Incorporated used of LocationAgnosticBioFormatsImg

pom.xml

@@ -13,7 +13,7 @@
 
     <groupId>net.calm</groupId>
     <artifactId>giani</artifactId>
-    <version>3.4.5</version>
+    <version>3.5.0</version>
 
     <build>
         <plugins>
@@ -155,7 +155,7 @@
         <dependency>
             <groupId>net.calm</groupId>
             <artifactId>iaclasslibrary</artifactId>
-            <version>1.0.28</version>
+            <version>1.0.29</version>
         </dependency>
         <dependency>
             <groupId>com.github.mcib3d</groupId>

src/main/java/net/calm/giani/exec/PipelineBuilder.java

@@ -19,7 +19,7 @@
 import mcib3d.geom.Objects3DPopulation;
 import net.calm.giani.gianiparams.GianiDefaultParams;
 import net.calm.iaclasslibrary.Extrema.MultiThreadedMaximaFinder;
-import net.calm.iaclasslibrary.IO.BioFormats.BioFormatsImg;
+import net.calm.iaclasslibrary.IO.BioFormats.LocationAgnosticBioFormatsImg;
 import net.calm.iaclasslibrary.Process.Colocalise.MultiThreadedColocalise;
 import net.calm.iaclasslibrary.Process.Filtering.MultiThreadedGaussianFilter;
 import net.calm.iaclasslibrary.Process.Filtering.MultiThreadedTopHatFilter;
@@ -74,7 +74,7 @@ public static MultiThreadedMaximaFinder getDefaultMaximaFinder(Properties props)
         propLabels[MultiThreadedMaximaFinder.THRESH_DETECT] = GianiDefaultParams.NUC_MAXIMA_DETECT_THRESHOLD;
         propLabels[MultiThreadedMaximaFinder.THRESH_METHOD] = GianiDefaultParams.NUC_MAXIMA_SEG_THRESH_METHOD;
         MultiThreadedMaximaFinder process = new MultiThreadedMaximaFinder(null);
-        process.setup(new BioFormatsImg(), props, propLabels);
+        process.setup(new LocationAgnosticBioFormatsImg(null), props, propLabels);
         return process;
     }
 
@@ -93,7 +93,7 @@ public static MultiThreadedTopHatFilter getDefaultNucTopHatFilteringProcess(Prop
         propLabels[MultiThreadedTopHatFilter.RESIZE_FACTOR_LABEL] = GianiDefaultParams.NUC_TOP_HAT_DOWNSIZE_FACTOR_LABEL;
         propLabels[MultiThreadedTopHatFilter.ENABLE_FILTER_LABEL] = GianiDefaultParams.ENABLE_TOP_HAT_FILTER;
         MultiThreadedTopHatFilter process = new MultiThreadedTopHatFilter(inputs);
-        process.setup(new BioFormatsImg(), props, propLabels);
+        process.setup(new LocationAgnosticBioFormatsImg(null), props, propLabels);
         return process;
     }
 
@@ -109,7 +109,7 @@ public static MultiThreadedGaussianFilter getDefaultNucFilteringProcess(Properti
         propLabels[MultiThreadedGaussianFilter.SERIES_LABEL] = GianiDefaultParams.SERIES_SELECT_LABEL;
         propLabels[MultiThreadedGaussianFilter.FILT_RAD_LABEL] = GianiDefaultParams.NUC_FILT_RAD_LABEL;
         MultiThreadedGaussianFilter process = new MultiThreadedGaussianFilter(null);
-        process.setup(new BioFormatsImg(), props, propLabels);
+        process.setup(new LocationAgnosticBioFormatsImg(null), props, propLabels);
         return process;
     }
 
@@ -135,7 +135,7 @@ public static MultiThreadedWatershed getDefaultNucSegmenter(Properties props, Mu
                 false,
                 cells,
                 MultiThreadedWatershed.NUCLEI);
-        process.setup(new BioFormatsImg(), props, propLabels);
+        process.setup(new LocationAgnosticBioFormatsImg(null), props, propLabels);
         return process;
     }
 
@@ -151,7 +151,7 @@ public static MultiThreadedGaussianFilter getDefaultCellFilteringProcess(Propert
         propLabels[MultiThreadedGaussianFilter.CHANNEL_LABEL] = GianiDefaultParams.CELL_SEG_CHAN_SELECT_LABEL;
         propLabels[MultiThreadedGaussianFilter.SERIES_LABEL] = GianiDefaultParams.SERIES_SELECT_LABEL;
         propLabels[MultiThreadedGaussianFilter.FILT_RAD_LABEL] = GianiDefaultParams.CELL_FILT_RAD_LABEL;
-        process.setup(new BioFormatsImg(), props, propLabels);
+        process.setup(new LocationAgnosticBioFormatsImg(null), props, propLabels);
         return process;
     }
 
