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update code to use URI methods
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@StephanPreibisch
StephanPreibisch committed Oct 16, 2024
1 parent 7977d1a commit 752bccf
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Showing 14 changed files with 39 additions and 108 deletions.
16 changes: 4 additions & 12 deletions src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/FileListDatasetDefinition.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1159,16 +1159,8 @@ else if (choice.equals( Z_VARIABLE_CHOICE ))

URI chosenPathXMLURI, chosenPathDataURI;

try
{
chosenPathXMLURI = new URI( chosenPathXML );
chosenPathDataURI = new URI( chosenPathData );
}
catch ( URISyntaxException e )
{
IOFunctions.println( "Could not convert provided paths into a URI: " + e );
return null;
}
chosenPathXMLURI = URITools.toURI( chosenPathXML );
chosenPathDataURI = URITools.toURI( chosenPathData );

if ( !URITools.isKnownScheme( chosenPathDataURI ) )
{
Expand Down Expand Up @@ -1270,8 +1262,8 @@ public int compare(Group< ViewDescription > o1, Group< ViewDescription > o2)
if (params == null)
return null;

String dataPath = URITools.removeFilePrefix( chosenPathDataURI );
String xmlPath = URITools.removeFilePrefix( chosenPathXMLURI );
String dataPath = URITools.fromURI( chosenPathDataURI );
String xmlPath = URITools.fromURI( chosenPathXMLURI );

if ( !new File( dataPath ).exists() )
{
Expand Down
12 changes: 2 additions & 10 deletions src/main/java/net/preibisch/mvrecon/fiji/plugin/XMLSaveAs.java
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Original file line number Diff line number Diff line change
Expand Up @@ -84,15 +84,7 @@ public static URI saveAs( final SpimData2 data, final String suggestedFileName )
final String uriString = gd.getNextString();
final URI newXMLPath, newBaseDir;

try
{
newXMLPath = new URI( uriString );
}
catch ( URISyntaxException ex )
{
IOFunctions.println( "Could not convert provided XML path into a URI: " + ex );
return null;
}
newXMLPath = URITools.toURI( uriString );

if ( !URITools.isKnownScheme( newXMLPath ) )
{
Expand All @@ -117,7 +109,7 @@ else if ( N5ImageLoader.class.isInstance( imgLoader ) )
final URI n5URI = ((N5ImageLoader)imgLoader).getN5URI();

IOFunctions.println( "Path of N5 (stays in old location): " + n5URI );
data.getSequenceDescription().setImgLoader( new N5ImageLoader( URITools.toFile( n5URI ), data.getSequenceDescription() ) );
data.getSequenceDescription().setImgLoader( new N5ImageLoader( new File( URITools.fromURI( n5URI ) ), data.getSequenceDescription() ) );
}
else if ( Hdf5ImageLoader.class.isInstance( imgLoader ) )
{
Expand Down
19 changes: 4 additions & 15 deletions src/main/java/net/preibisch/mvrecon/fiji/plugin/queryXML/GenericLoadParseQueryXML.java
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Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,6 @@
import net.preibisch.mvrecon.fiji.plugin.util.PluginHelper;
import net.preibisch.mvrecon.fiji.spimdata.EmptyEntity;
import net.preibisch.mvrecon.fiji.spimdata.NamePattern;
import net.preibisch.mvrecon.fiji.spimdata.SpimData2;
import util.URITools;

/**
Expand Down Expand Up @@ -255,10 +254,7 @@ public boolean queryXML(
this.attributeChoice = new HashMap< String, Integer >();

// try parsing if it ends with XML
try
{
tryParsing( new URI( defaultXMLURI ), false );
} catch (URISyntaxException e) {}
tryParsing( URITools.toURI( defaultXMLURI ), false );

if ( additionalTitle != null && additionalTitle.length() > 0 )
gd = new GenericDialogPlus( "Select dataset for " + additionalTitle );
Expand Down Expand Up @@ -318,14 +314,7 @@ public boolean queryXML(
// try to parse the file anyways
boolean success;

try
{
success = tryParsing( new URI( xmlURI ), true );
}
catch (URISyntaxException e)
{
success = false;
}
success = tryParsing( URITools.toURI( xmlURI ), true );

