Bug#648017: micromanager vs bioformats
block 648017 by 641448
thanks
Micro-Manager needs bio-formats to compile:
javac -source 1.5 -target 1.5 -sourcepath
../MMCoreJ_wrap:./src:../hcs/src:. -classpath
/usr/share/java/ij.jar:/usr/share/java/bsh.jar:/usr/share/java/swingx.jar:/usr/share/java/commons-math.jar:/usr/share/java/swing-layout-1.0.4.jar:/usr/share/java/*:/bin/MMCoreJ.jar:.
./src/*.java ./src/org/micromanager/acquisition/*.java
./src/org/micromanager/utils/*.java ./src/org/micromanager/api/*.java
./src/org/micromanager/conf2/*.java -d build
./src/org/micromanager/utils/ReportingUtils.java:155: warning:
unmappable character for encoding ASCII
final JDialog dialog = new JDialog(owningFrame_, "??Manager
Warning: ", false);
^
./src/org/micromanager/utils/ReportingUtils.java:155: warning:
unmappable character for encoding ASCII
final JDialog dialog = new JDialog(owningFrame_, "??Manager
Warning: ", false);
^
./src/org/micromanager/acquisition/MultipageTiffReader.java:39:
package loci.formats does not exist
import loci.formats.FormatException;
^
./src/org/micromanager/acquisition/TaggedImageStorageMultipageTiff.java:31:
package loci.common does not exist
import loci.common.DateTools;
^
./src/org/micromanager/acquisition/TaggedImageStorageMultipageTiff.java:32:
package loci.common.services does not exist
import loci.common.services.ServiceFactory;
^
./src/org/micromanager/acquisition/TaggedImageStorageMultipageTiff.java:33:
package loci.formats does not exist
import loci.formats.MetadataTools;
^
./src/org/micromanager/acquisition/TaggedImageStorageMultipageTiff.java:34:
package loci.formats.meta does not exist
import loci.formats.meta.IMetadata;
^
./src/org/micromanager/acquisition/TaggedImageStorageMultipageTiff.java:35:
package loci.formats.ome does not exist
import loci.formats.ome.OMEXMLMetadata;
^
./src/org/micromanager/acquisition/TaggedImageStorageMultipageTiff.java:36:
package loci.formats.services does not exist
import loci.formats.services.OMEXMLService;
^
./src/org/micromanager/acquisition/TaggedImageStorageMultipageTiff.java:37:
package loci.formats.services does not exist
import loci.formats.services.OMEXMLServiceImpl;
^
./src/org/micromanager/acquisition/TaggedImageStorageMultipageTiff.java:39:
package ome.xml.model.enums does not exist
import ome.xml.model.enums.Binning;
^
./src/org/micromanager/acquisition/TaggedImageStorageMultipageTiff.java:40:
package ome.xml.model.primitives does not exist
import ome.xml.model.primitives.*;
^
./src/org/micromanager/acquisition/OMEMetadata.java:27: package
loci.common does not exist
import loci.common.DateTools;
^
./src/org/micromanager/acquisition/OMEMetadata.java:28: package
loci.common.services does not exist
import loci.common.services.ServiceFactory;
^
./src/org/micromanager/acquisition/OMEMetadata.java:29: package
loci.formats does not exist
import loci.formats.MetadataTools;
^
./src/org/micromanager/acquisition/OMEMetadata.java:30: package
loci.formats.meta does not exist
import loci.formats.meta.IMetadata;
^
./src/org/micromanager/acquisition/OMEMetadata.java:31: package
loci.formats.services does not exist
import loci.formats.services.OMEXMLService;
^
./src/org/micromanager/acquisition/OMEMetadata.java:32: package
ome.xml.model.primitives does not exist
import ome.xml.model.primitives.*;
^
./src/org/micromanager/acquisition/OMEMetadata.java:42: cannot find symbol
symbol : class IMetadata
location: class org.micromanager.acquisition.OMEMetadata
private IMetadata metadata_;
