Merge branch 'integration' into calvin

Author: kevinthenn

CoralLabeler/LoadFunctions.qml

@@ -31,9 +31,10 @@ Rectangle{
             console.log("temp not initialized")
         }
 
+        
         else{
             //load in csv from python function
-            var everything = tbox.readCSV(tbox.fixTempUrl(tbox.getTempUrl()) + "/" + imgLoad + ".csv");
+            var everything = tbox.readCSV(tbox.trimFileUrl(tbox.getTempUrl())+ "/" + imgLoad + ".csv");
             //holding dictionaries, arrays, and variables
 
             //holds everything
@@ -171,8 +172,8 @@ Rectangle{
 
     //function to check if current image has a label file
     function hasLabels(imgsource){
-        console.log(tbox.fileExists("C:/Users/kevin/AppData/Roaming/CoralLabeler"))
-        return tbox.fileExists(tbox.fixTempUrl(tbox.getTempUrl()) + "/" + imgsource + ".csv")
+        //console.log((tbox.trimFileUrl(tbox.getTempUrl()) + imgsource + ".csv"))
+        return tbox.fileExists(tbox.trimFileUrl(tbox.getTempUrl()) + "/" + imgsource + ".csv")
     }
 
     //a function to loop through the current label's shapes and create shapes from coordinates

CoralLabeler/SaveLocationsPopup.qml

@@ -93,7 +93,7 @@ import QtQuick.Dialogs
     }
 
     onRejected: {
-        if (!tbox.fileExists("file_config")) {
+        if (!tbox.fileExists(tbox.getFileLocation()+"/file_config")) {
             //if user cancelled but no value exists, choose defaults
             tbox.saveFilePreference(StandardPaths.writableLocation(StandardPaths.AppDataLocation), StandardPaths.writableLocation(StandardPaths.DocumentsLocation) + "/CoralLabeler")
             var result = tbox.initFilePreference(StandardPaths.writableLocation(StandardPaths.AppDataLocation), StandardPaths.writableLocation(StandardPaths.DocumentsLocation) + "/CoralLabeler")

CoralLabeler/main.qml

@@ -1789,7 +1789,7 @@ ApplicationWindow {
     }
     ////Check if file preferences exist. If not, ask user
     Component.onCompleted: {
-        if (tbox.fileExists("file_config")) {
+        if (tbox.fileExists(tbox.getFileLocation()+"/file_config")) {
             tbox.loadFilePreference()
             saveLocationsPopup.updateText()
         } else {

CoralLabeler/toolbox.py

@@ -92,6 +92,13 @@ def initFilePreference(self, temp_url, out_url):
             else:
                 if not os.path.isdir(fp):
                     return 1 #a non directory file exists with that name
+        try:
+            os.makedirs(os.path.join(out_fp,'raster_labels'))
+            os.makedirs(os.path.join(out_fp,'statistics'))
+        except PermissionError:
+            return 2
+        except OSError:
+            return 3
         return 0
 
     @QtCore.Slot()
@@ -201,8 +208,8 @@ def readCSV(self, fileName):
     @QtCore.Slot(dict, str, list, result="QVariantList")
     def saveLabels(self, data, fileName, paintshapes):
         name = ""
-
-        filename = os.path.join(self.temp_url[8:], fileName+'.csv')
+        external_dir = self.trimFileUrl(self.getTempUrl())
+        filename = os.path.join(external_dir, fileName+'.csv')
         check = False
         paintSize = ''
         paintFirstCoords = []
@@ -261,7 +268,7 @@ def saveLabels(self, data, fileName, paintshapes):
 
     @QtCore.Slot(str, result = bool)
     def fileExists(self, fileName):
-        return os.path.exists(os.path.join(dirname,fileName))
+        return os.path.exists(fileName)
 
     @QtCore.Slot(str, result="QString")
     def splited(self, fileName):
@@ -274,7 +281,7 @@ def printString(self, s):
 
     @QtCore.Slot(str, str, str, result="QVariantList")
     def addToCSV(self, data, name, fileName):
-        fileName = os.path.join(dirname,fileName)
+        fileName = os.path.join(dirname,fileName) #hardcoded to internal file. fine bc only used to operate on SpeciesList.csv which is internal
         with open(fileName, 'a') as file:
 
             # write row
@@ -301,8 +308,8 @@ def toPixels(self, coords, x_coord, y_coord, x_factor, y_factor):
             for shape_num, shape_coords in coords_dict.items():
                 numpy_shapes[label_num][shape_num] = []
                 for coord in shape_coords:
-                    x = math.floor((coord[0] - x_coord) / x_factor)
-                    y  = math.floor((coord[1] - y_coord) / y_factor) 
+                    x = math.floor((coord[0] - x_coord) / x_factor) - 1
+                    y  = math.floor((coord[1] - y_coord) / y_factor) - 1
 
                     numpy_coord = [x, y]
                     numpy_shapes[label_num][shape_num].append(numpy_coord)
@@ -356,7 +363,9 @@ def saveRasters(self, coords, x_coord, y_coord, x_factor, y_factor, img_width, i
                 final_array[rr, cc] = n_label_id
 
         # save to csv file
-        np.savetxt('./raster_labels/' + filename + '.csv', final_array, fmt='%d', delimiter=',')
+        external_dir = self.trimFileUrl(self.getOutUrl())
+        save_to = os.path.join(external_dir,'raster_labels',filename+".csv")
+        np.savetxt(save_to, final_array, fmt='%d', delimiter=',')
 
 
     @QtCore.Slot(dict, list, int, int, float, float, int, int, str, str, str)
@@ -389,8 +398,9 @@ def saveStats(self, coords, specs_list, x_coord, y_coord, x_factor, y_factor, im
                              'area (cm2)': img_area}
 
                     stats_list.append(shape_stats)
-
-        with open('./statistics/' + filename + '.csv', 'w') as csvfile:
+        external_dir = self.trimFileUrl(self.getOutUrl())
+        save_to = os.path.join(external_dir,'statistics',filename+".csv")
+        with open(save_to, 'w') as csvfile:
             writer = csv.DictWriter(csvfile, fieldnames=headers)
             writer.writeheader()
             writer.writerows(stats_list)