/* test program to output a CBF header from a template */ /* gcc -g -Wall -o cbf_template_t cbf_template_t.c */ /* ** ** GPL license declared below. ** ** Copyright (C) 2010 E. F. Eikenberry, DECTRIS, AG ** All rights reserved. ** ** 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 2 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, write to the Free Software ** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA. ** ** EF Eikenberry, Jun, 2010 ** DECTRIS, Ltd. Neuenhoferstrasse 107, CH-5400 Baden, Switzerland. */ #define MX_PARAMS_MAIN /* turn on space allocations in mx_parms.h */ #include #include #include #include #include #include #include #include "mx_parms.h" #include "mx_cbf_t_extras.h" /* ** dummy functions */ int set_current_energy(double a, int b, int c, char *d) { return 0; } double dcb_get_exposure_period(void) { return 0.100; } /*****************************************************************************\ ** ** ** Global variables ** ** ** \*****************************************************************************/ #define TEXT_SIZE 30 static float mx_beam_x=(float)IMAGE_NCOL/2.0; static int mx_beam_x_defined=0; static float mx_beam_y=(float)IMAGE_NROW/2.0; static int mx_beam_y_defined=0; static int mx_n_oscilations=1; static int mx_n_oscilations_defined=0; static float mx_wavelength=1.54; static int mx_wavelength_defined=0; static float mx_det_distance=1.0; static int mx_det_distance_defined=0; static float mx_det_voffset=0.0; static int mx_det_voffset_defined=0; static float mx_start_angle=0.0; static int mx_start_angle_defined=0; static float mx_angle_increment=0.1; static int mx_angle_increment_defined=0; static float mx_det_2theta=0.0; static int mx_det_2theta_defined=0; static float mx_polarization=0.99; static int mx_polarization_defined=0; static float mx_alpha=0.0; static int mx_alpha_defined=0; static float mx_kappa=0.0; static int mx_kappa_defined=0; static float mx_phi=0.0; static int mx_phi_defined=0; static float mx_phi_increment=0.0; static int mx_phi_increment_defined=0; static float mx_chi=0.0; static int mx_chi_defined=0; static float mx_chi_increment=0.0; static int mx_chi_increment_defined=0; static float mx_flux=0.0; static int mx_flux_defined=0; static float mx_filter_tx=1.0; static int mx_filter_tx_defined=0; static float mx_e_range_low=0.0; static int mx_e_range_low_defined=0; static float mx_e_range_hi=0.0; static int mx_e_range_hi_defined=0; static char mx_oscillation_axis[TEXT_SIZE]="X, CW"; static int mx_oscillation_axis_defined=0; static float mx_start_position=0.0; static int mx_start_position_defined=0; static float mx_position_increment=0.0; static int mx_position_increment_defined=0; static float mx_shutter_time=0.0; static int mx_shutter_time_defined=0; static char cbf_template_file[LENFN]="\0"; static int cbf_template_file_defined=0; static char msg[80]; /*****************************************************************************\ ** ** ** End of global variables ** ** ** \*****************************************************************************/ /* ----- Functions defined in this module ---- */ static MX_PARAMS_CMND find_mx_param_command(char **); static MX_PARAMS_CMND find_mx_param_command(char **pP) { int i, j, n, idx=0; char *p=*pP; msg[0]='\0'; while(*p && (isspace(*p) || *p==';' || *p==',')) /* space to next command */ p++; if (*p == '\0') /* end of line? */ return 0; for (n=0; *(p+n); n++) /* count characters in command */ if (!isalnum(*(p+n)) && *(p+n)!='_') /* allows '_' */ break; j = 0; /* count matching names */ for (i = 0; i < mx_params_count; i++) if ( strncasecmp(p, mx_params_list[i].name, n) == 0 ) { idx = i; /* permit unambiguous abbreviations */ j++; if ( n == strlen(mx_params_list[i].name) ) { j = 1; /* to skip next block */ break; /* exact match is exempt from ambiguity check */ } } if (j != 1) { for (i=0; *(p+i) && !isspace(*(p+i)); i++) ; *(p+i) = '\0'; /* isolate command */ if (j == 0) sprintf(msg, "Command not found: %s", p); else sprintf(msg, "Command '%s' is ambiguous", p); return 0; } *pP += n; /* skip over command name */ return mx_params_list[idx].cmnd; } /*****************************************************************************\ ** ** ** CBF header from template ** ** ** \*****************************************************************************/ /* Note that CBF_TXT_HEADER_SIZE must fit within CBF_HEADER_SIZE in cbftvx.c */ #define CBF_TXT_HEADER_SIZE 8000 #define MAX_NODES 30 static char cbf_template[CBF_TXT_HEADER_SIZE]; static int cbf_header_initialized=0; struct CBF_NODE { MX_PARAMS_CMND cmnd; char *subP; char *strP; struct CBF_NODE *next; struct CBF_NODE *prev; } ; static struct CBF_NODE nodes[MAX_NODES]; int setup_cbf_template(char *msg) { int i, len, m, nidx=0, count; FILE *ifp; char line[120], *p, *q, *sub=NULL, substr[30], *txt=NULL, *ptxt=NULL; MX_PARAMS_CMND cmnd; struct CBF_NODE *tnode, *rnode; cbf_header_initialized=0; if (!cbf_template_file[0]) /* no template given - no error */ return 0; if ( !(ifp=fopen(cbf_template_file, "r")) ) { sprintf(msg, "Could not open template file for reading:\n %s", cbf_template_file); printf("%s\n", msg); return -1; } /* read and edit the template ensure that lines end in CRLF (a CBF standard) */ cbf_template[0]='\0'; m=0; while( (fgets(line, sizeof(line), ifp)) ) { /* if we find a mini-header, discard it */ if(strstr(line, "--CIF-BINARY-FORMAT-SECTION--")) break; len = strlen(line); if (len > -4+sizeof(line)) { fclose(ifp); strcpy(msg, "Line too long in CBF template"); printf("%s\n", msg); return -1; } p = line+strlen(line); while (p>=line && (*p=='\n' || *p=='\r' || *p=='\0')) /* cut off ending */ p--; strcpy(p+1, "\r\n"); /* CRLF is the correct line ending for CBF */ p = line; while(!ptxt && (*p==' ' || *p=='\t')) /* in case of leading space */ p++; q = cbf_template+m; /* memorize position */ m+=sprintf(cbf_template+m, "%s", p); /* put line in buffer */ if (txt) /* start of text has been found */ continue; if (ptxt && line[0]=='_') txt = q; /* confirmed start of text */ if (!sub && *q=='@') sub = q; /* position of first substitution */ if (*q=='@' || *q=='#') continue; if (strstr(q, "--- End of preamble")) txt = cbf_template+m; /* start of next line */ if (!txt) ptxt = q; /* possible start of text - probably CRLF */ } fclose(ifp); if (!txt) { sprintf(msg, "*** Error in template file format - text not found\n"); printf("%s\n", msg); return -1; } /* the ending is critical for CBF library parsing "\r\n;\r\n;\r\n" is required; we add an extra blank line */ while(isspace(*(cbf_template+m)) || *(cbf_template+m)=='\0') m--; m++; m+=sprintf(cbf_template+m, "\r\n;\r\n;\r\n\r\n"); /* ** (1) Identify each defined program parameter in turn (e.g., 'Timestamp') ** (2) Pick up the associated substitution key (e.g., '_timestamp_') ** (3) Search through the text for 1 or more instances of the key ** (4) Make up a 'node' for each instance giving the key type and the ** position of the instance in the text ** (5) Insert the node in the doubly-linked list such that traversing the ** linked-list enumerates the nodes in the order they occur in the text. ** The nodes are in arbitrary order in the array of nodes; only the ** link pointers keep track of the order. ** (6) After all instances are found, terminate each text segment ('\0') ** ** The final arrangement is an initial text segment, followed by the ** array of nodes (instances). Each instance contains a variable value ** to be printed, followed by a text segment. */ memset(nodes, 0, sizeof(nodes)); /* doubly linked list */ nodes[0].subP=nodes[0].strP=txt; /* start of text */ /* parse the substitutions */ while (sub && *sub=='@') { q=sub+1; while(isspace(*q)) q++; cmnd = find_mx_param_command(&q); if (!cmnd) { sprintf(msg, "*** Error - unrecognized variable name (%s)", q); printf("%s\n", msg); return -1; } while(isspace(*q)) q++; p = substr; while(!isspace(*q) && *q!='\r' && *q!='\n' && *q!='\0') *p++ = *q++; *p = '\0'; /* substr == string to search for */ while(isspace(*q) && *q!='\r') q++; if(isalnum(*q) || *q=='-') { switch (cmnd) /* store initial value(s) */ { case Energy_range: mx_e_range_low = atof(q); while(*q && (isdigit(*q) || *q=='-' || *q=='.')) /* skip number */ q++; while(*q && (isspace(*q) || *q==',')) /* skip to next number */ q++; if (*q == '\0') /* end of line? */ return 0; mx_e_range_hi = atof(q); mx_e_range_low_defined=1; mx_e_range_hi_defined=1; break; case Detector_distance: mx_det_distance = atof(q); mx_det_distance_defined=1; break; case Detector_Voffset: mx_det_voffset = atof(q); mx_det_voffset_defined=1; break; case Beam_xy: mx_beam_x = atof(q); while(*q && (isdigit(*q) || *q=='-' || *q=='.')) /* skip number */ q++; while(*q && (isspace(*q) || *q==',')) /* skip to next number */ q++; if (*q == '\0') /* end of line? */ break; mx_beam_y = atof(q); mx_beam_x_defined=1; mx_beam_y_defined=1; break; case Beam_x: mx_beam_x = atof(q); mx_beam_x_defined=1; break; case Beam_y: mx_beam_y = atof(q); mx_beam_y_defined=1; break; case Flux: mx_flux = atof(q); mx_flux_defined=1; break; case Filter_transmission: mx_filter_tx = atof(q); mx_filter_tx_defined=1; break; case Start_angle: mx_start_angle = atof(q); mx_start_angle_defined=1; break; case Angle_increment: mx_angle_increment = atof(q); mx_angle_increment_defined=1; mx_start_angle_defined=1; /* defaults to 0 */ break; case Detector_2theta: mx_det_2theta = atof(q); mx_det_2theta_defined=1; break; case Polarization: mx_polarization = atof(q); mx_polarization_defined=1; break; case Alpha: mx_alpha = atof(p); mx_alpha_defined=1; break; case Kappa: mx_kappa = atof(q); mx_kappa_defined=1; break; case Phi: mx_phi = atof(q); mx_phi_defined=1; break; case Phi_increment: mx_phi_increment = atof(q); mx_phi_increment_defined=1; mx_phi_defined=1; /* defaults to 0 */ break; case Chi: mx_chi = atof(q); mx_chi_defined=1; break; case Chi_increment: mx_chi_increment = atof(q); mx_chi_increment_defined=1; mx_chi_defined=1; /* defaults to 0 */ break; case Oscillation_axis: memset(mx_oscillation_axis, 0, TEXT_SIZE); strncat(mx_oscillation_axis, q, TEXT_SIZE-2); for (i=0; mx_oscillation_axis[i] && isubPnext; } if (nidx >= -1+MAX_NODES) { strcpy(msg, "Too many substitution nodes in CBF template"); printf("%s\n", line); return -1; } nidx++; /* allocate a new node */ nodes[nidx].cmnd = cmnd; /* name of variable */ nodes[nidx].subP = p; /* pointer to substitution string */ nodes[nidx].strP = p+strlen(substr); /* start of next string */ nodes[nidx].next = rnode->next; /* insert new node in chain */ nodes[nidx].prev = rnode; if (rnode->next) rnode->next->prev = &nodes[nidx]; rnode->next = &nodes[nidx]; q = p+strlen(substr); } if ( !count ) { sprintf(msg, "*** Error: key string ( %s ) not found", substr); printf("%s\n", msg); return -1; } #if 0 /* print the doubly linked list */ {char t1[20], t2[20]; for(i=0; i<=nidx; i++) { strcpy(t1, " "); if (nodes[i].subP) strncpy(t1, nodes[i].subP, 