Fix DeepSlice wrapper - exposes better its API (breaking for DeepSlice)

README.md

@@ -18,6 +18,8 @@ On top of this, some converters that facilite the transmission of data to these
       * [I.A. Cellpose Virtual Environment](#ia-cellpose-virtual-environment)
       * [I.A.2. Conda installation](#ia2-conda-installation)
         * [I.A.2.a. Windows](#ia2a-windows)
+          * [Enable conda command outside conda prompt](#enable-conda-command-outside-conda-prompt)
+          * [Conda cellpose-GPU](#conda-cellpose-gpu)
         * [I.A.2.b. Mac](#ia2b-mac)
         * [I.A.2.c. Linux](#ia2c-linux)
     * [I.B. Fiji - Cellpose wrapper](#ib-fiji---cellpose-wrapper)
@@ -28,13 +30,16 @@ On top of this, some converters that facilite the transmission of data to these
       * [I.A.1. More on venv installation](#ia1-more-on-venv-installation)
       * [I.A.2. More on conda installation](#ia2-more-on-conda-installation)
         * [I.A.2.a. Windows](#ia2a-windows-1)
+          * [Enable conda command outside conda prompt](#enable-conda-command-outside-conda-prompt-1)
+          * [Conda StarDist-GPU](#conda-stardist-gpu)
         * [I.A.2.b. MAC OSX](#ia2b-mac-osx)
     * [I.B. Fiji - StarDist3D wrapper](#ib-fiji---stardist3d-wrapper)
   * [II. Using Fiji - StarDist3D wrapper](#ii-using-fiji---stardist3d-wrapper)
 * [DeepSlice](#deepslice)
   * [I. Installation](#i-installation-2)
       * [I.A. Conda installation](#ia-conda-installation)
         * [I.A.2.a. Windows](#ia2a-windows-2)
+          * [Enable conda command outside conda prompt](#enable-conda-command-outside-conda-prompt-2)
         * [I.A.2.b. Mac](#ia2b-mac-1)
         * [I.A.2.c. Linux](#ia2c-linux-1)
   * [II. Using Fiji - DeepSlice wrapper](#ii-using-fiji---deepslice-wrapper)
@@ -300,9 +305,16 @@ You need to install DeepSlice in a conda env that has python 3.7 (versions above
 ```
 conda create --name deep_slice python=3.7
 conda activate deep_slice
-pip install DeepSlice
+pip install deepslice==1.1.5
 ```
 
+If you don't want to pin a deepslice version, replace the last line by:
+
+```
+pip install deepslice
+```
+
+
 ##### I.A.2.a. Windows
 **NOTE** : if you rely on conda, the DeepSlice wrapper requires to enable the conda command outside of conda prompt, [_cf_ installation instructions](#enable-conda-command-outside-conda-prompt).
 

src/main/java/ch/epfl/biop/wrappers/deepslice/DeepSlice.java

@@ -15,6 +15,7 @@
 import java.nio.file.StandardCopyOption;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 import java.util.function.Consumer;
 import java.util.stream.Collectors;
@@ -26,23 +27,17 @@ public class DeepSlice {
     public static String keyPrefix = DeepSlice.class.getName() + ".";
 
     static String defaultEnvDirPath = "C:/Users/username/.conda/envs/deepslice";//"E:/conda-envs/CellPoseGPU3";
-    static String defaultEnvType = "conda";
-    static String defaultVersion = "1.1.5";
+    static String defaultVersion = "1.1.5.1";
 
     public static String envDirPath = Prefs.get(keyPrefix + "envDirPath", defaultEnvDirPath);
-    public static String envType = Prefs.get(keyPrefix + "envType", defaultEnvType);
+
     public static String version = Prefs.get(keyPrefix + "version", defaultVersion);
 
     public static void setEnvDirPath(File f) {
         DeepSlice.envDirPath = f.getAbsolutePath();
         Prefs.set(keyPrefix + "envDirPath", envDirPath);
     }
 
-    public static void setEnvType(String envType) {
-        DeepSlice.envType = envType;
-        Prefs.set(keyPrefix + "envType", envType);
-    }
-
     public static void setVersion(String version) {
         DeepSlice.version = version; // RAAAH!
         Prefs.set(keyPrefix + "version", version);
@@ -99,70 +94,49 @@ static void execute(List<String> options, Consumer<InputStream> outputHandler) t
         }
 
         List<String> cmd = new ArrayList<>();
-        List<String> start_cmd = null ;
-
-        // Get the prefs about the env type
-        String envType = Prefs.get(keyPrefix + "envType", DeepSlice.envType);
+        List<String> start_cmd;
 
         // start terminal
         if (IJ.isWindows()) {
             start_cmd=  Arrays.asList("cmd.exe", "/C");
         } else if ( IJ.isMacOSX() || IJ.isLinux()) {
             start_cmd = Arrays.asList("bash", "-c");
+        } else {
+            IJ.error("OS unrecognized!!");
+            start_cmd = Collections.singletonList("");
         }
         cmd.addAll( start_cmd );
 
+        List<String> conda_activate_cmd;
 
