python-microscopy · David-Baddeley · Jul 31, 2024 · Jul 15, 2024 · Jul 15, 2024 · Jul 15, 2024
diff --git a/PYME/Acquire/acquiremainframe.py b/PYME/Acquire/acquiremainframe.py
@@ -31,7 +31,7 @@
 import PYME.ui.manualFoldPanel as afp
 import wx
 import wx.lib.agw.aui as aui
-import wx.py.shell
+import PYME.ui.shell
 
 logging.basicConfig(level=logging.DEBUG)
 logger = logging.getLogger(__name__)
@@ -122,7 +122,7 @@ def __init__(self, parent, options = None):
         self.splash.Show()
 
 
-        self.sh = wx.py.shell.Shell(id=-1,
+        self.sh = PYME.ui.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')

diff --git a/PYME/DSView/modules/annotation.py b/PYME/DSView/modules/annotation.py
@@ -458,7 +458,7 @@ def DrawOverlays(self, view, dc):
     def render(self, gl_canvas):
         import  OpenGL.GL as gl
 
-        gl.glDisable(gl.GL_LIGHTING)
+        #gl.glDisable(gl.GL_LIGHTING)
         gl.glPolygonMode(gl.GL_FRONT_AND_BACK, gl.GL_LINE)
         gl.glDisable(gl.GL_DEPTH_TEST)
 

diff --git a/PYME/DSView/modules/psfTools.py b/PYME/DSView/modules/psfTools.py
@@ -23,13 +23,19 @@
 import wx
 import wx.html2
 import wx.grid
+import wx.lib.agw.aui as aui
+
 
 from jinja2 import Environment, PackageLoader
 env = Environment(loader=PackageLoader('PYME.DSView.modules', 'templates'))
 
 from PYME.recipes.traits import HasTraits, Float, Int, Bool, Enum
+import numpy as np
+
+from matplotlib.figure import Figure
+from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigureCanvas
 
-from .graphViewPanel import *
+#from .graphViewPanel import *
 from PYME.Analysis.PSFEst import psfQuality
 
 def remove_newlines(s):

diff --git a/PYME/DSView/modules/shell.py b/PYME/DSView/modules/shell.py
@@ -20,11 +20,11 @@
 #
 ##################
 
-import wx.py.shell
+import PYME.ui.shell
 from PYME import config
 
 def Plug(dsviewer):
-    sh = wx.py.shell.Shell(id=-1,
+    sh = PYME.ui.shell.Shell(id=-1,
                            parent=dsviewer, pos=wx.Point(0, 0), size=wx.Size(618, 451), style=0, locals=dsviewer.__dict__,
                            startupScript=config.get('dh5View-console-startup-file', None),
               introText='PYMEImage - note that help, license, etc. below is for Python, not PYME\n\n')

diff --git a/PYME/DSView/modules/visgui.py b/PYME/DSView/modules/visgui.py
@@ -29,7 +29,13 @@
 import os
 
 from PYME.DSView.arrayViewPanel import ArrayViewPanel
-from PYME.LMVis.gl_render3D_shaders import LMGLShaderCanvas
+
+import PYME.config
+
+if PYME.config.get('VisGUI-opengl-core-profile', False):
+    from PYME.LMVis.glcanvas_core import LMGLShaderCanvas
+else:
+    from PYME.LMVis.gl_render3D_shaders import LMGLShaderCanvas
 
 from six.moves import xrange
 

diff --git a/PYME/LMVis/Extras/annotation.py b/PYME/LMVis/Extras/annotation.py
@@ -26,8 +26,8 @@ def render(self, gl_canvas):
         if not self.visible:
             return
 
