Merge pull request #192 from friskluft/POL3837_new_3d_layout

POL3837 new 3D layout

CMakeLists.txt

@@ -167,6 +167,7 @@ set(SOURCE
 	src/nyx/features/image_moments.cpp
 	src/nyx/features/image_moments_nontriv.cpp
 	src/nyx/features/intensity.cpp
+	src/nyx/features/intensity_3d.cpp
 	src/nyx/features/neighbors.cpp
 	src/nyx/features/ngldm.cpp
 	src/nyx/features/ngtdm.cpp
@@ -185,6 +186,7 @@ set(SOURCE
 	src/nyx/dirs_and_files.cpp
 	src/nyx/environment.cpp
 	src/nyx/environment_basic.cpp
+	src/nyx/env_features.cpp
 	src/nyx/feature_method.cpp
 	src/nyx/feature_mgr.cpp
 	src/nyx/feature_mgr_init.cpp
@@ -206,6 +208,7 @@ set(SOURCE
 	src/nyx/roi_cache.cpp
 	src/nyx/roi_cache_basic.cpp
 	src/nyx/scan_fastloader_way.cpp
+	src/nyx/strpat.cpp
 )
 
 

src/nyx/cli_gabor_options.cpp

@@ -1,6 +1,8 @@
 #include "cli_gabor_options.h"
 #include "features/gabor.h"
 
+using namespace Nyxus;
+
 bool GaborOptions::parse_input()
 {
 	// OK to have both angles and frequencies specified but not one of them

src/nyx/cli_nested_roi_options.cpp

@@ -397,7 +397,7 @@ namespace Nyxus
 			ofile << s << ",";
 
 		// User feature selection
-		std::vector<std::tuple<std::string, AvailableFeatures>> F = theFeatureSet.getEnabledFeatures();
+		std::vector<std::tuple<std::string, int>> F = theFeatureSet.getEnabledFeatures();
 		for (auto& f : F)
 		{
 			auto fn = std::get<0>(f);	// feature name

src/nyx/dirs_and_files.cpp

@@ -13,11 +13,16 @@
 #else
   error "Missing the <filesystem> header."
 #endif
+
 #include <vector>
 #include <iostream>
 #include <regex>
 #include <sstream>
+#include <string>
 #include <tiffio.h>
+#include "dirs_and_files.h"
+#include "strpat.h"
+#include "helpers/helpers.h"
 
 namespace Nyxus
 {
@@ -27,7 +32,7 @@ namespace Nyxus
 		return fs::exists(p);
 	}
 
-	void readDirectoryFiles(const std::string& dir, const std::string& file_pattern, std::vector<std::string>& files)
+	void readDirectoryFiles_2D (const std::string& dir, const std::string& file_pattern, std::vector<std::string>& files)
 	{
 		std::regex re(file_pattern);
 
@@ -48,29 +53,7 @@ namespace Nyxus
 		}
 	}
 
-	int datasetDirsOK(const std::string& dirIntens, const std::string& dirLabels, const std::string& dirOut, bool mustCheckDirOut)
-	{
-		if (!existsOnFilesystem(dirIntens))
-		{
-			std::cout << "Error: " << dirIntens << " is not a directory" << std::endl;
-			return 1;
-		}
-
-		if (!existsOnFilesystem(dirLabels))
-		{
-			std::cout << "Error: " << dirLabels << " is not a directory" << std::endl;
-			return 2;
-		}
-
-		if (mustCheckDirOut && !existsOnFilesystem(dirOut))
-		{
-			std::cout << "Error: " << dirOut << " is not a directory" << std::endl;
-			return 3;
-		}
-		return 0; // success
-	}
-
-	int read_dataset (
+	int read_2D_dataset (
 		// input
 		const std::string& dirIntens, 
 		const std::string& dirLabels, 
@@ -83,9 +66,7 @@ namespace Nyxus
 		std::vector <std::string>& intensFiles, 
 		std::vector <std::string>& labelFiles)
 	{
-		// Check the directories
-		if (datasetDirsOK(dirIntens, dirLabels, dirOut, mustCheckDirOut) != 0)
-			return 1;	// No need to issue console messages here, datasetDirsOK() does that
+		// Check directories
 
