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pymol-open-source/layer2/ObjectVolume.cpp
Jarrett Johnson 5a67f3816d clang-format ObjectVolume module
2025-09-26 12:07:30 -04:00

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/*
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 <algorithm>
#include "os_python.h"
#include "os_gl.h"
#include "os_predef.h"
#include "os_std.h"
#include <math.h>
#include "Base.h"
#include "Color.h"
#include "Err.h"
#include "Executive.h"
#include "Feedback.h"
#include "Field.h"
#include "Isosurf.h"
#include "Map.h"
#include "Matrix.h"
#include "MemoryDebug.h"
#include "ObjectGadgetRamp.h"
#include "ObjectVolume.h"
#include "P.h"
#include "PConv.h"
#include "Parse.h"
#include "Scene.h"
#include "Setting.h"
#include "ShaderMgr.h"
#include "Vector.h"
#include "main.h"
#define clamp(x, l, h) ((x) < (l) ? (l) : (x) > (h) ? (h) : (x))
static void ObjectVolumeRecomputeExtent(ObjectVolume* I);
static ObjectVolumeState* ObjectVolumeGetActiveState(ObjectVolume* I)
{
if (!I) {
return nullptr;
}
for (auto& state : I->State) {
if (state.Active) {
return &state;
}
}
return nullptr;
}
CObjectState* ObjectVolume::_getObjectState(int state)
{
return &State[state];
}
static ObjectMapState* ObjectVolumeStateGetMapState(ObjectVolumeState* vs)
{
ObjectMap* map = nullptr;
PyMOLGlobals* G = vs->G;
map = ExecutiveFindObjectMapByName(G, vs->MapName);
if (!map) {
PRINTFB(G, FB_ObjectVolume, FB_Errors)
"ObjectVolume-Error: map '%s' has been deleted.\n", vs->MapName ENDFB(G);
return nullptr;
}
return ObjectMapGetState(map, vs->MapState);
}
ObjectMapState* ObjectVolumeGetMapState(ObjectVolume* I)
{
ObjectVolumeState* ovs = ObjectVolumeGetActiveState(I);
if (ovs)
return ObjectVolumeStateGetMapState(ovs);
return nullptr;
}
static PyObject* ObjectVolumeStateAsPyList(ObjectVolumeState* I)
{
PyObject* result = nullptr;
result = PyList_New(19);
PyList_SetItem(result, 0, PyInt_FromLong(I->Active));
PyList_SetItem(result, 1, PyString_FromString(I->MapName));
PyList_SetItem(result, 2, PyInt_FromLong(I->MapState));
PyList_SetItem(
result, 3, PConvAutoNone(nullptr) /* CrystalAsPyList(&I->Crystal) */);
PyList_SetItem(result, 4, PyInt_FromLong(I->ExtentFlag));
PyList_SetItem(result, 5, PConvFloatArrayToPyList(I->ExtentMin, 3));
PyList_SetItem(result, 6, PConvFloatArrayToPyList(I->ExtentMax, 3));
PyList_SetItem(result, 7,
PConvAutoNone(nullptr) /* PConvIntArrayToPyList(I->Range, 6) */);
PyList_SetItem(result, 8, PyFloat_FromDouble(0.0 /* I->Level */));
PyList_SetItem(result, 9, PyFloat_FromDouble(0.0 /* I->Radius */));
PyList_SetItem(result, 10,
PyInt_FromLong(/* I->CarveFlag */ I->AtomVertex.data() != nullptr));
PyList_SetItem(result, 11, PyFloat_FromDouble(I->CarveBuffer));
PyList_SetItem(result, 12,
I->AtomVertex ? PConvFloatVLAToPyList(I->AtomVertex)
: PConvAutoNone(nullptr));
PyList_SetItem(result, 13, PyInt_FromLong(0 /* I->VolumeMode */));
PyList_SetItem(result, 14, PyFloat_FromDouble(0.0 /* I->AltLevel */));
PyList_SetItem(result, 15, PyInt_FromLong(1 /* I->quiet */));
if (I->Field) {
PyList_SetItem(result, 16, IsosurfAsPyList(I->G, I->Field.get()));
} else {
PyList_SetItem(result, 16, PConvAutoNone(nullptr));
}
PyList_SetItem(result, 17, PyInt_FromLong(I->RampSize()));
if (!I->Ramp.empty()) {
PyList_SetItem(result, 18, PConvToPyObject(I->Ramp));
} else {
PyList_SetItem(result, 18, PConvAutoNone(nullptr));
}
return (PConvAutoNone(result));
}
static PyObject* ObjectVolumeAllStatesAsPyList(ObjectVolume* I)
{
auto result = PyList_New(I->State.size());
for (int a = 0; a < I->State.size(); a++) {
if (I->State[a].Active) {
PyList_SetItem(result, a, ObjectVolumeStateAsPyList(&I->State[a]));
} else {
PyList_SetItem(result, a, PConvAutoNone(nullptr));
}
}
return (PConvAutoNone(result));
}
static int ObjectVolumeStateFromPyList(
PyMOLGlobals* G, ObjectVolumeState* I, PyObject* list)
{
int ok = true;
int ll = 0;
PyObject* tmp;
if (ok)
ok = (list != nullptr);
if (ok) {
if (!PyList_Check(list))
I->Active = false;
else {
*I = ObjectVolumeState(G);
if (ok)
ok = (list != nullptr);
if (ok)
ok = PyList_Check(list);
if (ok)
ll = PyList_Size(list);
/* TO SUPPORT BACKWARDS COMPATIBILITY...