if ( buttonText != null && xmlURI.toLowerCase().equals( "define" ) && buttonText.get( 0 ).equals( "Define a new dataset" ) )
{
Expand Down Expand Up @@ -906,9 +895,9 @@ public void textValueChanged( final TextEvent t )
// try parsing if it ends with XML
try
{
tryParsing( new URI( xmlFilename ), false );
tryParsing( URITools.toURI( xmlFilename ), false );
}
catch (URISyntaxException e)
catch (Exception e)
{
lpq.message1 = errorMsg1;
lpq.message2 = noMsg2;
Expand Down
13 changes: 3 additions & 10 deletions src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/ParametersResaveN5Api.java
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,7 @@
import net.preibisch.legacy.io.IOFunctions;
import net.preibisch.mvrecon.fiji.plugin.util.GUIHelper;
import net.preibisch.mvrecon.fiji.plugin.util.PluginHelper;
import util.URITools;

public class ParametersResaveN5Api
{
Expand Down Expand Up @@ -171,16 +172,8 @@ public static ParametersResaveN5Api getParamtersIJ(

if ( askForPaths )
{
try
{
n5params.xmlURI = new URI( gdp.getNextString() );
n5params.n5URI = new URI( gdp.getNextString() );
}
catch ( URISyntaxException e )
{
IOFunctions.println( "Cannot create URIs for provided paths: " + e );
return null;
}
n5params.xmlURI = URITools.toURI( gdp.getNextString() );
n5params.n5URI = URITools.toURI( gdp.getNextString() );

IOFunctions.println( "XML & metadata path: " + n5params.xmlURI );
IOFunctions.println( "Image data path: " + n5params.n5URI );
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_N5Api.java
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Original file line number Diff line number Diff line change
Expand Up @@ -268,7 +268,7 @@ public static SpimData2 resaveN5(
{
// we need to init with File and not with URI, since otherwise the N5ImageLoader will trigger the exception above if this object is re-used
// this seems to not matter when opening directly from disc...
sdReduced.getSequenceDescription().setImgLoader( new N5ImageLoader( URITools.toFile( n5Params.n5URI ), sdReduced.getSequenceDescription() ) );
sdReduced.getSequenceDescription().setImgLoader( new N5ImageLoader( new File( URITools.fromURI( n5Params.n5URI ) ), sdReduced.getSequenceDescription() ) );
n5Writer.close();
}
else if ( format == StorageFormat.N5 ) // some cloud location
Expand All @@ -277,7 +277,7 @@ else if ( format == StorageFormat.N5 ) // some cloud location
}
else if ( format == StorageFormat.HDF5 )
{
sdReduced.getSequenceDescription().setImgLoader( new Hdf5ImageLoader( new File( URITools.removeFilePrefix( n5Params.n5URI ) ), null, sdReduced.getSequenceDescription() ) );
sdReduced.getSequenceDescription().setImgLoader( new Hdf5ImageLoader( new File( URITools.fromURI( n5Params.n5URI ) ), null, sdReduced.getSequenceDescription() ) );
n5Writer.close();
}
else
Expand Down
19 changes: 4 additions & 15 deletions src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_TIFF.java
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Original file line number Diff line number Diff line change
Expand Up @@ -85,7 +85,7 @@ public void run( final String arg0 )
final SpimData2 data = lpq.getData();
final List< ViewId > viewIds = SpimData2.getAllViewIdsSorted( data, lpq.getViewSetupsToProcess(), lpq.getTimePointsToProcess() );

final File file = new File( URITools.removeFilePrefix( params.getXMLPath() ) );
final File file = new File( URITools.fromURI( params.getXMLPath() ) );

