Some cleanup of the sensor parameter code, and added some more parame…

…ters

CMakeLists.txt

@@ -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.

configure.ac

@@ -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

@@ -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
@@ -156,33 +156,44 @@ typedef struct {
 /* A list of sensor parameters that are also equiped with a state. */
 typedef enum {
     ICS_SENSOR_FIRST,
-    ICS_SENSOR_PINHOLE_RADIUS,
-    ICS_SENSOR_LAMBDA_EXCITATION,
-    ICS_SENSOR_LAMBDA_EMISSION,
-    ICS_SENSOR_PHOTON_COUNT,
-    ICS_SENSOR_MEDIUM_REFRACTIVE_INDEX,
+    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_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,
     ICS_SENSOR_SPIM_PLANE_GAUSS_WIDTH,
     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_SCATTER_BLURRING,    
     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

@@ -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

@@ -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: */