finesse.py 34.7 KB
Newer Older
Daniel Brown's avatar
Daniel Brown committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
# -*- coding: utf-8 -*-
"""
Created on Sun Jan 27 09:56:53 2013

PyKat - Python interface and wrapper for FINESSE
Copyright (C) 2013 Daniel David Brown

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

Contact at ddb@star.sr.bham.ac.uk

@author: Daniel Brown
"""
import sys
import os
import subprocess
import tempfile
import numpy as np
import datetime
import pickle
import pykat
import warnings
import re

from pykat.node_network import NodeNetwork
from pykat.detectors import Detector
from pykat.components import Component
from pykat.commands import Command, xaxis
from pykat.gui.gui import pyKatGUI
42
from pykat.SIfloat import *
43
from pykat.param import Param, AttrParam
Daniel Brown's avatar
Daniel Brown committed
44
45
46
47
48
49
50
51

import pykat.exceptions as pkex

from PyQt4.QtCore import QCoreApplication
from PyQt4.QtGui import QApplication

NO_GUI = False
NO_BLOCK = "NO_BLOCK"
52
53
54
pykat_version = "0.1"
pykat_web = "www.gwoptics.org/pykat"

Daniel Brown's avatar
Daniel Brown committed
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77

class katRun(object):
    def __init__(self):
        self.runDateTime = datetime.datetime.now()
        self.x = None
        self.y = None
        self.xlabel = None
        self.ylabels = None
        self.katScript = None
        self.katVersion = None
        
    def saveKatRun(self, filename):
        with open(filename,'w') as outfile:
            pickle.dump(self, outfile)
    
    @staticmethod
    def loadKatRun(filename):
        with open(filename,'r') as infile:
            return pickle.load(infile)
    
    def get(self, value): return self[value]
    
    def __getitem__(self, value):
78
        idx = [i for i in range(len(self.ylabels)) if self.ylabels[i].split(" ")[0] == str(value)]
Daniel Brown's avatar
Daniel Brown committed
79
80
        
        if len(idx) > 0 and self.y.shape == ():
81
82
            # In the case we have a noxaxis and just one output...
            return float(self.y)
Daniel Brown's avatar
Daniel Brown committed
83
        elif len(idx) == 1 and len(self.y.shape) == 1:
84
85
            
            # only selecting a single output from a 1D array
Daniel Brown's avatar
Daniel Brown committed
86
            if self.y.size == 1:
87
88
89
90
91
                return self.y
            else:
                return self.y[idx[0]]
                
	
92
93
        elif len(idx) > 0 and len(self.y.shape) == 1:
            return self.y[idx]
94
95
        elif len(idx) > 0:
            return self.y[:,idx].squeeze()
96
        elif len(idx) >= 1:
97
            return self.y[:,idx].squeeze()
Daniel Brown's avatar
Daniel Brown committed
98
        else:
99
            raise  pkex.BasePyKatException("No output by the name '{0}' found in the output".format(str(value)))
Daniel Brown's avatar
Daniel Brown committed
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
      
class katRun2D(object):
    def __init__(self):
        self.runDateTime = datetime.datetime.now()
        self.x = None
        self.y = None
        self.z = None
        self.xlabel = None
        self.ylabel = None
        self.zlabels = None
        self.katScript = None
        self.katVersion = None
        
    def saveKatRun(self, filename):
        with open(filename,'w') as outfile:
            pickle.dump(self, outfile)
    
    @staticmethod
    def loadKatRun(filename):
        with open(filename,'r') as infile:
            return pickle.load(infile)
    
    def get(self, value): return self[value]
    
    def __getitem__(self, value):
        idx = [i for i in range(len(self.zlabels)) if self.zlabels[i].split(" ")[0] == str(value)]
        
        if len(idx) > 0:
            return self.z[idx].squeeze()
        else:
            raise  pkex.BasePyKatException("No output by the name {0} found".format(str(value)))
131
    
132
133
class Signals(object):
    class fsig(object):
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
        def __init__(self, param, name, amplitude, phase):
            self._params = []
            self.__target = param
            self.__name = name
            self.__amplitude = Param("amp", self, SIfloat(amplitude))
            self.__phase = Param("phase", self, SIfloat(phase))
            
