Merge branch 'ISBI2016_TextureRenderer' of... (05e0a77a) · Commits · Vladimír Ulman / ISBI2016-filaSimu-TM

src/TriangleMesh.cpp

+6 −6

Original line number	Diff line number	Diff line
		@@ -2285,7 +2285,7 @@ void ActiveMesh::ConstructFF_T(FlowField<float> &FF)
		}


		void ActiveMesh::config::getValueOrDefault(const char* key,const std::string& defValue,std::string& var)
		void ActiveMesh::configDataSubClass::getValueOrDefault(const char* key,const std::string& defValue,std::string& var)
		{
		std::string sKey(key);
		std::map<std::string,std::string>::const_iterator it = keyVal_map.find(sKey);
		@@ -2299,7 +2299,7 @@ void ActiveMesh::config::getValueOrDefault(const char* key,const std::string& de
		var = it->second;
		}

		void ActiveMesh::config::getValueOrDefault(const char* key,const int defValue,int& var)
		void ActiveMesh::configDataSubClass::getValueOrDefault(const char* key,const int defValue,int& var)
		{
		std::string sKey(key);
		std::map<std::string,std::string>::const_iterator it = keyVal_map.find(sKey);
		@@ -2313,7 +2313,7 @@ void ActiveMesh::config::getValueOrDefault(const char* key,const int defValue,in
		var = atoi(it->second.c_str());
		}

		void ActiveMesh::config::getValueOrDefault(const char* key,const float defValue,float& var)
		void ActiveMesh::configDataSubClass::getValueOrDefault(const char* key,const float defValue,float& var)
		{
		std::string sKey(key);
		std::map<std::string,std::string>::const_iterator it = keyVal_map.find(sKey);
		@@ -2327,16 +2327,16 @@ void ActiveMesh::config::getValueOrDefault(const char* key,const float defValue,
		var = (float)atof(it->second.c_str());
		}

		int ActiveMesh::config::ParseConfigFile(const char* configFileName)
		int ActiveMesh::configDataSubClass::ParseConfigFile(const char* fileName)
		{
		//clear before parsing
		keyVal_map.clear();

		//try to open the config file
		std::ifstream configFile(configFileName);
		std::ifstream configFile(fileName);
		if (!configFile.is_open())
		{
		std::cout << "Unable to read the config file: " << configFileName << "\n";
		std::cout << "Unable to read the config file: " << fileName << "\n";
		return(-1);
		}

src/TriangleMesh.h

+2 −2

Original line number	Diff line number	Diff line
		@@ -179,12 +179,12 @@ class ActiveMesh
		Vector3F meshShift;

		///internal class to store all params that one can read in from a config file
		class config
		class configDataSubClass
		{
		public:
		///returns non-zero if some problem occured,
		///the default values are listed in this function
		int ParseConfigFile(const char* configFileName);
		int ParseConfigFile(const char* fileName);

		///output image resolution as voxels/um
		Vector3F texture_Resolution;

src/psf/2008-06-25_1_1_9_0_2_0_0_1_0_0_0_0_9_12.ics

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src/psf/2013-07-25_1_1_9_0_2_0_0_1_0_0_0_0_9_12.ics

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src/psf/list.py

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Original line number	Diff line number	Diff line
		#!/usr/bin/python

		locations = ["CBIA FI",
		"CBIA ILBIT",
		"BFU"]

		microscopes = ["Zeiss 200M",
		"Zeiss S100",
		"Leica DMRXA",
		"Leica DMIRE2"]

		modes = ["confocal",
		"widefield"]

		cameras = ["Andor iXon DV887",
		"Princeton Instruments Micromax 1300-YHS",
		"Photometrics CoolSNAP HQ",
		"Photometrics Quantix KAF-1400",
		"Photometrics CoolSNAP HQ2"]

		objectives = ["Zeiss 10x/0.30",
		"Zeiss 20x/0.50",
		"Zeiss 40x/0.75",
		"Zeiss 40x/1.30 Oil",
		"Zeiss 63x/1.30 Water-Glycerol",
		"Zeiss 100x/1.45 Oil",
		"Zeiss 63x/1.40 Oil",
		"63x/1.30 Oil",
		"Obecny",
		"Zeiss 63x/1.40 Oil DIC (new)"]

		excitation_filters = ["488/6 (488 Laser)",
		"567/15 (568 Laser)",
		"650/13 (648 Laser)",
		"445/50 (DAPI)",
		"470/40 (EGFP)",
		"FRET (FITC/Cy3) cube",
		"550/25 (Cy3)",
		"640/30 (Cy5)",
		"DAPI",
		"FITC",
		"Cy3",
		"Cy5",
		"blue(488nm) Ar/Kr Laser",
		"yellow(568nm) Ar/Kr Laser",
		"red(647nm) Ar/Kr Laser",
		"405 Laser",
		"488 Laser",
		"561 Laser",
		"640 Laser"]

		emission_filters = ["475/50 (DAPI)",
		"528/38 (FITC)",
		"617/73 (Cy3)",
		"685/40 (Cy5)",
		"440/521/607/700 (QUAD)",
		"488/568 (DUAL)",
		"365 (DAPI)",
		"525/50 (EGFP)",
		"FRET (FITC/Cy3) cube",
		"605/70 (Cy3)",
		"690/50 (Cy5)",
		"DAPI",
		"FITC",
		"Cy3",
		"Cy5",
		"Green HQ525/50",
		"Red HQ615/60",
		"Far red HQ700/75",
		"Yokogawa tripple"]

		glasses = ["1.0",
		"1.5"]

		immersion_mediums = ["Zeiss Immersol 518F",
		"Water"]

		mediums = ["Vectashield",
		"Slowfade"]

		temperatures = ["23 C",
		"37 C"]

		confocal_units = ["none",
		"Yokogawa CSU-10",
		"Atto CARV"]

		adapters = ["none (mag. 1x)",
		"0.63x",
		"0.5x",
		"1.25x"]

		import sys

		argv_parts = sys.argv[1].split('_')
		argv_parts[len(argv_parts) - 1]=argv_parts[len(argv_parts) - 1][:-4]

		# kontrolni vypis
		#for i in range(0,len(argv_parts)):
		# print `i` + " => " + argv_parts[i]

		months = {"01":"January",
		"02":"Ferbuary",
		"03":"March",
		"04":"April",
		"05":"May",
		"06":"June",
		"07":"July",
		"08":"August",
		"09":"September",
		"10":"October",
		"11":"November",
		"12":"December"}

		print "Parameters for the file: '" + sys.argv[1] + "' are following:"
		print " Date: " + months[argv_parts[0][5:7]] + " " + argv_parts[0][8:] + \
		", " + argv_parts[0][:4]

		print " Location: " + locations[int(argv_parts[1])]
		print " Microscope: " + microscopes[int(argv_parts[2])]
		print " Objective: " + objectives[int(argv_parts[3])]
		print " Mode: " + modes[int(argv_parts[4])]
		print " Confocal unit: " + confocal_units[int(argv_parts[5])]
		print " Microscope-Unit adapter: " + adapters[int(argv_parts[6])]
		print " Unit-Camera adapter: " + adapters[int(argv_parts[7])]
		print " Camera: " + cameras[int(argv_parts[8])]
		print " Medium: " + mediums[int(argv_parts[9])]
		print " Immersion medium: " + immersion_mediums[int(argv_parts[10])]
		print " Temperature: " + temperatures[int(argv_parts[11])]
		print " Glass: " + glasses[int(argv_parts[12])]
		print " Excitation filter: " + excitation_filters[int(argv_parts[13])]
		print " Emission filter: " + emission_filters[int(argv_parts[14])]