ide::transform_flags
ide::CBFAdaptor::transform_flags() const{
std::string precedence,direction;
const char *temp_value;
ide::transform_flags T;
T.transpose = file_is_transposed();
cbf_failnez ( cbf_find_category(cbf_h,"array_structure_list") );
cbf_failnez ( cbf_rewind_column(cbf_h) );
cbf_failnez ( cbf_find_column(cbf_h,"precedence") );
cbf_failnez ( cbf_rewind_row(cbf_h) );
precedence = "1";
cbf_failnez ( cbf_find_row(cbf_h,precedence.c_str()) );
cbf_failnez ( cbf_rewind_column(cbf_h) );
cbf_failnez ( cbf_find_column(cbf_h,"direction") );
cbf_failnez ( cbf_get_value(cbf_h,&temp_value) );
direction = std::string(temp_value);
SCITBX_ASSERT( direction == "increasing" || direction == "decreasing" );
T.reverse_fast = (direction=="decreasing");
cbf_failnez ( cbf_rewind_column(cbf_h) );
cbf_failnez ( cbf_find_column(cbf_h,"precedence") );
cbf_failnez ( cbf_rewind_row(cbf_h) );
precedence = "2";
cbf_failnez ( cbf_find_row(cbf_h,precedence.c_str()) );
cbf_failnez ( cbf_rewind_column(cbf_h) );
cbf_failnez ( cbf_find_column(cbf_h,"direction") );
cbf_failnez ( cbf_get_value(cbf_h,&temp_value) );
direction = std::string(temp_value);
SCITBX_ASSERT( direction == "increasing" || direction == "decreasing" );
T.reverse_slow = (direction=="decreasing");
return T;
}
std::string
ide::CBFAdaptor::raster_description(){
std::string precedence,direction;
std::string result="";
const char *temp_value;
cbf_failnez ( cbf_find_category(cbf_h,"array_structure_list") );
typedef std::vector<std::string> el_lst;
el_lst elements;
elements.push_back("ELEMENT_X");elements.push_back("ELEMENT_Y");
for (el_lst::const_iterator e = elements.begin(); e!=elements.end(); ++e) {
cbf_failnez ( cbf_find_column(cbf_h,"axis_set_id") );
cbf_failnez ( cbf_rewind_row(cbf_h) );
cbf_failnez ( cbf_find_row(cbf_h,e->c_str()) );
cbf_failnez ( cbf_rewind_column(cbf_h) );
cbf_failnez ( cbf_find_column(cbf_h,"direction") );
cbf_failnez ( cbf_get_value(cbf_h,&temp_value) );
direction = std::string(temp_value);
cbf_failnez ( cbf_rewind_column(cbf_h) );
cbf_failnez ( cbf_find_column(cbf_h,"precedence") );
cbf_failnez ( cbf_get_value(cbf_h,&temp_value) );
precedence = std::string(temp_value);
result = result+std::string(*e)+" "+direction+" precedence="+precedence+'\n';
}
return result;
}
bool
ide::CBFAdaptor::file_is_transposed() const{
std::string elem,precedence;
const char *temp_value;
cbf_failnez ( cbf_find_category(cbf_h,"array_structure_list") );
elem = "ELEMENT_X";
cbf_failnez ( cbf_find_column(cbf_h,"axis_set_id") );
cbf_failnez ( cbf_rewind_row(cbf_h) );
cbf_failnez ( cbf_find_row(cbf_h,elem.c_str()) );
cbf_failnez ( cbf_rewind_column(cbf_h) );
cbf_failnez ( cbf_find_column(cbf_h,"precedence") );
cbf_failnez ( cbf_get_value(cbf_h,&temp_value) );
precedence = std::string(temp_value);
if (precedence=="1") return false; //ELEMENT_X precedence=1 means it is fastest
