source: anuga_core/source/anuga/shallow_water/urs_ext.c @ 5531

/*
gcc -fPIC -c urs_ext.c -I/usr/include/python2.5 -o urs_ext.o -Wall -O
gcc -shared urs_ext.o  -o urs_ext.so
*/

/*
This file was reverted from changeset:5484 to changeset:5470 on 10th July 
by Ole.
*/

#include "Python.h"
#include "Numeric/arrayobject.h"
#include "structure.h"
#include "math.h"
#include <stdio.h>
#include <float.h>
#include <time.h>

#define MAX_FILE_NAME_LENGTH 128
#define NODATA 99.0
#define EPSILON  0.00001

#define DEBUG 0

#define POFFSET 5 //Number of site_params

void fillDataArray(int, int, int, int, int *, int *, float *, int *, int *, float *);
long getNumData(const int *fros, const int *lros, const int nsta);
char isdata(float);
float** _read_mux2(int numSrc, char **muxFileNameArray, float *weights, double *params, int verbose);

PyObject *read_mux2(PyObject *self, PyObject *args){
    /*Read in mux 2 file

    Python call:
    read_mux2(numSrc,filenames,weights,file_params,verbose)

    NOTE:
    A Python int is equivalent to a C long
    A Python double corresponds to a C double
    */
    PyObject *filenames;
    PyArrayObject *pyweights;
    PyArrayObject *file_params;
    PyArrayObject *pydata;
    PyObject *fname;

    char **muxFileNameArray;
    float **cdata;
    float *weights;
    int dimensions[2];
    int numSrc;
    int verbose;
    int nsta0;
    int nt;
    double dt;
    int i;
    int j;
    int start_tstep;
    int finish_tstep;
    int it;
    int time;
    int num_ts;
    
    //printf("Checkpoint 1 for urs2sts_ext.c\n");

    // Convert Python arguments to C
    if (!PyArg_ParseTuple(args, "iOOOi",
        &numSrc, &filenames, &pyweights, &file_params, &verbose)) 
    {
            PyErr_SetString(PyExc_RuntimeError, 
                "Input arguments to read_mux2 failed");
            return NULL;
    }

    if(!PyList_Check(filenames)) 
    {
        PyErr_SetString(PyExc_TypeError, "get_first_elem expects a list");
        return NULL;
    }

    if(PyList_Size(filenames) == 0)
    {
        PyErr_SetString(PyExc_ValueError, "empty lists not allowed");
        return NULL;
    }

    if (pyweights->nd != 1 || pyweights->descr->type_num != PyArray_DOUBLE) 
    {
        PyErr_SetString(PyExc_ValueError,
            "pyweights must be one-dimensional and of type double");
        return NULL; 
    }

    if(PyList_Size(filenames) != pyweights->dimensions[0])
    {
        PyErr_SetString(PyExc_ValueError, "Must specify one weight for each filename");
        return NULL;
    }

    muxFileNameArray = (char**)malloc(numSrc*sizeof(char*));
    if (muxFileNameArray == NULL) 
    {
        printf("ERROR: Memory for muxFileNameArray could not be allocated.\n");
        return NULL;
    }

    //printf("Checkpoint 2 for urs2sts_ext.c\n");    
    //printf("numSrc = %d\n", numSrc);
    for (i = 0; i < numSrc; i++)
    {

        //printf("check 2.1, i=%d\n", i);         
        fname = PyList_GetItem(filenames, i);
        //printf("check 2.2\n");                  
        if (!fname) 
        {
          //printf("error\n");          
            PyErr_SetString(PyExc_ValueError, "filename not a string");
            return NULL;
        }       
        //printf("check 2.3\n");          
        //printf("fname = %s\n", PyString_AsString(fname));
        
        
        //printf("check 2.4\n");  
        muxFileNameArray[i] = PyString_AsString(fname);
        if (muxFileNameArray[i] == NULL) 
        {
            printf("ERROR: Memory for muxFileNameArray could not be allocated.\n");
            return NULL;
        }
    }

