Merge branch 'renaming_sftfilepath_to_pattern' into 'master'

Renames sftfilepath -> sftfilepattern

See merge request !6

examples/computing_the_Bayes_factor.py

@@ -24,7 +24,7 @@ nwalkers = 100
 nsteps = [500, 500]
 
 mcmc = MCMCSearch(label='computing_the_Bayes_factor', outdir='data', 
-                  sftfilepath='data/*basic*sft', theta_prior=theta_prior,
+                  sftfilepattern='data/*basic*sft', theta_prior=theta_prior,
                   tref=tref, tstart=tstart, tend=tend, nsteps=nsteps,
                   nwalkers=nwalkers, ntemps=ntemps,
                   log10temperature_min=log10temperature_min)

examples/follow_up.py

@@ -26,7 +26,7 @@ run_setup = [(1000, 50), (1000, 25), (1000, 1, False),
 
 mcmc = pyfstat.MCMCFollowUpSearch(
     label='follow_up', outdir='data',
-    sftfilepath='data/*basic*sft', theta_prior=theta_prior, tref=tref,
+    sftfilepattern='data/*basic*sft', theta_prior=theta_prior, tref=tref,
     minStartTime=tstart, maxStartTime=tend, nwalkers=nwalkers,
     ntemps=ntemps, log10temperature_min=log10temperature_min)
 mcmc.run(run_setup)

examples/fully_coherent_search_using_MCMC.py

@@ -53,7 +53,7 @@ nsteps = [50, 50]
 
 mcmc = pyfstat.MCMCSearch(
     label='fully_coherent_search_using_MCMC', outdir='data',
-    sftfilepath='data/*'+data_label+'*sft', theta_prior=theta_prior, tref=tref,
+    sftfilepattern='data/*'+data_label+'*sft', theta_prior=theta_prior, tref=tref,
     minStartTime=tstart, maxStartTime=tend, nsteps=nsteps, nwalkers=nwalkers,
     ntemps=ntemps, log10temperature_min=log10temperature_min)
 mcmc.run(context='paper', subtractions=[30, -1e-10])

examples/fully_coherent_search_using_MCMC_on_glitching_data.py

@@ -26,7 +26,7 @@ nwalkers = 100
 nsteps = [500, 500]
 
 mcmc = MCMCSearch('fully_coherent_search_using_MCMC_on_glitching_data', 'data',
-                  sftfilepath='data/*_glitch*.sft',
+                  sftfilepattern='data/*_glitch*.sft',
                   theta_prior=theta_prior, tref=tref, minStartTime=tstart, maxStartTime=tend,
                   nsteps=nsteps, nwalkers=nwalkers, ntemps=ntemps,
                   log10temperature_min=log10temperature_min)

examples/glitch_robust_search.py

@@ -17,7 +17,7 @@ Delta = np.radians(22.0144)
 
 tref = tstart + .5 * Tspan
 
-sftfilepath = 'data/*glitching_signal*sft'
+sftfilepattern = 'data/*glitching_signal*sft'
 
 F0_width = np.sqrt(3)/(np.pi*Tspan)
 F1_width = np.sqrt(45/4.)/(np.pi*Tspan**2)
@@ -45,7 +45,7 @@ theta_prior = {'F0': {'type': 'unif',
                }
 
 search = pyfstat.MCMCGlitchSearch(
-    label=label, outdir=outdir, sftfilepath=sftfilepath,
+    label=label, outdir=outdir, sftfilepattern=sftfilepattern,
     theta_prior=theta_prior, nglitch=1, tref=tref, nsteps=[500, 500],
     ntemps=3, log10temperature_min=-0.5, minStartTime=tstart,
     maxStartTime=tstart+Tspan)

examples/semi_coherent_glitch_search_using_MCMC.py

@@ -31,7 +31,7 @@ nsteps = [5000, 1000, 1000]
 