 		if (!existsOnFilesystem(dirIntens))
 		{
@@ -106,8 +87,8 @@ namespace Nyxus
 		if (intLabMappingFile.empty())
 		{
 			// Common case - no ad hoc intensity-label file mapping, 1-to-1 correspondence instead
-			readDirectoryFiles(dirIntens, filePatt, intensFiles);
-			readDirectoryFiles(dirLabels, filePatt, labelFiles);
+			readDirectoryFiles_2D (dirIntens, filePatt, intensFiles);
+			readDirectoryFiles_2D (dirLabels, filePatt, labelFiles);
 
 			// Check if the dataset is meaningful
 			if (intensFiles.size() == 0 || labelFiles.size() == 0)
@@ -219,4 +200,142 @@ namespace Nyxus
 		else { throw (std::runtime_error("Tile Loader ERROR: The file can not be opened.")); }
 	}
 
+
+
+	bool readDirectoryFiles_3D (const std::string & dir, const StringPattern & filePatt, std::vector <Imgfile3D_layoutA> & files)
+	{
+		// grammar is OK to read data
+		std::map<std::string, std::vector<std::string>> imgDirs;
+
+		for (auto& fpath : fs::directory_iterator(dir))
+		{
+			// Skip hidden objects, e.g. directories '.DS_store' in OSX
+			if (fpath.path().filename().string()[0] == '.')
+				continue;
+
+			std::string fullPath = fpath.path().string(),
+				pureFname = fpath.path().filename().string();
+
+			std::string ermsg;
+			if (!filePatt.match(pureFname, imgDirs, ermsg))
+			{
+				std::cerr << "Error parsing file name " << pureFname << ": " << ermsg << '\n';
+				break;
+			}
+
+		} //- directory scan loop
+
+		// copy the file info to the external container
+		files.clear();
+		size_t i = 0;
+		for (const auto & x : imgDirs)
+		{
+			Nyxus::Imgfile3D_layoutA img3;
+			img3.fname = x.first;	// image name
+			img3.z_indices = x.second;	// z-indices as they are in corresponding file names
+			files.push_back(img3);
+		}
+
+		return true;
+	}
+
+	int read_3D_dataset(
+		// input:
+		const std::string& dirIntens,
+		const std::string& dirLabels,
+		const StringPattern& filePatt,
+		const std::string& dirOut,
+		const std::string& intLabMappingDir,
+		const std::string& intLabMappingFile,
+		bool mustCheckDirOut,
+		// output:
+		std::vector <Imgfile3D_layoutA>& intensFiles,
+		std::vector <Imgfile3D_layoutA>& labelFiles)
+	{
+		if (!existsOnFilesystem(dirIntens))
+		{
+			std::cout << "Error: nonexisting directory " << dirIntens << std::endl;
+			return 1;
+		}
+		if (!existsOnFilesystem(dirLabels))
+		{
+			std::cout << "Error: nonexisting directory " << dirLabels << std::endl;
+			return 1;
+		}
+		if (!existsOnFilesystem(dirOut))
+		{
+			std::cout << "Error: nonexisting directory " << dirOut << std::endl;
+			return 1;
+		}
+
+		// Common case - no ad hoc intensity-label file mapping, 1-to-1 correspondence instead
+		if (!readDirectoryFiles_3D(dirIntens, filePatt, intensFiles))
+		{
+			std::cerr << "Error reading directory " << dirIntens << '\n';
+			return 1;
+		}
+		if (!readDirectoryFiles_3D (dirLabels, filePatt, labelFiles))
+		{
+			std::cerr << "Error reading directory " << dirLabels << '\n';
+			return 1;
+		}
+
+		// Check if the dataset isn't blank
+		if (intensFiles.size() == 0 || labelFiles.size() == 0)
+		{
+			std::cout << "No intensity and/or label file pairs to process, probably due to file pattern " << filePatt.get_cached_pattern_string() << std::endl;
+			return 2;
+		}
+
+		// Shallow consistency check 
+		if (intensFiles.size() != labelFiles.size())
+		{
+			std::cout << "Mismatch: " << intensFiles.size() << " intensity images vs " << labelFiles.size() << " mask images\n";
+			return 3;
+		}
+
+		// Deep consistency check 
+		auto nf = intensFiles.size();
+		for (auto i = 0; i < nf; i++)
+		{
+			auto& file_i = intensFiles[i],
+				& file_m = labelFiles[i];
+
+			// name mismatch ?
+			if (file_i.fname != file_m.fname)
+			{
+				std::cerr << "Mismatch: intensity " << file_i.fname << " mask " << file_m.fname << '\n';
+				return 3;
+			}
+
+			// z-stack size mismatch ?
+			if (file_i.z_indices.size() != file_m.z_indices.size())
+			{
+				std::cerr << "Z-stack size mismatch: intensity " << file_i.z_indices.size() << " mask " << file_m.z_indices.size() << '\n';
+				return 3;
+			}
+
+			// z-stack indices mismatch ?
+			std::sort (file_i.z_indices.begin(), file_i.z_indices.end());
+			std::sort (file_m.z_indices.begin(), file_m.z_indices.end());
+			for (auto j=0; j< file_i.z_indices.size(); j++)
+				if (file_i.z_indices[j] != file_m.z_indices[j])
+				{
+					std::cerr << "Mismatch in z-stack indices: " << file_i.fname << "[" << j << "] != " << file_m.fname << "[" << j << "]\n";
+					return 3;
+				}
+		}
+
+		// let each file know its directory
+		for (auto i = 0; i < nf; i++)
+		{
+			auto& file_i = intensFiles[i],
+				& file_m = labelFiles[i];
+			file_i.fdir = dirIntens + '/';
+			file_m.fdir = dirLabels + '/';
+		}
+
+		return 0;
+	}
+
 } // namespace Nyxus

