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libics_read.c
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libics_read.c
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/*
* libics: Image Cytometry Standard file reading and writing.
*
* Copyright 2015-2019:
* Scientific Volume Imaging Holding B.V.
* Hilversum, The Netherlands.
* https://www.svi.nl
*
* Copyright (C) 2000-2013 Cris Luengo and others
*
* Large chunks of this library written by
* Bert Gijsbers
* Dr. Hans T.M. van der Voort
* And also Damir Sudar, Geert van Kempen, Jan Jitze Krol,
* Chiel Baarslag and Fons Laan.
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Library General Public
* License as published by the Free Software Foundation; either
* version 2 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Library General Public License for more details.
*
* You should have received a copy of the GNU Library General Public
* License along with this library; if not, write to the Free
* Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
*/
/*
* FILE : libics_read.c
*
* The following library functions are contained in this file:
*
* IcsReadIcs()
* IcsVersion()
*/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "libics_intern.h"
/* Use thread safe string tokenization if available */
#ifdef HAVE_STRTOK_R
#define STRTOK(str, seps) strtok_r(str, seps, &saveptr)
#else
#define STRTOK(str, seps) strtok(str, seps)
#endif
/* Find the index for "bits", which should be the first parameter. */
static int icsGetBitsParam(char order[ICS_MAXDIM+1][ICS_STRLEN_TOKEN],
int parameters)
{
int i;
for (i = 0; i < parameters; i++) {
if (strcmp(order[i], ICS_ORDER_BITS) == 0) {
return i;
}
}
return -1;
}
/* Like fgets(), gets a string from a stream. However, does not stop at newline
character, but at 'sep'. It retains the 'sep' character at the end of the
string; a null byte is appended. Also, it implements the solution to the
CR/LF pair problem caused by some windows applications. If 'sep' is LF, it
might be prepended by a CR. */
static char *icsFGetStr(char *line,
int n,
FILE *fi,
char sep)
{
/* n == ICS_LINE_LENGTH */
int i = 0;
int ch;
/* Imitate fgets() */
while (i < n - 1) {
ch = getc(fi);
if (ch == EOF)
break;
/* Skip CR if next char is LF and sep is LF. */
if (ch == '\r' && sep == '\n') {
ch = getc(fi);
if (ch != sep && ch != EOF) {
ungetc(ch, fi);
ch = '\r';
}
}
line[i] =(char)ch;
i++;
if ((char)ch == sep)
break;
}
line[i] = '\0';
if (i != 0) {
/* Read at least a 'sep' character */
return line;
} else {
/* EOF at first getc() call */
return NULL;
}
}
/* Read the two ICS separators from file. There is a special case for ICS
