def launch_viewer_frame (self) : if (self.viewer is None) : self.viewer = XrayFrame( parent=self, title="Image viewer") self.viewer.Show() self.Bind(wx.EVT_CLOSE, self.OnCloseViewer, self.viewer)
def run(self): """The run() function defines the frame and starts the main loop. self._init_lock is released only when all initialisation is done. Whatever thread is the current one when wxWindows is initialised is what it will consider the "main thread." For wxPython 2.4 that happens when wxPython.wx is imported the first time. For 2.5 it will be when the wx.App object is created. """ import wx from wxtbx import bitmaps app = wx.App(0) self._bitmap_pause = bitmaps.fetch_icon_bitmap('actions', 'stop') self._bitmap_run = bitmaps.fetch_icon_bitmap('actions', 'runit') self._frame = XrayFrame(None, -1, "X-ray image display", size=(800, 720)) self._frame.Bind(wx.EVT_IDLE, self.OnIdle) self.setup_toolbar(self._frame.toolbar) self._frame.Show() self._init_lock.release() app.MainLoop() # Avoid deadlock where the send_data() function is waiting for the # semaphore after the frame has closed. self._next_semaphore.release()
def setup_toolbar(self): XFBaseClass.setup_toolbar(self) btn = self.toolbar.AddLabelTool(id=wx.ID_SAVEAS, label="Save As...", bitmap=bitmaps.fetch_icon_bitmap("actions","save_all", 32), shortHelp="Save As...", kind=wx.ITEM_NORMAL) self.Bind(wx.EVT_MENU, self.OnSaveAs, btn)
def display(self,path): import wx from rstbx.viewer.frame import XrayFrame app = wx.App(0) frame = XrayFrame(None, -1, "X-ray image display", size=(1200,1080)) frame.SetSize((1024,780)) frame.load_image(path) frame.Show() app.MainLoop()
def run_one_index(path, *arguments, **kwargs): assert arguments[0].find("target=")==0 target = arguments[0].split("=")[1] from xfel.phil_preferences import load_cxi_phil if "--nodisplay" in arguments[1:]: display = False arguments = list(arguments) arguments.remove("--nodisplay") else: display = True args = ["indexing.data=%s"%path, "beam_search_scope=0.5", "lepage_max_delta = 3.0", "spots_pickle = None", "subgroups_pickle = None", "refinements_pickle = None", "rmsd_tolerance = 5.0", "mosflm_rmsd_tolerance = 5.0", "difflimit_sigma_cutoff=2.0", #"indexing.verbose_cv=True", "indexing.open_wx_viewer=%s"%display ] + list(arguments[1:]) horizons_phil = load_cxi_phil(target, args) info = run_one_index_core(horizons_phil) info.Files = info.organizer.Files info.phil_params = info.horizons_phil # The spotfinder view within cxi.index is an anachronism; no useful purpose anymore # therefore remove this option within cxi.index: return work = wrapper_of_callback(info) if kwargs.get("display",False): import wx from rstbx.viewer import display from rstbx.viewer.frame import XrayFrame display.user_callback = work.user_callback app = wx.App(0) frame = XrayFrame(None, -1, "X-ray image display", size=(1200,1080)) frame.SetSize((1024,780)) frame.load_image(path) frame.Show() app.MainLoop()
def run(args): app = wx.App(0) wx.SystemOptions.SetOption("osx.openfiledialog.always-show-types", "1") frame = XrayFrame(None, -1, "X-ray image display", size=(800,720)) if (len(args) == 1 and os.path.basename(args[0]) == "DISTL_pickle"): assert os.path.isfile(args[0]) frame.load_distl_output(args[0]) elif (len(args) > 0): for file_name in args: assert os.path.isfile(file_name) frame.add_file_name_or_data(file_name) frame.load_image(args[0]) frame.Show() app.MainLoop()
def run (args) : app = wx.App(0) wx.SystemOptions.SetOptionInt("osx.openfiledialog.always-show-types", 1) frame = XrayFrame(None, -1, "X-ray image display", size=(800,720)) if (len(args) == 1 and os.path.basename(args[0]) == "DISTL_pickle") : assert os.path.isfile(args[0]) frame.load_distl_output(args[0]) elif (len(args) > 0) : for file_name in args: assert os.path.isfile(file_name) frame.add_file_name_or_data(file_name) frame.load_image(args[0]) frame.Show() app.MainLoop()
