From 19cd231b214527a87c9f908d79409732174db0c3 Mon Sep 17 00:00:00 2001 From: Sylvain Tricot Date: Tue, 15 Dec 2020 16:12:40 +0100 Subject: [PATCH] Begin portage of clusterviewer from Wx to Gtk3. For the moment changes are in the Python file named clusterviewer_gi.py. --- .../msspecgui/msspec/gui/clusterviewer_gi.py | 1040 +++++++++++++++++ 1 file changed, 1040 insertions(+) create mode 100644 src/msspec/msspecgui/msspec/gui/clusterviewer_gi.py diff --git a/src/msspec/msspecgui/msspec/gui/clusterviewer_gi.py b/src/msspec/msspecgui/msspec/gui/clusterviewer_gi.py new file mode 100644 index 0000000..412126e --- /dev/null +++ b/src/msspec/msspecgui/msspec/gui/clusterviewer_gi.py @@ -0,0 +1,1040 @@ +# -*- encoding: utf-8 -*- +# vim: set fdm=indent ts=2 sw=2 sts=2 et tw=80 cc=+1 mouse=a nu : # +# import wx + +import numpy as np +# from time import clock +# import copy + +import cairo +import wx.lib.wxcairo + +import gi +gi.require_version("Gtk", "3.0") +from gi.repository import GLib, Gio, Gtk, Gdk + +# import ase +from ase.data import covalent_radii +from ase.data.colors import jmol_colors + + +class ClusterViewer(Gtk.Window): + """ + :param mx: last mouse position in x + :param my: last mouse position in y + """ + MODE_NONE = 0b0000000 + MODE_SELECTION = 0b0000001 + MODE_SELECTION_BOX = 0b0000010 + MODE_SELECTION_APPEND = 0b0000100 + MODE_SELECTION_TOGGLE = 0b0001000 + MODE_TRANSLATION = 0b0010000 + MODE_ROTATION = 0b0100000 + + def __init__(self, *args, **kwargs): + #GTK# kwargs['style'] = wx.NO_FULL_REPAINT_ON_RESIZE | wx.CLIP_CHILDREN + Gtk.Window.__init__(self, *args, **kwargs) + self.drawing_area = Gtk.DrawingArea() + self.add(self.drawing_area) + + self.ox = self.oy = 0 # offset in x and y + self.im_ox = self.im_oy = 0 # image offset in x and y + self.last_mouse_move_x = self.last_mouse_move_y = 0 # last mouse move + self.mx = self.my = 0 # last mouse position + self.theta = self.phi = 0 + self.scale = self.scale0 = 100 + self.im_factor = self.im_scale = 1 + self.atoms = None + # self.do_rescale = False + # self.do_center = False + self.atoms_center_of_mass = np.zeros(3) + self.atoms_largest_dimension = 1.0 # float, in angstrom + self.selection = [] + self.selection_box = None + self.__outer_margin = 0 + self.surface = None + self.busy = False + self.refresh_delay = 200 + self.back_buffer = None + self.screenshot = None + self.atom_numbers = None + self.atom_surfaces = None + self.atoms_sprite = None + self.background_sprite = None + + self.mode = self.MODE_NONE + + self.colors = { + 'selection_box': (0.0, 0.4, 1.0), + 'boulding_box_line': (0.0, 0.4, 1.0, 1.0), + 'boulding_box_fill': (0.0, 0.4, 1.0, 0.3), + } + self.sprites_opts = {'alpha': 1, 'glow': True} + + self.light_mode = False + self.light_mode_threshold = 2000 + + self.rotation_matrix = np.identity(4) + self.scale_matrix = np.identity(4) + self.translation_matrix = np.identity(4) + self.model_matrix = np.identity(4) + self.projection_matrix = np.identity(4) + # model to world matrix + self.m2w_matrix = np.identity(4) + # world to view matrix + self.w2v_matrix = np.identity(4) + # view to projection matrix + viewport = (-1., 1., -1., 1., -1., 1.) + self.v2p_matrix = self.create_v2p_matrix(*viewport) + + self.projections = None + + #GTK# + #self.timer = wx.Timer(self) + #self.Bind(wx.EVT_PAINT, self.__evt_paint_cb) + #self.Bind(wx.EVT_SIZE, self.__evt_size_cb) + #self.Bind(wx.EVT_MOUSEWHEEL, self.__evt_mousewheel_cb) + #self.Bind(wx.EVT_MOTION, self.__evt_motion_cb) + #self.Bind(wx.EVT_LEFT_DOWN, self.__evt_left_down_cb) + #self.Bind(wx.EVT_LEFT_UP, self.__evt_left_up_cb) + #self.Bind(wx.EVT_RIGHT_UP, self.__evt_right_up_cb) + #self.Bind(wx.EVT_TIMER, self.__evt_timer_cb, self.timer) + + self.drawing_area.add_events(Gdk.EventMask.SCROLL_MASK | + Gdk.EventMask.POINTER_MOTION_MASK | + Gdk.EventMask.BUTTON1_MOTION_MASK) + + self.connect("size-allocate", self.__evt_size_cb) + self.drawing_area.connect("draw", self.