headers which are erroneously written under Windows in text mode causing a
newline separator to be prepended by a carriage return. Therefore when the
second separator is a carriage return and the first separator is not a
newline then peek at the third character to see if it is a newline. If so
then use newline as the second separator. Return IcsErr_FReadIcs on read
errors and IcsErr_NotIcsFile on premature end-of-file. */
static Ics_Error getIcsSeparators(FILE *fi,
char *seps)
{
int sep1;
int sep2;
int sep3;
sep1 = fgetc(fi);
if (sep1 == EOF) {
return (ferror(fi)) ? IcsErr_FReadIcs : IcsErr_NotIcsFile;
}
sep2 = fgetc(fi);
if (sep2 == EOF) {
return (ferror(fi)) ? IcsErr_FReadIcs : IcsErr_NotIcsFile;
}
if (sep1 == sep2) {
return IcsErr_NotIcsFile;
}
if (sep2 == '\r' && sep1 != '\n') {
sep3 = fgetc(fi);
if (sep3 == EOF) {
return (ferror(fi)) ? IcsErr_FReadIcs : IcsErr_NotIcsFile;
} else {
if (sep3 == '\n') {
sep2 = '\n';
} else {
ungetc(sep3, fi);
}
}
}
seps[0] = (char)sep1;
seps[1] = (char)sep2;
seps[2] = '\0';
return IcsErr_Ok;
}
static Ics_Error getIcsVersion(FILE *fi,
const char *seps,
int *ver)
{
ICSINIT;
char *word;
char line[ICS_LINE_LENGTH];
#ifdef HAVE_STRTOK_R
char *saveptr;
#endif
if (icsFGetStr(line, ICS_LINE_LENGTH, fi, seps[1]) == NULL)
return IcsErr_FReadIcs;
word = STRTOK(line, seps);
if (word == NULL) return IcsErr_NotIcsFile;
if (strcmp(word, ICS_VERSION) != 0) return IcsErr_NotIcsFile;
word = STRTOK(NULL, seps);
if (word == NULL) return IcsErr_NotIcsFile;
if (strcmp(word, "1.0") == 0) {
*ver = 1;
} else if (strcmp(word, "2.0") == 0) {
*ver = 2;
} else {
error = IcsErr_NotIcsFile;
}
return error;
}
static Ics_Error getIcsFileName(FILE *fi,
const char *seps)
{
ICSINIT;
char *word;
char line[ICS_LINE_LENGTH];
#ifdef HAVE_STRTOK_R
char *saveptr;
#endif
if (icsFGetStr(line, ICS_LINE_LENGTH, fi, seps[1]) == NULL)
return IcsErr_FReadIcs;
word = STRTOK(line, seps);
if (word == NULL) return IcsErr_NotIcsFile;
if (strcmp(word, ICS_FILENAME) != 0) return IcsErr_NotIcsFile;
return error;
}
static Ics_Token getIcsToken(char *str,
Ics_SymbolList *listSpec)
{
int i;
Ics_Token token = ICSTOK_NONE;
/* Because some older ics versions have uncapitalized subsubcat
symbols (e.g. "channels" instead of the current "Channels"), do a
case-insensitive string comparison for backward compatibility. */
if (str != NULL) {
for (i = 0; i < listSpec->entries; i++) {
if (ICSSTRCASECMP(listSpec->list[i].name, str) == 0) {
token = listSpec->list[i].token;
}
}
}
return token;
}
static Ics_Error getIcsCat(char *str,
const char *seps,
Ics_Token *cat,
Ics_Token *subCat,
Ics_Token *subSubCat,
const char **index1,
const char **index2)
{
ICSINIT;