 mcmc = pyfstat.MCMCGlitchSearch(
     'semi_coherent_glitch_search_using_MCMC', 'data',
-    sftfilepath='data/*_glitch*sft', theta_prior=theta_prior, tref=tref,
+    sftfilepattern='data/*_glitch*sft', theta_prior=theta_prior, tref=tref,
     tstart=tstart, tend=tend, nsteps=nsteps, nwalkers=nwalkers,
     scatter_val=1e-10, nglitch=1, ntemps=ntemps,
     log10temperature_min=log10temperature_min)

examples/semi_coherent_search_using_MCMC.py

@@ -25,7 +25,7 @@ nsteps = [500, 500, 500]
 
 mcmc = pyfstat.MCMCSemiCoherentSearch(
     label='semi_coherent_search_using_MCMC', outdir='data', nsegs=20,
-    sftfilepath='data/*basic*sft', theta_prior=theta_prior, tref=tref,
+    sftfilepattern='data/*basic*sft', theta_prior=theta_prior, tref=tref,
     minStartTime=tstart, maxStartTime=tend, nsteps=nsteps, nwalkers=nwalkers,
     ntemps=ntemps, log10temperature_min=log10temperature_min)
 mcmc.run()

examples/semi_coherent_twoglitch_search_using_MCMC.py

@@ -34,7 +34,7 @@ nwalkers = 100
 nsteps = [1000, 1000, 5000]
 
 mcmc = pyfstat.MCMCGlitchSearch(
-    'semi_coherent_twoglitch_search', 'data', sftfilepath='data/*twoglitch*sft',
+    'semi_coherent_twoglitch_search', 'data', sftfilepattern='data/*twoglitch*sft',
     theta_prior=theta_prior, tref=tref, tstart=tstart,
     tend=tend, nsteps=nsteps, nwalkers=nwalkers, scatter_val=1e-10, nglitch=2)
 

examples/sliding_window.py

@@ -27,7 +27,7 @@ data.make_data()
 
 DeltaF0 = 1e-5
 search = pyfstat.FrequencySlidingWindow(
-        label='sliding_window', outdir='data', sftfilepath='data/*sliding_window*sft',
+        label='sliding_window', outdir='data', sftfilepattern='data/*sliding_window*sft',
         F0s=[F0-DeltaF0, F0+DeltaF0, DeltaF0/100.], F1=F1, F2=0,
         Alpha=Alpha, Delta=Delta, tref=tref, minStartTime=tstart,
         maxStartTime=tend, window_size=25*86400, window_delta=1*86400)

examples/transient_search_using_MCMC.py

@@ -40,7 +40,7 @@ nsteps = [100, 100]
 
 mcmc = pyfstat.MCMCTransientSearch(
     label='transient_search', outdir='data',
-    sftfilepath='data/*simulated_transient_signal*sft',
+    sftfilepattern='data/*simulated_transient_signal*sft',
     theta_prior=theta_prior, tref=tref, minStartTime=minStartTime,
     maxStartTime=maxStartTime, nsteps=nsteps, nwalkers=nwalkers, ntemps=ntemps,
     log10temperature_min=log10temperature_min)

examples/weak_signal_follow_up.py

@@ -55,7 +55,7 @@ nsteps = [100, 100]
 
 mcmc = pyfstat.MCMCFollowUpSearch(
     label='weak_signal_follow_up', outdir='data',
-    sftfilepath='data/*'+data_label+'*sft', theta_prior=theta_prior, tref=tref,
+    sftfilepattern='data/*'+data_label+'*sft', theta_prior=theta_prior, tref=tref,
     minStartTime=tstart, maxStartTime=tend, nwalkers=nwalkers, nsteps=nsteps,
     ntemps=ntemps, log10temperature_min=log10temperature_min,
     scatter_val=scatter_val)

pyfstat/core.py

@@ -174,16 +174,15 @@ class BaseSearchClass(object):
         return thetas
 
     def _get_list_of_matching_sfts(self):
-        # first make sure we have a list of paths, to avoid
-        # list comprehension trying to glob each single character
-        sftfilepathlist = np.atleast_1d(self.sftfilepath)
-        matches = [glob.glob(p) for p in sftfilepathlist]
+        """ Returns a list of sfts matching the sftfilepattern """
+        sftfilepatternlist = np.atleast_1d(self.sftfilepattern.split(';'))
+        matches = [glob.glob(p) for p in sftfilepatternlist]
         matches = [item for sublist in matches for item in sublist]
         if len(matches) > 0:
             return matches
         else:
             raise IOError('No sfts found matching {}'.format(
-                self.sftfilepath))
+                self.sftfilepattern))
 
 
 class ComputeFstat(object):
@@ -193,7 +192,7 @@ class ComputeFstat(object):
     sun_ephem_default = sun_ephem
 
     @helper_functions.initializer
-    def __init__(self, tref, sftfilepath=None, minStartTime=None,
+    def __init__(self, tref, sftfilepattern=None, minStartTime=None,
                  maxStartTime=None, binary=False, transient=True, BSGL=False,
                  detectors=None, minCoverFreq=None, maxCoverFreq=None,
                  earth_ephem=None, sun_ephem=None, injectSources=None,
@@ -203,8 +202,9 @@ class ComputeFstat(object):
         ----------
         tref: int
             GPS seconds of the reference time.
-        sftfilepath: str
-            File patern to match SFTs
+        sftfilepattern: str
+            Pattern to match SFTs using wildcards (*?) and ranges [0-9];
+            mutiple patterns can be given separated by colons.
         minStartTime, maxStartTime: float GPStime
             Only use SFTs with timestemps starting from (including, excluding)
             this epoch
@@ -250,7 +250,7 @@ class ComputeFstat(object):
     def get_SFTCatalog(self):
         if hasattr(self, 'SFTCatalog'):
             return
-        if self.sftfilepath is None:
+        if self.sftfilepattern is None:
             for k in ['minStartTime', 'maxStartTime', 'detectors']:
                 if getattr(self, k) is None:
                     raise ValueError('You must provide "{}" to injectSources'
@@ -285,8 +285,8 @@ class ComputeFstat(object):
             constraints.maxStartTime = lal.LIGOTimeGPS(self.maxStartTime)
 
         logging.info('Loading data matching pattern {}'.format(
-                     self.sftfilepath))
-        SFTCatalog = lalpulsar.SFTdataFind(self.sftfilepath, constraints)
+                     self.sftfilepattern))
+        SFTCatalog = lalpulsar.SFTdataFind(self.sftfilepattern, constraints)
         detector_names = list(set([d.header.name for d in SFTCatalog.data]))
         self.detector_names = detector_names
         SFT_timestamps = [d.header.epoch for d in SFTCatalog.data]
@@ -572,7 +572,7 @@ class ComputeFstat(object):
         times = np.linspace(self.minStartTime, self.maxStartTime, N+1)[1:]
         times = np.insert(times, 0, self.minStartTime + 86400/2.)
         out = [predict_fstat(minStartTime=self.minStartTime, maxStartTime=t,
-                             sftfilepattern=self.sftfilepath, IFO=IFO,
+                             sftfilepattern=self.sftfilepattern, IFO=IFO,
                              **pfs_input) for t in times]
         pfs, pfs_sigma = np.array(out).T
         return times, pfs, pfs_sigma
@@ -647,7 +647,7 @@ class SemiCoherentSearch(BaseSearchClass, ComputeFstat):
     """ A semi-coherent search """
 
     @helper_functions.initializer
-    def __init__(self, label, outdir, tref, nsegs=None, sftfilepath=None,
+    def __init__(self, label, outdir, tref, nsegs=None, sftfilepattern=None,
                  binary=False, BSGL=False, minStartTime=None,
                  maxStartTime=None, minCoverFreq=None, maxCoverFreq=None,
                  detectors=None, earth_ephem=None, sun_ephem=None,
@@ -661,8 +661,9 @@ class SemiCoherentSearch(BaseSearchClass, ComputeFstat):
             GPS seconds of the reference time, and start and end of the data.
         nsegs: int
             The (fixed) number of segments
-        sftfilepath: str
-            File patern to match SFTs
+        sftfilepattern: str
+            Pattern to match SFTs using wildcards (*?) and ranges [0-9];
+            mutiple patterns can be given separated by colons.
 
