ComboCode.cc.plotting.objects.PlotChem

29 30 """ 31 Class for plotting gas lines and their information. 32 33 """ 34

35 - def __init__(self,star_name,path_chemistry='OutputClumpy',\ 36 inputfilename=None,fn_add_star=1):

37 38 """ 39 Initializing an instance of PlotGas. 40 41 @param star_name: name of the star from Star.dat, use default only 42 when never using any star model specific things 43 @type star_name: string 44 45 @keyword path_chemistry: Output modeling folder in MCMax home folder 46 47 (default: 'OutputClumpy') 48 @type path_chemistry: string 49 @keyword inputfilename: name of inputfile that is also copied to the 50 output folder of the plots, 51 if None nothing is copied 52 53 (default: None) 54 @type inputfilename: string 55 56 @keyword fn_add_star: Add the star name to the requested plot filename. 57 Only relevant if fn_plt is given in a sub method. 58 59 (default: 1) 60 @type fn_add_star: bool 61 62 63 """ 64 65 super(PlotChem, self).__init__(star_name=star_name,\ 66 path=path_chemistry,\ 67 code='Chemistry',\ 68 inputfilename=inputfilename,\ 69 fn_add_star=fn_add_star) 70 #-- Convenience path 71 cc.path.cout = os.path.join(cc.path.chemistry,self.path)

72 73 74

75 - def makeStars(self,models):

76 77 ''' 78 Make a Star list based on the Chemistry model ids. 79 80 @param models: model_ids for the Chemistry db 81 @type models: list(string) 82 83 @return: the parameter sets 84 @rtype: list[Star()] 85 86 ''' 87 88 star_grid = Star.makeStars(models=models,\ 89 id_type='Chemistry',\ 90 code='Chemistry',path=self.path) 91 [star.addCoolingPars() for star in star_grid] 92 return star_grid

93 94 95

96 - def plotVelocity(self,star_grid=[],models=[],fn_plt='',force_plot=0,cfg=''):

97 98 ''' 99 Plot velocity versus radius for every model in star_grid. 100 101 @keyword star_grid: List of Star() instances. If default, model ids 102 have to be given. 103 104 (default: []) 105 @type star_grid: list[Star()] 106 @keyword models: The model ids, only required if star_grid is [] 107 108 (default: []) 109 @type models: list[string] 110 @keyword fn_plt: A base plot filename. Includes folder. If not, a 111 default is added 112 113 (default: '') 114 @type fn_plt: string 115 @keyword force_plot: force a plotting if more than models are requested 116 117 (default: 0) 118 @type force_plot: bool 119 @keyword cfg: path to the Plotting2.plotCols config file. If default, 120 the hard-coded default plotting options are used. 121 122 (default: '') 123 @type cfg: string 124 125 ''' 126 127 print '***********************************' 128 print '** Plotting Gas Velocity Profiles' 129 if not star_grid and models: 130 star_grid = self.makeStars(models=models) 131 elif (not models and not star_grid) or (models and star_grid): 132 print '** Input is undefined or doubly defined. Aborting.' 133 return 134 135 cfg_dict = Plotting2.readCfg(cfg) 136 if cfg_dict.has_key('filename'): 137 fn_plt = cfg_dict.pop('filename') 138 139 if len(star_grid) < 20 or force_plot: 140 141 valid_sg = [star for star in star_grid 142 if star['LAST_CHEMISTRY_MODEL']] 143 144 folders = [os.path.join(cc.path.cout,'models',\ 145 star['LAST_CHEMISTRY_MODEL'])+'/' for star in valid_sg] 146 147 radii = [DataIO.getChemistryPhysPar(folder+'csphyspar.out', 'RADIUS') \ 148 for folder in folders] 149 temps = [DataIO.getChemistryPhysPar(folder+'csphyspar.out', 'VELOCITY') \ 150 for folder in folders] 151 152 if temps: 153 keytags = [star['LAST_CHEMISTRY_MODEL'].replace('_','\_') 154 for star in valid_sg] 155 156 #-- Set filenames 157 pfn = fn_plt if fn_plt else 'velocity_profiles' 158 pfn = self.setFnPlt(pfn) 159 160 #-- Run the two plots 161 keys_cm = ['Model %i'%(i+1) 162 for i in xrange(len(star_grid))] 163 pfn = Plotting2.plotCols(x=radii,y=temps,cfg=cfg_dict,\ 164 filename=pfn,xaxis='$r$ (cm)',\ 165 yaxis=r'$v$ (km s$^{-1}$)',\ 166 figsize=(12.5,8),fontsize_ticklabels=26,\ 167 key_location=(0.05,0.05),xlogscale=1,ylogscale=1,\ 168 keytags=keys_cm,fontsize_axis=26,fontsize_key=26) 169 print '** Plots can be found at:' 170 print pfn 171 print '***********************************'