    //printf("Checkpoint 3 for urs2sts_ext.c\n");        
    if (file_params->nd != 1 || file_params->descr->type_num != PyArray_DOUBLE) 
    {
        PyErr_SetString(PyExc_ValueError,
            "file_params must be one-dimensional and of type double");
        return NULL; 
    }

    //printf("Checkpoint 4 for urs2sts_ext.c\n");        
    // Create array for weights which are passed to read_mux2
    weights = (float*) malloc(numSrc*sizeof(float));
    for (i = 0; i < numSrc; i++)
    {
        weights[i] = (float)(*(double*)(pyweights->data + i*pyweights->strides[0]));
    }
    
    //printf("Checkpoint 5 for urs2sts_ext.c\n");            
    // Read in mux2 data from file
    cdata = _read_mux2(numSrc, 
                       muxFileNameArray, 
                       weights, 
                       (double*)file_params->data, 
                       verbose);

    //printf("Checkpoint 6 for urs2sts_ext.c\n");                
    // Allocate space for return vector
    nsta0 = (int)*(double*)(file_params->data + 0*file_params->strides[0]);
    dt = *(double*)(file_params->data + 1*file_params->strides[0]);
    nt = (int)*(double*)(file_params->data + 2*file_params->strides[0]);

    //printf("Checkpoint 7 for urs2sts_ext.c\n");                    
    // Find min and max start times of all gauges
    start_tstep = nt + 1;
    finish_tstep = -1;
    for (i = 0; i < nsta0; i++)
    {
        if ((int)cdata[i][nt + 3] < start_tstep)
        {
            start_tstep = (int)cdata[i][nt + 3];
        }
        if ((int)cdata[i][nt + 4] > finish_tstep)
        {
            finish_tstep = (int)cdata[i][nt + 4]; 
        }
    }

    //printf("Checkpoint 8 for urs2sts_ext.c\n");                        
    if ((start_tstep > nt) | (finish_tstep < 0))
    {
        printf("ERROR: Gauge data has incorrect start and finsh times\n");
        return NULL;
    }

    if (start_tstep >= finish_tstep)
    {
        printf("ERROR: Gauge data has non-postive_length\n");
        return NULL;
    }

    num_ts = finish_tstep - start_tstep + 1;
    dimensions[0] = nsta0;
    dimensions[1] = num_ts + POFFSET;
    pydata = (PyArrayObject*)PyArray_FromDims(2, dimensions, PyArray_DOUBLE);
    if(pydata == NULL)
    {
        printf("ERROR: Memory for pydata array could not be allocated.\n");
        return NULL;
    }

    //printf("Checkpoint 9 for urs2sts_ext.c\n");                            
    // Each gauge begins and ends recording at different times. When a gauge is
    // not recording but at least one other gauge is. Pad the non-recording gauge
    // array with zeros.
    for (i = 0; i < nsta0; i++)
    {
        time = 0;
        for (it = 0; it < finish_tstep; it++)
        {
            if ((it + 1 >= start_tstep) && (it + 1 <= finish_tstep))
            {
                if (it + 1 > (int)cdata[i][nt + 4])
                {
                    //This gauge has stopped recording but others are still recording
                    *(double*)(pydata->data + i*pydata->strides[0] + time*pydata->strides[1]) = 0.0;
                }
                else
                {
                    *(double*)(pydata->data + i*pydata->strides[0] + time*pydata->strides[1]) = cdata[i][it];
                }
                time++;
            }
        }
        // Pass back lat,lon,elevation
        for (j = 0; j < POFFSET; j++)
        {
            *(double*)(pydata->data + i*pydata->strides[0] + (num_ts + j)*pydata->strides[1]) = cdata[i][nt + j];
        }
    }