20); t1[19]='\0'; while((q=strchr(t1,'\n')))*q='.'; while((q=strchr(t1,'\r')))*q='.'; strcpy(t2, " "); if (nodes[i].strP) strncpy(t2, nodes[i].strP, 20); t2[19]='\0'; while((q=strchr(t2,'\n')))*q='.'; while((q=strchr(t2,'\r')))*q='.'; printf("%2d %p %2d %20s %20s %p %p\n", i, &nodes[i], (int)nodes[i].cmnd, t1, t2, nodes[i].next, nodes[i].prev); } strncpy(t1, p, 20); t1[19]='\0'; while((q=strchr(t1,'\n')))*q='.'; while((q=strchr(t1,'\r')))*q='.'; printf(" p = %p, text = %s\n", p, t1); printf("\n"); } #endif sub = 1+strchr(sub, '\n'); /* next line */ } /* terminate the internal strings */ tnode = nodes[0].next; while(tnode) { *(tnode->subP) = '\0'; tnode = tnode->next; } cbf_header_initialized=1; return 0; } /* print the CBF header from the template into the buffer provided returns size */ int print_cbf_header(char *dest, int size, char *conv) { struct CBF_NODE *tnode=&nodes[0]; int m=0; if (!cbf_header_initialized) return 0; m += sprintf(dest+m, "%s", tnode->strP); tnode = tnode->next; while(tnode && mcmnd) { case Wavelength: if(mx_wavelength_defined) m += sprintf(dest+m, "%.2f", mx_wavelength); else m += sprintf(dest+m, ""); break; case Energy_range: if(mx_e_range_low_defined && mx_e_range_hi_defined) m += sprintf(dest+m, "%.0f %.0f", mx_e_range_low, mx_e_range_hi); else m += sprintf(dest+m, ""); break; case Detector_distance: if(mx_det_distance_defined) m += sprintf(dest+m, "%.3f", mx_det_distance); else m += sprintf(dest+m, ""); break; case Detector_Voffset: if(mx_det_voffset_defined) m += sprintf(dest+m, "%.3f", mx_det_voffset); else m += sprintf(dest+m, ""); break; case Beam_xy: if(mx_beam_x_defined && mx_beam_y_defined) m += sprintf(dest+m, "%.2f %.2f", mx_beam_x, mx_beam_y); else m += sprintf(dest+m, ""); break; case Beam_x: if(mx_beam_x_defined) m += sprintf(dest+m, "%.2f", mx_beam_x); else m += sprintf(dest+m, ""); break; case Beam_y: if(mx_beam_y_defined) m += sprintf(dest+m, "%.2f", mx_beam_y); else m += sprintf(dest+m, ""); break; case Flux: if(mx_flux_defined) m += sprintf(dest+m, "%g", mx_flux); else m += sprintf(dest+m, ""); break; case Filter_transmission: if(mx_filter_tx_defined) m += sprintf(dest+m, "%.4f", mx_filter_tx); else m += sprintf(dest+m, ""); break; case Start_angle: if(mx_start_angle_defined) m += sprintf(dest+m, "%.4f", mx_start_angle); else m += sprintf(dest+m, ""); break; case Angle_increment: if(mx_angle_increment_defined) m += sprintf(dest+m, "%.4f", mx_angle_increment); else m += sprintf(dest+m, ""); break; case Detector_2theta: if(mx_det_2theta_defined) m += sprintf(dest+m, "%.4f", mx_det_2theta); else m += sprintf(dest+m, ""); break; case Polarization: if(mx_polarization_defined) m += sprintf(dest+m, "%.3f", mx_polarization); else m += sprintf(dest+m, ""); break; case Alpha: if(mx_alpha_defined) m += sprintf(dest+m, "%.4f", mx_alpha); else m += sprintf(dest+m, ""); break; case Kappa: if(mx_kappa_defined) m += sprintf(dest+m, "%.4f", mx_kappa); else m += sprintf(dest+m, ""); break; case Phi: if(mx_phi_defined) m += sprintf(dest+m, "%.4f", mx_phi); else m += sprintf(dest+m, ""); break; case Phi_increment: if(mx_phi_increment_defined) m += sprintf(dest+m, "%.4f", mx_phi_increment); else m += sprintf(dest+m, ""); break; case Chi: if(mx_chi_defined) m += sprintf(dest+m, "%.4f", mx_chi); else m += sprintf(dest+m, ""); break; case Chi_increment: if(mx_chi_increment_defined) m += sprintf(dest+m, "%.4f", mx_chi_increment); else m += sprintf(dest+m, ""); break; case Oscillation_axis: if(mx_oscillation_axis_defined) m += sprintf(dest+m, "%s", mx_oscillation_axis); else m += sprintf(dest+m, ""); break; case N_oscillations: if(mx_n_oscilations_defined) m += sprintf(dest+m, "%d", mx_n_oscilations); else m += sprintf(dest+m, ""); break; case Start_position: if(mx_start_position_defined) m += sprintf(dest+m, "%.4f", mx_start_position); else m += sprintf(dest+m, ""); break; case Position_increment: if(mx_position_increment_defined) m += sprintf(dest+m, "%.4f", mx_position_increment); else m += sprintf(dest+m, ""); break; case Shutter_time: if(mx_shutter_time_defined) m += sprintf(dest+m, "%.7f", mx_shutter_time); else m += sprintf(dest+m, ""); break; case Timestamp: m += sprintf(dest+m, "%s", image_timestamp); break; case Exposure_period: m += sprintf(dest+m, "%.6f", dcb_get_exposure_period()); break; case Exposure_time: m += sprintf(dest+m, "%.6f", exposure_time); break; case Count_cutoff: m += sprintf(dest+m, "%u", count_cutoff); break; case Compression_type: if (strstr(conv, "x-")) conv+=2; m += sprintf(dest+m, "%s", conv); break; case X_dimension: m += sprintf(dest+m, "%d", camera_wide); break; case Y_dimension: m += sprintf(dest+m, "%d", camera_high); break; case CBF_template_file: default: break; } m += sprintf(dest+m, "%s", tnode->strP); tnode = tnode->next; } if (m >= -1+size-TEXT_SIZE) printf("Size exceeded - CBF header not completed\n"); return m; } /*************************************************\ ** ** ** main program for cbf test -or- demo ** ** ** \*************************************************/ int main (int argc, char *argv[]) { FILE *ofp; char msg[500]="\0"; char bufr[10000]; char line[80]; strcpy(cbf_template_file, "cbf_6M_template.cbf"); cbf_template_file_defined=1; setup_cbf_template(msg); if (msg[0]) { printf("%s\n", msg); return 0; } print_cbf_header(bufr, sizeof(bufr), "CBF_BYTE_OFFSET"); strcpy(line, "cbf_template_t.out"); if (!(ofp = fopen(line, "w+b"))) { printf("Could not open %s for writing\n", line); return 0; } /* The first part of a DECTRIS CBF header in an image file is a comment header containing detector settings and mx_settings (these are crystallography parameters supplied by the user that are also reproduced in the CBF syntax below) */ fprintf(ofp, "###CBF: VERSION 1.5, CBFlib v0.7.8 - SLS/DECTRIS PILATUS detectors\r\n" "\r\n" "data_test65\r\n" "\r\n" "_array_data.header_convention \"SLS/DECTRIS_1.1\"\r\n" "_array_data.header_contents\r\n" ";\r\n"); fprintf(ofp, "# Detector: PILATUS 100K, In-house (m141) Test System\r\n" "# 2010-Jun-16T19:09:48.271\r\n" "# Pixel_size 172e-6 m x 172e-6 m\r\n" "# Silicon sensor, thickness 0.000320 m\r\n" "# Exposure_time 1.0000000 s\r\n" "# Exposure_period 1.0000000 s\r\n" "# Tau = 0 s\r\n" "# Count_cutoff 1048574 counts\r\n" "# Threshold_setting 0 eV\r\n" "# Gain_setting not set (vrf = -0.200)\r\n" "# N_excluded_pixels = 0\r\n" "# Excluded_pixels: (nil)\r\n" "# Flat_field: (nil)\r\n" "# Trim_file: (nil)\r\n" "# Image_path: /home/det/p2_det/images/\r\n" ";\r\n" ); /* now the part made up from the template */ fprintf(ofp, "%s", bufr); /* now the mini-header and the data */ fprintf(ofp, "_array_data.data\r\n" ";\r\n" "--CIF-BINARY-FORMAT-SECTION--\r\n" "Content-Type: application/octet-stream;\r\n" " conversions=\"x-CBF_BYTE_OFFSET\"\r\n" "Content-Transfer-Encoding: BINARY\r\n" ); fprintf(ofp, "X-Binary-Size: 94981\r\n" "X-Binary-ID: 1\r\n" "X-Binary-Element-Type: \"signed 32-bit integer\"\r\n" "X-Binary-Element-Byte-Order: LITTLE_ENDIAN\r\n" "Content-MD5: VwGHOeEVHfClJWkB5v5Geg==\r\n" "X-Binary-Number-of-Elements: 94965\r\n" "X-Binary-Size-Fastest-Dimension: 487\r\n" "X-Binary-Size-Second-Dimension: 195\r\n" "X-Binary-Size-Padding: 4095\r\n" "\r\n" "--- data comes here ---\r\n" "--CIF-BINARY-FORMAT-SECTION----\r\n" ";\r\n" ); fclose(ofp); printf ("%s was written\n", line); return 0; }