-        // Depending of the env type
-        if (envType.equals("conda")) {
-            List<String> conda_activate_cmd;
-
-            if (IJ.isWindows()) {
-                // Activate the conda env
-                conda_activate_cmd = Arrays.asList("CALL", Conda.getWindowsCondaCommand(), "activate", envDirPath);
-                cmd.addAll(conda_activate_cmd);
-                // After starting the env we can now use deepslice
-                cmd.add("&");// to have a second command
-                List<String> cellpose_args_cmd = Arrays.asList("python", "-Xutf8", getDeepSliceCLIScriptPath());
-                cmd.addAll(cellpose_args_cmd);
-                // input options
-                cmd.addAll(options);
-
-            } else if ( IJ.isMacOSX() || IJ.isLinux()) {
-                // instead of conda activate (so much headache!!!) specify the python to use
-                String python_path = envDirPath+separatorChar+"bin"+separatorChar+"python";
-                List<String> cellpose_args_cmd = new ArrayList<>(Arrays.asList( python_path , getDeepSliceCLIScriptPath()));
-                cellpose_args_cmd.addAll(options);
-
-                // convert to a string
-                cellpose_args_cmd = cellpose_args_cmd.stream().map(s -> {
-                    if (s.trim().contains(" "))
-                        return "\"" + s.trim() + "\"";
-                    return s;
-                }).collect(Collectors.toList());
-                // The last part needs to be sent as a single string, otherwise it does not run
-                String cmdString = cellpose_args_cmd.toString().replace(",","");
-
-                // finally add to cmd
-                cmd.add(cmdString.substring(1, cmdString.length()-1));
-            }
-
-        } else if (envType.equals("venv")) { // venv
-
-            if (IJ.isWindows()) {
-                List<String> venv_activate_cmd = Arrays.asList(new File(envDirPath, "Scripts/activate").toString());
-                cmd.addAll(venv_activate_cmd);
-                cmd.add("&");// to have a second command
-                List<String> cellpose_args_cmd = Arrays.asList("python", "-Xutf8", getDeepSliceCLIScriptPath());
-                cmd.addAll(cellpose_args_cmd);
-                cmd.addAll(options);
-
-            } else if ( IJ.isMacOSX() || IJ.isLinux()) {
-                throw new UnsupportedOperationException("Mac/Unix not supported yet with virtual environment. Please try conda instead.");
-            }
+        if (IJ.isWindows()) {
+            // Activate the conda env
+            conda_activate_cmd = Arrays.asList("CALL", Conda.getWindowsCondaCommand(), "activate", envDirPath);
+            cmd.addAll(conda_activate_cmd);
+            // After starting the env we can now use deepslice
+            cmd.add("&");// to have a second command
+            List<String> cellpose_args_cmd = Arrays.asList("python", "-Xutf8", getDeepSliceCLIScriptPath());
+            cmd.addAll(cellpose_args_cmd);
+            // input options
+            cmd.addAll(options);
 
-        } else {
-            throw new UnsupportedOperationException("Virtual env type unrecognized!");
+        } else if ( IJ.isMacOSX() || IJ.isLinux()) {
+            // instead of conda activate (so much headache!!!) specify the python to use
+            String python_path = envDirPath+separatorChar+"bin"+separatorChar+"python";
+            List<String> cellpose_args_cmd = new ArrayList<>(Arrays.asList( python_path , getDeepSliceCLIScriptPath()));
+            cellpose_args_cmd.addAll(options);
+
+            // convert to a string
+            cellpose_args_cmd = cellpose_args_cmd.stream().map(s -> {
+                if (s.trim().contains(" "))
+                    return "\"" + s.trim() + "\"";
+                return s;
+            }).collect(Collectors.toList());
+            // The last part needs to be sent as a single string, otherwise it does not run
+            String cmdString = cellpose_args_cmd.toString().replace(",","");
+
+            // finally add to cmd
+            cmd.add(cmdString.substring(1, cmdString.length()-1));
         }
 
         System.out.println(cmd.toString().replace(",", ""));
@@ -192,7 +166,7 @@ public void run() {
         if (exitValue != 0) {
             System.out.println("Runner " + envDirPath + " exited with value " + exitValue + ". Please check output above for indications of the problem.");
         } else {
-            System.out.println(envType + " , " + envDirPath + " run finished");
+            System.out.println("conda , " + envDirPath + " run finished");
         }
 
     }

src/main/java/ch/epfl/biop/wrappers/deepslice/DeepSliceTaskSettings.java

@@ -6,6 +6,8 @@
 public class DeepSliceTaskSettings {
     public String model;
     public String input_folder, output_folder;
-    public boolean ensemble, section_numbers, propagate_angles, enforce_index_order;
-    public int enforce_index_spacing;
+    public boolean ensemble, section_numbers, propagate_angles;
+    public boolean enforce_index_order;
+    public boolean use_enforce_index_spacing;
+    public String enforce_index_spacing;
 }

src/main/java/ch/epfl/biop/wrappers/deepslice/DefaultDeepSliceTask.java

@@ -21,9 +21,9 @@ public void run() throws Exception {
         if (settings.section_numbers) options.add("--section_numbers");
         if (settings.propagate_angles) options.add("--propagate_angles");
         if (settings.enforce_index_order) options.add("--enforce_index_order");
-        if (settings.enforce_index_spacing>0) {
+        if (settings.use_enforce_index_spacing) {
             options.add("--enforce_index_spacing");
-            options.add(Integer.toString(settings.enforce_index_spacing));
+            options.add(settings.enforce_index_spacing);
         }
 