// write the TIFF's
writeTIFF( data, viewIds, file.getParent(), params.compress, progressWriter );
Expand Down Expand Up @@ -136,17 +136,7 @@ public static ParametersResaveAsTIFF getParameters()
if ( !fullPath.endsWith( ".xml" ) )
fullPath += ".xml";

final URI uri;

try
{
uri = new URI( fullPath );
}
catch (URISyntaxException e )
{
IOFunctions.println( "Cannot interpret '" + fullPath + "' as URI. Stopping." );
return null;
}
final URI uri = URITools.toURI( fullPath );

if ( !URITools.isFile( uri ) )
{
Expand Down Expand Up @@ -214,7 +204,6 @@ public static void writeTIFF( final SpimData spimData, final List< ViewId > view
}
}


public static SpimData2 createXMLObject( final SpimData2 spimData, final List< ViewId > viewIds, final ParametersResaveAsTIFF params )
{
int layoutTP = 0, layoutChannels = 0, layoutIllum = 0, layoutAngles = 0, layoutTiles = 0;
Expand Down Expand Up @@ -263,7 +252,7 @@ public static SpimData2 createXMLObject( final SpimData2 spimData, final List< V

// Re-assemble a new SpimData object containing the subset of viewsetups and timepoints selected
final SpimData2 newSpimData;
final URI newBasePath = new File( URITools.removeFilePrefix( params.getXMLPath() ) ).getParentFile().toURI();
final URI newBasePath = URITools.toURI( new File( URITools.fromURI( params.getXMLPath() ) ).getParentFile().toString() );

boolean isEqual = false;

Expand All @@ -282,7 +271,7 @@ public static SpimData2 createXMLObject( final SpimData2 spimData, final List< V
newSpimData = SpimData2Tools.reduceSpimData2( spimData, viewIds, newBasePath );

final StackImgLoaderIJ imgLoader = new StackImgLoaderIJ(
new File( URITools.removeFilePrefix( params.getXMLPath() ) ).getParentFile(),
new File( URITools.fromURI( params.getXMLPath() ) ).getParentFile(),
filename,
layoutTP, layoutChannels, layoutIllum, layoutAngles, layoutTiles, newSpimData.getSequenceDescription() );
newSpimData.getSequenceDescription().setImgLoader( imgLoader );
Expand Down
20 changes: 0 additions & 20 deletions src/main/java/net/preibisch/mvrecon/fiji/spimdata/SpimData2.java
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Original file line number Diff line number Diff line change
Expand Up @@ -577,24 +577,4 @@ public static < V extends ViewId > ArrayList< Group< V > > filterGroupsForMissin

return groupsOut;
}

public static void main( String[] args )
{
File f = new File( "/nrs/" );
URI u = f.toURI();
//u = URI.create( "s3://myBucket/" ) ;

URI u2 = URI.create( u.toString() + ( u.toString().endsWith( "/" ) ? "" : "/") + "test.xml" );


System.out.println( u );
System.out.println( u2 );
System.out.println( URITools.getParent( u2 ) );
System.out.println( URITools.getParent( URI.create("/nrs/test.xml") ) );
System.out.println( new File( u2 ) );
System.out.println( new File( URI.create("file:/nrs/test.xml") ) );
// System.out.println( new File( URI.create("/nrs/test.xml") ) ); // FAILS
System.out.println( URITools.removeFilePrefix( u2 ) );
System.out.println( Paths.get(u2.getPath()).getFileName().toString());
}
}
6 changes: 1 addition & 5 deletions src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorerPanel.java
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Original file line number Diff line number Diff line change
Expand Up @@ -716,11 +716,7 @@ public ArrayList< ExplorerWindowSetable > initPopups()

// add link to wiki
popups.add( new LabelPopUp( "Help" ) );
try
{
popups.add( new SimpleHyperlinkPopup("Browse Wiki...", new URI( "https://imagej.net/Multiview-Reconstruction" )) );
}
catch ( URISyntaxException e ) { e.printStackTrace(); }
popups.add( new SimpleHyperlinkPopup("Browse Wiki...", URITools.toURI( "https://imagej.net/Multiview-Reconstruction" )) );

return popups;
}
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ResavePopup.java
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Original file line number Diff line number Diff line change
Expand Up @@ -192,7 +192,7 @@ else if (choice == JOptionPane.YES_OPTION)
params.xmlPath = panel.xml();

// write the TIFF's
Resave_TIFF.writeTIFF( data, viewIds, new File( URITools.removeFilePrefix( params.getXMLPath() ) ).getParent(), params.compress, progressWriter );
Resave_TIFF.writeTIFF( data, viewIds, new File( URITools.fromURI( params.getXMLPath() ) ).getParent(), params.compress, progressWriter );