@@ -179,7 +179,7 @@ public static MultiThreadedWatershed getDefaultCellSegmenter(Properties props, M
                 cells,
                 MultiThreadedWatershed.CELLS
         );
-        process.setup(new BioFormatsImg(), props, propLabels);
+        process.setup(new LocationAgnosticBioFormatsImg(null), props, propLabels);
         return process;
     }
 
@@ -201,7 +201,7 @@ public static MultiThreadedROIConstructor getDefaultMeasure(Properties props, Mu
                 inputs,
                 cells
         );
-        process.setup(new BioFormatsImg(), props, propLabels);
+        process.setup(new LocationAgnosticBioFormatsImg(null), props, propLabels);
         return process;
     }
 
@@ -285,7 +285,7 @@ public static MultiThreadedMaximaFinder getDefaultFociMaximaFinder(Properties pr
         propLabels[MultiThreadedMaximaFinder.THRESH_METHOD] = String.format("%s%d", GianiDefaultParams.BLOB_CHAN_SEG_THRESH_METHOD, i);
         propLabels[MultiThreadedMaximaFinder.THRESH_DETECT] = String.format("%s%d", GianiDefaultParams.BLOB_CHAN_DETECT_THRESHOLD, i);
         MultiThreadedMaximaFinder process = new MultiThreadedMaximaFinder(null);
-        process.setup(new BioFormatsImg(), props, propLabels);
+        process.setup(new LocationAgnosticBioFormatsImg(null), props, propLabels);
         return process;
     }
 
@@ -295,7 +295,7 @@ public static MultiThreadedColocalise getDefaultColocalisationProcess(Properties
         localisationPropLabels[MultiThreadedColocalise.CHANNELS_LABEL] = GianiDefaultParams.CHAN_FOR_MEASURE;
         localisationPropLabels[MultiThreadedColocalise.OUTPUT_LABEL] = GianiDefaultParams.OUTPUT_DIR_LABEL;
         MultiThreadedColocalise process = new MultiThreadedColocalise(inputs, cells);
-        process.setup(new BioFormatsImg(), props, localisationPropLabels);
+        process.setup(new LocationAgnosticBioFormatsImg(null), props, localisationPropLabels);
         return process;
     }
 }

src/main/java/net/calm/giani/exec/PipelineExecutor.java

@@ -21,10 +21,9 @@
 import ij.plugin.filter.Analyzer;
 import ij.plugin.frame.RoiManager;
 import loci.common.DebugTools;
-import loci.formats.FormatException;
 import net.calm.giani.gianiparams.GianiDefaultParams;
 import net.calm.iaclasslibrary.IO.BioFormats.BioFormatsFileLister;
-import net.calm.iaclasslibrary.IO.BioFormats.BioFormatsImg;
+import net.calm.iaclasslibrary.IO.BioFormats.LocationAgnosticBioFormatsImg;
 import net.calm.iaclasslibrary.IO.DataWriter;
 import net.calm.iaclasslibrary.IO.PropertyWriter;
 import net.calm.iaclasslibrary.Process.MultiThreadedProcess;
@@ -55,8 +54,9 @@ public class PipelineExecutor extends Thread {
 
     /**
      * Construct an executor with the specified pipeline and properties
+     *
      * @param pipeline the {@link ProcessPipeline} to be executed
-     * @param props the parameter-value pairs for every process in the pipeline
+     * @param props    the parameter-value pairs for every process in the pipeline
      */
     public PipelineExecutor(ProcessPipeline pipeline, Properties props) {
         this.pipeline = pipeline;
@@ -94,12 +94,14 @@ public void run() {
         ExecutorService exec = Executors.newSingleThreadExecutor();
         while (files.size() > 0) {
             String file = files.get(0);
-            BioFormatsImg img = new BioFormatsImg();
-            try {
-                img.setId(String.format("%s%s%s", input, File.separator, file));
-            } catch (IOException | FormatException e) {
-                GenUtils.logError(e, String.format("Failed to initialise %s", file));
-            }
+            String bioFormatsOptions = String.format("location=[Local machine] open=[%s%s%s] windowless=true view=Hyperstack",
+                    input, File.separator, file);
+            LocationAgnosticBioFormatsImg img = new LocationAgnosticBioFormatsImg(bioFormatsOptions);
+//            try {
+//                img.setId(String.format("%s%s%s", input, File.separator, file));
+//            } catch (IOException | FormatException e) {
+//                GenUtils.logError(e, String.format("Failed to initialise %s", file));
+//            }
             props.put(img.reformatFileName(), file);
             IJ.log(String.format("Analysing file %s", FilenameUtils.getName(file)));
             int nSeries = img.getSeriesCount();
@@ -152,7 +154,7 @@ public void run() {
         IJ.log(String.format("Done %s", TimeAndDate.getCurrentTimeAndDate()));
     }
 
