first go at putting in plotting functions

bin/test_plot.py

+import pykat
+pykat.init_pykat_plotting(mode="display", dpi=100)
+
 from pykat import finesse
 from pykat.detectors import *
 from pykat.components import *
@@ -5,7 +8,6 @@ from pykat.commands import *
 from pykat.structs import *
 
 import numpy as np
-import pylab as pl
 
 code = """
 l l1 1 0 0 n1 
@@ -15,10 +17,12 @@ s s2 10 1 n3 n4
 m m2 0.5 0.5 0 n4 n5
 s s3 10 1 n5 n6
 
-yaxis abs:deg
+yaxis re:im
 
+ad circ 0 0 0 n4
 pd pd_cav n3
 
+
 cav c1 m1 n3 m2 n4
 
 attr m1 Rc 1
@@ -27,7 +31,7 @@ attr m1 Rc 1
 kat = finesse.kat()
 kat.parseCommands(code)
 
-kat.add(xaxis("lin", [0, 360], kat.m2.phi, 100))
+kat.add(xaxis("lin", [0, 360], kat.m2.phi, 500))
 
 kat.m1.Rcx = -1000.0
 kat.m1.Rcy = -1000.0
@@ -37,5 +41,4 @@ kat.m2.Rcy =  1000.0
 kat.maxtem = 0
 
 out = kat.run()
-out.plot()
-
+fig = out.plot("test_plot.pdf")

pykat/__init__.py

@@ -8,7 +8,9 @@ __version__ = "0.8.1"
 # This flag is used to switch on the gui features in pkat at import time
 USE_GUI = False
 HAS_OPTIVIS = False
+
 import imp
+
 try:
 	imp.find_module('optivis')
 	HAS_OPTIVIS = True
@@ -26,6 +28,6 @@ import pykat.commands as commands
 
 from pykat.optics.gaussian_beams import beam_param
 
-
+from pykat.plotting import init_pykat_plotting
 
 

pykat/components.py

@@ -1063,7 +1063,7 @@ class modulator(Component):
         self._requested_node_names.append(node1)
         self._requested_node_names.append(node2)
         self._svgItem = None
-        self.__f = Param("f", self, SIfloat(f))
+        self.__f = Param("f", self, SIfloat(f), canFsig=True, fsig_name="fre")
         self.__midx = Param("midx", self, SIfloat(midx))
         self.__phase = Param("phase", self, SIfloat(phase), canFsig=True, fsig_name="phase")
         self.__order = int(order)
@@ -1171,7 +1171,7 @@ class laser(Component):
         self._requested_node_names.append(node)
         
         self.__power = Param("P", self, SIfloat(P), canFsig=True, fsig_name="amp")
-        self.__f_offset = Param("f", self, SIfloat(f), canFsig=True, fsig_name="f")
+        self.__f_offset = Param("f", self, SIfloat(f), canFsig=True, fsig_name="freq")
         self.__phase = Param("phase", self, SIfloat(phase), canFsig=True, fsig_name="phase")
         self.__noise = AttrParam("noise", self, None)
         self._svgItem = None

pykat/detectors.py

@@ -65,6 +65,7 @@ class BaseDetector(object) :
         self._mask = {}
         self.__scale = []
         self.__removed = False
+        self.noplot = False
         
         self._alternate_beam = []
         self._nodes = []

pykat/finesse.py

@@ -240,13 +240,74 @@ class katRun(object):
         self.katVersion = None
         self.yaxis = None
         
