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Sourcecode: pymol version File versions

Field.c


/* 
A* -------------------------------------------------------------------
B* This file contains source code for the PyMOL computer program
C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific. 
D* -------------------------------------------------------------------
E* It is unlawful to modify or remove this copyright notice.
F* -------------------------------------------------------------------
G* Please see the accompanying LICENSE file for further information. 
H* -------------------------------------------------------------------
I* Additional authors of this source file include:
-* 
-* 
-*
Z* -------------------------------------------------------------------
*/

#include"os_predef.h"
#include"os_std.h"
#include"Base.h"

#include"OOMac.h"
#include"PConv.h"

#include"Field.h"
#include"Vector.h"

PyObject *FieldAsPyList(CField * I)
{
#ifdef _PYMOL_NOPY
  return NULL;
#else

  PyObject *result = NULL;
  int n_elem;

  /* first, dump the atoms */

  result = PyList_New(7);
  PyList_SetItem(result, 0, PyInt_FromLong(I->type));
  PyList_SetItem(result, 1, PyInt_FromLong(I->n_dim));
  PyList_SetItem(result, 2, PyInt_FromLong(I->base_size));
  PyList_SetItem(result, 3, PyInt_FromLong(I->size));
  PyList_SetItem(result, 4, PConvIntArrayToPyList((int *) I->dim, I->n_dim));
  PyList_SetItem(result, 5, PConvIntArrayToPyList((int *) I->stride, I->n_dim));
  n_elem = I->size / I->base_size;
  switch (I->type) {
  case cFieldInt:
    PyList_SetItem(result, 6, PConvIntArrayToPyList((int *) I->data, n_elem));
    break;
  case cFieldFloat:
    PyList_SetItem(result, 6, PConvFloatArrayToPyList((float *) I->data, n_elem));
    break;
  default:
    PyList_SetItem(result, 6, PConvAutoNone(Py_None));
    break;
  }

#if 0
  int type;
  char *data;
  unsigned int *dim;
  unsigned int *stride;
  int n_dim;
  unsigned int size;
  unsigned int base_size;
#endif

  return (PConvAutoNone(result));
#endif

}

CField *FieldNewCopy(PyMOLGlobals * G, CField * src)
{
  int ok = true;
  OOAlloc(G, CField);

  I->type = src->type;
  I->n_dim = src->n_dim;
  I->base_size = src->base_size;
  I->size = src->size;

  {
    int a;
    I->dim = Alloc(unsigned int, src->n_dim);
    I->stride = Alloc(unsigned int, src->n_dim);
    ok = I->dim && I->stride;
    if(ok)
      for(a = 0; a < src->n_dim; a++) {
        I->dim[a] = src->dim[a];
        I->stride[a] = src->stride[a];
      }
  }

  if(ok) {
    unsigned int n_elem = I->size / I->base_size;
    switch (I->type) {
    case cFieldInt:
      ok = ((I->data = (char *) Alloc(int, n_elem)) != NULL);
      if(ok)
        memcpy(I->data, src->data, sizeof(int) * n_elem);
      break;
    case cFieldFloat:
      ok = ((I->data = (char *) Alloc(float, n_elem)) != NULL);
      if(ok)
        memcpy(I->data, src->data, sizeof(float) * n_elem);
      break;
    default:
      ok = ((I->data = (char *) Alloc(char, I->size)) != NULL);
      if(ok)
        memcpy(I->data, src->data, I->size);
      break;
    }
  }
  if(!ok) {
    if(I) {
      FreeP(I->data);
      FreeP(I->dim);
      FreeP(I->stride);
      OOFreeP(I);
    }
    I = NULL;
  }
  return I;
}

CField *FieldNewFromPyList(PyMOLGlobals * G, PyObject * list)
{
#ifdef _PYMOL_NOPY
  return NULL;
#else
  int ok = true;
  unsigned int n_elem;
  int ll;
  int *I_dim = NULL;
  int *I_stride = NULL;