            # unfortunatenly the target names for fsig are not the same as the
            # various parameter names of the components, e.g. mirror xbeta is x 
            # for fsig. So we need to check here what type of component we are targetting
            # and then based on the parameter specfied get the name
            if not param.canFsig:
                raise  pkex.BasePyKatException("Cannot fsig parameter {1} on component {0}".format(str(param._owner), param.name))
            
            
        def _register_param(self, param):
            self._params.append(param)
  
        @property
        def name(self): return self.__name

        @property
        def amplitude(self): return self.__amplitude
157
158
159
        @amplitude.setter
        def amplitude(self,value): self.__amplitude.value = SIfloat(value)

160
161
162

        @property
        def phase(self): return self.__phase
163
164
        @phase.setter
        def phase(self,value): self.__phase.value = SIfloat(value)
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192

        @property
        def target(self): return self.__target.fsig_name

        @property
        def owner(self): return self.__target._owner.name
    
        def getFinesseText(self):
            rtn = []
    
            for p in self._params:
                rtn.extend(p.getFinesseText())
        
            return rtn
    
    @property
    def name(self):
        # if we don't have any signals yet then use a dummy name
        # however we need to always tune a real fsig command
        # so need to get the name of at least one of them
        # as if you tune one you tune them all
        if len(self.targets) == 0:
            return "signal"
        else:
            return self.targets[0].name

    @property
    def f(self): return self.__f
193
194
    @f.setter
    def f(self,value): self.__f.value = SIfloat(value)
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
    
    def __init__(self):

        self.targets = []
        self._params = []
        
        self.__f = Param("f", self, 1)
    
    def _register_param(self, param):
        self._params.append(param)
        
    def apply(self, target, amplitude, phase, name=None):
        
        if target == None:
            raise  pkex.BasePyKatException("No target was specified for signal to be applied")
        
        if name == None:
            name = "sig_" +target._owner.name + "_" + target.name
        
        self.targets.append(Signals.fsig(target, name, amplitude, phase))
        
        
    def getFinesseText(self):
        rtn = []
        
        for t in self.targets:
            rtn.extend(t.getFinesseText())
            rtn.append("fsig {name} {comp} {target} {frequency} {phase} {amplitude}".format(name = t.name, comp=t.owner, target=t.target, frequency=str(self.f), phase=str(t.phase), amplitude=str(t.amplitude)))
        
        for p in self._params:
            rtn.extend(p.getFinesseText())
        
        return rtn
        
        
Daniel Brown's avatar
Daniel Brown committed
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
class Block:
    def __init__(self, name):
        self.__name = name
        self.contents = [] # List of objects and strings of finesse code
        self.enabled = True 
        
    @property
    def name(self): return self.__name
    
class kat(object):                    
        
    def __init__(self, kat_file=None, kat_code=None, katdir="", katname="", tempdir=None, tempname=None):
        
        self.scene = None # scene object for GUI
        self.verbose = True
        self.__blocks = {} # dictionary of blocks that are used
        self.__components = {}  # dictionary of optical components      
        self.__detectors = {}   # dictionary of detectors
        self.__commands = {}    # dictionary of commands
        self.__gui = None
        self.nodes = NodeNetwork(self)  
        self.__katdir = katdir
        self.__katname = katname
        self.__tempdir = tempdir
        self.__tempname = tempname
        self.pykatgui = None
256
257
258
259
260
        self.__signals = Signals()
        
        # initialise default block
        self.__currentTag= NO_BLOCK
        self.__blocks[NO_BLOCK] = Block(NO_BLOCK)
Daniel Brown's avatar
Daniel Brown committed
261
262
263
        
        # Various options for running finesse, typicaly the commands with just 1 input
        # and have no name attached to them.
264
265
        self.retrace = None
        self.deriv_h = None
266
        self.scale = None
Daniel Brown's avatar
Daniel Brown committed
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
        self.__phase = None
        self.__maxtem = None
        self.__noxaxis = None
        self.__time_code = None
        
        if kat_code != None and kat_file != None:
            raise pkex.BasePyKatException("Specify either a Kat file or some Kat code, not both.")
        
        if kat_code != None:
            self.parseCommands(kat_code)
        
        if kat_file != None:
            self.loadKatFile(kat_file)
        
        cls = type(self)
        self.__class__ = type(cls.__name__, (cls,), {})
        