__evt_draw_cb) + self.drawing_area.connect("scroll-event", self.__evt_mousewheel_cb) + self.drawing_area.connect("motion-notify-event", self.__evt_motion_cb) + #self.drawing_area.connect("button-press-event", self.__evt_press_cb) + #self.drawing_area.connect("button-release-event", self.__evt_release_cb) + + def show_emitter(self, show=True, alpha=0.25): + _opts = self.sprites_opts.copy() + if show: + self.sprites_opts['alpha'] = alpha + self.sprites_opts['glow'] = False + else: + self.sprites_opts = _opts.copy() + + def set_atoms(self, atoms, rescale=False, center=True): + """ + Attach an Atoms object to the view. + + This will translate the model to the center of mass, move the model + center to the center of screen and adjust the scale to the largest + dimension of the model + + :param rescale: if True, the zoom is computed to view the atoms; if + False, a fixed zoom value is used + """ + if atoms is None: + self.light_mode = False + self.atoms_center_of_mass = np.zeros(3) + self.atoms_largest_dimension = 1.0 + self.atom_numbers = None + self.atom_surfaces = None + self.atoms_sprite = None + self.projections = None + else: + # Set the light mode according to the number of atoms + if len(atoms) > self.light_mode_threshold: + self.light_mode = True + else: + self.light_mode = False + + # get the center of mass + self.atoms_center_of_mass = atoms.get_center_of_mass() + # get the largest dimension + p = atoms.get_positions() + self.atoms_largest_dimension = np.max(np.amax(p, axis=0) - + np.amin(p, axis=0)) + if self.atoms_largest_dimension == 0: + self.atoms_largest_dimension = 1.0 + + # make atoms a class attribute + self.atoms = atoms + # self.do_rescale = rescale + # self.do_center = center + self.update_camera(center=center, rescale=rescale) + # create the textures + self.create_atom_sprites() + # finally update the view + self.update_drawing() + + def rotate_atoms(self, dtheta, dphi): + self.theta += dtheta + self.phi += dphi + + tx, ty = (self.theta, self.phi) + m_mat = np.zeros((4, 4)) + m_mat[0, 0] = m_mat[3, 3] = 1 + m_mat[1, 1] = m_mat[2, 2] = np.cos(np.radians(tx)) + m_mat[2, 1] = -np.sin(np.radians(tx)) + m_mat[1, 2] = np.sin(np.radians(tx)) + + n_mat = np.zeros((4, 4)) + n_mat[1, 1] = n_mat[3, 3] = 1 + n_mat[0, 0] = n_mat[2, 2] = np.cos(np.radians(ty)) + n_mat[0, 2] = -np.sin(np.radians(ty)) + n_mat[2, 0] = np.sin(np.radians(ty)) + + self.rotation_matrix = np.dot(m_mat, n_mat) + self.update_model_matrix() + self.scale_atoms(self.scale) + + def scale_atoms(self, factor): + self.scale = factor + self.scale_matrix[(0, 1, 2), (0, 1, 2)] = factor + self.create_atom_sprites() + self.update_projection_matrix() + + def translate_atoms(self, x, y): + """ + sets the translation of the atoms + """ + self.ox = x + self.oy = y + self.im_ox += self.last_mouse_move_x + self.im_oy += self.last_mouse_move_y + self.last_mouse_move_x = self.last_mouse_move_y = 0 + self.translation_matrix[-1, (0, 1)] = (x, y) + self.update_projection_matrix() + + def select_atoms(self, x, y, w=None, h=None, append=False, + toggle=False): + selection = np.array([]) + if w is None and h is None: + # get the projections + p = self.projections.copy() + # translate to the event point + p[:, :2] -= (x, y) + # compute the norm and the radius for each projected atom + norm = np.linalg.norm(p[:, :2], axis=1) + radii = covalent_radii[p[:, 4].astype(int)] * self.scale + # search where the norm is inside an atom + i = np.where(norm < radii) + # pick up the atom index of the one with the z min + try: + selection = np.array([int(p[i][np.argmin(p[i, 2]), 5])]) + # self.selection = np.array([selection]) + except: + pass + else: + if w < 0: + x += w + w = abs(w) + if h < 0: + y += h + h = abs(h) + p = self.projections.copy() + p = p[np.where(p[:, 0] > x)] + p = p[np.where(p[:, 0] < x + w)] + p = p[np.where(p[:, 1] > y)] + p = p[np.where(p[:, 1] < y + h)] + selection = p[:, -1].astype(int) + + if