; 1 0.5 1; 0 1 1; 0.5 1 1; 1 0.5 0; 1 0 0.5; 0.5 0 1; 0 0.5 1; 1 0.25 0; 1 0 0.25; 0.25 0 1; 0 0.25 1; 1 0.75 0; 1 0 0.75; 0.75 1 0; 0 1 0.75; 0.75 0 1; 0 0.75 1; 0.75 0.25 0; 0.5 0.25 0; 0.25 0.75 0; 0.25 0.5 0; 0.5 0.5 0; 0.75 0.75 0; 0.75 0 0.25; 0.5 0 0.25; 0.25 0 0.75; 0.25 0 0.5; 0.5 0 0.75; 0.75 0 0.5; 0.5 0 0.5; 0.75 0 0.75; 0 0.75 0.25; 0 0.5 0.25; 0 0.25 0.75; 0 0.25 0.5; 0 0.5 0.75; 0 0.75 0.5; 0 0.5 0.5; 0 0.75 0.75 ];" << endl;
+
+
+
+
+
+
+ const int x_midpoint = width/2;
+ const int y_midpoint = height/2;
+ const int output_size = (num_cells > 3600) ? 6 : 3;
+
+ fp << "colormap(mymapvar);" << endl;
+
+ for (int frame_id = 0; frame_id < num_files; frame_id++) {
+
+ // Clear the figure before re-drawing it...
+ fp << "clf" << endl;
+
+ // Start by placing the grid for the current frame on the screen.
+ fp << "pcolor_all( frame" << frame_id;
+
+ // If we *don't* have demes, rotate the map around so the starting oranism
+ // at 0,0 is centered.
+ if (num_demes == 0) {
+ fp << "(["
+ << y_midpoint+1 << ":" << height << " 1:" << y_midpoint
+ << "],["
+ << x_midpoint+1 << ":" << width << " 1:" << x_midpoint
+ << "])";
+ }
+
+ fp << " ); "
+ << endl;
+
+ // Set it up to look good:
+ // - "shading faceted" draws lines between cells.
+ // - "axis off" removes the axes.
+ // - "caxis([0 64]);" makes sure colors ar econsistant between frames.
+ // - "title(...)" sets the title of the frame to be the update number.
+ fp << "shading faceted" << endl
+ << "axis off" << endl
+ << "caxis([0 " << (64) << "]);" << endl;
+
+ const int UD_num = (frame_id + 1) * UD_step + UD_start;
+ fp << "title('" << UD_num << "');" << endl;
+
+ // Setup output size, which was determined by the number of cells we have.
+ fp << "set(gcf, 'PaperPosition', [0.5 0.5 "
+ << output_size << " " << output_size
+ << "]);" << endl;
+
+ // Finally, print it as a PNG frame.
+ fp << "print -dpng frame" << frame_id << ".png" << endl;
+ }
+
+ cerr << endl << "PROCESSING COMPLETE" << endl;
+}
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