-        self._clear_shader_clipping(gl_canvas)
-        with self.get_shader_program(gl_canvas):
+        with self.get_shader_program(gl_canvas) as sp:
+            sp.clear_shader_clipping()
             self._annotator.render(gl_canvas)
 
 class Annotator(ann.AnnotateBase):

diff --git a/PYME/LMVis/Extras/extra_layers.py b/PYME/LMVis/Extras/extra_layers.py
@@ -165,6 +165,7 @@ def open_surface(visFr):
             raise ValueError('Invalid file extension .' + str(ext))
         layer = TriangleRenderLayer(visFr.pipeline, dsname=surf_name, method='shaded')
         visFr.add_layer(layer)
+        visFr.update_datasource_panel()
 
 def save_surface(visFr):
     import wx

diff --git a/PYME/LMVis/VisGUI.py b/PYME/LMVis/VisGUI.py
@@ -27,7 +27,7 @@
 import argparse
 
 import wx
-import wx.py.shell
+import PYME.ui.shell
 
 #hacked so py2exe works
 #from PYME.DSView.dsviewer import View3D
@@ -112,7 +112,8 @@ def __init__(self, parent, filename=None, id=wx.ID_ANY,
         ################################   
 
         self.MainWindow = self #so we can access from shell
-        self.sh = wx.py.shell.Shell(id=-1,
+        self.pymevis = self # more memorable alias for the main window
+        self.sh = PYME.ui.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')
@@ -130,7 +131,9 @@ def __init__(self, parent, filename=None, id=wx.ID_ANY,
 
         self.generatedImages = []
 
-        self.sh.Execute('from pylab import *')
+        #self.sh.Execute('from pylab import *')
+        self.sh.Execute('import numpy as np')
+        self.sh.Execute('import matplotlib.pyplot as plt')
         self.sh.Execute('from PYME.DSView.dsviewer import View3D')
 
         import os
@@ -456,6 +459,8 @@ def parse():
                         default=True, help='switch shaders off(default: off)')
     parser.add_argument('--new-layers', dest='new_layers', action='store_true', default=True)
     parser.add_argument('--no-layers', dest='new_layers', action='store_false', default=True)
+    parser.add_argument('--opengl-core-profile', dest='opengl_core_profile', action='store_true', default=True)
+    parser.add_argument('--opengl-compatibility-profile', dest='opengl_core_profile', action='store_false', default=True)
     parser.add_argument('-l', '--load', nargs=2, action='append', default=[], dest='load', metavar=('KEY', 'FILENAME'), help='Load one (or more) additional files into the recipe namespace.')
     args = parser.parse_args()
     return args
@@ -469,6 +474,7 @@ def main():
     args = parse()
 
     PYME.config.config['VisGUI-new_layers'] = args.new_layers
+    PYME.config.config['VisGUI-opengl-core-profile'] = args.opengl_core_profile
 
     if wx.GetApp() is None: #check to see if there's already a wxApp instance (running from ipython -pylab or -wthread)
         main_(args.file, use_shaders=args.use_shaders, args=args)

diff --git a/PYME/LMVis/gl_render3D_shaders.py b/PYME/LMVis/gl_render3D_shaders.py
@@ -21,6 +21,7 @@
 #
 ##################
 from math import floor
+import time
 
 import numpy
 import numpy as np
@@ -89,6 +90,8 @@ class LMGLShaderCanvas(GLCanvas):
     ScaleBoxOverlayLayer = None
     _is_initialized = False
 
+    core_profile = False #legacy fixed function OpenGL pipeline (see glcanvas_core.py for modern core profile implementation)
+
     def __init__(self, parent, show_lut=True, display_mode='2D', view=None):
         print("New Canvas")
         attribute_list = [wx.glcanvas.WX_GL_RGBA, wx.glcanvas.WX_GL_STENCIL_SIZE, 8, wx.glcanvas.WX_GL_DOUBLEBUFFER]
@@ -300,10 +303,7 @@ def interlace_stencil(self):
         # TODO - do we need to do anything differnt on win?
         vmajor,vminor = wx.VERSION[:2]
 
