Example 11 with VectorString3D
use of ini.trakem2.vector.VectorString3D in project TrakEM2 by trakem2.
the class Compare method compareAllToAll.
/**
* Gets pipes for all open projects, and generates a matrix of dissimilarities, which gets passed on to the Worker thread and also to a file, if desired.
*
* @param to_file Whether to save the results to a file and popup a save dialog for it or not. In any case the results are stored in the worker's load, which you can retrieve like:
* <pre>
* Bureaucrat bu = Compare.compareAllToAll(true, null, null);
* Object result = bu.getWorker().getResult();
* float[][] scores = (float[][])result[0];
* ArrayList<Compare.Chain> chains = (ArrayList<Compare.Chain>)result[1];
* </pre>
*/
public static Bureaucrat compareAllToAll(final boolean to_file, final String regex, final String[] ignore, final Project[] projects, final boolean crop, final boolean from_end, final int max_n_elements, final String outgroup) {
// gather all open projects
final Project[] p = null == projects ? Project.getProjects().toArray(new Project[0]) : projects;
final Worker worker = new Worker("Comparing all to all") {
@Override
public void run() {
startedWorking();
try {
final CATAParameters cp = new CATAParameters();
if (!cp.setup(to_file, regex, false, false)) {
finishedWorking();
return;
}
String filename = null, dir = null;
if (to_file) {
final SaveDialog sd = new SaveDialog("Save matrix", OpenDialog.getDefaultDirectory(), null, ".csv");
filename = sd.getFileName();
if (null == filename) {
finishedWorking();
return;
}
dir = sd.getDirectory().replace('\\', '/');
if (!dir.endsWith("/"))
dir += "/";
}
Object[] ob = gatherChains(p, cp, ignore);
final ArrayList<Chain> chains = (ArrayList<Chain>) ob[0];
// to keep track of each project's chains
final ArrayList[] p_chains = (ArrayList[]) ob[1];
ob = null;
if (null == chains) {
finishedWorking();
return;
}
final int n_chains = chains.size();
// crop chains if desired
if (crop) {
for (final Chain chain : chains) {
if (from_end) {
final int start = chain.vs.length() - max_n_elements;
if (start > 0) {
chain.vs = chain.vs.substring(start, chain.vs.length());
// BEFORE making it relative
chain.vs.resample(cp.delta, cp.with_source);
}
} else {
if (max_n_elements < chain.vs.length()) {
chain.vs = chain.vs.substring(0, max_n_elements);
// BEFORE making it relative
chain.vs.resample(cp.delta, cp.with_source);
}
}
}
}
// compare all to all
final VectorString3D[] vs = new VectorString3D[n_chains];
for (int i = 0; i < n_chains; i++) vs[i] = chains.get(i).vs;
final float[][] scores = Compare.scoreAllToAll(vs, cp.distance_type, cp.delta, cp.skip_ends, cp.max_mut, cp.min_chunk, cp.direct, cp.substring_matching, this);
if (null == scores) {
finishedWorking();
return;
}
// store matrix and chains into the worker
this.result = new Object[] { scores, chains };
// write to file
if (!to_file) {
finishedWorking();
return;
}
final File f = new File(dir + filename);
// encoding in Latin 1 (for macosx not to mess around
final OutputStreamWriter dos = new OutputStreamWriter(new BufferedOutputStream(new FileOutputStream(f)), "8859_1");
// Normalize matrix to largest value of 1.0
if (cp.normalize) {
float max = 0;
for (int i = 0; i < scores.length; i++) {
// traverse half matrix ony: it's mirrored
for (int j = i; j < scores[0].length; j++) {
if (scores[i][j] > max)
max = scores[i][j];
}
}
for (int i = 0; i < scores.length; i++) {
for (int j = i; j < scores[0].length; j++) {
scores[i][j] = scores[j][i] /= max;
}
}
}
// write chain titles, with project prefix
if (cp.format.equals(cp.formats[0])) {
// as csv:
try {
final StringBuffer[] titles = new StringBuffer[n_chains];
int next = 0;
for (int i = 0; i < p.length; i++) {
final String prefix = Utils.getCharacter(i + 1);
// empty upper left corner
dos.write("\"\"");
for (final Chain chain : (ArrayList<Chain>) p_chains[i]) {
dos.write(",");
titles[next] = new StringBuffer().append('\"').append(prefix).append(' ').append(chain.getCellTitle()).append('\"');
dos.write(titles[next].toString());
next++;
}
}
dos.write("\n");
for (int i = 0; i < n_chains; i++) {
final StringBuffer line = new StringBuffer();
line.append(titles[i]);
for (int j = 0; j < n_chains; j++) line.append(',').append(scores[i][j]);
line.append('\n');
dos.write(line.toString());
}
dos.flush();
} catch (final Exception e) {
e.printStackTrace();
}
} else if (cp.format.equals(cp.formats[1])) {
// as XML:
try {
final StringBuffer sb = new StringBuffer("<?xml version=\"1.0\"?>\n<!DOCTYPE ggobidata SYSTEM \"ggobi.dtd\">\n");
sb.append("<ggobidata count=\"2\">\n");
sb.append("<data name=\"Pipe Chains\">\n");
sb.append("<description />\n");
// ggobi: what a crappy XML parser it has
sb.append("<variables count=\"0\">\n</variables>\n");
sb.append("<records count=\"").append(chains.size()).append("\" glyph=\"fr 1\" color=\"3\">\n");
int next = 0;
for (int i = 0; i < p.length; i++) {
final String prefix = Utils.getCharacter(i + 1);
final String color = new StringBuffer("color=\"").append(i + 1).append('\"').toString();
