Merge new upstream release

1 files changed, 265 insertions, 0 deletions

diff --git a/spectro/rspec.h b/spectro/rspec.h
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+#ifndef RSPEC_H
+
+/* 
+ * Argyll Color Correction System
+ *
+ * Author: Graeme W. Gill
+ * Date:   20015
+ *
+ * Copyright 2006 - 2015 Graeme W. Gill
+ * All rights reserved.
+ *
+ * This material is licenced under the GNU GENERAL PUBLIC LICENSE Version 2 or later :-
+ * see the License2.txt file for licencing details.
+ * 
+ * Derived from i1pro_imp.c & munki_imp.c
+ */
+
+/*
+ * A library for processing raw spectrometer values.
+ *
+ * Currently this is setup for the EX1 spectrometer,
+ * but the longer term plan is to expand the functionality
+ * so that it becomes more generic, and can replace a lot 
+ * of common code in i1pro_imp.c & munki_imp.c.
+ */
+
+#ifdef __cplusplus
+	extern "C" {
+#endif
+
+#define RSPEC_MAXSAMP 2048
+
+/* - - - - - - - - - - - - - */
+/* Collection of raw samples */
+typedef enum {
+	rspec_sensor,		/* Includes shielded/temperaturee values */
+	rspec_raw,			/* Potential light values */
+	rspec_wav			/* Valid wavelength values */
+} rspec_type;
+
+/* The order the state is changed in is device workflow dependent */
+typedef enum {
+	rspec_none = 0x0000,	/* No processing */
+	rspec_shld = 0x0002,	/* Shielded cell corrected */
+	rspec_dcal = 0x0004,	/* Dark calibration subtracted */
+	rspec_lin  = 0x0010,	/* Linearized */
+	rspec_int  = 0x0020,	/* Integration time adjusted */
+	rspec_temp = 0x0001,	/* Temperature corrected */
+	rspec_cal  = 0x0040		/* Calibrated */
+} rspec_state;
+
+struct _rspec {
+	struct _rspec_inf *inf;		/* Base information */
+
+	rspec_type     stype;	/* Spectral type - sensor, raw, cooked */
+	inst_meas_type mtype;	/* Measurement type (emis, ambient, reflective etc.) */
+	rspec_state    state;	/* Processing state */
+
+	double inttime;		/* Integration time */
+
+	int nmeas;			/* Number of measurements */
+	int nsamp;			/* Number of sensor/wavelength samples */
+	double **samp;		/* [mesa][samples] allocated using numlib. */
+
+}; typedef struct _rspec rspec;
+
+
+/* - - - - - - - - - - - - - */
+/* Base information about characteristics in a given mode */
+
+/* Wavelength resample kernel type */
+typedef enum {
+	rspec_triangle,
+	rspec_gausian,
+	rspec_lanczos2,
+	rspec_lanczos3,
+	rspec_cubicspline
+} rspec_kernel;
+
+/* Group of values */
+typedef struct {
+	int off;		/* Offset to start of group */
+	int num;		/* Number in group */
+} rspec_group;
+
+struct _rspec_inf {
+	a1log *log;
+
+	int nsen;					/* Number of sensor values */
+	int nshgrps;				/* Number of shielded sensor groups */
+	rspec_group shgrps[2];		/* Shielded group definition */
+
+	int nilltkgrps;				/* Number of illuminant level tracking groups */
+	rspec_group illtkgrps[2];	/* illuminant level tracking groups definition */
+
+	rspec_group lightrange;		/* Range of sensor potential light values transferred to raw */ 
+
+	int nraw;					/* Number of raw light sensor values */
+	rspec_group rawrange;		/* Valid range of raw values for filter to wav */
+
+	rspec_kernel ktype;			/* Re-sampling kernel type */
+	int nwav;					/* Cooked spectrum bands */
+	double wl_space;			/* Wavelength spacing */
+	double wl_short;			/* Cooked spectrum bands short wavelength nm */
+	double wl_long;				/* Cooked spectrum bands short wavelength nm */
+
+
+								/* (Stray light is not currently implemented) */
+	rspec_type straytype;		/* Stray light spectral type - sensor, raw, cooked */
+	double **straylight;		/* [][] Stray light convolution matrix (size ??) */
+
+	/* raw index to wavelength polynomial */
+	unsigned int nwlcal;		/* Number in array */
+	double *wlcal;				/* Array of wavelenght cal polinomial factors. */
+
+	/* raw index to wavelength re-sampling filters */
+	int *findex;				/* [nwav] raw starting index for each out wavelength */
+	int *fnocoef; 				/* [nwav] Number of matrix cooeficients for each out wavelength */
+	double *fcoef;				/* [nwav * nocoef] Packed cooeficients to compute each wavelength */
+
+	unsigned int nlin;			/* Number in array */
+	double *lin;				/* Array of linearisation polinomial factors. */
+	int lindiv;					/* nz if polinomial result should be divided */
+
+	/* Black calibration */