def run_one_index(path, *arguments, **kwargs): assert arguments[0].find("target=") == 0 target = arguments[0].split("=")[1] from xfel.phil_preferences import load_cxi_phil if "--nodisplay" in arguments[1:]: display = False arguments = list(arguments) arguments.remove("--nodisplay") else: display = True args = [ "indexing.data=%s" % path, "beam_search_scope=0.5", "lepage_max_delta = 3.0", "spots_pickle = None", "subgroups_pickle = None", "refinements_pickle = None", "rmsd_tolerance = 5.0", "mosflm_rmsd_tolerance = 5.0", "difflimit_sigma_cutoff=2.0", #"indexing.verbose_cv=True", "indexing.open_wx_viewer=%s" % display ] + list(arguments[1:]) horizons_phil = load_cxi_phil(target, args) info = run_one_index_core(horizons_phil) info.Files = info.organizer.Files info.phil_params = info.horizons_phil # The spotfinder view within cxi.index is an anachronism; no useful purpose anymore # therefore remove this option within cxi.index: return work = wrapper_of_callback(info) if kwargs.get("display", False): import wx from rstbx.viewer import display from rstbx.viewer.frame import XrayFrame display.user_callback = work.user_callback app = wx.App(0) frame = XrayFrame(None, -1, "X-ray image display", size=(1200, 1080)) frame.SetSize((1024, 780)) frame.load_image(path) frame.Show() app.MainLoop()
def integrate_one_character(self,setting,integration_limit): #from libtbx.development.timers import Profiler #P = Profiler("Preliminary") import copy local = copy.deepcopy(self.process_dictionary) local['cell']=cellstr(setting) print("Cell in setting",setting["counter"],local["cell"]) frames = list(sorted(self.spotfinder_results.pd['osc_start'].keys())) local['maxcel']='0' local['xbeam']="%f"%setting['minimizer'].new['xbeam'] local['ybeam']="%f"%setting['minimizer'].new['ybeam'] local['distance']="%f"%setting['minimizer'].new['distance'] local["resolution"]= "%f"%integration_limit from labelit.steps import primaries local['spacegroup'] = primaries[setting['bravais']] local['procstart'] = local['procend'] = "%d"%frames[0] self.pixel_size = float(local['pixel_size']) from labelit.dptbx import AutoIndexEngine, Parameters ai = AutoIndexEngine(local['endstation']) P = Parameters(xbeam=setting["refined x beam"],ybeam=setting["refined y beam"], distance=setting["refined distance"],twotheta=float(local["twotheta"])) ai.setBase(P) ai.setWavelength(float(local['wavelength'])) ai.setMaxcell(float(local['ref_maxcel'])) print("Deltaphi is",float(local['deltaphi'])) ai.setDeltaphi(float(local['deltaphi'])*math.pi/180.) ai.setMosaicity(setting["mosaicity"]) ai.setOrientation(setting["orient"]) refimage = self.files.images[0] ai.set_active_areas(self.horizons_phil, beam=(int(refimage.beamx/refimage.pixel_size), int(refimage.beamy/refimage.pixel_size))) image_centers = [(math.pi/180.)*float(x) for x in local["osc_start"].values()] print("Limiting resolution",integration_limit) local["results"] = [] for i in range(len(frames)): print("---------BEGIN Integrate one frame %d %s" % \ (frames[i], os.path.split(self.files.filenames()[i])[-1])) #P = Profiler("worker") if self.horizons_phil.integration.combine_sym_constraints_and_3D_target and setting["counter"]>1: from rstbx.apps.stills.dials_refinement_preceding_integration import integrate_one_frame integrate_worker = integrate_one_frame(self.triclinic["integration"]["results"][0]) else: from rstbx.apps.stills.deltapsi_refinement_preceding_integration import integrate_one_frame integrate_worker = integrate_one_frame() integrate_worker.inputai = ai integrate_worker.inputpd = dict(masks=local["masks"], size1=local["size1"], size2=local["size2"], symmetry=setting["best_subsym"]) # carefully