172 173

174 - def plotTemp(self,star_grid=[],models=[],fn_plt='',force_plot=0,cfg=''):

175 176 ''' 177 Plot temperature profiles of all models. 178 179 @keyword star_grid: List of Star() instances. If default, model ids 180 have to be given. 181 182 (default: []) 183 @type star_grid: list[Star()] 184 @keyword models: The model ids, only required if star_grid is [] 185 186 (default: []) 187 @type models: list[string] 188 @keyword fn_plt: A base plot filename. Includes folder. If not, a 189 default is added 190 191 (default: '') 192 @type fn_plt: string 193 @keyword force_plot: force a plotting if more than models are requested 194 195 (default: 0) 196 @type force_plot: bool 197 @keyword cfg: path to the Plotting2.plotCols config file. If default, 198 the hard-coded default plotting options are used. 199 200 (default: '') 201 @type cfg: string 202 203 ''' 204 205 print '***********************************' 206 print '** Plotting Gas Temperature Profiles' 207 if not star_grid and models: 208 star_grid = self.makeStars(models=models) 209 elif (not models and not star_grid) or (models and star_grid): 210 print '** Input is undefined or doubly defined. Aborting.' 211 return 212 213 cfg_dict = Plotting2.readCfg(cfg) 214 if cfg_dict.has_key('filename'): 215 fn_plt = cfg_dict.pop('filename') 216 217 if len(star_grid) < 20 or force_plot: 218 219 valid_sg = [star for star in star_grid 220 if star['LAST_CHEMISTRY_MODEL']] 221 222 folders = [os.path.join(cc.path.cout,'models',\ 223 star['LAST_CHEMISTRY_MODEL'])+'/' for star in valid_sg] 224 225 radii = [DataIO.getChemistryPhysPar(folder+'csphyspar.out', 'RADIUS') \ 226 for folder in folders] 227 temps = [DataIO.getChemistryPhysPar(folder+'csphyspar.out', 'TEMP') \ 228 for folder in folders] 229 230 if temps: 231 keytags = [star['LAST_CHEMISTRY_MODEL'].replace('_','\_') 232 for star in valid_sg] 233 234 #-- Set filenames 235 pfn = fn_plt if fn_plt else 'temperature_profiles' 236 pfn = self.setFnPlt(pfn) 237 238 #-- Run the two plots 239 keys_cm = ['Model %i'%(i+1) 240 for i in xrange(len(star_grid))] 241 pfn = Plotting2.plotCols(x=radii,y=temps,cfg=cfg_dict,\ 242 filename=pfn,xaxis='$r$ (cm)',\ 243 yaxis='$T_\mathrm{g}$ (K)',\ 244 figsize=(12.5,8),fontsize_ticklabels=26,\ 245 key_location=(0.05,0.05),xlogscale=1,ylogscale=1,\ 246 keytags=keys_cm,fontsize_axis=26,fontsize_key=26) 247 print '** Plots can be found at:' 248 print pfn 249 print '***********************************' 250 else: 251 print '** No Chemistry models were calculated successfully.'+\ 252 'No temperature profiles can be plotted.' 253 print '***********************************'

