lavavu 1.9.0__cp311-cp311-macosx_11_0_arm64.whl → 1.9.6__cp311-cp311-macosx_11_0_arm64.whl

lavavu/control.py

@@ -1689,13 +1689,26 @@ class _ControlFactory(object):
         """
         if not is_notebook():
             return
-        #Find matching viewer id, redisplay all that match
+        from IPython.display import display,HTML,Javascript
+        display(Javascript(self.redisplay_call()))
+
+    def redisplay_call(self):
+        """Update the active viewer image if any
+        Applies changes made in python to the viewer and forces a redisplay
+        """
+        #Find matching viewer id, redisplay first  match
+        ids = self.active_viewers()
+        return ';'.join('_wi["{0}"].redisplay()'.format(i) for i in ids)
+
+    def active_viewers(self):
+        """Return matching active viewer IDs
+        """
+        #Find matching viewer ids, all that match
+        ids = []
         for idx,obj in enumerate(windows):
             if obj == self._target():
-                viewerid = winids[idx]
-                from IPython.display import display,HTML,Javascript
-                #display(Javascript('_wi["{0}"].redisplay();'.format(viewerid)))
-                display(HTML('<script>_wi["{0}"].redisplay();</script>'.format(viewerid)))
+                ids.append(winids[idx])
+        return ids
 
     def update(self):
         """Update the control values from current viewer data

lavavu/html/menu.js

@@ -123,7 +123,12 @@ function menu_addctrls(menu, obj, viewer, onchange) {
     //Check if it has been set on the target object
     if (prop in obj) {
       //console.log(prop + " ==> " + JSON.stringify(viewer.dict[prop]));
-      menu_addctrl(menu, obj, viewer, prop, onchange);
+      try {
+        //Catch errors and continue gracefully
+        menu_addctrl(menu, obj, viewer, prop, onchange);
+      } catch(e) {
+        console.log("Error adding control to menu: " + e);
+      }
 
     } else {
       //Save list of properties without controls
@@ -159,9 +164,9 @@ function menu_addctrls(menu, obj, viewer, onchange) {
 
 function menu_addcmaps(menu, obj, viewer, onchange) {
   //Colourmap editing menu
-  if (viewer.cgui.prmenu) viewer.cgui.removeFolder(viewer.cgui.prmenu);
-  if (viewer.cgui.cmenu) viewer.cgui.removeFolder(viewer.cgui.cmenu);
-  if (viewer.cgui.pomenu) viewer.cgui.removeFolder(viewer.cgui.pomenu);
+  if (viewer.cgui.prmenu) viewer.cgui.remove(viewer.cgui.prmenu);
+  if (viewer.cgui.cmenu) viewer.cgui.remove(viewer.cgui.cmenu);
+  if (viewer.cgui.pomenu) viewer.cgui.remove(viewer.cgui.pomenu);
   viewer.cgui.prmenu = viewer.cgui.addFolder("Properties");
   viewer.cgui.cmenu = viewer.cgui.addFolder("Colours");
   viewer.cgui.pomenu = viewer.cgui.addFolder("Positions");

lavavu/html/webview.html

@@ -27,7 +27,7 @@
 
     <input id="fileinput" type="file" style="visibility:hidden" onchange="useFileInput(this)" />
 
-    <script async src="https://cdn.jsdelivr.net/gh/lavavu/lavavu.github.io@1.9.0/LavaVu-amalgamated.min.js"></script>
+    <script async src="https://cdn.jsdelivr.net/gh/lavavu/lavavu.github.io@1.9.6/LavaVu-amalgamated.min.js"></script>
     <!--script src="dat.gui.min.js"></script>
     <script src="OK-min.js"></script>
 

lavavu/lavavu.py

@@ -53,6 +53,7 @@ import weakref
 import asyncio
 import quaternion as quat
 import platform
+import matplotlib
 
 if sys.version_info[0] < 3:
     print("Python 3 required. LavaVu no longer supports Python 2.7.")
@@ -610,12 +611,12 @@ class Object(dict):
         return key in self.dict
 
     def __repr__(self):
-        return str(self.ref)
+        return self.__str__()
 
     def __str__(self):
         #Default string representation
         self.parent._get() #Ensure in sync
-        return '{\n' + str('\n'.join(['  %s=%s' % (k,json.dumps(v)) for k,v in self.dict.items()])) + '\n}\n'
+        return '{\n' + str('\n'.join(['  %s=%s' % (k,json.dumps(v)) for k,v in self.dict.items()])) + '\n}'
 
     #Interface for setting filters
     def include(self, *args, **kwargs):
@@ -1144,7 +1145,12 @@ class Object(dict):
             #Re-arrange to array of [r,g,b,a] values
             data = numpy.dstack((data[0],data[1],data[2]))
 
-        self._loadScalar(data, LavaVuPython.lucRGBAData)
+        #Use the shape as dims for texture image data
+        if len(data.shape) > 1:
+            width, height =  data.shape[1], data.shape[0]
+            depth = 4 #4 channel RGBA
+
+        self._loadScalar(data, LavaVuPython.lucRGBAData, width, height, depth)
 
 
     def luminance(self, data):
@@ -1166,7 +1172,7 @@ class Object(dict):
 
         self._loadScalar(data, LavaVuPython.lucLuminanceData, width, height, depth)
 
-    def texture(self, data=None, flip=True, filter=2, bgr=False, label=""):
+    def texture(self, data=None, flip=None, filter=2, bgr=False, label=""):
         """
         Load or clear texture data for object
 