toggle: + #print(self.selection) + # whether atoms in the current selection were previously selected + i = np.in1d(self.selection, selection) + #print(i) + self.selection = self.selection[np.invert(i)] + + if append: + self.selection = np.append(self.selection, selection) + self.selection = np.unique(self.selection) + else: + self.selection = selection + + def __evt_paint_cb(self, event): + self.swap_buffers() + + def OLD__evt_size_cb(self, event): + self.timer.Stop() + self.timer.Start(self.refresh_delay) + size = self.GetClientSize() + self.back_buffer = cairo.ImageSurface(cairo.FORMAT_RGB24, *size) + self.create_background_sprite(*size) + self.update_drawing() + + def __evt_size_cb(self, widget, data): + #self.timer.Stop() + #self.timer.Start(self.refresh_delay) + size = self.get_size() + self.back_buffer = cairo.ImageSurface(cairo.FORMAT_RGB24, *size) + self.create_background_sprite(*size) + self.update_drawing() + + def __evt_timer_cb(self, event): + self.update_drawing(light=False) + self.timer.Stop() + + def __evt_left_down_cb(self, event): + self.mx = event.GetX() + self.my = event.GetY() + self.capture_screen() + if event.ControlDown(): + self.mode |= self.MODE_SELECTION + if event.ShiftDown(): + self.mode |= self.MODE_SELECTION_APPEND + if event.AltDown(): + self.mode |= self.MODE_SELECTION_TOGGLE + + def __evt_left_up_cb(self, event): + if self.mode & self.MODE_SELECTION: + self.mode ^= self.MODE_SELECTION + # search for atoms in the selection box + x, y = event.GetPosition() + w = h = None + if self.mode & self.MODE_SELECTION_BOX: + self.mode ^= self.MODE_SELECTION_BOX + x, y, w, h = self.selection_box + + append = False + if self.mode & self.MODE_SELECTION_APPEND: + self.mode ^= self.MODE_SELECTION_APPEND + append = True + + toggle = False + if self.mode & self.MODE_SELECTION_TOGGLE: + self.mode ^= self.MODE_SELECTION_TOGGLE + toggle = True + + self.select_atoms(x, y, w, h, append=append, toggle=toggle) + + if self.mode == self.MODE_TRANSLATION: + self.mode ^= self.MODE_TRANSLATION + + self.update_drawing(light=False) + + def __evt_right_up_cb(self, event): + if self.mode & self.MODE_ROTATION: + self.mode ^= self.MODE_ROTATION + self.update_drawing(light=False) + + def OLD__evt_motion_cb(self, event): + self.timer.Stop() + self.timer.Start(self.refresh_delay) + if event.LeftIsDown(): + mx, my = event.GetPosition() + dx, dy = (mx - self.mx, my - self.my) + # if event.ControlDown(): + if self.mode & self.MODE_SELECTION: + self.mode |= self.MODE_SELECTION_BOX + # if event.ShiftDown(): + # self.mode |= self.MODE_SELECTION_APPEND + self.selection_box = [self.mx, self.my, dx, dy] + else: + self.mode = self.MODE_TRANSLATION + self.mx, self.my = (mx, my) + self.last_mouse_move_x = int(dx) + self.last_mouse_move_y = int(dy) + self.ox = int(self.ox + dx) + self.oy = int(self.oy + dy) + self.translate_atoms(self.ox, self.oy) + self.update_drawing() + elif event.RightIsDown(): + self.mode = self.MODE_ROTATION + theta = 2. * (float(self.scale0) / self.scale) + theta = max(1., theta) + mx, my = event.GetPosition() + dx, dy = (mx - self.mx, my - self.my) + self.mx, self.my = (mx, my) + + tx = theta * np.sign(dy) + ty = theta * np.sign(dx) + self.rotate_atoms(tx, ty) + + self.update_drawing() + + def __evt_motion_cb(self, widget, event): + #self.timer.Stop() + #self.timer.Start(self.refresh_delay) + if True:#event.state & Gdk.ModifierType.BUTTON1_MASK: + print("motion cb...", bool(event.state & + Gdk.ModifierType.BUTTON1_MASK)) + mx, my = event.x, event.y + dx, dy = (mx - self.mx, my - self.my) + # if event.ControlDown(): + if self.mode & self.MODE_SELECTION: + self.mode |= self.MODE_SELECTION_BOX + # if event.ShiftDown(): + # self.mode |= self.MODE_SELECTION_APPEND + self.selection_box = [self.mx, self.my, dx, dy] + else: + self.mode = self.MODE_TRANSLATION + self.mx, self.my = (mx, my) + self.last_mouse_move_x = int(dx) + self.last_mouse_move_y = int(dy) + self.ox = int(self.ox + dx) + self.oy = int(self.oy + dy) + self.translate_atoms(self.ox, self.oy) + self.update_drawing() + #elif event.RightIsDown(): + elif event.state & Gdk.ModifierType.BUTTON2_MASK: + self.mode = self.MODE_ROTATION + theta = 2. * (float(self.scale0) / self.scale) + theta = max(1., theta) + mx, my = event.GetPosition() + dx, dy = (mx - self.mx, my - self.my) + self.mx, self.my = (mx, my) + + tx = theta * np.sign(dy) + ty = theta * np.sign(dx) + self.rotate_atoms(tx, ty) + + self.update_drawing() + + def OLD__evt_mousewheel_cb(self, event): + if wx.GetKeyState(wx.WXK_CONTROL): + alpha = self.sprites_opts['alpha'] + rot = event.GetWheelRotation() + if rot > 0: + alpha *= 1.2 + alpha = min(1, alpha) + elif rot < 0: + alpha /= 1.2 + alpha = max(0, alpha) + self.sprites_opts['alpha'] = alpha + self.create_atom_sprites() + self.update_drawing() + else: + rot = event.GetWheelRotation() + self.timer.Stop() + self.timer.Start(self.refresh_delay) + if rot > 0: + factor = self.scale * 1.1 + im_factor = 1 * 1.1 + elif rot < 0: + factor = self.scale / 1.1 + im_factor = 1 / 1.1 + self.im_factor = im_factor + self.scale_atoms(factor) + self.update_drawing() + + def __evt_mousewheel_cb(self, widget, event): + #if wx.GetKeyState(wx.WXK_CONTROL): + if event.state & Gdk.ModifierType.CONTROL_MASK: + alpha = self.sprites_opts['alpha'] + #rot = event.GetWheelRotation() + rot = event.direction + if rot == Gdk.ScrollDirection.UP: + alpha *= 1.2 + alpha = min(1, alpha) + elif rot == Gdk.ScrollDirection.DOWN: + alpha /= 1.2 + alpha = max(0, alpha) + self.sprites_opts['alpha'] = alpha + self.create_atom_sprites() + self.update_drawing() + else: + #rot = event.GetWheelRotation() + rot = event.direction + #self.timer.Stop() + #self.timer.Start(self.refresh_delay) + if rot == Gdk.ScrollDirection.UP: + factor = self.scale * 1.1 + im_factor = 1 * 1.1 + elif rot == Gdk.ScrollDirection.DOWN: + factor = self.scale / 1.1 + im_factor = 1 / 1.1 + self.im_factor = im_factor + self.scale_atoms(factor) + self.update_drawing() + + def capture_screen(self): + # get size of screen + w, h = self.get_size() + # create a cairo surface and context + surface = cairo.ImageSurface(cairo.FORMAT_RGB24, w, h) + ctx = cairo.Context(surface) + # trick here: blit the last back_buffer onto the newly created surface + ctx.set_source_surface(self.back_buffer) + ctx.paint() + # store it as an attribute + self.screenshot = surface + + def create_atom_sprites(self): + """ + This function creates a list of cairo surfaces for each kind + of atoms + """ + + # Get out if there are no atoms + if not self.atoms: + return + + # First get an array of all atoms numbers + atom_numbers = np.unique(self.atoms.numbers) + + # Now, for each kind of atoms create a surface in memory + atom_surfaces = np.empty((2, len(atom_numbers)), dtype=object) + self.__outer_margin = 0 + def create_surface(atom_number, alpha=1, glow=True): + #global margin + # get the radius, and the color + radius = int(covalent_radii[atom_number] * 1. * self.scale) + r, g, b = jmol_colors[atom_number] + # actually create the surface + size = 2 * radius #+ 4 + self.__outer_margin = np.maximum(self.__outer_margin, size / 2.) + surface = cairo.ImageSurface(cairo.FORMAT_ARGB32, size, size) + # draw the ball + ctx = cairo.Context(surface) + # ctx.set_antialias(cairo.ANTIALIAS_NONE) + ctx.set_line_width(1.) + ctx.set_source_rgba(r, g, b, alpha) + ctx.arc(radius, radius, radius - 0.5, 0, 2 * np.pi) + ctx.fill_preserve() + if glow: + gradient = cairo.RadialGradient(radius, radius, radius / 2, + radius, radius, radius) + gradient.add_color_stop_rgba(0., 1., 1., 1., .5*alpha) + gradient.add_color_stop_rgba(0.5, 1., 1., 1., 0) + gradient.add_color_stop_rgba(1., 1., 1., 1., 0.) + ctx.set_source(gradient) + ctx.fill_preserve() + ctx.set_source_rgba(0., 0., 0., alpha) + ctx.stroke() + + # Create the overlay for selection + overlay = cairo.ImageSurface(cairo.FORMAT_ARGB32, size, size) + # draw the circle + ctx = cairo.Context(overlay) + ctx.set_source_surface(surface) + ctx.paint() + ctx.set_line_width(2.) + ctx.set_source_rgb(1 - r, 1 - g, 1 - b) + ctx.arc(radius, radius, radius - 2., 0, 2 * np.pi) + ctx.stroke() + + return surface, overlay + + for i, a in enumerate(atom_numbers): + surface, overlay = create_surface(a, + alpha=self.sprites_opts['alpha'], + glow=self.sprites_opts['glow']) + atom_surfaces[0, i] = surface + atom_surfaces[1, i] = overlay + """ + # get the radius, and the color + radius = int(covalent_radii[a] * 1. * self.scale) + # b, g, r = jmol_colors[a] + r, g, b = jmol_colors[a] + # actually create the surface + size = 2 * radius + 4 + margin = np.maximum(margin, size / 2.) + surface = cairo.ImageSurface(cairo.FORMAT_ARGB32, size, size) + # draw the ball + ctx = cairo.Context(surface) + # ctx.set_antialias(cairo.ANTIALIAS_NONE) + ctx.set_line_width(1.) + ctx.set_source_rgba(r, g, b, self.sprites_opts['alpha']) + ctx.arc(radius, radius, radius - 0.5, 0, 2 * np.pi) + ctx.fill_preserve() + if self.sprites_opts['glow']: + gradient = cairo.RadialGradient(radius, radius, radius / 2, + radius, radius, radius) + gradient.add_color_stop_rgba(0., 1., 1., 1., .5) + gradient.add_color_stop_rgba(0.5, 1., 1., 1., 0) + gradient.add_color_stop_rgba(1., 1., 1., 1., 0.) + ctx.set_source(gradient) + ctx.fill_preserve() + ctx.set_source_rgba(0., 0., 0., self.sprites_opts['alpha']) + ctx.stroke() + # store it + atom_surfaces[0, i] = surface + + # Create the overlay for selection + overlay = cairo.ImageSurface(cairo.FORMAT_ARGB32, size, size) + # draw the circle + ctx = cairo.Context(overlay) + ctx.set_source_surface(surface) + ctx.paint() + ctx.set_line_width(2.) + ctx.set_source_rgb(1 - r, 1 - g, 1 - b) + ctx.arc(radius, radius, radius - 2., 0, 2 * np.pi) + ctx.stroke() + atom_surfaces[1, i] = overlay + """ + + self.atom_numbers = atom_numbers + self.atom_surfaces = atom_surfaces + try: + absorber_number = self.atoms[self.atoms.info['absorber']].number + self.absorber_surface = create_surface(absorber_number, alpha=1, + glow=True) + except: + self.atoms.info['absorber'] = -1 + self.__outer_margin *= 1.1 + + def create_background_sprite(self, w, h): + surface = cairo.ImageSurface(cairo.FORMAT_ARGB32, w, h) + ctx = cairo.Context(surface) + + if True: # pylint: disable=using-constant-test + g = cairo.LinearGradient(0, 0, 0, h) + g.add_color_stop_rgba(0.0, 1.0, 1.0, 1.0, 1.0) + g.add_color_stop_rgba(0.7, 1.0, 1.0, 1.0, 1.0) + g.add_color_stop_rgba(1.0, 0.5, 0.5, 0.5, 1.0) + ctx.set_source(g) + ctx.rectangle(0, 0, w, h) + ctx.fill() + + g = cairo.LinearGradient(0, 0, 0, h) + #g.add_color_stop_rgba(0., 1., 1., 1., 1.) + #g.add_color_stop_rgba(2 / 3., 0.5, 0.5, 0.5, 1) + #g.add_color_stop_rgba(0.0, 1.0, 1.0, 1.0, 1.0) + #g.add_color_stop_rgba(0.9, 0.8, 0.8, 0.8, 1.0) + #g.add_color_stop_rgba(1.0, 0.2, 0.2, 0.2, 1.0) + #ctx.set_source(g) + ctx.set_source_rgb(1, 1, 1) + ctx.rectangle(0, 0, w, h) + ctx.fill() + + ctx.save() + + if False: + ctx.set_source_rgb(0.8, 0.8, 0.8) + rect = (0, 2 * h / 3, w, h / 3) + ctx.rectangle(*rect) + ctx.clip() + ctx.paint() + ctx.set_line_width(1.) + for i in np.arange(0, 2 * np.pi, np.pi / 30): + ctx.move_to(w / 2, 2 * h / 3) + x1 = w * np.cos(i) + y1 = w * np.sin(i) + ctx.rel_line_to(x1, y1) + for i in np.arange(2 * h / 3, h, 10): + ctx.move_to(0, i) + ctx.line_to(w, i) + + ctx.set_source_rgb(0.7, 0.7, 0.7) + ctx.stroke() + ctx.restore() + + self.background_sprite = surface + + @classmethod + def create_v2p_matrix(cls, left, right, bottom, top, near, far): + """ + creates the matrix that transforms coordinates from view space (space + defined by the bounding box passed as argument) to projection space + + this transformation is a scale and offset that maps [left; right], + [bottom; top], [near; far] to [-1;1], [-1;1], [0;1] + """ + v2p_matrix = np.eye(4) * -1 + v2p_matrix[0, 