add focussing

Auxiliary_utils/focussing/Makefile

@@ -0,0 +1,57 @@
+# run `make DEF=...` to add extra defines
+PROGRAM := bestfocus
+LDFLAGS := -fdata-sections -ffunction-sections -Wl,--gc-sections -Wl,--discard-all
+LDFLAGS += -lusefull_macros
+SRCS := $(wildcard *.c)
+DEFINES := $(DEF) -D_GNU_SOURCE -D_XOPEN_SOURCE=1111
+OBJDIR := mk
+CFLAGS += -O2 -Wall -Wextra -Wno-trampolines -std=gnu99
+OBJS := $(addprefix $(OBJDIR)/, $(SRCS:%.c=%.o))
+DEPS := $(OBJS:.o=.d)
+TARGFILE := $(OBJDIR)/TARGET
+CC = gcc
+#TARGET := RELEASE
+
+ifeq ($(shell test -e $(TARGFILE) && echo -n yes),yes)
+	TARGET := $(file < $(TARGFILE))
+else
+	TARGET := RELEASE
+endif
+
+ifeq ($(TARGET), DEBUG)
+	.DEFAULT_GOAL := debug
+endif
+
+release: $(PROGRAM)
+
+debug: CFLAGS += -DEBUG -Werror
+debug: TARGET := DEBUG
+debug: $(PROGRAM)
+
+$(TARGFILE): $(OBJDIR)
+	@echo -e "\t\tTARGET: $(TARGET)"
+	@echo "$(TARGET)" > $(TARGFILE)
+
+$(PROGRAM) : $(TARGFILE) $(OBJS)
+	@echo -e "\t\tLD $(PROGRAM)"
+	$(CC) $(OBJS) $(LDFLAGS) -o $(PROGRAM)
+
+$(OBJDIR):
+	@mkdir $(OBJDIR)
+
+ifneq ($(MAKECMDGOALS),clean)
+-include $(DEPS)
+endif
+
+$(OBJDIR)/%.o: %.c
+	@echo -e "\t\tCC $<"
+	$(CC) $< -MD -c $(LDFLAGS) $(CFLAGS) $(DEFINES) -o $@ 
+
+clean:
+	@echo -e "\t\tCLEAN"
+	@rm -rf $(OBJDIR) 2>/dev/null || true
+
+xclean: clean
+	@rm -f $(PROGRAM)
+
+.PHONY: clean xclean

Auxiliary_utils/focussing/Readme

@@ -0,0 +1,2 @@
+calculate best focus on plate by parabolic fit
+input: stdin or file with rows "F FWHM"