-    private void updateFileList(BioFormatsImg img, ArrayList<String> files) {
+    private void updateFileList(LocationAgnosticBioFormatsImg img, ArrayList<String> files) {
         String[] relatedFiles = img.getFileList();
         for (String rf : relatedFiles) {
             for (String f : files) {

src/main/java/net/calm/giani/ui/FilteringPanel.java

@@ -8,6 +8,7 @@
 import net.calm.giani.gianiparams.GIANIParamInfos;
 import net.calm.giani.gianiparams.GianiDefaultParams;
 import net.calm.iaclasslibrary.IO.BioFormats.BioFormatsImg;
+import net.calm.iaclasslibrary.IO.BioFormats.LocationAgnosticBioFormatsImg;
 import net.calm.iaclasslibrary.Process.Filtering.MultiThreadedGaussianFilter;
 import net.calm.iaclasslibrary.UIClasses.LayerPanel;
 import net.calm.iaclasslibrary.UIClasses.Updateable;
@@ -44,7 +45,7 @@ public FilteringPanel() {
      * @param process    the process that this panel is seeking user-specified parameters for
      * @param propLabels the labels associated with the parameters that this panel will display
      */
-    public FilteringPanel(Properties props, BioFormatsImg img, MultiThreadedGaussianFilter process, String[] propLabels) {
+    public FilteringPanel(Properties props, LocationAgnosticBioFormatsImg img, MultiThreadedGaussianFilter process, String[] propLabels) {
         this(props, img, process, propLabels, null, null);
     }
 
@@ -58,7 +59,7 @@ public FilteringPanel(Properties props, BioFormatsImg img, MultiThreadedGaussian
      * @param helpURI    link to an online help page describing how to use this panel
      * @param title      description of what this panel does
      */
-    public FilteringPanel(Properties props, BioFormatsImg img, MultiThreadedGaussianFilter process, String[] propLabels, URI helpURI, String title) {
+    public FilteringPanel(Properties props, LocationAgnosticBioFormatsImg img, MultiThreadedGaussianFilter process, String[] propLabels, URI helpURI, String title) {
         super(props, img, process, propLabels, helpURI);
         this.title = title;
         this.info = new GIANIParamInfos();

src/main/java/net/calm/giani/ui/GIANIUI.java

@@ -7,7 +7,7 @@
 import net.calm.giani.gianiparams.GIANIParamInfos;
 import net.calm.giani.gianiparams.GianiDefaultParams;
 import net.calm.iaclasslibrary.Extrema.MultiThreadedMaximaFinder;
-import net.calm.iaclasslibrary.IO.BioFormats.BioFormatsImg;
+import net.calm.iaclasslibrary.IO.BioFormats.LocationAgnosticBioFormatsImg;
 import net.calm.iaclasslibrary.IO.PropertyWriter;
 import net.calm.iaclasslibrary.Process.Colocalise.MultiThreadedColocalise;
 import net.calm.iaclasslibrary.Process.Filtering.MultiThreadedGaussianFilter;
@@ -38,7 +38,7 @@
  */
 public class GIANIUI extends javax.swing.JFrame implements GUIMethods {
 
-    private final BioFormatsImg img;
+    private final LocationAgnosticBioFormatsImg img;
     private static Properties props;
     private final LinkedList<LayerPanel> componentList = new LinkedList();
     private int layerIndex = 0;
@@ -61,7 +61,7 @@ public class GIANIUI extends javax.swing.JFrame implements GUIMethods {
      */
     public GIANIUI() {
         DebugTools.setRootLevel("WARN");
-        img = new BioFormatsImg();
+        img = new LocationAgnosticBioFormatsImg(null);
         pipeline = new ProcessPipeline();
         cells = new Objects3DPopulation();
         this.info = new GIANIParamInfos();

src/main/java/net/calm/giani/ui/LocalisationPanel.java

@@ -16,7 +16,7 @@
  */
 package net.calm.giani.ui;
 