         DeepSlice.execute(options, null);

src/main/java/ch/epfl/biop/wrappers/deepslice/ij2commands/DeepSliceFolderCommand.java

@@ -11,7 +11,7 @@
 
 @Plugin(type = Command.class, menuPath = "Plugins>BIOP>DeepSlice>DeepSlice (folder)",
 description = "Runs DeepSlice locally on a folder of your choice.")
-public class DeepSliceFolderCommand implements Command{
+public class DeepSliceFolderCommand implements Command {
     @Parameter(style = "directory")
     File input_folder;
 
@@ -24,20 +24,24 @@ public class DeepSliceFolderCommand implements Command{
     @Parameter(description = "try with and without ensemble to find the model which best works for you")
     boolean ensemble = false;
 
-    @Parameter(description = "if you have section numbers included in the filename as _sXXX specify this")
+    @Parameter(description = "if you have section numbers included in the filename as _sXXX set this to true")
     boolean section_number = false;
 
     @Parameter(description = "if you would like to normalise the angles")
     boolean propagate_angle = false;
 
-    @Parameter(description = "to reorder your sections according to the section")
+    @Parameter(description = "order your sections according to the section number (section number should be present)")
     boolean enforce_index_order = false;
 
+    @Parameter(description = "use enforce index spacing")
+    boolean use_enforce_index_spacing = false;
+
     @Parameter(description = "alternative to enforce_index_order: if you know the\n" +
-            "                        precise spacing (ie; 1, 2, 4, indicates that section 3\n" +
-            "                        has been left out of the series), then you can set the\n" +
-            "                        section thickness in microns with this parameter")
-    int enforce_index_spacing = -1;
+            " precise spacing (ie; 1, 2, 4, indicates that section 3\n" +
+            " has been left out of the series), then you can set the\n" +
+            " section thickness in microns with this parameter, or type 'None' " +
+            " if you want DeepSlice to guess the spacing")
+    String enforce_index_spacing = "None";
 
     @Override
     public void run() {
@@ -47,6 +51,7 @@ public void run() {
         if (output_folder!=null) settings.output_folder = output_folder.getAbsolutePath();
         settings.propagate_angles = propagate_angle;
         settings.section_numbers = section_number;
+        settings.use_enforce_index_spacing = use_enforce_index_spacing;
         settings.enforce_index_spacing = enforce_index_spacing;
         settings.enforce_index_order = enforce_index_order;
         settings.ensemble = ensemble;

src/main/java/ch/epfl/biop/wrappers/deepslice/ij2commands/DeepSlicePrefsSet.java

@@ -1,7 +1,6 @@
 package ch.epfl.biop.wrappers.deepslice.ij2commands;
 
 import ch.epfl.biop.wrappers.BiopWrappersCheck;
-import ch.epfl.biop.wrappers.cellpose.Cellpose;
 import ch.epfl.biop.wrappers.deepslice.DeepSlice;
 import org.scijava.command.Command;
 import org.scijava.log.LogService;
@@ -24,19 +23,13 @@ public class DeepSlicePrefsSet implements Command {
     @Parameter(style = "directory", persist = false)
     File deepSliceEnvDirectory = new File(DeepSlice.envDirPath);
 
-    //@Parameter(required = true, choices = {"conda", "venv"})
-    String envType = "conda";//DeepSlice.envType;
-
-
-    @Parameter(choices = {"1.1.5"}, persist = false)
+    @Parameter(choices = {"1.1.5.1"}, persist = false)
     String version = DeepSlice.version;
 
     @Override
     public void run() {
 
         DeepSlice.setEnvDirPath(deepSliceEnvDirectory);
-        DeepSlice.setEnvType(envType);
-
         DeepSlice.setVersion(version);
 
         if (ls != null) {

src/main/resources/deepslice_cli_v1.1.5.py → src/main/resources/deepslice_cli_v1.1.5.1.py

@@ -43,7 +43,11 @@ def parse_arguments():
     # alternatively if you know the precise spacing (ie; 1, 2, 4, indicates that section 3 has been left out of the series) Then you can use
     # Furthermore if you know the exact section thickness in microns this can be included instead of None
     if args.enforce_index_spacing is not None:
-        model.enforce_index_spacing(section_thickness=args.enforce_index_spacing)
+        if args.enforce_index_spacing=="None":
+            model.enforce_index_spacing(section_thickness=None)
+        else:
+            model.enforce_index_spacing(section_thickness=float(args.enforce_index_spacing))
+
     # now we save which will produce a json file which can be placed in the same directory as your images and then opened with QuickNII.
 
     # saves json only