Auxiliary_utils/focussing/main.c

@@ -0,0 +1,191 @@
+/*
+ * Copyright 2024 Edward V. Emelianov <edward.emelianoff@gmail.com>.
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <math.h>
+#include <signal.h>
+#include <stdio.h>
+#include <strings.h>
+#include <usefull_macros.h>
+
+// minimal amount of elements
+#define MIN_ELEMENTS_AMOUNT (5)
+
+typedef struct{
+    int help;
+    double tolerance;  // max std of data from fit
+    char *input;       // input file
+} glob_pars;
+
+static glob_pars G = {.tolerance = 10.};
+
+static myoption cmdlnopts[] = {
+    // common options
+    {"help",    NO_ARGS,    NULL,   'h',    arg_none,   APTR(&G.help),      _("show this help")},
+    {"infile",  NEED_ARG,   NULL,   'i',    arg_string, APTR(&G.input),     _("input file name")},
+    {"tolerance",NEED_ARG,  NULL,   't',    arg_double, APTR(&G.tolerance), _("max STD of data from fit (default: 10.)")},
+    end_option
+};
+
+static double *x = NULL, *y = NULL;
+static int nelems = 0;
+static uint8_t *badmask = NULL;
+
+/**
+ * @brief parabolic_fit - fit y = a + bx + cx^2
+ * @param coeffs (o) - coefficients a,b,c
+ * @return n good elements
+ */
+static int parabolic_fit(double coeffs[3]){
+    if(nelems < MIN_ELEMENTS_AMOUNT || !x || !y) return 0;
+    double matrix[3][4];
+    double sum_x = 0., sum_y = 0., sum_x2 = 0., sum_x3 = 0., sum_x4 = 0., sum_xy = 0., sum_x2y = 0.;
+    int goodelems = 0;
+    for(int i = 0; i < nelems; ++i){
+        if(badmask[i]) continue;
+        ++goodelems;
+        double xx = x[i], yy = y[i], x2 = xx * xx, x3 = x2 * xx, x4 = x3 * xx;
+        sum_x += xx;
+        sum_y += yy;
+        sum_x2 += x2;
+        sum_x3 += x3;
+        sum_x4 += x4;
+        sum_xy += xx*yy;
+        sum_x2y += x2*yy;
+    }
+    printf("%d good from %d\n", goodelems, nelems);
+    if(goodelems < MIN_ELEMENTS_AMOUNT) return 0;
+    matrix[0][0] = goodelems;
+    matrix[0][1] = sum_x;
+    matrix[0][2] = sum_x2;
+    matrix[0][3] = sum_y;
+    matrix[1][0] = sum_x;
+    matrix[1][1] = sum_x2;
+    matrix[1][2] = sum_x3;
+    matrix[1][3] = sum_xy;
+    matrix[2][0] = sum_x2;
+    matrix[2][1] = sum_x3;
+    matrix[2][2] = sum_x4;
+    matrix[2][3] = sum_x2y;
+    for(int i = 0; i < 3; i++){
+        for(int j = 0; j < 3; j++){
+            if(i != j){
+                if(matrix[i][i] == 0.) return 0;
+                double r = matrix[j][i]/matrix[i][i];
+                for(int k = 0; k < 4; k++){
+                    matrix[j][k] -= r * matrix[i][k];
+                }
+            }
+        }
+    }
+    for(int i = 0; i < 3; i++){
+        double a = matrix[i][i];
+        if(a == 0.) return 0;
+        for(int j = 0; j < 4; j++){
+            matrix[i][j] /= a;
+        }
+    }
+    for(int i = 0; i < 3; i++){
+        printf("%c => %.4f\n", 97+i, matrix[i][3]);
+        coeffs[i] = matrix[i][3];
+    }
+    return goodelems;
+}
+
+/**
+ * @brief check - check points for tolerance & mark bad (t*2)
+ * @param coeffs - fit coefficients
+ * @return amount of points in tolerance*2 region
+ */
+static int check(double coeffs[3]){
+    int ngood = 0;
+    double a = coeffs[0], b = coeffs[1], c = coeffs[2];
+    double lim = 2*G.tolerance;
+    for(int i = 0; i < nelems; ++i){
+        if(badmask[i]) continue;
+        double yy = a + b*x[i] + c*x[i]*x[i];
+        double delta = fabs(y[i] - yy);
+        printf("delta[%d]=%g\n", i, delta);
+        if(delta > lim) badmask[i] = 1;
+        else ++ngood;
+    }
+    printf("found %d good elements\n", ngood);
+    return ngood;
+}
+
+static int readfile(FILE *f){
+    if(!f) return 0;
+    int n = 0;
+    while(1){
+        double xx, yy;
+        if(2 != fscanf(f, "%lg %lg\n", &xx, &yy)) break;
+        if(nelems >= n){
+            n += 256;
+            x = realloc(x, n * sizeof(double));
+            y = realloc(y, n * sizeof(double));
+            badmask = realloc(badmask, n);
+            if(!x || !y) ERR("realloc failed");
+        }
+        x[nelems] = xx; y[nelems] = yy;
+        ++nelems;
+    }
+    for(int i = 0; i < nelems; ++i){
+        printf("x[%d]=%g, y[%d]=%g\n", i, x[i], i, y[i]);
+    }
+    bzero(badmask, sizeof(int) * nelems);
+    return nelems;
+}
+
+/* calculate best focus by parabolic fit:
+ * y = a + bx + cx^2 -> 0 = b + 2cx -> x = -b/(2c)
+ */
+static double calcfocus(double coeffs[3]){
+    return -coeffs[1]/2./coeffs[2];
+}
+
+int main(int argc, char **argv){
+    char helpstring[256];
+    initial_setup();
+    snprintf(helpstring, 255, "Usage: `cat file | %%s` or with args; file format \"x y\\n..\"\n\tArgs:\n");
+    change_helpstring(helpstring);
+    parseargs(&argc, &argv, cmdlnopts);
+    if(G.help) showhelp(-1, cmdlnopts);
+    if(G.tolerance <= 0.) ERRX("Tolerance should be > 0");
+    FILE *f = stdin;
+    if(G.input){
+        f = fopen(G.input, "r");
+        DBG("open %s - %d\n", G.input, f ? 1 : 0);
+        if(!f) ERR("Can't open %s", G.input);
+    }
+    if(!readfile(f)) ERRX("Can't read data");
+    double coeffs[3];
+    int goodelems = 0, now = 0;
+    do{
+        goodelems = parabolic_fit(coeffs);
+        red("focnow: %g\n", calcfocus(coeffs));
+        if(!goodelems) ERRX("Can't fit");
+        now = check(coeffs);
+        if(MIN_ELEMENTS_AMOUNT > now) ERRX("All elements are too wrong");
+    }while(now != goodelems);
+    green("focus = %.2f\n", calcfocus(coeffs));
+    return 0;
+#if 0
+
+    for(i = 0; i < 3; i++){
+        printf("\n%c => %.2f", 97+i, matrix[i][3]);
+    }
+#endif
+}