Changeset 1284


Ignore:
Timestamp:
08/17/06 11:57:40 (14 years ago)
Author:
curtis
Message:

Eliminate "LOCI common classes" package.

Location:
trunk
Files:
1 deleted
19 edited
3 copied

Legend:

Unmodified
Added
Removed
  • trunk/build.xml

    r1281 r1284  
    88=============================================================================== 
    99This build file handles the following projects: 
    10  
    11 LOCI Common Classes 
    12     JAR file:      loci-common.jar 
    13     Folders:       loci/ome/viewer 
    14                    loci/util 
    15     Main class:    loci.util.About 
    16     Dependencies:  commons-httpclient-2.0-rc2.jar (ome-java.jar) 
    17                    commons-logging.jar (ome-java.jar) 
    18                    ome-java.jar 
    19                    xmlrpc-1.2-b1.jar (ome-java.jar) 
    20     Targets:       jar-common 
    2110 
    2211Bio-Formats 
     
    2514                   loci/formats/* 
    2615    Main class:    loci.formats.ImageViewer 
    27     Dependencies:  loci-common.jar 
     16    Dependencies:  None 
    2817    Targets:       jar-formats 
    2918 
     
    3827                   forms-1.0.4.jar 
    3928                   ij.jar 
    40                    loci-common.jar 
    4129                   looks-1.2.2.jar 
    4230                   ome-java.jar 
     
    5139    Folders:       loci/plugins 
    5240                   loci/plugins/* 
     41                   loci/ome/viewer/* (temporary) 
    5342    Main class:    loci.plugins.About 
    5443    IJ plugins:    loci.plugins.browser.LociDataBrowser 
     
    5948                   commons-httpclient-2.0-rc2.jar (ome-java.jar) 
    6049                   commons-logging.jar (ome-java.jar) 
    61                    loci-common.jar 
    6250                   ome-java.jar 
    6351                   xmlrpc-1.2-b1.jar (ome-java.jar) 
     
    6755    JAR file:      ome-notebook.jar 
    6856    Folders:       loci/ome/notebook 
     57                   loci/ome/viewer (temporary) 
    6958    Main class:    loci.ome.notebook.MetadataNotebook 
    7059    Dependencies:  bio-formats.jar 
     
    7261                   commons-logging.jar (ome-java.jar) 
    7362                   forms-1.0.4.jar 
    74                    loci-common.jar 
    7563                   ome-java.jar 
    7664                   xmlrpc-1.2-b1.jar (ome-java.jar) 
     
    8876    JAR file:      QTConverter.jar 
    8977    Folders:       loci/apps/qt 
    90                    some loci/formats and loci/util 
     78                   some loci/formats 
    9179    Main class:    loci.apps.qt.QTConverter 
    9280    Dependencies:  None (custom built) 
     
    197185 
    198186  <target name="jars" 
    199     depends="jar-common, jar-formats, jar-visbio, jar-plugins, jar-notebook, jar-leica, jar-qt, jar-slim" 
     187    depends="jar-formats, jar-visbio, jar-plugins, jar-notebook, jar-leica, jar-qt, jar-slim" 
    200188    description="generate JAR files for LOCI software packages"/> 
    201189 
     
    244232  </target> 
    245233 
    246   <!-- LOCI Common Classes --> 
    247  
    248   <property name="common.files" value="loci/ome/viewer/** loci/util/**"/> 
    249  
    250   <target name="jar-common" depends="compile, copy-jars" 
    251     description="generate JAR file for LOCI common classes"> 
    252     <mkdir dir="${jar.dir}"/> 
    253     <jar jarfile="${jar.dir}/loci-common.jar" basedir="${classes.dir}" 
    254       includes="${common.files}"> 
    255       <manifest> 
    256         <attribute name="Main-Class" value="loci.util.About"/> 
    257       </manifest> 
    258     </jar> 
    259   </target> 
    260  
    261234  <!-- Bio-Formats --> 
    262235 
    263   <property name="formats.classpath" value="loci-common.jar"/> 
    264236  <property name="formats.files" value="loci/browser/** loci/formats/**"/> 
    265237  <property name="formats.resources" value="loci/formats/*.txt"/> 
    266238 
    267   <target name="jar-formats" depends="compile, jar-common" 
     239  <target name="jar-formats" depends="compile" 
    268240    description="generate Bio-Formats JAR file"> 
    269241    <mkdir dir="${jar.dir}"/> 
     