// write the XML
final SpimData2 newSpimData = Resave_TIFF.createXMLObject( data, viewIds, params );
Expand Down Expand Up @@ -231,7 +231,7 @@ else if ( index == 2 || index == 3 ) // HDF5, compressed HDF5
File hdf5File;
int i = 1;

String xml = URITools.removeFilePrefix( panel.xml() );
String xml = URITools.fromURI( panel.xml() );

do
{
Expand Down
4 changes: 2 additions & 2 deletions ...a/net/preibisch/mvrecon/fiji/spimdata/imgloaders/filemap2/XmlIOFileMapImgLoaderLOCI2.java
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@ public class XmlIOFileMapImgLoaderLOCI2 implements XmlIoBasicImgLoader< FileMapI
@Override
public Element toXml( final FileMapImgLoaderLOCI2 imgLoader, final URI basePathURI )
{
return toXml(imgLoader, new File( URITools.removeFilePrefix( basePathURI ) ) );
return toXml(imgLoader, new File( URITools.fromURI( basePathURI ) ) );
}

@Override
Expand Down Expand Up @@ -92,7 +92,7 @@ public Element toXml(FileMapImgLoaderLOCI2 imgLoader, File basePath)
public FileMapImgLoaderLOCI2 fromXml(Element elem, final URI basePathURI,
AbstractSequenceDescription< ?, ?, ? > sequenceDescription)
{
return fromXml(elem, new File( URITools.removeFilePrefix( basePathURI ) ), sequenceDescription);
return fromXml(elem, new File( URITools.fromURI( basePathURI ) ), sequenceDescription);
}

@Override
Expand Down
16 changes: 8 additions & 8 deletions ...n/java/net/preibisch/mvrecon/fiji/spimdata/interestpoints/InterestPointsTextFileList.java
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Original file line number Diff line number Diff line change
Expand Up @@ -147,15 +147,15 @@ public boolean saveInterestPoints( final boolean forceWrite )

try
{
final File dir = new File( URITools.removeFilePrefix( getBaseDir() ), getFile().getParent() );
final File dir = new File( URITools.fromURI( getBaseDir() ), getFile().getParent() );

if ( !dir.exists() )
{
IOFunctions.println( "Creating directory: " + dir );
dir.mkdirs();
}

final File f = new File( URITools.removeFilePrefix( getBaseDir() ), getFile().toString() + getInterestPointsExt() );
final File f = new File( URITools.fromURI( getBaseDir() ), getFile().toString() + getInterestPointsExt() );
final PrintWriter out = TextFileAccess.openFileWriteEx( f );

// header
Expand Down Expand Up @@ -194,15 +194,15 @@ public boolean saveCorrespondingInterestPoints( final boolean forceWrite )

try
{
final File dir = new File( URITools.removeFilePrefix( getBaseDir() ), getFile().getParent() );
final File dir = new File( URITools.fromURI( getBaseDir() ), getFile().getParent() );

if ( !dir.exists() )
{
IOFunctions.println( "Creating directory: " + dir );
dir.mkdirs();
}

final File f = new File( URITools.removeFilePrefix( getBaseDir() ), getFile().toString() + getCorrespondencesExt() );
final File f = new File( URITools.fromURI( getBaseDir() ), getFile().toString() + getCorrespondencesExt() );

final PrintWriter out = TextFileAccess.openFileWriteEx( f );

Expand Down Expand Up @@ -241,7 +241,7 @@ protected boolean loadCorrespondences()
{
final ArrayList< CorrespondingInterestPoints > correspondingInterestPoints = new ArrayList<>();

final BufferedReader in = TextFileAccess.openFileReadEx( new File( URITools.removeFilePrefix( getBaseDir() ), getFile().toString() + getCorrespondencesExt() ) );
final BufferedReader in = TextFileAccess.openFileReadEx( new File( URITools.fromURI( getBaseDir() ), getFile().toString() + getCorrespondencesExt() ) );

// the header
do {} while ( !in.readLine().startsWith( "id" ) );
Expand Down Expand Up @@ -285,7 +285,7 @@ protected boolean loadInterestPoints()
{
final ArrayList< InterestPoint > interestPoints = new ArrayList<>();

final BufferedReader in = TextFileAccess.openFileReadEx( new File( URITools.removeFilePrefix( getBaseDir() ), getFile().toString() + getInterestPointsExt() ) );
final BufferedReader in = TextFileAccess.openFileReadEx( new File( URITools.fromURI( getBaseDir() ), getFile().toString() + getInterestPointsExt() ) );