@@ -1186,7 +1192,7 @@ class Object(dict):
             If not provided, will use the default/primary texture for the object
         flip : boolean
             flip the texture vertically after loading
-            (default is enabled as usually required for OpenGL but can be disabled)
+            (default is to load value from "fliptexture" property)
         filter : int
             type of filtering, 0=None/nearest, 1=linear, 2=mipmap linear
         bgr : boolean
@@ -1196,6 +1202,11 @@ class Object(dict):
             #Clear texture
             self.parent.app.clearTexture(self.ref)
             return
+        if flip is None:
+            if "fliptexture" in self:
+                flip = self["fliptexture"]
+            else:
+                flip = self.parent["fliptexture"]
         if isinstance(data, str):
             self.parent.app.setTexture(self.ref, data, flip, filter, bgr, label)
             return
@@ -1266,6 +1277,8 @@ class Object(dict):
             self.ref.colourMap = data.ref
             data = None
         else:
+            if isinstance(data, matplotlib.colors.Colormap):
+                data = matplotlib_cmap(data)
             if data is None:
                 self.parent._get() #Ensure in sync
                 cmid = self["colourmap"]
@@ -2734,7 +2747,7 @@ class Viewer(dict):
 
     """
 
-    def __init__(self, *args, resolution=None, binpath=None, context="default", port=8080, threads=False, **kwargs):
+    def __init__(self, *args, resolution=None, binpath=None, context=None, port=8080, threads=False, **kwargs):
         """
         Create and init viewer instance
 
@@ -2771,7 +2784,9 @@ class Viewer(dict):
         self._collections = {}
         self.validate = True #Property validation flag
         self.recording = None
-        self.context = os.environ.get('LV_CONTEXT', context)
+        self.context = context
+        if self.context is None:
+            self.context = os.environ.get('LV_CONTEXT', 'default')
 
         #Exit handler to clean up threads
         #(__del__ does not always seem to get called on termination)
@@ -3249,10 +3264,12 @@ class Viewer(dict):
             self.validate = self.state["properties"]["validate"]
         self._objects._sync()
 
-    def _set(self):
+    def _set(self, reload=None):
         #Export state to lavavu
         #(include current object list state)
         #self.state["objects"] = [obj.dict for obj in self._objects.list]
+        if reload is not None:
+            self.state["reload"] = reload
         self.app.setState(json.dumps(self.state))
 
     def commands(self, cmds, queue=False):
@@ -3732,7 +3749,7 @@ class Viewer(dict):
         else:
             return c.tolist()
 
-    def texture(self, label, data=None, flip=True, filter=2, bgr=False):
+    def texture(self, label, data=None, flip=None, filter=2, bgr=False):
         """
         Load or clear global/shared texture data
 
@@ -3751,7 +3768,7 @@ class Viewer(dict):
             Pass a string to load a texture from given filename
         flip : boolean
             flip the texture vertically after loading
-            (default is enabled as usually required for OpenGL but can be disabled)
+            (default is to load value from "fliptexture" property)
         filter : int
             type of filtering, 0=None/nearest, 1=linear, 2=mipmap linear
         bgr : boolean
@@ -3761,6 +3778,8 @@ class Viewer(dict):
             #Clear texture
             self.app.clearTexture(None, label)
             return
+        if flip is None:
+            flip = self["fliptexture"]
         if isinstance(data, str):
             self.app.setTexture(None, data, flip, filter, bgr, label)
             return
@@ -4168,7 +4187,7 @@ class Viewer(dict):
         from IPython.display import display,HTML,Javascript
         display(Javascript(js + code))
 
-    def video(self, filename="", resolution=(0,0), fps=30, quality=0, encoder="h264", player=None, options={}, **kwargs):
+    def video(self, filename="", resolution=(0,0), fps=30, quality=2, encoder="h264", embed=False, player=None, options={}, **kwargs):
         """
         Record and show the generated video inline within an ipython notebook.
 
@@ -4195,6 +4214,9 @@ class Viewer(dict):
             If omitted will use default settings, can fine tune settings in kwargs
         encoder : str
             Name of encoder to use, eg: "h264" (default), "mpeg"
+        embed : bool
+            Set to true to embed the video file rather than link to url
+            Not recommended for large videos, default is False
         player : dict
             Args to pass to the player when the video is finished, eg:
             {"width" : 800, "height", 400, "params": "controls autoplay"}
@@ -4209,12 +4231,11 @@ class Viewer(dict):
         recorder : Video(object)
             Context manager object that controls the video recording
         """
-        return Video(self, filename, resolution, fps, quality, encoder, player, options, **kwargs)
+        return Video(self, filename, resolution, fps, quality, encoder, embed, player, options, **kwargs)
 
-    def video_steps(self, filename="", start=0, end=0, fps=10, quality=1, resolution=(0,0), **kwargs):
+    def video_steps(self, filename="", start=0, end=0, resolution=(0,0), fps=30, quality=2, encoder="h264", embed=False, player=None, options={}, **kwargs):
+        my_func.__doc__
         """
-        TODO: Fix to use pyAV
-
         Record a video of the model by looping through all time steps
 
         Shows the generated video inline within an ipython notebook.
@@ -4226,26 +4247,23 @@ class Viewer(dict):
 
         Parameters
         ----------
-        filename : str
-            Name of the file to save, if not provided a default will be used
         start : int
             First timestep to record, if not specified will use first available
         end : int
             Last timestep to record, if not specified will use last available
-        fps : int
-            Frames to output per second of video
-        quality : int
-            Encoding quality, 1=low(default), 2=medium, 3=high, higher quality reduces
-            encoding artifacts at cost of larger file size
-        resolution : list or tuple
-            Video resolution in pixels [x,y]
-        **kwargs :
-            Any additional keyword args will be passed to lavavu.player()
+
+        All other parameters same as video()
         """
 
         try:
-            fn = self.app.video(filename, fps, resolution[0], resolution[1], start, end, quality, **kwargs)
-            player(fn, **kwargs)
+            steps = self.steps
+            if end == 0: end = len(steps)
+            steps = steps[start:end]
+            from tqdm.notebook import tqdm
+            with Video(self, filename, resolution, fps, quality, encoder, embed, player, options, **kwargs):
+                for s in tqdm(steps, desc='Rendering loop'):
+                    self.timestep(s)
+                    self.render()
         except (Exception) as e:
             print("Video output error: " + str(e))
             pass
@@ -4461,10 +4479,10 @@ class Viewer(dict):
                 for key in ["translate", "rotate", "xyzrotate", "fov", "focus"]:
                     if key in src:
                         dst[key] = copy.copy(src[key])
-                        #Round down arrays to max 3 decimal places
+                        #Round down arrays to max 6 decimal places
                         try:
                             for r in range(len(dst[key])):
-                                dst[key][r] = round(dst[key][r], 3)
+                                dst[key][r] = round(dst[key][r], 6)
                         except:
                             #Not a list/array
                             pass
@@ -4478,7 +4496,7 @@ class Viewer(dict):
             #Set
             if data is not None:
                 copyview(self.state["views"][0], data)
-                self._set()
+                self._set(reload=False)
 
