/* Copyright (c) 2008-2025 the MRtrix3 contributors.
 *
 * This Source Code Form is subject to the terms of the Mozilla Public
 * License, v. 2.0. If a copy of the MPL was not distributed with this
 * file, You can obtain one at http://mozilla.org/MPL/2.0/.
 *
 * Covered Software is provided under this License on an "as is"
 * basis, without warranty of any kind, either expressed, implied, or
 * statutory, including, without limitation, warranties that the
 * Covered Software is free of defects, merchantable, fit for a
 * particular purpose or non-infringing.
 * See the Mozilla Public License v. 2.0 for more details.
 *
 * For more details, see http://www.mrtrix.org/.
 */

#include "file/config.h"
#include "gui/opengl/lighting.h"
#include "gui/mrview/mode/volume.h"
#include "gui/mrview/tool/base.h"
#include "gui/mrview/adjust_button.h"
#include "gui/mrview/tool/view.h"

namespace MR
{
  namespace GUI
  {
    namespace MRView
    {
      namespace Mode
      {

        std::string Volume::Shader::vertex_shader_source (const Displayable&)
        {
          std::string source =
            "layout(location=0) in vec3 vertpos;\n"
            "uniform mat4 M;\n"
            "out vec3 texcoord;\n";

          for (int n = 0; n < mode.overlays_for_3D.size(); ++n)
            source +=
              "uniform mat4 overlay_M" + str(n) + ";\n"
              "out vec3 overlay_texcoord" + str(n) + ";\n";

          source +=
            "void main () {\n"
            "  texcoord = vertpos;\n"
            "  gl_Position =  M * vec4 (vertpos,1);\n";

          for (int n = 0; n < mode.overlays_for_3D.size(); ++n)
            source +=
              "  overlay_texcoord"+str(n) + " = (overlay_M"+str(n) + " * vec4 (vertpos,1)).xyz;\n";

          source +=
            "}\n";

          return source;
        }






        std::string Volume::Shader::fragment_shader_source (const Displayable& object)
        {
          vector< std::pair<GL::vec4,bool> > clip = mode.get_active_clip_planes();
          const bool AND = mode.get_clipintersectionmodestate();
          std::string clip_color_spec = File::Config::get ("MRViewClipPlaneColour");
          vector<float> clip_color = { 1.0, 0.0, 0.0, 0.1 };
          if (clip_color_spec.size()) {
            auto colour = parse_floats (clip_color_spec);
            if (colour.size() != 4)
              WARN ("malformed config file entry for \"MRViewClipPlaneColour\" - expected 4 comma-separated values");
            clip_color = { float(colour[0]), float(colour[1]), float(colour[2]), float(colour[3]) };
          }

          std::string source = object.declare_shader_variables() +
            "uniform sampler3D image_sampler;\n"
            "in vec3 texcoord;\n";

          for (size_t n = 0; n < clip.size(); ++n)
            source +=
              "uniform vec4 clip" + str(n) + ";\n"
              "uniform int clip" + str(n) + "_selected;\n";

          for (int n = 0; n < mode.overlays_for_3D.size(); ++n) {
            source += mode.overlays_for_3D[n]->declare_shader_variables ("overlay"+str(n)+"_") +
              "uniform sampler3D overlay_sampler"+str(n) + ";\n" +
              "uniform vec3 overlay_ray"+str(n) + ";\n"
              "uniform vec3 overlay" + str(n) + "_colourmap_colours;\n"
              "in vec3 overlay_texcoord"+str(n) + ";\n";
          }

          source +=
            "uniform sampler2D depth_sampler;\n"
            "uniform mat4 M;\n"
            "uniform float ray_z, selection_thickness;\n"
            "uniform vec3 ray;\n"
            "out vec4 final_color;\n"
            "void main () {\n"
            "  float amplitude;\n"
            "  vec4 color;\n";