         For all other parameters, see pyfstat.ComputeFStat.
         """
@@ -776,7 +777,7 @@ class SemiCoherentGlitchSearch(BaseSearchClass, ComputeFstat):
 
     @helper_functions.initializer
     def __init__(self, label, outdir, tref, minStartTime, maxStartTime,
-                 nglitch=0, sftfilepath=None, theta0_idx=0, BSGL=False,
+                 nglitch=0, sftfilepattern=None, theta0_idx=0, BSGL=False,
                  minCoverFreq=None, maxCoverFreq=None, assumeSqrtSX=None,
                  detectors=None, earth_ephem=None, sun_ephem=None,
                  SSBprec=None, injectSources=None):
@@ -790,8 +791,9 @@ class SemiCoherentGlitchSearch(BaseSearchClass, ComputeFstat):
         nglitch: int
             The (fixed) number of glitches; this can zero, but occasionally
             this causes issue (in which case just use ComputeFstat).
-        sftfilepath: str
-            File patern to match SFTs
+        sftfilepattern: str
+            Pattern to match SFTs using wildcards (*?) and ranges [0-9];
+            mutiple patterns can be given separated by colons.
         theta0_idx, int
             Index (zero-based) of which segment the theta refers to - uyseful
             if providing a tight prior on theta to allow the signal to jump

pyfstat/grid_based_searches.py

@@ -17,7 +17,7 @@ from core import tqdm, args, earth_ephem, sun_ephem, read_par
 class GridSearch(BaseSearchClass):
     """ Gridded search using ComputeFstat """
     @helper_functions.initializer
-    def __init__(self, label, outdir, sftfilepath, F0s=[0], F1s=[0], F2s=[0],
+    def __init__(self, label, outdir, sftfilepattern, F0s=[0], F1s=[0], F2s=[0],
                  Alphas=[0], Deltas=[0], tref=None, minStartTime=None,
                  maxStartTime=None, nsegs=1, BSGL=False, minCoverFreq=None,
                  maxCoverFreq=None, earth_ephem=None, sun_ephem=None,
@@ -28,8 +28,9 @@ class GridSearch(BaseSearchClass):
         ----------
         label, outdir: str
             A label and directory to read/write data from/to
-        sftfilepath: str
-            File patern to match SFTs
+        sftfilepattern: str
+            Pattern to match SFTs using wildcards (*?) and ranges [0-9];
+            mutiple patterns can be given separated by colons.
         F0s, F1s, F2s, delta_F0s, delta_F1s, tglitchs, Alphas, Deltas: tuple
             Length 3 tuple describing the grid for each parameter, e.g
             [F0min, F0max, dF0], for a fixed value simply give [F0]. Unless
@@ -56,7 +57,7 @@ class GridSearch(BaseSearchClass):
         logging.info('Setting up search object')
         if self.nsegs == 1:
             self.search = ComputeFstat(
-                tref=self.tref, sftfilepath=self.sftfilepath,
+                tref=self.tref, sftfilepattern=self.sftfilepattern,
                 minCoverFreq=self.minCoverFreq, maxCoverFreq=self.maxCoverFreq,
                 earth_ephem=self.earth_ephem, sun_ephem=self.sun_ephem,
                 detectors=self.detectors, transient=False,
@@ -68,7 +69,7 @@ class GridSearch(BaseSearchClass):
         else:
             self.search = SemiCoherentSearch(
                 label=self.label, outdir=self.outdir, tref=self.tref,
-                nsegs=self.nsegs, sftfilepath=self.sftfilepath,
+                nsegs=self.nsegs, sftfilepattern=self.sftfilepattern,
                 BSGL=self.BSGL, minStartTime=self.minStartTime,
                 maxStartTime=self.maxStartTime, minCoverFreq=self.minCoverFreq,
                 maxCoverFreq=self.maxCoverFreq, detectors=self.detectors,
@@ -106,7 +107,7 @@ class GridSearch(BaseSearchClass):
         if os.path.isfile(self.out_file) is False:
             logging.info('No old data found, continuing with grid search')
             return False
-        if self.sftfilepath is not None:
+        if self.sftfilepattern is not None:
             oldest_sft = min([os.path.getmtime(f) for f in
                               self._get_list_of_matching_sfts()])
             if os.path.getmtime(self.out_file) < oldest_sft:
@@ -275,7 +276,7 @@ class GridSearch(BaseSearchClass):
 
