/**********************************************************************
 *     nexus2cbf.c by J. Sloan of Diamond Light Source                *
 *                                                                    *
 * CBFlib Version 0.9.3 30 May 2013                                   *
 *                                                                    *
 *                          Paul Ellis and                            *
 *         Herbert J. Bernstein (yaya@bernstein-plus-sons.com)        *
 *                                                                    *
 * (C) Copyright 2013 Herbert J. Bernstein                            *
 *                                                                    *
 **********************************************************************
 *                                                                    *
 * YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE GPL *
 *                                                                    *
 * ALTERNATIVELY YOU MAY REDISTRIBUTE THE CBFLIB API UNDER THE TERMS  *
 * OF THE LGPL                                                        *
 *                                                                    *
 **********************************************************************
 *                                                                    *
 * 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.               *
 *                                                                    *
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 *                                                                    *
 *                    Stanford University Notices                     *
 *  for the CBFlib software package that incorporates SLAC software   *
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 *                           The IUCr Policy                          *
 *      for the Protection and the Promotion of the STAR File and     *
 *     CIF Standards for Exchanging and Archiving Electronic Data     *
 *                                                                    *
 * Overview                                                           *
 *                                                                    *
 * The Crystallographic Information File (CIF)[1] is a standard for   *
 * information interchange promulgated by the International Union of  *
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 * and many other journals. The syntax of a CIF is a subset of the    *
 * more general STAR File[2] format. The CIF and STAR File approaches *
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 *                                                                    *
 * Statement of intent                                                *
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 * The IUCr's interest in the STAR File is as a general data          *
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 * syntax, respectively.                                              *
 *                                                                    *
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 * the CIF, standard must produce files that are conformant to the    *
 * STAR File syntax, or the CIF syntax, respectively.                 *
 *                                                                    *
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 * dictionary approved by the IUCr must be able to extract any        *
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 * definition language (DDL)[3] associated with that dictionary.      *
 *                                                                    *
 * The IUCr, through its Committee on CIF Standards, will assist      *
 * any developer to verify that software meets these conformance      *
 * conditions.                                                        *
 *                                                                    *
 * Glossary of terms                                                  *
 *                                                                    *
 * [1] CIF:  is a data file conformant to the file syntax defined     *
 * at http://www.iucr.org/iucr-top/cif/spec/index.html                *
 *                                                                    *
 * [2] STAR File:  is a data file conformant to the file syntax       *
 * defined at http://www.iucr.org/iucr-top/cif/spec/star/index.html   *
 *                                                                    *
 * [3] DDL:  is a language used in a data dictionary to define data   *
 * items in terms of "attributes". Dictionaries currently approved    *
 * by the IUCr, and the DDL versions used to construct these          *
 * dictionaries, are listed at                                        *
 * http://www.iucr.org/iucr-top/cif/spec/ddl/index.html               *
 *                                                                    *
 * Last modified: 30 September 2000                                   *
 *                                                                    *
 * IUCr Policy Copyright (C) 2000 International Union of              *
 * Crystallography                                                    *
 **********************************************************************/

#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include <time.h>
#include <errno.h>
#include <unistd.h>
#include <stdint.h>

#include "cbf.h"
#include "cbf_simple.h"
#include "img.h"
#include "cbf_string.h"
#include "cbf_copy.h"
#include "cbf_hdf5.h"
#include "cbf_getopt.h"

#ifndef UINT64_MAX
#define NO_UINT64_TYPE
#endif

#define C2CBUFSIZ 8192

#ifdef __MINGW32__
#define NOMKSTEMP
#define NOTMPDIR
#endif


int main (int argc, char *argv [])
{
	int error = CBF_SUCCESS;
    cbf_getopt_handle opts = NULL;
	int h5_write_flags = 0;
	int list = 0;
    int noCBFnames = 0;
	unsigned int frame = 0;
	const char * cifout = NULL;
	const char * hdf5in = NULL;
	const char * group = NULL;

	/* Attempt to read the arguments */
	if (CBF_SUCCESS != (error |= cbf_make_getopt_handle(&opts))) {
		fprintf(stderr,"Could not create a 'cbf_getopt' handle.\n");
	} else if (CBF_SUCCESS != (error |= cbf_getopt_parse(opts, argc, argv, "c(compression):g(group):o(output):Z(register):f(frame):\1(list)\2(no-list)\3(CBFnames)\4(noCBFnames)" ))) {
		fprintf(stderr,"Could not parse arguments.\n");
	} else {
    	int errflg = 0;
		/* successful so far, try to make sense of the options */
		if (!cbf_rewind_getopt_option(opts)) {
			int c = 0;
			const char * optarg = NULL;
			for(; !cbf_get_getopt_data(opts,&c,NULL,NULL,&optarg); cbf_next_getopt_option(opts)) {
				switch (c) {
					case 'f': { /* the index of the frame to be converted */
						if (!optarg) {
							++errflg;
						} else {
							char * end = NULL;
							const unsigned int _frame = strtoul(optarg,&end,0);
							if (end==optarg) {
								fprintf(stderr,"error: Expected a number for the frame index, got '%s'.\n",optarg);
								++errflg;
							} else {
								frame = _frame;
							}
						}
                        break;
					}
					case 'g': { /* group within input file where data should be found */
						if (group) ++errflg;
						else group = optarg;
						break;
					}
					case 'o': { /* output file */
						if (cifout) ++errflg;
						else cifout = optarg;
						break;
					}
					case 'Z': { /* automatic or manual filter registration? */
						if (cbf_cistrcmp(optarg?optarg:"","manual") == 0) {
							h5_write_flags |= CBF_H5_REGISTER_COMPRESSIONS;
						} else if (cbf_cistrcmp(optarg?optarg:"","plugin") == 0) {
							h5_write_flags &= ~CBF_H5_REGISTER_COMPRESSIONS;
						} else {
							++errflg;
						}
						break;
					}
					case 0: { /* input file */
						if (hdf5in) ++errflg;
						else hdf5in = optarg;
						break;
					}
					case '\1': {
						if (list) ++errflg;
						list = 1;
						break;
					}
					case '\2': {
						if (list) ++errflg;
						list = -1;
						break;
					}
					case '\3': {
						if (noCBFnames) ++errflg;
						noCBFnames = -1;
						break;
					}
					case '\4': {
						if (noCBFnames) ++errflg;
						noCBFnames = 1;
						break;
					}
					default: {
						++errflg;
						break;
					}
				}
			}
		}