    //printf("Checkpoint 10 for urs2sts_ext.c\n");                                
    free(weights);
    
    // Free filename array, but not independent Python strings
    // FIXME(Ole): Do we need to update a reference counter in this case?
    free(muxFileNameArray);
    
    for (i = 0; i < nsta0; ++i)
    {
        free(cdata[i]);
    }
    free(cdata);

    //printf("Checkpoint 11 for urs2sts_ext.c\n");                                    
    return  PyArray_Return(pydata);
}

float** _read_mux2(int numSrc, 
                   char **muxFileNameArray, 
                   float *weights, 
                   double *params, 
                   int verbose)
{
    FILE *fp;
    int nsta, nsta0, i, isrc, ista, k;
    struct tgsrwg *mytgs=0, *mytgs0=0;
    char *muxFileName;                                                                  
    int istart, istop;
    int *fros=0, *lros=0;
    char susMuxFileName;
    float *muxData;
    long numData;

    int len_sts_data;
    float **sts_data;
    float *temp_sts_data;

    long int offset;

    /* Allocate space for the names and the weights and pointers to the data*/    

    /* Check that the input files have mux2 extension*/
    susMuxFileName = 0;
    for(isrc = 0; isrc < numSrc; isrc++)
    { 
        muxFileName = muxFileNameArray[isrc];
        if(!susMuxFileName && strcmp(muxFileName + strlen(muxFileName) - 4, "mux2") != 0)
        {
            susMuxFileName = 1;
            break;
        }
    }

    if(susMuxFileName)
    {
        printf("\n**************************************************************************\n");
        printf("   WARNING: This program operates only on multiplexed files in mux2 format\n"); 
        printf("   At least one input file name does not end with mux2\n");
        printf("   Check your results carefully!\n");
        printf("**************************************************************************\n\n");
    }   

    if (verbose)
    {
        printf("Reading mux header information\n");
    }

    /* loop over all sources, read headers and check compatibility */
    for (isrc = 0; isrc < numSrc; isrc++)
    {
        muxFileName = muxFileNameArray[isrc];

                /* open the mux file */
        if((fp = fopen(muxFileName, "r")) == NULL)
        {
            fprintf(stderr, "cannot open file %s\n", muxFileName);
            exit(-1);  
        }
        
        if (!isrc)
        {
            fread(&nsta0, sizeof(int), 1, fp);
        
            fros = (int*)malloc(nsta0*numSrc*sizeof(int)); 
            lros = (int*)malloc(nsta0*numSrc*sizeof(int));
      
            mytgs0 = (struct tgsrwg*)malloc(nsta0*sizeof(struct tgsrwg));
            mytgs = (struct tgsrwg*)malloc(nsta0*sizeof(struct tgsrwg));

            fread(mytgs0, nsta0*sizeof(struct tgsrwg), 1, fp);
        }
        else
        {
            /* check that the mux files are compatible */      
            fread(&nsta, sizeof(int), 1, fp);
            if(nsta != nsta0)
            {
                fprintf(stderr,"%s has different number of stations to %s\n", muxFileName, muxFileNameArray[0]);
                fclose(fp);
                exit(-1);   
            }

            fread(mytgs, nsta*sizeof(struct tgsrwg), 1, fp); 
            
            for (ista = 0; ista < nsta; ista++)
            {
                if (mytgs[ista].dt != mytgs0[ista].dt)
                {
                    fprintf(stderr,"%s has different sampling rate to %s\n", muxFileName, muxFileNameArray[0]);
                    fclose(fp);
                    exit(-1);                 
                }   
                if (mytgs[ista].nt != mytgs0[ista].nt)
                {
                    fprintf(stderr,"%s has different series length to %s\n", muxFileName, muxFileNameArray[0]);
                    fclose(fp);
                    exit(-1);                 
                }
            }
        }