-    def plot(self, logy=False):
-        import pylab
+    def plot(self, filename=None, show=True):
+        import matplotlib.pyplot as pyplot
+        import pykat.plotting as plt
+
+        kat = pykat.finesse.kat()
+        kat.verbose = False
+        kat.parseCommands(self.katScript)
+
+        plot_cmd = None
+
+        if "log" in kat.yaxis:
+            if kat.xaxis.scale == "log":
+                plot_cmd = pyplot.loglog
+            else:
+                plot_cmd = pyplot.semilogy
+        else:
+            if kat.xaxis.scale == "log":
+                plot_cmd = pyplot.semilogx
+            else:
+                plot_cmd = pyplot.plot
+
+        dual_plot = False
+
+        if ":" in kat.yaxis:
+            fig = plt.figure(width="full", height=1)
+            dual_plot = True
+        else:
+            fig = plt.figure(width="full")
+
+        for lbl in self.ylabels:
+            lbl = lbl.split()[0]
+            if not dual_plot:
+                plot_cmd(self.x, np.abs(self[lbl]))
+            else:
+                pyplot.subplot(2,1,1)
+                plot_cmd(self.x, np.abs(self[lbl]))
         
-        pylab.plot(self.x, self.y)
-        pylab.legend(self.ylabels,0)
-        pylab.xlabel(self.xlabel)
-        pylab.show()
+                pyplot.subplot(2,1,2)
+                plot_cmd(self.x, np.angle(self[lbl]))
+
+        if dual_plot:
+            pyplot.subplot(2,1,1)
+            pyplot.xlabel(self.xlabel, fontsize=pyplot.rcParams["font.size"])
+            pyplot.xlim(self.x.min(), self.x.max())
+    
+            if "abs" in kat.yaxis: pyplot.ylabel("Absolute [au]", fontsize=pyplot.rcParams["font.size"])
+            if "re" in kat.yaxis: pyplot.ylabel("Real part [au]", fontsize=pyplot.rcParams["font.size"])
+    
+            pyplot.subplot(2,1,2)
+            pyplot.xlabel(self.xlabel, fontsize=pyplot.rcParams["font.size"])
+            pyplot.xlim(self.x.min(), self.x.max())
+    
+            if "deg" in kat.yaxis: pyplot.ylabel("Phase [deg]", fontsize=pyplot.rcParams["font.size"])
+            if "im" in kat.yaxis: pyplot.ylabel("Imaginary part [au]", fontsize=pyplot.rcParams["font.size"])
+        else:
+            pyplot.xlabel(self.xlabel, fontsize=pyplot.rcParams["font.size"])
+            pyplot.ylabel(" [au]")
+            pyplot.xlim(self.x.min(), self.x.max())
+    
+        fig.tight_layout()
+        
+        if filename is not None:
+            fig.savefig(filename)
+            
+        if show:
+            pyplot.show(fig)
+        
+        return fig
         
     def savekatRun(self, filename):
         with open(filename,'w') as outfile:
@@ -916,8 +977,7 @@ class kat(object):
                     elif(first == "fsig"):
                         after_process.append((line, self.__currentTag))
                     elif(first == "noplot"):
-                        obj = line
-                        #self.__blocks[self.__currentTag].contents.append(line) 
+                        after_process.append((line, self.__currentTag))
                     else:
                         if self.verbose:
                             print ("Parsing `{0}` into pykat object not implemented yet, added as extra line.".format(line))
@@ -938,7 +998,7 @@ class kat(object):
             # components to exist first before they can be processed
             for item in after_process:
                 line = item[0]
-                first = line.split(" ",1)[0] 
+                first, rest = line.split(" ",1)
                 block = item[1]
                 
                 if first == "gauss" or first == "gauss*" or first == "gauss**":
@@ -955,6 +1015,11 @@ class kat(object):
                     
                 elif (first == "variable"):
                     self.add(pykat.commands.variable.parseFinesseText(line, self), block=block)
+                elif (first == "noplot"):
+                    if not hasattr(self, rest):
+                        raise pkex.BasePyKatException("noplot command `{0}` refers to non-existing detector".format(line))
+                        
+                    getattr(self, rest).noplot = True
                     
                 elif (first == "scale"):
                     v = line.split()
@@ -1264,7 +1329,7 @@ class kat(object):
                             err="".join((err,str(line, 'utf-8')))
 
