from __future__ import absolute_import, division, print_function from wxtbx import bitmaps import wxtbx import wx from libtbx import object_oriented_patterns as oop from libtbx.math_utils import ifloor from libtbx import adopt_init_args import operator import math import sys from six.moves import range # explicitly set locale for matplotlib 2.0.0, otherwise, on macOS, # locale.getpreferredencoding(do_setlocale=False) returns an empty string # for consistency, set locale according to LC_ALL for both linux and macOS if (sys.platform != 'win32'): import locale locale.setlocale(locale.LC_ALL, '') class plot_container(wx.BoxSizer, wxtbx.MouseWheelTransparencyMixin): def __init__(self, parent, figure_size=(8,6), font_size=12, title_font_size=10, facecolor='white', transparent=False, handle_left_click=False, show_data_points=True, point_types=('o', '^', '+', 's', 'D'), title_alignment="right", toolbar_position=None): wx.BoxSizer.__init__(self, wx.VERTICAL) adopt_init_args(self, locals()) self._fonts = {} self.disabled = False try : import matplotlib from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg from matplotlib.backends.backend_wxagg import FigureManager import matplotlib.ticker import matplotlib.cm import matplotlib.figure import matplotlib.font_manager except ImportError as e : print("") print("Error loading matplotlib module:") print(e) print("") self.disabled = True self.canvas = oop.null() self.figure = oop.null() self.text_font = oop.null() self.p = oop.null() w = int(figure_size[0] * 72) h = int(figure_size[1] * 72) panel = wx.Panel(parent=parent, size=(w,h)) panel.SetBackgroundColour((150,150,150)) szr = wx.BoxSizer(wx.VERTICAL) panel.SetSizer(szr) txt = wx.StaticText(parent=panel, label="Plotting disabled due to missing libraries.") szr.Add(txt, 1, wx.ALL|wx.ALIGN_CENTER, 10) txt.SetForegroundColour((255,0,0)) font = txt.GetFont() font.SetWeight(wx.FONTWEIGHT_BOLD) txt.SetFont(font) txt2 = wx.StaticText(parent=panel, label="Original error:") txt2.SetForegroundColour((255,0,0)) szr.Add(txt2, 1, wx.ALL|wx.ALIGN_CENTER, 10) txt3 = wx.StaticText(parent=panel, label=str(e)) txt3.SetForegroundColour((255,0,0)) szr.Add(txt3, 1, wx.ALL|wx.ALIGN_CENTER, 10) self.Add(panel, 1, wx.EXPAND|wx.ALL) self.null_fmt = oop.null() else : self.figure = matplotlib.figure.Figure(figure_size, 72, linewidth=0, facecolor=facecolor) if transparent : self.figure.figurePatch.set_alpha(0.0) self.canvas = FigureCanvasWxAgg(self.parent, -1, self.figure) self.canvas.toolbar = oop.null() try: # XXX TEMPORARY Python 3 FIX TT conda_base/lib/python3.8/site-packages/matplotlib/backends/backend_wx.py", line 1041, in set_window_title AttributeError: 'RefinementStatsPlot' object has no attribute 'SetTitle' self.figmgr = FigureManager(self.canvas, 1, self) except Exception as e: pass if toolbar_position and self.figmgr.toolbar: self.figmgr.toolbar.SetPosition(toolbar_position) self.Add(self.canvas, 1, wx.EXPAND|wx.ALL) self.setup_fonts() self.null_fmt = matplotlib.ticker.NullFormatter() if self.handle_left_click : self.canvas.mpl_connect("button_release_event", self.OnClick) else : self.canvas.Bind(wx.EVT_CONTEXT_MENU, self.OnRightClick, self.canvas) if (wx.Platform == '__WXMAC__') : # FIXME MSW okay, check GTK self.canvas.Bind(wx.EVT_MOUSEWHEEL, self.OnMouseWheel, self.canvas) def GetParent(self): return self.parent def setup_fonts(self): import matplotlib.font_manager self._fonts["basic"] = matplotlib.font_manager.FontProperties( family = ["Courier", "Monaco", "monospace"], weight = "normal", size = 10) self._fonts["value_label"] = matplotlib.font_manager.FontProperties( family = ["Courier", "Monaco", "monospace"], weight = "normal", size = self.font_size) self._fonts["axis_label"] = matplotlib.font_manager.FontProperties( family = ["Helvetica", "sans-serif"], weight = "bold", size = self.font_size) self._fonts["text"] = matplotlib.font_manager.FontProperties( family = ["Helvetica", "sans-serif"], weight = "normal", size = self.font_size) self._fonts["title"] = matplotlib.font_manager.FontProperties( family = ["Helvetica", "sans-serif"], weight = "bold", size = self.title_font_size) def get_font(self, font_type): font = self._fonts.get(font_type, None) if (font is None): font = self._fonts.get("basic", None) return font def GetToolBar(self): return None def OnRightClick(self, event): pass def OnClick(self, event): if not hasattr(event, "button"): raise RuntimeError("The OnClick method of plot_container handles "+ "matplotlib events only. Please fix your code!") if event.button == 1 : self.process_mouse_click(event) def process_mouse_click(self, mpl_event): pass def save_image(self, default_path="", default_filename="plot.png"): output_file = wx.FileSelector("Saved image name", default_path=default_path, default_filename=default_filename, wildcard="Adobe PDF figure (*.pdf)|*.pdf|" + \ "PNG image (*.png)|*.png|" + \ "Postscript figure (*.ps)|*.ps", flags=wx.FD_SAVE) if output_file != "" : if output_file[-3:] == "pdf" : self.figure.savefig(output_file, orientation="landscape", format="pdf") elif output_file[-2:] == "ps" : self.figure.savefig(output_file, orientation="landscape", format="ps") else : self.figure.savefig(output_file, format="png") class histogram(plot_container): def show_histogram(self, data, n_bins, reference_value=None, pos=(1,1,1), draw_now=True, x_label=None, y_label=None, title=None, log_scale=False, x_lim=None, y_lim=None): assert len(pos) == 3 self.figure.clear() p = self.figure.add_subplot(*pos) p.hist(data, n_bins, facecolor='blue', log=log_scale) if reference_value is not None : p.axvline(reference_value, color='r') if (x_label is not None): p.set_xlabel(x_label) if (y_label is not None): p.set_ylabel(y_label) if (x_lim is not None): p.set_xlim(x_lim[0], x_lim[1]) if (y_lim is not None): p.set_ylim(y_lim[0], y_lim[1]) if (title is not None): p.set_title(title) if draw_now : self.canvas.draw() return p def convert_xyz_value_list(values, null_value=0.0): import numpy values = sorted(values, key=operator.itemgetter(0)) x_rows = [[values[0]]] for i, xyz in enumerate(values[1:]): if (xyz[0] != x_rows[-1][-1][0]): x_rows.append([]) x_rows[-1].append(xyz) x_values = [ x_row[0][0] for x_row in x_rows ] y_values = sorted([ x_rows[0][n][1] for n in range(len(x_rows[0])) ]) assert (len(values) == (len(x_values) * len(y_values))) z_values = [] for j in range(len(y_values)): z_values.append([]) for i, x_row in enumerate(x_rows): x_row = sorted(x_row, key=operator.itemgetter(1)) for j, (x,y,z) in enumerate(x_row): assert (y in y_values) if (z is not None): assert (isinstance(z, int) or isinstance(z, float)) z_values[j].append(z) else : z_values[j].append(numpy.NaN) # z_values[j].append(null_value) return (numpy.array(x_values), numpy.array(y_values), numpy.array(z_values)) class image_plot(plot_container): def show_plot(self, x_data=(), y_data=(), z_data=(), values=(), x_label=None, y_label=None, title=None, cmap=None, interpolation="nearest"): if (len(values) > 0): assert (len(x_data) == len(y_data) == len(z_data) == 0) (x_data, y_data, z_data) = convert_xyz_value_list(values) from matplotlib.image import NonUniformImage self.figure.clear() ax = self.figure.add_subplot(111) im = NonUniformImage(ax, interpolation=interpolation) if (cmap is not None): im.set_cmap(get_colormap(cmap)) im.set_data(x_data, y_data, z_data) ax.images.append(im) ax.set_xlim(x_data[0], x_data[-1]) ax.set_ylim(y_data[0], y_data[-1]) if (x_label is not None): ax.set_xlabel(x_label) if (y_label is not None): ax.set_ylabel(y_label) if (title is not None): ax.set_title(title) self.canvas.draw() class iotbx_data_plot_base(plot_container): def __init__(self, parent, tables, size=(640,480), **kwds): adopt_init_args(self, locals()) (x, y, w, h) = tuple(wx.GetClientDisplayRect()) (width, height) = size fig_w = float(width) / 72.0 fig_h = float(height) / 72.0 if (fig_w * 72) > (w - 20): fig_w = int(math.floor((w-40) / 72)) if (fig_h * 72) > (h - 120): fig_h = int(math.floor((h-160) / 72)) plot_container.