-import net.calm.iaclasslibrary.IO.BioFormats.BioFormatsImg;
+import net.calm.iaclasslibrary.IO.BioFormats.LocationAgnosticBioFormatsImg;
 import net.calm.iaclasslibrary.Process.Colocalise.MultiThreadedColocalise;
 import net.calm.iaclasslibrary.UIClasses.LayerPanel;
 
@@ -45,7 +45,7 @@ public LocalisationPanel() {
      * @param process the process that this panel is seeking user-specified parameters for
      * @param propLabels the labels associated with the parameters that this panel will display
      */
-    public LocalisationPanel(Properties props, BioFormatsImg img, MultiThreadedColocalise process, String[] propLabels) {
+    public LocalisationPanel(Properties props, LocationAgnosticBioFormatsImg img, MultiThreadedColocalise process, String[] propLabels) {
         super(props, img, process, propLabels, null);
         initComponents();
     }

src/main/java/net/calm/giani/ui/MaximaFinderPanel.java

@@ -24,7 +24,7 @@
 import net.calm.giani.gianiparams.GIANIParamInfos;
 import net.calm.giani.gianiparams.GianiDefaultParams;
 import net.calm.iaclasslibrary.Extrema.MultiThreadedMaximaFinder;
-import net.calm.iaclasslibrary.IO.BioFormats.BioFormatsImg;
+import net.calm.iaclasslibrary.IO.BioFormats.LocationAgnosticBioFormatsImg;
 import net.calm.iaclasslibrary.UIClasses.LayerPanel;
 import net.calm.iaclasslibrary.UIClasses.Updateable;
 import net.calm.iaclasslibrary.UtilClasses.GenUtils;
@@ -80,7 +80,7 @@ public MaximaFinderPanel() {
      *                           panel
      * @param title              description of what this panel does
      */
-    public MaximaFinderPanel(Properties props, BioFormatsImg img, MultiThreadedMaximaFinder process, String[] propLabels, boolean allowChannelSelect, int defaultChannel, URI helpURI, String title) {
+    public MaximaFinderPanel(Properties props, LocationAgnosticBioFormatsImg img, MultiThreadedMaximaFinder process, String[] propLabels, boolean allowChannelSelect, int defaultChannel, URI helpURI, String title) {
         super(props, img, process, propLabels, helpURI);
         this.allowChannelSelect = allowChannelSelect;
         this.defaultChannel = defaultChannel;

src/main/java/net/calm/giani/ui/MeasurementPanel.java

@@ -19,7 +19,7 @@
 import ij.plugin.filter.Analyzer;
 import net.calm.giani.gianiparams.GIANIParamInfos;
 import net.calm.giani.gianiparams.GianiDefaultParams;
-import net.calm.iaclasslibrary.IO.BioFormats.BioFormatsImg;
+import net.calm.iaclasslibrary.IO.BioFormats.LocationAgnosticBioFormatsImg;
 import net.calm.iaclasslibrary.Process.ROI.MultiThreadedROIConstructor;
 import net.calm.iaclasslibrary.UIClasses.LayerPanel;
 import net.calm.iaclasslibrary.UIClasses.Updateable;
@@ -53,7 +53,7 @@ public MeasurementPanel() {
      * @param propLabels the labels associated with the parameters that this panel will display
      * @param helpURI link to an online help page describing how to use this panel
      */
-    public MeasurementPanel(Properties props, BioFormatsImg img, MultiThreadedROIConstructor process, String[] propLabels, URI helpURI) {
+    public MeasurementPanel(Properties props, LocationAgnosticBioFormatsImg img, MultiThreadedROIConstructor process, String[] propLabels, URI helpURI) {
         super(props, img, process, propLabels, helpURI);
         this.info = new GIANIParamInfos();
         initComponents();