             
-            [out,errpipe] = p.communicate()
+            [out, errpipe] = p.communicate()
 
             if six.PY2:
                 _out = str(out).split("\n")
@@ -1286,6 +1351,7 @@ class kat(object):
             # get the version number
             ix = out.find(b'build ') + 6
             ix2 = out.find(b')',ix)
+            
             r.katVersion = out[ix:ix2]
             
             r.runDateTime = datetime.datetime.now()

pykat/plotting.py

@@ -9,79 +9,87 @@ from __future__ import division
 from __future__ import print_function
 from __future__ import unicode_literals
 
-import numpy as np
-import matplotlib
+# Should be either display (showing in windows) or paper (saving for paper/report/etc.)
+__mode__ = None
+__DPI__ = None
 
-BACKEND = 'Qt4Agg'
-matplotlib.use(BACKEND)
-
-from matplotlib import rc
-import matplotlib.pyplot as plt
-
-mainpid = -1
-
-def plot1D(run, title=""):
+def in_ipython():
+    try:
+        cfg = get_ipython() 
+        return True
+    except NameError:
+        return False
+        
+        
+def init_pykat_plotting(mode="display", dpi=100):
+    import matplotlib as mpl
     
-    rc('font', **pp.font)
-    rc('xtick',labelsize=pp.TICK_SIZE)
-    rc('ytick',labelsize=pp.TICK_SIZE)
-    rc('text', usetex=pp.USETEX)
-    rc('axes', labelsize = pp.LABEL_SIZE)
+    __DPI__ = int(dpi)
     
-    fig=plt.figure()
-    fig.set_size_inches(pp.fig_size)
-    fig.set_dpi(pp.FIG_DPI)
-        
-    ax1 = fig.add_subplot(111)
-    ax1.set_xlim(np.min(run.x),np.max(run.x))
-    traces = ax1.plot(run.x,run.y)
-    ax1.grid(pp.GRID)
+    if in_ipython():
+        from IPython.display import set_matplotlib_formats
+        set_matplotlib_formats('pdf', 'svg')
+        ipy = get_ipython()
+        ipy.magic("matplotlib inline")
     
-    ax1.set_xlabel(run.xlabel)
-    legends = run.ylabels
-    ax1.legend(traces, legends, loc=0, shadow=pp.SHADOW,prop={'size':pp.LEGEND_SIZE})
+    if mode == "display":
+        __mode__ = mode
+        
+    elif mode == "paper":
+        __mode__ = mode
+        
+        mpl.use("pgf")
+
+        pgf_with_pdflatex = {
+            "pgf.texsystem": "pdflatex",
+            "pgf.preamble": [
+                 r"\usepackage{amsmath, amssymb}",
+                 r"\usepackage{mathtools, siunitx}" ,
+                 r"\usepackage{amsmath}",
+                 r"\usepackage[utf8x]{inputenc}",
+                 r"\usepackage[T1]{fontenc}"
+                 ]
+        }
 
-    if pp.PRINT_TITLE:
-        plt.title(title)
+        mpl.rcParams.update(pgf_with_pdflatex)
+    else:
+        raise(BaseException("Plotting mode must be either 'display' or 'paper'."))
         
-    if pp.SCREEN_TITLE:
-        fig.canvas.manager.set_window_title(title)
+    mpl.rcParams.update({"figure.figsize": (6, 3.708)})
+    mpl.rcParams.update({'font.size': 11})
+    mpl.rcParams.update({'figure.dpi': __DPI__})
+    mpl.rcParams.update({'savefig.dpi': __DPI__})
+    mpl.rcParams.update({'font.family': "serif"})
+    mpl.rcParams.update({'axes.grid': True})
+    mpl.rcParams.update({'axes.axisbelow': True})
+    mpl.rcParams.update({'grid.linewidth': 0.25})
+    mpl.rcParams.update({'grid.linestyle': ":"})
+    mpl.rcParams.update({'grid.color': (0.7,0.7,0.7,1)})
+    mpl.rcParams.update({'savefig.bbox': "tight"})
+    mpl.rcParams.update({'savefig.pad_inches': 0.05})
+    mpl.rcParams.update({'xtick.labelsize': "small"})
+    mpl.rcParams.update({'ytick.labelsize': "small"})
+    mpl.rcParams.update({'axes.formatter.useoffset': False})
+
+def figure(width="full", height=0.618, textwidth=6, **kwargs):
+    """
+    Options:
+        width: 'full', 'half' (0.49*textwidth) (default: full)
+        height: relative height to width (default: 1/golden ratio = 0.618)
+        textwidth: Width of text in inches (default: 9.84252 in = 25 cm )
+    """
+    import matplotlib.pyplot as plt
+    
+    if width == "full":
+        fig_size = [textwidth, textwidth*height]
+    elif width == "half":
+        fig_size = [textwidth*0.49, textwidth*height*0.49]
     else:
-        fig.canvas.manager.set_window_title('')
+        raise(BaseException("width must be either 'full' or 'half'."))
         