         #Return
         return vdat
@@ -4501,7 +4519,7 @@ class Viewer(dict):
         if at is None:
             at = self["focus"]
         else:
-            self["focus"] = at
+            self.focus(*at)
 
         # Default to Y-axis up vector
         if up is None:
@@ -4545,7 +4563,7 @@ class Viewer(dict):
                 res = res / numpy.linalg.norm(res)
             final[key] = res.tolist()
 
-        self.camera(final)
+        self.camera(final, quiet=True)
 
     def flyto(self, pos, steps, stop=False, callback=None):
         # Fly using current camera orientation as start point
@@ -4553,7 +4571,7 @@ class Viewer(dict):
         return self.fly(pos0, pos, steps, stop, callback)
 
     def fly(self, pos0, pos1, steps, stop=False, callback=None):
-        self.camera(pos0)
+        self.camera(pos0, quiet=True)
         self.render()
 
         for i in range(steps):
@@ -5390,49 +5408,44 @@ def player(filename, params="controls autoplay loop", **kwargs):
 
     if is_notebook():
         from IPython.display import display,HTML,Video,Javascript
-        import uuid
-        vid = 'video_' + str(uuid.uuid4())[:8]
-
-        '''
-        def get_fn(filename):
-            import os
-            #This is unreliable, path incorrect on NCI
-            nbpath = os.getenv('JPY_SESSION_NAME')
-            if nbpath is not None:
-                import os.path
-                relpath = os.path.relpath(os.getcwd(), start=os.path.dirname(nbpath))
-                return relpath + '/' + filename
-            return filename
-        ''';
-
-        #Embed player
-        filename = os.path.relpath(filename)
-        display(Video(url=filename, html_attributes=f"id='{vid}' " + params, **kwargs))
-
-        #Add download link
-        display(HTML(f'<a id="link_{vid}" href="{filename}" download>Download Video</a>'))
 
         # Fallback - replace url on gadi and similar jupyterhub installs with 
         # fixed working directory that doesn't match notebook dir
         # check the video tag url and remove subpath on 404 error
-        display(Javascript(f"""
-        let el = document.getElementById('{vid}');
-        let url = el.src;
-        fetch(url, {{method: 'HEAD'}}).then(response=>{{
-          if(response.status == 404) {{
-            console.log("Bad video url: " + url);
-            let toppath = "/files/home/"
-            let baseurl = url.substring(0, url.indexOf(toppath)+toppath.length);
-            let endurl = url.substring(url.indexOf("{filename}"));
-            let fixed = baseurl + endurl;
-            console.log("Replaced video url: " + fixed);
-            el.src = fixed;
-            //Also fix download link
-            document.getElementById('link_{vid}').href = fixed;
-          }}
-        }});
-        """))
-        
+        onerror = """{
+          let url = this.src;
+          console.log('Error in video url: ' + url);
+          var urlp = new window.URL(url);
+          let toppath = '/files/home/';
+          let startidx = urlp.pathname.indexOf(toppath);
+          if (startidx < 0) {
+            toppath = '/files/';
+            startidx = urlp.pathname.indexOf(toppath);
+          }
+          if (startidx >= 0) {
+            let filename = urlp.pathname.split('/').pop();
+            let base = urlp.pathname.substring(0, startidx+toppath.length);
+            urlp.pathname = base + filename;
+            if (url != urlp.href) {
+              console.log('Replaced video url: ' + urlp.href);
+              this.src = urlp.href;
+              //Also fix download link
+              let link = document.getElementById('link_' + this.id);
+              if (link) link.href = urlp.href;
+            }
+          }
+        }"""
+
+        if "embed" in kwargs:
+            #Not needed if embedding
+            onerror = ""
+
+        #Display player and download link
+        import uuid
+        vid = 'video_' + str(uuid.uuid4())[:8]
+        filename = os.path.relpath(filename)
+        display(Video(filename=filename, html_attributes=f'id="{vid}" onerror="{onerror}" ' + params, **kwargs),
+                HTML(f'<a id="link_{vid}" href="{filename}" download>Download Video</a>'))
 
 #Class for managing video animation recording
 class Video(object):
@@ -5452,7 +5465,7 @@ class Video(object):
     ...         lv.rotate('y', 10) # doctest: +SKIP
     ...         lv.render()        # doctest: +SKIP
     """
-    def __init__(self, viewer=None, filename="", resolution=(0,0), framerate=30, quality=0, encoder="h264", player=None, options={}, **kwargs):
+    def __init__(self, viewer, filename="output.mp4", resolution=(0,0), framerate=30, quality=2, encoder="h264", embed=False, player=None, options={}, **kwargs):
         """
         Record and show the generated video inline within an ipython notebook.
 
