org.deeplearning4j.util.StringGrid Maven / Gradle / Ivy
/*
*
* * Copyright 2015 Skymind,Inc.
* *
* * Licensed under the Apache License, Version 2.0 (the "License");
* * you may not use this file except in compliance with the License.
* * You may obtain a copy of the License at
* *
* * http://www.apache.org/licenses/LICENSE-2.0
* *
* * Unless required by applicable law or agreed to in writing, software
* * distributed under the License is distributed on an "AS IS" BASIS,
* * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* * See the License for the specific language governing permissions and
* * limitations under the License.
*
*/
package org.deeplearning4j.util;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.deeplearning4j.berkeley.Counter;
import org.deeplearning4j.berkeley.StringUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.util.*;
import static org.deeplearning4j.berkeley.StringUtils.splitOnCharWithQuoting;
/**
* String matrix
* @author Adam Gibson
*
*/
public class StringGrid extends ArrayList> {
private static final long serialVersionUID = 4702427632483221813L;
private String sep;
private int numColumns = -1;
private static final Logger log = LoggerFactory.getLogger(StringGrid.class);
public final static String NONE = "NONE";
public StringGrid(StringGrid grid) {
this.sep = grid.sep;
this.numColumns = grid.numColumns;
addAll(grid);
fillOut();
}
public StringGrid(String sep,int numColumns) {
this(sep,new ArrayList());
this.numColumns = numColumns;
fillOut();
}
public int getNumColumns() {
return numColumns;
}
private void fillOut() {
for(List list : this) {
if(list.size() < numColumns) {
int diff = numColumns - list.size();
for(int i = 0; i< diff;i++) {
list.add(NONE);
}
}
}
}
public static StringGrid fromFile(String file,String sep) throws IOException {
List read = FileUtils.readLines(new File(file));
if(read.isEmpty())
throw new IllegalStateException("Nothing to read; file is empty");
return new StringGrid(sep,read);
}
public static StringGrid fromInput(InputStream from,String sep) throws IOException {
List read = IOUtils.readLines(from);
if(read.isEmpty())
throw new IllegalStateException("Nothing to read; file is empty");
return new StringGrid(sep,read);
}
public StringGrid(String sep, Collection data) {
super();
this.sep = sep;
List list = new ArrayList<>(data);
for(int i = 0;i< list.size(); i++) {
String line = list.get(i).trim();
//text delimiter
if(line.indexOf('\"') > 0) {
Counter counter = new Counter<>();
for(int j = 0; j < line.length(); j++) {
counter.incrementCount(line.charAt(j),1.0);
}
if(counter.getCount('"') > 1) {
String[] split = splitOnCharWithQuoting(line, sep.charAt(0), '"', '\\');
add(new ArrayList<>(Arrays.asList(split)));
}
else {
List row = new ArrayList<>(Arrays.asList(splitOnCharWithQuoting(line, sep.charAt(0), '"', '\\')));
if(numColumns < 0)
numColumns = row.size();
else if(row.size() != numColumns)
log.warn("Row " + i + " had invalid number of columns line was " + line);
add(row);
}
}
else {
List row = new ArrayList<>(Arrays.asList(splitOnCharWithQuoting(line, sep.charAt(0), '"', '\\')));
if(numColumns < 0)
numColumns = row.size();
else if(row.size() != numColumns) {
log.warn("Could not add " + line);
}
add(row);
}
}
fillOut();
}
/**
* Removes all rows with a column of NONE
* @param column the column to remove by
*/
public void removeRowsWithEmptyColumn(int column) {
List> remove = new ArrayList<>();
for(List list : this) {
if(list.get(column).equals(NONE))
remove.add(list);
}
removeAll(remove);
}
public void head(int num) {
if(num >= size())
num = size();
StringBuilder builder = new StringBuilder();
for(int i = 0; i < num; i++) {
builder.append(get(i) + "\n");
}
log.info(builder.toString());
}
/**
* Removes the specified columns from the grid
* @param columns the columns to remove
*/
public void removeColumns(Integer...columns) {
if(columns.length < 1)
throw new IllegalArgumentException("Columns must contain at least one column");
List removeOrder = Arrays.asList(columns);
//put them in the right order for removing
Collections.sort(removeOrder);
for(List list : this) {
List remove = new ArrayList<>();
for(int i = 0; i < columns.length; i++) {
remove.add(list.get(columns[i]));
}
list.removeAll(remove);
}
}
/**
* Removes all rows with a column of missingValue
* @param column he column to remove by
* @param missingValue the missingValue sentinel value
*/
public void removeRowsWithEmptyColumn(int column,String missingValue) {
List> remove = new ArrayList<>();
for(List list : this) {
if(list.get(column).equals(missingValue))
remove.add(list);
}
removeAll(remove);
}
public List> getRowsWithColumnValues(Collection values,int column) {
List> ret = new ArrayList<>();
for(List val : this) {
if(values.contains(val.get(column)))
ret.add(val);
}
return ret;
}
public void sortColumnsByWordLikelihoodIncluded(final int column) {
final Counter counter = new Counter<>();
List col = getColumn(column);
for(String s : col) {
StringTokenizer tokenizer = new StringTokenizer(s);
while(tokenizer.hasMoreTokens()) {
counter.incrementCount(tokenizer.nextToken(),1.0);
}
}
if(counter.totalCount() <= 0.0) {
log.warn("Unable to calculate probability; nothing found");
return;
}
//laplace smoothing
counter.incrementAll(counter.keySet(), 1.0);
Set remove = new HashSet<>();
for(String key : counter.keySet())
if(key.length() < 2 || key.matches("[a-z]+"))
remove.add(key);
for(String key : remove)
counter.removeKey(key);
counter.pruneKeysBelowThreshold(4.0);
final double totalCount = counter.totalCount();
Collections.sort(this,new Comparator>() {
@Override
public int compare(List o1, List o2) {
double c1 = sumOverTokens(counter,o1.get(column),totalCount);
double c2 = sumOverTokens(counter,o2.get(column),totalCount);
return Double.compare(c1, c2);
}
});
}
/* Return the log sum of the column relative to the word frequencies (equivalent to the probability in log space */
private double sumOverTokens(Counter counter,String column,double totalCount) {
StringTokenizer tokenizer = new StringTokenizer(column);
double count = 0;
while(tokenizer.hasMoreTokens())
count += Math.log(counter.getCount(column)/totalCount);
return count;
}
public StringCluster clusterColumn(int column) {
return new StringCluster(getColumn(column));
}
public void dedupeByClusterAll() {
for(int i = 0; i< size(); i++)
dedupeByCluster(i);
}
/**
* Deduplicate based on the column clustering signature
* @param column
*/
public void dedupeByCluster(int column) {
StringCluster cluster = clusterColumn(column);
System.out.println(cluster.get("family mcdonalds restaurant"));
System.out.println(cluster.get("family mcdonalds restaurants"));
List> list2 = cluster.getClusters();
for(int i = 0; i < list2.size(); i++) {
if(list2.get(i).size() > 1) {
System.out.println(list2.get(i));
}
}
FingerPrintKeyer keyer = new FingerPrintKeyer();
Set alreadyDeDupped = new HashSet<>();
for(int i = 0; i< size(); i++) {
String key = keyer.key(get(i).get(column));
Map map = cluster.get(key);
if(map != null && map.size() > 1) {
List list = filterRowsByColumn(column,map.keySet());
//deduplication to do
if(list.size() > 1)
modifyRows(alreadyDeDupped,column,list,map);
}
}
}
/**
* Cleans up the rows specified that haven't already been deduplified
* @param alreadyDeDupped the already dedupped rows
* @param column the column to homogenize
* @param rows the rows to preProcess
* @param cluster the cluster of values
*/
private void modifyRows(Set alreadyDeDupped,Integer column,List rows,Map cluster) {
String chosenKey = null;
Integer max = null;
for (Map.Entry entry : cluster.entrySet()) {
String key = entry.getKey();
int value = entry.getValue();
StringTokenizer val = new StringTokenizer(key);
List list = new ArrayList<>();
boolean allLower = true;
outer: while(val.hasMoreTokens()) {
String token = val.nextToken();
//weird capitalization
if(token.length() >= 3 && token.matches("[A-Z]+")) {
continue outer;
}
list.add(token);
}
for(String s : list) {
allLower = allLower && s.matches("[a-z]+");
}
if(allLower) {
continue;
}
//not a proper name
if(list.get(list.size() -1).toLowerCase().equals("the")) {
continue;
}
//first selection that's valid or count is higher
if(max == null || (!allLower && value > max)) {
max = value;
chosenKey = key;
}
}
//wtf is wrong with you people?
if(chosenKey == null) {
//getFromOrigin the max value of the cluster
String max2 = maximalValue(cluster);
StringTokenizer val = new StringTokenizer(max2);
List list = new ArrayList<>();
while(val.hasMoreTokens()) {
String token = val.nextToken();
//weird capitalization
if(token.length() >= 3 && token.matches("[A-Z]+")) {
token = token.charAt(0) + token.substring(1).toLowerCase();
}
list.add(token);
}
boolean allLower = true;
for(String s : list)
allLower = allLower && s.matches("[a-z]+");
if(list.get(list.size() -1).toLowerCase().equals("the")) {
max2 = max2.replaceAll("^[Tt]he","");
}
if(allLower)
max2 = StringUtils.capitalize(max2);
chosenKey = max2;
}
for(Integer i2 : rows) {
//row already processed
if(!alreadyDeDupped.contains(i2)) {
disambiguateRow(i2,column,chosenKey);
}
}
}
private String maximalValue(Map map) {
Counter counter = new Counter<>();
for (Map.Entry entry : map.entrySet()) {
counter.incrementCount(entry.getKey(), entry.getValue());
}
return counter.argMax();
}
private void disambiguateRow(Integer row,Integer column,String chosenValue) {
System.out.println("SETTING " + row + " column " + column + " to " + chosenValue);
get(row).set(column, chosenValue);
}
public List filterRowsByColumn(int column,Collection values) {
List list = new ArrayList<>();
for(int i = 0; i< size(); i++) {
if(values.contains(get(i).get(column)))
list.add(i);
}
return list;
}
public void sortBy(final int column) {
Collections.sort(this, new Comparator>() {
@Override
public int compare(List o1,List o2) {
return o1.get(column).compareTo(o2.get(column));
}
});
}
public List toLines() {
List lines = new ArrayList<>();
for(List list : this) {
StringBuilder sb = new StringBuilder();
for(String s : list) {
sb.append(s.replaceAll(sep," "));
sb.append(sep);
}
lines.add(sb.toString().substring(0, sb.lastIndexOf(sep)));
}
return lines;
}
public void swap(int column1,int column2) {
List col1 = getColumn(column1);
List col2 = getColumn(column2);
for(int i = 0; i< size(); i++) {
get(i).set(column1,col2.get(i));
get(i).set(column2,col1.get(i));
}
}
public void merge(int column1,int column2) {
checkInvalidColumn(column1);
checkInvalidColumn(column2);
if(column1 != column2)
for(List list : this) {
StringBuilder sb = new StringBuilder();
sb.append(list.get(column1));
sb.append(list.get(column2));
list.set(Math.min(column1,column2),sb.toString().replaceAll("\"","").replace(sep," "));
list.remove(Math.max(column1,column2));
}
numColumns--;
}
public StringGrid getAllWithSimilarity(double threshold,int firstColumn,int secondColumn) {
for(int column : new int[]{firstColumn,secondColumn})
checkInvalidColumn(column);
StringGrid grid = new StringGrid(sep,numColumns);
for(List list : this) {
double sim = MathUtils.stringSimilarity(list.get(firstColumn),list.get(secondColumn));
if(sim >= threshold)
grid.addRow(list);
}
return grid;
}
public void writeLinesTo(String path) throws IOException {
FileUtils.writeLines(new File(path),toLines());
}
public void fillDown(String value,int column) {
checkInvalidColumn(column);
for(List list : this)
list.set(column,value);
}
public StringGrid select(int column,String value) {
StringGrid grid = new StringGrid(sep,numColumns);
for(int i = 0; i< size(); i++) {
List row = get(i);
if(row.get(column).equals(value)) {
grid.addRow(row);
}
}
return grid;
}
public void split(int column,String sepBy) {
List col = getColumn(column);
int validate = -1;
Set remove = new HashSet<>();
for(int i = 0; i< col.size(); i++) {
String s = col.get(i);
String[] split2 = StringUtils.splitOnCharWithQuoting(s, sepBy.charAt(0), '"', '\\');
if(validate < 0)
validate = split2.length;
else if(validate != split2.length) {
log.warn("Row " + get(i) + " will be invalid after split; removing");
remove.add(s);
}
}
for(String s : remove) {
StringGrid grid = select(column,s);
removeAll(grid);
}
Map> replace = new HashMap<>();
for(int i = 0; i< size(); i++) {
List list = get(i);
List newList = new ArrayList<>();
String split = list.get(column);
String[] split2 = StringUtils.splitOnCharWithQuoting(split, sepBy.charAt(0), '"', '\\');
//add right next to where column was split
for(int j = 0; j< list.size(); j++) {
if(j == column)
for(String s : split2)
newList.add(s);
else
newList.add(list.get(j));
}
replace.put(i,newList);
}
//prevent concurrent modification
for (Map.Entry> entry : replace.entrySet()) {
set(entry.getKey(), entry.getValue());
}
}
public void filterBySimilarity(double threshold,int firstColumn,int secondColumn) {
for(int column : new int[]{firstColumn,secondColumn})
checkInvalidColumn(column);
List> remove = new ArrayList<>();
for(List list : this) {
double sim = MathUtils.stringSimilarity(list.get(firstColumn),list.get(secondColumn));
if(sim < threshold)
remove.add(list);
}
removeAll(remove);
}
public void prependToEach(String prepend, int toColumn) {
for(List row : this) {
String currVal = row.get(toColumn);
row.set(toColumn,prepend + currVal);
}
}
public void appendToEach(String append, int toColumn) {
for(List row : this) {
String currVal = row.get(toColumn);
row.set(toColumn, currVal + append);
}
}
public void addColumn(List column) {
if(column.size() != this.size())
throw new IllegalArgumentException("Unable to add column; not enough rows");
for(int i = 0; i< size();i++) {
get(i).add(column.get(i));
}
}
/**
* Combine the column based on a template and a number of template variable
* columns. Note that this will also collapse the columns specified (removing them)
*
* @param templateColumn the column with the template ( uses printf style templating)
* @param paramColumns the columns with template variables
*/
public void combineColumns(int templateColumn,Integer[] paramColumns) {
for(List list : this) {
List format = new ArrayList<>();
for(int j : paramColumns)
format.add(list.get(j));
list.set(templateColumn,String.format(list.get(templateColumn), (Object[]) format.toArray(new String[]{})));
//collapse columns
list.removeAll(format);
}
}
/**
* Combine the column based on a template and a number of template variable
* columns. Note that this will also collapse the columns specified (removing them)
*
* @param templateColumn the column with the template ( uses printf style templating)
* @param paramColumns the columns with template variables
*/
public void combineColumns(int templateColumn,int[] paramColumns) {
for(List list : this) {
List format = new ArrayList<>();
for(int j : paramColumns)
format.add(list.get(j));
list.set(templateColumn,String.format(list.get(templateColumn), (Object[]) format.toArray(new String[]{})));
//collapse columns
list.removeAll(format);
}
}
public void addRow(List row) {
if(row.isEmpty()) {
log.warn("Unable to add empty row");
}
else if(!isEmpty() && row.size() != get(0).size()) {
log.warn("Unable to add row; not the same number of columns");
}
else
add(row);
}
public Map>> mapByPrimaryKey(int columnKey) {
Map>> map = new HashMap<>();
for(List line : this) {
String val = line.get(columnKey);
List> get = map.get(val);
if(get == null) {
get = new ArrayList<>();
map.put(val,get);
}
get.add(new ArrayList<>(Arrays.asList(sep)));
}
return map;
}
public List getRow(int row) {
checkInvalidRow(row);
return new ArrayList<>(get(row));
}
public List getColumn(int column) {
checkInvalidColumn(column);
List ret = new ArrayList<>();
for(List list : this) {
ret.add(list.get(column));
}
return ret;
}
private void checkInvalidRow(int row) {
if(row < 0 || row >= size())
throw new IllegalArgumentException("Row does not exist");
}
private void checkInvalidColumn(int column) {
if(column < 0 || column >= numColumns)
throw new IllegalArgumentException("Invalid column " + column);
}
public StringGrid getRowsWithDuplicateValuesInColumn(int column) {
checkInvalidColumn(column);
StringGrid grid = new StringGrid(sep,numColumns);
List columns = getColumn(column);
Counter counter = new Counter<>();
for(String val : columns)
counter.incrementCount(val,1.0);
counter.pruneKeysBelowThreshold(2.0);
Set keys = counter.keySet();
for(List row : this) {
for(String key : keys)
if(row.get(column).equals(key))
grid.addRow(row);
}
return grid;
}
public StringGrid getRowWithOnlyOneOccurrence(int column) {
checkInvalidColumn(column);
StringGrid grid = new StringGrid(sep,numColumns);
List columns = getColumn(column);
Counter counter = new Counter<>();
for(String val : columns)
counter.incrementCount(val,1.0);
Set keys = new HashSet<>(counter.keySet());
for(String key : keys) {
if(counter.getCount(key) > 1) {
counter.removeKey(key);
}
}
for(List row : this) {
for(String key : keys)
if(row.get(column).equals(key))
grid.addRow(row);
}
return grid;
}
public StringGrid getUniqueRows() {
StringGrid ret = new StringGrid(this);
ret.stripDuplicateRows();
return ret;
}
public void stripDuplicateRows() {
Set> set = new HashSet<>(this);
clear();
addAll(set);
}
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