254 255 256

257 - def plotVisualExtinction(self,star_grid=[],models=[],fn_plt='',force_plot=0,cfg=''):

258 259 ''' 260 Plot temperature profiles of all models. 261 262 @keyword star_grid: List of Star() instances. If default, model ids 263 have to be given. 264 265 (default: []) 266 @type star_grid: list[Star()] 267 @keyword models: The model ids, only required if star_grid is [] 268 269 (default: []) 270 @type models: list[string] 271 @keyword fn_plt: A base plot filename. Includes folder. If not, a 272 default is added 273 274 (default: '') 275 @type fn_plt: string 276 @keyword force_plot: force a plotting if more than models are requested 277 278 (default: 0) 279 @type force_plot: bool 280 @keyword cfg: path to the Plotting2.plotCols config file. If default, 281 the hard-coded default plotting options are used. 282 283 (default: '') 284 @type cfg: string 285 286 ''' 287 288 print '***********************************' 289 print '** Plotting Visual Extinction Profiles' 290 if not star_grid and models: 291 star_grid = self.makeStars(models=models) 292 elif (not models and not star_grid) or (models and star_grid): 293 print '** Input is undefined or doubly defined. Aborting.' 294 return 295 296 cfg_dict = Plotting2.readCfg(cfg) 297 if cfg_dict.has_key('filename'): 298 fn_plt = cfg_dict.pop('filename') 299 300 if len(star_grid) < 20 or force_plot: 301 302 valid_sg = [star for star in star_grid 303 if star['LAST_CHEMISTRY_MODEL']] 304 305 folders = [os.path.join(cc.path.cout,'models',\ 306 star['LAST_CHEMISTRY_MODEL'])+'/' for star in valid_sg] 307 308 radii = [DataIO.getChemistryPhysPar(folder+'csphyspar.out', 'RADIUS') \ 309 for folder in folders] 310 avs = [DataIO.getChemistryPhysPar(folder+'csphyspar.out', 'A_V') \ 311 for folder in folders] 312 313 if avs: 314 keytags = [star['LAST_CHEMISTRY_MODEL'].replace('_','\_') 315 for star in valid_sg] 316 317 #-- Set filenames 318 pfn = fn_plt if fn_plt else 'visual_extinction' 319 pfn = self.setFnPlt(pfn) 320 321 #-- Run the two plots 322 keys_cm = ['Model %i'%(i+1) 323 for i in xrange(len(star_grid))] 324 pfn = Plotting2.plotCols(x=radii,y=avs,cfg=cfg_dict,\ 325 filename=pfn,xaxis='$r$ (cm)',\ 326 yaxis='$A_V$ (mag)',\ 327 figsize=(12.5,8),fontsize_ticklabels=26,\ 328 key_location=(0.05,0.05),xlogscale=1,ylogscale=1,\ 329 keytags=keys_cm,fontsize_axis=26,fontsize_key=26) 330 print '** Plots can be found at:' 331 print pfn 332 print '***********************************' 333 else: 334 print '** No Chemistry models were calculated successfully.'+\ 335 'No temperature profiles can be plotted.' 336 print '***********************************'

337 338

339 - def plotPhotodissociationrateCo(self,star_grid=[],models=[],fn_plt='',force_plot=0,cfg=''):