 
 class GridUniformPriorSearch():
-    def __init__(self, theta_prior, NF0, NF1, label, outdir, sftfilepath,
+    def __init__(self, theta_prior, NF0, NF1, label, outdir, sftfilepattern,
                  tref, minStartTime, maxStartTime, minCoverFreq=None,
                  maxCoverFreq=None, BSGL=False, detectors=None, nsegs=1):
         dF0 = (theta_prior['F0']['upper'] - theta_prior['F0']['lower'])/NF0
@@ -283,7 +284,7 @@ class GridUniformPriorSearch():
         F0s = [theta_prior['F0']['lower'], theta_prior['F0']['upper'], dF0]
         F1s = [theta_prior['F1']['lower'], theta_prior['F1']['upper'], dF1]
         self.search = GridSearch(
-            label, outdir, sftfilepath, F0s=F0s, F1s=F1s, tref=tref,
+            label, outdir, sftfilepattern, F0s=F0s, F1s=F1s, tref=tref,
             Alphas=[theta_prior['Alpha']], Deltas=[theta_prior['Delta']],
             minStartTime=minStartTime, maxStartTime=maxStartTime, BSGL=BSGL,
             detectors=detectors, minCoverFreq=minCoverFreq,
@@ -299,7 +300,7 @@ class GridUniformPriorSearch():
 class GridGlitchSearch(GridSearch):
     """ Grid search using the SemiCoherentGlitchSearch """
     @helper_functions.initializer
-    def __init__(self, label, outdir, sftfilepath=None, F0s=[0],
+    def __init__(self, label, outdir, sftfilepattern=None, F0s=[0],
                  F1s=[0], F2s=[0], delta_F0s=[0], delta_F1s=[0], tglitchs=None,
                  Alphas=[0], Deltas=[0], tref=None, minStartTime=None,
                  maxStartTime=None, minCoverFreq=None, maxCoverFreq=None,
@@ -310,8 +311,9 @@ class GridGlitchSearch(GridSearch):
         ----------
         label, outdir: str
             A label and directory to read/write data from/to
-        sftfilepath: str
-            File patern to match SFTs
+        sftfilepattern: str
+            Pattern to match SFTs using wildcards (*?) and ranges [0-9];
+            mutiple patterns can be given separated by colons.
         F0s, F1s, F2s, delta_F0s, delta_F1s, tglitchs, Alphas, Deltas: tuple
             Length 3 tuple describing the grid for each parameter, e.g
             [F0min, F0max, dF0], for a fixed value simply give [F0].
@@ -328,7 +330,7 @@ class GridGlitchSearch(GridSearch):
             self.sun_ephem = self.sun_ephem_default
 
         self.search = SemiCoherentGlitchSearch(
-            label=label, outdir=outdir, sftfilepath=self.sftfilepath,
+            label=label, outdir=outdir, sftfilepattern=self.sftfilepattern,
             tref=tref, minStartTime=minStartTime, maxStartTime=maxStartTime,
             minCoverFreq=minCoverFreq, maxCoverFreq=maxCoverFreq,
             earth_ephem=self.earth_ephem, sun_ephem=self.sun_ephem,
@@ -357,7 +359,7 @@ class GridGlitchSearch(GridSearch):
 class FrequencySlidingWindow(GridSearch):
     """ A sliding-window search over the Frequency """
     @helper_functions.initializer
-    def __init__(self, label, outdir, sftfilepath, F0s, F1, F2,
+    def __init__(self, label, outdir, sftfilepattern, F0s, F1, F2,
                  Alpha, Delta, tref, minStartTime=None,
                  maxStartTime=None, window_size=10*86400, window_delta=86400,
                  BSGL=False, minCoverFreq=None, maxCoverFreq=None,
@@ -368,8 +370,9 @@ class FrequencySlidingWindow(GridSearch):
         ----------
         label, outdir: str
             A label and directory to read/write data from/to
-        sftfilepath: str
-            File patern to match SFTs
+        sftfilepattern: str
+            Pattern to match SFTs using wildcards (*?) and ranges [0-9];
+            mutiple patterns can be given separated by colons.
         F0s: array
             Frequency range
         F1, F2, Alpha, Delta: float
@@ -397,7 +400,7 @@ class FrequencySlidingWindow(GridSearch):
     def inititate_search_object(self):
         logging.info('Setting up search object')
         self.search = ComputeFstat(
-            tref=self.tref, sftfilepath=self.sftfilepath,
+            tref=self.tref, sftfilepattern=self.sftfilepattern,
             minCoverFreq=self.minCoverFreq, maxCoverFreq=self.maxCoverFreq,
             earth_ephem=self.earth_ephem, sun_ephem=self.sun_ephem,
             detectors=self.detectors, transient=True,
@@ -473,7 +476,7 @@ class FrequencySlidingWindow(GridSearch):
 class DMoff_NO_SPIN(GridSearch):
     """ DMoff test using SSBPREC_NO_SPIN """
     @helper_functions.initializer
-    def __init__(self, par, label, outdir, sftfilepath, minStartTime=None,
+    def __init__(self, par, label, outdir, sftfilepattern, minStartTime=None,
                  maxStartTime=None, minCoverFreq=None, maxCoverFreq=None,
                  earth_ephem=None, sun_ephem=None, detectors=None,
                  injectSources=None, assumeSqrtSX=None):
@@ -485,8 +488,9 @@ class DMoff_NO_SPIN(GridSearch):
             and 'tref') or a path to a .par file to read in the F0, F1 etc
         label, outdir: str
             A label and directory to read/write data from/to
-        sftfilepath: str
-            File patern to match SFTs
+        sftfilepattern: str
+            Pattern to match SFTs using wildcards (*?) and ranges [0-9];
+            mutiple patterns can be given separated by colons.
         minStartTime, maxStartTime: int
             GPS seconds of the start time and end time
 

pyfstat/mcmc_based_searches.py

@@ -36,7 +36,7 @@ class MCMCSearch(core.BaseSearchClass):
 
     @helper_functions.initializer
     def __init__(self, label, outdir, theta_prior, tref, minStartTime,
-                 maxStartTime, sftfilepath=None, nsteps=[100, 100],
+                 maxStartTime, sftfilepattern=None, nsteps=[100, 100],
                  nwalkers=100, ntemps=1, log10temperature_min=-5,
                  theta_initial=None, scatter_val=1e-10, rhohatmax=1000,
                  binary=False, BSGL=False, minCoverFreq=None, SSBprec=None,
@@ -46,7 +46,7 @@ class MCMCSearch(core.BaseSearchClass):
         Parameters
         label, outdir: str
             A label and directory to read/write data from/to
-        sftfilepath: str
+        sftfilepattern: str
             Pattern to match SFTs using wildcards (*?) and ranges [0-9];
             mutiple patterns can be given separated by colons.
         theta_prior: dict
@@ -94,10 +94,10 @@ class MCMCSearch(core.BaseSearchClass):
             os.mkdir(outdir)
         self._add_log_file()
         logging.info('Set-up MCMC search for model {}'.format(self.label))
-        if sftfilepath:
-            logging.info('Using data {}'.format(self.sftfilepath))
+        if sftfilepattern:
+            logging.info('Using data {}'.format(self.sftfilepattern))
         else:
-            logging.info('No sftfilepath given')
+            logging.info('No sftfilepattern given')
         if injectSources:
             logging.info('Inject sources: {}'.format(injectSources))
         self.pickle_path = '{}/{}_saved_data.p'.format(self.outdir, self.label)
@@ -132,7 +132,7 @@ class MCMCSearch(core.BaseSearchClass):
     def _initiate_search_object(self):
         logging.info('Setting up search object')
         self.search = core.ComputeFstat(
-            tref=self.tref, sftfilepath=self.sftfilepath,
+            tref=self.tref, sftfilepattern=self.sftfilepattern,
             minCoverFreq=self.minCoverFreq, maxCoverFreq=self.maxCoverFreq,
             earth_ephem=self.earth_ephem, sun_ephem=self.sun_ephem,
             detectors=self.detectors, BSGL=self.BSGL, transient=False,
@@ -1112,7 +1112,7 @@ class MCMCSearch(core.BaseSearchClass):
             logging.info('No pickled data found')
             return False
 
-        if self.sftfilepath is not None:
+        if self.sftfilepattern is not None:
             oldest_sft = min([os.path.getmtime(f) for f in
                               self._get_list_of_matching_sfts()])
             if os.path.getmtime(self.pickle_path) < oldest_sft:
@@ -1275,7 +1275,7 @@ class MCMCSearch(core.BaseSearchClass):
                ' --refTime={} --outputLoudest="{}/{}.loudest" '
                '--minStartTime={} --maxStartTime={}').format(
                     params['Alpha'], params['Delta'], params['F0'],
-                    params['F1'], self.sftfilepath, params['tref'],
+                    params['F1'], self.sftfilepattern, params['tref'],
                     self.outdir, self.label, self.minStartTime,
                     self.maxStartTime)
         subprocess.call([cmd], shell=True)
@@ -1459,7 +1459,7 @@ class MCMCGlitchSearch(MCMCSearch):
             )
 
     @helper_functions.initializer
-    def __init__(self, label, outdir, sftfilepath, theta_prior, tref,
+    def __init__(self, label, outdir, sftfilepattern, theta_prior, tref,
                  minStartTime, maxStartTime, nglitch=1, nsteps=[100, 100],
                  nwalkers=100, ntemps=1, log10temperature_min=-5,
                  theta_initial=None, scatter_val=1e-10, rhohatmax=1000,
@@ -1471,8 +1471,9 @@ class MCMCGlitchSearch(MCMCSearch):
         ----------
         label, outdir: str
             A label and directory to read/write data from/to
-        sftfilepath: str
-            File patern to match SFTs
+        sftfilepattern: str
+            Pattern to match SFTs using wildcards (*?) and ranges [0-9];
+            mutiple patterns can be given separated by colons.
         theta_prior: dict
             Dictionary of priors and fixed values for the search parameters.
             For each parameters (key of the dict), if it is to be held fixed
@@ -1530,7 +1531,7 @@ class MCMCGlitchSearch(MCMCSearch):
         self._add_log_file()
         logging.info(('Set-up MCMC glitch search with {} glitches for model {}'
                       ' on data {}').format(self.nglitch, self.label,
-                                            self.sftfilepath))
+                                            self.sftfilepattern))
         self.pickle_path = '{}/{}_saved_data.p'.format(self.outdir, self.label)
         self._unpack_input_theta()
         self.ndim = len(self.theta_keys)
@@ -1554,7 +1555,7 @@ class MCMCGlitchSearch(MCMCSearch):
     def _initiate_search_object(self):
         logging.info('Setting up search object')
         self.search = core.SemiCoherentGlitchSearch(
-            label=self.label, outdir=self.outdir, sftfilepath=self.sftfilepath,
+            label=self.label, outdir=self.outdir, sftfilepattern=self.sftfilepattern,
             tref=self.tref, minStartTime=self.minStartTime,
             maxStartTime=self.maxStartTime, minCoverFreq=self.minCoverFreq,
             maxCoverFreq=self.maxCoverFreq, earth_ephem=self.earth_ephem,
@@ -1718,7 +1719,7 @@ class MCMCGlitchSearch(MCMCSearch):
 class MCMCSemiCoherentSearch(MCMCSearch):
     """ MCMC search for a signal using the semi-coherent ComputeFstat """
     @helper_functions.initializer
-    def __init__(self, label, outdir, theta_prior, tref, sftfilepath=None,
+    def __init__(self, label, outdir, theta_prior, tref, sftfilepattern=None,