for (final Chain chain : (ArrayList<Chain>) p_chains[i]) {
sb.append("<record id=\"").append(next + 1).append("\" label=\"").append(prefix).append(' ').append(chain.getCellTitle()).append("\" ").append(color).append("></record>\n");
next++;
}
}
sb.append("</records>\n</data>\n");
sb.append("<data name=\"distances\">\n");
sb.append("<description />\n");
sb.append("<variables count=\"1\">\n<realvariable name=\"D\" />\n</variables>\n");
sb.append("<records count=\"").append(n_chains * (n_chains - 1)).append("\" glyph=\"fr 1\" color=\"0\">\n");
for (int i = 0; i < n_chains; i++) {
for (int j = 0; j < n_chains; j++) {
if (i == j)
continue;
sb.append("<record source=\"").append(i + 1).append("\" destination=\"").append(j + 1).append("\">").append(scores[i][j]).append("</record>\n");
}
}
sb.append("</records>\n</data>\n");
sb.append("</ggobidata>");
dos.write(sb.toString());
dos.flush();
} catch (final Exception e) {
e.printStackTrace();
}
} else if (cp.format.equals(cp.formats[2])) {
// as Phylip .dis
try {
// collect different projects
final ArrayList<Project> projects = new ArrayList<Project>();
for (final Chain chain : chains) {
final Project p = chain.getRoot().getProject();
if (!projects.contains(p))
projects.add(p);
}
final HashSet names = new HashSet();
final StringBuffer sb = new StringBuffer();
sb.append(scores.length).append('\n');
dos.write(sb.toString());
// unique ids, since phylip cannot handle long names
final AtomicInteger ids = new AtomicInteger(0);
final File ftags = new File(dir + filename + ".tags");
// encoding in Latin 1 (for macosx not to mess around
final OutputStreamWriter dostags = new OutputStreamWriter(new BufferedOutputStream(new FileOutputStream(ftags)), "8859_1");
for (int i = 0; i < scores.length; i++) {
sb.setLength(0);
// String title = chains.get(i).getShortCellTitle().replace(' ', '_').replace('\t', '_').replace('[', '-').replace(']', '-');
final int id = ids.incrementAndGet();
final String sid = Utils.getCharacter(id);
String name = chains.get(i).getShortCellTitle();
// If sid.length() > 10 chars, trouble!
if (sid.length() > 10) {
Utils.log2("Ignoring " + name + " : id longer than 10 chars: " + id);
continue;
}
final int k = 1;
// Prepend a project char identifier to the name
String project_name = "";
if (projects.size() > 1) {
project_name = Utils.getCharacter(projects.indexOf(chains.get(i).getRoot().getProject()) + 1).toLowerCase();
name = project_name + name;
}
dostags.write(new StringBuilder().append(sid).append('\t').append(name).append('\n').toString());
if (null != outgroup && -1 != name.indexOf(outgroup)) {
Utils.logAll("Outgroup 0-based index is " + id + ", with id " + sid + ", with name " + name);
}
//
final int len = 12;
sb.append(sid);
// pad with spaces up to len
for (int j = len - sid.length(); j > 0; j--) sb.append(' ');
int count = 0;
for (int j = 0; j < scores[0].length; j++) {
sb.append(' ').append(scores[i][j]);
count++;
if (7 == count && j < scores[0].length - 1) {
sb.append('\n');
count = 0;
while (++count < len) sb.append(' ');
sb.append(' ');
count = 0;
}
}
sb.append('\n');
dos.write(sb.toString());
}
dos.flush();
dostags.flush();
dostags.close();
} catch (final Exception e) {
e.printStackTrace();
}
}
dos.close();
} catch (final Exception e) {
e.printStackTrace();
} finally {
finishedWorking();
}
}
};
return Bureaucrat.createAndStart(worker, p);
}
Also used :
CATAParameters(ini.trakem2.analysis.Compare.CATAParameters)
ArrayList(java.util.ArrayList)
Worker(ini.trakem2.utils.Worker)
SaveDialog(ij.io.SaveDialog)
BufferedOutputStream(java.io.BufferedOutputStream)
HashSet(java.util.HashSet)
Project(ini.trakem2.Project)
VectorString3D(ini.trakem2.vector.VectorString3D)
AtomicInteger(java.util.concurrent.atomic.AtomicInteger)
FileOutputStream(java.io.FileOutputStream)
OutputStreamWriter(java.io.OutputStreamWriter)
File(java.io.File)
Example 12 with VectorString3D
use of ini.trakem2.vector.VectorString3D in project TrakEM2 by trakem2.
the class Compare method reliabilityAnalysis.
public static final Bureaucrat reliabilityAnalysis(final String[] ignore, final boolean output_arff, final boolean weka_classify, final boolean show_dialog, final double delta, final double wi, final double wd, final double wm) {
// gather all open projects
final Project[] p = Project.getProjects().toArray(new Project[0]);
final Worker worker = new Worker("Reliability by name") {
@Override
public void run() {
startedWorking();
try {
final CATAParameters cp = new CATAParameters();
cp.delta = delta;
if (show_dialog && !cp.setup(false, null, false, false)) {
finishedWorking();
return;
}
Object[] ob = gatherChains(p, cp, ignore);
final ArrayList<Chain> chains = (ArrayList<Chain>) ob[0];
// to keep track of each project's chains
final ArrayList[] p_chains = (ArrayList[]) ob[1];
ob = null;
if (null == chains) {
finishedWorking();
return;
}
// For each pipe in a brain:
// - score against all other brains in which that pipe name exists,
// - record the score position within that brain.