340 341 ''' 342 Plot temperature profiles of all models. 343 344 @keyword star_grid: List of Star() instances. If default, model ids 345 have to be given. 346 347 (default: []) 348 @type star_grid: list[Star()] 349 @keyword models: The model ids, only required if star_grid is [] 350 351 (default: []) 352 @type models: list[string] 353 @keyword fn_plt: A base plot filename. Includes folder. If not, a 354 default is added 355 356 (default: '') 357 @type fn_plt: string 358 @keyword force_plot: force a plotting if more than models are requested 359 360 (default: 0) 361 @type force_plot: bool 362 @keyword cfg: path to the Plotting2.plotCols config file. If default, 363 the hard-coded default plotting options are used. 364 365 (default: '') 366 @type cfg: string 367 368 ''' 369 370 print '***********************************' 371 print '** Plotting Photodissociation Rate CO' 372 if not star_grid and models: 373 star_grid = self.makeStars(models=models) 374 elif (not models and not star_grid) or (models and star_grid): 375 print '** Input is undefined or doubly defined. Aborting.' 376 return 377 378 cfg_dict = Plotting2.readCfg(cfg) 379 if cfg_dict.has_key('filename'): 380 fn_plt = cfg_dict.pop('filename') 381 382 if len(star_grid) < 20 or force_plot: 383 384 valid_sg = [star for star in star_grid 385 if star['LAST_CHEMISTRY_MODEL']] 386 387 folders = [os.path.join(cc.path.cout,'models',\ 388 star['LAST_CHEMISTRY_MODEL'])+'/' for star in valid_sg] 389 390 radii = [DataIO.getChemistryPhysPar(folder+'csphyspar.out', 'RADIUS') \ 391 for folder in folders] 392 cos = [DataIO.getChemistryPhysPar(folder+'csphyspar.out', 'COK(PHOT)') \ 393 for folder in folders] 394 395 if cos: 396 keytags = [star['LAST_CHEMISTRY_MODEL'].replace('_','\_') 397 for star in valid_sg] 398 399 #-- Set filenames 400 pfn = fn_plt if fn_plt else 'CO_photodissociation_rate' 401 pfn = self.setFnPlt(pfn) 402 403 #-- Run the two plots 404 keys_cm = ['Model %i'%(i+1) 405 for i in xrange(len(star_grid))] 406 pfn = Plotting2.plotCols(x=radii,y=cos,cfg=cfg_dict,\ 407 filename=pfn,xaxis='$r$ (cm)',\ 408 yaxis='$k_{CO,photo}$ (s$^{-1}$)',\ 409 figsize=(12.5,8),fontsize_ticklabels=26,\ 410 key_location=(0.05,0.05),xlogscale=1,ylogscale=1,\ 411 keytags=keys_cm,fontsize_axis=26,fontsize_key=26) 412 print '** Plots can be found at:' 413 print pfn 414 print '***********************************' 415 else: 416 print '** No Chemistry models were calculated successfully.'+\ 417 'No temperature profiles can be plotted.' 418 print '***********************************'

419 420 421

422 - def plotRadiationField(self,star_grid=[],models=[],fn_plt='',force_plot=0,cfg=''):

423 424 ''' 425 Plot temperature profiles of all models. 426 427 @keyword star_grid: List of Star() instances. If default, model ids 428 have to be given. 429 430 (default: []) 431 @type star_grid: list[Star()] 432 @keyword models: The model ids, only required if star_grid is [] 433 434 (default: []) 435 @type models: list[string] 436 @keyword fn_plt: A base plot filename. Includes folder. If not, a 437 default is added 438 439 (default: '') 440 @type fn_plt: string 441 @keyword force_plot: force a plotting if more than models are requested 442 443 (default: 0) 444 @type force_plot: bool 445 @keyword cfg: path to the Plotting2.plotCols config file. If default, 446 the hard-coded default plotting options are used. 447 448 (default: '') 449 @type cfg: string 450 451 ''' 452 453 print '***********************************' 454 print '** Plotting Radiation Field' 455 if not star_grid and models: 456 star_grid = self.makeStars(models=models) 457 elif (not models and not star_grid) or (models and star_grid): 458 print '** Input is undefined or doubly defined. Aborting.' 459 return 460 461 cfg_dict = Plotting2.readCfg(cfg) 462 if cfg_dict.has_key('filename'): 463 fn_plt = cfg_dict.pop('filename') 464 465 if len(star_grid) < 20 or force_plot: 466 467 valid_sg = [star for star in star_grid 468 if star['LAST_CHEMISTRY_MODEL']] 469 470 folders = [os.path.join(cc.path.cout,'models',\ 471 star['LAST_CHEMISTRY_MODEL'])+'/' for star in valid_sg] 472 473 radii = [DataIO.getChemistryPhysPar(folder+'csphyspar.out', 'RADIUS') \ 474 for folder in folders] 475 cos = [DataIO.getChemistryPhysPar(folder+'csphyspar.out', 'COK(PHOT)') \ 476 for folder in folders] 477 478 if cos: 479 keytags = [star['LAST_CHEMISTRY_MODEL'].replace('_','\_') 480 for star in valid_sg] 481 482 #-- Set filenames 483 pfn = fn_plt if fn_plt else 'radiation_field' 484 pfn = self.setFnPlt(pfn) 485 486 #-- Run the two plots 487 keys_cm = ['Model %i'%(i+1) 488 for i in xrange(len(star_grid))] 489 pfn = Plotting2.plotCols(x=radii,y=cos,cfg=cfg_dict,\ 490 filename=pfn,xaxis='$r$ (cm)',\ 491 yaxis='$I_D$ (photons /s /cm$^2$ /Hz / sr) ',\ 492 figsize=(12.5,8),fontsize_ticklabels=26,\ 493 key_location=(0.05,0.05),xlogscale=1,ylogscale=1,\ 494 keytags=keys_cm,fontsize_axis=26,fontsize_key=26) 495 print '** Plots can be found at:' 496 print pfn 497 print '***********************************' 498 else: 499 print '** No Chemistry models were calculated successfully.'+\ 500 'No temperature profiles can be plotted.' 501 print '***********************************'

502 503 504

505 - def plotAbundanceProfiles(self,star_grid=[],models=[],force_plot=0,cfg='',\ 506 fn_plt='',molecules=[],per_molecule=0,frac=1):