  OOAlloc(G, CField);

  if(ok)
    ok = (list != NULL);
  if(ok)
    ok = PyList_Check(list);
  if(ok)
    ll = PyList_Size(list);
  if(ok)
    ok = PConvPyIntToInt(PyList_GetItem(list, 0), &I->type);
  if(ok)
    ok = PConvPyIntToInt(PyList_GetItem(list, 1), &I->n_dim);
  if(ok)
    ok = PConvPyIntToInt(PyList_GetItem(list, 2), (int *) &I->base_size);
  if(ok)
    ok = PConvPyIntToInt(PyList_GetItem(list, 3), (int *) &I->size);
  if(ok)
    ok = PConvPyListToIntArray(PyList_GetItem(list, 4), &I_dim);
  if(ok)
    I->dim = (unsigned int *) I_dim;
  if(ok)
    ok = PConvPyListToIntArray(PyList_GetItem(list, 5), &I_stride);
  if(ok)
    I->stride = (unsigned int *) I_stride;

  /* TO SUPPORT BACKWARDS COMPATIBILITY...
     Always check ll when adding new PyList_GetItem's */

  if(ok) {
    n_elem = I->size / I->base_size;
    switch (I->type) {
    case cFieldInt:
      {
        int *I_data;
        ok = PConvPyListToIntArray(PyList_GetItem(list, 6), &I_data);
        I->data = (char *) I_data;
      }
      break;
    case cFieldFloat:
      {
        float *I_data;
        ok = PConvPyListToFloatArray(PyList_GetItem(list, 6), &I_data);
        I->data = (char *) I_data;
      }
      break;
    default:
      I->data = (char *) mmalloc(I->size);
      break;
    }
  }
  if(!ok) {
    OOFreeP(I);
    I = NULL;
  }
  return (I);
#endif
}

float FieldInterpolatef(CField * I, int a, int b, int c, float x, float y, float z)
{
  /* basic trilinear interpolation */

  register float x1, y1, z1;
  register float result1 = 0.0F, result2 = 0.0F;
  register float product1, product2;
  x1 = 1.0F - x;
  y1 = 1.0F - y;
  z1 = 1.0F - z;

#if 0
  if((product1 = x1 * y1 * z1) != 0.0F)
    result1 += product1 * Ffloat3(I, a, b, c);
  if((product2 = x * y1 * z1) != 0.0F)
    result2 += product2 * Ffloat3(I, a + 1, b, c);
  if((product1 = x1 * y * z1) != 0.0F)
    result1 += product1 * Ffloat3(I, a, b + 1, c);
  if((product2 = x1 * y1 * z) != 0.0F)
    result2 += product2 * Ffloat3(I, a, b, c + 1);
  if((product1 = x * y * z1) != 0.0F)
    result1 += product1 * Ffloat3(I, a + 1, b + 1, c);
  if((product2 = x1 * y * z) != 0.0F)
    result2 += product2 * Ffloat3(I, a, b + 1, c + 1);
  if((product1 = x * y1 * z) != 0.0F)
    result1 += product1 * Ffloat3(I, a + 1, b, c + 1);
  if((product2 = x * y * z) != 0.0F)
    result2 += product2 * Ffloat3(I, a + 1, b + 1, c + 1);
#else
  {
    register char *data = I->data;
    register int a_st = I->stride[0];
    register int b_st = I->stride[1];
    register int c_st = I->stride[2];
    register int a_bs = a * a_st;
    register int b_bs = b * b_st;
    register int c_bs = c * c_st;

    if((product1 = x1 * y1 * z1) != 0.0F)
      result1 += product1 * (*((float *) (data + a_bs + b_bs + c_bs)));
    if((product2 = x * y1 * z1) != 0.0F)
      result2 += product2 * (*((float *) (data + a_bs + a_st + b_bs + c_bs)));
    if((product1 = x1 * y * z1) != 0.0F)
      result1 += product1 * (*((float *) (data + a_bs + b_bs + b_st + c_bs)));
    if((product2 = x1 * y1 * z) != 0.0F)
      result2 += product2 * (*((float *) (data + a_bs + b_bs + c_bs + c_st)));
    if((product1 = x * y * z1) != 0.0F)
      result1 += product1 * (*((float *) (data + a_bs + a_st + b_bs + b_st + c_bs)));
    if((product2 = x1 * y * z) != 0.0F)
      result2 += product2 * (*((float *) (data + a_bs + b_bs + b_st + c_bs + c_st)));
    if((product1 = x * y1 * z) != 0.0F)
      result1 += product1 * (*((float *) (data + a_bs + a_st + b_bs + c_bs + c_st)));
    if((product2 = x * y * z) != 0.0F)
      result2 +=
        product2 * (*((float *) (data + a_bs + a_st + b_bs + b_st + c_bs + c_st)));
  }
#endif

