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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


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