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fix/test: more flexible NumericalFilenamePattern matching #76

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25d824b
fix/test: more flexible NumericalFilenamePattern matching
bogovicj Jul 23, 2025
0af4d5b
NumericalFilenamePatternDetector rm test main method
bogovicj Jul 23, 2025
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139 changes: 85 additions & 54 deletions ...eibisch/mvrecon/fiji/datasetmanager/patterndetector/NumericalFilenamePatternDetector.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,32 +24,104 @@

import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import java.util.function.Predicate;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import java.util.stream.Stream;

import net.imglib2.util.Pair;
import net.imglib2.util.ValuePair;

public class NumericalFilenamePatternDetector implements FilenamePatternDetector
{

private static final Pattern NUMERICAL_PATTERN = Pattern.compile( "(\\d+)(.*)" );
private static final Pattern PREFIX_PATTERN = Pattern.compile( "([^0-9]+)(\\d+).*" );

private List<String> invariants;
private List<List<String>> variables;

private List<String> tStrings;
private StringBuilder stringRepresentation;

@Override
public void detectPatterns(List< String > files)
{
Pair< List< String >, List< List< String > > > res = detectNumericPatterns( files );
invariants = res.getA();
variables = res.getB();
tStrings = new ArrayList<>();
files.forEach( tStrings::add );
invariants = new ArrayList<>();
variables = new ArrayList<>();
stringRepresentation = new StringBuilder();

while(true) {
boolean hadNumeric = numericPrefixes(tStrings);
boolean hadPrefix = nonnumericPrefixes(tStrings);
if( !hadNumeric && !hadPrefix )
break;
}
suffix(tStrings);
}


private boolean suffix(Iterable<String> strings) {

String suffix = null;
for (String s : strings){
if (suffix == null)
suffix = s;
else if( !s.equals(suffix)) {
stringRepresentation.append(".*");
return false;
}
}
stringRepresentation.append(suffix);
return true;
}

private boolean nonnumericPrefixes(Iterable<String> strings)
{
List<String> prefixes = new ArrayList<>();
List<String> remainders = new ArrayList<>();
for (String s : strings){
Matcher m = PREFIX_PATTERN.matcher( s );
if (! m.matches())
return false;

prefixes.add(m.group( 1 ));
remainders.add(m.group( 2 ));
}

final String prefix = prefixes.get(0);
if (!prefixes.stream().allMatch(x -> x.equals(prefix))) {
return false;
}

invariants.add(prefix);
stringRepresentation.append(prefix);

tStrings = tStrings.stream().map( s -> s.substring(prefix.length() ) ).collect( Collectors.toList() );
return true;
}

private boolean numericPrefixes(Iterable<String> strings)
{
List<String> prefixes = new ArrayList<>();
List<String> remainders = new ArrayList<>();
for (String s : strings){
Matcher m = NUMERICAL_PATTERN.matcher( s );
if (! m.matches())
return false;

prefixes.add(m.group( 1 ));
remainders.add(m.group( 2 ));
}

stringRepresentation.append(String.format("{%d}", variables.size()));
variables.add( prefixes );
tStrings = remainders;
return true;
}

@Override
public String getInvariant(int n){ return invariants.get( n );}
@Override
Expand All @@ -67,13 +139,10 @@ public Pattern getPatternAsRegex()
@Override
public String getStringRepresentation()
{
StringBuilder sb = new StringBuilder();
for (int i = 0; i < invariants.size() - 1; i++)
sb.append( invariants.get( i ) + "{" + i + "}" );
sb.append( invariants.get( invariants.size()-1 ) );
return sb.toString();
return stringRepresentation.toString();
}


@Deprecated
public static String maxPrefix(List<String> strings)
{

Expand Down Expand Up @@ -105,6 +174,7 @@ public static String maxPrefix(List<String> strings)
}
}

