New upstream version 1.6.2 (05af19a6) · Commits · Debian Med / libics

CMakeLists.txt

+12 −12

Original line number	Diff line number	Diff line
		@@ -15,7 +15,7 @@
		##############################################################################
		cmake_minimum_required(VERSION 3.0)

		project(libics VERSION 1.6.1)
		project(libics VERSION 1.6.2)

		# Note: the version number above is not yet used anywhere.
		# TODO: rewrite the header file with this version number.
		@@ -44,7 +44,7 @@ if(USE_ZLIB)
		endif()

		# ICS
		configure_file(libics_conf.h.in ${CMAKE_SOURCE_DIR}/libics_conf.h COPYONLY)
		configure_file(libics_conf.h.in ${PROJECT_SOURCE_DIR}/libics_conf.h COPYONLY)
		set(SOURCES
		libics_binary.c
		libics_compress.c
		@@ -69,7 +69,7 @@ set(HEADERS
		libics_test.h
		)

		include_directories(${CMAKE_SOURCE_DIR})
		include_directories(${PROJECT_SOURCE_DIR})

		# Build a dll
		add_library(libics SHARED ${SOURCES} ${HEADERS})
		@@ -123,22 +123,22 @@ add_custom_target(all_tests DEPENDS
		test_metadata
		test_history
		)
		add_test(ctest_build_test_code "${CMAKE_COMMAND}" --build ${CMAKE_BINARY_DIR} --target all_tests)
		add_test(NAME test_ics1 COMMAND test_ics1 ${CMAKE_SOURCE_DIR}/test/testim.ics result_v1.ics)
		add_test(ctest_build_test_code "${CMAKE_COMMAND}" --build ${PROJECT_BINARY_DIR} --target all_tests)
		add_test(NAME test_ics1 COMMAND test_ics1 ${PROJECT_SOURCE_DIR}/test/testim.ics result_v1.ics)
		set_tests_properties(test_ics1 PROPERTIES DEPENDS ctest_build_test_code)
		add_test(NAME test_ics2a COMMAND test_ics2a ${CMAKE_SOURCE_DIR}/test/testim.ics result_v2a.ics)
		add_test(NAME test_ics2a COMMAND test_ics2a ${PROJECT_SOURCE_DIR}/test/testim.ics result_v2a.ics)
		set_tests_properties(test_ics2a PROPERTIES DEPENDS ctest_build_test_code)
		add_test(NAME test_ics2b COMMAND test_ics2b ${CMAKE_SOURCE_DIR}/test/testim.ics result_v2b.ics)
		add_test(NAME test_ics2b COMMAND test_ics2b ${PROJECT_SOURCE_DIR}/test/testim.ics result_v2b.ics)
		set_tests_properties(test_ics2b PROPERTIES DEPENDS ctest_build_test_code)
		add_test(NAME test_gzip COMMAND test_gzip ${CMAKE_SOURCE_DIR}/test/testim.ics result_v2z.ics)
		add_test(NAME test_gzip COMMAND test_gzip ${PROJECT_SOURCE_DIR}/test/testim.ics result_v2z.ics)
		set_tests_properties(test_gzip PROPERTIES DEPENDS ctest_build_test_code)
		add_test(NAME test_compress COMMAND test_compress ${CMAKE_SOURCE_DIR}/test/testim.ics ${CMAKE_SOURCE_DIR}/test/testim_c.ics)
		add_test(NAME test_compress COMMAND test_compress ${PROJECT_SOURCE_DIR}/test/testim.ics ${PROJECT_SOURCE_DIR}/test/testim_c.ics)
		set_tests_properties(test_compress PROPERTIES DEPENDS ctest_build_test_code)
		add_test(NAME test_strides COMMAND test_strides ${CMAKE_SOURCE_DIR}/test/testim.ics result_s.ics)
		add_test(NAME test_strides COMMAND test_strides ${PROJECT_SOURCE_DIR}/test/testim.ics result_s.ics)
		set_tests_properties(test_strides PROPERTIES DEPENDS ctest_build_test_code)
		add_test(NAME test_strides2 COMMAND test_strides2 ${CMAKE_SOURCE_DIR}/test/testim.ics result_s2.ics)
		add_test(NAME test_strides2 COMMAND test_strides2 ${PROJECT_SOURCE_DIR}/test/testim.ics result_s2.ics)
		set_tests_properties(test_strides2 PROPERTIES DEPENDS ctest_build_test_code)
		add_test(NAME test_strides3 COMMAND test_strides3 ${CMAKE_SOURCE_DIR}/test/testim.ics result_s3.ics)
		add_test(NAME test_strides3 COMMAND test_strides3 ${PROJECT_SOURCE_DIR}/test/testim.ics result_s3.ics)
		set_tests_properties(test_strides3 PROPERTIES DEPENDS ctest_build_test_code)
		add_test(NAME test_metadata1 COMMAND test_metadata result_v1.ics)
		set_tests_properties(test_metadata1 PROPERTIES DEPENDS test_ics1)