          source +=
            "  final_color = vec4 (0.0);\n"
            "  float dither = fract(sin(gl_FragCoord.x * 12.9898 + gl_FragCoord.y * 78.233) * 43758.5453);\n"
            "  vec3 coord = texcoord + ray * dither;\n";

          for (int n = 0; n < mode.overlays_for_3D.size(); ++n)
            source +=
              "  vec3 overlay_coord"+str(n) +" = overlay_texcoord"+str(n) + " + overlay_ray"+str(n) + " * dither;\n";

              source +=
            "  float depth = texelFetch (depth_sampler, ivec2(gl_FragCoord.xy), 0).r;\n"
            "  float current_depth = gl_FragCoord.z + ray_z * dither;\n"
            "  int nmax = 10000;\n"
            "  if (ray.x < 0.0) nmax = int (-texcoord.s/ray.x);\n"
            "  else if (ray.x > 0.0) nmax = int ((1.0-texcoord.s) / ray.x);\n"
            "  if (ray.y < 0.0) nmax = min (nmax, int (-texcoord.t/ray.y));\n"
            "  else if (ray.y > 0.0) nmax = min (nmax, int ((1.0-texcoord.t) / ray.y));\n"
            "  if (ray.z < 0.0) nmax = min (nmax, int (-texcoord.p/ray.z));\n"
            "  else if (ray.z > 0.0) nmax = min (nmax, int ((1.0-texcoord.p) / ray.z));\n"
            "  nmax = min (nmax, int ((depth - current_depth) / ray_z));\n"
            "  if (nmax <= 0) return;\n"
            "  for (int n = 0; n < nmax; ++n) {\n"
            "    coord += ray;\n";

          if (clip.size()) {
            source += std::string("    bool show = ") + ( AND ? "false" : "true" ) + ";\n";
            for (size_t n = 0; n < clip.size(); ++n)
              source += std::string("    if (dot (coord, clip") + str(n) + ".xyz) " + ( AND ? "<" : ">" ) + " clip" + str(n) + ".w)\n";
            source +=
              std::string("          show = ") + ( AND ? "true" : "false" ) + ";\n"
              "    if (show) {\n";
          }


          source +=
            "      color = texture (image_sampler, coord);\n"
            "      amplitude = " + std::string (ColourMap::maps[object.colourmap].amplitude) + ";\n"
            "      if (!isnan(amplitude) && !isinf(amplitude)";

          if (object.use_discard_lower())
            source += " && amplitude >= lower";

          if (object.use_discard_upper())
            source += " && amplitude <= upper";

          source += " && amplitude >= alpha_offset) {\n"
            "        color.a = clamp ((amplitude - alpha_offset) * alpha_scale, 0, alpha);\n";

          if (!ColourMap::maps[object.colourmap].special) {
            source +=
              "        amplitude = clamp (";
            if (object.scale_inverted())
              source += "1.0 -";
            source +=
              " scale * (amplitude - offset), 0.0, 1.0);\n";
          }

          source +=
            std::string ("        ") + ColourMap::maps[object.colourmap].glsl_mapping;

          source +=
            "        final_color.rgb += (1.0 - final_color.a) * color.rgb * color.a;\n"
            "        final_color.a += color.a;\n"
            "      }\n";


          if (clip.size())
            source += "    }\n";




          // OVERLAYS:
          for (size_t n = 0, N = mode.overlays_for_3D.size(); n < N; ++n) {
            const ImageBase* image = mode.overlays_for_3D[n];
            source +=
              "    overlay_coord"+str(n) + " += overlay_ray"+str(n) + ";\n"
              "    if (overlay_coord"+str(n) + ".s >= 0.0 && overlay_coord"+str(n) + ".s <= 1.0 &&\n"
              "        overlay_coord"+str(n) + ".t >= 0.0 && overlay_coord"+str(n) + ".t <= 1.0 &&\n"
              "        overlay_coord"+str(n) + ".p >= 0.0 && overlay_coord"+str(n) + ".p <= 1.0) {\n"
              "      color = texture (overlay_sampler"+str(n) +", overlay_coord"+str(n) +");\n"
              "      amplitude = " + std::string (ColourMap::maps[image->colourmap].amplitude) + ";\n"
              "      if (!isnan(amplitude) && !isinf(amplitude)";