@@ -5472,13 +5485,16 @@ class Video(object):
         fps : int
             Frames to output per second of video
         quality : int
-            Encoding quality, 1=low, 2=medium, 3=high, higher quality reduces
+            Encoding quality, 1=low, 2=medium(default), 3=high, higher quality reduces
             encoding artifacts at cost of larger file size
             If omitted will use default settings, can fine tune settings in kwargs
         resolution : list or tuple
             Video resolution in pixels [x,y]
         encoder : str
             Name of encoder to use, eg: "h264" (default), "mpeg"
+        embed : bool
+            Set to true to embed the video file rather than link to url
+            Not recommended for large videos, default is False
         player : dict
             Args to pass to the player when the video is finished, eg:
             {"width" : 800, "height", 400, "params": "controls autoplay"}
@@ -5491,21 +5507,30 @@ class Video(object):
         if av is None:
             raise(ImportError("Video output not supported without pyAV - pip install av"))
             return
-        self.resolution = resolution
-        if self.resolution[0] == 0:
-            self.resolution = viewer.width
-        if self.resolution[1] == 0:
-            self.resolution = viewer.height
+        self.resolution = list(resolution)
+        if self.resolution[0] == 0 or self.resolution[1] == 0:
+            self.resolution = (viewer.app.viewer.width, viewer.app.viewer.height)
+        #Ensure resolution values are even or encoder fails
+        self.resolution = (2 * int(self.resolution[0]//2), 2 * int(self.resolution[1] // 2))
         self.framerate = framerate
         self.quality = quality
         self.viewer = viewer
         self.filename = filename
-        if len(self.filename) == 0:
-            self.filename = "lavavu.mp4"
         self.player = player
         if self.player is None:
-            #Default player is half output resolution
-            self.player = {"width": self.resolution[0] // 2, "height": self.resolution[1] // 2}
+            #Default player is half output resolution, unless < 900 then full
+            if "width" in kwargs or "height" in kwargs or "params" in kwargs:
+                #Back compatibility with old args
+                self.player = {}
+                self.player.update(kwargs)
+                kwargs = {}
+            elif self.resolution[0] > 900:
+                #Larger output res - default to half size player
+                self.player = {"width": self.resolution[0]//2, "height": self.resolution[1]//2}
+            else:
+                self.player = {}
+        if embed:
+            self.player["embed"] = True
         self.encoder = encoder
         self.options = options
         #Also include extra args
@@ -5603,6 +5628,7 @@ class Video(object):
         self.container.close()
         self.container = None
         self.stream = None
+        self.viewer.recording = None
 
     def write(self, image):
         """
@@ -5630,9 +5656,8 @@ class Video(object):
 
     def play(self):
         """
-        Show the video in an inline player if in an interative notebook
+        Show the video in an inline player if in an interactive notebook
         """
-        print(self.player)
         player(self.filename, **self.player)
 
     def __enter__(self):

lavavu/tracers.py

@@ -1,124 +1,194 @@
 """
-Warning! EXPERIMENTAL:
- these features and functions are under development, will have bugs,
- and may be heavily modified in the future
-
 Tracer particles in a vector field
-Uses a KDTree to find nearest vector to advect the particles
 
-- Requires scipy.spatial
+- Requires scipy.interpolate
 """
 import numpy
 import os
 import sys
 import random
-import math
-from scipy import spatial
-
-#Necessary? for large trees, detect?
-#sys.setrecursionlimit(10000)
+from scipy.interpolate import RegularGridInterpolator
 
-class TracerState(object):
-    def __init__(self, verts, N=5000):
-        self.tree = spatial.cKDTree(verts)
-        self.tracers = None
-        self.steps = [0]*N
-        self.values = None
-        self.positions = None
-        self.velocities = None
-
-def trace_particles(state, verts, vecs, N=5000, limit=0.5, speed=1.0, noise=0.0, height=None):
+def random_particles(count, lowerbound=[0,0,0], upperbound=[1,1,1], dims=3):
     """
-    Take a list of tracer vertices and matching velocity grid points (verts) & vectors (vecs)
-    For each tracer
-
-    - find the nearest velocity grid point
-    - if within max dist: Multiply position by velocity vector
-    - otherwise: Generate a new start position for tracer
-
-    Parameters
-    ----------
-    state : TracerState
-        Object returned from first call, pass None on first pass
-    verts : array or list
-        vertices of the vector field
-    vecs : array or list
-        vector values of the vector field
-    N : int
-        Number of particles to seed
-    limit : float
-        Distance limit over which tracers are not connected,
-        For example if using a periodic boundary, setting limit to
-        half the bounding box size will prevent tracer lines being
-        connected when passing through the boundary
-    speed : float
-        Speed multiplier, scaling factor for the velocity taken from the vector values
-    noise : float
-        A noise factor, if set a random value is generated, multiplied by noise factor
-        and added to each new position
-    height : float
-        A fixed height value, all positions will be given this height as their Z component
-
-    Returns
-    -------
-    TracerState
-        Object to hold the tracer state and track particles
-        Pass this as first paramter on subsequent calls
+    Return an array of *count* 3d vertices of random particle positions
+    Minimum and maximum values defined by lowerbound and upperbound
     """
+    p = [None] * dims
+    for c in range(dims):
+        if lowerbound[c] == upperbound[c]:
+            p[c] = numpy.zeros(shape=(count)) + lowerbound[c]
+        else:
+            p[c] = numpy.random.uniform(low=lowerbound[c], high=upperbound[c], size=count)
+
+    return numpy.stack(p).T
 
-    #KDstate.tree for finding nearest velocity grid point
-    if state is None:
-        state = TracerState(verts, N)
-
-    lastid = 0
-    def rand_vert():
-        #Get a random velocity grid point
-        lastid = random.randint(0, len(verts)-1)
-        pos = verts[lastid]
-        #Generate some random noise to offset
-        noise3 = numpy.array((0.,0.,0.))
-        if noise > 0.0:
-            noise3 = numpy.random.rand(3) * noise
-        #Fixed height?
-        if height:
-            noise3[2] = height
-        #Return the sum
-        return pos + noise3
-
-    if state.positions is None:
-        state.positions = numpy.zeros(shape=(N,3))
-        state.velocities = numpy.zeros(shape=(N,3))
-        state.values = numpy.zeros(shape=(N))
-        for i in range(N):
-            state.positions[i] = rand_vert()
-            state.steps[i] = 0
-            state.values[i] = numpy.linalg.norm(vecs[lastid])
-
-    #Query all tracer state.positions
-    q = state.tree.query(state.positions, k=1)
-    for r in range(len(q[0])):
-        #print("result, distance, point")
-        #print(r, q[0][r], state.tree.data[q[1][r]], state.positions[r])
-
-        #Increasing random chance as steps exceed 5 of a new start pos
-        if random.randint(0,state.steps[r]) > 5:
-            #Pick a new random grid vertex to start from
-            #(Must be farther away than distance criteria)
-            old = numpy.array(state.positions[r])
-            while True:
-                state.positions[r] = rand_vert() 
-                if numpy.linalg.norm(state.positions[r]-old) > limit:
-                    break
-            state.steps[r] = 0
-            state.values[r] = numpy.linalg.norm(vecs[lastid])
+class Tracers():
+    def __init__(self, grid, count=1000, lowerbound=None, upperbound=None, limit=None, age=4, respawn_chance=0.2, speed_multiply=1.0, height=0.0, viewer=None):
+        """
+        Seed random particles into a vector field and trace their positions
+
+        Parameters
+        ----------
+        grid : list of coord arrays for each dimension as expected by RegularGridInterpolator,
+            or a numpy array of 2d or 3d vertices, which will be converted before being sent to the interpolator
+            Object returned from first call, pass None on first pass
+        count : int
+            Number of particles to seed and track
+        lowerbound : optional minimum vertex point defining particle bounding box,
+            if not provided will be taken from grid lower corner
+        upperbound : optional maximum vertex point defining particle bounding box,
+            if not provided will be taken from grid upper corner
+        limit : float
+            Distance limit over which tracers are not connected,
+            For example if using a periodic boundary, setting limit to
+            half the bounding box size will prevent tracer lines being
+            connected when passing through the boundary
+        age : int
+            Minimum particle age in steps after which particle can be deleted and respawned, defaults to 4
+        respawn : float
+            Probability of respawning, after age reached, default 0.2 ==> 1 in 5 chance of deletion
+        speed_multiply : float
+            Speed multiplier, scaling factor for the velocity taken from the vector values
+        height : float
+            A fixed height value, all positions will be given this height as their Z component
+        viewer : lavavu.Viewer
+            Viewer object for plotting functions
+        """
+        if len(grid) == 2:
+            self.gridx = grid[0]
+            self.gridy = grid[1]
+            self.gridz = numpy.array((height, height))
+            self.dims = 2
+        elif len(grid) == 3:
+            self.gridx = grid[0]
+            self.gridy = grid[1]
+            self.gridz = grid[2]
+            self.dims = 3
+        elif isinstance(grid, numpy.ndarray) and grid.shape[1] == 3:
+            self.gridx = grid[::,0]
+            self.gridy = grid[::,1]
+            self.gridz = grid[::,2]
+            self.dims = 3
+        elif isinstance(grid, numpy.ndarray) and grid.shape[1] == 2:
+            self.gridx = grid[::,0]
+            self.gridy = grid[::,1]
+            self.gridz = numpy.array((height, height))
+            self.dims = 2
         else:
-            #Index of nearest grid point is in q[1][r]
-            #Lookup vector at this index, multiply by position to get delta and add
-            state.velocities[r] = vecs[q[1][r]] #Store velocity
-            state.positions[r] += speed * vecs[q[1][r]]
-            #Increment step tracking
-            state.steps[r] += 1
-            state.values[r] = numpy.linalg.norm(vecs[q[1][r]])
-
-    return state
+            raise(ValueError('Grid needs to be array of 2d/3d vertices, or arrays of vertex coords (x, y, [z])'))
+
+        self.count = count
+        if lowerbound is None:
+            lowerbound = (self.gridx[0], self.gridy[0], self.gridz[0])
+        if upperbound is None:
+            upperbound = (self.gridx[-1], self.gridy[-1], self.gridz[-1])
+        self.positions = random_particles(self.count, lowerbound, upperbound, self.dims)
+        self.old_pos = numpy.zeros_like(self.positions)
+        self.lowerbound = lowerbound
+        self.upperbound = upperbound
+        self.velocities = None
+        self.steps = [0]*count
+        self.speed = numpy.zeros(shape=(count))
+        self.ages = numpy.zeros(shape=(count))
+        self.interp = None
+        if limit is None:
+            limit = 0.1 * (abs(self.gridx[-1] - self.gridx[0]) + abs(self.gridy[-1] - self.gridy[0]))
+        self.limit = limit
+        self.age = age
+        self.respawn_chance = respawn_chance
+        self.speed_multiply = speed_multiply
+        self.height = height
+
+        self.lv = viewer
+        self.points = None
+        self.arrows = None
+        self.tracers = None
+
+
+    def respawn(self, r):
+        #Dead or out of bounds particle, start at new position
+        #Loop until new position further from current position than limit
+        old_pos = self.positions[r]
+        pos = numpy.array([0.] * self.dims)
+        for i in range(10):
+            pos = random_particles(1, self.lowerbound, self.upperbound, self.dims)
+            dist = numpy.linalg.norm(old_pos - pos)
+            if dist > self.limit*1.01:
+                break
+
+        self.ages[r] = 0
+        self.positions[r] = pos
+
+    def update(self, vectors=None):
+        #Interpolate velocity at all positions,
+        #If vectors not passed, will use previous values
+        if vectors is not None:
+            if self.dims == 2:
+                self.interp = RegularGridInterpolator((self.gridx, self.gridy), vectors, bounds_error=False, fill_value=0.0)
+            else:
+                self.interp = RegularGridInterpolator((self.gridx, self.gridy, self.gridz), vectors, bounds_error=False, fill_value=0.0)
+
+        if self.interp is None:
+            raise(ValueError("No velocity grid, must pass vectors for first call of update()"))
+
+        self.velocities = self.interp(self.positions)
+        self.old_pos = numpy.copy(self.positions)
+
+        for r in range(len(self.velocities)):
+            #Lookup velocity at this index, multiply by position to get delta and add
+            self.speed[r] = numpy.linalg.norm(self.velocities[r])
+            if numpy.isnan(self.speed[r]): self.speed[r] = 0.0
+            if self.speed[r] == 0.0: #numpy.any(numpy.isinf(self.old_pos[r])) or numpy.any(numpy.isinf(self.positions[r])):
+                self.respawn(r)
+            else:
+                self.positions[r] = self.positions[r] + self.speed_multiply * self.velocities[r]
+                self.ages[r] += 1
+
+            #Bounds checks
+            #Chance of killing particle when over age, default 1 in 5 (0.2)
+            if (any(self.positions[r] < self.lowerbound[0:self.dims]) or any(self.positions[r] > self.upperbound[0:self.dims])
+            or (self.ages[r] > self.age and numpy.random.uniform() <= self.respawn_chance)):
+                #if r < 20: print("Kill", r, self.speed[r], numpy.isnan(self.speed[r])) # [0] == numpy.nan)
+                #self.positions[r] = numpy.array([numpy.inf] * self.dims)
+                #self.positions[r] = numpy.array([numpy.nan] * self.dims)
+                self.respawn(r)
+                self.velocities[r] = numpy.array([0.0] * self.dims)
+                self.speed[r] = 0.0
+
+        if self.lv:
+            positions = self.positions
+            if self.dims == 2 and self.height != 0:
+                #Convert to 3d and set z coord to height
+                shape = list(positions.shape)
+                shape[-1] = 3
+                positions = numpy.zeros(shape)
+                positions[::,0:2] = self.positions
+                positions[::,2] = numpy.array([self.height] * shape[0])
+            if self.points:
+                self.points.vertices(positions)
+                if len(self.points["colourmap"]):
+                    self.points.values(self.speed)
+            if self.arrows:
+                self.arrows.vectors(self.velocities)
+                self.arrows.vertices(positions)
+                if len(self.arrows["colourmap"]):
+                    self.arrows.values(self.speed)
+
+            if self.tracers:
+                self.tracers.vertices(positions)
+                if len(self.tracers["colourmap"]):
+                    self.tracers.values(self.speed)
+
+    def plot_points(self, **kwargs):
+        if self.lv is not None and self.points is None:
+            self.points = self.lv.points('tracer_points', **kwargs)
+
+    def plot_arrows(self, **kwargs):
+        if self.lv is not None and self.arrows is None:
+            self.arrows = self.lv.vectors('tracer_arrows', **kwargs)
+
+    def plot_tracers(self, **kwargs):
+        if self.lv is not None and self.tracers is None:
+            self.tracers = self.lv.tracers('tracers', dims=self.count, limit=self.limit, **kwargs)
 