configure.ac

+1 −1

Original line number	Diff line number	Diff line
		@@ -12,7 +12,7 @@ dnl Written by Peter Verveer, Cris Luengo
		dnl

		dnl Library version number (make sure to also change it in 'libics.h'):
		AC_INIT([libics], [1.6.1])
		AC_INIT([libics], [1.6.2])
		AC_CONFIG_SRCDIR([libics.h])
		AC_CONFIG_HEADERS([config.h libics_conf.h])
		AC_CONFIG_MACRO_DIR([m4])

libics.h

+65 −32

Original line number	Diff line number	Diff line
		@@ -50,7 +50,7 @@ extern "C" {
		#endif

		/* Library versioning is in the form major, minor, patch: */
		#define ICSLIB_VERSION "1.6.1" /* also defined in configure.ac */
		#define ICSLIB_VERSION "1.6.2" /* also defined in configure.ac */

		#if defined(__WIN32__) && !defined(WIN32)
		#define WIN32
		@@ -156,19 +156,32 @@ typedef struct {
		/* A list of sensor parameters that are also equiped with a state. */
		typedef enum {
		ICS_SENSOR_FIRST,
		ICS_SENSOR_IMAGING_DIRECTION,
		ICS_SENSOR_NUMERICAL_APERTURE,
		ICS_SENSOR_OBJECTIVE_QUALITY,
		ICS_SENSOR_MEDIUM_REFRACTIVE_INDEX,
		ICS_SENSOR_LENS_REFRACTIVE_INDEX,
		ICS_SENSOR_PINHOLE_RADIUS,
		ICS_SENSOR_ILL_PINHOLE_RADIUS,
		ICS_SENSOR_PINHOLE_SPACING,
		ICS_SENSOR_EXCITATION_BEAM_FILL,
		ICS_SENSOR_LAMBDA_EXCITATION,
		ICS_SENSOR_LAMBDA_EMISSION,
		ICS_SENSOR_PHOTON_COUNT,
		ICS_SENSOR_MEDIUM_REFRACTIVE_INDEX,
		ICS_SENSOR_NUMERICAL_APERTURE,
		ICS_SENSOR_LENS_REFRACTIVE_INDEX,
		ICS_SENSOR_PINHOLE_SPACING,
		ICS_SENSOR_INTERFACE_PRIMARY,
		ICS_SENSOR_INTERFACE_SECONDARY,

		ICS_SENSOR_DETECTOR_MAGN,
		ICS_SENSOR_DETECTOR_PPU,
		ICS_SENSOR_DETECTOR_BASELINE,
		ICS_SENSOR_DETECTOR_LINE_AVG_COUNT,

		ICS_SENSOR_STED_DEPLETION_MODE,
		ICS_SENSOR_STED_LAMBDA,
		ICS_SENSOR_STED_SATURATION_FACTOR,
		ICS_SENSOR_STED_IMM_FRACTION,
		ICS_SENSOR_STED_VPPM,

		ICS_SENSOR_SPIM_EXCITATION_TYPE,
		ICS_SENSOR_SPIM_FILL_FACTOR,
		ICS_SENSOR_SPIM_PLANE_NA,
		@@ -176,13 +189,11 @@ typedef enum {
		ICS_SENSOR_SPIM_PLANE_PROP_DIR,
		ICS_SENSOR_SPIM_PLANE_CENTER_OFF,
		ICS_SENSOR_SPIM_PLANE_FOCUS_OFF,

		ICS_SENSOR_SCATTER_MODEL,
		ICS_SENSOR_SCATTER_FREE_PATH,
		ICS_SENSOR_SCATTER_REL_CONTRIB,
		ICS_SENSOR_SCATTER_BLURRING,
		ICS_SENSOR_DETECTOR_PPU,
		ICS_SENSOR_DETECTOR_BASELINE,
		ICS_SENSOR_DETECTOR_LINE_AVG_COUNT,
		ICS_SENSOR_LAST
		} Ics_SensorParameter;

		@@ -242,9 +253,33 @@ typedef struct _ICS {
		char model[ICS_STRLEN_OTHER];
		/* Number of channels: */
		int sensorChannels;
		/* Backprojected microns: */
		/* Imaging direction: */
		char imagingDirection[ICS_MAX_LAMBDA][ICS_STRLEN_TOKEN];
		Ics_SensorState imagingDirectionState[ICS_MAX_LAMBDA];
		/* Numerical Aperture: */
		double numAperture;
		Ics_SensorState numApertureState;
		/* Objective quality: */
		int objectiveQuality[ICS_MAX_LAMBDA];
		Ics_SensorState objectiveQualityState[ICS_MAX_LAMBDA];
		/* Refractive index of embedding medium: */
		double refrInxMedium;
		Ics_SensorState refrInxMediumState;
		/* Refractive index of design medium: */
		double refrInxLensMedium;
		Ics_SensorState refrInxLensMediumState;
		/* Detection pinhole in microns: */
		double pinholeRadius[ICS_MAX_LAMBDA];
		Ics_SensorState pinholeRadiusState[ICS_MAX_LAMBDA];
		/* Illumination pinhole in microns: */
		double illPinholeRadius[ICS_MAX_LAMBDA];
		Ics_SensorState illPinholeRadiusState[ICS_MAX_LAMBDA];
		/* Nipkow Disk pinhole spacing: */
		double pinholeSpacing;
		Ics_SensorState pinholeSpacingState;
		/* Excitation beam fill factor: */
		double excitationBeamFill[ICS_MAX_LAMBDA];
		Ics_SensorState excitationBeamFillState[ICS_MAX_LAMBDA];
		/* Excitation wavelength in nanometers: */
		double lambdaEx[ICS_MAX_LAMBDA];
		Ics_SensorState lambdaExState[ICS_MAX_LAMBDA];
		@@ -254,18 +289,24 @@ typedef struct _ICS {
		/* Number of excitation photons: */
		int exPhotonCnt[ICS_MAX_LAMBDA];
		Ics_SensorState exPhotonCntState[ICS_MAX_LAMBDA];
		/* Refractive index of embedding medium: */
		double refrInxMedium;
		Ics_SensorState refrInxMediumState;
		/* Numerical Aperture: */
		double numAperture;
		Ics_SensorState numApertureState;
		/* Refractive index of design medium: */
		double refrInxLensMedium;
		Ics_SensorState refrInxLensMediumState;
		/* Nipkow Disk pinhole spacing: */
		double pinholeSpacing;
		Ics_SensorState pinholeSpacingState;
		/* Emission wavelength in nm: */
		double interfacePrimary;
		Ics_SensorState interfacePrimaryState;
		/* Emission wavelength in nm: */
		double interfaceSecondary;
		Ics_SensorState interfaceSecondaryState;
		/* Excitation beam fill factor: */
		double detectorMagn[ICS_MAX_LAMBDA];
		Ics_SensorState detectorMagnState[ICS_MAX_LAMBDA];
		/* Detector photons per unit: */
		double detectorPPU[ICS_MAX_LAMBDA];
		Ics_SensorState detectorPPUState[ICS_MAX_LAMBDA];
		/* Detector Baseline: */
		double detectorBaseline[ICS_MAX_LAMBDA];
		Ics_SensorState detectorBaselineState[ICS_MAX_LAMBDA];
		/* Averaging line count */
		double detectorLineAvgCnt[ICS_MAX_LAMBDA];
		Ics_SensorState detectorLineAvgCntState[ICS_MAX_LAMBDA];
		/* STED depletion mode: */
		char stedDepletionMode[ICS_MAX_LAMBDA][ICS_STRLEN_TOKEN];
		Ics_SensorState stedDepletionModeState[ICS_MAX_LAMBDA];
		@@ -314,20 +355,12 @@ typedef struct _ICS {
		/* Scatter blurring: */
		double scatterBlurring[ICS_MAX_LAMBDA];
		Ics_SensorState scatterBlurringState[ICS_MAX_LAMBDA];
		/* Detector photons per unit: */
		double detectorPPU[ICS_MAX_LAMBDA];
		Ics_SensorState detectorPPUState[ICS_MAX_LAMBDA];
		/* Detector Baseline: */
		double detectorBaseline[ICS_MAX_LAMBDA];
		Ics_SensorState detectorBaselineState[ICS_MAX_LAMBDA];
		/* Averaging line count */
		double detectorLineAvgCnt[ICS_MAX_LAMBDA];
		Ics_SensorState detectorLineAvgCntState[ICS_MAX_LAMBDA];

		/* SCIL_Image compatibility parameter: */
		char scilType[ICS_STRLEN_TOKEN];
		} ICS;