284
285
286
    @property
    def signals(self): return self.__signals

Daniel Brown's avatar
Daniel Brown committed
287
288
289
    @property
    def maxtem(self): return self.__maxtem
    @maxtem.setter
290
291
292
293
294
    def maxtem(self,value):
        if value == "off":
            self.__maxtem = -1
        else:
            self.__maxtem = int(value)
Daniel Brown's avatar
Daniel Brown committed
295
296
297
298
299
    
    @property
    def phase(self): return self.__phase
    @phase.setter
    def phase(self,value): self.__phase = int(value)
300
        
Daniel Brown's avatar
Daniel Brown committed
301
302
303
304
305
306
307
308
    @property
    def getPerformanceData(self): return self.__time_code
    @getPerformanceData.setter
    def getPerformanceData(self,value): self.__time_code = bool(value)
    
    @property
    def noxaxis(self): return self.__noxaxis
    @noxaxis.setter
309
    def noxaxis(self,value): self.__noxaxis = bool(value) 
Daniel Brown's avatar
Daniel Brown committed
310

311
312
    @staticmethod
    def logo():
Daniel Brown's avatar
Daniel Brown committed
313
        print """                                              ..-
314
    PyKat {0:7}         _                  '(
Daniel Brown's avatar
Daniel Brown committed
315
316
317
318
319
320
                          \\`.|\\.__...-\"\"""-_." )
       ..+-----.._        /  ' `            .-'
   . '            `:      7/* _/._\\    \\   (
  (        '::;;+;;:      `-"' =" /,`"" `) /
  L.        \\`:::a:f            c_/     n_'
  ..`--...___`.  .    ,  
Daniel Brown's avatar
Daniel Brown committed
321
   `^-....____:   +.      {1}""".format(pykat.__version__, pykat_web)
Daniel Brown's avatar
Daniel Brown committed
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
    
    def loadKatFile(self, katfile):
        commands=open(katfile).read()
        self.parseCommands(commands)
    
    def parseKatCode(self, code):
        #commands = code.split("\n")
        self.parseCommands(code)
        
    def parseCommands(self, commands):
        blockComment = False
        
        commands=self.remove_comments(commands)
        
        after_process = [] # list of commands that should be processed after 
                           # objects have been set and created
        
        for line in commands.split("\n"):
            #for line in commands:
            if len(line.strip()) >= 2:
                line = line.strip()

                # Looking for block start or end
                values = line.split(" ")
                if values[0] == "%%%":
                    if values[1] == "FTblock":
                        newTag = values[2]
                        
                        if self.__currentTag != None and newTag != self.__currentTag: 
                            warnings.warn("found block {0} before block {1} ended".format(newTag, self.__currentTag))    
                            
                        if newTag in self.__blocks:
Daniel Brown's avatar
Daniel Brown committed
354
                            raise pkex.BasePyKatException("Block `{0}` has already been read".format(newTag))
Daniel Brown's avatar
Daniel Brown committed
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
                            
                        self.__blocks[newTag] = Block(newTag) # create new list to store all references to components in block
                        self.__currentTag = newTag                            
                        
                    if values[1] == "FTend":
                        self.__currentTag = NO_BLOCK
                        
                    continue
                #warnings.warn("current tag {0}".format(self.__currentTag))    

                # don't read comment lines
                if line[0] == "#" or line[0] == "%":
                    continue
                
                # check if block comment is being used
                if not blockComment and line[0:2] == "/*":
                    blockComment = True
                    continue
                elif blockComment and line[0:2] == "*/":
                    blockComment = False
                    continue
                
