Improves ask for help command: allows for python to sneak in

Allows to set DeepSlice supported atlases from Python Updates bigdataviewer image loader to support unsigned int 32 bits
BIOP · Sep 5, 2024 · 912b62d · 912b62d
1 parent b6c8af8
commit 912b62d
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Showing 4 changed files with 76 additions and 34 deletions.
diff --git a/pom.xml b/pom.xml
@@ -108,7 +108,7 @@
 
 		<!-- bdv playground related dependencies -->
 		<bigdataviewer-playground.version>0.10.4</bigdataviewer-playground.version>
-		<bigdataviewer-image-loaders.version>0.8.1</bigdataviewer-image-loaders.version>
+		<bigdataviewer-image-loaders.version>0.8.2</bigdataviewer-image-loaders.version>
 		<bigdataviewer-biop-tools.version>0.10.5</bigdataviewer-biop-tools.version>
 		<bigdataviewer-selector.version>0.2.7</bigdataviewer-selector.version>
 

diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/DeepSliceHelper.java b/src/main/java/ch/epfl/biop/atlas/aligner/DeepSliceHelper.java
@@ -8,36 +8,31 @@
 
 import java.io.File;
 import java.net.URL;
+import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.List;
 import java.util.function.Consumer;
 import java.util.function.Supplier;
 
 public class DeepSliceHelper {
 
+    final private static List<String> atlasNameMouseCompatible = new ArrayList<>();
+    final private static List<String> atlasNameRatCompatible = new ArrayList<>();
+
+    public synchronized static void addMouseCompatibleAtlas(String name) {
+        if(!atlasNameMouseCompatible.contains(name)) atlasNameMouseCompatible.add(name);
+    }
+
+    public synchronized static void addRatCompatibleAtlas(String name) {
+        if(!atlasNameRatCompatible.contains(name)) atlasNameRatCompatible.add(name);
+    }
+
     /**
      * @param atlasName either the BrainGlobe API name or the specific Java packaged Atlases
      * @return true if the DeepSlice mouse model will be compatible with this atlas
      */
     public static boolean isDeepSliceMouseCompatible(String atlasName) {
-        switch (atlasName) {
-            case "example_mouse_100um":
-            case "allen_mouse_100um":
-            case "allen_mouse_50um":
-            case "allen_mouse_25um":
-            case "allen_mouse_10um":
-            case "kim_mouse_100um":
-            case "kim_mouse_50um":
-            case "kim_mouse_25um":
-            case "kim_mouse_10um":
-            case "osten_mouse_100um":
-            case "osten_mouse_50um":
-            case "osten_mouse_25um":
-            case "osten_mouse_10um":
-            case "Adult Mouse Brain - Allen Brain Atlas V3":
-            case "Adult Mouse Brain - Allen Brain Atlas V3p1":
-                return true;
-        }
-        return false;
+        return atlasNameMouseCompatible.contains(atlasName);
     }
 
     /**
@@ -46,13 +41,7 @@ public static boolean isDeepSliceMouseCompatible(String atlasName) {
      * @return true if the DeepSlice mouse model will be compatible with this atlas
      */
     public static boolean isDeepSliceRatCompatible(String atlasName) {
-        switch (atlasName) {
-            case "Rat - Waxholm Sprague Dawley V4":
-            case "Rat - Waxholm Sprague Dawley V4p2":
-            case "whs_sd_rat_39um":
-                return true;
-        }
-        return false;
+        return atlasNameRatCompatible.contains(atlasName);
     }
 
     public static File deepSliceLocalRunner(DeepSliceTaskSettings settings, File input_folder) {

diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/command/ABBAForumHelpCommand.java b/src/main/java/ch/epfl/biop/atlas/aligner/command/ABBAForumHelpCommand.java
@@ -6,7 +6,10 @@
 import ch.epfl.biop.atlas.aligner.ABBAHelper;
 import ch.epfl.biop.bdv.img.bioformats.BioFormatsHelper;
 import ch.epfl.biop.sourceandconverter.register.Elastix2DSplineRegister;
+import ch.epfl.biop.wrappers.deepslice.DeepSlice;
+import ch.epfl.biop.wrappers.elastix.Elastix;
 import ch.epfl.biop.wrappers.elastix.ElastixTask;
+import ch.epfl.biop.wrappers.transformix.Transformix;
 import ij.IJ;
 import net.imagej.ImageJ;
 import net.imagej.updater.UpdateService;
@@ -19,7 +22,10 @@
 import org.scijava.util.VersionUtils;
 import sc.fiji.bdvpg.services.SourceAndConverterServices;
 
+import java.io.File;
 import java.net.URL;
+import java.net.URLEncoder;
+import java.nio.charset.StandardCharsets;
 import java.util.Map;
 @SuppressWarnings("unused")
 @Plugin(type = Command.class,
@@ -33,18 +39,29 @@ public class ABBAForumHelpCommand implements Command {
     @Parameter
     UpdateService us;
 
+    public static String pythonInformation = "";
+
     @Override
     public void run() {
         try {
-            Map<String, UpdateSite> sites = AvailableSites.getAvailableSites();
 
             StringBuilder sites_string = new StringBuilder();
+            if (pythonInformation.isEmpty()) {
+                Map<String, UpdateSite> sites = AvailableSites.getAvailableSites();
+                try {
+                    for (UpdateSite site : sites.values()) {
+                        if (us.getUpdateSite(site.getName()).isActive()) {
+                            sites_string.append(site.getName()).append("+");
+                        }
+                    }
+                } catch (Exception e) {
+                    sites_string.append("Could not get installed update sites.");
+                }
+            } else {
+                sites_string.append("Can't collect update sites with ABBA run from Python");
+            }
 
-            sites.values().stream()
-                    .filter(site -> us.getUpdateSite(site.getName()).isActive())
-                    .forEach(site -> sites_string.append(site.getName()+"+"));
-
-            String nl = "%0D%0A"; // new line in url get
+            String nl = "\n";
             String imageScForumUrl = "https://forum.image.sc/";
             String title = "Help for ABBA in Fiji: [your question here]";
             String body = "[Detail your issue here]"+nl;
@@ -54,6 +71,11 @@ public void run() {
             body += "OS and Dependencies Info"+nl;
             body +="```"+nl;
             body +="OS "+ System.getProperty("os.name")+nl;
+            if (!pythonInformation.isEmpty()) {
+                body += pythonInformation+nl;
+            } else {
+                body += "Not run from PyImageJ"+nl;
+            }
             body +="ImageJ "+ VersionUtils.getVersion(ImageJ.class)+nl;
             body +="IJ "+ VersionUtils.getVersion(IJ.class)+nl;
             body +="ABBA "+ VersionUtils.getVersion(ABBAHelper.class)+nl;
@@ -64,13 +86,29 @@ public void run() {
             body +="Bdv Playground "+VersionUtils.getVersion(SourceAndConverterServices.class)+nl;
             body +="Biop Image Loader "+VersionUtils.getVersion(BioFormatsHelper.class)+nl;
             body +="Biop Wrappers "+VersionUtils.getVersion(ElastixTask.class)+nl;
+            if (Elastix.exePath!=null) {
+                body += "Elastix Path: " + Elastix.exePath + " exists ?"+new File(Elastix.exePath).exists()+nl;
+            } else {
+                body += "Elastix path not set"+nl;
+            }
+            if (Transformix.exePath!=null) {
+                body += "Transformix Path: " + Transformix.exePath + " exists ?"+new File(Transformix.exePath).exists()+nl;
+            } else {
+                body += "Transformix path not set"+nl;
+            }
+            if (DeepSlice.envDirPath!=null) {
+                body += "Deepslice env dir: " + DeepSlice.envDirPath + " exists ?"+new File(DeepSlice.envDirPath).exists()+nl;
+            } else {
+                body += "Deepslice env dir not set"+nl;
+            }
+
             //noinspection deprecation
             body +="Updates sites: "+sites_string+nl;
             body +="```";
 
             String fullUrl = imageScForumUrl+"new-topic?"
                     +"title="+title+"&"
-                    +"body="+body+"&"
+                    +"body="+formatStringForUrl(body)+"&"
                     +"category=usage-issues&"
                     +"tags=fiji,abba";
 
@@ -81,4 +119,14 @@ public void run() {
             e.printStackTrace();
         }
     }
+
+    public static String formatStringForUrl(String input) {
+        try {
+            // Encode the input string using UTF-8
+            return URLEncoder.encode(input, StandardCharsets.UTF_8.toString());
+        } catch (Exception e) {
+            e.printStackTrace();
+            return "";
+        }
+    }
 }
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/gui/bdv/BdvMultislicePositionerView.java b/src/main/java/ch/epfl/biop/atlas/aligner/gui/bdv/BdvMultislicePositionerView.java
@@ -390,6 +390,11 @@ private void installBdvMenu(int hierarchyLevelsSkipped) {
             if (this.mode == POSITIONING_MODE_INT) msp.equalSpacingSelectedSlices();
         });
 
+        DeepSliceHelper.addMouseCompatibleAtlas("Adult Mouse Brain - Allen Brain Atlas V3");
+        DeepSliceHelper.addMouseCompatibleAtlas("Adult Mouse Brain - Allen Brain Atlas V3p1");
+        DeepSliceHelper.addRatCompatibleAtlas("Rat - Waxholm Sprague Dawley V4");
+        DeepSliceHelper.addRatCompatibleAtlas("Rat - Waxholm Sprague Dawley V4p2");
+
         if (DeepSliceHelper.isDeepSliceMouseCompatible(msp.getReslicedAtlas().ba.getName())) {
 
             logger.debug("Installing DeepSlice Command for Mouse");