def __init__(self, *args, **kwargs):
from PYME.LMVis import gl_render3D_shaders as glrender
from PYME.LMVis import layer_panel
AUIFrame.__init__(self, *args, **kwargs)
self.canvas = glrender.LMGLShaderCanvas(self)
self.AddPage(page=self.canvas, caption='View')
self.panesToMinimise = []
self.layerpanel = layer_panel.LayerPane(self,
self.canvas,
caption=None,
add_button=False)
self.layerpanel.SetSize(self.layerpanel.GetBestSize())
pinfo = aui.AuiPaneInfo().Name("layerPanel").Right().Caption(
'Layers').CloseButton(False).MinimizeButton(True).MinimizeMode(
aui.AUI_MINIMIZE_CAPT_SMART
| aui.AUI_MINIMIZE_POS_RIGHT) #.CaptionVisible(False)
self._mgr.AddPane(self.layerpanel, pinfo)
self.panesToMinimise.append(pinfo)
# self._mgr.AddPane(self.optionspanel.CreateToolBar(self),
# aui.AuiPaneInfo().Name("ViewTools").Caption("View Tools").CloseButton(False).
# ToolbarPane().Right().GripperTop())
for pn in self.panesToMinimise:
self._mgr.MinimizePane(pn)
self.Layout()
def __init__(self, parent, options=None):
AUIFrame.__init__(self,
id=wx.ID_ANY,
name='smiMainFrame',
parent=parent,
pos=wx.Point(20, 20),
size=wx.Size(600, 800),
style=wx.DEFAULT_FRAME_STYLE,
title=getattr(options, 'window_title',
'PYME Acquire'))
self._create_menu()
self.options = options
self.snapNum = 0
self.Bind(wx.EVT_CLOSE, self.OnCloseWindow)
self.MainFrame = self #reference to this window for use in scripts etc...
protocol.MainFrame = self
self.toolPanels = []
self.camPanels = []
self.aqPanels = []
self.anPanels = []
self.postInit = []
self.initDone = False
self.scope = microscope.microscope()
self.splash = splashScreen.SplashScreen(self, self.scope)
self.splash.Show()
self.sh = wx.py.shell.Shell(
id=-1,
parent=self,
size=wx.Size(-1, -1),
style=0,
locals=self.__dict__,
introText=
'PYMEAcquire - note that help, license, etc. below is for Python, not PYME\n\n'
)
self.AddPage(self.sh, caption='Shell')
self.CreateToolPanel(getattr(options, 'gui_mode', 'default'))
self.SetSize((1030, 895))
self.roi_on = False
self.bin_on = False
self.time1 = mytimer.mytimer()
self.time1.Start(50)
wx.CallAfter(self._initialize_hardware)
#self.time1.WantNotification.append(self.runInitScript)
self.time1.WantNotification.append(self.splash.Tick)
def __init__(self, parent, filename=None, id=wx.ID_ANY,
title="PYME Visualise", pos=wx.DefaultPosition,
size=(900,750), style=wx.DEFAULT_FRAME_STYLE, use_shaders=True, cmd_args=None, pipeline_vars = {}):
# populate about box info
self._component_name = 'PYMEVisualise'
self._long_desc = "Visualisation of localisation microscopy data."
AUIFrame.__init__(self, parent, id, title, pos, size, style)
self.cmd_args = cmd_args
self._flags = 0
self.pipeline = pipeline.Pipeline(visFr=self)
self.pipeline.dataSources.update(pipeline_vars)
visCore.VisGUICore.__init__(self, use_shaders=use_shaders)
#self.Quads = None
#self.SetMenuBar(self.CreateMenuBar())
self.CreateMenuBar(use_shaders=use_shaders)
self.statusbar = self.CreateStatusBar(1, wx.STB_SIZEGRIP)
self.statusbar.SetStatusText("", 0)
#self._leftWindow1 = wx.Panel(self, -1, size = wx.Size(220, 1000))
#self._pnl = 0
#initialize the common parts
###############################
#NB: this has to come after the shell has been generated, but before the fold panel
################################
self.MainWindow = self #so we can access from shell
self.sh = wx.py.shell.Shell(id=-1,
parent=self, size=wx.Size(-1, -1), style=0, locals=self.__dict__,
startupScript=config.get('VisGUI-console-startup-file', None),
introText='PYMEVisualize - note that help, license, etc. below is for Python, not PYME\n\n')
#self._mgr.AddPane(self.sh, aui.AuiPaneInfo().