Always check ll when adding new PyList_GetItem's */
if (ok)
ok = PConvPyIntToInt(PyList_GetItem(list, 0), &I->Active);
if (ok)
ok = PConvPyStrToStr(PyList_GetItem(list, 1), I->MapName, WordLength);
if (ok)
ok = PConvPyIntToInt(PyList_GetItem(list, 2), &I->MapState);
#if 0
if(ok)
ok = CrystalFromPyList(&I->Crystal, PyList_GetItem(list, 3));
#endif
if (ok)
ok = PConvPyIntToInt(PyList_GetItem(list, 4), &I->ExtentFlag);
if (ok)
ok = PConvPyListToFloatArrayInPlace(
PyList_GetItem(list, 5), I->ExtentMin, 3);
if (ok)
ok = PConvPyListToFloatArrayInPlace(
PyList_GetItem(list, 6), I->ExtentMax, 3);
#if 0
if(ok)
ok = PConvPyListToIntArrayInPlace(PyList_GetItem(list, 7), I->Range, 6);
if(ok)
ok = PConvPyFloatToFloat(PyList_GetItem(list, 8), &I->Level);
if(ok)
ok = PConvPyFloatToFloat(PyList_GetItem(list, 9), &I->Radius);
if(ok)
ok = PConvPyIntToInt(PyList_GetItem(list, 10), &I->CarveFlag);
#endif
if (ok)
ok = PConvPyFloatToFloat(PyList_GetItem(list, 11), &I->CarveBuffer);
if (ok) {
tmp = PyList_GetItem(list, 12);
if (tmp == Py_None)
I->AtomVertex = nullptr;
else
ok = PConvPyListToFloatVLA(tmp, &I->AtomVertex);
}
#if 0
if(ok)
ok = PConvPyIntToInt(PyList_GetItem(list, 13), &I->VolumeMode);
#endif
if (ok) {
I->RefreshFlag = true;
I->ResurfaceFlag = true;
}
#if 0
if(ok && (ll > 14)) {
ok = PConvPyFloatToFloat(PyList_GetItem(list, 14), &I->AltLevel);
} else {
I->AltLevel = I->Level;
}
if(ok && (ll > 15)) {
ok = PConvPyIntToInt(PyList_GetItem(list, 15), &I->quiet);
} else {
I->quiet = true;
}
#endif
if (ok && (ll > 16)) {
tmp = PyList_GetItem(list, 16);
if (CPythonVal_IsNone(tmp))
I->Field.reset();
else {
I->Field.reset(IsosurfNewFromPyList(G, tmp));
ok = I->Field != nullptr;
}
CPythonVal_Free(tmp);
}
#if 0
if (ok && (ll > 17)) {
ok = PConvPyIntToInt(PyList_GetItem(list, 17), &I->RampSize);
}
#endif
if (ok && (ll > 18)) {
tmp = PyList_GetItem(list, 18);
if (!CPythonVal_IsNone(tmp))
ok = PConvFromPyObject(G, tmp, I->Ramp);
CPythonVal_Free(tmp);
}
}
}
return (ok);
}
static int ObjectVolumeAllStatesFromPyList(ObjectVolume* I, PyObject* list)
{
int ok = true;
VecCheckEmplace(I->State, I->State.size(), I->G);
if (ok)
ok = PyList_Check(list);
if (ok) {
for (int a = 0; a < I->State.size(); a++) {
CPythonVal* val = CPythonVal_PyList_GetItem(I->G, list, a);
ok = ObjectVolumeStateFromPyList(I->G, &I->State[a], val);
CPythonVal_Free(val);
if (!ok)
break;
}
}
return (ok);
}
int ObjectVolumeNewFromPyList(
PyMOLGlobals* G, PyObject* list, ObjectVolume** result)
{
int ok = true;
ObjectVolume* I = nullptr;
(*result) = nullptr;
if (ok)
ok = (list != nullptr);
if (ok)
ok = PyList_Check(list);
/* TO SUPPORT BACKWARDS COMPATIBILITY...