src/nyx/dirs_and_files.h

@@ -4,8 +4,10 @@
 // Helper functions for manipulating directories and files
 //
 
+#include <map>
 #include <string>
 #include <vector>
+#include "strpat.h"
 
 namespace Nyxus
 {
@@ -23,17 +25,8 @@ namespace Nyxus
 	/// @param dir 
 	/// @param file_pattern 
 	/// @param files 
-	void readDirectoryFiles(const std::string& dir, const std::string& file_pattern, std::vector<std::string>& files);
-
-	/// @brief Nyxus specific: checks if the intensity, mask, and output directories exist
-	/// @param dirIntens 
-	/// @param dirLabels 
-	/// @param dirOut 
-	/// @param mustCheckDirOut 
-	/// @return 
-	int datasetDirsOK(const std::string& dirIntens, const std::string& dirLabels, const std::string& dirOut, bool mustCheckDirOut);
-
-	int read_dataset(
+
+	int read_2D_dataset(
 		// input:
 		const std::string& dirIntens,
 		const std::string& dirLabels,
@@ -46,6 +39,26 @@ namespace Nyxus
 		std::vector <std::string>& intensFiles,
 		std::vector <std::string>& labelFiles);
 
+	struct Imgfile3D_layoutA
+	{
+	public:
+		std::string fname, fdir;
+		std::vector<std::string> z_indices;
+	};
+
+	int read_3D_dataset(
+		// input:
+		const std::string& dirIntens,
+		const std::string& dirLabels,
+		const StringPattern& filePatt,
+		const std::string& dirOut,
+		const std::string& intLabMappingDir,
+		const std::string& intLabMappingFile,
+		bool mustCheckDirOut,
+		// output:
+		std::vector <Imgfile3D_layoutA>& intensFiles,
+		std::vector <Imgfile3D_layoutA>& labelFiles);
+
 	/// @brief checks if the Tiff file is tiled or not
 	/// @param filePath File name with complete path
 	bool check_tile_status(const std::string& filePath);