# Name("Shell").Caption("Console").Centre().CloseButton(False).CaptionVisible(False))
self.AddPage(self.sh, caption='Shell')
self.elv = None
self.colp = None
self.mdp = None
self.rav = None
self.generatedImages = []
self.sh.Execute('from pylab import *')
self.sh.Execute('from PYME.DSView.dsviewer import View3D')
import os
if os.getenv('PYMEGRAPHICSFIX'): # fix issue with graphics freezing on some machines (apparently matplotlib related)
self.sh.Execute('plot()')
self.sh.Execute('close()')
#self.workspace = workspaceTree.WorkWrap(self.__dict__)
##### Make certain things visible in the workspace tree
#components of the pipeline
#col = self.workspace.newColour()
#self.workspace.addKey('pipeline', col)
#Generated stuff
#col = self.workspace.newColour()
#self.workspace.addKey('GeneratedMeasures', col)
#self.workspace.addKey('generatedImages', col)
#self.workspace.addKey('objects', col)
#main window, so we can get everything else if needed
#col = self.workspace.newColour()
#self.workspace.addKey('MainWindow', col)
######
#self.workspaceView = workspaceTree.WorkspaceTree(self, workspace=self.workspace, shell=self.sh)
#self.AddPage(page=wx.StaticText(self, -1, 'foo'), select=False, caption='Workspace')
# self.glCanvas = gl_render.LMGLCanvas(self)
# self.AddPage(page=self.glCanvas, select=True, caption='View')
# self.glCanvas.cmap = pylab.cm.gist_rainbow #pylab.cm.hot
#self.Bind(wx.EVT_SIZE, self.OnSize)
self.Bind(wx.EVT_MOVE, self.OnMove)
self.Bind(wx.EVT_CLOSE, self.OnClose)
#self.Bind(wx.EVT_IDLE, self.OnIdle)
#self.refv = False
statusLog.SetStatusDispFcn(self.SetStatus)
self.paneHooks.append(self.GenPanels)
self.CreateFoldPanel()
#from .layer_panel import CreateLayerPane, CreateLayerPanel
#CreateLayerPane(sidePanel, self)
#CreateLayerPanel(self)
self._recipe_manager = recipeGui.PipelineRecipeManager(self.pipeline)
self._recipe_editor = recipeGui.RecipeView(self, self._recipe_manager)
self.AddPage(page=self._recipe_editor, select=False, caption='Pipeline Recipe')
self.AddMenuItem('Recipe', 'Reconstruct from open image', self.reconstruct_pipeline_from_open_image)
self.AddMenuItem('Recipe', 'Reconstruct from image file', self.reconstruct_pipeline_from_image_file)
if not filename is None:
def _recipe_callback():
recipe = getattr(self.cmd_args, 'recipe', None)
print('Using recipe: %s' % recipe)
if recipe:
from PYME.recipes import modules
self.pipeline.recipe.update_from_yaml(recipe)
#self.recipeView.SetRecipe(self.pipeline.recipe)
self.update_datasource_panel()
self._recipe_editor.update_recipe_text()
wx.CallLater(50,self.OpenFile,filename, recipe_callback=_recipe_callback)
#self.refv = False
wx.CallAfter(self.RefreshView)
nb = self._mgr.GetNotebooks()[0]
nb.SetSelection(0)
self.add_common_menu_items()
def __init__(self, image, parent=None, title='', mode='LM',
size = (800,700), glCanvas=None):
AUIFrame.__init__(self,parent, -1, title,size=size, pos=wx.DefaultPosition)
self.mode = mode
self.glCanvas = glCanvas
self.updateHooks = []
self.statusHooks = []
self.installedModules = []
# will store weakrefs to things that modules previously injected into our namespace
#self._module_injections = weakref.WeakValueDictionary()
self.dataChangeHooks = []
self.updating = False
if glCanvas:
self.glCanvas.wantViewChangeNotification.add(self)
self.timer = mytimer()
self.timer.Start(10000)
self.image = image
#self.image = ImageStack(data = dstack, mdh = mdh, filename = filename, queueURI = queueURI, events = None)
if not self.image.filename is None and title == '':
self.SetTitle(self.image.filename)
self.do = DisplayOpts(self.image.data)
if self.image.data.shape[1] == 1:
self.do.slice = self.do.SLICE_XZ
self.do.Optimise()
if self.image.mdh and 'ChannelNames' in self.image.mdh.getEntryNames():
chan_names = self.image.mdh.getEntry('ChannelNames')
if len(chan_names) == self.image.data.shape[3]:
self.do.names = chan_names
#self.vp = ArraySettingsAndViewPanel(self, self.image.data, wantUpdates=[self.update], mdh=self.image.mdh)
#self.view = ArrayViewPanel(self, do=self.do)
#self.AddPage(self.view, True, 'Data')
#self._mgr.AddPane(self.vp, aui.AuiPaneInfo().
# Name("Data").Caption("Data").Centre().CloseButton(False).CaptionVisible(False))
self.mainFrame = weakref.ref(self)
#self.do = self.vp.do
tmp_menu = wx.Menu()
tmp_menu.Append(wx.ID_OPEN, '&Open', "", wx.ITEM_NORMAL)
tmp_menu.Append(wx.ID_SAVE, "&Save As", "", wx.ITEM_NORMAL)
tmp_menu.Append(wx.ID_SAVEAS, "&Export Cropped", "", wx.ITEM_NORMAL)
#a submenu for modules to hook and install saving functions into
self.save_menu = wx.Menu()
self._menus['Save'] = self.save_menu
tmp_menu.AppendMenu(-1, 'Save &Results', self.save_menu)
#tmp_menu.AppendSeparator()
#tmp_menu.Append(wx.ID_CLOSE, "Close", "", wx.ITEM_NORMAL)
self.menubar.Append(tmp_menu, "File")
self._menus['File'] = tmp_menu
self.view_menu = wx.Menu()
self.menubar.Append(self.view_menu, "&View")
self._menus['View'] = self.view_menu
#'extras' menu for modules to install stuff into
self.mProcessing = wx.Menu()
self.menubar.Append(self.mProcessing, "&Processing")
self._menus['Processing'] = self.mProcessing
# Menu Bar end
self.Bind(wx.EVT_MENU, self.OnOpen, id=wx.ID_OPEN)
self.Bind(wx.EVT_MENU, self.OnSave, id=wx.ID_SAVE)
self.Bind(wx.EVT_MENU, self.OnExport, id=wx.ID_SAVEAS)
#self.Bind(wx.EVT_MENU, lambda e: self.Close(), id=wx.ID_CLOSE)
self.Bind(wx.EVT_CLOSE, self.OnCloseWindow)
self.statusbar = self.CreateStatusBar(1, wx.STB_SIZEGRIP)
self.panesToMinimise = []
modules.loadMode(self.mode, self)
self.CreateModuleMenu()
self.add_common_menu_items()
self.optionspanel = OptionsPanel(self, self.do, thresholdControls=True)
self.optionspanel.SetSize(self.optionspanel.GetBestSize())
pinfo = aui.AuiPaneInfo().Name("optionsPanel").Right().Caption('Display Settings').CloseButton(False).MinimizeButton(True).MinimizeMode(aui.AUI_MINIMIZE_CAPT_SMART|aui.AUI_MINIMIZE_POS_RIGHT)#.CaptionVisible(False)
self._mgr.AddPane(self.optionspanel, pinfo)
self.panesToMinimise.append(pinfo)
self._mgr.AddPane(self.optionspanel.CreateToolBar(self), aui.AuiPaneInfo().Name("ViewTools").Caption("View Tools").CloseButton(False).
ToolbarPane().Right().GripperTop())
if self.do.ds.shape[2] > 1:
from PYME.DSView.modules import playback
self.playbackpanel = playback.PlayPanel(self, self)
self.playbackpanel.SetSize(self.playbackpanel.GetBestSize())
pinfo1 = aui.AuiPaneInfo().Name("playbackPanel").Bottom().Caption('Playback').CloseButton(False).MinimizeButton(True).MinimizeMode(aui.AUI_MINIMIZE_CAPT_SMART|aui.AUI_MINIMIZE_POS_RIGHT)#.CaptionVisible(False)
self._mgr.AddPane(self.playbackpanel, pinfo1)
self.do.WantChangeNotification.append(self.playbackpanel.update)
#self.mWindows = wx.Menu()
#self.menubar.append(self.mWindows, '&Composite With')
self.do.WantChangeNotification.append(self.update)
self.CreateFoldPanel()
for pn in self.panesToMinimise:
self._mgr.MinimizePane(pn)
#self._mgr.MinimizePane(pinfo2)
self.Layout()
if 'view' in dir(self):
sc = np.floor(np.log2(1.0*self.view.Size[0]/self.do.ds.shape[0]))
#print self.view.Size[0], self.do.ds.shape[0], sc
self.do.SetScale(sc)
self.view.Refresh()
self.update()
self.drop = dt()
self.SetDropTarget(self.drop)
self.AddMenuItem('Save', 'To Cluster', self.OnSaveToCluster)
openViewers[self.image.filename] = self
def _cleanup(self):
self.timer.Stop()
del(self.image)
AUIFrame._cleanup(self)
def _cleanup(self):
self.timer.Stop()
AUIFrame._cleanup(self)