__init__(self, parent, (fig_w, fig_h), **kwds) self.p = self.figure.add_subplot(111) self.plot_type = None def set_tables(self, tables): self.tables = tables def set_plot(self, graph_name=None, table_name=None, table_index=0): table = None if table_name is None : table = self.tables[table_index] else : for t in self.tables : if t.title == table_name : table = t if table is not None : self.plot_type = getattr(table, "plot_type", "GRAPH") graph = table.get_graph(graph_name) self.show_plot(graph, reference_lines=table.get_reference_marks()) def show_plot(self, graph, line_width=1, show_points=True, show_grid=True, reference_lines=None): if self.disabled : return self.figure.clear() self.graph = graph self.p = self.figure.add_subplot(111) if graph is None : return if self.plot_type == "SCATTER" : show_points = True show_lines = False else : show_lines = True if self.show_data_points : point_types = self.point_types #['o', '^', '+', 's', 'D'] else : point_types = [""] point_index = 0 for (x_values, y_values) in self.graph.get_plots(): plot_type = "" if show_points : plot_type = "%s" % point_types[point_index] point_index += 1 if point_index >= len(point_types): point_index = 0 if show_lines : plot_type += "-" self.p.plot(x_values, y_values, plot_type, linewidth=line_width) if (reference_lines is not None): for x in reference_lines : if (x is not None): self.p.axvline(x=x, linewidth=1) self.format_labels() if show_grid : self.p.grid(True, color="0.75") self.p.set_autoscale_on(True) self.p.set_title(graph.name, fontproperties=self.get_font("title"), horizontalalignment=self.title_alignment) self.canvas.draw() self.parent.Refresh() def format_x_axis(self): if self.tables[0].x_is_inverse_d_min : xdata = self.tables[0].get_x_as_resolution() self.p.set_xlabel("Resolution", fontproperties=self.get_font("axis_label")) if (getattr(self.tables[0], "force_exact_x_labels", False)): xticks_ = self.tables[0].get_x_values() else : xticks_ = self.p.get_xticks() n_skip = max(1, ifloor(len(xticks_) / 10)) xticks = [] xticklabels = [] k = 0 while (k < len(xticks_)): x = xticks_[k] xticks.append(x) if (x != 0): if x > 0.0: x = math.sqrt(1 / x) else: x = -math.sqrt(1 / abs(x) ) xticklabels.append("%.2f" % x) else : # FIXME? xticklabels.append("") k += n_skip self.p.set_xticks(xticks) self.p.set_xticklabels(xticklabels) else : if self.graph.x_axis_label is not None : self.p.set_xlabel(self.graph.x_axis_label, fontproperties=self.get_font("axis_label")) else : self.p.set_xlabel(self.graph.x_label, fontproperties=self.get_font("axis_label")) for ticklabel in self.p.get_xticklabels(): ticklabel.set_fontproperties(self.get_font("value_label")) def axvline(self, x, **kwargs): if self.tables[0].x_is_inverse_d_min : self.p.axvline(x=(1.0 / (x**2)), **kwargs) else : self.p.axvline(x=x, **kwargs) self.canvas.draw() self.parent.Refresh() def format_y_axis(self): for ticklabel in self.p.get_yticklabels(): ticklabel.set_fontproperties(self.get_font("value_label")) if self.graph.y_axis_label is not None : self.p.set_ylabel(self.graph.y_axis_label, fontproperties=self.get_font("axis_label")) def format_labels(self): self.figure.legend(self.p.lines, self.graph.y_labels, prop=self.get_font("text")) self.format_x_axis() self.format_y_axis() def show_grid(self, show=True): if show : self.p.grid(True, color="0.75") else : self.p.grid(False) self.canvas.draw() self.parent.Refresh() def OnRightClick(self, event): if (wx.Platform != '__WXMAC__') : # FIXME menu = wx.Menu() menu_item = menu.Append(-1, "Save image") self.parent.Bind(wx.EVT_MENU, self.OnSave, menu_item) self.parent.PopupMenu(menu) menu.Destroy() def OnSave(self, event=None): self.save_image() class small_plot(iotbx_data_plot_base): def __init__(self, parent, table, size=(320,320)): iotbx_data_plot_base.__init__(self, parent=parent, tables=[table], size=size, font_size=9, title_font_size=10, title_alignment="center", point_types=('+')) class plot_frame(wx.Frame): controls_on_top = True show_controls_default = True def __init__(self, *args, **kwds): wx.Frame.__init__(self, *args, **kwds) self.setup_toolbar() self.toolbar.Realize() self.sizer = wx.BoxSizer(wx.VERTICAL) self.draw_top_panel() self.plot_panel = self.create_plot_panel() if self.controls_on_top : self.sizer.Add(self.top_panel, 0, wx.EXPAND|wx.ALL) self.sizer.Add(self.plot_panel, 1, wx.EXPAND|wx.ALL) else : self.sizer.Add(self.plot_panel, 1, wx.EXPAND|wx.ALL) self.sizer.Add(self.top_panel, 0, wx.EXPAND|wx.ALL) self._show_controls = self.show_controls_default if not self.show_controls_default : self.top_panel.Hide() self.SetSizer(self.sizer) self.sizer.Layout() self.Fit() self.Bind(wx.EVT_CLOSE, self.OnClose, self) self.Bind(wx.EVT_WINDOW_DESTROY, self.OnDestroy, self) def setup_toolbar(self): tb_buttons = [ ("Show/hide controls", bitmaps.fetch_icon_bitmap("apps", "advancedsettings"), self.OnToggleControls), ("Save", bitmaps.fetch_icon_bitmap("actions", "save_all"), self.OnSave), #("Print", # bitmaps.fetch_icon_bitmap("devices", "printer1"), # self.OnPrint), ] tb = wx.ToolBar(self, style=wx.TB_TEXT) tb.SetToolBitmapSize((32,32)) self.SetToolBar(tb) for (name, bitmap, function) in tb_buttons : tool_button = tb.AddLabelTool(-1, name, bitmap, kind=wx.ITEM_NORMAL) self.Bind(wx.EVT_MENU, function, tool_button) self.toolbar = tb def draw_top_panel(self): self.top_panel = wx.Panel(parent=self, style=wx.SUNKEN_BORDER) def create_plot_panel(self): return (0,0) def OnExit(self, event): self.Close() def OnClose(self, event): wx.CallAfter(self.Destroy) def OnDestroy(self, event): pass def OnSave(self, event): self.plot_panel.save_image() def OnToggleControls(self, event): if self._show_controls : self._show_controls = False self.top_panel.Hide() else : self._show_controls = True self.top_panel.Show() self.sizer.Layout() self.Fit() class loggraph(plot_frame): plot_type = "loggraph" controls_on_top = True show_controls_default = True table_selection_label = "Table:" plot_selection_label = "Plot:" def __init__(self, parent, title, tables=None, file_name=None, processed_lines=None): adopt_init_args(self, locals()) self.tables = [] self.graph = None self.table_frame = None self.table_chooser = None self.plot_chooser = None self.current_table = None self.current_plot = None if tables is not None : self.tables = tables elif file_name is not None or processed_lines is not None : self.load_log(file_name, processed_lines, update=False) if len(self.tables) > 0 : self.current_table = self.tables[0].title self.current_plot = self.tables[0].graph_names[0] plot_frame.__init__(self, parent=parent, title=title) self.Bind(wx.EVT_CLOSE, self.OnClose) self.Centre() self.switch_plot() def draw_top_panel(self): self.top_panel = wx.Panel(parent=self, style=wx.SUNKEN_BORDER) cp = self.top_panel cp_sizer = wx.BoxSizer(wx.VERTICAL) cp.SetSizer(cp_sizer) grid = wx.FlexGridSizer(cols=2) txt = wx.StaticText(self.top_panel, -1, "Table:") # TODO: set bold-face grid.Add(txt, 0, wx.ALL|wx.EXPAND, 5) self.table_chooser = wx.Choice(parent=cp, choices=[ t.title for t in self.tables]) if (len(self.tables) > 0): self.table_chooser.SetSelection(0) self.Bind(wx.EVT_CHOICE, self.OnSelectTable, self.table_chooser) grid.Add(self.table_chooser, 0, wx.ALL|wx.EXPAND, 5) txt2 = wx.StaticText(self.top_panel, -1, "Plot:") grid.Add(txt2, 0, wx.ALL|wx.EXPAND, 5) plot_choices = self.tables[0].graph_names self.plot_chooser = wx.Choice(parent=cp, choices=plot_choices) if (len(plot_choices) > 0): self.plot_chooser.SetSelection(0) self.Bind(wx.EVT_CHOICE, self.OnSelectPlot, self.plot_chooser) grid.Add(self.plot_chooser, 0, wx.ALL|wx.EXPAND, 5) cp_sizer.Add(grid, 0, wx.EXPAND) szr = wx.BoxSizer(wx.HORIZONTAL) cp_sizer.Add(szr, 0, wx.EXPAND) grid_box = wx.CheckBox(parent=cp, label="Show