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Add meaningful error when no images could be found in a table
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tischi committed Jun 12, 2024
1 parent 04da10a commit c84e7c6
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Showing 2 changed files with 63 additions and 6 deletions.
16 changes: 10 additions & 6 deletions src/main/java/org/embl/mobie/lib/SourcesFromTableCreator.java
Original file line number Diff line number Diff line change
Expand Up @@ -44,9 +44,8 @@
import tech.tablesaw.columns.Column;

import java.io.File;
import java.util.ArrayList;
import java.util.LinkedHashSet;
import java.util.List;
import java.lang.reflect.Array;
import java.util.*;

import static tech.tablesaw.aggregate.AggregateFunctions.mean;

Expand Down Expand Up @@ -103,8 +102,12 @@ public SourcesFromTableCreator( String tablePath, List< String > imageColumns, L
}
}


// region table for grid view
//
if ( imageFileSources.isEmpty() )
throw new RuntimeException("No images found in the table! Please check your table and image column names: " + imageColumns );

int numSources = imageFileSources.get( 0 ).getSources().size();

if ( table.rowCount() == numSources )
Expand All @@ -126,14 +129,15 @@ public SourcesFromTableCreator( String tablePath, List< String > imageColumns, L
regionTable = Table.create( "image table" );

// init columns
LinkedHashSet< String > uniqueImagePaths = new LinkedHashSet<>(); // important not to change the order!
LinkedHashSet< String > uniqueRegionNames = new LinkedHashSet<>(); // important not to change the order!
String imageColumnName = new TableImageSource( imageColumns.get( 0 ) ).columnName;
StringColumn imageColumn = table.stringColumn( imageColumnName );
for ( String imagePath : imageColumn )
{
uniqueImagePaths.add( imagePath );
// FIXME It would be nice to shorten the names, e.g. by removing everything that is common to all image paths
uniqueRegionNames.add( imagePath );
}
final List< String > regions = new ArrayList<>( uniqueImagePaths );
final List< String > regions = new ArrayList<>( uniqueRegionNames );
regionTable.addColumns( StringColumn.create( ColumnNames.REGION_ID, regions ) ); // needed for region table
regionTable.addColumns( StringColumn.create( imageColumnName, regions ) ); // needed for joining the tables

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53 changes: 53 additions & 0 deletions src/test/java/projects/OpenRemoteAlexandraTable.java
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@@ -0,0 +1,53 @@
/*-
* #%L
* Fiji viewer for MoBIE projects
* %%
* Copyright (C) 2018 - 2024 EMBL
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package projects;

import net.imagej.ImageJ;
import org.embl.mobie.MoBIE;
import org.embl.mobie.MoBIESettings;
import org.embl.mobie.command.open.OpenTableCommand;
import org.embl.mobie.lib.transform.GridType;

import java.io.File;
import java.io.IOException;

public class OpenRemoteAlexandraTable
{
public static void main( String[] args ) throws IOException
{
final ImageJ imageJ = new ImageJ();
imageJ.ui().showUI();

OpenTableCommand command = new OpenTableCommand();
command.table = new File("/Users/tischer/Desktop/alexandra-mobie.tsv");
command.gridType = GridType.Transformed;
command.images = "Images";
command.run();
}
}

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