  /*
     printf("%8.5f %8.5f %8.5f %8.3f\n %8.5f %8.5f %8.5f %8.5f \n",
     (Ffloat3(I,a  ,b  ,c  )),
     (Ffloat3(I,a+1,b  ,c  )),
     (Ffloat3(I,a  ,b+1,c  )),
     (Ffloat3(I,a  ,b  ,c+1)),
     (Ffloat3(I,a+1,b+1,c  )),
     (Ffloat3(I,a  ,b+1,c+1)),
     (Ffloat3(I,a+1,b  ,c+1)),
     (Ffloat3(I,a+1,b+1,c+1))); */

  return (result1 + result2);

}


/*
float FieldExtrapolatef(CField *I,int a,int b,int c,float x,float y,float z)
{
  float ix = (x > 1.0F) ? 1.0F : 0.0F;
  float iy = (y > 1.0F) ? 1.0F : 0.0F;
  float iz = (z > 1.0F) ? 1.0F : 0.0F;

  x -= ix;
  y -= iy;
  z -= iz;

  {
    float base = FieldInterpolatef(I,a,b,c,ix,iy,iz) - FieldInterpolatef(I,a,b,c,0.0F,0.0F,0.0F);
    float offset = FieldInterpolatef(I,a,b,c,x,y,z);
    return base + offset;
  }
}
*/

void FieldInterpolate3f(CField * I, int *locus, float *fract, float *result)
{
  /* basic trilinear interpolation */

  register float x = fract[0];
  register float y = fract[1];
  register float z = fract[2];
  register float x1, y1, z1;
  register float result1, result2;
  register float product1, product2;
  register int a = locus[0];
  register int b = locus[1];
  register int c = locus[2];
  register int d;

  x1 = 1.0F - x;
  y1 = 1.0F - y;
  z1 = 1.0F - z;

#if 0
  for(d = 0; d < 3; d++) {
    result1 = 0.0F;
    result2 = 0.0F;

    if((product1 = x1 * y1 * z1) != 0.0F)
      result1 += product1 * Ffloat4(I, a, b, c, d);
    if((product2 = x * y1 * z1) != 0.0F)
      result2 += product2 * Ffloat4(I, a + 1, b, c, d);
    if((product1 = x1 * y * z1) != 0.0F)
      result1 += product1 * Ffloat4(I, a, b + 1, c, d);
    if((product2 = x1 * y1 * z) != 0.0F)
      result2 += product2 * Ffloat4(I, a, b, c + 1, d);
    if((product1 = x * y * z1) != 0.0F)
      result1 += product1 * Ffloat4(I, a + 1, b + 1, c, d);
    if((product2 = x1 * y * z) != 0.0F)
      result2 += product2 * Ffloat4(I, a, b + 1, c + 1, d);
    if((product1 = x * y1 * z) != 0.0F)
      result1 += product1 * Ffloat4(I, a + 1, b, c + 1, d);
    if((product2 = x * y * z) != 0.0F)
      result2 += product2 * Ffloat4(I, a + 1, b + 1, c + 1, d);

    result[d] = result1 + result2;
  }
#else
  {
    register char *data = I->data;
    register int a_st = I->stride[0];
    register int b_st = I->stride[1];
    register int c_st = I->stride[2];
    register int d_st = I->stride[3];
    register int a_bs = a * a_st;
    register int b_bs = b * b_st;
    register int c_bs = c * c_st;

    for(d = 0; d < 3; d++) {
      register int d_bs = d * d_st;
      result1 = 0.0F;
      result2 = 0.0F;

      if((product1 = x1 * y1 * z1) != 0.0F)
        result1 += product1 * (*((float *) (data + a_bs + b_bs + c_bs + d_bs)));
      if((product2 = x * y1 * z1) != 0.0F)
        result2 += product2 * (*((float *) (data + a_bs + a_st + b_bs + c_bs + d_bs)));
      if((product1 = x1 * y * z1) != 0.0F)
        result1 += product1 * (*((float *) (data + a_bs + b_bs + b_st + c_bs + d_bs)));
      if((product2 = x1 * y1 * z) != 0.0F)
        result2 += product2 * (*((float *) (data + a_bs + b_bs + c_bs + c_st + d_bs)));
      if((product1 = x * y * z1) != 0.0F)
        result1 +=
          product1 * (*((float *) (data + a_bs + a_st + b_bs + b_st + c_bs + d_bs)));
      if((product2 = x1 * y * z) != 0.0F)
        result2 +=
          product2 * (*((float *) (data + a_bs + b_bs + b_st + c_bs + c_st + d_bs)));
      if((product1 = x * y1 * z) != 0.0F)
        result1 +=
          product1 * (*((float *) (data + a_bs + a_st + b_bs + c_bs + c_st + d_bs)));
      if((product2 = x * y * z) != 0.0F)
        result2 +=
          product2 *
          (*((float *) (data + a_bs + a_st + b_bs + b_st + c_bs + c_st + d_bs)));

