RTModel 2.0__tar.gz

RTModel-2.0/LICENSE

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+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
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RTModel-2.0/MANIFEST.in

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+include RTModel/bin/Reader.exe
+graft RTModel/data
+graft RTModel/lib
+graft RTModel/include
+graft RTModel/bin
+global-exclude RTModel/lib/*.o*

RTModel-2.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: RTModel
+Version: 2.0
+Summary: RTModel is a tool for microlensing event interpretation.
+Author-email: Valerio Bozza <valboz@sa.infn.it>
+License: GPL-3.0
+Project-URL: Homepage, https://github.com/valboz/RTModel
+Keywords: Microlensing analysis and fitting
+Classifier: Development Status :: 1 - Planning
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Programming Language :: Python :: 3
+Requires-Python: <4,>=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pytest
+Requires-Dist: matplotlib
+Requires-Dist: tqdm
+Requires-Dist: VBBinaryLensing>=3.7.0
+
+# RTModel
+`RTModel` is a package for modeling and interpretation of microlensing events. It uses photometric time series collected from ground and/or space telescopes to propose one or more possible models among the following:
+- Single-lens-single-source microlensing (i.e. Paczynski)
+- Single-lens-binary-source microlensing (with or without xallarap)
+- Binary-lens-single-source microlensing (including planetary microlensing, parallax and orbital motion)
+
+All models include the finite-size of the source(s).
+
+The modeling strategy is based on a grid search in the parameter space for single-lens models, whereas a **template library** for binary-lens models is used including all possible geometries of the source trajectory with respect to the caustics. In addition to this global search, planets are searched where maximal deviations from a Paczynski model occurs. 
+
+The library is in the form of a standard Python package that launches specific subprocesses for different tasks. Model fitting is executed in **parallel** exploiting available processors in the machine. The full modeling may take from one to three hours depending on the event and on the machine speed. The results of modeling are given in the form of a text **assessment file**; in addition, **final models** are made available with their parameters and covariance matrices.
+
+`RTModel` also includes a subpackage **`RTModel.plotmodel`** that allows an immediate visualization of models and the possibility to review each individual fitting process as an animated gif.
+
+## Attribution
+
+A paper is in preparation describing all algorithms behind RTModel in detail.
+At the moment, any use of this code for scientific publications should be acknowledged by citing this GitHub repository. 
+
+## Installation
+
+The easiest way to install `RTModel` is through `pip`
+```
+pip install RTModel
+```
+
+Currently, `RTModel` works on Linux and Windows, requiring Python >= 3.6. 
+A C++ compiler compatible with C++17 standard is needed for installation.
+`RTModel` also incorporates version 3.7 of [`VBBinaryLensing`](https://github.com/valboz/VBBinaryLensing).
+
+Example Jupyter notebooks will be included in `examples/`.
+
+## Documentation
+Provisional [documentation for the use of RTModel](docs/README.md) is available and under development.
+
+## License
+`RTModel` is freely available to the community under the 
+GNU Lesser General Public License Version 3 included in this repository.
+
+

RTModel-2.0/README.md

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+# RTModel
+`RTModel` is a package for modeling and interpretation of microlensing events. It uses photometric time series collected from ground and/or space telescopes to propose one or more possible models among the following:
+- Single-lens-single-source microlensing (i.e. Paczynski)
+- Single-lens-binary-source microlensing (with or without xallarap)
+- Binary-lens-single-source microlensing (including planetary microlensing, parallax and orbital motion)
+
+All models include the finite-size of the source(s).
+
+The modeling strategy is based on a grid search in the parameter space for single-lens models, whereas a **template library** for binary-lens models is used including all possible geometries of the source trajectory with respect to the caustics. In addition to this global search, planets are searched where maximal deviations from a Paczynski model occurs. 
+
+The library is in the form of a standard Python package that launches specific subprocesses for different tasks. Model fitting is executed in **parallel** exploiting available processors in the machine. The full modeling may take from one to three hours depending on the event and on the machine speed. The results of modeling are given in the form of a text **assessment file**; in addition, **final models** are made available with their parameters and covariance matrices.
+
+`RTModel` also includes a subpackage **`RTModel.plotmodel`** that allows an immediate visualization of models and the possibility to review each individual fitting process as an animated gif.
+
+## Attribution
+
+A paper is in preparation describing all algorithms behind RTModel in detail.
+At the moment, any use of this code for scientific publications should be acknowledged by citing this GitHub repository. 
+
+## Installation
+
+The easiest way to install `RTModel` is through `pip`
+```
+pip install RTModel
+```
+
+Currently, `RTModel` works on Linux and Windows, requiring Python >= 3.6. 
+A C++ compiler compatible with C++17 standard is needed for installation.
+`RTModel` also incorporates version 3.7 of [`VBBinaryLensing`](https://github.com/valboz/VBBinaryLensing).
+
+Example Jupyter notebooks will be included in `examples/`.
+
+## Documentation
+Provisional [documentation for the use of RTModel](docs/README.md) is available and under development.
+
+## License
+`RTModel` is freely available to the community under the 
+GNU Lesser General Public License Version 3 included in this repository.
+
+

