pytest fcns added, testmode paths added to open fcn, init shape contr…

…ols, initroi fcn list append fixed, init file list fcn sanity check

.gitignore

@@ -88,4 +88,6 @@ demo/img_ROIs_classes.zip
 masks
 src/napari_annotatorj/models/*
 src/napari_annotatorj/unet/__pycache__/
-src/napari_annotatorj/default_models/*
+src/napari_annotatorj/default_models/*
+src/napari_annotatorj/pyinstaller/
+src/napari_annotatorj/build/

pyproject.toml

@@ -3,4 +3,13 @@ requires = ["setuptools", "wheel", "setuptools_scm"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
-write_to = "src/napari_annotatorj/_version.py"
+write_to = "src/napari_annotatorj/_version.py"
+
+[tool.pytest.ini_options]
+filterwarnings = [
+    "error",
+    "ignore::DeprecationWarning",
+    # note the use of single quote below to denote "raw" strings in TOML
+    'ignore:function ham\(\) is deprecated:DeprecationWarning',
+    "ignore::FutureWarning",
+]

src/napari_annotatorj/_dock_widget.py

@@ -128,7 +128,7 @@ def __init__(self, napari_viewer):
         self.curPredictionImage=None
         self.curPredictionImageName=None
         self.curOrigImage=None
-        self.allowContAssistBbox=True
+        self.allowContAssistBbox=False #True
         # '0' is the default GPU if any, otherwise fall back to cpu
         # valid values are: ['cpu','0','1','2',...]
         self.gpuSetting='cpu'
@@ -461,6 +461,8 @@ def openNew(self):
             if os.path.exists(self.test_image):
                 img=skimage.io.imread(self.test_image)
                 print('Test image read successfully')
+                self.defDir=os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(__file__))),'demo/')
+                self.defFile='img.png'
             else:
                 print('Test image could not be found')
         else:
@@ -837,6 +839,8 @@ def finishOpenNewInit(self,initSrc=None):
             roiLayer.mode='add_polygon'
             if self.freeHandROIvis not in roiLayer.mouse_drag_callbacks:
                 roiLayer.mouse_drag_callbacks.append(self.freeHandROIvis)
+
+            self.initShapeControls()
 
             # chkbx setting moved to its own fcn initChkBoxes
 
@@ -881,6 +885,8 @@ def finishOpenNewInit(self,initSrc=None):
             if self.freeHandROIvis in roiLayer.mouse_drag_callbacks:
                 roiLayer.mouse_drag_callbacks.remove(self.freeHandROIvis)
 
+            self.initShapeControls()
+
             # chkbx setting moved to its own fcn initChkBoxes
 
 
@@ -1083,6 +1089,7 @@ def loadROIs(self):
         self.bindKeys(roiLayer)
 
 
+    '''
     def loadROIs2(self):
         # temporarily load a test ImageJ ROI.zip file with contours created in ImageJ and saved with AnnotatorJ
         # later this will start a browser dialog to select the annotation file
@@ -1117,6 +1124,7 @@ def loadROIs2(self):
         #shapesLayer.mode = 'select'
         # select the "add polygon" mode from the controls by default to enable freehand ROI drawing
         shapesLayer.mode = 'add_polygon'
+    '''
 
     def initRoiManager(self):
         # the rois will be stored in this object as in ImageJ's RoiManager
@@ -1397,7 +1405,10 @@ def importROIsFromMaskImage(self,mask,layerName='ROI'):
         roiLayer=self.findROIlayer(layerName=layerName)
         if roiLayer is not None:
             roiLayer.add_polygons(shapes,edge_width=self.annotEdgeWidth,edge_color=roiColours,face_color=[0,0,0,0])
-            roiLayer.properties=roiProps
+            #roiLayer.properties=roiProps
+            numpy.append(roiLayer.properties['class'],numpy.array(roiProps['class']))
+            numpy.append(roiLayer.properties['name'],roiProps['name'])
+            numpy.append(roiLayer.properties['nameInt'],numpy.array(roiProps['nameInt']))
 
         else:
             print(f'Cannot find the ROI layer')
@@ -3585,12 +3596,7 @@ def updateControls(self,layerName):
         from napari._qt.layer_controls.qt_shapes_controls import QtShapesControls
 
         #shapeControls=None
-        if self.shapeControls is None:
-            for c in self.viewer.window._qt_viewer.controls.children():
-                if isinstance(c,QtShapesControls) and c.layer.name==layerName:
-                    self.shapeControls=c
-                    self.shapeControls.widthSlider.valueChanged.connect(self.updateEdgeWidths)
-                    break
+        self.initShapeControls(layerName=layerName)
         if self.shapeControls is None:
             print('Could not find the shapeControls')
             return
@@ -3599,6 +3605,31 @@ def updateControls(self,layerName):
             self.shapeControls.widthSlider.setValue(self.annotEdgeWidth)
 
 
+    def initShapeControls(self,layerName='ROI',reinit=False):
+        from napari._qt.layer_controls.qt_shapes_controls import QtShapesControls
+        #if self.shapeControls is None or reinit:
+        if self.shapeControls is not None:
+            # check if valid
+            try:
+                self.shapeControls.widthSlider.name()
+                self.doInitShapeControls(layerName)
+            except Exception as e:
+                # does not exist
+                self.doInitShapeControls(layerName)
+        else:
+            self.doInitShapeControls(layerName)
+
+
+    def doInitShapeControls(self,layerName='ROI'):
+        from napari._qt.layer_controls.qt_shapes_controls import QtShapesControls
+        for c in self.viewer.window._qt_viewer.controls.children():
+                if isinstance(c,QtShapesControls) and c.layer.name==layerName:
+                    self.shapeControls=c
+                    self.shapeControls.widthSlider.valueChanged.connect(self.updateEdgeWidths)
+                    print(f'---- reinited shape controls to layer {layerName}')
+                    break
+
+
     def updateEdgeWidths(self,value):
         roiLayer=self.findROIlayer()
         for i in range(roiLayer.nshapes):
@@ -8587,6 +8618,7 @@ def setAnnotType(self):
                 if self.annotatorjObj.freeHandROIvis not in roiLayer.mouse_drag_callbacks:
                     roiLayer.mouse_drag_callbacks.append(self.annotatorjObj.freeHandROIvis)
                 self.annotatorjObj.viewer.layers.selection.add(roiLayer)
+                self.annotatorjObj.initShapeControls(reinit=True)
             elif newAnnotType=='bbox':
                 roiLayer=self.annotatorjObj.findROIlayer()
                 if roiLayer is None:
@@ -8596,6 +8628,7 @@ def setAnnotType(self):
                 if self.annotatorjObj.freeHandROIvis in roiLayer.mouse_drag_callbacks:
                     roiLayer.mouse_drag_callbacks.remove(self.annotatorjObj.freeHandROIvis)
                 self.annotatorjObj.viewer.layers.selection.add(roiLayer)
+                self.annotatorjObj.initShapeControls(reinit=True)
             elif newAnnotType=='semantic':
                 labelLayer=self.annotatorjObj.findLabelsLayerName(layerName='semantic')
                 if labelLayer is None:
@@ -10472,10 +10505,11 @@ def initFileList(annotatorjObj,callback):
         fileList=QListWidget()
         fileList.setSelectionMode(QAbstractItemView.SingleSelection)
 
-        for fi,f in enumerate(annotatorjObj.curFileList):
-            fileList.insertItem(fi,f)
+        if annotatorjObj.curFileList is not None:
+            for fi,f in enumerate(annotatorjObj.curFileList):
+                fileList.insertItem(fi,f)
 
-        fileList.setCurrentItem(fileList.item(annotatorjObj.curFileIdx))
+            fileList.setCurrentItem(fileList.item(annotatorjObj.curFileIdx))
 
         fileList.currentItemChanged.connect(callback)
 

src/napari_annotatorj/_tests/mimic_roiloading_frommask.py

@@ -0,0 +1,38 @@
+import napari
+from _dock_widget import AnnotatorJ
+from roifile import ImagejRoi
+from napari.layers import Shapes, Image, Labels, Layer
+
+def countLayers(layers,layerType=Image):
+    c=0
+    for x in layers:
+        if (x.__class__ is layerType):
+            c+=1
+    return c
+
+viewer = napari.Viewer()
+pluginInstance=AnnotatorJ(viewer)
+viewer.window.add_dock_widget(pluginInstance,name='AnnotatorJ')
+
+tmp_path="C:/work/szbk/annotatorj/testing_napari/dummying_nucleus/masks_demo/labelled_masks/"
+pluginInstance.defFile='full adj.tiff'
+# load dummy roi
+rois=ImagejRoi.fromfile(pluginInstance.test_rois)
+shapesLayer=pluginInstance.extractROIdata(rois)
+n=len(shapesLayer.data)
+print(f'numshapes: {n}')
+# add 2nd shapes layer with these rois
+pluginInstance.viewer.add_layer(shapesLayer)
+prev_count_shapes=countLayers(pluginInstance.viewer.layers,layerType=Shapes)
+print(f'before: {prev_count_shapes}')
+#'''
+pluginInstance.viewer.layers.remove('ROI')
+print(f'is 2?: {countLayers(pluginInstance.viewer.layers,layerType=Shapes)}')
+pluginInstance.loadRoisFromMask(tmp_path,False)
+after_count_shapes=countLayers(pluginInstance.viewer.layers,layerType=Shapes)
+print(f'after: {after_count_shapes}')
+newShapesLayer=pluginInstance.viewer.layers[-1]
+print(f'new shapes num: {len(newShapesLayer.data)}')
+#'''
+
+napari.run()