char *token, buffer[ICS_LINE_LENGTH], *idx1, *idx2;
#ifdef HAVE_STRTOK_R
char *saveptr;
#endif
*subCat = *subSubCat = ICSTOK_NONE;
*index1 = NULL;
*index2 = NULL;
IcsStrCpy(buffer, str, ICS_LINE_LENGTH);
token = STRTOK(buffer, seps);
*cat = getIcsToken(token, &G_Categories);
if (*cat == ICSTOK_NONE) return IcsErr_MissCat;
if ((*cat != ICSTOK_HISTORY) &&(*cat != ICSTOK_END)) {
token = STRTOK(NULL, seps);
*subCat = getIcsToken(token, &G_SubCategories);
if (*subCat == ICSTOK_NONE) return IcsErr_MissSubCat;
if (*subCat == ICSTOK_SPARAMS || *subCat == ICSTOK_SSTATES) {
token = STRTOK(NULL, seps);
if (token[strlen(token) - 1] == ']') {
idx1 = strchr(token, '[');
if (idx1) {
idx2 = strchr(idx1 + 1, '[');
/* Todo: Check that this line is indeed not
necessary. */
/* token[strlen(token) - 1] = '\0'; */
*idx1 = '\0';
*index1 = idx1 + 1;
if (idx2) {
*index2 = idx2 + 1;
}
}
}
*subSubCat = getIcsToken(token, &G_SubSubCategories);
if (*subSubCat == ICSTOK_NONE) return IcsErr_MissSensorSubSubCat;
}
}
/* Copy the remaining stuff into 'str' */
if ((token = STRTOK(NULL, seps)) != NULL) {
strcpy(str, token);
}
while ((token = STRTOK(NULL, seps)) != NULL) {
IcsAppendChar(str, seps[0]);
strcat(str, token);
}
return error;
}
static Ics_Error getIcsSensorState(char *str,
Ics_SensorState *state)
{
ICSINIT;
switch (getIcsToken(str, &G_Values)) {
case ICSTOK_STATE_DEFAULT:
*state = IcsSensorState_default;
break;
case ICSTOK_STATE_ESTIMATED:
*state = IcsSensorState_estimated;
break;
case ICSTOK_STATE_REPORTED:
*state = IcsSensorState_reported;
break;
case ICSTOK_STATE_VERIFIED:
*state = IcsSensorState_verified;
break;
default:
error = IcsErr_UnknownSensorState;
break;
}
return error;
}
#define ICS_SET_SENSOR_STRING(FIELD) \
do { \
while (ptr != NULL && i < ICS_MAX_LAMBDA) { \
IcsStrCpy(icsStruct->FIELD[i++], \
ptr, ICS_STRLEN_TOKEN); \
ptr = STRTOK(NULL, seps); \
} \
} while (0)
#define ICS_SET_SENSOR_DOUBLE_ONE(FIELD) \
do { \
if (ptr != NULL) { \
icsStruct->FIELD = atof(ptr); \
} \
} while (0)
#define ICS_SET_SENSOR_INT(FIELD) \
do { \
while (ptr != NULL && i < ICS_MAX_LAMBDA) { \
icsStruct->FIELD[i++] = atoi(ptr); \
ptr = STRTOK(NULL, seps); \
} \
} while (0)
#define ICS_SET_SENSOR_DOUBLE(FIELD) \
do { \
while (ptr != NULL && i < ICS_MAX_LAMBDA) { \
icsStruct->FIELD[i++] = atof(ptr); \
ptr = STRTOK(NULL, seps); \
} \
} while (0)
#define ICS_SET_SENSOR_STATE(FIELD) \
do { \
while (ptr != NULL && i < ICS_MAX_LAMBDA) { \
error = getIcsSensorState(ptr, &state); \
icsStruct->FIELD ## State[i++] = state; \
ptr = STRTOK(NULL, seps); \
} \
} while(0)
#define ICS_SET_SENSOR_STATE_ONE(FIELD) \
do { \
if (ptr != NULL) { \
error = getIcsSensorState(ptr, &state); \