0] = 2. / (right - left) + v2p_matrix[1, 1] = 2. / (right - left) + v2p_matrix[2, 2] = 1. / (near - far) + v2p_matrix[3, 0] = (left + right) / (left - right) + v2p_matrix[3, 1] = (top + bottom) / (bottom - top) + v2p_matrix[3, 2] = near / (near - far) + return v2p_matrix + + def update_projection_matrix(self): + m_matrix = np.dot(self.v2p_matrix, self.scale_matrix) + m_matrix = np.dot(m_matrix, self.translation_matrix) + self.projection_matrix = m_matrix + + def update_model_matrix(self): + m_matrix = np.dot(self.m2w_matrix, self.rotation_matrix) + self.model_matrix = m_matrix + + def get_projections(self, points, save=False): + m_matrix = np.dot(self.model_matrix, self.projection_matrix) + + p = points[:, :4] + v = np.dot(p, m_matrix) + v = v / v[:, -1, None] + + # add the other columns + v = np.c_[v, points[:, 4:]] + # and sort by Z + # v = v[v[:,2].argsort()[::-1]] + + if save: + self.projections = v + return v + + def filter_projections(self, projections, w, h): + try: + # filtering + margin = self.__outer_margin + projections = projections[projections[:, 0] >= -1 * margin, :] + projections = projections[projections[:, 0] <= w + margin, :] + projections = projections[projections[:, 1] >= -1 * margin, :] + projections = projections[projections[:, 1] <= h + margin, :] + return projections + + except: + pass + + def render_background(self, ctx): + surface = self.background_sprite + ctx.set_source_surface(surface, 0, 0) + ctx.paint() + + def render_scalebar(self, ctx): + x, y, w, h = ctx.clip_extents() # @UnusedVariable + scalebar_bb_width = 200 + scalebar_bb_height = 20 + ctx.set_source_rgba(0., 0., 0., 0.7) + ctx.rectangle(x + w - scalebar_bb_width - 6, h - scalebar_bb_height - 6, + scalebar_bb_width, scalebar_bb_height) + ctx.fill() + + ctx.set_source_rgb(1, 1, 1) + ctx.rectangle(x + w - scalebar_bb_width, h - scalebar_bb_height, 100, + scalebar_bb_height - 12) + ctx.fill() + + ctx.move_to(x + w - scalebar_bb_width / 2 + 6, h - 9) + ctx.set_source_rgb(1, 1, 1) + ctx.set_font_size(16) + ctx.show_text("%.2f \xc5" % (100. / self.scale)) + + def render_axes(self, ctx): + _, _, w, h = ctx.clip_extents() # @UnusedVariable + m_matrix = np.dot(self.rotation_matrix, self.v2p_matrix) + + d = 20 + offset = 12 + + points = np.array([[d, 0, 0, 1, 0], + [0, d, 0, 1, 1], + [0, 0, d, 1, 2]]) + + # project onto viewport + projections = np.dot(points[:, :4], m_matrix) + projections /= projections[:, -1, None] + # add the other columns + projections = np.c_[projections, points[:, 4:]] + # and sort by Z + projections = projections[projections[:,2].argsort()[::-1]] + + red = (1, 0, 0) + green = (0, 0.7, 0) + blue = (0, 0, 1) + colors = (red, green, blue) + labels = ('X', 'Y', 'Z') + + # draw a white circle + so = np.array([d + offset, h - d - offset, 0]) + ctx.move_to(d + offset, h - d - offset) + ctx.arc(d + offset, h - d - offset, d + offset - 2, 0, 2 * np.pi) + #ctx.set_source_rgb(1, 1, 1) + ctx.set_source_rgba(0., 0., 0., 0.7) + ctx.set_line_width(1) + #ctx.stroke_preserve() + ctx.set_source_rgba(0.95, 0.95, 0.95, 1) + ctx.fill() + + for x, y, z, w, n in projections: + n = int(n) + ctx.move_to(*so[:2]) + ctx.rel_line_to(x, y) + ctx.set_source_rgb(*colors[n]) + ctx.set_line_width(2) + ctx.set_font_size(10) + ctx.show_text(labels[n]) + ctx.stroke() + + + def render_atoms(self, ctx): + try: + atoms = self.atoms + except: + return + + # create a points matrix with homogeneous coordinates + # x,y,z,w and the atom number and index + points = atoms.get_positions() + points = np.c_[points, np.ones(len(points))] + points = np.c_[points, atoms.numbers] + points = np.c_[points, np.arange(len(atoms))] + + # Get the points array projected to the screen display + projections = self.get_projections(points, save=True) + # print('render_atoms : len(projections) = %d' % len(projections)) + # print('render_atoms : projections = %s' % str(projections)) + + # Reduce the number of atoms to be drawn if outside the viewport + w, h = self.get_size() + # print('render_atoms : w = %f, h = %f' % (w, h)) + projections = self.filter_projections(projections, w, h) + # self.projections = projections + + if len(projections) == 0: + print('render_atoms : no atom is visible') + return # no atom is visible from the camera + + # sort by z + projections = projections[projections[:, 2].argsort()[::-1]] + + margin = self.