RTModel-2.0/RTModel/RTModel.py

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+
+import subprocess
+import os
+import sys
+import glob
+import time
+import inspect
+from tqdm import tqdm
+import shutil
+
+
+class RTModel:
+    def __init__(self, event = None):
+        # Directory preliminaries
+        print('*********************')
+        print('****   RTModel   ****')
+        print('*********************')
+        self.pathtoRTM = inspect.getfile(RTModel)
+        self.bindir = os.path.dirname(self.pathtoRTM) + '/bin/'
+        if os.name =='nt':
+            self.readerexe = 'Reader.exe'
+            self.initcondexe = 'InitCond.exe'
+            self.levmarexe = 'LevMar.exe'
+            self.modelselectorexe = 'ModelSelector.exe'
+            self.finalizerexe = 'Finalizer.exe'
+        else:
+            self.readerexe = 'Reader'
+            self.initcondexe = 'InitCond'
+            self.levmarexe = 'LevMar'
+            self.modelselectorexe = 'ModelSelector'
+            self.finalizerexe = 'Finalizer'
+        if(event == None):
+            self.eventname = os.getcwd()
+        else:
+            self.eventname = os.path.realpath(event)
+            print("Event name: " + self.eventname)
+        self.inidir = "ini"
+        self.modelcodes = ['PS', 'PX', 'BS', 'BO', 'LS', 'LX', 'LO']
+        self.endphase =  len(self.modelcodes)*2+3
+        self.eventinifile = 'event.ini'        
+        self.nprocessors = os.cpu_count()
+        print('Number of processors: {}'.format(self.nprocessors))
+        self.config_Reader()
+        self.config_InitCond()
+        self.config_LevMar()
+        self.config_ModelSelector()
+        self.satellitedir = '.'
+
+    def set_processors(self, nprocessors):
+        self.nprocessors = nprocessors
+
+    def set_event(self, event):
+        self.eventname = os.path.realpath(event)
+
+    def set_satellite_dir(self, satellitedir):
+        self.satellitedir = satellitedir
+
+    def config_Reader(self, tau = 0.1, binning = 4000, otherseasons = 1, renormalize = 1, thresholdoutliers = 10):
+        self.Reader_tau= tau # conventional correlation time for consecutive points
+        self.Reader_binning = binning # maximum number of points left after re-binning
+        self.Reader_otherseasons = otherseasons # How to use other seasons (0 = Yes, 1 = decrease significance, 2 = remove)
+        self.Reader_renormalize = renormalize # Re-normalize error bars if non-zero
+        self.Reader_thresholdoutliers = thresholdoutliers # Threshold in sigmas for removing outliers
+        
+    def Reader(self):
+        if(not os.path.exists(self.eventname + '/' + self.inidir)):
+            os.makedirs(self.eventname + '/' + self.inidir)
+        with open(self.eventname + '/' + self.inidir + '/Reader.ini','w') as f:
+            f.write('tau = ' + str(self.Reader_tau) + '\n')
+            f.write('binning = ' + str(self.Reader_binning) + '\n')
+            f.write('otherseasons = ' + str(self.Reader_otherseasons) + '\n')
+            f.write('renormalize = ' + str(self.Reader_renormalize) + '\n')
+            f.write('thresholdoutliers = ' + str(self.Reader_thresholdoutliers) + '\n')
+        print('- Launching: Reader')
+        print('  Pre-processing data...')
+        completedprocess = subprocess.run([self.bindir+self.readerexe,self.eventname], cwd = self.bindir, shell = False, stdout=subprocess.DEVNULL)
+        if(completedprocess.returncode != 0):
+            print('! Error in pre-processing. Please check your data!')            
+            self.done = True
+        else:
+            print('  OK')
+
+    def config_InitCond(self, npeaks = 2, peakthreshold = 10.0, oldmodels = 4, override = None, nostatic = False, onlyorbital = False, usesatellite = 0):
+        self.InitCond_npeaks = npeaks # Number of peaks in the observed light curve to be considered for setting initial conditions.
+        self.InitCond_peakthreshold = peakthreshold # Number of sigmas necessary for a deviation to be identified as a maximum or a minimum.
+        self.InitCond_oldmodels = oldmodels # Maximum number of old models to include in new run as initial conditions
+        self.InitCond_override = override # Override peak identification and manually set peak times
+        self.InitCond_nostatic = nostatic or onlyorbital # No static models will be calculated.
+        self.InitCond_noparallax = onlyorbital; # Only orbital motion models will be calculated.
+        self.InitCond_usesatellite = usesatellite; # Satellite to be used for initial conditions. Ground telescopes by default.
+        
+    def InitCond(self):
+        if(not os.path.exists(self.eventname + '/' + self.inidir)):
+            os.makedirs(self.eventname + '/' + self.inidir)
+        with open(self.eventname + '/' + self.inidir + '/InitCond.ini','w') as f:
+            f.write('npeaks = ' + str(self.InitCond_npeaks) + '\n')
+            f.write('peakthreshold = ' + str(self.InitCond_peakthreshold) + '\n')
+            f.write('oldmodels = ' + str(self.InitCond_oldmodels) + '\n')
+            f.write('usesatellite = ' + str(self.InitCond_usesatellite) + '\n')
+            if(self.InitCond_nostatic):            
+                f.write('nostatic = 1\n')
+            if(self.InitCond_noparallax):            
+                f.write('noparallax = 1\n')
+            if(self.InitCond_override != None):
+                f.write('override = ' + str(self.InitCond_override[0])+ ' ' + str(self.InitCond_override[1]) + '\n')            
+        print('- Launching: InitCond')
+        print('  Setting initial conditions...')
+        completedprocess = subprocess.run([self.bindir+self.initcondexe,self.eventname], cwd = self.bindir, shell = False, stdout=subprocess.DEVNULL)
+        if(completedprocess.returncode != 0):
+            print('! Error in setting initial conditions!')
+            self.done = True
+        else:
+            print('  OK')
+
+    def config_LevMar(self, nfits = 5, timelimit = 600.0, maxsteps = 50, bumperpower = 2.0):
+        self.LevMar_nfits = nfits # Number of models to be calculated from the same initial condition using the bumper method
+        self.LevMar_maxsteps = maxsteps # Maximum number of steps in each fit
+        self.LevMar_timelimit = timelimit # Maximum time in seconds for total execution
+        self.LevMar_bumperpower = bumperpower # Repulsion factor of bumpers
+    
+    def LevMar(self,strmodel):
+        if(not os.path.exists(self.eventname + '/' + self.inidir)):
+            os.makedirs(self.eventname + '/' + self.inidir)
+        with open(self.eventname + '/' + self.inidir + '/LevMar.ini','w') as f:
+            f.write('nfits = ' + str(self.LevMar_nfits) + '\n')
+            f.write('maxsteps = ' + str(self.LevMar_maxsteps) + '\n')
+            f.write('timelimit = ' + str(self.LevMar_timelimit) + '\n')
+            f.write('bumperpower = ' + str(self.LevMar_bumperpower) + '\n')
+        print('- Launching: LevMar')
+        print('  Fitting ' + strmodel + ' ...')
+        completedprocess = subprocess.run([self.bindir+self.levmarexe,self.eventname, strmodel,self.satellitedir], cwd = self.bindir, shell = False, stdout=subprocess.DEVNULL)
+        if(completedprocess.returncode != 0):
+            print('! Error in fit!')
+            self.done = True
+        else:
+            print('  OK')
+  
+    def launch_fits(self,modelcode):
+        if(not os.path.exists(self.eventname + '/' + self.inidir)):
+            os.makedirs(self.eventname + '/' + self.inidir)
+        with open(self.eventname + '/' + self.inidir + '/LevMar.ini','w') as f:
+            f.write('nfits = ' + str(self.LevMar_nfits) + '\n')
+            f.write('maxsteps = ' + str(self.LevMar_maxsteps) + '\n')
+            f.write('timelimit = ' + str(self.LevMar_timelimit) + '\n')
+            f.write('bumperpower = ' + str(self.LevMar_bumperpower) + '\n')