                first = line.split(" ",1)[0]
                obj = None
                if(first == "m" or first == "m1" or first == "m2"):
                    obj = pykat.components.mirror.parseFinesseText(line)
                elif(first == "s"):
                    obj = pykat.components.space.parseFinesseText(line)
                elif(first == "l"):
                    obj = pykat.components.laser.parseFinesseText(line)
                elif(first[0:2] == "bs"):
                    obj = pykat.components.beamSplitter.parseFinesseText(line)
                elif(first[0:2] == "gr"):
                    obj = pykat.components.grating.parseFinesseText(line)
                elif(first[0:4] == "isol"):
                    obj = pykat.components.isolator.parseFinesseText(line)
                elif(first[0:4] == "lens"):
                    obj = pykat.components.lens.parseFinesseText(line)
                elif(first[0:3] == "mod"):
                    obj = pykat.components.modulator.parseFinesseText(line)
395
                elif(first[0:2] == "pd" and first != "pdtype"):
396
                    obj = pykat.detectors.pd.parseFinesseText(line)
Daniel Brown's avatar
Daniel Brown committed
397
398
399
400
401
402
                elif(first == "xaxis" or first == "xaxis*"):
                    obj = pykat.commands.xaxis.parseFinesseText(line)
                elif(first == "x2axis" or first == "x2axis*"):
                    obj = pykat.commands.x2axis.parseFinesseText(line)
                elif(first == "gauss" or first == "gauss*" or first == "gauss**"):
                    after_process.append(line)
403
404
                elif(first == "scale"):
                    after_process.append(line)
405
406
                elif(first == "pdtype"):
                    after_process.append(line)
Daniel Brown's avatar
Daniel Brown committed
407
408
                elif(first == "noxaxis"):
                    self.noxaxis = True
409
410
411
                elif(first == "phase"):
                    v = line.split(" ")
                    if len(v) != 2:
412
                        raise pkex.BasePyKatException("phase command `{0}` is incorrect.".format(line))
413
414
                    else:
                        self.phase = int(v[1])
415
416
417
418
419
                elif(first == "maxtem"):
                    v = line.split(" ")
                    if len(v) != 2:
                        raise pkex.BasePyKatException("maxtem command `{0}` is incorrect.".format(line))
                    else:
420
421
422
423
			if v[1] == "off":
				self.maxtem = -1
			else:
	                        self.maxtem = int(v[1])
424
425
                elif(first == "retrace"):
                    v = line.split(" ")
Daniel Brown's avatar
Daniel Brown committed
426
                    if len(v) > 2:
427
                        raise pkex.BasePyKatException("Retrace command `{0}` is incorrect.".format(line))
Daniel Brown's avatar
Daniel Brown committed
428
                    elif len(v) == 2:
429
                        self.retrace = v[1]                        
430
431
432
                elif(first == "deriv_h"):
                    v = line.split(" ")
                    if len(v) != 2:
433
                        raise pkex.BasePyKatException("deriv_h command `{0}` is incorrect.".format(line))
434
435
                    else:
                        self.deriv_h = float(v[1])
436
437
438
                elif(first == "gnuterm" or first == "pyterm"):
                    if self.verbose:
                        print "Ignoring Gnuplot/Python terminal command '{0}'".format(line)
Daniel Brown's avatar
Daniel Brown committed
439
440
441
442
443
444
445
446
447
448
449
450
451
                else:
                    if self.verbose:
                        print "Parsing `{0}` into pykat object not implemented yet, added as extra line.".format(line)
                    obj = line
                    # manually add the line to the block contents
                    self.__blocks[self.__currentTag].contents.append(line) 
                
                if obj != None and not isinstance(obj, str):
                    self.add(obj)
                    
        # now process all the varous gauss/attr etc. commands which require
        # components to exist first before they can be processed
        for line in after_process:
452
            first = line.split(" ",1)[0]            
Daniel Brown's avatar
Daniel Brown committed
453
454
            if first == "gauss" or first == "gauss*" or first == "gauss**":
                pykat.commands.gauss.parseFinesseText(line)
455
456
457
458
459
460
461
462
463
464
465
466
            elif (first == "scale"):
                v = line.split(" ")
                if len(v) == 3:
                    component_name = v[2]
                    if component_name in self.__detectors :
                        self.__detectors[component_name].scale = SIfloat(v[1])
                    else:
                        raise pkex.BasePyKatException("scale command `{0}` refers to non-existing output".format(text))
                elif len(values) == 2:
                    self.scale = SIfloat(v[1])
                else:
                    raise pkex.BasePyKatException("scale command `{0}` is incorrect.".format(text))
467
468
469
470
471
            elif (first == "pdtype"):
                v = line.split(" ")
                if len(v) == 3:
                    component_name = v[1]
                    if component_name in self.__detectors :
Andreas Freise's avatar
Andreas Freise committed
472
                        self.__detectors[component_name].pdtype = v[2]
473
474
475
476
                    else:
                        raise pkex.BasePyKatException("pdtype command `{0}` refers to non-existing detector".format(text))
                else:
                    raise pkex.BasePyKatException("pdtype command `{0}` is incorrect.".format(text))
477
                    