grid") grid_box.SetValue(True) self.Bind(wx.EVT_CHECKBOX, self.OnToggleGrid, grid_box) szr.Add(grid_box, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) point_box = wx.CheckBox(parent=cp, label="Show data points") point_box.SetValue(True) self.Bind(wx.EVT_CHECKBOX, self.OnTogglePoints, point_box) szr.Add(point_box, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) return cp def create_plot_panel(self): self.plot = iotbx_data_plot_base( parent=self, tables=self.tables, transparent=False) return self.plot def load_log(self, file_name=None, processed_lines=None, update=True): from iotbx import data_plots if processed_lines : self.tables = data_plots.import_ccp4i_logfile(log_lines=processed_lines) else : self.tables = data_plots.import_ccp4i_logfile(file_name=file_name) if update : self.update_interface() def update_interface(self, update_tables=True): if len(self.tables) > 0 : if update_tables : table_choices = [t.title for t in self.tables] self.table_chooser.SetItems(table_choices) self.table_chooser.SetSelection(0) self.plot_chooser.SetItems(self.get_table().graph_names) self.plot_chooser.SetSelection(0) self.top_panel.Layout() self.switch_plot() def set_current_plot(self, plot_name): for t in self.tables : for t_plot_name in t.graph_names : if plot_name == t_plot_name : self.table_chooser.SetStringSelection(t.title) self.plot_chooser.SetStringSelection(plot_name) break self.switch_plot() def switch_plot(self): table = self.table_chooser.GetStringSelection() plot = self.plot_chooser.GetStringSelection() if table != "" and plot != "" : self.plot.set_plot(graph_name=plot, table_name=table) #self.Refresh() #--- EVENTS def OnSelectTable(self, event): table_name = self.table_chooser.GetStringSelection() current_plot = self.plot_chooser.GetStringSelection() plot_choices = [] for t in self.tables : if t.title == table_name : plot_choices = t.graph_names self.plot_chooser.SetItems(plot_choices) if current_plot in plot_choices : self.plot_chooser.SetStringSelection(current_plot) self.switch_plot() def OnSelectPlot(self, event): self.switch_plot() def OnPrint(self, event): pass def OnToggleGrid(self, event): show = event.GetEventObject().GetValue() self.plot.show_grid(show) def OnTogglePoints(self, event): self.plot.show_data_points = event.GetEventObject().GetValue() self.switch_plot() standard_colormaps = [ ("jet", "Rainbow"), ("Greys", "Greyscale"), ("Reds", "Red"), ("YlGn", "Yellow/Green"), ("Greens", "Green"), ("Blues", "Blue"), ] colormap_names = [ cm_name for cm_id, cm_name in standard_colormaps ] colormap_id_dict = dict([ (name, id) for id, name in standard_colormaps ]) def get_colormap(cm_name): import matplotlib.cm cm = None for cm_id, cm_name2 in standard_colormaps : if cm_name2 == cm_name : cm = getattr(matplotlib.cm, cm_id, None) break else : cm = getattr(matplotlib.cm, cm_name, None) if cm is None : cm = matplotlib.cm.jet return cm def exercise(): values = [ (1.5, 3.0, 40.2), (2.5, 3.5, 35.1), (1.5, 3.5, 45.6), (2.0, 3.5, 54.2), (1.5, 4.5, 48.2), (2.5, 4.5, 28.4), (2.5, 4.0, 37.6), (2.0, 2.5, None), (2.0, 3.0, 29.8), (2.0, 4.0, 36.7), (2.0, 4.5, 33.2), (2.5, 2.5, None), (1.5, 2.5, 39.5), (2.5, 3.0, None), (1.5, 4.0, 50.9), ] sys.path.pop(0) from iotbx import data_plots loggraph1 = """\ $TABLE: Resolution shell statistics $GRAPHS :R-free vs. resolution :A:1,3: :FOM vs. resolution :A:1,4: $$ 1/resol^2 Nrefl R-free FOM $$ $$ 0.02 2004 0.25 0.89 0.04 2084 0.23 0.88 0.06 2037 0.27 0.83 0.08 1949 0.28 0.75 0.1 1783 0.38 * $$ """ app = wx.App(0) frame = loggraph(parent=None, title="Loggraph test", tables=None, processed_lines=loggraph1.splitlines()) frame.Show() frame2 = wx.Frame(None, -1, "Heat map") panel = wx.Panel(frame2, -1) sizer2 = wx.BoxSizer(wx.VERTICAL) frame2.SetSizer(sizer2) sizer2.Add(panel, 1, wx.EXPAND) implot = image_plot(panel) implot.show_plot(values=values, x_label="RMSD", y_label="resolution", cmap="autumn") sizer2.Layout() frame2.Fit() frame2.Show() app.MainLoop() if __name__ == "__main__" : exercise()