🚧 working server plotting in new tab

notebook is not ideal as it is not inline and you have to "interrupt kernel" to close server thread

May have to wait for bokeh/bokeh#3461 to be resolved.

QGL/Plotting.py

@@ -24,6 +24,12 @@
 import bokeh.plotting as bk
 import numpy as np
 
+import threading
+import subprocess
+import psutil
+import os
+import sys
+
 from . import config
 
 def output_notebook():
@@ -88,3 +94,48 @@ def plot_waveforms(waveforms, figTitle = ''):
 def show(seq):
     waveforms = build_waveforms(seq)
     plot_waveforms(waveforms)
+
+def in_notebook():
+    return True
+    # From http://stackoverflow.com/questions/15411967/how-can-i-check-if-code-is-executed-in-the-ipython-notebook
+    try:
+        cfg = get_ipython().config
+        if cfg['IPKernelApp']['parent_appname'] == 'ipython-notebook':
+            return True
+        else:
+            return False
+    except NameError:
+        return False
+
+class BokehServerThread(threading.Thread):
+    def __init__(self):
+        super(BokehServerThread, self).__init__()
+        self.daemon = True
+        self.run_in_notebook = in_notebook()
+
+    def __del__(self):
+        self.join()
+
+    def __del__(self):
+        self.join()
+
+    def run(self):
+        args = []
+        if 'win32' in sys.platform:
+            args.append("bokeh.bat")
+        else:
+            args.append("bokeh")
+        args.append("serve")
+        if self.run_in_notebook:
+            args.append("--allow-websocket-origin=localhost:8888")
+        self.p = subprocess.Popen(args, env=os.environ.copy())
+
+    def join(self, timeout=None):
+        if self.p:
+            print("Killing bokeh server thread {}".format(self.p.pid))
+            for child_proc in psutil.Process(self.p.pid).children():
+                print("Killing child process {}".format(child_proc.pid))
+                child_proc.kill()
+            self.p.kill()
+            self.p = None
+            super(BokehServerThread, self).join(timeout=timeout)

QGL/PulseSequencePlotter.py

@@ -23,20 +23,26 @@
 limitations under the License.
 '''
 
+import time
 import os.path
 from importlib import import_module
-from bokeh.io import vform
-from bokeh.models import CustomJS, ColumnDataSource, Slider
-from bokeh.plotting import Figure, show
+import pkgutil
+from collections import OrderedDict
 
-from jinja2 import Template
 import numpy as np
 
+from bokeh.layouts import column
+from bokeh.models import Slider
+from bokeh.plotting import Figure
+from bokeh.client import push_session
+from bokeh.io import curdoc, output_notebook, output_server
+
 from . import config
 from . import ChannelLibrary
 
 from . import drivers
-import pkgutil
+
+from .Plotting import BokehServerThread, in_notebook
 
 def all_zero_seqs(seqs):
     return all([np.allclose([_[1] for _ in seq], 0) for seq in seqs])
@@ -67,92 +73,91 @@ def resolve_translator(filename, translators):
             return t
     raise NameError("No translator found to open the given file %s", filename)
 
-def plot_pulse_files(fileNames):
-    '''
-    plot_pulse_files(fileNames)
+def plot_pulse_files(h5_files):
+    """
+    Plots a list of h5 sequence files with an interactive slider.
+    """
 
-    Helper function to plot a list of AWG files. A JS slider allows choice of sequence number.
-    '''
-    #If we only go one filename turn it into a list
-    if isinstance(fileNames, str):
-        fileNames = [fileNames]
+    bokeh_thread = BokehServerThread()
+    bokeh_thread.start()
+    time.sleep(1) #make sure server is finish launching
+    output_server()
+    curdoc().clear()
+    # output_notebook()
 
-    dataDict = {}
-    lineNames, num_seqs = extract_waveforms(dataDict, fileNames)
+    #If we only got one filename turn it into a list
+    if isinstance(h5_files, str):
+        h5_files = [h5_files]
 
-    localname = os.path.split(fileNames[0])[1]
-    sequencename = localname.split('-')[0]
+    wfs = extract_waveforms(h5_files)
+    num_seqs = max([len(_) for _ in wfs.values()])
 
-    all_data = ColumnDataSource(data=dataDict)
-    plot = Figure(title=sequencename, plot_width=1000)
-    plot.background_fill_color = config.plotBackground
-    if config.gridColor:
-        plot.xgrid.grid_line_color = config.gridColor
-        plot.ygrid.grid_line_color = config.gridColor
+    filename = os.path.split(h5_files[0])[1]
+    seq_name = filename.split('-')[0]
 
-    # Colobrewer2 qualitative Set1 (http://colorbrewer2.org)
-    colours = [
-        "#e41a1c",
-        "#377eb8",
-        "#4daf4a",
-        "#984ea3",
-        "#ff7f00",
-        "#ffff33",
-        "#a65628",
-        "#f781bf",
-        "#999999"
-    ]
+    fig = Figure(title=seq_name, plot_width=800)
+    fig.background_fill_color = config.plotBackground
+    if config.gridColor:
+        fig.xgrid.grid_line_color = config.gridColor
+        fig.ygrid.grid_line_color = config.gridColor
 