//
final ExecutorService exec = Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors());
// for each individual lineage:
final TreeMap<String, ArrayList<Integer>> indices = new TreeMap<String, ArrayList<Integer>>();
final ArrayList<CITuple> cin = new ArrayList<CITuple>();
// for each family:
final TreeMap<String, ArrayList<Integer>> indices_f = new TreeMap<String, ArrayList<Integer>>();
final ArrayList<CITuple> cin_f = new ArrayList<CITuple>();
final ArrayList<Future> fus = new ArrayList<Future>();
// For neural network analysis:
final StringBuilder arff = output_arff ? new StringBuilder("@RELATION Lineages\n\n") : null;
if (output_arff) {
arff.append("@ATTRIBUTE APD NUMERIC\n");
arff.append("@ATTRIBUTE CPD NUMERIC\n");
arff.append("@ATTRIBUTE STD NUMERIC\n");
arff.append("@ATTRIBUTE MPD NUMERIC\n");
arff.append("@ATTRIBUTE PM NUMERIC\n");
arff.append("@ATTRIBUTE LEV NUMERIC\n");
arff.append("@ATTRIBUTE SIM NUMERIC\n");
arff.append("@ATTRIBUTE PRX NUMERIC\n");
arff.append("@ATTRIBUTE PRM NUMERIC\n");
// length ratio: len(query) / len(ref)
arff.append("@ATTRIBUTE LR NUMERIC\n");
arff.append("@ATTRIBUTE TR NUMERIC\n");
arff.append("@ATTRIBUTE CLASS {false,true}\n");
arff.append("\n@DATA\n");
}
// Count number of times when decision tree says it's good, versus number of times when it should be good
// observed
final AtomicInteger obs_good = new AtomicInteger(0);
// observed wrong
final AtomicInteger obs_wrong = new AtomicInteger(0);
// expected
final AtomicInteger exp_good = new AtomicInteger(0);
final AtomicInteger exp_bad = new AtomicInteger(0);
final AtomicInteger obs_bad_classified_good_ones = new AtomicInteger(0);
final AtomicInteger obs_well_classified_bad_ones = new AtomicInteger(0);
// inc by one when a lineage to compare is not found at all in the brain that works as reference
final AtomicInteger not_found = new AtomicInteger(0);
final AtomicInteger already_classified = new AtomicInteger(0);
Method classify_ = null;
if (weka_classify) {
try {
classify_ = Class.forName("lineage.LineageClassifier").getDeclaredMethod("classify", new Class[] { double[].class });
} catch (final Exception e) {
IJError.print(e);
}
}
final Method classify = classify_;
// All possible pairs of projects, with repetition (it's not the same, although the pipe pairwise comparison itself will be.)
for (int _i = 0; _i < p_chains.length; _i++) {
final int i = _i;
Utils.log2("Project " + p[i] + " has " + p_chains[i].size() + " chains.");
for (int _j = 0; _j < p_chains.length; _j++) {
final int j = _j;
// skip same project (would have a score of zero, identical.)
if (i == j)
continue;
final String[] titles_j = new String[p_chains[j].size()];
int next = 0;
for (final Chain cj : (ArrayList<Chain>) p_chains[j]) {
final String t = cj.getCellTitle();
titles_j[next++] = t.substring(0, t.indexOf(' '));
}
// families:
final TreeSet<String> ts_families = new TreeSet<String>();
for (int f = 0; f < titles_j.length; f++) {
// extract family name from title: read the first continuous string of capital letters
final String title = titles_j[f];
int u = 0;
for (; u < title.length(); u++) {
if (!Character.isUpperCase(title.charAt(u)))
break;
}
ts_families.add(title.substring(0, u));
}
final ArrayList<String> families = new ArrayList<String>(ts_families);
fus.add(exec.submit(new Callable() {
@Override
public Object call() {
// All chains of one project to all chains of the other:
for (final Chain chain : (ArrayList<Chain>) p_chains[i]) {
final VectorString3D vs1 = chain.vs;
// Prepare title
String title = chain.getCellTitle();
title = title.substring(0, title.indexOf(' '));
// check if the other project j contains a chain of name chain.getCellTitle() up to the space.