if (precedence=="2") return true; //ELEMENT_X precedence=2 means it is slow
throw iotbx::detectors::Error ("Unable to determine precedence of ELEMENT_X");
}
int main (int argc, char *argv [])
{
FILE *in, *out;
clock_t a,b;
img_handle img, cbf_img;
cbf_handle cbf;
int id, index;
unsigned int column, row;
size_t nelem_read;
double pixel_size, gain, wavelength, distance;
int overload, dimension [2], precedence [2];
const char *detector;
char *detector_char;
char detector_id [64];
const char *direction [2], *array_id;
/* Usage */
if (argc < 3)
{
fprintf (stderr, "\n Usage: %s imagefile cbffile\n", argv [0]);
exit (2);
}
/* Read the image */
img = img_make_handle ();
a = clock ();
cbf_failnez (img_read (img, argv [1]))
b = clock ();
fprintf (stderr, " Time to read the image: %.3fs\n", ((b - a) * 1.0) / CLOCKS_PER_SEC);
/* Get some detector parameters */
/* Detector identifier */
detector = img_get_field (img, "DETECTOR");
if (!detector)
detector = "unknown";
strncpy (detector_id, detector, 63);
detector_id [63] = 0;
detector_char = detector_id;
while (*detector_char)
if (isspace (*detector_char))
memmove (detector_char, detector_char + 1, strlen (detector_char));
else
{
*detector_char = tolower (*detector_char);
detector_char++;
}
/* Pixel size */
pixel_size = img_get_number (img, "PIXEL SIZE") * 0.001;
/* Wavelength */
wavelength = img_get_number (img, "WAVELENGTH");
/* Distance */
distance = img_get_number (img, "DISTANCE") * 0.001;
/* Image size and orientation & gain and overload */
if (strcmp (detector_id, "mar180") == 0 ||
strcmp (detector_id, "mar300") == 0)
{
gain = 1.08;
overload = 120000;
dimension [0] = img_rows (img);
dimension [1] = img_columns (img);
precedence [0] = 1;
precedence [1] = 2;
direction [0] = "decreasing";
direction [1] = "increasing";
}
else
if (strcmp (detector_id, "mar345") == 0)
{
gain = 1.55;
overload = 240000;
dimension [0] = img_columns (img);
dimension [1] = img_rows (img);
precedence [0] = 2;
precedence [1] = 1;
direction [0] = "increasing";
direction [1] = "increasing";
}
else
if (strncmp (detector_id, "adscquantum", 11) == 0)
{
gain = 0.20;
overload = 65000;
dimension [0] = img_columns (img);
dimension [1] = img_rows (img);
precedence [0] = 2;
precedence [1] = 1;
direction [0] = "increasing";
direction [1] = "increasing";
}
else
{
gain = 0.0;
overload = 0;
dimension [0] = img_rows (img);
dimension [1] = img_columns (img);
precedence [0] = 1;
precedence [1] = 2;
direction [0] = NULL;
direction [1] = NULL;
}
/* Make a cbf version of the image */
a = clock ();
/* Create the cbf */
cbf_failnez (cbf_make_handle (&cbf))
/* Make a new data block */
cbf_failnez (cbf_new_datablock (cbf, "image_1"))
/* Make the _diffrn category */
cbf_failnez (cbf_new_category (cbf, "diffrn"))
cbf_failnez (cbf_new_column (cbf, "id"))
cbf_failnez (cbf_set_value (cbf, "DS1"))
/* Make the _diffrn_source category */
cbf_failnez (cbf_new_category (cbf, "diffrn_source"))