		/* check for missing data */
		if (!cifout) {
			fprintf(stderr,"No output files given.\n");
			++errflg;
		}
		if (!hdf5in) {
			fprintf(stderr,"No input file given.\n");
			++errflg;
		}
		if (errflg) {
			fprintf(stderr, "Usage:\n\t%s [options] -o|--output output_cbf input_nexus\n"
					"Options:\n"
							"\t-g|--group output_group (default: 'entry')\n"
							"\t-Z|--register manual|plugin (default: plugin)\n"
							"\t-f|--frame <unsigned int> (default: 0)\n",
					argv[0]);
			error |= CBF_ARGUMENT;
		}
	}

	/* If I could read the arguments then attempt to use them */
	if (CBF_SUCCESS == error) {
		cbf_h5handle h5in = NULL;
		cbf_handle cif = NULL;

		/* prepare the input file */
		{
			hid_t hdf_file = CBF_H5FAIL, fapl = CBF_H5FAIL;
			if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
				fprintf(stderr,"Couldn't create file access property list.\n");
				error |= CBF_H5ERROR;
			} else if ((H5Pset_fclose_degree(fapl,H5F_CLOSE_STRONG)) < 0) {
				fprintf(stderr,"Couldn't set a file access property.\n");
				error |= CBF_H5ERROR;
			} else if ((hdf_file = H5Fopen(hdf5in,H5F_ACC_RDONLY,fapl)) < 0) {
				fprintf(stderr,"Couldn't open a HDF5 file.\n");
				error |= CBF_H5ERROR;
			} else if(CBF_SUCCESS != (error |= cbf_create_h5handle3(&h5in,hdf_file))) {
				fprintf(stderr,"Couldn't open the HDF5 file '%s'.\n", hdf5in);
			} else if (CBF_SUCCESS != (error |= cbf_h5handle_require_entry(h5in,0,group))) {
				fprintf(stderr,"Couldn't create an NXentry group in the HDF5 file '%s'.\n", hdf5in);
			} else {
				h5in->flags = h5_write_flags;
				h5in->slice = frame;
#ifdef CBF_USE_ULP
				// set up some parameters for comparing floating point numbers
				h5in->cmp_double_as_float = 0;
				h5in->float_ulp = 4;
#ifndef NO_UINT64_TYPE
				h5in->double_ulp = 4;
#endif
#endif
			}
			H5Pclose(fapl);
		}

		/* make the handle for the output file */
		if (CBF_SUCCESS != (error |= cbf_make_handle(&cif))) {
			fprintf(stderr,"Failed to create handle for input_cif\n");
			error |= CBF_ALLOC;
		}

		/* Time the conversion */
		if (CBF_SUCCESS == error) {
			clock_t a = clock(), b;
			h5in->slice = 0;
            if (list > 0) h5in->logfile = stdout;
            if (noCBFnames >= 0) h5in->flags |= CBF_H5_CBFNONAMES;
			error |= cbf_write_nx2cbf(h5in, cif);
			b = clock();
			printf("Time to convert '%s': %.3fs\n", cifout, ((float)(b - a))/CLOCKS_PER_SEC);
		} else {
			fprintf(stderr,"An error occured, will not try to convert the file '%s'\n",hdf5in);
		}

		/* Write the file */
		if (CBF_SUCCESS == error) {
			/* start timing */
			clock_t a = clock(), b;
			FILE * const out = fopen(cifout,"wb");
			if (NULL == out) {
				fprintf(stderr,"Couldn't open the output CIF file '%s': %s\n", cifout, strerror(errno));
				error |= CBF_FILEOPEN;
			} else if (CBF_SUCCESS != (error |= cbf_write_file(cif,out,0,CBF,0,0))) {
				fprintf(stderr,"Couldn't write the output CIF file '%s': %s\n", cifout, cbf_strerror(error));
				error |= CBF_FILEWRITE;
			}
			if (NULL!=out) fclose(out);
			/* stop timing */
			b = clock();
			printf("Time to write '%s': %.3fs\n", cifout, ((float)(b - a))/CLOCKS_PER_SEC);
		} else {
			fprintf(stderr,"An error occured, will not try to write the file '%s'\n",cifout);
		}

		/* Clean up */
		if (cif) cbf_free_handle(cif);
		if (h5in) cbf_free_h5handle(h5in);

	}

	/*******************************************************************************************************************/

	/* Cleanup */
	error |= cbf_free_getopt_handle(opts);
	return CBF_SUCCESS==error ? 0 : 1;
}