+        stringfits = {'PS' : '- Single-lens-Single-source fits',
+                      'PX' : '- Single-lens-Single-source fits with parallax',
+                      'BS' : '- Single-lens-Binary-source fits',
+                      'BO' : '- Single-lens-Binary-source fits with xallarap',
+                      'LS' : '- Binary-lens-Single-source fits',
+                      'LX' : '- Binary-lens-Single-source fits with parallax',
+                      'LO' : '- Binary-lens-Single-source fits with orbital motion'}       
+        print(stringfits[modelcode])
+        initcondfile = self.eventname + '/InitCond/' + 'InitCond'+ modelcode + '.txt'
+        if(os.path.exists(initcondfile)):
+            with open(self.eventname + '/InitCond/' + 'InitCond'+ modelcode + '.txt') as f:
+                line = f.readline().split()
+                npeaks = int(line[0])
+                ninitconds = int(line[1])   
+            processes = []
+            procnumbers = []
+            iinitcond = 0
+            finitcond = 0
+            finitcondold = -1       
+            pbar = tqdm(total = ninitconds,desc = 'Fits completed',file=sys.stdout, colour='GREEN', smoothing = 0)
+            while(finitcond < ninitconds):
+                i=0
+                while i < len(processes):
+                    if(processes[i].poll() != None):
+                        processes.pop(i)
+                        procnumbers.pop(i)
+                        finitcond += 1
+                    else:
+                        i += 1
+                while(iinitcond < ninitconds and len(processes) < self.nprocessors):
+                    strmodel =  modelcode + '{:0>4}'.format(str(iinitcond))
+                    if(glob.glob(self.eventname +'/PreModels/' + strmodel + '/t' + strmodel + '.dat')==[]):
+                        processes.append(subprocess.Popen([self.bindir+self.levmarexe,self.eventname, strmodel,self.satellitedir], cwd = self.bindir, shell = False, stdout=subprocess.DEVNULL))
+                        procnumbers.append(iinitcond)
+                    else:
+                        finitcond += 1
+                    iinitcond += 1
+                if(finitcond != finitcondold):
+                    #print('  Fits launched: {}; completed: {}/{}'.format(iinitcond, finitcond, ninitconds))
+                    pbar.update(finitcond - max(finitcondold,0))
+                    finitcondold =finitcond
+                time.sleep(0.1)
+            pbar.close()
+        else:
+            print('- No initial conditions for this class')
+ 
+    def config_ModelSelector(self, sigmasoverlap = 3.0, sigmachisquare = 1.0, maxmodels = 10):
+        self.ModelSelector_sigmasoverlap = sigmasoverlap # factor multiplying the inverse covariance in search for superpositions (models are incompatible if farther than sigmasoverlap*sigma)
+        self.ModelSelector_sigmachisquare = sigmachisquare # number of sigmas in the chi square distribution for accepting alternative models after the best one
+        self.ModelSelector_maxmodels = maxmodels # maximum number of models returned
+    
+    def ModelSelector(self, modelcode):
+        if(not os.path.exists(self.eventname + '/' + self.inidir)):
+            os.makedirs(self.eventname + '/' + self.inidir)
+        with open(self.eventname + '/' + self.inidir + '/ModelSelector.ini','w') as f:
+            f.write('sigmasoverlap = ' + str(self.ModelSelector_sigmasoverlap) + '\n')
+            f.write('sigmachisquare = ' + str(self.ModelSelector_sigmachisquare) + '\n')
+            f.write('maxmodels = ' + str(self.ModelSelector_maxmodels) + '\n')
+        stringmodels = {'PS' : '- Selecting models for Single-lens-Single-source fits',
+                        'PX' : '- Selecting models for Single-lens-Single-source fits with parallax',
+                        'BS' : '- Selecting models for Single-lens-Binary-source fits',
+                        'BO' : '- Selecting models for Single-lens-Binary-source fits with xallarap',