^
./src/org/micromanager/acquisition/OMEMetadata.java:59: cannot find symbol
symbol : variable MetadataTools
location: class org.micromanager.acquisition.OMEMetadata
metadata_ = MetadataTools.createOMEXMLMetadata();
^
./src/org/micromanager/acquisition/OMEMetadata.java:64: cannot find symbol
symbol : class OMEXMLService
location: class org.micromanager.acquisition.OMEMetadata
OMEXMLService service = new
ServiceFactory().getInstance(OMEXMLService.class);
^
./src/org/micromanager/acquisition/OMEMetadata.java:64: cannot find symbol
symbol : class OMEXMLService
location: class org.micromanager.acquisition.OMEMetadata
OMEXMLService service = new
ServiceFactory().getInstance(OMEXMLService.class);
^
./src/org/micromanager/acquisition/OMEMetadata.java:64: cannot find symbol
symbol : class ServiceFactory
location: class org.micromanager.acquisition.OMEMetadata
OMEXMLService service = new
ServiceFactory().getInstance(OMEXMLService.class);
^
./src/org/micromanager/acquisition/OMEMetadata.java:81: cannot find symbol
symbol : class PositiveInteger
location: class org.micromanager.acquisition.OMEMetadata
metadata_.setPixelsSizeT(new PositiveInteger(numFrames), seriesIndex);
^
./src/org/micromanager/acquisition/OMEMetadata.java:89: cannot find symbol
symbol : variable MetadataTools
location: class org.micromanager.acquisition.OMEMetadata
MetadataTools.populateMetadata(metadata_, seriesIndex,
baseFileName, MultipageTiffWriter.BYTE_ORDER.equals(ByteOrder.LITTLE_ENDIAN),
^
./src/org/micromanager/acquisition/OMEMetadata.java:98: cannot find symbol
symbol : class PositiveFloat
location: class org.micromanager.acquisition.OMEMetadata
metadata_.setPixelsPhysicalSizeX(new
PositiveFloat(pixelSize), seriesIndex);
^
./src/org/micromanager/acquisition/OMEMetadata.java:99: cannot find symbol
symbol : class PositiveFloat
location: class org.micromanager.acquisition.OMEMetadata
metadata_.setPixelsPhysicalSizeY(new
PositiveFloat(pixelSize), seriesIndex);
^
./src/org/micromanager/acquisition/OMEMetadata.java:105: cannot find symbol
symbol : class PositiveFloat
location: class org.micromanager.acquisition.OMEMetadata
metadata_.setPixelsPhysicalSizeZ(new PositiveFloat(zStep),
seriesIndex);
^
./src/org/micromanager/acquisition/OMEMetadata.java:118: cannot find symbol
symbol : variable MetadataTools
location: class org.micromanager.acquisition.OMEMetadata
String instrumentID = MetadataTools.createLSID("Microscope");
^
./src/org/micromanager/acquisition/OMEMetadata.java:131: cannot find symbol
symbol : class Color
location: class org.micromanager.acquisition.OMEMetadata
metadata_.setChannelColor(new Color(channel.getInt("Color")),
seriesIndex, channelIndex);
^
./src/org/micromanager/acquisition/OMEMetadata.java:137: cannot find symbol
symbol : class OMEXMLService
location: class org.micromanager.acquisition.OMEMetadata
OMEXMLService service = new
ServiceFactory().getInstance(OMEXMLService.class);
^
./src/org/micromanager/acquisition/OMEMetadata.java:137: cannot find symbol
symbol : class OMEXMLService
location: class org.micromanager.acquisition.OMEMetadata
OMEXMLService service = new
ServiceFactory().getInstance(OMEXMLService.class);
^
./src/org/micromanager/acquisition/OMEMetadata.java:137: cannot find symbol
symbol : class ServiceFactory
location: class org.micromanager.acquisition.OMEMetadata
OMEXMLService service = new
ServiceFactory().getInstance(OMEXMLService.class);
^
./src/org/micromanager/acquisition/OMEMetadata.java:159: cannot find symbol
symbol : class Timestamp