+	rspec *idark[2];			/* Adaptive dark cal for two integration times */
+
+	/* Emission calibration */
+	rspec_type ecaltype;		/* Emissioni calibration type - sensor, raw, cooked */
+	double *ecal;				/* Emission calibration values */
+
+}; typedef struct _rspec_inf rspec_inf;
+
+/* - - - - - - - - - - - - - */
+
+/* Completely clear an rspec_inf. */
+void clear_rspec_inf(rspec_inf *inf);
+
+/* Completely free contesnt of rspec_inf. */
+void free_rspec_inf(rspec_inf *inf);
+
+/* return the number of samples for the given spectral type */
+int rspec_typesize(rspec_inf *inf, rspec_type ty);
+
+/* Compute the valid raw range from the calibration information */
+void rspec_comp_raw_range_from_ecal(rspec_inf *inf);
+
+/* Convert a raw index to nm */
+double rspec_raw2nm(rspec_inf *inf, double rix);
+
+/* Convert a cooked index to nm */
+double rspec_wav2nm(rspec_inf *inf, double ix);
+
+/* Create the wavelength resampling filters */
+void rspec_make_resample_filters(rspec_inf *inf);
+
+
+/* Plot the first rspec */
+void plot_rspec1(rspec *p);
+
+/* Plot the first rspec of 2 */
+void plot_rspec2(rspec *p1, rspec *p2);
+
+/* Plot the wave resampling filters */
+void plot_resample_filters(rspec_inf *inf);
+
+/* Plot the calibration curves */
+void plot_ecal(rspec_inf *inf);
+
+/* - - - - - - - - - - - - - */
+
+/* Create a new rspec from scratch */
+/* This always succeeds (i.e. application bombs if malloc fails) */
+rspec *new_rspec(rspec_inf *inf, rspec_type ty, int nmeas);
+
+/* Create a new rspec based on an existing prototype */ 
+/* If nmes == 0, create space for the same number or measurements */
+rspec *new_rspec_proto(rspec *rs, int nmeas);
+
+/* Create a new rspec by cloning an existing one */
+rspec *new_rspec_clone(rspec *rs);
+
+/* Free a rspec */
+void del_rspec(rspec *rs);
+
+/* - - - - - - - - - - - - - */
+/* Return the largest value */
+double largest_val_rspec(int *pmix, int *psix, rspec *raw);
+
+/* return a raw rspec from a sensor rspec */
+rspec *extract_raw_from_sensor_rspec(rspec *sens);
+
+/* Return an interpolated dark reference value from idark */
+double ex1_interp_idark_val(rspec_inf *inf, int mix, int six, double inttime);
+
+/* Return an interpolated dark reference from idark */
+rspec *ex1_interp_idark(rspec_inf *inf, double inttime);
+
+/* Subtract the adaptive black */
+void subtract_idark_rspec(rspec *raw);
+
+/* Apply non-linearity to a single value */
+double linearize_val_rspec(rspec_inf *inf, double ival);
+
+/* Invert non-linearity of a single value */
+double inv_linearize_val_rspec(rspec_inf *inf, double targv);
+
+/* Correct non-linearity */
+void linearize_rspec(rspec *raw);
+
+/* Apply the emsissive calibration */
+void emis_calibrate_rspec(rspec *sens);
+
+/* Scale to the integration time */
+void inttime_calibrate_rspec(rspec *sens);
+
+/* return a wav rspec from a raw rspec */
+rspec *convert_wav_from_raw_rspec(rspec *sens);
+
+
+/* - - - - - - - - - - - - - */
+/* Calibration file support */
+
+typedef struct {
+	a1log *log;
+	int lo_secs;			/* Seconds since last opened (from file mod time) */ 
+	FILE *fp;
+	int rd;					/* 0 = dummy read, 1 = real read */
+	int ef;					/* Error flag, 1 = write failed, 2 = close failed */
+	unsigned int chsum;		/* Checksum */
+	int nbytes;				/* Number of bytes checksummed */
+
+	char *buf;				/* Dummy read buffer */
+	size_t bufsz;			/* Size of dumy read buffer */
+} calf;
+
+int calf_open(calf *x, a1log *log, char *fname, int wr);
+void calf_rewind(calf *x);
+int calf_touch(a1log *log, char *fname);
+int calf_done(calf *x);
+
+void calf_wints(calf *x, int *dp, int n);
+void calf_wdoubles(calf *x, double *dp, int n);
+void calf_wtime_ts(calf *x, time_t *dp, int n);
+void calf_wstrz(calf *x, char *dp);
+
+void calf_rints(calf *x, int *dp, int n);
+void calf_rints2(calf *x, int *dp, int n);
+void calf_rdoubles(calf *x, double *dp, int n);
+void calf_rtime_ts(calf *x, time_t *dp, int n);
+void calf_rstrz(calf *x, char **dp);
+void calf_rstrz2(calf *x, char **dp);
+
+/* Save a rspec to a calibration file */
+void calf_wrspec(calf *x, rspec *dp);
+
+/* Restore a rspec from a calibration file */
+void calf_rrspec(calf *x, rspec **dp, rspec_inf *inf);
+
+#ifdef __cplusplus
+	}
+#endif
+
+#define RSPEC_H
+#endif /* RSPEC_H */