Always check ll when adding new PyList_GetItem's */
I = new ObjectVolume(G);
if (ok)
ok = (I != nullptr);
if (ok) {
auto* val = PyList_GetItem(list, 0);
ok = ObjectFromPyList(G, val, I);
}
if (ok) {
CPythonVal* val = CPythonVal_PyList_GetItem(G, list, 2);
ok = ObjectVolumeAllStatesFromPyList(I, val);
CPythonVal_Free(val);
}
if (ok) {
(*result) = I;
ObjectVolumeRecomputeExtent(I);
} else {
/* cleanup? */
}
return (ok);
}
PyObject* ObjectVolumeAsPyList(ObjectVolume* I)
{
auto result = PyList_New(3);
PyList_SetItem(result, 0, ObjectAsPyList(I));
PyList_SetItem(result, 1, PyInt_FromLong(I->State.size()));
PyList_SetItem(result, 2, ObjectVolumeAllStatesAsPyList(I));
return (PConvAutoNone(result));
}
ObjectVolumeState::~ObjectVolumeState()
{
if (G->HaveGUI) {
std::array<std::size_t, std::tuple_size<decltype(textures)>::value> t{};
std::transform(textures.begin(), textures.end(), t.begin(),
[](const pymol::cache_value<std::size_t>& value) {
return value.value;
});
G->ShaderMgr->freeGPUBuffers(t.data(), 3);
}
}
int ObjectVolumeInvalidateMapName(
ObjectVolume* I, const char* name, const char* new_name)
{
int result = false;
for (int a = 0; a < I->State.size(); a++) {
auto vs = &I->State[a];
if (vs->Active) {
if (strcmp(vs->MapName, name) == 0) {
if (new_name)
strcpy(vs->MapName, new_name);
I->invalidate(cRepAll, cRepInvAll, a);
result = true;
}
}
}
return result;
}
void ObjectVolume::invalidate(cRep_t rep, cRepInv_t level, int state)
{
auto I = this;
int a;
int once_flag = true;
if (level >= cRepInvExtents) {
I->ExtentFlag = false;
}
PRINTFB(I->G, FB_ObjectVolume, FB_Blather)
"ObjectVolumeInvalidate-Msg: %zu states.\n", I->State.size() ENDFB(I->G);
if ((rep == cRepVolume) || (rep == cRepAll) || (rep == cRepExtent)) {
for (a = 0; a < I->State.size(); a++) {
if (state < 0)
once_flag = false;
if (!once_flag)
state = a;
if (level == cRepInvColor || level == cRepInvAll) {
I->State[state].RecolorFlag = true;
}
if (level != cRepInvColor) {
I->State[state].ResurfaceFlag = true;
I->State[state].RefreshFlag = true;
}
SceneChanged(I->G);
if (once_flag)
break;
}
}
}
/**
* Get the field either from the associated map, or from vs->Field in case
* this is a reduced or symmetry expanded volume.
*/
static CField* ObjectVolumeStateGetField(ObjectVolumeState* vs)
{
if (!vs)
return nullptr;
if (vs->Field)
return vs->Field->data.get();
return ObjectVolumeStateGetMapState(vs)->Field->data.get();
}
CField* ObjectVolumeGetField(ObjectVolume* I)
{
return ObjectVolumeStateGetField(ObjectVolumeGetActiveState(I));
}
/**
* Get a 4x4 (incl. translation) FracToReal from corner array
*/
static void get44FracToRealFromCorner(const float* corner, float* frac2real)
{
float tmp[16];
identity44f(tmp);
subtract3f(corner + 3, corner, tmp);
subtract3f(corner + 6, corner, tmp + 4);
subtract3f(corner + 12, corner, tmp + 8);
copy3f(corner, tmp + 12);
transpose44f44f(tmp, frac2real);
}
void ObjectVolume::update()
{
auto I = this;
ObjectMapState* oms = nullptr;
float carve_buffer;
int avoid_flag = false;
int flag;
int h, k, l;
int i, j;
float range;
MapType* voxelmap; /* this has nothing to do with isosurfaces... */
for (int a = 0; a < I->State.size(); a++) {
auto vs = &I->State[a];
if (!vs || !vs->Active)
continue;
PRINTFD(G, FB_ObjectVolume)
"ObjectVolumeUpdate: state=%d, refresh=%d, resurface=%d.\n", a,
vs->RefreshFlag, vs->ResurfaceFlag ENDFD;
oms = ObjectVolumeStateGetMapState(vs);
if (!oms) {
vs->ResurfaceFlag = false;
continue;
}
if (vs->RefreshFlag || vs->ResurfaceFlag) {
if (!oms->Matrix.empty()) {
ObjectStateSetMatrix(vs, oms->Matrix.data());
} else if (!vs->Matrix.empty()) {
ObjectStateResetMatrix(vs);
}
// data min/max/mean/stdev
range = SettingGet_f(
I->G, I->Setting.get(), nullptr, cSetting_volume_data_range);
ObjectMapStateGetHistogram(
I->G, oms, 0, range, vs->min_max_mean_stdev, 0.f, 0.f);
}
// handle legacy or default color ramp
if (vs->Ramp.empty() || (vs->RampSize() && vs->Ramp[0] == 0.f &&
vs->Ramp[5 * (vs->RampSize() - 1)] == 359.f)) {
if (!vs->Ramp.empty()) {
// legacy color ramp (0..359)
range = vs->min_max_mean_stdev[1] - vs->min_max_mean_stdev[0];
PRINTFB(G, FB_ObjectVolume, FB_Warnings)
" ObjectVolumeUpdate: detected legacy color ramp\n" ENDFB(G);
for (i = 0; i < vs->Ramp.size(); i += 5) {