select only the data items needed for integrate_worker # avoid giving the whole process dictionary; reference to "local" # is a circular reference creating memory leak, while copying the # whole thing is a big performance hit. integrate_worker.frame_numbers = frames integrate_worker.imagefiles = self.files integrate_worker.spotfinder = self.spotfinder_results integrate_worker.image_centers = image_centers integrate_worker.limiting_resolution = integration_limit integrate_worker.setting_id = setting["counter"] integrate_worker.pixel_size = self.pixel_size integrate_worker.set_pixel_size(self.pixel_size) integrate_worker.set_detector_size(int(local["size1"]),int(local["size2"])) integrate_worker.set_detector_saturation(refimage.saturation) integrate_worker.set_up_mask_focus() integrate_worker.initialize_increments(i) integrate_worker.horizons_phil = self.horizons_phil if self.horizons_phil.indexing.verbose_cv: print("EFFECTIVE TILING"," ".join( ["%d"%z for z in refimage.get_tile_manager(self.horizons_phil).effective_tiling_as_flex_int()])) integrate_worker.integration_concept(image_number = i, cb_op_to_primitive = setting["cb_op_inp_best"].inverse(), verbose_cv = self.horizons_phil.indexing.verbose_cv, background_factor = self.horizons_phil.integration.background_factor, ) #P = Profiler("proper") integrate_worker.integration_proper() local["results"].append(integrate_worker) local["r_xbeam"]=ai.xbeam() local["r_ybeam"]=ai.ybeam() local["r_distance"]=ai.distance() local["r_wavelength"]=ai.wavelength local["r_residual"]=integrate_worker.r_residual local["r_mosaicity"]=setting["mosaicity"] try: local["ewald_proximal_volume"]=integrate_worker.ewald_proximal_volume except Exception as e: local["ewald_proximal_volume"]=None if (self.horizons_phil.indexing.open_wx_viewer): if True: #use updated slip viewer try: import wx from rstbx.slip_viewer.frame import XrayFrame as SlipXrayFrame from rstbx.command_line.slip_viewer import master_str as slip_params from iotbx import phil from spotfinder import phil_str from spotfinder.command_line.signal_strength import additional_spotfinder_phil_defs work_phil = phil.process_command_line("",master_string=slip_params + phil_str + additional_spotfinder_phil_defs) work_params = work_phil.work.extract() app = wx.App(0) wx.SystemOptions.SetOption("osx.openfiledialog.always-show-types", "1") frame = SlipXrayFrame(None, -1, "X-ray image display", size=(800,720)) frame.Show() # Update initial settings with values from the command line. Needs # to be done before image is loaded (but after the frame is # instantiated). frame.inherited_params = integrate_worker.horizons_phil frame.params = work_params if (frame.pyslip is None): frame.init_pyslip() if (frame.settings_frame is None): frame.OnShowSettings(None) frame.Layout() frame.pyslip.tiles.user_requests_antialiasing = work_params.anti_aliasing frame.settings_frame.panel.center_ctrl.SetValue(True) frame.settings_frame.panel.integ_ctrl.SetValue(True) frame.settings_frame.panel.spots_ctrl.SetValue(False) frame.settings.show_effective_tiling = work_params.show_effective_tiling frame.settings_frame.panel.collect_values() paths = work_phil.remaining_args frame.user_callback = integrate_worker.slip_callback frame.load_image(self.files.filenames()[i]) app.MainLoop() del app except Exception: pass # must use phenix.wxpython for wx display elif False : #original wx viewer try: from rstbx.viewer.frame import XrayFrame import wx from rstbx.viewer import display display.user_callback = integrate_worker.user_callback app = wx.App(0) frame = XrayFrame(None, -1, "X-ray image display", size=(1200,1080)) frame.settings.show_spotfinder_spots = False frame.settings.show_integration = False #frame.settings.enable_collect_values = False