-        if (vmajor >= 4) and (vminor >=1): # 4.1 or later 
-            sc = self.GetContentScaleFactor()
-        else:
-            sc = 1
+        sc = self.content_scale_factor
 
         #print('scale factor:', sc)
 
@@ -355,6 +355,7 @@ def _stereo_views(self):
             return ['centre']
 
     def OnDraw(self):
+        t0 = time.time()
         self.SetCurrent(self.gl_context)
         self.interlace_stencil()
         GL.glEnable(GL.GL_DEPTH_TEST)
@@ -388,6 +389,8 @@ def OnDraw(self):
                 GL.glOrtho(-1, 1, ys, -ys, -1000, 1000)
 
             GL.glMatrixMode(GL.GL_MODELVIEW)
+
+            #stereo offset
             GL.glTranslatef(eye, 0.0, 0.0)
 
             # move our object to be centred at -10
@@ -412,7 +415,7 @@ def OnDraw(self):
 
                 oit_layers = [] #layers which support order independent transparency - render these all together
                 for l in self.layers:
-                    if getattr(l.engine, 'use_oit', lambda l: False)(l) or getattr(l.engine, 'oit', False):
+                    if hasattr(l, 'engine') and (getattr(l.engine, 'use_oit', lambda l: False)(l) or getattr(l.engine, 'oit', False)):
                         #defer rendering
                         oit_layers.append(l)
                     else:
@@ -444,6 +447,8 @@ def OnDraw(self):
         GL.glFlush()
 
         self.SwapBuffers()
+
+        logger.debug('Frame rendered in: %3.4fs' % (time.time() - t0))
 
     def init_oit(self):
         self._fb = GL.glGenFramebuffers(1)
@@ -474,11 +479,7 @@ def resize_gl_oit(self, w, h):
         # fix scaling error
         # TODO - should this check be on wx, or OpenGL (or potentially python)
         # TODO - do we need to do anything differnt on win?
-        vmajor,vminor = wx.VERSION[:2]
-        if vmajor >= 4 and vminor >=1: # 4.1 or later 
-            sc = self.GetContentScaleFactor()
-        else:
-            sc = 1
+        sc = self.content_scale_factor
 
         #sc = 1
 
@@ -696,6 +697,16 @@ def ymax(self):
     def pixelsize(self):
         return 2. / (self.view.scale * self.view_port_size[0])
 
+    @property
+    def content_scale_factor(self):
+        # version-safe way to get the content scale factor for high DPI screens
+        vmajor,vminor = wx.VERSION[:2]
+        if vmajor >= 4 and vminor >=1: # 4.1 or later 
+            sc = self.GetContentScaleFactor()
+        else:
+            sc = 1
+        return sc
+
     def _view_changed(self):
         """Notify anyone who is synced to our view"""
         for callback in self.wantViewChangeNotification:
@@ -826,7 +837,7 @@ def OnMiddleUp(self, event):
 
     def _ScreenCoordinatesToNm(self, x, y):
         # FIXME!!!
-        sc = self.GetContentScaleFactor()
+        sc = self.content_scale_factor
         x_ = self.pixelsize * (x - 0.5 * float(self.view_port_size[0])) + self.view.translation[0]
         y_ = self.pixelsize * (y - 0.5 * float(self.view_port_size[1])) + self.view.translation[1]
         # print x_, y_
@@ -944,11 +955,7 @@ def getSnapshot(self, mode=GL.GL_RGB):
         #     raise RuntimeError('{} is not a supported format.'.format(mode))
         # img.show()
         self.on_screen = False
-        vmajor, vminor = wx.VERSION[:2]
-        if (vmajor >= 4) and (vminor >= 1):
-            sc = self.GetContentScaleFactor()
-        else:
-            sc = 1
+        sc = self.content_scale_factor
         view_port_size = (int(self.view_port_size[0]*sc), int(self.view_port_size[1]*sc))
         off_screen_handler = OffScreenHandler(view_port_size, mode, self._num_antialias_samples)
         with off_screen_handler: