Merge pull request #154 from friskluft/POL3595_unify_col_naming

POL3595 unified column name | customizable output file name

src/nyx/environment.cpp

@@ -166,7 +166,7 @@ void Environment::show_cmdline_help()
 		<< "\t\t\tExample: " << FILEPATTERN << "=.* for all files, " << FILEPATTERN << "=*.tif for .tif files \n"
 		<< "\t\t" << OUTPUTTYPE << "=<separatecsv or singlecsv for csv output. arrowipc or parquet for arrow output> \n"
 		<< "\t\t\tDefault: separatecsv \n"
-		<< "\t\t" << SEGDIR << "=<directory of segmentation images> \n"
+		<< "\t\t" << SEGDIR << "=<directory of segmentation mask images> \n"
 		<< "\t\t" << INTDIR << "=<directory of intensity images> \n"
 		<< "\t\t" << OUTDIR << "=<output directory> \n"
 		<< "\t\t" << OPT << FEATURES << "=<specific feature or comma-separated features or feature group> \n"
@@ -201,7 +201,10 @@ void Environment::show_cmdline_help()
 		<< "\t\t" << OPT << SKIPROI << "=<ROI blacklist> \n"
 		<< "\t\t\tDefault: void blacklist \n"
 		<< "\t\t\tExample 1: " << SKIPROI << "=34,35,36 \n"
-		<< "\t\t\tExample 2: " << SKIPROI << "=image1.ome.tif:34,35,36;image2.ome.tif:42,43 \n";
+		<< "\t\t\tExample 2: " << SKIPROI << "=image1.ome.tif:34,35,36;image2.ome.tif:42,43 \n"
+		<< "\t\t" << OPT << RESULTFNAME << "=<file name without extension> \n"
+		<< "\t\t\tDefault: NyxusFeatures \n"
+		<< "\t\t\tExample: " << RESULTFNAME << "=training_set_features";
 
 	#ifdef CHECKTIMING
 		std::cout << "\t\t" << OPT << EXCLUSIVETIMING << "=<false or true> \n"
@@ -751,6 +754,7 @@ bool Environment::parse_cmdline(int argc, char **argv)
 				|| find_string_argument(i, NESTEDROI_PARENT_CHNL, nestedOptions.rawParentChannelNo)
 				|| find_string_argument(i, NESTEDROI_CHILD_CHNL, nestedOptions.rawChildChannelNo)
 				|| find_string_argument(i, NESTEDROI_AGGREGATION_METHOD, nestedOptions.rawAggregationMethod)
+				|| find_string_argument(i, RESULTFNAME, nyxus_result_fname)
 
 				#ifdef CHECKTIMING
 					|| find_string_argument(i, EXCLUSIVETIMING, rawExclusiveTiming)
@@ -826,6 +830,13 @@ bool Environment::parse_cmdline(int argc, char **argv)
 		rawFeatures = FEA_NICK_ALL;
 	}
 
+	//==== Parse optional result file name
+	if (nyxus_result_fname == "")
+	{
+		std::cout << "Error: void argument " << RESULTFNAME << "\n";
+		return false;
+	}
+
 	//==== Output type
 #ifdef USE_ARROW 
 	VERBOSLVL1(std::cout << "\n*-*-*-*- Using Apache output -*-*-*-*\n");

src/nyx/environment.h

@@ -40,7 +40,7 @@
 #define TEMPDIR "--tempDir"						// Optional. Used in processing non-trivial features. Default - system temp directory
 #define IBSICOMPLIANCE "--ibsi" // skip binning for grey level and grey tone features
 #define SKIPROI "--skiproi"		// Optional. Skip ROIs having specified labels. Sybtax: --skiproi <label[,label,label,...]>
-
+#define RESULTFNAME "--resultFname"				// Environment :: nyxus_result_fname
 
 #ifdef CHECKTIMING
 	#define EXCLUSIVETIMING "--exclusivetiming"
@@ -110,10 +110,11 @@ class Environment: public BasicEnvironment
 	void show_summary(const std::string &head, const std::string &tail);
 
 	std::string labels_dir = "",
-				intensity_dir = "",
-				output_dir = "",
-				intSegMapDir = "",
-				intSegMapFile = "";
+		intensity_dir = "",
+		output_dir = "",
+		intSegMapDir = "",
+		intSegMapFile = "";
+	std::string nyxus_result_fname = "NyxusFeatures";	// Default file name without extension ".csv", ".arrow", etc
 
 	bool singleROI = false; // is set to 'true' parse_cmdline() if labels_dir==intensity_dir
 

src/nyx/output_2_csv.cpp

@@ -178,12 +178,12 @@ namespace Nyxus
 		}
 		else
 		{
-			retval = theEnvironment.output_dir + "/" + "NyxusFeatures.csv";
+			retval = theEnvironment.output_dir + "/" + theEnvironment.nyxus_result_fname + ".csv";
 		}
 		return retval;
 	}
 
-	const std::vector<std::string> mandatory_output_columns {"intensity_image", "segmentation_image", "ROI_label"};
+	const std::vector<std::string> mandatory_output_columns {"intensity_image", "mask_image", "ROI_label"};
 
 	// Saves the result of image scanning and feature calculation. Must be called after the reduction phase.
 	bool save_features_2_csv (const std::string & intFpath, const std::string & segFpath, const std::string & outputDir)

src/nyx/python/new_bindings_py.cpp

@@ -287,7 +287,7 @@ py::tuple featurize_montage_imp (
 
     } 
 
-    std::string path = output_dir + "NyxusFeatures.";
+    std::string path = output_dir + theEnvironment.nyxus_result_fname + ".";
     return py::make_tuple(error_message, path);
 }
 
@@ -312,9 +312,9 @@ py::tuple featurize_fname_lists_imp (const py::list& int_fnames, const py::list
     if (intensFiles.size() == 0)
         throw std::runtime_error("Intensity file list is blank");
     if (labelFiles.size() == 0)
-        throw std::runtime_error("Segmentation file list is blank");
+        throw std::runtime_error("Segmentation mask file list is blank");
     if (intensFiles.size() != labelFiles.size())
-        throw std::runtime_error("Imbalanced intensity and segmentation file lists");
+        throw std::runtime_error("Imbalanced intensity and segmentation mask file lists");
     for (auto i = 0; i < intensFiles.size(); i++)
     {
         const std::string& i_fname = intensFiles[i];
@@ -588,7 +588,7 @@ PYBIND11_MODULE(backend, m)
     m.def("featurize_directory_imp", &featurize_directory_imp, "Calculate features of images defined by intensity and mask image collection directories");
     m.def("featurize_montage_imp", &featurize_montage_imp, "Calculate features of images defined by intensity and mask image collection directories");
     m.def("featurize_fname_lists_imp", &featurize_fname_lists_imp, "Calculate features of intensity-mask image pairs defined by lists of image file names");
-    m.def("findrelations_imp", &findrelations_imp, "Find relations in segmentation images");
+    m.def("findrelations_imp", &findrelations_imp, "Find relations in segmentation mask images");
     m.def("gpu_available", &Environment::gpu_is_available, "Check if CUDA gpu is available");
     m.def("use_gpu", &use_gpu, "Enable/disable GPU features");
     m.def("get_gpu_props", &get_gpu_properties, "Get properties of CUDA gpu");