icsStruct->FIELD ## State = state; \
} \
} while(0)
Ics_Error IcsReadIcs(Ics_Header *icsStruct,
const char *filename,
int forceName,
int forceLocale)
{
ICSINIT;
ICS_INIT_LOCALE;
FILE *fp;
int end = 0, si, sj;
size_t i, j;
char seps[3], *ptr, *data;
char line[ICS_LINE_LENGTH];
Ics_Token cat, subCat, subSubCat;
int detID;
const char *idx1;
const char *idx2;
/* These are temporary buffers to hold the data read until it is copied
to the Ics_Header structure. This is needed because the Ics_Header
structure is made to look more like we like to see images, compared
to the way the data is written in the ICS file. */
Ics_Format format = IcsForm_unknown;
int sign = 1;
int parameters = 0;
char order[ICS_MAXDIM+1][ICS_STRLEN_TOKEN];
size_t sizes[ICS_MAXDIM+1];
double origin[ICS_MAXDIM+1];
double scale[ICS_MAXDIM+1];
char label[ICS_MAXDIM+1][ICS_STRLEN_TOKEN];
char unit[ICS_MAXDIM+1][ICS_STRLEN_TOKEN];
Ics_SensorState state = IcsSensorState_default;
#ifdef HAVE_STRTOK_R
char *saveptr;
#endif
for (i = 0; i < ICS_MAXDIM+1; i++) {
sizes[i] = 1;
origin[i] = 0.0;
scale[i] = 1.0;
order[i][0] = '\0';
label[i][0] = '\0';
unit[i][0] = '\0';
}
IcsInit(icsStruct);
icsStruct->fileMode = IcsFileMode_read;
IcsStrCpy(icsStruct->filename, filename, ICS_MAXPATHLEN);
error = IcsOpenIcs(&fp, icsStruct->filename, forceName);
if (error) return error;
if (forceLocale) {
ICS_SET_LOCALE;
}
if (!error) error = getIcsSeparators(fp, seps);
if (!error) error = getIcsVersion(fp, seps, &(icsStruct->version));
if (!error) error = getIcsFileName(fp, seps);
while (!end && !error
&& (icsFGetStr(line, ICS_LINE_LENGTH, fp, seps[1]) != NULL)) {
if (getIcsCat(line, seps, &cat, &subCat, &subSubCat, &idx1, &idx2) !=
IcsErr_Ok)
continue;
ptr = STRTOK(line, seps);
i = 0;
switch (cat) {
case ICSTOK_END:
end = 1;
if (icsStruct->srcFile[0] == '\0') {
icsStruct->srcOffset =(size_t) ftell(fp);
IcsStrCpy(icsStruct->srcFile, icsStruct->filename,
ICS_MAXPATHLEN);
}
break;
case ICSTOK_SOURCE:
switch (subCat) {
case ICSTOK_FILE:
if (ptr != NULL) {
IcsStrCpy(icsStruct->srcFile, ptr, ICS_MAXPATHLEN);
}
break;
case ICSTOK_OFFSET:
if (ptr != NULL) {
icsStruct->srcOffset = IcsStrToSize(ptr);
}
break;
default:
break;
}
break;
case ICSTOK_LAYOUT:
switch (subCat) {
case ICSTOK_PARAMS:
if (ptr != NULL) {
parameters = atoi(ptr);
if (parameters > ICS_MAXDIM+1) {
error = IcsErr_TooManyDims;
}
}
break;
case ICSTOK_ORDER:
while (ptr!= NULL && i < ICS_MAXDIM+1) {
IcsStrCpy(order[i++], ptr, ICS_STRLEN_TOKEN);
ptr = STRTOK(NULL, seps);
}
break;
case ICSTOK_SIZES:
while (ptr!= NULL && i < ICS_MAXDIM+1) {
sizes[i++] = IcsStrToSize(ptr);
ptr = STRTOK(NULL, seps);
}
break;
case ICSTOK_COORD:
if (ptr != NULL) {