-    #plt.ion()
-    plt.show()
+    fig = plt.figure(figsize=fig_size, dpi=__DPI__)
+    
+    return fig
+    
     
-class pp():
-    # set some gobal settings first
-    BACKEND = 'Qt4Agg' # matplotlib backend
-    FIG_DPI=90 # DPI of on sceen plot
-    # Some help in calculating good figure size for Latex
-    # documents. Starting with plot size in pt,
-    # get this from LaTeX using \showthe\columnwidth
-    fig_width_pt = 484.0
-    inches_per_pt = 1.0/72.27  # Convert TeX pt to inches
-    golden_mean = (np.sqrt(5)-1.0)/2.0   # Aesthetic ratio
-    fig_width = fig_width_pt*inches_per_pt  # width in inches
-    fig_height = fig_width*golden_mean      # height in inches
-    fig_size = [fig_width,fig_height]
-    # some plot options:
-    LINEWIDTH = 1 # linewidths of traces in plot
-    AA = True # antialiasing of traces
-    USETEX = False # use Latex encoding in text
-    SHADOW = False # shadow of legend box
-    GRID = True # grid on or off
-    # font sizes for normal text, tick labels and legend
-    FONT_SIZE = 10 # size of normal text
-    TICK_SIZE = 10 # size of tick labels
-    LABEL_SIZE = 10 # size of axes labels
-    LEGEND_SIZE = 10 # size of legend
-    # font family and type
-    font = {'family':'sans-serif','sans-serif':['Helvetica'],'size':FONT_SIZE}
-    DPI=300 # DPI for saving via savefig
-    # print options given to savefig command:
-    print_options = {'dpi':DPI, 'transparent':True, 'bbox_inches':'tight', 'pad_inches':0.1}
-    # for Palatino and other serif fonts use:
-    #font = {'family':'serif','serif':['Palatino']}
-    SCREEN_TITLE = True # show title on screen?
-    PRINT_TITLE = False # show title in saved file?
+    
\ No newline at end of file

pykat/profiling.py

@@ -3,10 +3,10 @@ from __future__ import division
 from __future__ import print_function
 from __future__ import unicode_literals
 
-import numpy as np
-import pylab as pl
-
 def plotReducedPerformanceData(perfdata, ordered=False):
+    import numpy as np
+    import pylab as pl
+    
     labels = []
     times = []
 

pykat/tools/modematching.py

-import pylab as pl
+#import pylab as pl # removed by DDB 1/12/2015
 import scipy.optimize as opt
 from pykat import finesse
 from pykat.detectors import *
@@ -7,7 +7,7 @@ from pykat.commands import *
 from pykat.structs import *
 from numpy import *
 # from modematch import modematch
-import pykat.utilities.optics.ABCD as abcd
+import pykat.optics.ABCD as abcd
 import time
 
 

pykat/tools/plotting/beamtrace.py

@@ -2,9 +2,10 @@ import pykat
 import pykat.exceptions as pkex
 import copy
 import numpy as np
-import pylab
 
 def plot_beam_trace(_kat, from_node, to_node):
+    import pylab
+    
     if _kat == None:
         raise pkex.BasePyKatException('kat object in None')