cbf_failnez (cbf_new_column (cbf, "diffrn_id"))
cbf_failnez (cbf_set_value (cbf, "DS1"))
cbf_failnez (cbf_new_column (cbf, "source"))
cbf_failnez (cbf_set_value (cbf, "synchrotron"))
cbf_failnez (cbf_new_column (cbf, "type"))
cbf_failnez (cbf_set_value (cbf, "ssrl crystallography"))
/* Make the _diffrn_radiation category */
cbf_failnez (cbf_new_category (cbf, "diffrn_radiation"))
cbf_failnez (cbf_new_column (cbf, "diffrn_id"))
cbf_failnez (cbf_set_value (cbf, "DS1"))
cbf_failnez (cbf_new_column (cbf, "wavelength_id"))
cbf_failnez (cbf_set_value (cbf, "L1"))
/* Make the _diffrn_radiation_wavelength category */
cbf_failnez (cbf_new_category (cbf, "diffrn_radiation_wavelength"))
cbf_failnez (cbf_new_column (cbf, "id"))
cbf_failnez (cbf_set_value (cbf, "L1"))
cbf_failnez (cbf_new_column (cbf, "wavelength"))
if (wavelength)
cbf_failnez (cbf_set_doublevalue (cbf, "%.4f", wavelength))
cbf_failnez (cbf_new_column (cbf, "wt"))
cbf_failnez (cbf_set_value (cbf, "1.0"))
/* Make the _diffrn_measurement category */
cbf_failnez (cbf_new_category (cbf, "diffrn_measurement"))
cbf_failnez (cbf_new_column (cbf, "diffrn_id"))
cbf_failnez (cbf_set_value (cbf, "DS1"))
cbf_failnez (cbf_new_column (cbf, "method"))
cbf_failnez (cbf_set_value (cbf, "oscillation"))
cbf_failnez (cbf_new_column (cbf, "sample_detector_distance"))
if (distance)
cbf_failnez (cbf_set_doublevalue (cbf, "%.4f", distance))
/* Make the _diffrn_detector category */
cbf_failnez (cbf_new_category (cbf, "diffrn_detector"))
cbf_failnez (cbf_new_column (cbf, "id"))
cbf_failnez (cbf_set_value (cbf, detector_id))
cbf_failnez (cbf_new_column (cbf, "diffrn_id"))
cbf_failnez (cbf_set_value (cbf, "DS1"))
cbf_failnez (cbf_new_column (cbf, "type"))
cbf_failnez (cbf_set_value (cbf, detector))
/* Make the _diffrn_detector_element category */
cbf_failnez (cbf_new_category (cbf, "diffrn_detector_element"))
cbf_failnez (cbf_new_column (cbf, "id"))
cbf_failnez (cbf_set_integervalue (cbf, 1))
cbf_failnez (cbf_new_column (cbf, "detector_id"))
cbf_failnez (cbf_set_value (cbf, detector_id))
/* Make the _diffrn_frame_data category */
cbf_failnez (cbf_new_category (cbf, "diffrn_frame_data"))
cbf_failnez (cbf_new_column (cbf, "id"))
cbf_failnez (cbf_set_value (cbf, "frame_1"))
cbf_failnez (cbf_new_column (cbf, "detector_element_id"))
cbf_failnez (cbf_set_integervalue (cbf, 1))
cbf_failnez (cbf_new_column (cbf, "detector_id"))
cbf_failnez (cbf_set_value (cbf, detector_id))
cbf_failnez (cbf_new_column (cbf, "array_id"))
cbf_failnez (cbf_set_value (cbf, "image_1"))
cbf_failnez (cbf_new_column (cbf, "binary_id"))
cbf_failnez (cbf_set_integervalue (cbf, 1))
/* Make the _array_structure_list category */
cbf_failnez (cbf_new_category (cbf, "array_structure_list"))
cbf_failnez (cbf_new_column (cbf, "array_id"))
cbf_failnez (cbf_set_value (cbf, "image_1"))
cbf_failnez (cbf_new_row (cbf))
cbf_failnez (cbf_set_value (cbf, "image_1"))
cbf_failnez (cbf_new_column (cbf, "index"))
cbf_failnez (cbf_rewind_row (cbf))
cbf_failnez (cbf_set_integervalue (cbf, 1))
cbf_failnez (cbf_next_row (cbf))
cbf_failnez (cbf_set_integervalue (cbf, 2))
cbf_failnez (cbf_new_column (cbf, "dimension"))
cbf_failnez (cbf_rewind_row (cbf))
cbf_failnez (cbf_set_integervalue (cbf, dimension [0]))
cbf_failnez (cbf_next_row (cbf))
cbf_failnez (cbf_set_integervalue (cbf, dimension [1]))
cbf_failnez (cbf_new_column (cbf, "precedence"))
cbf_failnez (cbf_rewind_row (cbf))
cbf_failnez (cbf_set_integervalue (cbf, precedence [0]))
cbf_failnez (cbf_next_row (cbf))
cbf_failnez (cbf_set_integervalue (cbf, precedence [1]))
cbf_failnez (cbf_new_column (cbf, "direction"))
cbf_failnez (cbf_rewind_row (cbf))
cbf_failnez (cbf_set_value (cbf, direction [0]))
cbf_failnez (cbf_next_row (cbf))
cbf_failnez (cbf_set_value (cbf, direction [1]))
/* Make the _array_element_size category */
cbf_failnez (cbf_new_category (cbf, "array_element_size"))
cbf_failnez (cbf_new_column (cbf, "array_id"))
cbf_failnez (cbf_set_value (cbf, "image_1"))
cbf_failnez (cbf_new_row (cbf))
cbf_failnez (cbf_set_value (cbf, "image_1"))
cbf_failnez (cbf_new_column (cbf, "index"))
cbf_failnez (cbf_rewind_row (cbf))
cbf_failnez (cbf_set_integervalue (cbf, 1))
cbf_failnez (cbf_next_row (cbf))
cbf_failnez (cbf_set_integervalue (cbf, 2))
cbf_failnez (cbf_new_column (cbf, "size"))
if (pixel_size > 0)
{
cbf_failnez (cbf_rewind_row (cbf))
cbf_failnez (cbf_set_doublevalue (cbf, "%.1fe-6", pixel_size * 1e6))
cbf_failnez (cbf_next_row (cbf))
cbf_failnez (cbf_set_doublevalue (cbf, "%.1fe-6", pixel_size * 1e6))
}
/* Make the _array_intensities category */
cbf_failnez (cbf_new_category (cbf, "array_intensities"))
cbf_failnez (cbf_new_column (cbf, "array_id"))
cbf_failnez (cbf_set_value (cbf, "image_1"))
cbf_failnez (cbf_new_column (cbf, "binary_id"))
cbf_failnez (cbf_set_integervalue (cbf, 1))
cbf_failnez (cbf_new_column (cbf, "linearity"))
cbf_failnez (cbf_set_value (cbf, "linear"))
cbf_failnez (cbf_new_column (cbf, "gain"))
if (gain)
cbf_failnez (cbf_set_doublevalue (cbf, "%.3g", gain))
cbf_failnez (cbf_new_column (cbf, "overload"))
if (overload)
cbf_failnez (cbf_set_integervalue (cbf, overload))
cbf_failnez (cbf_new_column (cbf, "undefined"))
cbf_failnez (cbf_set_integervalue (cbf, 0))
/* Make the _array_data category */
cbf_failnez (cbf_new_category (cbf, "array_data"))
cbf_failnez (cbf_new_column (cbf, "array_id"))
cbf_failnez (cbf_set_value (cbf, "image_1"))
cbf_failnez (cbf_new_column (cbf, "binary_id"))
cbf_failnez (cbf_set_integervalue (cbf, 1))
cbf_failnez (cbf_new_column (cbf, "data"))
/* Save the binary data */
cbf_failnez (cbf_set_integerarray_wdims_fs (cbf, CBF_PACKED|CBF_FLAT_IMAGE, 1,
img_pixelptr (img, 0, 0), sizeof (int), 1,
img_rows (img) * img_columns (img),
"little_endian",img_rows (img),img_columns (img),0,0 ))
/* Write the new file */
out = fopen (argv [2], "w+b");