int title_index = -1;
for (int k = 0; k < titles_j.length; k++) {
if (title.equals(titles_j[k])) {
title_index = k;
break;
}
}
if (-1 == title_index) {
Utils.log2(title + " not found in project " + p[j]);
if (weka_classify)
not_found.incrementAndGet();
continue;
}
// should be there:
if (weka_classify) {
exp_good.incrementAndGet();
exp_bad.addAndGet(titles_j.length - 1);
}
final ArrayList<ChainMatch> list = new ArrayList<ChainMatch>();
// extract family name from title: read the first continuous string of capital letters
int u = 0;
for (; u < title.length(); u++) {
if (!Character.isUpperCase(title.charAt(u)))
break;
}
final String family_name = title.substring(0, u);
String last_classify = null;
int g = 0;
for (final Chain cj : (ArrayList<Chain>) p_chains[j]) {
final VectorString3D vs2 = cj.vs;
final Object[] ob = findBestMatch(vs1, vs2, cp.delta, cp.skip_ends, cp.max_mut, cp.min_chunk, cp.distance_type, cp.direct, cp.substring_matching, wi, wd, wm);
final Editions ed = (Editions) ob[0];
final double[] stats = ed.getStatistics(cp.skip_ends, cp.max_mut, cp.min_chunk, cp.score_mut_only);
final ChainMatch cm = new ChainMatch(cj, null, ed, stats, score(ed.getSimilarity(), ed.getDistance(), stats[3], Compare.W));
cm.title = titles_j[g];
list.add(cm);
g++;
if (weka_classify) {
// from decision tree: is it good?
final double[] param = new double[11];
for (int p = 0; p < stats.length; p++) param[p] = stats[p];
try {
if (((Boolean) classify.invoke(null, param)).booleanValue()) {
if (null != last_classify) {
Utils.log2("ALREADY CLASSIFIED " + title + " as " + last_classify + " (now: " + cm.title + " )");
already_classified.incrementAndGet();
}
last_classify = cm.title;
if (title.equals(cm.title)) {
obs_good.incrementAndGet();
} else {
Utils.log2("WRONG CLASSIFICATION of " + title + " as " + cm.title);
obs_wrong.incrementAndGet();
}
} else {
if (title.equals(cm.title)) {
obs_bad_classified_good_ones.incrementAndGet();
} else {
obs_well_classified_bad_ones.incrementAndGet();
}
}
} catch (final Exception ee) {
IJError.print(ee);
}
}
}
// sort scores:
Compare.sortMatches(list, cp.distance_type, cp.distance_type_2, cp.min_matches);
if (output_arff) {
// Take top 8 and put them into training set for WEKA in arff format
for (int h = 0; h < 8; h++) {
final ChainMatch cm = list.get(h);
final StringBuilder sb = new StringBuilder();
sb.append(cm.phys_dist).append(',').append(cm.cum_phys_dist).append(',').append(cm.stdDev).append(',').append(cm.median).append(',').append(cm.prop_mut).append(',').append(cm.ed.getDistance()).append(',').append(cm.seq_sim).append(',').append(cm.proximity).append(',').append(cm.proximity_mut).append(',').append(cm.prop_len).append(',').append(cm.tortuosity_ratio).append(',').append(title.equals(cm.title)).append(// append('-').append(cm.title.startsWith(family_name)).append('\n');
'\n');
synchronized (arff) {
arff.append(sb);
}
}
}
// record scoring index
int f = 0;
boolean found_specific = false;
boolean found_family = false;
for (final ChainMatch cm : list) {
// Exact match: for each individual lineage
if (!found_specific && title.equals(cm.title)) {
synchronized (indices) {
ArrayList<Integer> al = indices.get(title);
if (null == al) {
al = new ArrayList<Integer>();
indices.put(title, al);
// so I can keep a list of chains sorted by name
cin.add(new CITuple(title, chain, al));
}
al.add(f);
}
found_specific = true;
}
if (!found_family && cm.title.startsWith(family_name)) {
synchronized (indices_f) {
ArrayList<Integer> al = indices_f.get(family_name);
if (null == al) {
al = new ArrayList<Integer>();
indices_f.put(family_name, al);
cin_f.add(new CITuple(family_name, chain, al));
}
al.add(f);
}
found_family = true;
}
if (found_specific && found_family) {
break;
}
//
f++;
}
if (!found_specific) {
Utils.log2("NOT FOUND any match for " + title + " within a list of size " + list.size() + ", in project " + chain.getRoot().getProject());
}
}
return null;
}
}));
}
}
for (final Future fu : fus) {
try {
fu.get();
} catch (final Exception e) {
IJError.print(e);
}
}
exec.shutdownNow();
if (weka_classify) {
// so stateful ... it's a sin.
try {
Class.forName("lineage.LineageClassifier").getDeclaredMethod("flush", new Class[] {}).invoke(null, new Object[] {});
} catch (final Exception e) {
IJError.print(e);
}
}
// export ARFF for neural network training
if (output_arff) {
Utils.saveToFile(new File(System.getProperty("user.dir") + "/lineages.arff"), arff.toString());
}
// Show the results from indices map
final StringBuilder sb = new StringBuilder();
// scoring index vs count of occurrences
final TreeMap<Integer, Integer> sum = new TreeMap<Integer, Integer>();
// best scoring index of best family member vs count of ocurrences
final TreeMap<Integer, Integer> sum_f = new TreeMap<Integer, Integer>();
// scoring index vs count of ocurrences, within each family
final TreeMap<String, TreeMap<Integer, Integer>> sum_fw = new TreeMap<String, TreeMap<Integer, Integer>>();
// From collected data, several kinds of results:
// - a list of how well each chain scores: its index position in the sorted list of scores of one to many.