frame.SetSize((1024,780)) frame.load_image(self.files.filenames()[i]) frame.Show() app.MainLoop() del app except Exception: pass # must use phenix.wxpython for wx display # for the wx image viewer filename = self.horizons_phil.indexing.indexing_pickle if filename != None: filename = "%s_%d_%d.pkl"%(filename,setting["counter"],keys[i]) SIO = StringIO() table_raw = show_observations(integrate_worker.get_obs( local["spacegroup"]),out=SIO) limitobject = ResolutionAnalysisMetaClass(local, self.horizons_phil) info = dict(table = SIO.getvalue(), table_raw = table_raw, xbeam = setting["refined x beam"], ybeam = setting["refined y beam"], distance = setting["refined distance"], residual = integrate_worker.r_residual, resolution = limitobject.value, # FIXME not reliable? mosaicity = setting["mosaicity"], pointgroup = local["spacegroup"], hkllist = integrate_worker.hkllist, predictions = (1./integrate_worker.pixel_size)*integrate_worker.predicted, mapped_predictions = integrate_worker.detector_xy, integration_masks_xy = integrate_worker.integration_masks_as_xy_tuples(), background_masks_xy = integrate_worker.background_masks_as_xy_tuples() ) assert info["predictions"].size() >= info["mapped_predictions"].size() assert info["predictions"].size() == info["hkllist"].size() G = open(filename,"wb") pickle.dump(info,G,pickle.HIGHEST_PROTOCOL) print("---------END Integrate one frame",frames[i]) return local
class ProcessingFrame(wx.Frame): def __init__(self, *args, **kwds): wx.Frame.__init__(self, *args, **kwds) self.viewer = None self.toolbar = self.CreateToolBar(style=wx.TB_3DBUTTONS | wx.TB_TEXT) btn = self.toolbar.AddLabelTool(id=-1, label="Image viewer", bitmap=icons.hkl_file.GetBitmap(), shortHelp="Image viewer", kind=wx.ITEM_NORMAL) self.Bind(wx.EVT_MENU, self.OnLaunchViewer, btn) self.toolbar.Realize() self.statusbar = self.CreateStatusBar() self.sizer = wx.BoxSizer(wx.VERTICAL) self.SetSizer(self.sizer) self.nb = fnb.FlatNotebook(self, agwStyle=fnb.FNB_DEFAULT_STYLE | fnb.FNB_NO_X_BUTTON) self.sizer.Add(self.nb, 1, wx.EXPAND) self.nb.SetMinSize((800, 40)) self.start_panel = StartPanel(self.nb) self.nb.AddPage(self.start_panel, "Setup") self.output_panel = LogViewer(self.nb) self.nb.AddPage(self.output_panel, "Output") try: self.html_panel = wx.html2.WebView.New(self.nb) except NotImplementedError: self.html_panel = wx.html.HtmlWindow(self.nb) self.nb.AddPage(self.html_panel, "Report") #self.indexing_panel = indexing.IndexingPanel(self.nb) #self.nb.AddPage(self.indexing_panel, "Indexing") #self.integration_panel = integration.IntegrationPanel(self.nb) #self.nb.AddPage(self.integration_panel, "Integration") self.SetSize((800, 600)) self.event_dispatcher = process_control.event_agent(window=self, project_id=0, job_id=0) self.was_aborted = False #def LoadResults (self, dir_name) : #self.result = results_base.result(dir_name) #self.indexing_panel.SetIndexingResults(self.result.get_indexing()) #self.integration_panel.SetResults(self.result) #self.nb.SetSelection(1) def OnRunXia2(self, evt): #thread = WorkerThread(0, self) #thread.start() #return output_dir = self.start_panel.GetOutputDir() result = self.run_xia2(imagesets=self.start_panel.GetImagesets(), output_dir=output_dir) def run_xia2(self, **kwds): output_dir = kwds['output_dir'] imagesets = kwds['imagesets'] args = [] for imageset in imagesets: scan = imageset.get_scan() first, last = scan.get_image_range() args.append('image=%s:%i:%i' % (imageset.paths()[0], first, last)) kwds = {} self.nb.AdvanceSelection(forward=True) thread = xia2Thread(self, output_dir, args) thread.start() return def launch_viewer_frame(self): if (self.viewer is None): self.viewer = XrayFrame(parent=self, title="Image viewer") self.viewer.Show() self.Bind(wx.EVT_CLOSE, self.OnCloseViewer, self.viewer) def