		/* The error codes. */
		typedef enum {
		/* No error. */

libics_data.c

+15 −8

Original line number	Diff line number	Diff line
		@@ -82,14 +82,24 @@ Ics_Symbol G_SubCatSymbols[] =
		Ics_Symbol G_SubSubCatSymbols[] =
		{
		{"Channels", ICSTOK_CHANS},
		{"ImagingDirection", ICSTOK_IMDIR},
		{"NumAperture", ICSTOK_NUMAPER},
		{"ObjectiveQuality", ICSTOK_OBJQ},
		{"RefrInxMedium", ICSTOK_REFRIME},
		{"RefrInxLensMedium", ICSTOK_REFRILM},
		{"PinholeRadius", ICSTOK_PINHRAD},
		{"IllPinholeRadius", ICSTOK_ILLPINHRAD},
		{"PinholeSpacing", ICSTOK_PINHSPA},
		{"ExcitationBeamFill", ICSTOK_EXBFILL},
		{"LambdaEx", ICSTOK_LAMBDEX},
		{"LambdaEm", ICSTOK_LAMBDEM},
		{"ExPhotonCnt", ICSTOK_PHOTCNT},
		{"RefrInxMedium", ICSTOK_REFRIME},
		{"NumAperture", ICSTOK_NUMAPER},
		{"RefrInxLensMedium", ICSTOK_REFRILM},
		{"PinholeSpacing", ICSTOK_PINHSPA},
		{"InterFacePrimary", ICSTOK_IFACE1},
		{"InterFaceSecondary", ICSTOK_IFACE2},
		{"DetectorMagnif", ICSTOK_DETMAG},
		{"DetectorPPU", ICSTOK_DETPPU},
		{"DetectorBaseline", ICSTOK_DETBASELINE},
		{"DetectorLineAvgCnt", ICSTOK_DETLNAVGCNT},
		{"STEDDeplMode", ICSTOK_STEDDEPLMODE},
		{"STEDLambda", ICSTOK_STEDLAMBDA},
		{"STEDSatFactor", ICSTOK_STEDSATFACTOR},
		@@ -105,10 +115,7 @@ Ics_Symbol G_SubSubCatSymbols[] =
		{"ScatterModel", ICSTOK_SCATTERMODEL},
		{"ScatterFreePath", ICSTOK_SCATTERFREEPATH},
		{"ScatterRelContrib", ICSTOK_SCATTERRELCONTRIB},
		{"ScatterBlurring", ICSTOK_SCATTERBLURRING},
		{"DetectorPPU", ICSTOK_DETPPU},
		{"DetectorBaseline", ICSTOK_DETBASELINE},
		{"DetectorLineAvgCnt", ICSTOK_DETLNAVGCNT}
		{"ScatterBlurring", ICSTOK_SCATTERBLURRING}
		};

libics_intern.h

+14 −7

Original line number	Diff line number	Diff line
		@@ -107,14 +107,24 @@ typedef enum {
		/* SubsubCategory tokens: */
		ICSTOK_FIRSTSUBSUB,
		ICSTOK_CHANS,
		ICSTOK_IMDIR,
		ICSTOK_NUMAPER,
		ICSTOK_OBJQ,
		ICSTOK_REFRIME,
		ICSTOK_REFRILM,
		ICSTOK_PINHRAD,
		ICSTOK_ILLPINHRAD,
		ICSTOK_PINHSPA,
		ICSTOK_EXBFILL,
		ICSTOK_LAMBDEX,
		ICSTOK_LAMBDEM,
		ICSTOK_PHOTCNT,
		ICSTOK_REFRIME,
		ICSTOK_NUMAPER,
		ICSTOK_REFRILM,
		ICSTOK_PINHSPA,
		ICSTOK_IFACE1,
		ICSTOK_IFACE2,
		ICSTOK_DETMAG,
		ICSTOK_DETPPU,
		ICSTOK_DETBASELINE,
		ICSTOK_DETLNAVGCNT,
		ICSTOK_STEDDEPLMODE,
		ICSTOK_STEDLAMBDA,
		ICSTOK_STEDSATFACTOR,
		@@ -131,9 +141,6 @@ typedef enum {
		ICSTOK_SCATTERFREEPATH,
		ICSTOK_SCATTERRELCONTRIB,
		ICSTOK_SCATTERBLURRING,
		ICSTOK_DETPPU,
		ICSTOK_DETBASELINE,
		ICSTOK_DETLNAVGCNT,
		ICSTOK_LASTSUBSUB,

		/* Value tokens: */