IcsStrCpy(icsStruct->coord, ptr, ICS_STRLEN_TOKEN);
}
break;
case ICSTOK_SIGBIT:
if (ptr != NULL) {
icsStruct->imel.sigBits = IcsStrToSize(ptr);
}
break;
default:
error = IcsErr_MissLayoutSubCat;
}
break;
case ICSTOK_REPRES:
switch (subCat) {
case ICSTOK_FORMAT:
switch (getIcsToken(ptr, &G_Values)) {
case ICSTOK_FORMAT_INTEGER:
format = IcsForm_integer;
break;
case ICSTOK_FORMAT_REAL:
format = IcsForm_real;
break;
case ICSTOK_FORMAT_COMPLEX:
format = IcsForm_complex;
break;
default:
format = IcsForm_unknown;
}
break;
case ICSTOK_SIGN:
{
Ics_Token tok = getIcsToken(ptr, &G_Values);
if (tok == ICSTOK_SIGN_UNSIGNED) {
sign = 0;
} else {
sign = 1;
}
break;
}
case ICSTOK_SCILT:
if (ptr!= NULL) {
IcsStrCpy(icsStruct->scilType, ptr,
ICS_STRLEN_TOKEN);
}
break;
case ICSTOK_COMPR:
switch (getIcsToken(ptr, &G_Values)) {
case ICSTOK_COMPR_UNCOMPRESSED:
icsStruct->compression = IcsCompr_uncompressed;
break;
case ICSTOK_COMPR_COMPRESS:
if (icsStruct->version == 1) {
icsStruct->compression = IcsCompr_compress;
} else { /* A version 2.0 file never uses
COMPRESS, maybe it means GZIP? */
icsStruct->compression = IcsCompr_gzip;
}
break;
case ICSTOK_COMPR_GZIP:
icsStruct->compression = IcsCompr_gzip;
break;
default:
error = IcsErr_UnknownCompression;
}
break;
case ICSTOK_BYTEO:
while (ptr!= NULL && i < ICS_MAX_IMEL_SIZE) {
icsStruct->byteOrder[i++] = atoi(ptr);
ptr = STRTOK(NULL, seps);
}
break;
default:
error = IcsErr_MissRepresSubCat;
break;
}
break;
case ICSTOK_PARAM:
switch (subCat) {
case ICSTOK_ORIGIN:
while (ptr!= NULL && i < ICS_MAXDIM+1) {
origin[i++] = atof(ptr);
ptr = STRTOK(NULL, seps);
}
break;
case ICSTOK_SCALE:
while (ptr!= NULL && i < ICS_MAXDIM+1) {
scale[i++] = atof(ptr);
ptr = STRTOK(NULL, seps);
}
break;
case ICSTOK_UNITS:
while (ptr!= NULL && i < ICS_MAXDIM+1) {
IcsStrCpy(unit[i++], ptr, ICS_STRLEN_TOKEN);
ptr = STRTOK(NULL, seps);
}
break;
case ICSTOK_LABELS:
while (ptr!= NULL && i < ICS_MAXDIM+1) {
IcsStrCpy(label[i++], ptr, ICS_STRLEN_TOKEN);
ptr = STRTOK(NULL, seps);
}
break;
default:
error = IcsErr_MissParamSubCat;
}
break;
case ICSTOK_HISTORY:
if (ptr != NULL) {
data = STRTOK(NULL, seps+1); /* This will get the rest of
the line */
if (data == NULL) { /* data is not allowed to be "", but ptr
is */
data = ptr;
ptr = "";
}
/* The next portion is to avoid having
IcsInternAddHistory return IcsErr_LineOverflow. */
i = strlen(ptr);
if (i+1 > ICS_STRLEN_TOKEN) {
ptr[ICS_STRLEN_TOKEN-1] = '\0';
i = ICS_STRLEN_TOKEN-1;
}
j = strlen(ICS_HISTORY);
if ((strlen(data) + i + j + 4) > ICS_LINE_LENGTH) {
data[ICS_LINE_LENGTH - i - j - 4] = '\0';
}
error = IcsInternAddHistory(icsStruct, ptr, data, seps);
}
break;
case ICSTOK_SENSOR:
switch (subCat) {
case ICSTOK_TYPE:
while (ptr != NULL && i < ICS_MAX_LAMBDA) {
IcsStrCpy(icsStruct->type[i++], ptr,
ICS_STRLEN_TOKEN);
ptr = STRTOK(NULL, seps);
}
break;
case ICSTOK_MODEL:
if (ptr != NULL) {
IcsStrCpy(icsStruct->model, ptr, ICS_STRLEN_OTHER);
}
break;
case ICSTOK_SPARAMS:
switch (subSubCat) {
case ICSTOK_CHANS:
if (ptr != NULL) {
int v = atoi(ptr);
icsStruct->sensorChannels = v;
if (v > ICS_MAX_LAMBDA) {
error = IcsErr_TooManyChans;
}
}
break;
case ICSTOK_DETECTORS:
if (ptr != NULL) {
int v = atoi(ptr);
icsStruct->sensorDetectors = v;
if (v > ICS_MAX_DETECT) {
error = IcsErr_TooManyDetectors;
}
}
break;
case ICSTOK_IMDIR:
ICS_SET_SENSOR_STRING(imagingDirection);
break;
case ICSTOK_NUMAPER:
ICS_SET_SENSOR_DOUBLE_ONE(numAperture);
break;
case ICSTOK_OBJQ:
ICS_SET_SENSOR_INT(objectiveQuality);
break;
case ICSTOK_REFRIME:
ICS_SET_SENSOR_DOUBLE_ONE(refrInxMedium);
break;
case ICSTOK_REFRILM:
ICS_SET_SENSOR_DOUBLE_ONE(refrInxLensMedium);
break;
case ICSTOK_PINHRAD:
ICS_SET_SENSOR_DOUBLE(pinholeRadius);
break;
case ICSTOK_ILLPINHRAD:
ICS_SET_SENSOR_DOUBLE(illPinholeRadius);
break;
case ICSTOK_PINHSPA:
ICS_SET_SENSOR_DOUBLE_ONE(pinholeSpacing);
break;
case ICSTOK_EXBFILL:
ICS_SET_SENSOR_DOUBLE(excitationBeamFill);
break;
case ICSTOK_LAMBDEX:
ICS_SET_SENSOR_DOUBLE(lambdaEx);
break;
case ICSTOK_LAMBDEM:
ICS_SET_SENSOR_DOUBLE(lambdaEm);
break;
case ICSTOK_PHOTCNT:
ICS_SET_SENSOR_INT(exPhotonCnt);
break;
case ICSTOK_IFACE1:
ICS_SET_SENSOR_DOUBLE_ONE(interfacePrimary);
break;
case ICSTOK_IFACE2:
ICS_SET_SENSOR_DOUBLE_ONE(interfaceSecondary);
break;
case ICSTOK_DESCRIPTION:
ICS_SET_SENSOR_STRING(description);
break;
case ICSTOK_DETMAG:
ICS_SET_SENSOR_DOUBLE(detectorMagn);
break;
case ICSTOK_DETPPU:
ICS_SET_SENSOR_DOUBLE(detectorPPU);
break;
case ICSTOK_DETBASELINE:
ICS_SET_SENSOR_DOUBLE(detectorBaseline);
break;
case ICSTOK_DETLNAVGCNT:
ICS_SET_SENSOR_DOUBLE(detectorLineAvgCnt);
break;
case ICSTOK_DETNOISEGAIN:
ICS_SET_SENSOR_DOUBLE(detectorNoiseGain);
break;
case ICSTOK_DETOFFSET:
while (ptr != NULL && i < ICS_MAX_LAMBDA) {
if (idx1 && idx2) {
detID = atoi(idx1);
switch (idx2[0]) {
case 'X':
icsStruct->
detectorOffset[i++][detID][0]
= atof(ptr);
break;
case 'Y':
icsStruct->
detectorOffset[i++][detID][1]
= atof(ptr);
break;
case 'Z':
icsStruct->
detectorOffset[i++][detID][2]
= atof(ptr);
break;
default:
break;
}
ptr = STRTOK(NULL, seps);
} else {
error = IcsErr_MissSensorSubSubCatIndex;
break;
}
}
break;
case ICSTOK_DETSENS:
while (ptr != NULL && i < ICS_MAX_LAMBDA) {
if (idx1) {
detID = atoi(idx1);
icsStruct->detectorSensitivity[i++][detID]
= atof(ptr);
ptr = STRTOK(NULL, seps);
} else {