{lavavu-1.9.0.dist-info → lavavu-1.9.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: lavavu
-Version: 1.9.0
+Version: 1.9.6
 Summary: Python interface to LavaVu OpenGL 3D scientific visualisation utilities
 Author-email: Owen Kaluza <owen@kaluza.id.au>
 License: ### Licensing
@@ -215,14 +215,16 @@ License-File: LICENSE.md
 Requires-Dist: numpy>=1.18
 Requires-Dist: aiohttp
 Requires-Dist: jupyter_server_proxy
+Requires-Dist: matplotlib
 Requires-Dist: numpy-quaternion
+Dynamic: license-file
 
 ![# logo](http://owen.kaluza.id.au/Slides/2017-08-15/LavaVu.png)
 
 [![Build Status](https://github.com/lavavu/LavaVu/workflows/Test/badge.svg)](https://github.com/lavavu/LavaVu/actions?query=workflow:Test)
 [![Deploy Status](https://github.com/lavavu/LavaVu/workflows/Deploy/badge.svg?branch=1.7.3)](https://github.com/lavavu/LavaVu/actions?query=workflow:Deploy)
 [![DOI](https://zenodo.org/badge/45163055.svg)](https://zenodo.org/badge/latestdoi/45163055)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/lavavu/LavaVu/1.9.0)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/lavavu/LavaVu/1.9.6)
 
 A scientific visualisation tool with a python interface for fast and flexible visual analysis.
 
@@ -230,11 +232,12 @@ Documentation available here [LavaVu Documentation](https://lavavu.github.io/Doc
 
 ![examplevis](http://owen.kaluza.id.au/Slides/2017-08-15/combined.png)
 
-LavaVu development is supported by the [Monash Immersive Visualisation Plaform](http://monash.edu.au/mivp) and the Simulation, Analysis & Modelling component of the [NCRIS AuScope](http://www.auscope.org.au/ncris/) capability.
+LavaVu development is supported by [ACCESS-NRI](https://www.access-nri.org.au/).
+Prior development was funded by the Monash Immersive Visualisation Plaform at [Monash eResearch](https://www.monash.edu/researchinfrastructure/eresearch) and the Simulation, Analysis & Modelling component of the [NCRIS AuScope](http://www.auscope.org.au/ncris/) capability.
 
 The acronym stands for: lightweight, automatable  visualisation and analysis viewing utility, but "lava" is also a reference to its primary application as a viewer for geophysical simulations. It was also chosen to be unique enough to find the repository with google.
 
-The project started in the gLucifer<sup>1</sup> framework for visualising geodynamics simulations. The OpenGL visualisation module was separated from the simulation and sampling libraries and became a more general purpose visualisation tool. gLucifer continues as a set of sampling tools for Underworld simulations as part of the [Underworld2](https://github.com/underworldcode/underworld2/) code. LavaVu provides the rendering library for creating 2d and 3d visualisations to view this sampled data, inline within interactive IPython notebooks and offline through saved visualisation databases and images/movies.
+The project started as a replacement rendering library for the gLucifer<sup>1</sup> framework, visualising geodynamics simulations. The new OpenGL visualisation code was re-implemented as a more general purpose visualisation tool. gLucifer continues as a set of sampling tools for Underworld simulations as part of the [Underworld2](https://github.com/underworldcode/underworld2/) code. LavaVu provides the rendering library for creating 2d and 3d visualisations to view this sampled data, inline within interactive Jupyter notebooks and offline through saved visualisation databases and images/movies.
 