if (!out)
{
fprintf (stderr, " Couldn't open the CBF file %s\n", argv [2]);
exit (1);
}
cbf_failnez (cbf_write_file (cbf, out, 1, CBF, MSG_DIGEST | MIME_HEADERS , 0))
/* Free the cbf */
cbf_failnez (cbf_free_handle (cbf))
b = clock ();
fprintf (stderr, " Time to write the CBF image: %.3fs\n",
((b - a) * 1.0) / CLOCKS_PER_SEC);
/* Read the CBF file and compare the image to the original */
a = clock ();
/* Create the cbf */
cbf_failnez (cbf_make_handle (&cbf))
/* Read the file */
in = fopen (argv [2], "rb");
if (!in)
{
fprintf (stderr, " Couldn't reopen the CBF file %s\n", argv [2]);
exit (1);
}
cbf_failnez (cbf_read_file (cbf, in, MSG_DIGEST))
/* Get the image identifier */
cbf_failnez (cbf_rewind_datablock (cbf))
cbf_failnez (cbf_find_category (cbf, "diffrn_frame_data"))
cbf_failnez (cbf_find_column (cbf, "array_id"))
cbf_failnez (cbf_get_value (cbf, &array_id))
/* Get the image dimensions (second dimension = fast, first = slow) */
cbf_failnez (cbf_find_category (cbf, "array_structure_list"))
cbf_failnez (cbf_rewind_row (cbf))
cbf_failnez (cbf_find_column (cbf, "array_id"))
dimension [0] = dimension [1] = 0;
while (cbf_find_nextrow (cbf, array_id) == 0)
{
cbf_failnez (cbf_find_column (cbf, "precedence"))
cbf_failnez (cbf_get_integervalue (cbf, &index))
if (index >= 1 && index <= 2)
{
cbf_failnez (cbf_find_column (cbf, "dimension"))
cbf_failnez (cbf_get_integervalue (cbf, &dimension [2 - index]))
}
else
exit (1);
cbf_failnez (cbf_find_column (cbf, "array_id"))
}
if (dimension [0] == 0 || dimension [1] == 0)
exit (1);
/* Create the new image */
cbf_img = img_make_handle ();
img_set_dimensions (cbf_img, dimension [0], dimension [1]);
/* Find the binary data */
cbf_failnez (cbf_find_category (cbf, "array_data"))
cbf_failnez (cbf_find_column (cbf, "array_id"))
cbf_failnez (cbf_find_row (cbf, array_id))
cbf_failnez (cbf_find_column (cbf, "data"))
/* Read the binary data */
cbf_failnez (cbf_get_integerarray (cbf,
&id, img_pixelptr (cbf_img, 0, 0), sizeof (int), 1,
img_rows (cbf_img) * img_columns (cbf_img), &nelem_read))
/* Free the cbf */
cbf_failnez (cbf_free_handle (cbf))
b = clock ();
fprintf (stderr, " Time to read the CBF image: %.3fs\n",
((b - a) * 1.0) / CLOCKS_PER_SEC);
/* Compare the images */
if (img_rows (img) != img_rows (cbf_img) || img_columns (img) != img_columns (cbf_img))
{
fprintf (stderr, " The dimensions of the CBF image don't match the original\n");
exit (1);
}
for (column = 0; column < (unsigned int) img_columns (cbf_img); column++)
for (row = 0; row < (unsigned int) img_rows (cbf_img); row++)
if (img_pixel (cbf_img, column, row) != img_pixel (img, column, row))
{
fprintf (stderr, " The CBF image differs from the original at (%d, %d)\n", column, row);
exit (1);
}
fprintf (stderr, " The CBF image matches the original\n");
/* Free the images */
img_free_handle (img);
img_free_handle (cbf_img);
/* Success */
return 0;
}