-    js_sources = {}
-    js_sources["all_data"] = all_data
-    for ct,k in enumerate(lineNames):
-        k_ = k.replace("-", "_")
-        line = plot.line(dataDict[k_+"_x_1"], dataDict[k_+"_y_1"], color=colours[ct%len(colours)], line_width=2, legend=k)
-        js_sources[k_] = line.data_source
+    num_lines = len(wfs.keys())
+    #for some reason the qualitative maps aren't in bokeh.palettes
+    # see https://github.com/bokeh/bokeh/issues/4758
+    brewer_set3 = ['#8dd3c7','#ffffb3','#bebada','#fb8072','#80b1d3','#fdb462','#b3de69','#fccde5','#d9d9d9','#bc80bd','#ccebc5','#ffed6f']
+    colours = list(np.resize(brewer_set3, num_lines))
 
-    code_template = Template("""
-        var seq_num = cb_obj.get('value');
-        console.log(seq_num)
-        var all_data = all_data.get('data');
-        {% for line in lineNames %}
-        {{line}}.set('data', {'x':all_data['{{line}}_x_'.concat(seq_num.toString())], 'y':all_data['{{line}}_y_'.concat(seq_num.toString())]} );
-        {% endfor %}
-        console.log("Got here!")
-    """)
+    lines = []
+    for colour, (k,v) in zip(colours, wfs.items()):
+        lines.append( fig.line(v[0]["x"], v[0]["y"], color=colour, legend=k, line_width=2) )
 
-    callback = CustomJS(args=js_sources, code=code_template.render(lineNames=[l.replace("-","_") for l in lineNames]))
+    def callback(attr, old, new):
+        for line, wf in zip(lines, wfs.values()):
+            new_xy = {"x":wf[new-1]["x"], "y":wf[new-1]["y"]}
+            line.data_source.data = new_xy
 
-    slider = Slider(start=1, end=num_seqs, value=1, step=1, title="Sequence", callback=callback)
+    slider = Slider(start=1, end=num_seqs, value=1, step=1, title="Sequence")
+    slider.on_change("value", callback)
 
-    layout = vform(slider, plot)
+    session = push_session(curdoc())
+    session.show(column([slider, fig]))
+    session.loop_until_closed()
 
-    show(layout)
+def extract_waveforms(h5_files, nameDecorator=''):
+    """
+    Extracts a dictionary mapping channel names to lists of dictionaries (keys "x" and "y") lines
 
-def extract_waveforms(dataDict, fileNames, nameDecorator=''):
-    lineNames = []
-    num_seqs = 0
-    for fileName in sorted(fileNames):
+    Lines are shifted along the y axis to prevent overlap
+    """
+    wfs = OrderedDict()
 
+    y_shift = 0
+    for file_name in sorted(h5_files):
         # Assume a naming convention path/to/file/SequenceName-AWGName.h5
-        AWGName = (os.path.split(os.path.splitext(fileName)[0])[1]).split('-')[1]
+        AWGName = (os.path.split(os.path.splitext(file_name)[0])[1]).split('-')[1]
         # Strip any _ suffix
         if '_' in AWGName:
             AWGName = AWGName[:AWGName.index('_')]
 
-        translator = resolve_translator(fileName, translators)
-        wfs = translator.read_sequence_file(fileName)
+        translator = resolve_translator(file_name, translators)
+        ta_pairs = translator.read_sequence_file(file_name)
 
-        for (k,seqs) in sorted(wfs.items()):
+        for (k,seqs) in sorted(ta_pairs.items()):
             if all_zero_seqs(seqs):
                 continue
-            num_seqs = max(num_seqs, len(seqs))
-            lineNames.append(AWGName + nameDecorator + '-' + k)
-            k_ = lineNames[-1].replace("-", "_")
+
+            line_name = AWGName + nameDecorator + '-' + k
+            y_shift += 2
+            wfs[line_name] = []
             for ct,seq in enumerate(seqs):
-                # Convert from time amplitude pairs to x,y lines with points at start and beginnning to prevent interpolation
-                dataDict[k_+"_x_{:d}".format(ct+1)] = np.tile( np.cumsum([0] + [_[0] for _ in seq]), (2,1)).flatten(order="F")[1:-1]
-                dataDict[k_+"_y_{:d}".format(ct+1)] = np.tile( [_[1] for _ in seq], (2,1)).flatten(order="F") + 2*(len(lineNames)-1)
-    return lineNames, num_seqs
+                wfs[line_name].append(
+                    {
+                        # Convert from time amplitude pairs to x,y lines with points at start and beginnning to prevent interpolation
+                        "x": np.tile( np.cumsum([0] + [_[0] for _ in seq]), (2,1)).flatten(order="F")[1:-1],
+                        "y": np.tile( [_[1] for _ in seq], (2,1)).flatten(order="F") + y_shift
+                    }
+                )
+    return wfs
 
 def plot_pulse_files_compare(fileNames1, fileNames2):
     '''
@@ -173,10 +178,10 @@ def plot_pulse_files_compare(fileNames1, fileNames2):
     num_seqs = max(num_seqs1, num_seqs2)
 
     localname = os.path.split(fileNames1[0])[1]
-    sequencename = localname.split('-')[0]
+    seq_name = localname.split('-')[0]
 
     all_data = ColumnDataSource(data=dataDict)
-    plot = Figure(title=sequencename, plot_width=1000)
+    plot = Figure(title=seq_name, plot_width=1000)
     plot.background_fill_color = config.plotBackground
     if config.gridColor:
         plot.xgrid.grid_line_color = config.gridColor