 As a standalone tool it is a scriptable 3D visualisation tool capable of producing publication quality high res images and video output from time varying data sets along with HTML5 3D visualisations in WebGL.
 Rendering features include correctly and efficiently rendering large numbers of opaque and transparent points and surfaces and volume rendering by GPU ray-marching. There are also features for drawing vector fields and tracers (streamlines).
@@ -242,12 +245,11 @@ Rendering features include correctly and efficiently rendering large numbers of
 Control is via python and a set of simple verbose scripting commands along with mouse/keyboard interaction.
 GUI components can be generated for use from a web browser via the python "control" module and a built in web server.
 
+Widgets for interactive use in the Jupyter notebook environment allow use for remote visualisation, eg: on supercomputing environments.
+
 A native data format called GLDB is used to store and visualisations in a compact single file, using SQLite for storage and fast loading. A small number of other data formats are supported for import (OBJ surfaces, TIFF stacks etc). 
 Further data import formats are supported with python scripts, with the numpy interface allowing rapid loading and manipulation of data.
 
-A CAVE2 virtual reality mode is provided by utilising Omegalib (http://github.com/uic-evl/omegalib) to allow use in Virtual Reality and Immersive Visualisation facilities, such as the CAVE2 at Monash, see (https://github.com/mivp/LavaVR).
-Side-by-side and quad buffer stereoscopic 3D support is also provided for other 3D displays.
-
 ### This repository ###
 
 This is the public source code repository for all development on the project.
@@ -258,13 +260,10 @@ Development happens in the "master" branch with stable releases tagged, so if yo
 It's now in the python package index, so you can install with *pip*:
 
 ```
-pip install --user lavavu
+python -m pip install lavavu
 ```
 
-> If you don't have pip available, you can try `sudo easy_install pip` or just install [Anaconda](https://www.anaconda.com/download), which comes with pip and a whole lot of other useful packages for scientific work with python. Once in anaconda `pip install lavavu` will install the package.
-
-> Currently no binaries are provided and the installer needs to compile the library, so on Linux you may need some developer tools and headers first, eg: for Ubuntu:
-`sudo apt install build-essential libgl1-mesa-dev libx11-dev zlib1g-dev`
+> Currently binary wheels are provided for Linux x86_64, MacOS x86_64 and ARM64 and Windows x86_64. 
 
 To try it out:
 
@@ -281,7 +280,12 @@ Alternatively, clone this repository with *git* and build from source:
 ```
   git clone https://github.com/lavavu/LavaVu
   cd LavaVu
+  python -m pip install .
+```
+or 
+```
   make -j4
+
 ```
 
 If all goes well the viewer will be built, try running with:
@@ -290,14 +294,14 @@ If all goes well the viewer will be built, try running with:
 ### Dependencies ###
 
 * OpenGL and Zlib, present on most systems, headers may need to be installed
-* To use with python requires python 2.7+ and NumPy
-* For video output, requires: libavcodec, libavformat, libavutil, libswscale (from FFmpeg / libav)
+* To use with python requires python 3.6+ and NumPy
+* For video output, requires: PyAV or for built in encoding, libavcodec, libavformat, libavutil, libswscale (from FFmpeg / libav)
 * To build the python interface from source requires swig (http://www.swig.org/)
 
 ### Who do I talk to? ###
 
 * Report bugs/issues here on github: https://github.com/lavavu/LavaVu/issues
-* Contact developer: Owen Kaluza (at) monash.edu
+* Contact developer: Owen Kaluza (at) anu.edu.au
 
 For further documentation / examples, see the online documentation
 * https://lavavu.github.io/Documentation