    275247      <manifest> 
    276248        <attribute name="Main-Class" value="loci.formats.ImageViewer"/> 
    277         <attribute name="Class-Path" value="${formats.classpath}"/> 
    278249      </manifest> 
    279250    </jar> 
     
    282253  <!-- VisBio --> 
    283254 
    284   <property name="visbio.classpath" value="bio-formats.jar commons-httpclient-2.0-rc2.jar commons-logging.jar forms-1.0.4.jar ij.jar loci-common.jar looks-1.2.2.jar ome-java.jar visad.jar xmlrpc-1.2-b1.jar"/> 
     255  <property name="visbio.classpath" value="bio-formats.jar commons-httpclient-2.0-rc2.jar commons-logging.jar forms-1.0.4.jar ij.jar looks-1.2.2.jar ome-java.jar visad.jar xmlrpc-1.2-b1.jar"/> 
    285256  <property name="visbio.files" value="loci/visbio/**"/> 
    286257  <property name="visbio.resources" value="loci/visbio/classes.txt loci/visbio/*.png loci/visbio/*.gif loci/visbio/help/*.html loci/visbio/help/*.png loci/visbio/overlays/*.png loci/visbio/view/*.png"/> 
    287258 
    288259  <target name="jar-visbio" 
    289     depends="compile, copy-jars, jar-formats, jar-common" 
     260    depends="compile, copy-jars, jar-formats" 
    290261    description="generate VisBio JAR file"> 
    291262    <mkdir dir="${jar.dir}"/> 
     
    310281 
    311282  <target name="jar-plugins" 
    312     depends="compile, copy-jars, jar-common, jar-formats" 
     283    depends="compile, copy-jars, jar-formats" 
    313284    description="generate LOCI Plugins for ImageJ JAR file"> 
    314285    <mkdir dir="${jar.dir}"/> 
     
    319290 
    320291  <target name="jar-notebook" 
    321     depends="compile, copy-jars, jar-common, jar-formats" 
     292    depends="compile, copy-jars, jar-formats" 
    322293    description="generate OME Metadata Notebook JAR file"> 
    323294    <mkdir dir="${jar.dir}"/> 
     
    344315  <!-- QT TIFF Converter --> 
    345316 
    346   <property name="qt.files" value="loci/apps/qt/* loci/util/FilePattern* loci/util/NumberFilter* loci/formats/BitBuffer* loci/formats/BitWriter* loci/formats/ByteVector* loci/formats/ComboFileFilter* loci/formats/Compression* loci/formats/DataTools* loci/formats/DummyMetadataStore* loci/formats/ExtensionFileFilter* loci/formats/FileStitcher* loci/formats/FormatException* loci/formats/FormatFileFilter* loci/formats/FormatHandler* loci/formats/FormatReader* loci/formats/FormatWriter* loci/formats/IFormatHandler* loci/formats/IFormatReader* loci/formats/ImageTools* loci/formats/LZWTreeNode* loci/formats/LegacyQTTools* loci/formats/MetadataStore* loci/formats/OMEXMLMetadataStore* loci/formats/RandomAccessArray* loci/formats/RandomAccessStream* loci/formats/ReflectException* loci/formats/ReflectedUniverse* loci/formats/TiffRational* loci/formats/TiffTools* loci/formats/in/BaseTiffReader* loci/formats/in/LegacyQTReader* loci/formats/in/QTReader* loci/formats/in/TiffReader* loci/formats/out/TiffWriter*"/> 
     317  <property name="qt.files" value="loci/apps/qt/* loci/formats/BitBuffer* loci/formats/BitWriter* loci/formats/ByteVector* loci/formats/ComboFileFilter* loci/formats/Compression* loci/formats/DataTools* loci/formats/DummyMetadataStore* loci/formats/ExtensionFileFilter* loci/formats/FilePattern* loci/formats/FileStitcher* loci/formats/FormatException* loci/formats/FormatFileFilter* loci/formats/FormatHandler* loci/formats/FormatReader* loci/formats/FormatWriter* loci/formats/IFormatHandler* loci/formats/IFormatReader* loci/formats/ImageTools* loci/formats/LZWTreeNode* loci/formats/LegacyQTTools* loci/formats/MetadataStore* loci/formats/NumberFilter* loci/formats/OMEXMLMetadataStore* loci/formats/RandomAccessArray* loci/formats/RandomAccessStream* loci/formats/ReflectException* loci/formats/ReflectedUniverse* loci/formats/TiffRational* loci/formats/TiffTools* loci/formats/in/BaseTiffReader* loci/formats/in/LegacyQTReader* loci/formats/in/QTReader* loci/formats/in/TiffReader* loci/formats/out/TiffWriter*"/> 
    347318 
    348319  <target name="jar-qt" depends="compile" 
  • trunk/loci/apps/qt/QTConverter.java

    r1276 r1284  
    1616import javax.swing.border.EmptyBorder; 
    1717import javax.swing.filechooser.FileFilter; 
     18import loci.formats.FilePattern; 
    1819import loci.formats.FormatHandler; 
    1920import loci.formats.FormatReader; 
     
    2223import loci.formats.in.TiffReader; 
    2324import loci.formats.out.TiffWriter; 
    24 import loci.util.FilePattern; 
    2525 
    2626/** A utility for converting 4D QuickTime movies into 4D TIFF stacks. */ 
  • trunk/loci/formats/FilePattern.java

    r1260 r1284  
    44 
    55/* 
    6 LOCI common classes for use with VisBio, Bio-Formats, 4D Data Browser, etc. 
    7 Copyright (C) 2006 Curtis Rueden. 
     6LOCI Bio-Formats package for reading and converting biological file formats. 
     7Copyright (C) 2005-@year@ Melissa Linkert, Curtis Rueden, Chris Allan 
     8and Eric Kjellman. 
    89 
    910This program is free software; you can redistribute it and/or modify 
     
    2223*/ 
    2324 
    24 package loci.util; 
     25package loci.formats; 
    2526 
    2627import java.io.File; 
  • trunk/loci/formats/FileStitcher.java

    r1264 r1284  
    3030import java.util.Hashtable; 
    3131import java.util.Vector; 
    32  
    33 import loci.util.FilePattern; 
    3432 
    3533/** Logic to stitch together files with similar names. */ 
  • trunk/loci/formats/FormatReader.java

    r1264 r1284  
    3131import java.util.Hashtable; 
    3232import javax.swing.filechooser.FileFilter; 
    33  
    34 import loci.util.FilePattern; 
    3533 
    3634/** Abstract superclass of all biological file format readers. */ 
  • trunk/loci/formats/NumberFilter.java

    r1260 r1284  
    44 
    55/* 
    6 LOCI common classes for use with VisBio, Bio-Formats, 4D Data Browser, etc. 
    7 Copyright (C) 2006 Curtis Rueden. 
     6LOCI Bio-Formats package for reading and converting biological file formats. 
     7Copyright (C) 2005-@year@ Melissa Linkert, Curtis Rueden, Chris Allan 
     8and Eric Kjellman. 
    89 
    910This program is free software; you can redistribute it and/or modify 
     
    2223*/ 
    2324 
    24 package loci.util; 
     25package loci.formats; 
    2526 
    2627import java.io.File; 
  • trunk/loci/plugins/browser/LociDataBrowser.java

    r1271 r1284  
    3030import java.io.File; 
    3131import loci.formats.*; 
    32 import loci.util.FilePattern; 
    33 import loci.util.MathUtil; 
    3432 
    3533/** 
     
    105103    if (tIndex >= 0) pos[tIndex] = t; 
    106104    if (cIndex >= 0) pos[cIndex] = c; 
    107     return MathUtil.positionToRaster(lengths, pos); 
     105    int[] offsets = new int[lengths.length]; 
     106    if (offsets.length > 0) offsets[0] = 1; 
     107    for (int i=1; i<offsets.length; i++) { 
     108      offsets[i] = offsets[i - 1] * lengths[i - 1]; 
     109    } 
     110    int raster = 0; 
     111    for (int i=0; i<pos.length; i++) raster += offsets[i] * pos[i]; 
     112    return raster; 
    108113  } 
    109114 
  • trunk/loci/visbio/classes.txt

    r927 r1284  
    22672267loci.formats.DeltavisionReader 
    22682268loci.formats.ExtensionFileFilter 
     2269loci.formats.FilePattern 
    22692270loci.formats.FluoviewReader 
    22702271loci.formats.FormatException 
     
    22912292loci.formats.LeicaReader 
    22922293loci.formats.MetamorphReader 
     2294loci.formats.NumberFilter 
    22932295loci.formats.OMETools 
    22942296loci.formats.OMEXMLReader 
     
    23072309loci.formats.ZeissLSMReader 
    23082310loci.formats.ZeissZVIReader 
    2309 loci.util.FilePattern 
    2310 loci.util.MathUtil 
    2311 loci.util.NumberFilter 
    23122311loci.visbio.BioDropHandler 
    23132312loci.visbio.BioTask 
     
    24322431loci.visbio.util.InstanceServer 
    24332432loci.visbio.util.LAFUtil 
     2433loci.visbio.util.MathUtil 
    24342434loci.visbio.util.MessagePane 
    24352435loci.visbio.util.ObjectUtil 
  • trunk/loci/visbio/data/DataCache.java

    r1264 r1284  
    2525 
    2626import java.util.Hashtable; 
    27 import loci.util.MathUtil; 
     27import loci.visbio.util.MathUtil; 
    2828import visad.Data; 
    2929 
  • trunk/loci/visbio/data/DataManager.java

    r1264 r1284  
    3232import java.util.zip.ZipInputStream; 
    3333import javax.swing.tree.DefaultMutableTreeNode; 
    34 import loci.util.FilePattern; 
     34import loci.formats.FilePattern; 
    3535import loci.visbio.*; 
    3636import loci.visbio.help.HelpManager; 
  • trunk/loci/visbio/data/DataSampling.java

    r1264 r1284  
    2929import javax.swing.JOptionPane; 
    3030import loci.formats.ImageTools; 
    31 import loci.util.MathUtil; 
    3231import loci.visbio.state.Dynamic; 
    3332import loci.visbio.state.SaveException; 
    34 import loci.visbio.util.ObjectUtil; 
    35 import loci.visbio.util.XMLUtil; 
     33import loci.visbio.util.*; 
    3634import org.w3c.dom.Element; 
    3735 
  • trunk/loci/visbio/data/Dataset.java

    r1264 r1284  
    3333import javax.swing.JComponent; 
    3434import loci.formats.*; 
    35 import loci.util.MathUtil; 
    3635import loci.visbio.TaskEvent; 
    3736import loci.visbio.TaskListener; 
  • trunk/loci/visbio/data/DatasetPane.java

    r1264 r1284  
    3636import javax.swing.event.DocumentEvent; 
    3737import javax.swing.event.DocumentListener; 
    38 import loci.formats.FormatException; 
    39 import loci.formats.ImageReader; 
    40 import loci.util.FilePattern; 
     38import loci.formats.*; 
    4139import loci.visbio.VisBioFrame; 
    4240import loci.visbio.util.*; 
  • trunk/loci/visbio/data/ExportPane.java

    r1264 r1284  
    3535import javax.swing.*; 
    3636import loci.formats.*; 
    37 import loci.util.MathUtil; 
    3837import loci.visbio.*; 
    3938import loci.visbio.util.*; 
  • trunk/loci/visbio/data/ImageTransform.java

    r1264 r1284  
    2727import java.math.BigInteger; 
    2828import java.rmi.RemoteException; 
    29 import loci.util.MathUtil; 
    3029import loci.visbio.state.SaveException; 
    3130import loci.visbio.util.*; 
  • trunk/loci/visbio/data/ThumbnailHandler.java

    r1264 r1284  
    2525 
    2626import java.rmi.RemoteException; 
    27 import loci.util.MathUtil; 
    2827import loci.visbio.BioTask; 
    2928import loci.visbio.TaskManager; 
  • trunk/loci/visbio/ome/ImageUploader.java

    r1264 r1284  
    3131import org.openmicroscopy.ds.st.*; 
    3232import org.openmicroscopy.is.*; 
    33 import loci.util.FilePattern; 
    34 import loci.util.MathUtil; 
     33import loci.formats.FilePattern; 
    3534import loci.visbio.*; 
    3635import loci.visbio.data.DataTransform; 
     36import loci.visbio.util.MathUtil; 
    3737import visad.FlatField; 
    3838 
  • trunk/loci/visbio/overlays/OverlayArrow.java

    r1264 r1284  
    2626import java.rmi.RemoteException; 
    2727import java.util.Arrays; 
    28 import loci.util.MathUtil; 
     28import loci.visbio.util.MathUtil; 
    2929import visad.*; 
    3030 
  • trunk/loci/visbio/overlays/OverlayIO.java

    r1264 r1284  
    3131import javax.swing.JComponent; 
    3232import javax.swing.JOptionPane; 
    33 import loci.util.MathUtil; 
    3433import loci.visbio.VisBio; 
    3534import loci.visbio.util.*; 
  • trunk/loci/visbio/overlays/OverlayLine.java

    r1264 r1284  
    2626import java.rmi.RemoteException; 
    2727import java.util.Arrays; 
    28 import loci.util.MathUtil; 
     28import loci.visbio.util.MathUtil; 
    2929import visad.*; 
    3030 
  • trunk/loci/visbio/overlays/OverlayTransform.java

    r1264 r1284  
    3232import javax.swing.JComponent; 
    3333import javax.swing.JOptionPane; 
    34 import loci.util.MathUtil; 
    3534import loci.visbio.data.*; 
    3635import loci.visbio.state.Dynamic; 
  • trunk/loci/visbio/util/MathUtil.java

    r1260 r1284  
    44 
    55/* 
    6 LOCI common classes for use with VisBio, Bio-Formats, 4D Data Browser, etc. 
    7 Copyright (C) 2006 Curtis Rueden. 
     6VisBio application for visualization of multidimensional 
     7biological image data. Copyright (C) 2002-@year@ Curtis Rueden. 
    88 
    99This program is free software; you can redistribute it and/or modify 
    10 it under the terms of the GNU Library General Public License as published by 
     10it under the terms of the GNU General Public License as published by 
    1111the Free Software Foundation; either version 2 of the License, or 
    1212(at your option) any later version. 
     
    1515but WITHOUT ANY WARRANTY; without even the implied warranty of 
    1616MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the 
    17 GNU Library General Public License for more details. 
    18  
    19 You should have received a copy of the GNU Library General Public License 
     17GNU General Public License for more details. 
     18 
     19You should have received a copy of the GNU General Public License 
    2020along with this program; if not, write to the Free Software 
    2121Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA 
    2222*/ 
    2323 
    24 package loci.util; 
     24package loci.visbio.util; 
    2525 
    2626import java.math.BigInteger; 
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