// - a list of how well each chain scores relative to family: the lowest (best) index position of a lineage of the same family in the sorted list of scores.
sb.append("List of scoring indices for each (starting at index 1, aka best possible score):\n");
for (final CITuple ci : cin) {
// sort indices in place
Collections.sort(ci.list);
// count occurrences of each scoring index
// lowest possible index
int last = 0;
int count = 1;
for (final int i : ci.list) {
if (last == i)
count++;
else {
sb.append(ci.title).append(' ').append(last + 1).append(' ').append(count).append('\n');
// reset
last = i;
count = 1;
}
// global count of occurrences
final Integer oi = new Integer(i);
sum.put(oi, (sum.containsKey(oi) ? sum.get(oi) : 0) + 1);
// Same thing but not for all lineages, but only for lineages within a family:
// extract family name from title: read the first continuous string of capital letters
int u = 0;
for (; u < ci.title.length(); u++) {
if (!Character.isUpperCase(ci.title.charAt(u)))
break;
}
final String family_name = ci.title.substring(0, u);
TreeMap<Integer, Integer> sfw = sum_fw.get(family_name);
if (null == sfw) {
sfw = new TreeMap<Integer, Integer>();
sum_fw.put(family_name, sfw);
}
sfw.put(oi, (sfw.containsKey(oi) ? sfw.get(oi) : 0) + 1);
}
if (0 != count)
sb.append(ci.title).append(' ').append(last + 1).append(' ').append(count).append('\n');
// find the very-off ones:
if (last > 6) {
Utils.log2("BAD index " + last + " for chain " + ci.title + " " + ci.chain.getRoot() + " of project " + ci.chain.getRoot().getProject());
}
}
sb.append("===============================\n");
// / family score:
for (final CITuple ci : cin_f) {
// sort indices in place
Collections.sort(ci.list);
// count occurrences of each scoring index
// lowest possible index
int last = 0;
int count = 1;
for (final int i : ci.list) {
if (last == i)
count++;
else {
// reset
last = i;
count = 1;
}
// global count of occurrences
final Integer oi = new Integer(i);
sum_f.put(oi, (sum_f.containsKey(oi) ? sum_f.get(oi) : 0) + 1);
}
}
sb.append("===============================\n");
// - a summarizing histogram that collects how many 1st, how many 2nd, etc. in total, normalized to total number of one-to-many matches performed (i.e. the number of scoring indices recorded.)
//
{
sb.append("Global count of index ocurrences:\n");
int total = 0;
int top2 = 0;
int top5 = 0;
for (final Map.Entry<Integer, Integer> e : sum.entrySet()) {
sb.append(e.getKey()).append(' ').append(e.getValue()).append('\n');
total += e.getValue();
if (e.getKey() < 2)
top2 += e.getValue();
if (e.getKey() < 5)
top5 += e.getValue();
}
sb.append("total: ").append(total).append('\n');
sb.append("top1: ").append(sum.get(sum.firstKey()) / (float) total).append('\n');
sb.append("top2: ").append(top2 / (float) total).append('\n');
sb.append("top5: ").append(top5 / (float) total).append('\n');
sb.append("===============================\n");
}
sb.append("Family-wise count of index ocurrences:\n");
for (final Map.Entry<String, TreeMap<Integer, Integer>> fe : sum_fw.entrySet()) {
int total = 0;
int top5 = 0;
for (final Map.Entry<Integer, Integer> e : fe.getValue().entrySet()) {
sb.append(fe.getKey()).append(' ').append(e.getKey()).append(' ').append(e.getValue()).append('\n');
total += e.getValue();
if (e.getKey() < 5)
top5 += e.getValue();
}
sb.append("total: ").append(total).append('\n');
sb.append("top1: ").append(fe.getValue().get(fe.getValue().firstKey()) / (float) total).append('\n');
sb.append("top5: ").append(top5 / (float) total).append('\n');
}
sb.append("===============================\n");
// - the percent of first score being the correct one:
double first = 0;
double first_5 = 0;
double all = 0;
for (final Map.Entry<Integer, Integer> e : sum.entrySet()) {
final int k = e.getKey();
final int a = e.getValue();
all += a;
if (0 == k)
first = a;
if (k < 5)
first_5 += a;
}
// STORE
this.result = new double[] { // Top one ratio
first / all, // Top 5 ratio
first_5 / all };
sb.append("Global count of index occurrences family-wise:\n");
for (final Map.Entry<Integer, Integer> e : sum_f.entrySet()) {
sb.append(e.getKey()).append(' ').append(e.getValue()).append('\n');
}
sb.append("===============================\n");
// - a summarizing histogram of how well each chain scores (4/4, 3/4, 2/4, 1/4, 0/4 only for those that have 4 homologous members.)