vs->Ramp[i] = vs->Ramp[i] / 359.f * range + vs->min_max_mean_stdev[0];
}
} else {
// default color ramp (1.0 sigma peak)
if (vs->Ramp.empty()) {
vs->Ramp = std::vector<float>(
{vs->min_max_mean_stdev[2] + 0.7f * vs->min_max_mean_stdev[3],
0.f, 0.f, 1.f, 0.0f,
vs->min_max_mean_stdev[2] + 1.0f * vs->min_max_mean_stdev[3],
0.f, 1.f, 1.f, 0.2f,
vs->min_max_mean_stdev[2] + 1.3f * vs->min_max_mean_stdev[3],
0.f, 0.f, 1.f, 0.0f});
vs->RecolorFlag = true;
}
}
}
if ((I->visRep & cRepVolumeBit) && vs->ResurfaceFlag) {
Isofield* field = nullptr;
vs->ResurfaceFlag = false;
if (vs->Field) {
field = vs->Field.get();
} else if (oms->Field) {
field = oms->Field.get();
} else {
field = nullptr;
}
if (field) {
// get bounds and dimension data from field
copy3(field->data->dim.data(), vs->dim);
IsofieldGetCorners(G, field, vs->Corner);
// transform corners by state matrix
if (!vs->Matrix.empty()) {
for (i = 0; i < 8; i++)
transform44d3f(
vs->Matrix.data(), vs->Corner + 3 * i, vs->Corner + 3 * i);
}
}
if (/* CarveFlag */ vs->AtomVertex) {
carve_buffer = vs->CarveBuffer;
if (vs->CarveBuffer < 0.0F) {
avoid_flag = true;
carve_buffer = -carve_buffer;
}
// cull my friend, cull */
voxelmap = new MapType(I->G, -carve_buffer, vs->AtomVertex,
vs->AtomVertex.size() / 3, nullptr);
if (voxelmap) {
int x, y, z;
int dx, dy, dz;
float vv[3];
float frac2real[16];
MapSetupExpress(voxelmap);
dx = vs->dim[0];
dy = vs->dim[1];
dz = vs->dim[2];
get44FracToRealFromCorner(vs->Corner, frac2real);
// initialize carve mask
vs->carvemask = pymol::make_copyable<CField>(
G, (int*) vs->dim, 3, sizeof(GLubyte), cFieldOther);
// loop over voxels
for (z = 0; z < dz; z++) {
for (y = 0; y < dy; y++) {
for (x = 0; x < dx; x++) {
float frac[3] = {
(x + .5f) / dx, (y + .5f) / dy, (z + .5f) / dz};
transform44f3f(frac2real, frac, vv);
flag = avoid_flag;
// loop over close atoms
MapLocus(voxelmap, vv, &h, &k, &l);
for (i = *(MapEStart(voxelmap, h, k, l));
i && (j = voxelmap->EList[i]) >= 0; i++) {
if (within3f(
vs->AtomVertex.data() + 3 * j, vv, carve_buffer)) {
flag = !flag;
break;
}
}
// 0xFF (masked) or 0 (not masked), will be 1.0 or 0.0 in shader
vs->carvemask->get<GLubyte>(x, y, z) = flag ? 0x0 : 0xFF;
}
}
}
MapFree(voxelmap);
}
}
}
vs->isUpdated = true;
SceneInvalidate(I->G);
}
if (!I->ExtentFlag) {
ObjectVolumeRecomputeExtent(I);
if (I->ExtentFlag)
SceneInvalidate(I->G);
}
}
static int ObjectVolumeAddSlicePoint(float* p0, float* p1, float* zaxis,
float d, float* slice, float* t0, float* t1, float* tex_coords,
float* origin);
static void ObjectVolumeDrawSlice(
float* points, float* tex_coords, int n_points, float* zaxis);
/**
* Converting Ramp to `count * 4` sized interpolated RGBA color
* array. Returns allocated memory.
* Assigns data minimum and range covered by ramp to `ramp_min` and
* `ramp_range`.
*/
static float* ObjectVolumeStateGetColors(PyMOLGlobals* G,
ObjectVolumeState* ovs, int count, float* ramp_min, float* ramp_range)
{
int i, j, k;
int lowerId, upperId = 0;
float mixc, mixcincr, r_min, range;
float stdev = ovs->min_max_mean_stdev[3];
float* colors;
ok_assert(1, ovs->RampSize() > 1);
r_min = ovs->Ramp[0];
range = ovs->Ramp[5 * (ovs->RampSize() - 1)] - r_min;
ok_assert(1, range > R_SMALL4);
r_min -= stdev * 0.5;
range += stdev;
colors = pymol::calloc<float>(4 * count);
ok_assert(1, colors);
for (i = 0; i < ovs->RampSize(); i++) {
lowerId = upperId;
upperId = (int) (count * (ovs->Ramp[i * 5] - r_min) / range);
if (i == 0)
continue;
mixcincr = 1.f / (upperId - lowerId);
for (j = lowerId, mixc = 1.f; j < upperId; j++, mixc -= mixcincr) {
if (j < 0 || j >= count)
continue;
for (k = 0; k < 4; k++)
colors[j * 4 + k] = ovs->Ramp[i * 5 - 4 + k] * mixc +
ovs->Ramp[i * 5 + 1 + k] * (1.f - mixc);
}
}
*ramp_min = r_min;
*ramp_range = range;
return colors;
ok_except1:
PRINTFB(G, FB_ObjectVolume, FB_Blather)
"ObjectVolumeStateGetColors failed\n" ENDFB(G);
return nullptr;
}
/**
* Adjust alpha values in the given RGBA array (in place) by:
* alpha_new = 1 - exp(-alpha * factor)
*/
static void ColorsAdjustAlpha(float* colors, int count, float factor)
{
int j;
for (j = 3; j < count * 4; j += 4) {
colors[j] = 1. - expf(-colors[j] * factor);
}
}
/**
* Render bounding box
* TODO: duplicate in other reps?
*/
static void ExtentRender(float* corner)
{
#ifndef PURE_OPENGL_ES_2
int i, ci[] = {0, 3, 3, 9, 9, 6, 6, 0, 12, 15, 15, 21, 21, 18, 18, 12, 0, 12,
3, 15, 9, 21, 6, 18};
glBegin(GL_LINES);
for (i = 0; i < 8 * 3; i++)
glVertex3fv(corner + ci[i]);
glEnd();
#endif
}
static size_t createColorTexture(
PyMOLGlobals* G, const float* colors, const int count)
{
size_t texname = 0;
#ifndef PURE_OPENGL_ES_2
auto tex = G->ShaderMgr->newGPUBuffer<TextureGL>(tex::format::RGBA,
tex::data_type::FLOAT, tex::filter::LINEAR, tex::filter::LINEAR,
tex::wrap::CLAMP);
tex->texture_data_1D(count, colors);
texname = tex->get_hash_id();
#endif
return texname;
}
static size_t createPreintegrationTexture(
PyMOLGlobals* G, const float* Table, const int count)
{
float factor, tmp1[4];
Vector4f* sat = pymol::malloc<Vector4f>(count + 1);
int i, sb, sf, lookupindex = 0;
GLfloat* lookupImg = pymol::malloc<GLfloat>(count * count * 4);
memset(sat[0], 0, sizeof(sat[0]));
// summed area table
for (i = 0; i < count; i++) {
tmp1[3] = Table[i * 4 + 3];
scale3f(Table + i * 4, tmp1[3], tmp1);
add4f(tmp1, sat[i], sat[i + 1]);
}
// make quadratic lookup table
for (sb = 0; sb < count; sb++) {
for (sf = 0; sf < count; sf++) {
GLfloat col[4];
int smin, smax;
if (sb < sf) {
smin = sb;
smax = sf;
} else {
smin = sf;
smax = sb;
}
if (sat[smax + 1][3] != sat[smin][3]) {
factor = 1.f / (sat[smax + 1][3] - sat[smin][3]);
for (i = 0; i < 3; i++)
col[i] = (sat[smax + 1][i] - sat[smin][i]) * factor;
col[3] = 1. / (factor * (smax + 1 - smin));
} else {
for (i = 0; i < 4; i++)
col[i] = 0.f;
}
for (i = 0; i < 4; i++)
lookupImg[lookupindex++] = clamp(col[i], 0., 1.);
}
}
// upload texture
auto tex = G->ShaderMgr->newGPUBuffer<TextureGL>(tex::format::RGBA,
tex::data_type::FLOAT, tex::filter::NEAREST, tex::filter::NEAREST,
tex::wrap::CLAMP_TO_EDGE, tex::wrap::CLAMP_TO_EDGE);
tex->texture_data_2D(count, count, lookupImg);
mfree(sat);
mfree(lookupImg);
return tex->get_hash_id();
}
void ObjectVolume::render(RenderInfo* info)
{
#ifndef PURE_OPENGL_ES_2
auto I = this;
int state = info->state;
const RenderPass pass = info->pass;
int a = 0;
ObjectVolumeState* vs = nullptr;
float volume_layers =
SettingGet_f(I->G, I->Setting.get(), nullptr, cSetting_volume_layers);
#ifdef _PYMOL_IP_EXTRAS
short volume_mode = SettingGetGlobal_i(G, cSetting_volume_mode);
short ortho = SettingGetGlobal_i(G, cSetting_ortho);
#endif
/* make this a setting? */
GLint alpha_func;
GLfloat alpha_ref;
float tex_corner[24];
float* corner;
const float* ttt;
float zaxis[3];
float points[36], tex_coords[36];
int n_points;
float d, sliceRange, sliceDelta;
float origin[3];
CShaderPrg* shaderPrg;
bool volume_t = 0;
if (info->pick || pass != RenderPass::Transparent)
return;
if (!G->HaveGUI || !G->ValidContext)
return;
/* bail if no shaders */
if (G && !(G->ShaderMgr->ShadersPresent()))
return;
if (info->pass == RenderPass::Transparent) {
volume_t = SettingGetGlobal_i(G, cSetting_transparency_mode) == 3;
}
// ViewElem/TTT Matrix
ObjectPrepareContext(I, info);
for (a = 0; a < I->State.size(); ++a) {
if (state < 0 || state == a) {
vs = &I->State[a];
} else if (a == 0 && I->State.size() == 1 &&
SettingGetGlobal_b(G, cSetting_static_singletons)) {
vs = &I->State[a];
} else {
continue;
}
if (!vs || !vs->Active)
continue;
// PYMOL-3283
if (!vs->isUpdated)
I->update();
PRINTFB(I->G, FB_ObjectVolume, FB_Blather)
"ObjectVolumeRender-Msg: state=%d, pass=%d, refresh=%d, recolor=%d.\n", a,
static_cast<int>(pass), vs->RefreshFlag, vs->RecolorFlag ENDFB(I->G);
corner = vs->Corner;
SceneResetNormal(I->G, false);
// render bounding box
if ((I->visRep & cRepExtentBit)) {
if (!info->line_lighting)
glDisable(GL_LIGHTING);
ObjectUseColor(I);
ExtentRender(corner);
}
// upload color ramp texture
if (vs->RecolorFlag) {
const int volume_nColors = 512;
float* colors = ObjectVolumeStateGetColors(
G, vs, volume_nColors, &vs->ramp_min, &vs->ramp_range);
if (!colors)
continue;
// volume_layers default is 256, adjust alpha to maintain integrated