__outer_margin + xmin, ymin = np.min(projections[:, :2], axis=0) + xmax, ymax = np.max(projections[:, :2], axis=0) + sw = xmax - xmin + 2 * margin + sh = ymax - ymin + 2 * margin + surface = cairo.ImageSurface(cairo.FORMAT_ARGB32, int(sw), int(sh)) + surface_ctx = cairo.Context(surface) + + # set the local references + set_source_surface = surface_ctx.set_source_surface + paint = surface_ctx.paint + selection = self.selection + atom_numbers = self.atom_numbers + atom_surfaces = self.atom_surfaces + + self.im_ox = int(xmin - margin) + self.im_oy = int(ymin - margin) + surface_ctx.translate(-self.im_ox, -self.im_oy) + # surface_ctx.set_source_rgb(1,1,0) + # surface_ctx.set_line_width(2.) + # surface_ctx.rectangle(self.im_ox, self.im_oy, int(sw), int(sh)) + # surface_ctx.stroke() + for i, p in enumerate(projections): # @UnusedVariable + x, y, z, w, n, index = p # @UnusedVariable + # load the surface + if index in selection: + if index == self.atoms.info['absorber']: + sprite = self.absorber_surface[1] + else: + sprite = atom_surfaces[1, np.where(atom_numbers == n)[0][0]] + else: + if index == self.atoms.info['absorber']: + sprite = self.absorber_surface[0] + else: + sprite = atom_surfaces[0, np.where(atom_numbers == n)[0][0]] + + sx = x - sprite.get_width() / 2. + sy = y - sprite.get_height() / 2. + set_source_surface(sprite, int(sx), int(sy)) + paint() + if False: # pylint: disable=using-constant-test + ctx.set_source_rgb(0., 0., 0.) + r = sprite.get_width() / 2 + ctx.arc(x, y, r, 0, 2 * np.pi) + ctx.stroke_preserve() + ctx.set_source_rgb(0.8, 0.8, 0.8) + ctx.fill() + ctx.move_to(x, y) + ctx.set_source_rgb(0, 0, 0) + ctx.set_font_size(14) + ctx.show_text("%d" % index) + + # save the rendering + self.atoms_sprite = surface + ctx.set_source_surface(surface, self.im_ox, self.im_oy) + ctx.paint() + + def render_selection_box(self, ctx): + r, g, b = self.colors['selection_box'] + ctx.set_source_surface(self.screenshot, 0, 0) + ctx.paint() + ctx.set_source_rgba(r, g, b, 0.3) + ctx.rectangle(*self.selection_box) + ctx.fill_preserve() + ctx.set_source_rgb(r, g, b) + ctx.stroke() + + def render_boundingbox(self, ctx): + # print('render_boundingbox : start') + try: + atoms = self.atoms + except: + return + + # create a points matrix with homogeneous coordinates + # x,y,z,w for atoms extrema + points = atoms.get_positions() + margin = self.__outer_margin / float(self.scale) + xmin, ymin, zmin = np.min(points, axis=0) - margin + xmax, ymax, zmax = np.max(points, axis=0) + margin + points = np.array([ + [xmax, ymax, zmax, 1], + [xmax, ymin, zmax, 1], + [xmin, ymax, zmax, 1], + [xmin, ymin, zmax, 1], + [xmax, ymax, zmin, 1], + [xmax, ymin, zmin, 1], + [xmin, ymax, zmin, 1], + [xmin, ymin, zmin, 1]]) + + # Get the points array projected to the screen display + projections = self.get_projections(points) + x0, y0 = (np.min(projections[:, :2], axis=0)).astype(int) + x1, y1 = (np.max(projections[:, :2], axis=0)).astype(int) + + # Declare the 6 faces with their vertex index + # the order of the numbers define if the normal plane points outward or not + faces = np.array([ + [6, 7, 5, 4], + [2, 3, 7, 6], + [3, 1, 5, 7], + [2, 6, 4, 0], + [0, 4, 5, 1], + [2, 0, 1, 3]]) + + # kind of backface culling + ind = [] + for i, f in enumerate(faces): + # Get 2 vectors of the plane + v1 = projections[f[1], :3] - projections[f[0], :3] + v2 = projections[f[3], :3] - projections[f[0], :3] + # cross multiply them to get the normal + n = np.cross(v2, v1) + # If the normal z