Daniel Brown's avatar
Daniel Brown committed
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
        self.__currentTag = NO_BLOCK 

    def saveScript(self, filename=None):
        """
        Saves the current kat object to a Finesse input file
        """
        try:
            katScript = "".join(self.generateKatScript())       
            katfile = open(filename,'w')
            katfile.writelines(katScript)
            katfile.flush()
            katfile.close()

        except pkex.BasePyKatException as ex:
            print ex
            
    def run(self, printout=0, printerr=0, save_output=False, save_kat=False,kat_name=None) :
        """ 
        Runs the current simulation setup that has been built thus far.
        It returns a katRun or katRun2D object which is populated with the various
        data from the simulation run.
499
500
        printoutput=1 prints the Finesse banner
        printerr shows the Finesse progress (set kat.verbose=1 to see warnings and errors)
Daniel Brown's avatar
Daniel Brown committed
501
502
503
504
505
506
507
508
509
510
511
512
        """
        start = datetime.datetime.now()
        
        try:        
            if not hasattr(self, "xaxis") and self.noxaxis != None and self.noxaxis == False:
                raise pkex.BasePyKatException("No xaxis was defined")
            
            if len(self.__katdir) == 0:
                # Get the environment variable for where Finesse is stored
                self.__finesse_dir = os.environ.get('FINESSE_DIR')
                
                if self.__finesse_dir == None :
513
                    raise pkex.MissingFinesseEnvVar()
Daniel Brown's avatar
Daniel Brown committed
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
            else:
                self.__finesse_dir = self.__katdir
                
            if len(self.__katname) == 0:
                katexe = "kat"
                
                if os.sys.platform == "win32":
                    katexe += ".exe"
            else:
                katexe = self.__katname
            
            kat_exec = os.path.join(self.__finesse_dir, katexe) 
            
            # check if kat file exists and it is executable by user        
            if not (os.path.isfile(kat_exec) and os.access(kat_exec, os.X_OK)):
529
                raise pkex.MissingFinesse()
Daniel Brown's avatar
Daniel Brown committed
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
                
            if self.verbose: print "--------------------------------------------------------------"
            if self.verbose: print "Running kat - Started at " + str(start)
            
            if hasattr(self, "x2axis"):
                r = katRun2D()
            else:
                r = katRun()
                
            r.katScript = "".join(self.generateKatScript())   
            
            # create a kat file which we will write the script into
            if self.__tempname == None:
                katfile = tempfile.NamedTemporaryFile(suffix=".kat", dir=self.__tempdir)
            else:
                filepath =os.path.join(self.__tempdir, self.__tempname+".kat" )
                katfile = open( filepath, 'w' ) 
                
            katfile.writelines(r.katScript)
            katfile.flush()
550
551
552
553
554

            if printout == 1:
                cmd=[kat_exec]
            else:
                cmd=[kat_exec, '--perl1']
Daniel Brown's avatar
Daniel Brown committed
555
556
557
558
559
560
561
562
563
564
            
            if self.__time_code:
                cmd.append('--perf-timing')

            cmd.append('--no-backspace')
            # set default format so that less repeated numbers are printed to the
            # output file, should speed up running and parsing of output files
            cmd.append('-format=%.15g')

            cmd.append(katfile.name)
565
                            
Daniel Brown's avatar
Daniel Brown committed
566
567
568
            p=subprocess.Popen(cmd, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
            err = ""
            
Andreas Freise's avatar
Andreas Freise committed
569
            #if self.verbose: print "Finesse output:"
570

Daniel Brown's avatar
Daniel Brown committed
571
572
            for line in iter(p.stderr.readline, ""):
                
573
                if len(line) > 0:
Daniel Brown's avatar
Daniel Brown committed
574
575
                    
                    if line.rstrip().endswith('s'):
Daniel Brown's avatar
Daniel Brown committed
576
577
                        vals = line.split("-")
                        action = vals[0].strip()
Daniel Brown's avatar
Daniel Brown committed
578
579
                        prc = vals[1].strip()[:]
                        