// opacity with different layer numbers
ColorsAdjustAlpha(colors, volume_nColors, 256. / volume_layers);
if (vs->textures[1]) {
G->ShaderMgr->freeGPUBuffer(vs->textures[1]);
}
vs->textures[1] =
#ifdef _PYMOL_IP_EXTRAS
#endif
createColorTexture(G, colors, volume_nColors);
tex::env(tex::env_name::ENV_MODE, tex::env_param::REPLACE);
mfree(colors);
vs->RecolorFlag = false;
}
// upload map data texture
if (!vs->textures[0] || vs->RefreshFlag) {
tex::data_type volume_bit_depth;
CField* field = ObjectVolumeStateGetField(vs);
if (!field) {
PRINTFB(G, FB_ObjectVolume, FB_Errors)
" ObjectVolumeRender-Error: Could not get field data.\n" ENDFB(G);
return;
}
int volume_bit_val =
SettingGet_i(G, I->Setting.get(), nullptr, cSetting_volume_bit_depth);
volume_bit_depth = (volume_bit_val < 17) ? tex::data_type::HALF_FLOAT
: tex::data_type::FLOAT;
if (vs->textures[0]) {
G->ShaderMgr->freeGPUBuffer(vs->textures[0]);
vs->textures[0] = 0;
}
if (vs->textures[2]) {
G->ShaderMgr->freeGPUBuffer(vs->textures[2]);
vs->textures[2] = 0;
}
auto tex3dGenBind = [](PyMOLGlobals* G, tex::data_type dtype) -> size_t {
auto texture = G->ShaderMgr->newGPUBuffer<TextureGL>(tex::format::R,
dtype, tex::filter::LINEAR, tex::filter::LINEAR, tex::wrap::CLAMP,
tex::wrap::CLAMP, tex::wrap::CLAMP);
tex::env(tex::env_name::ENV_MODE, tex::env_param::REPLACE);
return texture->get_hash_id();
};
// Create a 3D texture
vs->textures[0] = tex3dGenBind(G, volume_bit_depth);
auto t0 = G->ShaderMgr->getGPUBuffer<TextureGL>(vs->textures[0]);
t0->texture_data_3D(
field->dim[2], field->dim[1], field->dim[0], field->data.data());
// Create 3D carve mask texture
if (vs->carvemask) {
vs->textures[2] = tex3dGenBind(G, tex::data_type::UBYTE);
auto t2 = G->ShaderMgr->getGPUBuffer<TextureGL>(vs->textures[2]);
t2->texture_data_3D(vs->carvemask->dim[2], vs->carvemask->dim[1],
vs->carvemask->dim[0], vs->carvemask->data.data());
// not needed anymore, data now in texture memory
vs->carvemask.reset();
}
vs->RefreshFlag = false;
}
// render volume
if ((I->visRep & cRepVolumeBit)) {
int i, j;
glDisable(GL_LIGHTING);
// half grid cell inset in texture corners (texture coordinate units)
for (j = 0; j < 3; j++) {
float offset = 0.5 / vs->dim[2 - j];
int bit = 1 << (2 - j);
for (i = 0; i < 8; i++)
tex_corner[i * 3 + j] = (i & bit) ? 1.0 - offset : offset;
}
// for z-axis
SceneGetViewNormal(G, zaxis);
for (j = 0; j < 3; j++) {
// map center
origin[j] = corner[j] + 0.5 * (corner[21 + j] - corner[j]);
}
// TTT (movie object motions)
if (ObjectGetTTT(I, &ttt, -1))
MatrixTransformC44fAs33f3f(ttt, zaxis, zaxis);
// determine number of slices based on max extent
// and slice option
sliceRange = 0.5 * sqrt(2.0) *
std::max(std::max(fabs(corner[21] - corner[0]),
fabs(corner[22] - corner[1])),
fabs(corner[23] - corner[2]));
sliceDelta = (sliceRange / volume_layers);
// load shader
shaderPrg = G->ShaderMgr->GetShaderPrg(volume_t ? "volume_t" : "volume");
if (!shaderPrg)
return;
shaderPrg->Enable();
shaderPrg->Set_Stereo_And_AnaglyphMode();
shaderPrg->Set_Matrices();
shaderPrg->Set1i("volumeTex", 0);
shaderPrg->Set1i("colorTex1D", 1);
shaderPrg->Set1i("colorTex2D", 1);
shaderPrg->Set1i("carvemask", 5);
shaderPrg->Set1i("carvemaskFlag", vs->textures[2] != 0);
shaderPrg->Set1f("volumeScale", 1.0 / vs->ramp_range);
shaderPrg->Set1f("volumeBias", (-vs->ramp_min) / vs->ramp_range);
// for pre-integrated rendering
#ifdef _PYMOL_IP_EXTRAS
#endif
// background and fog stuff
{
shaderPrg->SetBgUniforms();
}
// bind color ramp and map data textures
glActiveTexture(GL_TEXTURE1);
G->ShaderMgr->bindGPUBuffer(vs->textures[1]);
glActiveTexture(GL_TEXTURE0);
G->ShaderMgr->bindGPUBuffer(vs->textures[0]);
if (vs->textures[2]) {
glActiveTexture(GL_TEXTURE5);
G->ShaderMgr->bindGPUBuffer(vs->textures[2]);
}
// alpha: everything passes
// Not sure if we really need to restore this
glGetIntegerv(GL_ALPHA_TEST_FUNC, &alpha_func);
glGetFloatv(GL_ALPHA_TEST_REF, &alpha_ref);
glAlphaFunc(GL_ALWAYS, 0.0);