error = IcsErr_MissSensorSubSubCatIndex;
break;
}
}
break;
case ICSTOK_DETRADIUS:
if (idx1) {
/* This supports ics files with a non-vector
detector radius. */
while (ptr != NULL && i < ICS_MAX_LAMBDA) {
detID = atoi(idx1);
icsStruct->detectorRadius[i++][detID]
= atof(ptr);
ptr = STRTOK(NULL, seps);
}
} else {
printf("Using non-vector detRadius.\n");
if (ptr != NULL) {
printf("Filling vector with single "
"value.\n");
int k;
for (i = 0; i < ICS_MAX_LAMBDA; i++) {
for (k = 0; k < ICS_MAX_DETECT;
k++) {
icsStruct->detectorRadius[i][k]
= atof(ptr);
}
}
}
}
break;
case ICSTOK_DETSCALE:
ICS_SET_SENSOR_DOUBLE(detectorScale);
break;
case ICSTOK_DETSTRETCH:
ICS_SET_SENSOR_DOUBLE(detectorStretch);
break;
case ICSTOK_DETROT:
ICS_SET_SENSOR_DOUBLE(detectorRot);
break;
case ICSTOK_DETMIRROR:
ICS_SET_SENSOR_STRING(detectorMirror);
break;
case ICSTOK_DETMODEL:
ICS_SET_SENSOR_STRING(detectorModel);
break;
case ICSTOK_DETREDUCEHIST:
ICS_SET_SENSOR_STRING(detectorRedHist);
break;
case ICSTOK_STEDDEPLMODE:
ICS_SET_SENSOR_STRING(stedDepletionMode);
break;
case ICSTOK_STEDLAMBDA:
ICS_SET_SENSOR_DOUBLE(stedLambda);
break;
case ICSTOK_STEDSATFACTOR:
ICS_SET_SENSOR_DOUBLE(stedSatFactor);
break;
case ICSTOK_STEDIMMFRACTION:
ICS_SET_SENSOR_DOUBLE(stedImmFraction);
break;
case ICSTOK_STEDVPPM:
ICS_SET_SENSOR_DOUBLE(stedVPPM);
break;
case ICSTOK_SPIMEXCTYPE:
ICS_SET_SENSOR_STRING(spimExcType);
break;
case ICSTOK_SPIMFILLFACTOR:
ICS_SET_SENSOR_DOUBLE(spimFillFactor);
break;
case ICSTOK_SPIMPLANENA:
ICS_SET_SENSOR_DOUBLE(spimPlaneNA);
break;
case ICSTOK_SPIMPLANEGAUSSWIDTH:
ICS_SET_SENSOR_DOUBLE(spimPlaneGaussWidth);
break;
case ICSTOK_SPIMPLANEPROPDIR:
while (ptr != NULL && i < ICS_MAX_LAMBDA) {
if (idx1) {
switch (idx1[0]) {
case 'X':
icsStruct->spimPlanePropDir[i++][0]
= atof(ptr);
break;
case 'Y':
icsStruct->spimPlanePropDir[i++][1]
= atof(ptr);
break;
case 'Z':
icsStruct->spimPlanePropDir[i++][2]
= atof(ptr);
break;
default:
break;
}
ptr = STRTOK(NULL, seps);
} else {
error = IcsErr_MissSensorSubSubCatIndex;
break;
}
}
break;
case ICSTOK_SPIMPLANECENTEROFF:
ICS_SET_SENSOR_DOUBLE(spimPlaneCenterOff);
break;
case ICSTOK_SPIMPLANEFOCUSOF:
ICS_SET_SENSOR_DOUBLE(spimPlaneFocusOff);
break;
case ICSTOK_SCATTERMODEL:
ICS_SET_SENSOR_STRING(scatterModel);
break;
case ICSTOK_SCATTERFREEPATH:
ICS_SET_SENSOR_DOUBLE(scatterFreePath);
break;
case ICSTOK_SCATTERRELCONTRIB:
ICS_SET_SENSOR_DOUBLE(scatterRelContrib);
break;
case ICSTOK_SCATTERBLURRING:
ICS_SET_SENSOR_DOUBLE(scatterBlurring);
break;
default:
error = IcsErr_MissSensorSubSubCat;
}
break;
case ICSTOK_SSTATES:
switch (subSubCat) {
case ICSTOK_IMDIR:
ICS_SET_SENSOR_STATE(imagingDirection);
break;
case ICSTOK_NUMAPER:
ICS_SET_SENSOR_STATE_ONE(numAperture);
break;
case ICSTOK_OBJQ:
ICS_SET_SENSOR_STATE(objectiveQuality);
break;
case ICSTOK_REFRIME:
ICS_SET_SENSOR_STATE_ONE(refrInxMedium);
break;
case ICSTOK_REFRILM:
ICS_SET_SENSOR_STATE_ONE(refrInxLensMedium);
break;
case ICSTOK_PINHRAD:
ICS_SET_SENSOR_STATE(pinholeRadius);
break;
case ICSTOK_ILLPINHRAD:
ICS_SET_SENSOR_STATE(illPinholeRadius);
break;
case ICSTOK_PINHSPA:
ICS_SET_SENSOR_STATE_ONE(pinholeSpacing);
break;
case ICSTOK_EXBFILL:
ICS_SET_SENSOR_STATE(excitationBeamFill);
break;
case ICSTOK_LAMBDEX:
ICS_SET_SENSOR_STATE(lambdaEx);
break;
case ICSTOK_LAMBDEM:
ICS_SET_SENSOR_STATE(lambdaEm);
break;
case ICSTOK_PHOTCNT:
ICS_SET_SENSOR_STATE(exPhotonCnt);
break;
case ICSTOK_IFACE1:
ICS_SET_SENSOR_STATE_ONE(interfacePrimary);
break;
case ICSTOK_IFACE2:
ICS_SET_SENSOR_STATE_ONE(interfaceSecondary);
break;
case ICSTOK_DESCRIPTION:
ICS_SET_SENSOR_STATE(description);
break;
case ICSTOK_DETMAG:
ICS_SET_SENSOR_STATE(detectorMagn);
break;
case ICSTOK_DETPPU:
ICS_SET_SENSOR_STATE(detectorPPU);
break;
case ICSTOK_DETBASELINE:
ICS_SET_SENSOR_STATE(detectorBaseline);
break;
case ICSTOK_DETLNAVGCNT:
ICS_SET_SENSOR_STATE(detectorLineAvgCnt);
break;
case ICSTOK_DETNOISEGAIN:
ICS_SET_SENSOR_STATE(detectorNoiseGain);
break;
case ICSTOK_DETOFFSET:
ICS_SET_SENSOR_STATE(detectorOffset);
break;
case ICSTOK_DETSENS:
ICS_SET_SENSOR_STATE(detectorSensitivity);
break;
case ICSTOK_DETRADIUS:
ICS_SET_SENSOR_STATE(detectorRadius);
break;
case ICSTOK_DETSCALE:
ICS_SET_SENSOR_STATE(detectorScale);
break;
case ICSTOK_DETSTRETCH:
ICS_SET_SENSOR_STATE(detectorStretch);
break;
case ICSTOK_DETROT:
ICS_SET_SENSOR_STATE(detectorRot);
break;
case ICSTOK_DETMIRROR:
ICS_SET_SENSOR_STATE(detectorMirror);
break;
case ICSTOK_DETMODEL:
ICS_SET_SENSOR_STATE(detectorModel);
break;
case ICSTOK_DETREDUCEHIST:
ICS_SET_SENSOR_STATE(detectorRedHist);
break;
case ICSTOK_STEDDEPLMODE:
ICS_SET_SENSOR_STATE(stedDepletionMode);
break;
case ICSTOK_STEDLAMBDA:
ICS_SET_SENSOR_STATE(stedLambda);
break;
case ICSTOK_STEDSATFACTOR:
ICS_SET_SENSOR_STATE(stedSatFactor);
break;
case ICSTOK_STEDIMMFRACTION:
ICS_SET_SENSOR_STATE(stedImmFraction);
break;
case ICSTOK_STEDVPPM:
ICS_SET_SENSOR_STATE(stedVPPM);
break;
case ICSTOK_SPIMEXCTYPE:
ICS_SET_SENSOR_STATE(spimExcType);
break;
case ICSTOK_SPIMFILLFACTOR:
ICS_SET_SENSOR_STATE(spimFillFactor);
break;
case ICSTOK_SPIMPLANENA:
ICS_SET_SENSOR_STATE(spimPlaneNA);
break;
case ICSTOK_SPIMPLANEGAUSSWIDTH:
ICS_SET_SENSOR_STATE(spimPlaneGaussWidth);
break;
case ICSTOK_SPIMPLANEPROPDIR:
ICS_SET_SENSOR_STATE(spimPlanePropDir);
break;
case ICSTOK_SPIMPLANECENTEROFF:
ICS_SET_SENSOR_STATE(spimPlaneCenterOff);