coordinate is <0, the plane is not visible, so, + # draw it first, otherwise draw it last + if n[-1] > 0: + ind.append(i) + else: + ind.insert(0, i) + # faces are now re-ordered + faces = faces[ind] + + # plane transparency and color + color_plane = self.colors['boulding_box_fill'] + color_line = self.colors['boulding_box_line'] + + ctx.save() + #ctx.set_source_rgb(1, 0, 0) + #ctx.rectangle(x0, y0, x1 - x0, y1 - y0) + #ctx.stroke() + ctx.set_fill_rule(cairo.FILL_RULE_EVEN_ODD) + ctx.set_line_join(cairo.LINE_JOIN_ROUND) + ctx.set_line_width(1.) + ctx.set_dash([8., 8.]) + for i, p in enumerate(faces): + # remove dash for front faces + if i > 2: + ctx.set_dash([]) + if i == 3 and not(self.mode & self.MODE_ROTATION): + try: + f = self.scale / self.scale0 + # sprite_w = self.atoms_sprite.get_width() + # sprite_h = self.atoms_sprite.get_height() + # m = self.__outer_margin + # sw = float(sprite_w) / (x1 - x0) + # sh = float(sprite_h) / (y1 - y0) + ctx.save() + # ctx.translate((x0 + x1 - sprite_w)/2. , + # (y0 + y1 - sprite_h)/2.) + ctx.set_source_surface(self.atoms_sprite, self.im_ox, self.im_oy) + ctx.paint() + ctx.restore() + except: + pass + ctx.set_source_rgba(*color_plane) + # get the projected points + p0, p1, p2, p3 = projections[p, :2] + # move to the first + ctx.move_to(*p0) + # line to the others + list(map(lambda _: ctx.line_to(*_), (p1, p2, p3))) + # close the polygon + ctx.close_path() + # fill it and stroke the path + ctx.fill_preserve() + ctx.set_source_rgba(*color_line) + ctx.stroke() + ctx.restore() + + def update_camera(self, rescale=False, center=False): + # update the scale + w, h = self.get_size() + l = min(w, h) + # print('set_atoms : w=%d h = %d l = %f' % (w, h, l)) + self.scale0 = int(.5 * l / self.atoms_largest_dimension) + 1 + + # move the model to the center of mass + t_matrix = np.eye(4) + t_matrix[-1, :-1] = -1 * self.atoms_center_of_mass + self.m2w_matrix = t_matrix # self.m2w_matrix.dot(t_matrix) + self.update_model_matrix() + + if rescale: + assert self.scale0 > 0.0 + self.scale = self.scale0 + + #print "scale = ", self.scale, "scale0 = ", self.scale0 + #self.scale_atoms(1.) + + if center: + self.translate_atoms(w / 2, h / 2) + + def update_drawing(self, light=None): + # print('update_drawing : light=%s' % str(light)) + + try: + ctx = cairo.Context(self.back_buffer) + except: + #self.scale = self.scale0 = 10 + return + + light_mode = self.light_mode if light is None else light + + if self.mode & self.MODE_SELECTION: + self.render_selection_box(ctx) + else: + self.render_background(ctx) + if self.atoms: + if light_mode: + self.render_boundingbox(ctx) + else: + self.render_atoms(ctx) + self.render_scalebar(ctx) + self.render_axes(ctx) + + #Gtk# + #self.Refresh(eraseBackground=False) + allocation = self.drawing_area.get_allocation() + self.drawing_area.queue_draw_area(allocation.x, allocation.y, + allocation.width, allocation.height) + + def swap_buffers(self): + if self.back_buffer: + back_buffer = self.back_buffer + # w = back_buffer.get_width() + # h = back_buffer.get_height() + + bitmap = wx.lib.wxcairo.BitmapFromImageSurface(back_buffer) + dc = wx.PaintDC(self) + dc.DrawBitmap(bitmap, 0, 0) + + def __evt_draw_cb(self, da, ctx): + if self.back_buffer: + print("Draw called.", ctx) + back_buffer = self.back_buffer + ctx.set_source_surface(back_buffer) + ctx.paint() + + +if __name__ == "__main__": + from ase.build import bulk + from ase.visualize import view + import wx + + MgO = bulk('MgO', crystalstructure='rocksalt', a=4.21, cubic=True) + #view(MgO) + + #app = wx.App(False) + #app.SetAppName('MsSpec Data Viewer') + #win = wx.Frame(None, size=wx.Size(480, 340)) + #cv = ClusterViewer(win, size=wx.Size(480, 340)) + #cv.set_atoms(MgO, rescale=True, center=True) + #win.Show() + #app.MainLoop() + + cv = ClusterViewer() + cv.connect("destroy", Gtk.main_quit) + cv.set_atoms(MgO, rescale=True, center=True) + cv.show_all() + Gtk.main() +