get_viewer_frame(self): self.launch_viewer_frame() return self.viewer def set_viewer_frame(self, frame): assert (self.viewer is None) self.viewer = frame def OnCloseViewer(self, evt): self.viewer.Destroy() self.viewer = None def OnLaunchViewer(self, evt): self.launch_viewer_frame() def callback_start(self, data): self.event_dispatcher.callback_start(data) def callback_stdout(self, data): self.output_panel.AppendText(data) self.event_dispatcher.callback_stdout(data) def callback_other(self, data): print 'other' self.event_dispatcher.callback_other(data) def callback_abort(self): self.event_dispatcher.callback_abort() self.close() def callback_final(self, result): if self.was_aborted: # XXX hack for jobs killed with 'qdel' self.callback_abort() return import glob html_files = glob.glob( os.path.join(result.output_dir, 'LogFiles/*_report.html')) print html_files if html_files: html_file = html_files[0] try: # wx.html.HtmlWindow self.html_panel.LoadFile(html_file) except AttributeError: # wx.html2.WebView self.html_panel.LoadURL(html_file) self.nb.AdvanceSelection() self.event_dispatcher.callback_final(result) self.close() def callback_error(self, error, traceback_info): self.event_dispatcher.callback_error(error, traceback_info) self.close() def callback_pause(self): self.event_dispatcher.callback_pause() def callback_resume(self): self.event_dispatcher.callback_resume() def close(self): pass def OnLogEvent(self, event): print event
class _XrayFrameThread(threading.Thread): """The _XrayFrameThread class allows MainLoop() to be run as a thread, which is necessary because all calls to wxPython must be made from the same thread that originally imported wxPython. This is all based on "Running MainLoop in a separate thread", http://wiki.wxpython.org/MainLoopAsThread. """ def __init__(self): """The thread is started automatically on initialisation. self.run() will initialise self.frame and release self._init_lock. """ super(_XrayFrameThread, self).__init__() self.setDaemon(1) self._init_lock = threading.Lock() self._next_semaphore = threading.Semaphore() self._start_orig = self.start self._frame = None self.start = self._start_local self._init_lock.acquire() self.start() def _start_local(self): """The _start_local() function calls the run() function through self._start_orig, and exists only after self._init_lock has been released. This eliminates a race condition which could cause updates to be sent to a non-existent frame. """ self._start_orig() self._init_lock.acquire() def run(self): """The run() function defines the frame and starts the main loop. self._init_lock is released only when all initialisation is done. Whatever thread is the current one when wxWindows is initialised is what it will consider the "main thread." For wxPython 2.4 that happens when wxPython.wx is imported the first time. For 2.5 it will be when the wx.App object is created. """ import wx from wxtbx import bitmaps app = wx.App(0) self._bitmap_pause = bitmaps.fetch_icon_bitmap('actions', 'stop') self._bitmap_run = bitmaps.fetch_icon_bitmap('actions', 'runit') self._frame = XrayFrame(None, -1, "X-ray image display", size=(800, 720)) self._frame.Bind(wx.EVT_IDLE, self.OnIdle) self.setup_toolbar(self._frame.toolbar) self._frame.Show() self._init_lock.release() app.MainLoop() # Avoid deadlock where the send_data() function is waiting for the # semaphore after the frame has closed. self._next_semaphore.release() def send_data(self, img, title): """The send_data() function updates the wxPython application with @p img and @p title by sending it an ExternalUpdateEvent(). The function blocks until the event is processed.""" from rstbx.viewer.frame import ExternalUpdateEvent event = ExternalUpdateEvent() event.img = img event.title = title if self.isAlive(): try: # Saturating the event queue makes the whole caboodle # uselessly unresponsive. Therefore, block until idle events # are processed. while self.isAlive() and not self._run_pause.IsToggled(): pass self._frame.AddPendingEvent(event) self._is_idle = False while self.isAlive() and not self._is_idle: pass except Exception: pass def setup_toolbar(self, toolbar): import wx from wxtbx import icons toolbar.ClearTools() btn = toolbar.AddLabelTool(id=wx.ID_ANY, label="Settings", bitmap=icons.advancedsettings.GetBitmap(), shortHelp="Settings", kind=wx.ITEM_NORMAL) self._frame.Bind(wx.EVT_MENU, self._frame.OnShowSettings, btn) btn = toolbar.AddLabelTool(id=wx.ID_ANY, label="Zoom", bitmap=icons.search.GetBitmap(), shortHelp="Zoom", kind=wx.ITEM_NORMAL) self._frame.Bind(wx.EVT_MENU, self._frame.OnZoom, btn) # Reset the normal bitmap after the tool has been created, so that # it will update on the next event. See also OnPauseRun() self._run_pause = toolbar.AddCheckLabelTool(id=wx.ID_ANY, label="Run/Pause", bitmap=self._bitmap_run, shortHelp="Run/Pause") self._run_pause.SetNormalBitmap(self._bitmap_pause) self._frame.Bind(wx.EVT_MENU, self.OnPauseRun, self._run_pause) def OnIdle(self, event): self._is_idle = True event.RequestMore() def OnPauseRun(self, event): if self._run_pause.IsToggled(): self._run_pause.SetNormalBitmap(self._bitmap_run) else: self._run_pause.SetNormalBitmap(self._bitmap_pause) def stop(self): from wx import CloseEvent self._frame.AddPendingEvent(CloseEvent())
class ProcessingFrame (wx.Frame) : def __init__ (self, *args, **kwds) : wx.Frame.__init__(self, *args, **kwds) self.viewer = None self.toolbar = self.CreateToolBar(style=wx.TB_3DBUTTONS|wx.TB_TEXT) btn = self.toolbar.AddLabelTool(id=-1, label="Image viewer", bitmap=icons.hkl_file.GetBitmap(), shortHelp="Image viewer", kind=wx.ITEM_NORMAL) self.Bind(wx.EVT_MENU, self.OnLaunchViewer, btn) self.toolbar.Realize() self.statusbar = self.CreateStatusBar() self.sizer = wx.BoxSizer(wx.VERTICAL) self.SetSizer(self.sizer) self.nb = wx.lib.agw.flatnotebook.FlatNotebook(self) self.sizer.Add(self.nb, 1, wx.EXPAND) self.nb.SetMinSize((800,40)) self.start_panel = StartPanel(self.nb) self.nb.AddPage(self.start_panel, "Setup") self.indexing_panel = indexing.IndexingPanel(self.nb) self.nb.AddPage(self.indexing_panel, "Indexing") self.integration_panel = integration.IntegrationPanel(self.nb) self.nb.AddPage(self.integration_panel, "Integration") self.SetSize((800,600)) def LoadResults (self, dir_name) : self.result = results_base.result(dir_name) self.indexing_panel.SetIndexingResults(self.result.get_indexing()) self.integration_panel.SetResults(self.result) self.nb.SetSelection(1) def OnRunIndexing (self, evt) : dataset, frames = self.start_panel.GetDataset() output_dir = self.start_panel.GetOutputDir() result = self.run_indexing( dataset=dataset, frames=frames, output_dir=output_dir) self.LoadResults(output_dir) def run_indexing (self, **kwds) : from rstbx.viewer import drivers run = drivers.run_indexing(**kwds) indexing_result = process_control.run_function_as_process_in_dialog( parent=self, thread_function=run, title="Running LABELIT", message="Indexing images and performing simple test integration") return indexing_result def launch_viewer_frame (self) : if (self.viewer is None) : self.viewer = XrayFrame( parent=self, title="Image viewer") self.viewer.Show() self.Bind(wx.EVT_CLOSE, self.OnCloseViewer, self.viewer) def get_viewer_frame (self) : self.launch_viewer_frame() return self.viewer def set_viewer_frame (self, frame) : assert (self.viewer is None) self.viewer = frame def OnCloseViewer (self, evt) : self.viewer.Destroy() self.viewer = None def OnLaunchViewer (self, evt) : self.launch_viewer_frame()