+                        'LS' : '- Selecting models for Binary-lens-Single-source fits',
+                        'LX' : '- Selecting models for Binary-lens-Single-source fits with parallax',
+                        'LO' : '- Selecting models for Binary-lens-Single-source fits with orbital motion'}
+        print(stringmodels[modelcode])
+        completedprocess = subprocess.run([self.bindir+self.modelselectorexe,self.eventname, modelcode], cwd = self.bindir, shell = False, stdout=subprocess.DEVNULL)
+        if(completedprocess.returncode != 0):
+            print('! Error in model selection!')
+            self.done = True
+        else:
+            print('  OK')
+            
+    def Finalizer(self):
+        print('- Launching: Finalizer')
+        print('  Making final assessment for this event')
+        completedprocess = subprocess.run([self.bindir+self.finalizerexe,self.eventname], cwd = self.bindir, shell = False, stdout=subprocess.DEVNULL)
+        if(completedprocess.returncode != 0):
+            print('! Error in finalization. Maybe there are problems with models')
+            self.done = True
+        else:
+            with open(self.eventname + '/Nature.txt') as f:
+                for line in f.readlines():
+                    print("  " + line,end='')
+                print("  OK")  
+
+    def run(self, event = None):
+        phase =0
+        if(event!= None):
+            self.eventname = os.path.realpath(event)
+        self.done = False        
+        while not(self.done):
+            print("o " + time.asctime())
+            # Check that event directory exists
+            if phase == 0:
+                if(os.path.exists(self.eventname + '/Data')):
+                    print('- Analyzing event: ',self.eventname)
+                    phase = 1
+                else:
+                    print('! Event data for ' + self.eventname + ' not found !')
+                    self.done = True
+            # Launch Reader
+            elif phase == 1:
+                self.Reader()
+                phase = 2
+            # Launch InitCond
+            elif phase == 2:
+                self.InitCond()
+                phase = 3
+            # Launch Finalizer
+            elif phase == self.endphase:
+                self.Finalizer()
+                phase += 1
+            # Conclude analysis
+            elif phase > self.endphase:
+                print("- Analysis of " + self.eventname + " successfully completed!")
+                self.done = True
+            # Launch LevMar for next class
+            elif phase%2 == 1:
+                self.launch_fits(self.modelcodes[phase//2-1]) 
+                phase += 1            
+            # Launch ModelSelector for this class
+            else:
+                self.ModelSelector(self.modelcodes[phase//2-2])
+                phase += 1     
+                
+    def archive_run(self, destination = None):
+        olddir = os.getcwd()
+        os.chdir(self.eventname)
+        if(os.path.exists('LCToFit.txt')):
+            previousrunslist = glob.glob('run-*')
+            previousrunslist.sort()
+            if(destination == None):
+                if(len(previousrunslist)>0):
+                    lastrun = int(previousrunslist[-1].split('-')[-1])
+                else:
+                    lastrun = 0
+                rundir = 'run-' + str(lastrun+1). zfill(4)
+            else:
+                rundir = destination
+            alllist = glob.glob('*')
+            alllist.remove('Data')
+            filelist = list(set(alllist) - set(previousrunslist))
+            os.mkdir(rundir)
+            shutil.copytree('Data',rundir+'/Data')
+            for nam in filelist:
+                shutil.move(nam,rundir)
+        os.chdir(olddir)

RTModel-2.0/RTModel/__init__.py

@@ -0,0 +1,5 @@
+__version__ = "2.0.0"
+__author__ = 'Valerio Bozza'
+__credits__ = 'University of Salerno, Italy'
+
+from .RTModel import RTModel