src/main/java/net/calm/giani/ui/SegmentationPanel.java

@@ -11,7 +11,7 @@
 import ij.process.AutoThresholder;
 import net.calm.giani.gianiparams.GIANIParamInfos;
 import net.calm.giani.gianiparams.GianiDefaultParams;
-import net.calm.iaclasslibrary.IO.BioFormats.BioFormatsImg;
+import net.calm.iaclasslibrary.IO.BioFormats.LocationAgnosticBioFormatsImg;
 import net.calm.iaclasslibrary.Process.Segmentation.MultiThreadedWatershed;
 import net.calm.iaclasslibrary.UIClasses.LayerPanel;
 import net.calm.iaclasslibrary.UIClasses.Updateable;
@@ -49,7 +49,7 @@ public SegmentationPanel() {
      * @param helpURI    link to an online help page describing how to use this panel
      * @param title      description of what this panel does
      */
-    public SegmentationPanel(Properties props, BioFormatsImg img, MultiThreadedWatershed process, String[] propLabels, URI helpURI, String title) {
+    public SegmentationPanel(Properties props, LocationAgnosticBioFormatsImg img, MultiThreadedWatershed process, String[] propLabels, URI helpURI, String title) {
         super(props, img, process, propLabels, helpURI);
         this.title = title;
         this.info = new GIANIParamInfos();

src/main/java/net/calm/giani/ui/SelectInputPanel.java

@@ -24,7 +24,7 @@
 import net.calm.giani.gianiparams.GIANIParamInfos;
 import net.calm.giani.gianiparams.GianiDefaultParams;
 import net.calm.iaclasslibrary.IO.BioFormats.BioFormatsFileLister;
-import net.calm.iaclasslibrary.IO.BioFormats.BioFormatsImg;
+import net.calm.iaclasslibrary.IO.BioFormats.LocationAgnosticBioFormatsImg;
 import net.calm.iaclasslibrary.UIClasses.LayerPanel;
 import net.calm.iaclasslibrary.UtilClasses.GenUtils;
 import net.calm.iaclasslibrary.UtilClasses.Utilities;
@@ -60,7 +60,7 @@ public SelectInputPanel() {
      * @param img the image that the process associated with this panel will run on
      * @param propLabels the labels associated with the parameters that this panel will display
      */
-    public SelectInputPanel(Properties props, BioFormatsImg img, String[] propLabels) {
+    public SelectInputPanel(Properties props, LocationAgnosticBioFormatsImg img, String[] propLabels) {
         this(props, img, propLabels, null);
     }
 
@@ -72,7 +72,7 @@ public SelectInputPanel(Properties props, BioFormatsImg img, String[] propLabels
      * @param propLabels the labels associated with the parameters that this panel will display
      * @param helpURI link to an online help page describing how to use this panel
      */
-    public SelectInputPanel(Properties props, BioFormatsImg img, String[] propLabels, URI helpURI) {
+    public SelectInputPanel(Properties props, LocationAgnosticBioFormatsImg img, String[] propLabels, URI helpURI) {
         super(props, img, null, propLabels, helpURI);
         initComponents();
         this.info = new GIANIParamInfos();

src/main/java/net/calm/giani/ui/TopHatFilterPanel.java

@@ -7,7 +7,7 @@
 
 import net.calm.giani.gianiparams.GIANIParamInfos;
 import net.calm.giani.gianiparams.GianiDefaultParams;
-import net.calm.iaclasslibrary.IO.BioFormats.BioFormatsImg;
+import net.calm.iaclasslibrary.IO.BioFormats.LocationAgnosticBioFormatsImg;
 import net.calm.iaclasslibrary.Process.Filtering.MultiThreadedTopHatFilter;
 import net.calm.iaclasslibrary.UIClasses.LayerPanel;
 import net.calm.iaclasslibrary.UIClasses.Updateable;
@@ -48,7 +48,7 @@ public TopHatFilterPanel() {
      * @param propLabels the labels associated with the parameters that this
      *                   panel will display
      */
-    public TopHatFilterPanel(Properties props, BioFormatsImg img, MultiThreadedTopHatFilter process, String[] propLabels) {
+    public TopHatFilterPanel(Properties props, LocationAgnosticBioFormatsImg img, MultiThreadedTopHatFilter process, String[] propLabels) {
         this(props, img, process, propLabels, null, null);
     }
 
@@ -68,7 +68,7 @@ public TopHatFilterPanel(Properties props, BioFormatsImg img, MultiThreadedTopHa
      *                   panel
      * @param title      description of what this panel does
      */
-    public TopHatFilterPanel(Properties props, BioFormatsImg img, MultiThreadedTopHatFilter process, String[] propLabels, URI helpURI, String title) {
+    public TopHatFilterPanel(Properties props, LocationAgnosticBioFormatsImg img, MultiThreadedTopHatFilter process, String[] propLabels, URI helpURI, String title) {
         super(props, img, process, propLabels, helpURI);
         this.title = title;
         this.info = new GIANIParamInfos();