{lavavu-1.9.0.dist-info → lavavu-1.9.6.dist-info}/RECORD

@@ -1,18 +1,18 @@
-lavavu/lavavu.py,sha256=5JdzlRaEjuWAPjBQrgIKEyIS2RRL2RIrQ2aWaHFkg2A,217172
+lavavu/lavavu.py,sha256=I64ioPwTN1eyZcZEaF9RfdxncfLuihl-7VqqqJDFLCw,218528
 lavavu/vutils.py,sha256=6Vm_xl1bp9mWlfk7jgLDwbRw-tdE_oxin77YkLel3_4,5437
 lavavu/dict.json,sha256=lsZEHc7Bb6_lt7tkSBQMgkq7AEn_2hnhWzzdokmvIY8,52729
 lavavu/server.py,sha256=L-_yPCbNfwYxJCPjDQtr_lxPnDp4oMNVFyxXhBERYrQ,12468
 lavavu/points.py,sha256=jRRtA6CrcA46Y2jUJmkxnIiVoMC5a14xEd_ojhmjhz4,5871
 lavavu/LavaVuPython.py,sha256=ixhceiAr0gGGfCe3d2cY0IIgS4hbgoYJGa_RfgAmmrU,33207
-lavavu/tracers.py,sha256=0dB6v9Jg5G-IeZxiVFvbPoTycGvyAQBtgyEAZUmq4XU,4257
+lavavu/tracers.py,sha256=-NwdBAj5vYWmLt4NE0gWl36SQShQhICR7vBE4rzNOFI,8488
 lavavu/convert.py,sha256=tbYRjLE2l1hI4d6tsW41Lia1JXmrWSc0-JAYCiMrjys,35516
-lavavu/control.py,sha256=C5fLZeeNazRODDlWyWhKINry86uW7jAu3x_MvmrKeO8,66434
+lavavu/control.py,sha256=s32rtLPXXYtxpeXd6-iHdupmaMTJ3KhK6Vq-CLjf9OQ,66755
 lavavu/__init__.py,sha256=JroZQiUbuVN7ifixk2zNDGlyLGaM8bqfRbw4D_F9qIQ,191
 lavavu/amalgamate.py,sha256=Xloq1IZ4VUvYiROzQtwKcQIWC65c7EZrdiGVhZdolL8,586
 lavavu/aserver.py,sha256=SfFvLeDTcx1XtS8fY_HIrDmh3q9HicCBRSAriY5yyOE,12003
 lavavu/font.bin,sha256=fvi5zkvmq6gh9v3jXedBVuxNJWKmHtbjECzv6eT9wb4,225360
 lavavu/__main__.py,sha256=EbDetijCjyoiNxmExqnDGoRVs996tSVave5DML9zuMY,235
-lavavu/_LavaVuPython.cpython-311-darwin.so,sha256=xYjN7ELLgT87N1_ubcq3JujvVXjuPP318YJj5Z59uRc,3927360
+lavavu/_LavaVuPython.cpython-311-darwin.so,sha256=4f_OIq_Z1CDwE96EOJLY_E-4pHxMRE1Quk5JEHHtqSM,3927376
 lavavu/html/control.css,sha256=PVLwmle00ciEckUV5ZIRmI3Whxhl7-mlVexnyyxoU70,3259
 lavavu/html/control.js,sha256=oV24eJZ0vfuCxF3fO60eeJSkNFJ9hUkSCThHGJS1Wvc,11652
 lavavu/html/gui.css,sha256=PRDLsYwM6cgLC9zZsEAG0dnnSd-HYH6oSEfsdEBkuxk,582
@@ -27,11 +27,11 @@ lavavu/html/dat.gui.min.js,sha256=S4_QjoXe4IOpU0f0Sj5jEQLTWPoX9uRl1ohB91jyhuw,56
 lavavu/html/OK-min.js,sha256=-4Gc1-dWfxP_w6r9ZOHa8u-X2BlGUoSQbX68lwCxQ3E,39115
 lavavu/html/emscripten.css,sha256=wkaIJhXaxuMchinQX9Z8c12cJomyvFQMeIZ62WGQEPQ,1813
 lavavu/html/drawbox.js,sha256=SJxFSmWd7QVFI5__66hFkKzLKeqg1JPcx-gJuqdMkXw,34590
-lavavu/html/webview.html,sha256=aFUGmVs3dT3R9X9IgA5WN8ND6tWFM0Ki5mgywqIRjz4,1521
+lavavu/html/webview.html,sha256=8eilGjX8y_I5OjCvTm-ZAQDNOSCaT1yvogKFqK4lCS0,1521
 lavavu/html/emscripten-template.js,sha256=h63mzl3Lv7aQT1wMOiOucPOvHTJjpKkzsL-SFVYaZlA,6135
 lavavu/html/draw.js,sha256=57LlHlYRh0IvWVwzGDnF6PaCxYLzokpokLNCuZlG1ds,84108
 lavavu/html/dat-gui-light-theme.css,sha256=uPhvJs-1IAsdxudItyOw8lZy8Hrih0zmFM1u-xRwZ-M,1142
-lavavu/html/menu.js,sha256=WCli3UYcQ7frjNq0aAXNALu33iNiN8lpTYwKZ7pUcn4,21501
+lavavu/html/menu.js,sha256=42h-BCnrmEpW4IdZRKC_FIXUVczJP0sm4ciZ2ccfs-k,21630
 lavavu/html/baseviewer.js,sha256=u3UhC1At6rMBKmcQ7d2DXTRxQ20wsQkc4lqA-7sL7i4,9567
 lavavu/osmesa/LavaVuPython.py,sha256=ixhceiAr0gGGfCe3d2cY0IIgS4hbgoYJGa_RfgAmmrU,33207
 lavavu/osmesa/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -47,9 +47,9 @@ lavavu/shaders/fontShader.vert,sha256=yCBmRugaPUeUQUdIh62-AK_5KELiJqVS2M82iyIqPw
 lavavu/shaders/pointShader.frag,sha256=3zREBdsimlL9fAXBPjhzomGaFUWmlG_QYkhwMTVURHQ,3291
 lavavu/shaders/volumeShader.vert,sha256=uGdQjGqi7V5kE6V7nxymfugtU4cbf6u570xBy13RgmY,78
 lavavu/shaders/default.frag,sha256=5XLYVfLwzN0sFT3aMYGmxbyquA_cmndp55YCOuy1t4E,180
-lavavu-1.9.0.dist-info/LICENSE.md,sha256=EhfNgC6BYh5gDEaq4tcrN3S0wbO4CtJO46botJnCF8c,8603
-lavavu-1.9.0.dist-info/RECORD,,
-lavavu-1.9.0.dist-info/WHEEL,sha256=NW1RskY9zow1Y68W-gXg0oZyBRAugI1JHywIzAIai5o,109
-lavavu-1.9.0.dist-info/entry_points.txt,sha256=LC2qXR6EMe45Cb7zGAF99R9HFrAECP6Qkp_YuG6HZB0,44
-lavavu-1.9.0.dist-info/top_level.txt,sha256=JptS0k1nlBumjLs_0hITr3_XUJhxqvKBXD2jGho3E3A,7
-lavavu-1.9.0.dist-info/METADATA,sha256=yZSA74LHPQhIIUvqPUS3b9DhXpvQ3MLvl8lDLmENqS8,18267
+lavavu-1.9.6.dist-info/RECORD,,
+lavavu-1.9.6.dist-info/WHEEL,sha256=EfZGgIDXTDki1cNGEkgBr7YEgShBrw-nMmb-y67Rxxs,136
+lavavu-1.9.6.dist-info/entry_points.txt,sha256=LC2qXR6EMe45Cb7zGAF99R9HFrAECP6Qkp_YuG6HZB0,44
+lavavu-1.9.6.dist-info/top_level.txt,sha256=JptS0k1nlBumjLs_0hITr3_XUJhxqvKBXD2jGho3E3A,7
+lavavu-1.9.6.dist-info/METADATA,sha256=EHgjIlNax60denK4kKXeAJziT1zFhX8e-9OqQUVd9WE,17877
+lavavu-1.9.6.dist-info/licenses/LICENSE.md,sha256=EhfNgC6BYh5gDEaq4tcrN3S0wbO4CtJO46botJnCF8c,8603

{lavavu-1.9.0.dist-info → lavavu-1.9.6.dist-info}/WHEEL

@@ -1,5 +1,6 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (78.1.0)
 Root-Is-Purelib: false
 Tag: cp311-cp311-macosx_11_0_arm64
+Generator: delocate 0.13.0