            if (image->use_discard_lower())
              source += " && amplitude >= overlay"+str(n)+"_lower";

            if (image->use_discard_upper())
              source += " && amplitude <= overlay"+str(n)+"_upper";

            source += " && amplitude >= overlay"+str(n)+"_alpha_offset) {\n";

            if (!ColourMap::maps[image->colourmap].special) {
              source +=
                "        amplitude = clamp (";
              if (image->scale_inverted())
                source += "1.0 -";
              source +=
                " overlay"+str(n)+"_scale * (amplitude - overlay"+str(n)+"_offset), 0.0, 1.0);\n";
            }

            std::string mapping (ColourMap::maps[image->colourmap].glsl_mapping);
            replace (mapping, "scale", "overlay"+str(n)+"_scale");
            replace (mapping, "offset", "overlay"+str(n)+"_offset");
            replace (mapping, "colourmap_colour", "overlay"+str(n)+"_colourmap_colour");
            source += std::string ("        ") + mapping;

            source +=
              "        color.a = amplitude * overlay"+str(n) + "_alpha;\n"
              "        final_color.rgb += (1.0 - final_color.a) * color.rgb * color.a;\n"
              "        final_color.a += color.a;\n"
              "      }\n"
              "    }\n";
          }



          if (clip.size() && mode.get_cliphighlightstate()) {
            source += "    float highlight = 0.0;\n";
            for (size_t n = 0; n < clip.size(); ++n)
              source +=
                "    if (clip"+str(n)+"_selected != 0)\n"
                "      highlight += clamp (selection_thickness - abs (dot (coord, clip" + str(n) + ".xyz) - clip" + str(n) + ".w), 0.0, selection_thickness);\n";
            source +=
              "    highlight *= " + str(clip_color[3]) + ";\n"
              "    final_color.rgb += (1.0 - final_color.a) * vec3("
              + str(clip_color[0]) + "," + str(clip_color[1]) + "," + str(clip_color[2]) + ") * highlight;\n"
              "    final_color.a += highlight;\n";
          }

          source +=
            "    if (final_color.a > 0.95) break;\n"
            "  }\n"
            "}\n";

          return source;
        }




        bool Volume::Shader::need_update (const Displayable& object) const
        {
          if (mode.update_overlays)
            return true;
          if (mode.get_active_clip_planes().size() != active_clip_planes)
            return true;
          if (mode.get_cliphighlightstate() != cliphighlight)
            return true;
          if (mode.get_clipintersectionmodestate() != clipintersectionmode)
            return true;
          return Displayable::Shader::need_update (object);
        }



        void Volume::Shader::update (const Displayable& object)
        {
          active_clip_planes = mode.get_active_clip_planes().size();
          cliphighlight = mode.get_cliphighlightstate();
          clipintersectionmode = mode.get_clipintersectionmodestate();
          Displayable::Shader::update (object);
        }





        namespace {

          inline GL::vec4 clip_real2tex (const GL::mat4& T2S, const GL::mat4& S2T, const Eigen::Vector3f& ray, const GL::vec4& plane)
          {
            GL::vec4 normal = T2S * GL::vec4 (plane[0], plane[1], plane[2], 0.0);
            GL::vec4 on_plane = S2T * GL::vec4 (plane[3]*plane[0], plane[3]*plane[1], plane[3]*plane[2], 1.0);
            normal[3] = on_plane[0]*normal[0] + on_plane[1]*normal[1] + on_plane[2]*normal[2];
            float off_axis_thickness = abs (ray[0]*plane[0] + ray[1]*plane[1] + ray[2]*plane[2]);
            normal[0] /= off_axis_thickness;
            normal[1] /= off_axis_thickness;
            normal[2] /= off_axis_thickness;
            normal[3] /= off_axis_thickness;
            return normal;
          }


