small fixes

PreibischLab · Jun 23, 2020 · 06d67cd · 06d67cd
1 parent 3e1417f
commit 06d67cd
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Showing 14 changed files with 158 additions and 78 deletions.
diff --git a/src/main/java/com/preibisch/pinna2d/tools/Imp.java b/src/main/java/com/preibisch/pinna2d/tools/Imp.java
@@ -120,9 +120,9 @@ public float getMax() {
         return max.get();
     }
 
-    public void save(@NotNull File file) {
+    public boolean save(@NotNull File file) {
         int dims = img.numDimensions() - 1;
         IntervalView<FloatType> view = Views.hyperSlice(img, dims, categoryChannel);
-        save(view, file);
+       return save(view, file);
     }
 }
diff --git a/src/main/java/com/preibisch/pinna2d/utils/ImpHelpers.java b/src/main/java/com/preibisch/pinna2d/utils/ImpHelpers.java
@@ -239,10 +239,10 @@ public static <T extends FloatType> void computeMinMax(
 
     }
 
-    public static void save(IntervalView<FloatType> view, File file) {
+    public static boolean save(IntervalView<FloatType> view, File file) {
         ImagePlus imp = ImageJFunctions.wrap(view, "Categories");
         imp.show();
-        saveTiffStack(imp, file);
+        return saveTiffStack(imp, file);
     }
 
     /*

diff --git a/src/main/kotlin/com/preibisch/pinna2d/controllers/AnnotationController.kt b/src/main/kotlin/com/preibisch/pinna2d/controllers/AnnotationController.kt
@@ -8,6 +8,7 @@ import com.preibisch.pinna2d.model.toAnnotationEntry
 import com.preibisch.pinna2d.tools.Imp
 import com.preibisch.pinna2d.tools.Log
 import com.preibisch.pinna2d.util.execute
+import com.preibisch.pinna2d.util.showPopup
 import com.preibisch.pinna2d.util.toDate
 import javafx.collections.FXCollections
 import javafx.collections.ObservableList
@@ -36,21 +37,22 @@ class AnnotationController : Controller() {
         items = FXCollections.observableArrayList();
     }
 
-    fun add(newEntryDate: LocalDate, newImageName: String, newAnnotationId: Float, newAnnotationVal: Int, spaceVal: Long): AnnotationEntry {
+    fun add(newImageId: Int,newEntryDate: LocalDate, newImageName: String, newAnnotationId: Float, newAnnotationVal: Int, spaceVal: Long): AnnotationEntry {
         val newEntry = execute {
             AnnotationEntryTbl.insert {
                 it[entryDate] = newEntryDate.toDate()
+                it[imageId] = newImageId
                 it[imageName] = newImageName
                 it[annotationId] = newAnnotationId
                 it[annotationVal] = newAnnotationVal
                 it[spaceDims] = spaceVal
             }
         }
         items.add(AnnotationEntryModel().apply {
-            item = AnnotationEntry(newEntry[AnnotationEntryTbl.id], newEntryDate, newImageName, newAnnotationId, newAnnotationVal, spaceVal)
+            item = AnnotationEntry(newEntry[AnnotationEntryTbl.id], newEntryDate, newImageId,newImageName, newAnnotationId, newAnnotationVal, spaceVal)
         })
 //        pieItemsData.add(PieChart.Data(newItem,newPrice))
-        return AnnotationEntry(newEntry[AnnotationEntryTbl.id], newEntryDate, newImageName, newAnnotationId, newAnnotationVal, spaceVal)
+        return AnnotationEntry(newEntry[AnnotationEntryTbl.id], newEntryDate, newImageId, newImageName, newAnnotationId, newAnnotationVal, spaceVal)
     }
 
     fun update(updatedItem: AnnotationEntryModel): Int {
@@ -77,20 +79,20 @@ class AnnotationController : Controller() {
 //        removeModelFromPie(model)
     }
 
-    private fun newEntry(img: String, min: Int, max: Int) {
+    private fun newEntry(imageId: Int, img: String, min: Int, max: Int) {
         for (i in min..max) {
-            add(LocalDate.now(), img, i.toFloat(), -1, 0)
+            add(imageId,LocalDate.now(), img, i.toFloat(), -1, 0)
 