@Deprecated
public static Pair<List<String>, List<String>> collectNumericPrefixes(Iterable<String> strings)
{
Pattern p = Pattern.compile( "(\\d+)(.+?)" );
Expand All @@ -120,6 +190,7 @@ public static Pair<List<String>, List<String>> collectNumericPrefixes(Iterable<S
return new ValuePair< List<String>, List<String> >( prefixes, remainders );
}

@Deprecated
public static Pair<List<String>, List<List<String>>> detectNumericPatterns(Iterable<String> strings)
{

Expand Down Expand Up @@ -167,44 +238,4 @@ public static Pair<List<String>, List<List<String>>> detectNumericPatterns(Itera
@Override
public int getNumVariables(){return variables.size();}

public static void main(String[] args)
{
List< String > files = null;
try
{
Stream< Path > w = Files.list( Paths.get( "/Users/david/Desktop/Bordeaux/BIC Reconstruction/170331_EA810_Fred_MosZXY_Nocrop_12-36-22/" ));

files = w.filter( new Predicate< Path >()
{

boolean res = false;
@Override
public boolean test(Path t)
{
try
{
res = Files.size( t ) > 100000;
}
catch ( IOException e )
{
// TODO Auto-generated catch block
e.printStackTrace();
}
return res;
}
} ).map( p -> p.toFile().getAbsolutePath()).collect( Collectors.toList() );
}
catch ( IOException e )
{
// TODO Auto-generated catch block
e.printStackTrace();
}

System.out.println( files.get( 0 ) );

Pair< List< String >, List< List< String > > > detectNumericPatterns = detectNumericPatterns( files );


}

}
75 changes: 75 additions & 0 deletions ...ch/mvrecon/fiji/datasetmanager/patterndetector/NumericalFilenamePatternDetectorTests.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,75 @@
package net.preibisch.mvrecon.fiji.datasetmanager.patterndetector;

import static org.junit.Assert.assertArrayEquals;
import static org.junit.Assert.assertEquals;

import java.util.Arrays;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;

import org.junit.Ignore;
import org.junit.Test;

public class NumericalFilenamePatternDetectorTests {

@Test
public void testStringRepresentation() {

final NumericalFilenamePatternDetector patternDetector = new NumericalFilenamePatternDetector();

patternDetector.detectPatterns(Arrays.asList("0_t0", "1_t0"));
assertEquals("{0}_t{1}", patternDetector.getStringRepresentation());

patternDetector.detectPatterns(Arrays.asList("s0_t0", "s1_t0"));
assertEquals("s{0}_t{1}", patternDetector.getStringRepresentation());

patternDetector.detectPatterns(Arrays.asList("s0_suffix", "s1_suffix"));
assertEquals("s{0}_suffix", patternDetector.getStringRepresentation());

patternDetector.detectPatterns(Arrays.asList("s0_a", "s1_b"));
assertEquals("s{0}.*", patternDetector.getStringRepresentation());
}

@Test
public void testNumVariables() {

final List<String> prefixes = Arrays.asList("setup", "");
final List<String> suffixes = Arrays.asList("_t0", "");
final List<String> values = Arrays.asList("10", "21");

pairs(prefixes, suffixes).forEach(ps -> {

List<String> list = values.stream().map(v -> {
return ps[0] + v + ps[1];
}).collect(Collectors.toList());

final NumericalFilenamePatternDetector patternDetector = new NumericalFilenamePatternDetector();
patternDetector.detectPatterns(list);

int nVariables = ps[1].equals(suffixes.get(0)) ? 2 : 1;
assertEquals(nVariables, patternDetector.getNumVariables());

assertEquals(values.get(0), patternDetector.getValuesForVariable(0).get(0));
assertEquals(values.get(1), patternDetector.getValuesForVariable(0).get(1));

if( nVariables == 2) {
assertEquals("0", patternDetector.getValuesForVariable(1).get(0));
assertEquals("0", patternDetector.getValuesForVariable(1).get(1));
}

});

}

private static List<String[]> pairs( List<String> prefix, List<String> suffix) {

return prefix.stream().flatMap( p -> {
return suffix.stream().map(s -> {
return new String[] {p, s};
});
}).collect(Collectors.toList());
}

}