      result[d] = result1 + result2;
    }
  }
#endif
}

int FieldSmooth3f(CField * I)
{
  register int a, b, c;
  register int na = I->dim[0], nb = I->dim[1], nc = I->dim[2];
  int n_pts = na * nb * nc;
  char *data = (char *) mmalloc(sizeof(float) * n_pts);
  register int x, y, z;
  register int da, db, dc;
  register double tot;
  register float cur;
  register double inp_sum = 0.0;
  register double inp_sumsq = 0.0;
  register double out_sum = 0.0;
  register double out_sumsq = 0.0;
  register int mult, cnt;
  float inp_mean, out_mean, inp_stdev, out_stdev;

  if(data) {
    for(a = 0; a < na; a++)
      for(b = 0; b < nb; b++)
        for(c = 0; c < nc; c++) {
          cur = Ffloat3(I, a, b, c);
          inp_sum += cur;
          inp_sumsq += cur * cur;
          tot = 0.0;
          cnt = 0;
          for(x = -1; x < 2; x++)
            for(y = -1; y < 2; y++)
              for(z = -1; z < 2; z++) {
                da = a + x;
                db = b + y;
                dc = c + z;
                if((da >= 0) && (da < na) &&
                   (db >= 0) && (db < nb) && (dc >= 0) && (dc < nc)) {

                  mult = 1;
                  if(!x)
                    mult = (mult << 1);
                  if(!y)
                    mult = (mult << 1);
                  if(!z)
                    mult = (mult << 1);

                  cur = Ffloat3(I, da, db, dc);
                  tot += mult * cur;
                  cnt += mult;
                }
              }
          tot = tot / cnt;
          *((float *) (data +
                       (a) * I->stride[0] +
                       (b) * I->stride[1] + (c) * I->stride[2])) = (float) tot;
          out_sum += tot;
          out_sumsq += (tot * tot);
        }
    mfree(I->data);
    I->data = data;

    inp_mean = (float) (inp_sum / n_pts);
    inp_stdev = (float) sqrt1d((inp_sumsq - (inp_sum * inp_sum / n_pts)) / (n_pts - 1));

    out_mean = (float) (out_sum / n_pts);
    out_stdev = (float) sqrt1d((out_sumsq - (out_sum * out_sum / n_pts)) / (n_pts - 1));

    if(out_stdev != 0.0F) {
      float scale = inp_stdev / out_stdev;

      for(a = 0; a < na; a++)
        for(b = 0; b < nb; b++)
          for(c = 0; c < nc; c++) {
            cur = Ffloat3(I, a, b, c);
            cur = (cur - out_mean) * scale + inp_mean;
            Ffloat3(I, a, b, c) = cur;
          }
    }
    return 1;
  }
  return 0;
}

void FieldZero(CField * I)
{
  char *p, *q;
  p = (char *) I->data;
  q = p + I->size;
  MemoryZero(p, q);
}

CField *FieldNew(PyMOLGlobals * G, int *dim, int n_dim, unsigned int base_size, int type)
{
  unsigned int stride;
  int a;

  OOAlloc(G, CField);
  I->type = type;
  I->base_size = base_size;
  I->stride = (unsigned int *) Alloc(int, n_dim);
  I->dim = (unsigned int *) Alloc(int, n_dim);

  stride = base_size;
  for(a = n_dim - 1; a >= 0; a--) {
    I->stride[a] = stride;
    I->dim[a] = dim[a];
    stride *= dim[a];
  }
  I->data = (char *) mmalloc(stride);
  I->n_dim = n_dim;
  I->size = stride;
  return (I);
}

void FieldFree(CField * I)
{
  if(I) {
    FreeP(I->dim);
    FreeP(I->stride);
    FreeP(I->data);
  }
  OOFreeP(I);
}

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