// Must consider that there are 5 projects taken in pairs with repetition.
sb.append("A summarizing histogram of how well each chain scores, for those that have 4 homologous members. It's the number of 1st scores (zeroes) versus the total number of scores:\n");
// First, classify them in having 4, 3, 2, 1
// For 5 brains: 5! / (5-2)! = 5 * 4 = 20 --- 5 elements taken in groups of 2, where order matters
// For 4 brains: 4! / (4-2)! = 4 * 3 = 12
// For 3 brains: 3! / (3-2)! = 3 * 2 = 6;
final TreeMap<Integer, ArrayList<String>> hsc = new TreeMap<Integer, ArrayList<String>>();
for (final CITuple ci : cin) {
final int size = ci.list.size();
ArrayList<String> al = hsc.get(size);
if (null == al) {
al = new ArrayList<String>();
hsc.put(size, al);
}
// Count the number of 0s -- top scoring
int count = 0;
for (final Integer i : ci.list) {
if (0 == i)
count++;
else
break;
}
al.add(new StringBuffer(ci.title).append(" =").append(count).append('/').append(ci.list.size()).append('\n').toString());
}
// Then just print:
for (final Map.Entry<Integer, ArrayList<String>> e : hsc.entrySet()) {
sb.append("For ").append(e.getKey()).append(" matches:\n");
for (final String s : e.getValue()) sb.append(s);
}
sb.append("=========================\n");
// Family-wise, count the number of zeros per family:
sb.append("Number of top scoring per family:\n");
final TreeMap<String, String> family_scores = new TreeMap<String, String>();
for (final CITuple ci : cin_f) {
int count = 0;
for (final Integer i : ci.list) {
if (0 == i)
count++;
else
// ci.list is sorted
break;
}
family_scores.put(ci.title, new StringBuilder().append(ci.title).append(" =").append(count).append('/').append(ci.list.size()).append('\n').toString());
}
// Now print sorted by family name:
for (final String s : family_scores.values()) {
sb.append(s);
}
sb.append("=========================\n");
if (weka_classify) {
sb.append("Decision tree:\n");
sb.append("Expected good matches: " + exp_good.get() + "\n");
sb.append("Expected bad matches: " + exp_bad.get() + "\n");
sb.append("Observed good matches: " + obs_good.get() + "\n");
sb.append("Observed bad matches: " + obs_wrong.get() + "\n");
sb.append("Observed well classified bad ones: " + obs_well_classified_bad_ones.get() + "\n");
sb.append("Observed bad classified good ones: " + obs_bad_classified_good_ones.get() + "\n");
sb.append("Not found, so skipped: " + not_found.get() + "\n");
sb.append("Already classified: " + already_classified.get() + "\n");
sb.append("=========================\n");
}
if (output_arff) {
Utils.log(sb.toString());
} else {
Utils.log2(sb.toString());
}
} catch (final Exception e) {
e.printStackTrace();
} finally {
finishedWorking();
}
}
};
return Bureaucrat.createAndStart(worker, p);
}
Also used :
ArrayList(java.util.ArrayList)
TreeSet(java.util.TreeSet)
Method(java.lang.reflect.Method)
Project(ini.trakem2.Project)
AtomicInteger(java.util.concurrent.atomic.AtomicInteger)
File(java.io.File)
Map(java.util.Map)
HashMap(java.util.HashMap)
TreeMap(java.util.TreeMap)
CATAParameters(ini.trakem2.analysis.Compare.CATAParameters)
Callable(java.util.concurrent.Callable)
Worker(ini.trakem2.utils.Worker)
TreeMap(java.util.TreeMap)
AtomicInteger(java.util.concurrent.atomic.AtomicInteger)
Editions(ini.trakem2.vector.Editions)
VectorString3D(ini.trakem2.vector.VectorString3D)
ExecutorService(java.util.concurrent.ExecutorService)
Future(java.util.concurrent.Future)
Example 13 with VectorString3D
use of ini.trakem2.vector.VectorString3D in project TrakEM2 by trakem2.
the class Compare method obtainOrigin.
/**
* Generate calibrated origin of coordinates.
*/
public static Object[] obtainOrigin(final Line3D[] axes, final int transform_type, final Vector3d[] o_ref) {
// pipe's axes
final VectorString3D[] vs = new VectorString3D[3];
for (int i = 0; i < 3; i++) vs[i] = axes[i].asVectorString3D();
final Calibration cal = (null != axes[0].getLayerSet() ? axes[0].getLayerSet().getCalibration() : null);
// 1 - calibrate
if (null != cal) {
for (int i = 0; i < 3; i++) vs[i].calibrate(cal);
}
// 2 - resample (although it's done before transforming, it's only for aesthetic purposes: it doesn't matter, won't ever go into dynamic programming machinery)
double delta = 0;
for (int i = 0; i < 3; i++) delta += vs[i].getAverageDelta();
delta /= 3;
for (int i = 0; i < 3; i++) vs[i].resample(delta);
// return origin vectors for pipe's project
// requires resampled vs
final Vector3d[] o = Compare.createOrigin(vs[0], vs[1], vs[2], transform_type, o_ref);
return new Object[] { vs, o };
}
Also used :
VectorString3D(ini.trakem2.vector.VectorString3D)
Vector3d(org.scijava.vecmath.Vector3d)
Calibration(ij.measure.Calibration)
Example 14 with VectorString3D
use of ini.trakem2.vector.VectorString3D in project TrakEM2 by trakem2.
the class Compare method createOrigin.