// don't write to the depth buffer
GLboolean depth_writemask;
glGetBooleanv(GL_DEPTH_WRITEMASK, &depth_writemask);
if (depth_writemask)
glDepthMask(GL_FALSE);
// Cheap hack, should be replaced with non-immediate calls
glFlush();
glFinish();
// draw slices
{
int i, cornerindices[] = {0, 3, 3, 9, 9, 6, 6, 0, 12, 15, 15, 21, 21,
18, 18, 12, 0, 12, 3, 15, 9, 21, 6, 18};
for (d = sliceRange; d >= -sliceRange; d -= sliceDelta) {
// Slice the volume
n_points = 0;
for (i = 0; i < 24; i += 2) {
int j = cornerindices[i], k = cornerindices[i + 1];
n_points += ObjectVolumeAddSlicePoint(corner + j, corner + k, zaxis,
d, points + n_points, tex_corner + j, tex_corner + k,
tex_coords + n_points, origin);
}
ObjectVolumeDrawSlice(points, tex_coords, n_points / 3, zaxis);
}
}
shaderPrg->Disable();
// restore
if (depth_writemask)
glDepthMask(GL_TRUE);
glAlphaFunc(alpha_func, alpha_ref);
}
glEnable(GL_LIGHTING);
}
#endif
}
void ObjectVolumeDrawSlice(
float* points, float* tex_coords, int n_points, float* zaxis)
{
float center[3], v[3], w[3], q[3];
float angles[12];
float a, c, s;
int vertices[12];
int i, j;
if (!n_points)
return;
// Calculate the polygon center
zero3f(center);
for (i = 0; i < 3 * n_points; i += 3) {
add3f(center, points + i, center); // center += (points + i)
}
scale3f(center, 1. / n_points, center); // center /= n_points
subtract3f(points, center, v); // v = points - center
normalize3f(v);
// Sort vertices by rotation angle around the central axis
for (i = 0; i < n_points; i++) {
subtract3f(points + 3 * i, center, w); // w = (points + 3 * i) - center
normalize3f(w);
cross_product3f(v, w, q);
c = dot_product3f(v, w);
s = dot_product3f(zaxis, q);
a = atan2(s, c);
if (a < 0.0f)
a += 2.0f * PI;
j = i - 1;
while (j >= 0 && angles[j] > a) {
angles[j + 1] = angles[j];
vertices[j + 1] = vertices[j];
j--;
}
angles[j + 1] = a;
vertices[j + 1] = i;
}
// Now the vertices are sorted so draw the polygon
glBegin(GL_POLYGON);
for (i = 0; i < n_points; i++) {
glTexCoord3fv(&tex_coords[3 * vertices[i]]);
glVertex3fv(&points[3 * vertices[i]]);
}
glEnd();
}
int ObjectVolumeAddSlicePoint(float* pt0, float* pt1, float* zaxis, float d,
float* coords, float* t0, float* t1, float* tex_coords, float* origin)
{
float p0[3];
float p1[3];
float u;
p0[0] = pt0[0] - origin[0];
p0[1] = pt0[1] - origin[1];
p0[2] = pt0[2] - origin[2];
p1[0] = pt1[0] - origin[0];
p1[1] = pt1[1] - origin[1];
p1[2] = pt1[2] - origin[2];
u = (zaxis[0] * p0[0] + zaxis[1] * p0[1] + zaxis[2] * p0[2] + d) /
(zaxis[0] * (p0[0] - p1[0]) + zaxis[1] * (p0[1] - p1[1]) +
zaxis[2] * (p0[2] - p1[2]));
if (u >= 0.0F && u <= 1.0F) {
coords[0] = pt0[0] + (pt1[0] - pt0[0]) * u;
coords[1] = pt0[1] + (pt1[1] - pt0[1]) * u;
coords[2] = pt0[2] + (pt1[2] - pt0[2]) * u;
tex_coords[0] = t0[0] + (t1[0] - t0[0]) * u;
tex_coords[1] = t0[1] + (t1[1] - t0[1]) * u;
tex_coords[2] = t0[2] + (t1[2] - t0[2]) * u;
return 3;
}
return 0;
}
/*========================================================================*/
int ObjectVolume::getNFrame() const
{
return State.size();
}
/*========================================================================*/
ObjectVolume::ObjectVolume(PyMOLGlobals* G)
: pymol::CObject(G)
{
type = cObjectVolume;
}
/*========================================================================*/
ObjectVolumeState::ObjectVolumeState(PyMOLGlobals* G)
: CObjectState(G)
, Crystal(G)
, Active(true)
{
}
/*========================================================================*/
ObjectVolume* ObjectVolumeFromXtalSym(PyMOLGlobals* G, ObjectVolume* obj,
ObjectMap* map, CSymmetry* sym, int map_state, int state, float* mn,
float* mx, float level, int box_mode, float carve, float* vert_vla,
int quiet)
{
ObjectVolume* I;
ObjectVolumeState* vs;
ObjectMapState* oms;
int created = !obj;
if (created) {
I = new ObjectVolume(G);
} else {
I = obj;
}
if (state < 0)
state = I->State.size();
if (I->State.size() <= state) {
VecCheckEmplace(I->State, state, G);
}
vs = &I->State[state];
strcpy(vs->MapName, map->Name);
