slideEMask changes

swvanderlaan · Sep 18, 2017 · e08fdd1 · e08fdd1
1 parent ca3e963
commit e08fdd1
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Showing 3 changed files with 29 additions and 10 deletions.
diff --git a/slideEMask b/slideEMask
diff --git a/slideEMask_source/source/slideEMask.cpp b/slideEMask_source/source/slideEMask.cpp
@@ -44,7 +44,7 @@ int main(int argc,char **argv)
 	cmd.parse( argc, argv );
 
 	std::string filename = filenameArg.getValue();
-	std::string layer = to_string(layerArg.getValue());
+	int layer = layerArg.getValue();
 	int threshold = thresholdArg.getValue();
 
 	//TIF, 210 is an appropriate value
@@ -178,6 +178,7 @@ int main(int argc,char **argv)
 	  	}
 	  	else {
 	  		//Dilate the image (a way to widen the borders of the image)
+	  		cout << "\t...Dilating mask to widen borders (to prevent too narrow mask borders from clipping relevant tile material) " << endl;
 	  		dest.dilate(3);
 
 	  		new_fn = replaceString(to_open, ".png", ".emask.png");

diff --git a/slideEMask_source/source/slideToolKit.h b/slideEMask_source/source/slideToolKit.h
@@ -68,28 +68,38 @@ std::string replaceString(std::string subject, const std::string& search,
 }
 
 
-std::string getScannerType(std::string filename)
+void getScannerType(std::string filename, std::string &ScannerType)
 {
 
+	std::cout << "\t...Detecting Scanner Type" << std::endl;
+
     TIFF* tif = TIFFOpen(filename.c_str(), "r");
 
 	if (tif) {
 
+		std::cout << "\t...Successfully read TIFF directory" << std::endl;
+
 		TIFFReadDirectory(tif);
 
-		char* model_name = NULL;
+		char* model_name = "";
 
 		TIFFGetField(tif, TIFFTAG_MODEL, &model_name);
 
+		std::cout << "\t...Successfully extracted TIF Field" << std::endl;
+
 		std::string output( model_name );
 
+		std::cout << "\t...Successfully converted to string" << std::endl;
+
+		ScannerType = output;
+
 		TIFFClose(tif);
 
-    	return output;
+		std::cout << "\t...Successfully closed TIF" << std::endl;
 
     }
 
-    return "Error";
+    std::cerr <<  "Error" << std::endl;
 
 }
 
@@ -98,7 +108,8 @@ Magick::Image getThumbLayer(std::string filename) {
 	//APERIO NEEDS TESTING
 	Magick::Image image;
 
- 	std::string ScannerType = getScannerType(filename);
+ 	std::string ScannerType;
+ 	getScannerType(filename, ScannerType);
 
  	if (ScannerType == "iScan HT") {image.read( filename.append("[0]") );}
  	if (ScannerType == "iScan") {image.read( filename.append("[0]") );}
@@ -136,15 +147,16 @@ Magick::Image getThumbLayer(std::string filename) {
 
  }
 
-Magick::Image getMacroLayer(std::string filename, std::string layer = "-1") {
+Magick::Image getMacroLayer(std::string filename, int layer = -1) {
 
 	Magick::Image image;
 
-	if (layer == "-1") {
+	if (layer == -1) {
 
 		int LAYER = -1;
 
-	 	std::string ScannerType = getScannerType(filename);
+	 	std::string ScannerType;
+	 	getScannerType(filename, ScannerType);
 
 	 	if (ScannerType == "iScan HT") {LAYER = 8;}
 	 	if (ScannerType == "iScan") {LAYER = 7;}
@@ -161,6 +173,12 @@ Magick::Image getMacroLayer(std::string filename, std::string layer = "-1") {
 
 	 		LAYER = n_layers - 3;
 	 	}
+	 	else {
+	 		std::cerr << "Unimplemented Scanner Type '" << ScannerType << "'" << std::endl;
+	 		exit(-1);
+	 	}
+
+	 	std::cout << "Detected Scanner Type '" << ScannerType << "'" << std::endl;
 
 	 	image.read( filename.append("[" + std::to_string(LAYER) + "]") );
 
@@ -171,7 +189,7 @@ Magick::Image getMacroLayer(std::string filename, std::string layer = "-1") {
 
  	std::cout << "\t...Reading image in layer '" << layer << "' of TIF file." << std::endl;
 
- 	image.read( filename.append("[" + layer + "]") );
+ 	image.read( filename.append("[" + std::to_string(layer) + "]") );
 
  	return image;