580
                        if printerr == 1:
Daniel Brown's avatar
Daniel Brown committed
581
582
583
584
585
586
587
588
589
                            sys.stdout.write("\r{0} {1}".format(action, prc))
                    elif line.rstrip().endswith('%'):
                        vals = line.split("-")
                        action = vals[0].strip()
                        prc = vals[1].strip()[:]
                        
                        if printerr == 1:
                            sys.stdout.write("\r{0} {1}".format(action, prc))
                            
590
591
                    elif line[0:3] == '** ':
                        if self.verbose: sys.stdout.write(line)
592
593
                    else:
                        err += line
594

Daniel Brown's avatar
Daniel Brown committed
595
            
Daniel Brown's avatar
Daniel Brown committed
596
            [out,errpipe] = p.communicate()
597
598
            if printout == 1: 
                print out
Andreas Freise's avatar
Andreas Freise committed
599
600
            else:
                if printerr == 1: print ""
601

Daniel Brown's avatar
Daniel Brown committed
602
603
604
605
606
607
            # get the version number
            ix = out.find('build ') + 6
            ix2 = out.find(')',ix)
            r.katVersion = out[ix:ix2]
            
            r.runDateTime = datetime.datetime.now()
608
609

            # If Finesse returned an error, just print that and exit!
Daniel Brown's avatar
Daniel Brown committed
610
            if p.returncode != 0:
611
612
                print err
                sys.exit(1) 
Daniel Brown's avatar
Daniel Brown committed
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
            
            root = os.path.splitext(katfile.name)
            base = os.path.basename(root[0])            
            outfile = root[0] + ".out"
            
            if save_output:        
                newoutfile = "{0}.out".format(base)
                
                cwd = os.path.os.getcwd()
                newoutfile = os.path.join(cwd,newoutfile)
                
                if os.path.isfile(newoutfile):
                    os.remove(newoutfile)
                    
                os.rename(outfile, newoutfile)

                if self.verbose: print "\nOutput data saved to '{0}'".format(newoutfile)
            
            if hasattr(self, "x2axis"):
                [r.x,r.y,r.z,hdr] = self.readOutFile(outfile)
                
                r.xlabel = hdr[0]
                r.ylabel = hdr[1]
                r.zlabels = map(str.strip, hdr[2:])
            else:
                [r.x,r.y,hdr] = self.readOutFile(outfile)
            
                r.xlabel = hdr[0]
                r.ylabels = map(str.strip, hdr[1:])
                            
            if save_kat:
                if kat_name == None:
                    kat_name = "pykat_output"                
                
                cwd = os.path.os.getcwd()
                newkatfile = os.path.join(cwd, kat_name + ".kat")
                
                if os.path.isfile(newkatfile):
                    os.remove(newkatfile)
                  
                os.rename(katfile.name, newkatfile)         
                
                if self.verbose: print "Kat file saved to '{0}'".format(newkatfile)
                

            katfile.close()
            perfData = []
            
            if self.__time_code:
                perffile = open(root[0] + ".perf",'r')
                
                for l in perffile.readlines():
                    vals = l.strip().split(' ')
                    perfData.append((vals[0], float(vals[1]), float(vals[2]), float(vals[3])))
                    
                return [r, perfData]
            else:
                return r
671
672
            
        except pkex.FinesseRunError as fe:
Daniel Brown's avatar
Daniel Brown committed
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
            print fe
        finally:
            if self.verbose: print ""
            if self.verbose: print "Finished in " + str(datetime.datetime.now()-start)
            
        
    def add(self, obj):
        try:
            obj.tag = self.__currentTag
            self.__blocks[self.__currentTag].contents.append(obj)
            
            if isinstance(obj, Component):
                
                if obj.name in self.__components :
                    raise pkex.BasePyKatException("A component with name '{0}' has already been added".format([obj.name]))            
                            
                self.__components[obj.name] = obj
                self.__add_component(obj)
                
            elif isinstance(obj, Detector):
                
                if obj.name in self.__detectors :
                        raise pkex.BasePyKatException("A detector '{0}' has already been added".format(obj.name))
                        
                self.__detectors[obj.name] = obj
                self.__add_detector(obj)
                
            elif isinstance(obj, Command):
                
                self.__commands[obj.__class__.__name__] = obj
                self.__add_command(obj)
                
705
            else:
Daniel Brown's avatar
Daniel Brown committed
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
                raise pkex.BasePyKatException("Object {0} could not be added".format(obj))
                
            obj._on_kat_add(self)
            
        except pkex.BasePyKatException as ex:
            print ex

    def readOutFile(self, filename):
        
        with open(filename,'r') as outfile:
            # read first to lines to get to header line
            outfile.readline()
            outfile.readline()
            
            hdr = outfile.readline().replace('%','').replace('\n','').split(',')
        
        data = np.loadtxt(filename,comments='%',skiprows=4)
        
        if hasattr(self, "x2axis"):
            # need to parse 2D outputs slightly different as they are effectively 2D matrices
            # written in linear form
            x = data[0::(1+self.x2axis.steps),0]
            y = data[0:(1+self.x2axis.steps),1]
            # get rows and columns lined up so that we can reshape a single column of all x/y data
            # into a matrix
            z = data[:,2:].transpose().reshape(data.shape[1]-2, 1+self.xaxis.steps, 1+self.x2axis.steps)
            # once you do this the data for y and x axes need swapping
            z = z.swapaxes(1,2)
            return [x, y, z, hdr]
        else:
            shape_len = len(data.shape)
            
            if shape_len > 1:
                rows,cols = data.shape
                x = data[:,0]
                y = data[:,1:cols].squeeze()
            else:
                rows = 1
                cols = data.shape[0]
                
                x = data[0]
                y = data[1:cols].squeeze()
            
            return [x, y, hdr]
750
751
752
753
754
755
756
757
758

    def removeLine(self, fragment) :
        for key in self.__blocks:
            objs = self.__blocks[key].contents
            for obj in objs:
                if isinstance(obj, str):
                    if fragment in obj:
                        print "  ** removing line '{0}'".format(obj)
                        objs.remove(obj)
759
        
Daniel Brown's avatar
Daniel Brown committed
760
761
762
763
    def generateKatScript(self) :
        """ Generates the kat file which can then be run """
        
        out = []    
764
765
766
        import datetime
        strtoday = datetime.datetime.now()
        out.append(strtoday.strftime("%% Generated by PyKat %d.%m.%Y %H:%M:%S\n") )
Daniel Brown's avatar
Daniel Brown committed
767
768
769
        
        for key in self.__blocks:
            objs = self.__blocks[key].contents
770
771
772

            if key != NO_BLOCK:
                out.append("%%% FTblock " + key + "\n")
Daniel Brown's avatar
Daniel Brown committed
773
774
775
776
777
778
779
780
781
782
783
784
785
786
            
            for obj in objs:
                if isinstance(obj, str):
                    out.append(obj + '\n')
                    
                elif isinstance(obj, Component) or isinstance(obj, Detector) or isinstance(obj, Command):
                    txt = obj.getFinesseText() 
                    
                    if txt != None:
                        if isinstance(txt,list):
                            for t in txt:
                                out.append(t + "\n")
                        else:
                            out.append(txt + "\n")
787
788
789

            if key != NO_BLOCK:
                out.append("%%% FTend " + key + "\n")
Daniel Brown's avatar
Daniel Brown committed
790
791
792
793
794
795
796
797
798
799
800
            
        # now loop through all the nodes and get any gauss commands
        for key in self.nodes.getNodes():
            txt = self.nodes.getNodes()[key].getFinesseText()
            
            if txt != None:
                if isinstance(txt,list):
                    for t in txt: out.append(t+ "\n")
                else:
                    out.append(txt + "\n")
        
801

802
803
804
805
806
807
808
809
810
811
        # now get any signal commands
        txt = self.signals.getFinesseText()
        
        if txt != None:
            if isinstance(txt,list):
                for t in txt: out.append(t+ "\n")
            else:
                out.append(txt + "\n")
                            

812
        if self.scale != None and self.scale !='': out.append("scale {0}\n".format(self.scale))
Daniel Brown's avatar
Daniel Brown committed
813
        if self.phase != None: out.append("phase {0}\n".format(self.phase))
814
815
816
817
818
        if self.maxtem != None:
                if self.maxtem == -1:
                        out.append("maxtem off\n")
                else:
                        out.append("maxtem {0}\n".format(self.maxtem))
Daniel Brown's avatar
Daniel Brown committed
819