vs->MapState = map_state;
oms = ObjectMapGetState(map, map_state);
#if 0
vs->VolumeMode = meshMode;
#endif
if (oms) {
copy3f(mn, vs->ExtentMin); /* this is not exactly correct...should actually
take vertex points from range */
copy3f(mx, vs->ExtentMax);
if (!oms->Matrix.empty()) {
ObjectStateSetMatrix(vs, oms->Matrix.data());
} else if (!vs->Matrix.empty()) {
ObjectStateResetMatrix(vs);
}
{
float *min_ext, *max_ext;
float tmp_min[3], tmp_max[3];
if (MatrixInvTransformExtentsR44d3f(vs->Matrix.data(), vs->ExtentMin,
vs->ExtentMax, tmp_min, tmp_max)) {
min_ext = tmp_min;
max_ext = tmp_max;
} else {
min_ext = vs->ExtentMin;
max_ext = vs->ExtentMax;
}
if (sym && box_mode) {
int eff_range[6];
IsosurfGetRange(G, oms->Field.get(), &oms->Symmetry->Crystal, min_ext,
max_ext, eff_range, false);
{
int fdim[3];
int expand_result;
/* need to generate symmetry-expanded temporary map */
fdim[0] = eff_range[3] - eff_range[0];
fdim[1] = eff_range[4] - eff_range[1];
fdim[2] = eff_range[5] - eff_range[2];
vs->Field = pymol::make_copyable<Isofield>(I->G, fdim);
expand_result = IsosurfExpand(oms->Field.get(), vs->Field.get(),
&oms->Symmetry->Crystal, sym, eff_range);
if (expand_result == 0) {
if (!quiet) {
PRINTFB(G, FB_ObjectVolume, FB_Warnings)
" ObjectVolume-Warning: no symmetry expanded map points "
"found.\n" ENDFB(G);
}
} else {
if (!quiet) {
PRINTFB(G, FB_ObjectVolume, FB_Warnings)
" ObjectVolume-Warning: not all symmetry expanded points covered "
"by map.\n" ENDFB(G);
}
}
}
}
}
vs->ExtentFlag = true;
}
vs->CarveBuffer = carve;
vs->AtomVertex = pymol::vla_take_ownership(vert_vla);
I->ExtentFlag = false;
SceneChanged(G);
SceneCountFrames(G);
return (I);
}
/*========================================================================*/
ObjectVolume* ObjectVolumeFromBox(PyMOLGlobals* G, ObjectVolume* obj,
ObjectMap* map, int map_state, int state, float* mn, float* mx, float level,
int meshMode, float carve, float* vert_vla, int quiet)
{
return ObjectVolumeFromXtalSym(G, obj, map, nullptr, map_state, state, mn, mx,
level, meshMode, carve, vert_vla, quiet);
}
/*========================================================================*/
void ObjectVolumeRecomputeExtent(ObjectVolume* I)
{
int extent_flag = false;
for (int a = 0; a < I->State.size(); a++) {
auto vs = &I->State[a];
if (vs->Active) {
if (vs->ExtentFlag) {
if (!extent_flag) {
extent_flag = true;
copy3f(vs->ExtentMax, I->ExtentMax);
copy3f(vs->ExtentMin, I->ExtentMin);
} else {
max3f(vs->ExtentMax, I->ExtentMax, I->ExtentMax);
min3f(vs->ExtentMin, I->ExtentMin, I->ExtentMin);
}
}
}
}
I->ExtentFlag = extent_flag;
if (I->TTTFlag && I->ExtentFlag) {
const float* ttt;
double tttd[16];
if (ObjectGetTTT(I, &ttt, -1)) {
convertTTTfR44d(ttt, tttd);
MatrixTransformExtentsR44d3f(
tttd, I->ExtentMin, I->ExtentMax, I->ExtentMin, I->ExtentMax);
}
}
}
/*==============================================================================*/
PyObject* ObjectVolumeGetRamp(ObjectVolume* I, int state)
{
/* TODO: Allow for multi-state maps? */
if (!I) {
return (PConvAutoNone(nullptr));
}
if (auto ovs = static_cast<ObjectVolumeState*>(I->getObjectState(state))) {
if (!ovs->isUpdated)
I->update();
return PConvFloatArrayToPyList(ovs->Ramp.data(), ovs->Ramp.size());
}
return (PConvAutoNone(nullptr));
}
/*==============================================================================*/
pymol::Result<> ObjectVolumeSetRamp(
ObjectVolume* I, std::vector<float>&& ramp_list, int state)
{
/* TODO: Allow for multi-state maps? */
if (!I) {
return pymol::make_error("Invalid volume.");
}
if (ramp_list.empty()) {
return pymol::make_error("Empty ramp.");
}
auto ovs = static_cast<ObjectVolumeState*>(I->getObjectState(state));
if (!ovs) {
return pymol::make_error("Invalid volume state.");
}
ovs->Ramp = std::move(ramp_list);
ovs->RecolorFlag = true;
SceneChanged(I->G);
return {};
}
pymol::CObject* ObjectVolume::clone() const
{
return new ObjectVolume(*this);
}
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