         }
     }
 
-    fun start(projectFolder: String, imageName: String, min: Float, max: Float) {
+    fun start(imageId: Int, projectFolder: String, imageName: String, min: Float, max: Float) {
         folder = projectFolder
         currentImage = imageName
         items.clear()
         val exists = checkExist(imageName)
         if (!exists)
-            newEntry(imageName, min.toInt(), max.toInt())
+            newEntry(imageId, imageName, min.toInt(), max.toInt())
         else {
             val newItems = execute {
                 AnnotationEntryTbl.select { AnnotationEntryTbl.imageName eq imageName }.map {
@@ -148,7 +150,8 @@ class AnnotationController : Controller() {
     fun exportStatistics() {
         val basename = currentImage.split(".")[0]
         val f = File(folder, String.format("%s.csv", basename))
-        f.toAnnotationCSV(items)
+        val result = f.toAnnotationCSV(items)
+        showPopup(result,"Saving CSV file!",f.path)
     }
 
 

diff --git a/src/main/kotlin/com/preibisch/pinna2d/controllers/AnnotationExporterCSV.kt b/src/main/kotlin/com/preibisch/pinna2d/controllers/AnnotationExporterCSV.kt
@@ -6,7 +6,7 @@ import javafx.collections.ObservableList
 import java.io.File
 import java.io.FileWriter
 
-fun File.toAnnotationCSV(list: ObservableList<AnnotationEntryModel>) {
+fun File.toAnnotationCSV(list: ObservableList<AnnotationEntryModel>): Boolean {
     try {
         var fileWriter = FileWriter(this)
         val head = String.format("%s,%s,%s", AnnotationEntryModel::annotationId.name, AnnotationEntryModel::annotationVal.name, AnnotationEntryModel::spaceDims.name)
@@ -17,9 +17,12 @@ fun File.toAnnotationCSV(list: ObservableList<AnnotationEntryModel>) {
         }
         fileWriter.flush()
         fileWriter.close()
+        return true
     } catch (e: Exception) {
         Log.error("Error writing file !")
         Log.error(e.toString())
+        return false
     }
 
+
 }
diff --git a/src/main/kotlin/com/preibisch/pinna2d/controllers/FilesAnalyzeManager.kt b/src/main/kotlin/com/preibisch/pinna2d/controllers/FilesAnalyzeManager.kt
@@ -45,7 +45,8 @@ class FilesAnalyzeManager : Controller() {
         assembledData.forEach { (t, u) ->
             if (!checkExist(t.name, listOfItems)) {
                 val bestMask = getMaxCells(u)
-                add(LocalDate.now(), t.name, bestMask.name, u.size, getNbCells(bestMask), 0, 0)
+                val status = if (u.isNotEmpty()) 0 else 1
+                add(LocalDate.now(), t.name, bestMask.name, u.size, getNbCells(bestMask), 0, status)
             }
         }
 
@@ -70,10 +71,21 @@ class FilesAnalyzeManager : Controller() {
         return ImageEntry(newEntry[ImageEntryTbl.id], newEntryDate, newImageName, newMaskFile, newNbMasks, newNbCells, newNbClassifiedCells, newStatus)
     }
 
+    fun updateStatus(id: Int, newStatus: Int){
+        return execute {
+            ImageEntryTbl.update({
+                AnnotationEntryTbl.id eq (id)
+            }) {
+                it[status] = newStatus
+            }
+        }
+
+    }
+
     fun update(updatedItem: ImageEntryModel): Int {
         return execute {
             ImageEntryTbl.update({
-                AnnotationEntryTbl.id eq (updatedItem.id.value.toInt())
+                ImageEntryTbl.id eq (updatedItem.id.value.toInt())
             }) {
                 it[entryDate] = updatedItem.entryDate.value.toDate()
                 it[fileName] = updatedItem.fileName.value
@@ -112,5 +124,19 @@ class FilesAnalyzeManager : Controller() {
         val elms = maskFile.name.split(".")[0].split("_")
         return elms.last().toInt()
     }
+
+    fun startedImage(name: String) {
+        val newStatus = 1
+        for (f in files){
+            if (f.fileName.value == name){
+                Log.info("Update id: ${f.id.value}")
+                f.status.value = newStatus
+                update(f)
+                break
+            }
+        }
+
+
+    }
 }
 
diff --git a/src/main/kotlin/com/preibisch/pinna2d/controllers/ImageController.kt b/src/main/kotlin/com/preibisch/pinna2d/controllers/ImageController.kt
@@ -3,6 +3,7 @@ package com.preibisch.pinna2d.controllers
 import com.preibisch.pinna2d.model.AnnotationEntryModel
 import com.preibisch.pinna2d.tools.Imp
 import com.preibisch.pinna2d.tools.Log
+import com.preibisch.pinna2d.util.showPopup
 import javafx.beans.property.SimpleStringProperty
 import javafx.geometry.Point2D
 import javafx.scene.Node
@@ -63,7 +64,8 @@ class ImageController : Controller() {
     }
 