// the header
do {} while ( !in.readLine().startsWith( "id" ) );
Expand Down Expand Up @@ -323,15 +323,15 @@ protected boolean loadInterestPoints()
@Override
public boolean deleteInterestPoints()
{
final File ip = new File( URITools.removeFilePrefix( getBaseDir() ), getFile().toString() + getInterestPointsExt() );
final File ip = new File( URITools.fromURI( getBaseDir() ), getFile().toString() + getInterestPointsExt() );

return ip.delete();
}

@Override
public boolean deleteCorrespondingInterestPoints()
{
final File corr = new File( URITools.removeFilePrefix( getBaseDir() ), getFile().toString() + getCorrespondencesExt() );
final File corr = new File( URITools.fromURI( getBaseDir() ), getFile().toString() + getCorrespondencesExt() );

return corr.delete();
}
Expand Down
8 changes: 4 additions & 4 deletions src/main/java/net/preibisch/mvrecon/process/export/ExportN5Api.java
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Original file line number Diff line number Diff line change
Expand Up @@ -172,10 +172,10 @@ public <T extends RealType<T> & NativeType<T>> boolean exportImage(
{
if ( storageType == StorageFormat.HDF5 )
{
final File dir = new File( URITools.removeFilePrefix( path ) ).getParentFile();
final File dir = new File( URITools.fromURI( path ) ).getParentFile();
if ( !dir.exists() )
dir.mkdirs();
driverVolumeWriter = new N5HDF5Writer( URITools.removeFilePrefix( path ) );
driverVolumeWriter = new N5HDF5Writer( URITools.fromURI( path ) );
}
else if ( storageType == StorageFormat.N5 || storageType == StorageFormat.ZARR )
{
Expand Down Expand Up @@ -529,7 +529,7 @@ else if ( storageType == StorageFormat.N5 )

try
{
this.path = new URI( defaultPathURI = gd.getNextString().trim() );
this.path = URITools.toURI( defaultPathURI = gd.getNextString().trim() );
}
catch ( Exception e )
{
Expand All @@ -553,7 +553,7 @@ else if ( storageType == StorageFormat.N5 )
{
try
{
this.xmlOut = new URI( defaultXMLOutURI = gd.getNextString().trim() );//defaultXMLOut = gd.getNextString();
this.xmlOut = URITools.toURI( defaultXMLOutURI = gd.getNextString().trim() );//defaultXMLOut = gd.getNextString();
}
catch ( Exception e )
{
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/net/preibisch/mvrecon/process/n5api/SpimData2Tools.java
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Original file line number Diff line number Diff line change
Expand Up @@ -236,7 +236,7 @@ public static Pair<Boolean, Boolean> writeSpimData(
else if ( StorageFormat.N5.equals(storageType) ) // some cloud location
sequence.setImgLoader( new N5CloudImageLoader( null, n5PathURI, sequence) );
else if ( StorageFormat.HDF5.equals(storageType) )
sequence.setImgLoader( new Hdf5ImageLoader( new File( URITools.removeFilePrefix( n5PathURI ) ), null, sequence) );
sequence.setImgLoader( new Hdf5ImageLoader( new File( URITools.fromURI( n5PathURI ) ), null, sequence) );
else
throw new RuntimeException( storageType + " not supported." );

Expand Down Expand Up @@ -287,7 +287,7 @@ else if ( StorageFormat.HDF5.equals(storageType) )
else if ( StorageFormat.N5.equals(storageType) ) // some cloud location
sequence.setImgLoader( new N5CloudImageLoader( null, n5PathURI, sequence) );
else if ( StorageFormat.HDF5.equals(storageType) )
sequence.setImgLoader( new Hdf5ImageLoader( new File( URITools.removeFilePrefix( n5PathURI ) ), null, sequence) );
sequence.setImgLoader( new Hdf5ImageLoader( new File( URITools.fromURI( n5PathURI ) ), null, sequence) );
else
throw new RuntimeException( storageType + " not supported." );

Expand Down
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