/*
   Name- copyMirsIMGToOutputFile.c

   Language- C     Type- MAIN

   Version- 1.0    Date-  2/28/2026   Programmer- Mike Pettey (STC)

   Function- This program extracts data from NUCAPS granules and collocates
             the data to selected collocations times and locations.
*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <archive_entry.h>
#include <archive.h>
#include <netcdf.h>
#include <netcdf_mem.h>
#include <math.h>
#include "uthash.h"
#include "mirs_collocator.h"


void copyGranuleName(char *granule_name, int out_id, int out_index, int out_var_id);
int fileStartsWith(char *file_name, char *token);
int fileEndsWith(char *file_name, char *token);


int copyMirsIMGToOutputFile(struct collocation_data *collocations, int num_collocations,
                            char *file_name, size_t file_size, void* nc_buffer, int out_id)
  {
  int     num_collocations_copied;
  int     n, i, j, coll, level, in_footprint, scan_line, fov;
  int     retval, in_id, in_var_id, out_var_id, out_dim_id;
  int     num_channels;
  short   short_value, short_in_fill, short_out_fill;
  short   *short_array;
  float   float_value, float_in_fill, float_out_fill, scaling_factor;
  float   *float_array;
  size_t  output_index[1];
  size_t  input_2d_index[2], input_2d_count[2];
  size_t  input_3d_index[3], input_3d_count[3];
  size_t  output_2d_index[2], output_2d_count[2];

  num_collocations_copied = 0;

  scan_line = collocations[coll].closest_scanline;
  fov       = collocations[coll].closest_fov;

  input_2d_index[0] = scan_line;
  input_2d_index[1] = fov;
  input_2d_count[0] = 1;
  input_2d_count[1] = 1;
  
  // Open the input file

  retval = nc_open_mem(file_name, NC_NOWRITE, file_size, nc_buffer, &in_id);

  if (retval == NC_NOERR)
    {
  
    // Loop through the collocations

    for (coll=0; coll<num_collocations; coll++)
      {
      output_index[0] = coll;

      // Copy the data for this collocation if a collocation was made

      if ((strlen(collocations[coll].closest_img_granule) > 0) &&
	  (strcmp(collocations[coll].closest_img_granule, file_name) == 0))
	{
        //num_collocations_copied++;
        //input_index[1]  = collocations[coll].closest_footprint;

        // Copy the granule name and footprint

        retval = nc_inq_varid(out_id, "collocated_img_granule_name", &out_var_id);
	copyGranuleName(collocations[coll].closest_img_granule, out_id, coll, out_var_id);

	// Copy the granule name and footprint

	retval = nc_inq_varid(out_id, "collocated_img_granule_name", &out_var_id);
	copyGranuleName(collocations[coll].closest_img_granule, out_id, coll, out_var_id);

	// Copy the cloud liquid water

	retval = nc_inq_varid(in_id, "CLW", &in_var_id);
	retval = nc_get_var1_float(in_id, in_var_id, input_2d_index, &float_value);
	retval = nc_get_att_float(in_id, in_var_id, "_FillValue", &float_in_fill);

	if (float_value != float_in_fill)
	  {
          retval = nc_inq_varid(out_id, "CLW", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// Channel selection

	short_array = (short*)malloc(num_channels*sizeof(short));

	input_3d_index[0] = scan_line;
	input_3d_index[1] = fov;
	input_3d_index[2] = 0;
	input_3d_count[0] = 1;
	input_3d_count[1] = 1;
	input_3d_count[2] = num_channels;

	retval = nc_inq_varid(in_id, "ChanSel", &in_var_id);
	retval = nc_get_vara_short(in_id, in_var_id, input_3d_index, input_3d_count, short_array);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);

	retval = nc_inq_varid(out_id, "ChanSel", &out_var_id);
	retval = nc_get_att_short(out_id, out_var_id, "_FillValue", &short_out_fill);

	for (n=0; n<num_channels; n++)
	  {
          if (short_array[n] == short_in_fill)
	    short_array[n] = short_out_fill;
	  }  // for (n=0...

	output_2d_index[0] = coll;
	output_2d_index[1] = 0;
	output_2d_count[0] = 1;
	output_2d_count[1] = num_channels;

	retval = nc_put_vara_short(out_id, out_var_id, output_2d_index, output_2d_count, short_array);

	free(short_array);