location: class org.micromanager.acquisition.OMEMetadata
metadata_.setImageAcquisitionDate(new Timestamp(
^
./src/org/micromanager/acquisition/OMEMetadata.java:160: cannot find symbol
symbol : variable DateTools
location: class org.micromanager.acquisition.OMEMetadata
DateTools.formatDate(tags.getString("Time"),
"yyyy-MM-dd HH:mm:ss")), seriesIndex);
^
./src/org/micromanager/acquisition/OMEMetadata.java:181: cannot find symbol
symbol : class NonNegativeInteger
location: class org.micromanager.acquisition.OMEMetadata
metadata_.setTiffDataFirstZ(new NonNegativeInteger(slice),
seriesIndex, indices.tiffDataIndex_);
^
./src/org/micromanager/acquisition/OMEMetadata.java:182: cannot find symbol
symbol : class NonNegativeInteger
location: class org.micromanager.acquisition.OMEMetadata
metadata_.setTiffDataFirstC(new
NonNegativeInteger(channel), seriesIndex, indices.tiffDataIndex_);
^
./src/org/micromanager/acquisition/OMEMetadata.java:183: cannot find symbol
symbol : class NonNegativeInteger
location: class org.micromanager.acquisition.OMEMetadata
metadata_.setTiffDataFirstT(new NonNegativeInteger(frame),
seriesIndex, indices.tiffDataIndex_);
^
./src/org/micromanager/acquisition/OMEMetadata.java:184: cannot find symbol
symbol : class NonNegativeInteger
location: class org.micromanager.acquisition.OMEMetadata
metadata_.setTiffDataIFD(new NonNegativeInteger(ifdCount),
seriesIndex, indices.tiffDataIndex_);
^
./src/org/micromanager/acquisition/OMEMetadata.java:190: cannot find symbol
symbol : class NonNegativeInteger
location: class org.micromanager.acquisition.OMEMetadata
metadata_.setTiffDataPlaneCount(new
NonNegativeInteger(indices.tiffDataPlaneCount_),
^
./src/org/micromanager/acquisition/OMEMetadata.java:194: cannot find symbol
symbol : class NonNegativeInteger
location: class org.micromanager.acquisition.OMEMetadata
metadata_.setPlaneTheZ(new NonNegativeInteger(slice),
seriesIndex, indices.planeIndex_);
^
./src/org/micromanager/acquisition/OMEMetadata.java:195: cannot find symbol
symbol : class NonNegativeInteger
location: class org.micromanager.acquisition.OMEMetadata
metadata_.setPlaneTheC(new NonNegativeInteger(channel),
seriesIndex, indices.planeIndex_);
^
./src/org/micromanager/acquisition/OMEMetadata.java:196: cannot find symbol
symbol : class NonNegativeInteger
location: class org.micromanager.acquisition.OMEMetadata
metadata_.setPlaneTheT(new NonNegativeInteger(frame),
seriesIndex, indices.planeIndex_);
^
./src/org/micromanager/acquisition/OMEMetadata.java:240: cannot find symbol
symbol : class OMEXMLService
location: class org.micromanager.acquisition.OMEMetadata
OMEXMLService service = new
ServiceFactory().getInstance(OMEXMLService.class);
^
./src/org/micromanager/acquisition/OMEMetadata.java:240: cannot find symbol
symbol : class OMEXMLService
location: class org.micromanager.acquisition.OMEMetadata
OMEXMLService service = new
ServiceFactory().getInstance(OMEXMLService.class);
^
./src/org/micromanager/acquisition/OMEMetadata.java:240: cannot find symbol
symbol : class ServiceFactory
location: class org.micromanager.acquisition.OMEMetadata
OMEXMLService service = new
ServiceFactory().getInstance(OMEXMLService.class);
^
./src/org/micromanager/acquisition/OMEMetadata.java:272: cannot find symbol
symbol : variable MetadataTools
location: class org.micromanager.acquisition.OMEMetadata
String detectorID = MetadataTools.createLSID(camera);
^
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
45 errors
2 warnings
Reply to: