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Orbit, a versatile image analysis software for biological image-based quantification
/*
* Orbit, a versatile image analysis software for biological image-based quantification.
* Copyright (C) 2009 - 2018 Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see browseImages(Object parentObj) throws Exception {
List rdfList = new ArrayList<>();
this.series = 0;
JFileChooser fileChooser = OrbitUtils.buildOpenFileFileChooser(this);
Preferences prefs = Preferences.userNodeForPackage(this.getClass());
String dir = prefs.get("ImageProviderLocal.OpenFileCurrentDir", null);
if (dir != null) {
File cd = new File(dir);
fileChooser.setCurrentDirectory(cd);
}
Component parent = null;
if (parentObj != null && parentObj instanceof Component) {
parent = (Component) parentObj;
}
int returnVal = fileChooser.showOpenDialog(parent);
if (returnVal == JFileChooser.APPROVE_OPTION) {
prefs.put("ImageProviderLocal.OpenFileCurrentDir", fileChooser.getCurrentDirectory().getAbsolutePath());
File[] files = fileChooser.getSelectedFiles();
if (files != null && files.length > 0) {
for (File file : files) {
RawDataFile rdf = registerFile(file,series);
rdfList.add(rdf);
}
}
} else {
logger.trace("browse images canceled.");
}
return rdfList;
}
public RawDataFile registerFile(File file, int series) throws SQLException {
String fn = file.getAbsolutePath();
int id = DAODataFileSQLite.ExistRawDataFile(fn,series);
RawDataFile rdf;
if (id>0) {
rdf = DAODataFileSQLite.LoadRawDataFile(id);
if (!file.getParent().equals(rdf.getDataPath())) {
rdf.setDataPath(file.getParent());
DAODataFileSQLite.UpdateRawDataFile(rdf);
}
} else {
rdf = createRDF(file.getAbsolutePath(),series);
DAODataFileSQLite.InsertRawDataFile(rdf);
}
//RawDataFile rdf = createRDF(file.getAbsolutePath(),series);
return rdf;
}
@Override
public boolean useCustomBrowseImagesDialog() {
return true;
}
public RawDataFile createRDF(String fn,int series) {
File file = new File(fn);
String md5 = "";
try {
md5 = OrbitUtils.getDigest(fn);
} catch (Exception e) {
e.printStackTrace();
}
// TODO: user and type
RawDataFile rdf = new RawDataFile();
rdf.setDataPath(file.getParentFile().getAbsolutePath());
rdf.setFileName(file.getName());
rdf.setFileSize(file.length());
rdf.setModifyDate(new Date(file.lastModified()));
rdf.setReferenceDate(new Date(file.lastModified()));
rdf.setRawDataId(rawData.getRawDataId());
rdf.setMd5(md5);
rdf.setSeriesNum(series);
return rdf;
}
@Override
public RawDataFile LoadRawDataFile(int rdfId) throws Exception {
return DAODataFileSQLite.LoadRawDataFile(rdfId);
}
@Override
public RawData LoadRawData(int i) throws Exception {
return rawData;
}
@Override
public List LoadRawMetasByRawDataFile(int rdfId) throws Exception {
List rmList = new ArrayList<>();
RawDataFile rdf = LoadRawDataFile(rdfId);
IOrbitImage image = createOrbitImage(rdf,0);
RawMetaFactoryFile rmff = new RawMetaFactoryFile(rdfId,new Date(),"orbit");
rmList.add(rmff.createMetaStr("Filename",rdf.getFileName()));
rmList.add(rmff.createMetaStr("Filesize", RawUtilsCommon.formatFileSize(rdf.getFileSize())));
rmList.add(rmff.createMetaInt("Orbit ID", rdf.getRawDataFileId()));
if (rdf.getReferenceDate() != null)
rmList.add(rmff.createMetaDate("Create Date", rdf.getReferenceDate()));
if (rdf.getModifyDate() != null)
rmList.add(rmff.createMetaDate("Update Date", rdf.getModifyDate()));
if (image!=null) {
rmList.add(rmff.createMetaInt(RawUtilsCommon.STR_META_IMAGE_IMAGEHEIGHT, image.getHeight()));
rmList.add(rmff.createMetaInt(RawUtilsCommon.STR_META_IMAGE_IMAGEWIDTH, image.getWidth()));
if (image instanceof OrbitImageBioformats) {
OrbitImageBioformats oib = (OrbitImageBioformats) image;
if (oib.getPixelsPhysicalSizeX()!=null && oib.getPixelsPhysicalSizeX().value()!=null) {
rmList.add(rmff.createMetaDouble(RawUtilsCommon.STR_META_IMAGE_SCALE, oib.getPixelsPhysicalSizeX().value().doubleValue()));
}
}
}
return rmList;
}
@Override
public List LoadRawMetasByRawData(int i) throws Exception {
List rmList = new ArrayList<>();
RawMetaFactoryData rmfd = new RawMetaFactoryData (rawData.getRawDataId(),new Date(),"orbit");
rmList.add(rmfd.createMetaStr("Filesystem","local"));
return rmList;
}
/**
* Small images (bmp,png,dcm.lif,zif) are loaded wie TiffConverter (JAI), tiff files via OrbitImageTiff (better performance) and everything else via Scifio.
* @param rdf
* @param level
* @return
* @throws Exception
*/
@Override
public IOrbitImage createOrbitImage(RawDataFile rdf, int level) throws Exception {
if (rdf==null) return null;
String ending = RawUtilsCommon.getExtension(rdf.getFileName());
if (ending.equals("bmp")||ending.equals("png")) {
PlanarImage pi = TiffConverter.loadFromFile(rdf.getDataPath() + File.separator + rdf.getFileName());
return new OrbitImagePlanar(pi, rdf.getFileName());
} else if (!OrbitUtils.isOME_TIFF(rdf.getFileName()) && (ending.equals("tif")||ending.equals("tiff"))) {
try {
return new OrbitImageTiff(rdf.getDataPath() + File.separator + rdf.getFileName(), level);
} catch (FormatException e) { // for tiff files >=16 bits per sample
return new OrbitImageBioformats(rdf.getDataPath() + File.separator + rdf.getFileName(), level, rdf.getSeriesNum(), orbitModel);
}
}
if (ending.equals("ndpi") && !NDPI_JAVA_FALLBACK) {
try {
return new NDPIImageNative(rdf.getDataPath() + File.separator + rdf.getFileName(), level);
} catch (UnsatisfiedLinkError err) {
NDPI_JAVA_FALLBACK = true;
logger.debug("using java NDPI fallback");
return new OrbitImageBioformats(rdf.getDataPath() + File.separator + rdf.getFileName(), level, rdf.getSeriesNum(), orbitModel);
}
}
if (ending.equals("ndpis") && !NDPI_JAVA_FALLBACK) {
try {
//return null;
return new NDPISImageNative(rdf.getDataPath() + File.separator + rdf.getFileName(), level);
} catch (UnsatisfiedLinkError err) {
NDPI_JAVA_FALLBACK = true;
logger.debug("using java NDPIS fallback");
return new OrbitImageBioformats(rdf.getDataPath() + File.separator + rdf.getFileName(), level, rdf.getSeriesNum(), orbitModel);
}
}
else {
return new OrbitImageBioformats(rdf.getDataPath() + File.separator + rdf.getFileName(), level, rdf.getSeriesNum(), orbitModel);
}
}
public BufferedImage getThumbnail(String filename) throws Exception {
File file = new File(filename);
String ending = RawUtilsCommon.getExtension(file.getName()) ;
BufferedImage bi = null;
if (ending.equals("bmp")||ending.equals("png")) {
bi = TiffConverter.getDownsampledImage(file.getPath(), 300, -1, 1, false);
} else {
try {
if (!OrbitUtils.isOME_TIFF(filename) && (ending.equals("tif")||ending.equals("tiff"))) {
try {
OrbitImageTiff oi = new OrbitImageTiff(file.getAbsolutePath(), 0);
bi = oi.getThumbnail();
oi.close();
} catch (FormatException e) { // for tiff files >=16 bits per sample
OrbitImageBioformats oi = new OrbitImageBioformats(file.getAbsolutePath(), 0, series, orbitModel);
bi = oi.getThumbnail();
oi.close();
}
} else {
// OrbitImageScifio oi = new OrbitImageScifio(file.getAbsolutePath(), 0);
logger.debug("loading thumbnail of file "+filename+", series: "+series);
OrbitImageBioformats oi = new OrbitImageBioformats(file.getAbsolutePath(), 0, series, orbitModel);
bi = oi.getThumbnail();
oi.close();
}
} catch (Exception e) {
e.printStackTrace();
}
}
return bi;
}
@Override
public BufferedImage getThumbnail(RawDataFile rdf) throws Exception {
return getThumbnail(rdf.getDataPath() + File.separator + rdf.getFileName());
}
@Override
public void close() throws IOException {
}
// search
@Override
public List LoadRawDataFilesSearch(String search, boolean b) throws Exception {
return LoadRawDataFilesSearchFast(search,1000, Arrays.asList(RawUtilsCommon.fileTypesImage));
}
@Override
public List LoadRawDataFilesSearch(String search, boolean andMode, int searchLimit, List fileTypes) throws Exception {
return LoadRawDataFilesSearchFast(search,1000, Arrays.asList(RawUtilsCommon.fileTypesImage));
}
@Override
public List LoadRawDataFilesByFilenameStart(String search, boolean andMode, int searchLimit, List fileTypes, String s1) throws Exception {
return LoadRawDataFilesSearchFast(search,1000, Arrays.asList(RawUtilsCommon.fileTypesImage));
}
@Override
public List LoadRawDataFilesSearchFast(String search, int searchLimit, List list) throws Exception {
return DAODataFileSQLite.LoadRawDataFilesSearchFast(search,searchLimit,null);
}
// raw annotations
@Override
public RawAnnotation LoadRawAnnotation(int rawAnnotationId) throws Exception {
return DAORawAnnotationSQLite.LoadRawAnnotation(rawAnnotationId);
}
@Override
public List LoadRawAnnotationsByRawDataFile(int rdfID) throws Exception {
return DAORawAnnotationSQLite.LoadRawAnnotationsByRawDataFile(rdfID);
}
@Override
public List LoadRawAnnotationsByRawDataFile(int rdfID, int rawAnnotationType) throws Exception {
return DAORawAnnotationSQLite.LoadRawAnnotationsByRawDataFile(rdfID,rawAnnotationType);
}
@Override
public List LoadRawAnnotationsByType(int rawAnnotationType) throws Exception {
return DAORawAnnotationSQLite.LoadRawAnnotationsByType(rawAnnotationType);
}
@Override
public int InsertRawAnnotation(RawAnnotation rawAnnotation) throws Exception {
return DAORawAnnotationSQLite.InsertRawAnnotation(rawAnnotation);
}
@Override
public boolean UpdateRawAnnotation(RawAnnotation rawAnnotation) throws Exception {
return DAORawAnnotationSQLite.UpdateRawAnnotation(rawAnnotation);
}
@Override
public boolean DeleteRawAnnotation(int rawAnnotationId) throws Exception {
return DAORawAnnotationSQLite.DeleteRawAnnotation(rawAnnotationId);
}
@Override
public boolean DeleteRawAnnotationAllWithType(int rdfId, int rawAnnotationType) throws Exception {
return DAORawAnnotationSQLite.DeleteRawAnnotationAllWithType(rdfId,rawAnnotationType);
}
// DB tools
/**
* Checks if saved RawDataFiles still physically exist on local disk (path+filename) and removes RawDataFile and RawAnnotation entries if not.
*/
public static void DBCleanup() throws Exception {
List rdfList = DAODataFileSQLite.LoadRawDataFiles(); // load all RDFs
if (rdfList!=null && rdfList.size()>0) {
for (RawDataFile rdf: rdfList) {
File file = new File(rdf.getDataPath()+File.separator+rdf.getFileName());
if (!file.exists()) {
DAORawAnnotationSQLite.DeleteRawAnnotationsByRDF(rdf.getRawDataFileId());
DAODataFileSQLite.DeleteRawDataFile(rdf.getRawDataFileId());
logger.info("local db entries removed for non existing file "+file.getAbsolutePath());
}
}
}
}
@Override
public boolean authenticateUser(String s, String s1) {
return true;
}
@Override
public void stateChanged(ChangeEvent e) {
if (e.getSource() instanceof Integer) {
this.series = (Integer) e.getSource();
logger.debug("series set to "+this.series);
}
}
public static void main(String[] args) throws Exception {
ImageProviderLocal.DBCleanup();
}
}