public static Vector3d[] createOrigin(final VectorString3D x, final VectorString3D y, final VectorString3D z, final int transform_type, final Vector3d[] o_ref) {
// Aproximate an origin of coordinates
final VectorString3D[] vs = new VectorString3D[] { z, y, x };
final ArrayList<Point3d> ps = new ArrayList<Point3d>();
final int[] dir = new int[] { 1, 1, 1 };
for (int i = 0; i < vs.length; i++) {
for (int k = i + 1; k < vs.length; k++) {
double min_dist = Double.MAX_VALUE;
int ia = 0, ib = 0;
for (int a = 0; a < vs[i].length(); a++) {
for (int b = 0; b < vs[k].length(); b++) {
final double d = VectorString3D.distance(vs[i], a, vs[k], b);
if (d < min_dist) {
min_dist = d;
ia = a;
ib = b;
}
}
}
ps.add(new Point3d((vs[i].getPoint(0, ia) + vs[k].getPoint(0, ib)) / 2, (vs[i].getPoint(1, ia) + vs[k].getPoint(1, ib)) / 2, (vs[i].getPoint(2, ia) + vs[k].getPoint(2, ib)) / 2));
// determine orientation of the VectorString3D relative to the origin
if (ia > vs[i].length() / 2)
dir[i] = -1;
if (ib > vs[k].length() / 2)
dir[k] = -1;
// WARNING: we don't check for the case where it contradicts
}
}
final Vector3d origin = new Vector3d();
final int len = ps.size();
for (final Point3d p : ps) {
p.x /= len;
p.y /= len;
p.z /= len;
}
for (final Point3d p : ps) origin.add(p);
// aproximate a vector for each axis
final Vector3d vz = z.sumVector();
final Vector3d vy = y.sumVector();
final Vector3d vx = x.sumVector();
// adjust orientation, so vectors point away from the origin towards the other end of the vectorstring
vz.scale(dir[0]);
vy.scale(dir[1]);
vx.scale(dir[2]);
/*
Utils.log2("dir[0]=" + dir[0]);
Utils.log2("dir[1]=" + dir[1]);
Utils.log2("dir[2]=" + dir[2]);
*/
Vector3d v1 = vx, v2 = vy;
final Vector3d v3 = vz;
if (Compare.TRANS_ROT == transform_type || Compare.TRANS_ROT_SCALE == transform_type) {
// 1 - compute MEDIAL vector: perpendicular to the plane made by peduncle and dorsal lobe
final Vector3d vc_medial = new Vector3d();
vc_medial.cross(vz, vy);
/* // OLD WAY
// check orientation:
Vector3d vc_med = new Vector3d(vc_medial);
vc_med.normalize();
Vector3d vx_norm = new Vector3d(vx);
vx_norm.normalize();
vc_med.add(vx_norm); // adding the actual medial lobe vector
// if the sum is smaller, then it means it should be inverted (it was the other side)
if (vc_med.length() < vx_norm.length()) {
vc_medial.scale(-1);
Utils.log2("Mirroring X axis");
}
*/
// 2 - compute DORSAL vector: perpedicular to the plane made by v1 and vc_medial
final Vector3d vc_dorsal = new Vector3d();
vc_dorsal.cross(vz, vc_medial);
// check orientation
final Vector3d vc_dor = new Vector3d(vc_dorsal);
vc_dor.add(vy);
// if the sum is smaller, invert
if (vc_dor.length() < vy.length()) {
vc_dorsal.scale(-1);
Utils.log("Mirroring Y axis");
}
/*
if (Compare.TRANS_ROT == transform_type) {
// just in case, for rounding issues
vc_medial.normalize();
vc_dorsal.normalize();
}
*/
v1 = vc_medial;
v2 = vc_dorsal;
if (Compare.TRANS_ROT == transform_type && null != o_ref) {
// Scale each query axis to length of the reference one
// so that there are no scaling differences.
v1.normalize();
v1.scale(o_ref[0].length());
v2.normalize();
v2.scale(o_ref[1].length());
v3.normalize();
v3.scale(o_ref[2].length());
}
}
return new Vector3d[] { // X axis : medial lobe
v1, // Y axis : dorsal lobe
v2, // Z axis : peduncle
v3, // x,y,z origin of coordinates
origin };
}
Also used :
VectorString3D(ini.trakem2.vector.VectorString3D)
Vector3d(org.scijava.vecmath.Vector3d)
Point3d(org.scijava.vecmath.Point3d)
ArrayList(java.util.ArrayList)
Example 15 with VectorString3D
use of ini.trakem2.vector.VectorString3D in project TrakEM2 by trakem2.
the class Compare method condense.
/**
* Do an all-to-all distance matrix of the given vs, then do a neighbor joining, do a weighted merge of the two VectorString3D being merged, and then finally output the resulting condensed unique VectorString3D with its source array full with all points that make each point in it. Expects VectorString3D which are already calibrated and transformed.