820
821
822
        if self.noxaxis == True:
            out.append("noxaxis\n")

Daniel Brown's avatar
Daniel Brown committed
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
        # ensure we don't do any plotting. That should be handled
        # by user themselves
        out.append("gnuterm no\n")
        out.append("pyterm no\n")
        
        return out
        
    def openGUI(self):
        if NO_GUI:
            print  "No PyQt4 module was installed so cannot open a GUI"
        else:
            self.app = QCoreApplication.instance() 
            created = False
            
            if self.app == None:
                created = True
                self.app = QApplication([""])
                
            if self.pykatgui == None:
                self.pykatgui = pyKatGUI(self)
                self.pykatgui.main()
            else:
                self.pykatgui.show()
                
            if created: self.app.exec_()
    
    def getComponents(self):
        return self.__components.values()
    
    def hasComponent(self, name):
        return (name in self.__components)
    
    def _newName(self, container, prefix):
        n = 1
        name = "{0}{1}".format(prefix, n)
        
        while name in container:
            n += 1
            name = "{0}{1}".format(prefix,n)
        
        return name
    
    def getNewComponentName(self,prefix):
        '''
        Returns a name for a component which hasn't already been added.
        Returns [prefix] + number, where number is greater than 1. e.g.
        if m1 exists getNewName('m') will return 'm2'
        '''
        return self._newName(self.__components, prefix)
    
    def getNewDetectorName(self,prefix):
        '''
        Returns a name for a component which hasn't already been added.
        Returns [prefix] + number, where number is greater than 1. e.g.
        if m1 exists getNewName('m') will return 'm2'
        '''
        return self._newName(self.__detectors, prefix)
        
    def getNewNodeNames(self,prefix,N=1):
        '''
        Returns a list of names for N number of nodes which haven't already been added.
        Returns [prefix] + number, where number is greater than 1. e.g.
        if m1 exists getNewName('m') will return 'm2'
        '''
        rtn = []
        n = 1
        
        for M in range(1,N+1):
            name = "{0}{1}".format(prefix, n)
            
            while name in self.nodes.getNodes() or (name in rtn):
                n += 1
                name = "{0}{1}".format(prefix,n)
        
            rtn.append(name)
            
        return rtn
        
    
    def __add_detector(self, det):

        if not isinstance(det, Detector):
            raise exceptions.ValueError("Argument is not of type Detector")
        
        name = det.name
        fget = lambda self: self.__get_detector(name)
        
        setattr(self.__class__, name, property(fget))
        setattr(self, '__det_' + name, det)                   

    def __get_detector(self, name):
        return getattr(self, '__det_' + name) 
        
    def __add_command(self, com):

        if not isinstance(com, Command):
            raise exceptions.ValueError("Argument is not of type Command")
        
        name = com.__class__.__name__
        fget = lambda self: self.__get_command(name)
        
        setattr(self.__class__, name, property(fget))
        setattr(self, '__com_' + name, com)                   

    def __get_command(self, name):
        return getattr(self, '__com_' + name)            
    
    def __add_component(self, comp):

        if not isinstance(comp, Component):
            raise exceptions.ValueError("Argument is not of type Component")
            
        fget = lambda self: self.__get_component(comp.name)
        
        setattr(self.__class__, comp.name, property(fget))
        setattr(self, '__comp_' + comp.name, comp)                   

    def __get_component(self, name):
        return getattr(self, '__comp_' + name)        

    def remove_comments(self, string):
        pattern = r"(\".*?\"|\'.*?\'|%{3}[^\r\n]*$)|(/\*.*?\*/|%[^\r\n]*$|#[^\r\n]*$|//[^\r\n]*$)"
        # first group captures quoted strings (double or single)
        # second group captures comments (//single-line or /* multi-line */)
        regex = re.compile(pattern, re.MULTILINE|re.DOTALL)
        def _replacer(match):
            # if the 2nd group (capturing comments) is not None,
            # it means we have captured a non-quoted (real) comment string.
            if match.group(2) is not None:
                return "" # so we will return empty to remove the comment
            else: # otherwise, we will return the 1st group
                return match.group(1) # captured quoted-string
        return regex.sub(_replacer, string)
956
957
958

# printing pykat logo on first input
kat.logo()