	// Copy the brightness temperatures

	short_array = (short*)malloc(num_channels*sizeof(short));
	float_array = (float*)malloc(num_channels*sizeof(float));

	retval = nc_inq_varid(in_id, "BT", &in_var_id);
	retval = nc_get_vara_short(in_id, in_var_id, input_3d_index, input_3d_count, short_array);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);
	retval = nc_get_att_float(in_id, in_var_id, "scale_factor", &scaling_factor);

	retval = nc_inq_varid(out_id, "BT", &out_var_id);
	retval = nc_get_att_float(out_id, out_var_id, "_FillValue", &float_out_fill);

	for (n=0; n<num_channels; n++)
	  {
          if (short_array[n] == short_in_fill)
	    float_array[n] = float_out_fill;
	  else
	    float_array[n] = (float)short_array[n] * scaling_factor;
	  }  // for (n=0...

	output_2d_index[0] = coll;
	output_2d_index[1] = 0;
	output_2d_count[0] = 1;
	output_2d_count[1] = num_channels;

	retval = nc_put_vara_float(out_id, out_var_id, output_2d_index, output_2d_count, float_array);

	free(float_array);
	free(short_array);

	// Cloud base pressure

	retval = nc_inq_varid(in_id, "CldBase", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);
	retval = nc_get_att_float(in_id, in_var_id, "scale_factor", &scaling_factor);

	if ((short_value != short_in_fill) && (short_value != -888))
          {
          float_value = (float)short_value * scaling_factor;

	  retval = nc_inq_varid(out_id, "CldBase", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// Cloud thickness

	retval = nc_inq_varid(in_id, "CldThick", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);
	retval = nc_get_att_float(in_id, in_var_id, "scale_factor", &scaling_factor);

	if ((short_value != short_in_fill) && (short_value != -888))
	  {
          float_value = (float)short_value * scaling_factor;

	  retval = nc_inq_varid(out_id, "CldThick", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// Cloud top pressure

	retval = nc_inq_varid(in_id, "CldTop", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);
	retval = nc_get_att_float(in_id, in_var_id, "scale_factor", &scaling_factor);

	if ((short_value != short_in_fill) && (short_value != -888))
	  {
          float_value = (float)short_value * scaling_factor;

	  retval = nc_inq_varid(out_id, "CldTop", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// Emissivity

	short_array = (short*)malloc(num_channels*sizeof(short));
	float_array = (float*)malloc(num_channels*sizeof(float));

	input_3d_index[0] = scan_line;
	input_3d_index[1] = fov;
	input_3d_index[2] = 0;
	input_3d_count[0] = 1;
	input_3d_count[1] = 1;
	input_3d_count[2] = num_channels;

	retval = nc_inq_varid(in_id, "Emis", &in_var_id);
	retval = nc_get_vara_short(in_id, in_var_id, input_3d_index, input_3d_count, short_array);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);
	retval = nc_get_att_float(in_id, in_var_id, "scale_factor", &scaling_factor);

	retval = nc_inq_varid(out_id, "Emis", &out_var_id);
	retval = nc_get_att_short(out_id, out_var_id, "_FillValue", &short_out_fill);

	for (n=0; n<num_channels; n++)
	  {
          if (short_array[n] == short_in_fill)
	    float_array[n] = float_out_fill;
	  else
	    float_array[n] = (float)short_array[n] * scaling_factor;
	  }  // for (n=0...

	output_2d_index[0] = coll;
	output_2d_index[1] = 0;
	output_2d_count[0] = 1;
	output_2d_count[1] = num_channels;

	retval = nc_put_vara_float(out_id, out_var_id, output_2d_index, output_2d_count, float_array);

	free(float_array);
	free(short_array);

	// Graupel water path

	retval = nc_inq_varid(in_id, "GWP", &in_var_id);
	retval = nc_get_var1_float(in_id, in_var_id, input_2d_index, &float_value);
	retval = nc_get_att_float(in_id, in_var_id, "_FillValue", &float_in_fill);

	if (float_value != float_in_fill)
	  {
          retval = nc_inq_varid(out_id, "GWP", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// Ice water path

	retval = nc_inq_varid(in_id, "IWP", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);
	retval = nc_get_att_float(in_id, in_var_id, "scale_factor", &scaling_factor);

	if (short_value != short_in_fill)
	  {
          float_value = (float)short_value * scaling_factor;

	  retval = nc_inq_varid(out_id, "IWP", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// Liquid water path

	retval = nc_inq_varid(in_id, "LWP", &in_var_id);
	retval = nc_get_var1_float(in_id, in_var_id, input_2d_index, &float_value);
	retval = nc_get_att_float(in_id, in_var_id, "_FillValue", &float_in_fill);

	if (float_value != float_in_fill)
	  {
          retval = nc_inq_varid(out_id, "LWP", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// Precip type

	retval = nc_inq_varid(in_id, "PrecipType", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);

	if ((short_value != short_in_fill) && (short_value != -888))
          {
          retval = nc_inq_varid(out_id, "PrecipType", &out_var_id);
	  retval = nc_put_var1_short(out_id, out_var_id, output_index, &short_value);
	  }