     fun save(file: File) {
-        Imp.get().save(file)
+        val result =  Imp.get().save(file)
+        showPopup(result,"Saving file!",file.path)
     }
 
     fun select(v: Float) {

diff --git a/src/main/kotlin/com/preibisch/pinna2d/controllers/InstanceController.kt b/src/main/kotlin/com/preibisch/pinna2d/controllers/InstanceController.kt
@@ -1,27 +1,30 @@
 package com.preibisch.pinna2d.controllers
 
 import com.preibisch.pinna2d.tools.Imp
-import com.preibisch.pinna2d.view.MainAnnotationView
 import tornadofx.*
 import java.io.File
 
 class InstanceController : Controller() {
 
     val annotationController: AnnotationController by inject()
+    val fileController: FilesAnalyzeManager by inject()
     private val imageController: ImageController by inject()
 
     private var projectPath = ""
     var inputPath: String = ""
     var maskPath: String = ""
     var imageName: String = ""
 
-    fun start(projectFolder : String, inputPath: String, maskPath: String) {
+    fun start(imageId: Int, projectFolder: String, inputPath: String, maskPath: String) {
         this.projectPath = projectFolder
         this.inputPath = inputPath
         this.maskPath = maskPath
         this.imageName = File(inputPath).name
         println(imageName)
         imageController.start(inputPath, maskPath,imageName)
-        annotationController.start(projectPath,imageName, Imp.get().min+1, Imp.get().max)
+        fileController.startedImage(imageName)
+        annotationController.start(imageId,projectPath,imageName, Imp.get().min+1, Imp.get().max)
+
+
     }
 }
diff --git a/src/main/kotlin/com/preibisch/pinna2d/model/AnnotationEntryTbl.kt b/src/main/kotlin/com/preibisch/pinna2d/model/AnnotationEntryTbl.kt
@@ -10,6 +10,7 @@ import java.time.LocalDate
 fun ResultRow.toAnnotationEntry() = AnnotationEntry(
         this[AnnotationEntryTbl.id],
         this[AnnotationEntryTbl.entryDate].toJavaLocalDate(),
+        this[AnnotationEntryTbl.imageId].toInt(),
         this[AnnotationEntryTbl.imageName],
         this[AnnotationEntryTbl.annotationId].toFloat(),
         this[AnnotationEntryTbl.annotationVal].toInt(),
@@ -19,16 +20,20 @@ fun ResultRow.toAnnotationEntry() = AnnotationEntry(
 object AnnotationEntryTbl : Table() {
     val id = integer(id_string).autoIncrement().primaryKey()
     val entryDate = date(entry_date)
+    val imageId = integer(image_id)
     val imageName = varchar(image_name, length = 100)
     val annotationId = float(annotation_id)
     val annotationVal = integer(annotation_val)
     val spaceDims = long(space_dims)
 }
 
-class AnnotationEntry(id: Int, entryDate: LocalDate, imageName: String, annotationId: Float, annotationVal : Int, spaceVal: Long) {
+class AnnotationEntry(id: Int, entryDate: LocalDate, imageId: Int, imageName: String, annotationId: Float, annotationVal : Int, spaceVal: Long) {
     val idProperty = SimpleIntegerProperty(id)
     var id by idProperty
 
+    val imageIdProperty = SimpleIntegerProperty(imageId)
+    var imageId by imageIdProperty
+
     val entryDateProperty = SimpleObjectProperty<LocalDate>(entryDate)
     var entryDate by entryDateProperty
 
@@ -52,6 +57,7 @@ class AnnotationEntry(id: Int, entryDate: LocalDate, imageName: String, annotati
 class AnnotationEntryModel : ItemViewModel<AnnotationEntry>() {
     val id = bind { item?.idProperty }
     val entryDate = bind { item?.entryDateProperty }
+    val imageId = bind { item?.imageIdProperty }
     val imageName = bind { item?.imageNameProperty }
     val annotationId = bind { item?.annotationIdProperty }
     val annotationVal = bind { item?.annotationValProperty }

diff --git a/src/main/kotlin/com/preibisch/pinna2d/util/FileUtil.kt b/src/main/kotlin/com/preibisch/pinna2d/util/FileUtil.kt
@@ -3,7 +3,7 @@ package com.preibisch.pinna2d.util
 import com.preibisch.pinna2d.tools.Log
 