*/
public static VectorString3D condense(final CATAParameters cp, final VectorString3D[] vs, final Worker worker) throws Exception {
// Trivial case 1:
if (1 == vs.length)
return vs[0];
// Estimate delta
if (0 == cp.delta) {
for (int i = 0; i < vs.length; i++) {
cp.delta += vs[i].getAverageDelta();
}
cp.delta /= vs.length;
}
// Resample all:
for (int i = 0; i < vs.length; i++) vs[i].resample(cp.delta, true);
// Trivial case 2:
try {
if (2 == vs.length)
VectorString3D.createInterpolatedPoints(new Editions(vs[0], vs[1], cp.delta, false), 0.5f);
} catch (final Exception e) {
IJError.print(e);
return null;
}
// Else, do neighbor joining
final float[][] scores = Compare.scoreAllToAll(vs, cp.distance_type, cp.delta, cp.skip_ends, cp.max_mut, cp.min_chunk, cp.direct, cp.substring_matching, worker);
final HashMap<Compare.Cell<VectorString3D>, Float> table = new HashMap<Compare.Cell<VectorString3D>, Float>();
// Input the half matrix only into the table, since it's mirrored. And without the diagonal of zeros:
for (int i = 1; i < scores.length; i++) {
for (int j = 0; j < i; j++) {
table.put(new Cell<VectorString3D>(vs[i], vs[j]), scores[i][j]);
}
}
final HashSet<VectorString3D> remaining = new HashSet<VectorString3D>();
for (final VectorString3D v : vs) remaining.add(v);
while (table.size() > 0) {
if (null != worker && worker.hasQuitted()) {
return null;
}
// find smallest value
float min = Float.MAX_VALUE;
Cell<VectorString3D> cell = null;
for (final Map.Entry<Cell<VectorString3D>, Float> e : table.entrySet()) {
final float f = e.getValue();
if (f < min) {
min = f;
cell = e.getKey();
}
}
// done below//table.remove(cell);
for (final Iterator<Cell<VectorString3D>> it = table.keySet().iterator(); it.hasNext(); ) {
final Cell<VectorString3D> c = it.next();
if (c.t1 == cell.t1 || c.t2 == cell.t2 || c.t2 == cell.t1 || c.t1 == cell.t2) {
it.remove();
}
}
// pop the two merged VectorString3D
remaining.remove(cell.t1);
remaining.remove(cell.t2);
// merge, weighted by number of sources of each
// in createInterpolated, the alpha is the opposite of what one would think: a 0.2 alpha means 0.8 for the first and 0.2 for the second. So alpha should be 1-alpha
final double alpha = (double) (cell.t1.getNSources()) / (double) (cell.t1.getNSources() + cell.t2.getNSources());
final Editions eds = new Editions(cell.t1, cell.t2, cp.delta, false);
VectorString3D vs_merged = null;
if (cp.cut_uneven_ends) {
// crop ends to eliminate strings of insertions or deletions sparsed by strings of max cp.max_mut mutations inside
// (This reduces or eliminates variability noise caused by unequal sequence length)
final int[][] editions = eds.getEditions();
int first = 0;
int last = editions.length - 1;
int n_mut = 0;
for (int i = 0; i < last; i++) {
if (Editions.MUTATION == editions[i][0]) {
n_mut++;
if (n_mut > cp.max_mut) {
first = i - n_mut + 1;
break;
}
}
}
// reset
n_mut = 0;
for (int i = last; i > first; i--) {
if (Editions.MUTATION == editions[i][0]) {
n_mut++;
if (n_mut > cp.max_mut) {
last = i + n_mut - 1;
break;
}
}
}
vs_merged = VectorString3D.createInterpolatedPoints(eds, alpha, first, last);
} else {
vs_merged = VectorString3D.createInterpolatedPoints(eds, alpha);
}
vs_merged.resample(cp.delta, true);
// add a new cell for each possible comparison with all other unique vs
for (final VectorString3D v : remaining) {
final Object[] ob = findBestMatch(vs_merged, v, cp.delta, cp.skip_ends, cp.max_mut, cp.min_chunk, cp.distance_type, cp.direct, cp.substring_matching);
final Editions ed = (Editions) ob[0];
final float score = (float) getScore(ed, cp.skip_ends, cp.max_mut, cp.min_chunk, cp.distance_type);
table.put(new Cell<VectorString3D>(vs_merged, v), score);
}
// add the new VectorString3D
remaining.add(vs_merged);
}
// test:
if (1 != remaining.size()) {
Utils.log2("WARNING: remaining.size() == " + remaining.size());
}
return remaining.iterator().next();
}Aggregations
VectorString3D (ini.trakem2.vector.VectorString3D)19
ArrayList (java.util.ArrayList)6
Editions (ini.trakem2.vector.Editions)5
Calibration (ij.measure.Calibration)4
Project (ini.trakem2.Project)4
HashMap (java.util.HashMap)4
Map (java.util.Map)4
TreeMap (java.util.TreeMap)4
CATAParameters (ini.trakem2.analysis.Compare.CATAParameters)3
Worker (ini.trakem2.utils.Worker)3
HashSet (java.util.HashSet)3
AtomicInteger (java.util.concurrent.atomic.AtomicInteger)3
Vector3d (org.scijava.vecmath.Vector3d)3
File (java.io.File)2
Tuple3d (org.scijava.vecmath.Tuple3d)2
ImagePlus (ij.ImagePlus)1
OvalRoi (ij.gui.OvalRoi)1
Plot (ij.gui.Plot)1
DirectoryChooser (ij.io.DirectoryChooser)1
FileSaver (ij.io.FileSaver)1