	// Probability of falling snow

	retval = nc_inq_varid(in_id, "Prob_SF", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);

	if (short_value != short_in_fill)
	  {
          retval = nc_inq_varid(out_id, "Prob_SF", &out_var_id);
	  retval = nc_put_var1_short(out_id, out_var_id, output_index, &short_value);
	  }

	// Rain flag

	retval = nc_inq_varid(in_id, "RFlag", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);

	if ((short_value != short_in_fill) && (short_value != -888))
	  {
          retval = nc_inq_varid(out_id, "RFlag", &out_var_id);
	  retval = nc_put_var1_short(out_id, out_var_id, output_index, &short_value);
	  }

	// Rain rate

	retval = nc_inq_varid(in_id, "RR", &in_var_id);
	retval = nc_get_var1_float(in_id, in_var_id, input_2d_index, &float_value);
	retval = nc_get_att_float(in_id, in_var_id, "_FillValue", &float_in_fill);

	if (float_value != float_in_fill)
	  {
          retval = nc_inq_varid(out_id, "RR", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// Rain water path

	retval = nc_inq_varid(in_id, "RWP", &in_var_id);
	retval = nc_get_var1_float(in_id, in_var_id, input_2d_index, &float_value);
	retval = nc_get_att_float(in_id, in_var_id, "_FillValue", &float_in_fill);

	if (float_value != float_in_fill)
	  {
          retval = nc_inq_varid(out_id, "RWP", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// Sea ice concentration

	retval = nc_inq_varid(in_id, "SIce", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);

	if (short_value != short_in_fill)
	  {
          retval = nc_inq_varid(out_id, "SIce", &out_var_id);
	  retval = nc_put_var1_short(out_id, out_var_id, output_index, &short_value);
	  }

	// First year sea ice

	retval = nc_inq_varid(in_id, "SIce_FY", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);

	if (short_value != short_in_fill)
	  {
          retval = nc_inq_varid(out_id, "SIce_FY", &out_var_id);
	  retval = nc_put_var1_short(out_id, out_var_id, output_index, &short_value);
	  }

	// Multi year sea ice

	retval = nc_inq_varid(in_id, "SIce_MY", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);

	if (short_value != short_in_fill)
	  {
          retval = nc_inq_varid(out_id, "SIce_MY", &out_var_id);
	  retval = nc_put_var1_short(out_id, out_var_id, output_index, &short_value);
	  }

	// Snow water equivalent

	retval = nc_inq_varid(in_id, "SWE", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);
	retval = nc_get_att_float(in_id, in_var_id, "scale_factor", &scaling_factor);

	if (short_value != short_in_fill)
	  {
          float_value = (float)short_value * scaling_factor;

	  retval = nc_inq_varid(out_id, "SWE", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// Snow water path

	retval = nc_inq_varid(in_id, "SWP", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);
	retval = nc_get_att_float(in_id, in_var_id, "scale_factor", &scaling_factor);

	if (short_value != short_in_fill)
	  {
          float_value = (float)short_value * scaling_factor;

	  retval = nc_inq_varid(out_id, "SWP", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// Snow cover

	retval = nc_inq_varid(in_id, "Snow", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);

	if (short_value != short_in_fill)
	  {
          retval = nc_inq_varid(out_id, "Snow", &out_var_id);
	  retval = nc_put_var1_short(out_id, out_var_id, output_index, &short_value);
	  }

	// Snow grain size

	retval = nc_inq_varid(in_id, "SnowGS", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);
	retval = nc_get_att_float(in_id, in_var_id, "scale_factor", &scaling_factor);

	if (short_value != short_in_fill)
	  {
          float_value = (float)short_value * scaling_factor;

	  retval = nc_inq_varid(out_id, "SnowGS", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// Surface moisture

	retval = nc_inq_varid(in_id, "SurfM", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);
	retval = nc_get_att_float(in_id, in_var_id, "scale_factor", &scaling_factor);

	if ((short_value != short_in_fill) && (short_value != -888))
	  {
          float_value = (float)short_value * scaling_factor;

	  retval = nc_inq_varid(out_id, "SurfM", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// Total precipitable water

	retval = nc_inq_varid(in_id, "TPW", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);
	retval = nc_get_att_float(in_id, in_var_id, "scale_factor", &scaling_factor);

	if (short_value != short_in_fill)
	  {
          float_value = (float)short_value * scaling_factor;

	  retval = nc_inq_varid(out_id, "TPW", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// Skin temperature

	retval = nc_inq_varid(in_id, "TSkin", &in_var_id);
	retval = nc_get_var1_float(in_id, in_var_id, input_2d_index, &float_value);
	retval = nc_get_att_float(in_id, in_var_id, "_FillValue", &float_in_fill);

	if (float_value != float_in_fill)
	  {
          retval = nc_inq_varid(out_id, "TSkin", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// Wind direction

	retval = nc_inq_varid(in_id, "WindDir", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);
	retval = nc_get_att_float(in_id, in_var_id, "scale_factor", &scaling_factor);

	if ((short_value != short_in_fill) && (short_value != -888))
	  {
          float_value = (float)short_value * scaling_factor;

	  retval = nc_inq_varid(out_id, "WindDir", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// Wind speed

	retval = nc_inq_varid(in_id, "WindSp", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);
	retval = nc_get_att_float(in_id, in_var_id, "scale_factor", &scaling_factor);

	if ((short_value != short_in_fill) && (short_value != -888))
	  {
          float_value = (float)short_value * scaling_factor;

	  retval = nc_inq_varid(out_id, "WindSp", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// U direction wind speed

	retval = nc_inq_varid(in_id, "WindU", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);
	retval = nc_get_att_float(in_id, in_var_id, "scale_factor", &scaling_factor);

	if ((short_value != short_in_fill) && (short_value != -888))
	  {
          float_value = (float)short_value * scaling_factor;

	  retval = nc_inq_varid(out_id, "WindU", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// V direction wind speed

	retval = nc_inq_varid(in_id, "WindV", &in_var_id);
	retval = nc_get_var1_short(in_id, in_var_id, input_2d_index, &short_value);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);
	retval = nc_get_att_float(in_id, in_var_id, "scale_factor", &scaling_factor);

	if ((short_value != short_in_fill) && (short_value != -888))
	  {
          float_value = (float)short_value * scaling_factor;

	  retval = nc_inq_varid(out_id, "WindV", &out_var_id);
	  retval = nc_put_var1_float(out_id, out_var_id, output_index, &float_value);
	  }

	// Un-corrected channel temperature

	short_array = (short*)malloc(num_channels*sizeof(short));
	float_array = (float*)malloc(num_channels*sizeof(float));

	input_3d_index[0] = scan_line;
	input_3d_index[1] = fov;
	input_3d_index[2] = 0;
	input_3d_count[0] = 1;
	input_3d_count[1] = 1;
	input_3d_count[2] = num_channels;

	retval = nc_inq_varid(in_id, "YM", &in_var_id);
	retval = nc_get_vara_short(in_id, in_var_id, input_3d_index, input_3d_count, short_array);
	retval = nc_get_att_short(in_id, in_var_id, "_FillValue", &short_in_fill);
	retval = nc_get_att_float(in_id, in_var_id, "scale_factor", &scaling_factor);

	retval = nc_inq_varid(out_id, "YM", &out_var_id);
	retval = nc_get_att_short(out_id, out_var_id, "_FillValue", &short_out_fill);

	for (n=0; n<num_channels; n++)
          {
          if (short_array[n] == short_in_fill)
	    float_array[n] = float_out_fill;
	  else
	    float_array[n] = (float)short_array[n] * scaling_factor;
	  }  // for (n=0...

	output_2d_index[0] = coll;
	output_2d_index[1] = 0;
	output_2d_count[0] = 1;
	output_2d_count[1] = num_channels;

	retval = nc_put_vara_float(out_id, out_var_id, output_2d_index, output_2d_count, float_array);

	free(float_array);
	free(short_array);
	}  // if (strlen(collocations[coll].closest_img_granule...
      }  // for (coll=0...

    nc_close(in_id);
    } // if (retval nc_mem_open...

  return num_collocations_copied;
  }

// end of file