          inline GL::mat4 get_tex_to_scanner_matrix (const ImageBase& image)
          {
            const auto V2S = image.voxel2scanner();
            const Eigen::Vector3f pos   = V2S * Eigen::Vector3f { -0.5f, -0.5f, -0.5f };
            const Eigen::Vector3f vec_X = V2S.linear() * Eigen::Vector3f { float(image.header().size(0)), 0.0f, 0.0f };
            const Eigen::Vector3f vec_Y = V2S.linear() * Eigen::Vector3f { 0.0f, float(image.header().size(1)), 0.0f };
            const Eigen::Vector3f vec_Z = V2S.linear() * Eigen::Vector3f { 0.0f, 0.0f, float(image.header().size(2)) };
            GL::mat4 T2S;
            T2S(0,0) = vec_X[0];
            T2S(1,0) = vec_X[1];
            T2S(2,0) = vec_X[2];

            T2S(0,1) = vec_Y[0];
            T2S(1,1) = vec_Y[1];
            T2S(2,1) = vec_Y[2];

            T2S(0,2) = vec_Z[0];
            T2S(1,2) = vec_Z[1];
            T2S(2,2) = vec_Z[2];

            T2S(0,3) = pos[0];
            T2S(1,3) = pos[1];
            T2S(2,3) = pos[2];

            T2S(3,0) = T2S(3,1) = T2S(3,2) = 0.0f;
            T2S(3,3) = 1.0f;

            return T2S;
          }

        }





        void Volume::tilt_event()
        {
          Base::tilt_event();

          auto MV = adjust_projection_matrix (GL::transpose (GL::mat4 (orientation())));
          Eigen::Vector3f screen_normal (MV(2,0), MV(2,1), MV(2,2));
          screen_normal.normalize();

          window().set_target (window().target() + screen_normal * screen_normal.dot (window().focus() - window().target()));
        }






        void Volume::paint (Projection& projection)
        {
          GL::assert_context_is_current();
          GL_CHECK_ERROR;
          setup_projection (orientation(), projection);
          GL_CHECK_ERROR;

          overlays_for_3D.clear();
          render_tools (projection, true);
          gl::Disable (gl::BLEND);
          gl::Enable (gl::DEPTH_TEST);
          gl::DepthMask (gl::TRUE_);

          draw_crosshairs (projection);

          if(!visible) {
            gl::Disable (gl::BLEND);
            draw_orientation_labels (projection);
            return;
          }


          GL_CHECK_ERROR;
          GL::mat4 T2S = get_tex_to_scanner_matrix (*image());
          GL::mat4 M = projection.modelview_projection() * T2S;
          GL::mat4 S2T = GL::inv (T2S);

          float step_size = 0.5f * std::min ( { float(image()->header().spacing (0)), float(image()->header().spacing (1)), float(image()->header().spacing (2)) } );
          Eigen::Vector3f ray = image()->scanner2voxel().linear() * projection.screen_normal();
          Eigen::Vector3f ray_real_space = ray;
          ray *= step_size;
          ray[0] /= image()->header().size(0);
          ray[1] /= image()->header().size(1);
          ray[2] /= image()->header().size(2);



          if (!volume_VB || !volume_VAO || !volume_VI) {
            volume_VB.gen();
            volume_VI.gen();
            volume_VAO.gen();

            volume_VAO.bind();
            volume_VB.bind (gl::ARRAY_BUFFER);
            volume_VI.bind (gl::ELEMENT_ARRAY_BUFFER);

            gl::EnableVertexAttribArray (0);
            gl::VertexAttribPointer (0, 3, gl::BYTE, gl::FALSE_, 4*sizeof(GLbyte), (void*)0);

            GLbyte vertices[] = {
              0, 0, 0, 0,
              0, 0, 1, 0,
              0, 1, 0, 0,
              0, 1, 1, 0,
              1, 0, 0, 0,
              1, 0, 1, 0,
              1, 1, 0, 0,
              1, 1, 1, 0
            };
            gl::BufferData (gl::ARRAY_BUFFER, sizeof(vertices), vertices, gl::STATIC_DRAW);
          }
          else {
            volume_VAO.bind();
            volume_VI.bind (gl::ELEMENT_ARRAY_BUFFER);
          }

          GL_CHECK_ERROR;
          GLubyte indices[12];

          if (ray[0] < 0) {
            indices[0] = 4;
            indices[1] = 5;
            indices[2] = 7;
            indices[3] = 6;
          }
          else {
            indices[0] = 0;
            indices[1] = 1;
            indices[2] = 3;
            indices[3] = 2;
          }

          if (ray[1] < 0) {
            indices[4] = 2;
            indices[5] = 3;
            indices[6] = 7;
            indices[7] = 6;
          }
          else {
            indices[4] = 0;
            indices[5] = 1;
            indices[6] = 5;
            indices[7] = 4;
          }

          if (ray[2] < 0) {
            indices[8] = 1;
            indices[9] = 3;
            indices[10] = 7;
            indices[11] = 5;
          }
          else {
            indices[8] = 0;
            indices[9] = 2;
            indices[10] = 6;
            indices[11] = 4;
          }

          gl::BufferData (gl::ELEMENT_ARRAY_BUFFER, sizeof(indices), indices, gl::STREAM_DRAW);

          image()->update_texture3D();
          image()->set_use_transparency (true);

          image()->start (volume_shader, image()->scale_factor());
          gl::UniformMatrix4fv (gl::GetUniformLocation (volume_shader, "M"), 1, gl::FALSE_, M);
          gl::Uniform3fv (gl::GetUniformLocation (volume_shader, "ray"), 1, ray.data());
          gl::Uniform1i (gl::GetUniformLocation (volume_shader, "image_sampler"), 0);
          gl::Uniform1f (gl::GetUniformLocation (volume_shader, "selection_thickness"), 3.0*step_size);

          if (ColourMap::maps[image()->colourmap].is_colour)
            gl::Uniform3f (gl::GetUniformLocation (volume_shader, "colourmap_colour"),
                image()->colour[0]/255.0f, image()->colour[1]/255.0f, image()->colour[2]/255.0f);

          gl::ActiveTexture (gl::TEXTURE0);
          gl::BindTexture (gl::TEXTURE_3D, image()->texture());

          gl::ActiveTexture (gl::TEXTURE1);
          if (!depth_texture) {
            depth_texture.gen (gl::TEXTURE_2D);
            depth_texture.bind();
            depth_texture.set_interp (gl::NEAREST);
          }
          else
            depth_texture.bind();

          GL_CHECK_ERROR;
#if QT_VERSION >= 0x050100
          int m = window().windowHandle()->devicePixelRatio();
          gl::CopyTexImage2D (gl::TEXTURE_2D, 0, gl::DEPTH_COMPONENT, 0, 0, m*projection.width(), m*projection.height(), 0);
#else
          gl::CopyTexImage2D (gl::TEXTURE_2D, 0, gl::DEPTH_COMPONENT, 0, 0, projection.width(), projection.height(), 0);
#endif

          GL_CHECK_ERROR;
          gl::Uniform1i (gl::GetUniformLocation (volume_shader, "depth_sampler"), 1);

          vector< std::pair<GL::vec4,bool> > clip = get_active_clip_planes();
          GL_CHECK_ERROR;

          for (size_t n = 0; n < clip.size(); ++n) {
            gl::Uniform4fv (gl::GetUniformLocation (volume_shader, ("clip"+str(n)).c_str()), 1,
                clip_real2tex (T2S, S2T, ray_real_space, clip[n].first));
            gl::Uniform1i (gl::GetUniformLocation (volume_shader, ("clip"+str(n)+"_selected").c_str()), clip[n].second);
          }
          GL_CHECK_ERROR;

          for (int n = 0; n < overlays_for_3D.size(); ++n) {
            gl::ActiveTexture (gl::TEXTURE2 + n);
            gl::BindTexture (gl::TEXTURE_3D, overlays_for_3D[n]->texture());
            overlays_for_3D[n]->update_texture3D();
            overlays_for_3D[n]->texture().set_interp_on (overlays_for_3D[n]->interpolate());
            gl::Uniform1i (gl::GetUniformLocation (volume_shader, ("overlay_sampler"+str(n)).c_str()), 2+n);

            GL::mat4 overlay_M = GL::inv (get_tex_to_scanner_matrix (*overlays_for_3D[n])) * T2S;
            GL::vec4 overlay_ray = overlay_M * GL::vec4 (ray, 0.0);
            gl::UniformMatrix4fv (gl::GetUniformLocation (volume_shader, ("overlay_M"+str(n)).c_str()), 1, gl::FALSE_, overlay_M);
            gl::Uniform3fv (gl::GetUniformLocation (volume_shader, ("overlay_ray"+str(n)).c_str()), 1, overlay_ray);

            overlays_for_3D[n]->set_shader_variables (volume_shader, overlays_for_3D[n]->scale_factor(), "overlay"+str(n)+"_");
          }

          GL_CHECK_ERROR;
          GL::vec4 ray_eye = M * GL::vec4 (ray, 0.0);
          gl::Uniform1f (gl::GetUniformLocation (volume_shader, "ray_z"), 0.5*ray_eye[2]);

          gl::Enable (gl::BLEND);
          gl::BlendFunc (gl::SRC_ALPHA, gl::ONE_MINUS_SRC_ALPHA);

          gl::DepthMask (gl::FALSE_);
          gl::ActiveTexture (gl::TEXTURE0);

          const GLsizei counts[] = { 4, 4, 4 };
          const GLvoid* starts[] = { reinterpret_cast<void*>(0),
                                     reinterpret_cast<void*>(4),
                                     reinterpret_cast<void*>(8) };

          GL_CHECK_ERROR;
          gl::MultiDrawElements (gl::TRIANGLE_FAN, counts, gl::UNSIGNED_BYTE, starts, 3);
          GL_CHECK_ERROR;
          image()->stop (volume_shader);
          GL_CHECK_ERROR;
          gl::Disable (gl::BLEND);

          GL_CHECK_ERROR;
          draw_orientation_labels (projection);

          GL::assert_context_is_current();
        }

        inline Tool::View* Volume::get_view_tool () const
        {
          Tool::Dock* dock = dynamic_cast<Tool::__Action__*>(window().tools()->actions()[0])->dock;
          if (!dock)
            return NULL;
          return dynamic_cast<Tool::View*> (dock->tool);
        }

        inline vector< std::pair<GL::vec4,bool> > Volume::get_active_clip_planes () const
        {
          Tool::View* view = get_view_tool();
          return view ? view->get_active_clip_planes() : vector< std::pair<GL::vec4,bool> >();
        }

        inline vector<GL::vec4*> Volume::get_clip_planes_to_be_edited () const
        {
          Tool::View* view = get_view_tool();
          return view ? view->get_clip_planes_to_be_edited() : vector<GL::vec4*>();
        }

        inline bool Volume::get_cliphighlightstate () const
        {
          Tool::View* view = get_view_tool();
          return view ? view->get_cliphighlightstate() : true;
        }

        inline bool Volume::get_clipintersectionmodestate () const
        {
          Tool::View* view = get_view_tool();
          return view ? view->get_clipintersectionmodestate() : false;
        }


      }
    }
  }
}