        /* read the start and stop times for this source */
        fread(fros + isrc*nsta0, nsta0*sizeof(int), 1, fp);
        fread(lros + isrc*nsta0, nsta0*sizeof(int), 1, fp);

        /* compute the size of the data block for this source */
        numData = getNumData(fros + isrc*nsta0, lros + isrc*nsta0, nsta0);

        /* Burbidge: Added a sanity check here */
        if (numData < 0)
        {
            fprintf(stderr,"Size of data block appears to be negative!\n");
            exit(-1);
        }

        fclose(fp);          
    }

    params[0] = (double)nsta0;
    params[1] = (double)mytgs0[0].dt;
    params[2] = (double)mytgs0[0].nt;

    /* make array(s) to hold the demuxed data */
    //FIXME: This can be reduced to only contain stations given in permutation file
    sts_data = (float**)malloc(nsta0*sizeof(float *));
    if (sts_data == NULL)
    {
        printf("ERROR: Memory for sts_data could not be allocated.\n");
        exit(-1);
    }

    len_sts_data = mytgs0[0].nt + POFFSET;
    for (ista = 0; ista < nsta0; ista++)
    {
        // Initialise sts_data to zero
        sts_data[ista] = (float*)calloc(len_sts_data, sizeof(float));
        if (sts_data[ista] == NULL)
        {
            printf("ERROR: Memory for sts_data could not be allocated.\n");
            exit(-1);
        }

        sts_data[ista][mytgs0[0].nt] = (float)mytgs0[ista].geolat;
        sts_data[ista][mytgs0[0].nt + 1] = (float)mytgs0[ista].geolon;
        sts_data[ista][mytgs0[0].nt + 2] = (float)mytgs0[ista].z;
        sts_data[ista][mytgs0[0].nt + 3] = (float)fros[ista];
        sts_data[ista][mytgs0[0].nt + 4] = (float)lros[ista];
    }

    temp_sts_data = (float*)calloc(len_sts_data, sizeof(float));

    /* Loop over all sources */
    //FIXME: remove istart and istop they are not used.
    istart = -1;
    istop = -1;
    for (isrc = 0; isrc < numSrc; isrc++)
    {
        /* Read in data block from mux2 file */
        muxFileName = muxFileNameArray[isrc];
        if((fp = fopen(muxFileName, "r")) == NULL)
        {
            //fprintf(stderr, "%s: cannot open file %s\n", av[0], muxFileName);
            fprintf(stderr, "cannot open file %s\n", muxFileName);
            exit(-1);  
        }

        if (verbose){
            printf("Reading mux file %s\n",muxFileName);
        }

        offset = sizeof(int) + nsta0*(sizeof(struct tgsrwg) + 2*sizeof(int));
        fseek(fp, offset, 0);

        numData = getNumData(fros + isrc*nsta0, lros + isrc*nsta0, nsta0);
        muxData = (float*)malloc(numData*sizeof(float));
        fread(muxData, numData*sizeof(float), 1, fp); 
        fclose(fp);

        /* loop over stations */
        /* This is where we should only take stations with indices in the permutation array 
           (and in that order) */
        
        //for i in range(len(permution)):
        //     ista = permutation[i]
        //     use ista with mux data
        //     use i with the processed data to be returned         
        i=0;
        
        for(ista = 0; ista < nsta0; ista++)
        {               
            /* fill the data0 array from the mux file, and weight it */
            fillDataArray(ista, nsta0, mytgs0[ista].nt, mytgs0[ista].ig, fros + isrc*nsta0, lros + isrc*nsta0, temp_sts_data, &istart, &istop, muxData);