 
-private val statusList: List<String> = listOf("Not stated Yet","No Masks","Started","Finished")
+private val statusList: List<String> = listOf("Not stated Yet","Started","No Masks","Finished")
 
 fun getStatus(statusCode: Int) : String{
     if((statusCode)>= statusList.size){

diff --git a/src/main/kotlin/com/preibisch/pinna2d/util/IOFunctions.kt b/src/main/kotlin/com/preibisch/pinna2d/util/IOFunctions.kt
@@ -1,10 +1,17 @@
 package com.preibisch.pinna2d.util
 
+import com.preibisch.pinna2d.tools.Log
+import javafx.scene.control.Alert
+import javafx.scene.control.Alert.AlertType
+import javafx.scene.control.ButtonType
 import javafx.stage.DirectoryChooser
 import javafx.stage.FileChooser
+import javafx.stage.Window
+import tornadofx.*
 import java.io.File
 import java.io.IOException
 
+
 fun assembleInputWithMasks(inputFiles: Array<File>, maskFiles: Array<File>): Map<File, List<File>> {
     var result = HashMap<File, List<File>>()
     inputFiles.forEach {
@@ -40,4 +47,25 @@ fun openFolderChooser(): String {
     var chooser = DirectoryChooser()
     val file = chooser.showDialog(null)
     return file?.toString() ?: ""
+}
+
+fun imageSaverBox(currentWindow: Window?): File? {
+    Log.info("save")
+    var chooser = FileChooser()
+    val name = String.format("%s_instances.tif", CURRENT_IMAGE.split(".")[0])
+    chooser.initialDirectory = File(PROJECT_FOLDER)
+    chooser.initialFileName = name
+    chooser.extensionFilters.add(FileChooser.ExtensionFilter("TIF file ", "*.tif"))
+    chooser.extensionFilters.add(FileChooser.ExtensionFilter("TIFF file ", "*.tiff"))
+    chooser.extensionFilters.add(FileChooser.ExtensionFilter("PNG file ", "*.png"))
+    val file = chooser.showSaveDialog(currentWindow)
+    Log.info(file.toString())
+    return file
+}
+
+fun showPopup(condition: Boolean,title: String, msg: String){
+    if (condition)
+        information(title,msg)
+    else
+        error(title,msg)
 }
diff --git a/src/main/kotlin/com/preibisch/pinna2d/util/Names.kt b/src/main/kotlin/com/preibisch/pinna2d/util/Names.kt
@@ -3,6 +3,7 @@ package com.preibisch.pinna2d.util
 //DB Images
 const val id_string = "id"
 const val entry_date = "entry_date"
+const val image_id = "image_id"
 const val image_name = "image_name"
 const val mask_file = "mask_file"
 const val nb_masks = "nb_masks"

diff --git a/src/main/kotlin/com/preibisch/pinna2d/view/AnnotationEditorView.kt b/src/main/kotlin/com/preibisch/pinna2d/view/AnnotationEditorView.kt
@@ -5,13 +5,13 @@ import com.preibisch.pinna2d.controllers.AnnotationController
 import com.preibisch.pinna2d.controllers.ImageController
 import com.preibisch.pinna2d.model.AnnotationEntryModel
 import com.preibisch.pinna2d.tools.Imp
-import com.preibisch.pinna2d.util.CATEGORIES
-import com.preibisch.pinna2d.util.getColor
+import com.preibisch.pinna2d.util.*
 import javafx.scene.control.ToggleButton
 import javafx.scene.control.ToggleGroup
 import javafx.scene.paint.Color
 import javafx.scene.shape.Circle
 import tornadofx.*
+import java.io.File
 
 class AnnotationEditorView : View("Annotations") {
 
@@ -79,13 +79,25 @@ class AnnotationEditorView : View("Annotations") {
                 }
 
             }
-            borderpane {  right = button("Export Statistics") {
+          button("Export Statistics") {
+              prefWidth = 220.0
                 setOnAction { controller.exportStatistics() }
-            } }
+            }
+            button("Save Instance Image") {
+                prefWidth = 220.0
+                setOnAction { save() }
+            }
+
 
         }
     }
 
+    private fun save(){
+        val file = imageSaverBox(this.currentWindow)
+        if (file.toString() != null)
+            imageController.save(File(file.toString()))
+    }
+
     private fun generateCategoriesButtons() {
         val group = ToggleGroup()
         for (cat in CATEGORIES)