507 508 ''' 509 Plot abundance profiles for all molecules in every model. 510 511 @keyword star_grid: List of Star() instances. If default, model ids 512 have to be given. 513 514 (default: []) 515 @type star_grid: list[Star()] 516 @keyword models: The model ids, only required if star_grid is [] 517 518 (default: []) 519 @type models: list[string] 520 @keyword force_plot: force a plotting if more than models are requested 521 522 (default: 0) 523 @type force_plot: bool 524 @keyword cfg: path to the Plotting2.plotCols config file. If default, 525 the hard-coded default plotting options are used. 526 527 (default: '') 528 @type cfg: string 529 @keyword fn_plt: A base plot filename. Includes folder. If not, a 530 default is added 531 532 (default: '') 533 @type fn_plt: string 534 @keyword molecules: Molecules to be plotted. 535 536 (default: []) 537 @type molecules: bool 538 @keyword per_molecule: Plot one molecule for all models in one figure. 539 540 (default: 0) 541 @type per_molecule: bool 542 @keyword per_model: Plot all molecules for one model in one figure. 543 544 (default: 0) 545 @type per_model: bool 546 @keyword frac: Plot the fractional abundances. If not frac, plot number 547 densities. 548 549 (default: 1) 550 @type frac: bool 551 552 553 ''' 554 555 print '***********************************' 556 print '** Plotting Abundance Profiles' 557 if not star_grid and models: 558 star_grid = self.makeStars(models=models) 559 elif (not models and not star_grid) or (models and star_grid): 560 print '** Input is undefined or doubly defined. Aborting.' 561 return 562 pfns = [] 563 cfg_dict = Plotting2.readCfg(cfg) 564 if cfg_dict.has_key('filename'): 565 fn_plt = cfg_dict.pop('filename') 566 if cfg_dict.has_key('molecules'): 567 molecules = cfg_dict.pop('molecules') 568 if cfg_dict.has_key('per_molecule'): 569 per_molecule = cfg_dict['per_molecule'] 570 if cfg_dict.has_key('per_model'): 571 per_model = cfg_dict['per_model'] 572 573 #-- Some general plot settings 574 extra_pars = dict() 575 extra_pars['ymin'] = 1e-9 576 extra_pars['ymax'] = 1e-3 577 extra_pars['ylogscale'] = 1 578 extra_pars['xlogscale'] = 1 579 extra_pars['figsize'] = (12.5,8.5) 580 extra_pars['xaxis'] = 'cm' 581 582 #-- Dict to keep track of all data 583 ddata = dict() 584 for istar,star in enumerate(star_grid): 585 if not star['LAST_CHEMISTRY_MODEL']: continue 586 ddata[istar] = dict() 587 588 folder = os.path.join(cc.path.cout,'models',\ 589 star['LAST_CHEMISTRY_MODEL'])+'/' 590 ddata[istar]['rad'] = DataIO.getChemistryPhysPar(folder+\ 591 'csphyspar.out', 'RADIUS') 592 ddata[istar]['id'] = star['LAST_CHEMISTRY_MODEL'] 593 if frac: 594 species = DataIO.getChemistryAbundances(folder+'csfrac.out') 595 else: 596 species = DataIO.getChemistryAbundances(folder+'csnum.out') 597 598 for molec in molecules: 599 ddata[istar][molec] = species[molec] 600 601 if not per_molecule: 602 #-- Collect all data 603 radii = [ddata[istar]['rad']]*len(molecules) 604 abuns = [ddata[istar][molec] for molec in molecules] 605 keytags = molecules 606 #ids = star['LAST_CHEMISTRY_MODEL'] 607 ids = ddata[istar]['id'] 608 609 #-- Set the yaxis tag 610 yaxis = '$n_\mathrm{molec}/n_{\mathrm{H}_2}$' 611 612 #-- Set filename 613 pfn = fn_plt if fn_plt else 'abundance_profiles' 614 suff = '_'.join(list(set(ids))) 615 pfn = self.setFnPlt(pfn,fn_suffix=suff) 616 617 pfns.append(Plotting2.plotCols(x=radii,y=abuns,cfg=cfg_dict,\ 618 filename=pfn,keytags=keytags,\ 619 plot_title=ids.replace('_','\_'),\ 620 yaxis=yaxis,**extra_pars)) 621 622 if per_molecule: 623 #-- Collect all data 624 #molecs = list(set([molec for istar in ddata.keys() 625 #for molec in ddata[istar].keys()])) 626 for molec in molecules: 627 #-- Collect data 628 radii = [dstar['rad'] 629 for istar,dstar in ddata.items()] 630 abuns = [dstar[molec] 631 for istar,dstar in ddata.items()] 632 keytags = [dstar['id'].replace('_','\_') 633 for istar,dstar in ddata.items()] 634 635 #-- Set the y axis tag 636 #strmolec = ddata[0][molec]['key'] 637 yaxis = '$n_\mathrm{%s}/n_{\mathrm{H}_2}$'%str(molec) 638 639 #-- Make filename 640 pfn = fn_plt if fn_plt else 'abundance_profiles' 641 pfn = self.setFnPlt(pfn,fn_suffix=molec) 642 643 pfns.append(Plotting2.plotCols(x=radii,y=abuns,yaxis=yaxis,\ 644 filename=pfn,keytags=keytags,\ 645 cfg=cfg_dict,**extra_pars)) 646 647 if not per_molecule and pfns and pfns[0][-4:] == '.pdf': 648 pfn = fn_plt if fn_plt else 'abundance_profiles' 649 pfn = self.setFnPlt(pfn) + '.pdf' 650 DataIO.joinPdf(old=pfns,new=pfn) 651 print '** Plots can be found at:' 652 print pfn 653 print '***********************************' 654 else: 655 print '** Plots can be found at:' 656 print '\n'.join(pfns) 657 print '***********************************'

Source Code for Module ComboCode.cc.plotting.objects.PlotChem