src/napari_annotatorj/_tests/mimic_roiloading_fromtext.py

@@ -0,0 +1,84 @@
+import napari
+from _dock_widget import AnnotatorJ,ExportFrame
+from roifile import ImagejRoi
+from napari.layers import Shapes, Image, Labels, Layer
+import os,sys
+
+def countLayers(layers,layerType=Image):
+    c=0
+    for x in layers:
+        if (x.__class__ is layerType):
+            c+=1
+    return c
+
+viewer = napari.Viewer()
+pluginInstance=AnnotatorJ(viewer)
+viewer.window.add_dock_widget(pluginInstance,name='AnnotatorJ')
+
+tmp_path="C:/work/szbk/annotatorj/testing_napari/dummying_nucleus/coording/"
+pluginInstance.defFile='dummy_mask.tiff'
+filename='dummy_mask.csv'
+filename2='dummy_mask.txt'
+# load dummy roi
+rois=ImagejRoi.fromfile(pluginInstance.test_rois)
+shapesLayer=pluginInstance.extractROIdata(rois)
+n=len(shapesLayer.data)
+print(f'numshapes: {n}')
+prev_count_shapes=countLayers(pluginInstance.viewer.layers,layerType=Shapes)
+print(f'before: {prev_count_shapes}')
+
+if os.path.isfile(os.path.join(tmp_path,filename)):
+    os.remove(os.path.join(tmp_path,filename))
+if os.path.isfile(os.path.join(tmp_path,filename2)):
+    os.remove(os.path.join(tmp_path,filename2))
+
+pluginInstance.ExportFrame=ExportFrame(pluginInstance.viewer,annotatorjObj=pluginInstance)
+bboxes=pluginInstance.ExportFrame.fillBboxList(shapesLayer,len(shapesLayer.data))
+pluginInstance.ExportFrame.saveExportedCSV(bboxes,os.path.join(tmp_path,filename))
+success=os.path.isfile(os.path.join(tmp_path,filename))
+print(f'wrote file: {success}')
+
+pluginInstance.loadRoisFromCoords(tmp_path)
+print(f'loaded: {countLayers(pluginInstance.viewer.layers,layerType=Shapes)}')
+#'''
+after_count_shapes=countLayers(pluginInstance.viewer.layers,layerType=Shapes)
+print(f'after: {after_count_shapes}')
+newShapesLayer=pluginInstance.viewer.layers[-1]
+print(f'new shapes num: {len(newShapesLayer.data)}')
+#'''
+
+# remove it
+print(f'layers before REMOVE: {pluginInstance.viewer.layers}')
+pluginInstance.viewer.layers.remove('ROI')
+print(f'--------------- REMOVING ROI LAYER -----------------')
+print(f'after remove layer count: {countLayers(pluginInstance.viewer.layers,layerType=Shapes)}')
+print(f'layers after REMOVE: {pluginInstance.viewer.layers}')
+os.remove(os.path.join(tmp_path,filename))
+
+# write yolo file
+bboxes=pluginInstance.ExportFrame.fillBboxListYOLO(shapesLayer,n,256,256)
+pluginInstance.ExportFrame.saveExportedCSVyolo(bboxes,os.path.join(tmp_path,filename2))
+success=os.path.isfile(os.path.join(tmp_path,filename2))
+print(f'wrote second file: {success}')
+
+pluginInstance.loadRoisFromCoords(tmp_path)
+print(f'loaded 2nd: {countLayers(pluginInstance.viewer.layers,layerType=Shapes)}')
+newShapesLayer=pluginInstance.viewer.layers[-1]
+print(f'numshapes 2nd: {len(newShapesLayer.data)}')
+
+pluginInstance.testMode=True
+pluginInstance.openNew()
+print(f'opened image')
+pluginInstance.testMode=False
+pluginInstance.defFile='dummy_mask.tiff'
+pluginInstance.loadRoisFromCoords(tmp_path)
+print(f'loaded 3rd: {countLayers(pluginInstance.viewer.layers,layerType=Shapes)}')
+newShapesLayer=pluginInstance.viewer.layers[-1]
+print(f'numshapes 3rd: {len(newShapesLayer.data)}')
+
+
+napari.run()
+
+
+
+