            /* weight appropriately and add */
            for(k = 0; k < mytgs0[ista].nt; k++)
            {
                if((isdata(sts_data[ista][k])) && isdata(temp_sts_data[k]))
                {
                    sts_data[ista][k] += temp_sts_data[k] * weights[isrc];
                    //printf("%d,%d,%f\n",ista,k,sts_data[ista][k]);
                }
                else
                {
                    sts_data[ista][k] = NODATA;
                }
            }
        }
    }

    free(muxData);
    free(temp_sts_data);
    free(fros);
    free(lros);
    free(mytgs0);
    free(mytgs);

    return sts_data;
}


/* thomas */
void fillDataArray(int ista, int nsta, int nt, int ig, int *nst, int *nft, float *data, int *istart_p, int *istop_p, float *muxData)
{
    int it, last_it, jsta;
    long int offset=0;


    last_it = -1;
    /* make arrays of starting and finishing time steps for the tide gauges */
    /* and fill them from the file */

    /* update start and stop timesteps for this gauge */
    if (nst[ista]!= -1)
    {
        if(*istart_p == -1)
        {
            *istart_p = nst[ista];
        }
        else
        {
            *istart_p = ((nst[ista] < *istart_p) ? nst[ista] : *istart_p);
        }
    }
    if (nft[ista] != -1)
    {
        if (*istop_p == -1)
        {
            *istop_p = nft[ista];
        }
        else
        {
            *istop_p = ((nft[ista] < *istop_p) ? nft[ista] : *istop_p);
        }
    }     
    if (ig == -1 || nst[ista] == -1) /* currently ig==-1 => nst[ista]==-1 */
    {
        /* gauge never started recording, or was outside of all grids, fill array with 0 */
        for(it = 0; it < nt; it++)
        {
            data[it] = 0.0;
        }
    }   
    else
    {
        for(it = 0; it < nt; it++)
        {
            last_it = it;
            /* skip t record of data block */
            offset++;
            /* skip records from earlier tide gauges */
            for(jsta = 0; jsta < ista; jsta++)
                if(it + 1 >= nst[jsta] && it + 1 <= nft[jsta])
                    offset++;

            /* deal with the tide gauge at hand */
            if(it + 1 >= nst[ista] && it + 1 <= nft[ista])
                /* gauge is recording at this time */
            {
                memcpy(data + it, muxData + offset, sizeof(float));
                offset++;
            }
            else if (it + 1 < nst[ista])
            {
                /* gauge has not yet started recording */
                data[it] = 0.0;
            }   
            else
                /* gauge has finished recording */                                            
            {
                data[it] = NODATA;
                break;
            }

            /* skip records from later tide gauges */
            for(jsta = ista + 1; jsta < nsta; jsta++)
                if(it + 1 >= nst[jsta] && it+1 <= nft[jsta])
                    offset++;
        }

        if(last_it < nt - 1)
            /* the loop was exited early because the gauge had finished recording */
            for(it = last_it+1; it < nt; it++)
                data[it] = NODATA;
    }
} 

char isdata(float x)
{
    //char value;
    if(x < NODATA + EPSILON && NODATA < x + EPSILON)
    {
       return 0;
    }
    else
    {
        return 1;  
    }
}


long getNumData(const int *fros, const int *lros, const int nsta)
/* calculates the number of data in the data block of a mux file */
/* based on the first and last recorded output steps for each gauge */ 
{
    int ista, last_output_step;
    long numData = 0;

    last_output_step = 0;   
    for(ista = 0; ista < nsta; ista++)
        if(*(fros + ista) != -1)
        {
            numData += *(lros + ista) - *(fros + ista) + 1;
            last_output_step = (last_output_step < *(lros+ista) ? *(lros+ista):last_output_step);
        }   
        numData += last_output_step*nsta; /* these are the t records */
        return numData;
}   



//-------------------------------
// Method table for python module
//-------------------------------
static struct PyMethodDef MethodTable[] = {
    {"read_mux2", read_mux2, METH_VARARGS, "Print out"},
    {NULL, NULL}
};

// Module initialisation
void initurs_ext(void){
    Py_InitModule("urs_ext", MethodTable);

    import_array(); // Necessary for handling of NumPY structures
}