                  nsegs=None, nsteps=[100, 100, 100], nwalkers=100,
                  binary=False, ntemps=1, log10temperature_min=-5,
                  theta_initial=None, scatter_val=1e-10, rhohatmax=1000,
@@ -1735,7 +1736,7 @@ class MCMCSemiCoherentSearch(MCMCSearch):
         self._add_log_file()
         logging.info(('Set-up MCMC semi-coherent search for model {} on data'
                       '{}').format(
-            self.label, self.sftfilepath))
+            self.label, self.sftfilepattern))
         self.pickle_path = '{}/{}_saved_data.p'.format(self.outdir, self.label)
         self._unpack_input_theta()
         self.ndim = len(self.theta_keys)
@@ -1767,7 +1768,7 @@ class MCMCSemiCoherentSearch(MCMCSearch):
         logging.info('Setting up search object')
         self.search = core.SemiCoherentSearch(
             label=self.label, outdir=self.outdir, tref=self.tref,
-            nsegs=self.nsegs, sftfilepath=self.sftfilepath, binary=self.binary,
+            nsegs=self.nsegs, sftfilepattern=self.sftfilepattern, binary=self.binary,
             BSGL=self.BSGL, minStartTime=self.minStartTime,
             maxStartTime=self.maxStartTime, minCoverFreq=self.minCoverFreq,
             maxCoverFreq=self.maxCoverFreq, detectors=self.detectors,
@@ -2124,7 +2125,7 @@ class MCMCTransientSearch(MCMCSearch):
     def _initiate_search_object(self):
         logging.info('Setting up search object')
         self.search = core.ComputeFstat(
-            tref=self.tref, sftfilepath=self.sftfilepath,
+            tref=self.tref, sftfilepattern=self.sftfilepattern,
             minCoverFreq=self.minCoverFreq, maxCoverFreq=self.maxCoverFreq,
             earth_ephem=self.earth_ephem, sun_ephem=self.sun_ephem,
             detectors=self.detectors, transient=True,

tests.py

@@ -95,7 +95,7 @@ class TestComputeFstat(Test):
 
         search = pyfstat.ComputeFstat(
             tref=Writer.tref,
-            sftfilepath='{}/*{}*sft'.format(Writer.outdir, Writer.label))
+            sftfilepattern='{}/*{}*sft'.format(Writer.outdir, Writer.label))
         FS = search.run_computefstatistic_single_point(Writer.tstart,
                                                        Writer.tend,
                                                        Writer.F0,
@@ -113,7 +113,7 @@ class TestComputeFstat(Test):
 
         search = pyfstat.ComputeFstat(
             tref=Writer.tref, assumeSqrtSX=1,
-            sftfilepath='{}/*{}*sft'.format(Writer.outdir, Writer.label))
+            sftfilepattern='{}/*{}*sft'.format(Writer.outdir, Writer.label))
         FS = search.run_computefstatistic_single_point(Writer.tstart,
                                                        Writer.tend,
                                                        Writer.F0,
@@ -162,7 +162,7 @@ class TestSemiCoherentGlitchSearch(Test):
 
         search = pyfstat.SemiCoherentGlitchSearch(
             label=self.label, outdir=outdir,
-            sftfilepath='{}/*{}*sft'.format(Writer.outdir, Writer.label),
+            sftfilepattern='{}/*{}*sft'.format(Writer.outdir, Writer.label),
             tref=Writer.tref, minStartTime=Writer.tstart,
             maxStartTime=Writer.tend, nglitch=1)
 
@@ -221,7 +221,7 @@ class TestMCMCSearch(Test):
 
         search = pyfstat.MCMCSearch(
             label=self.label, outdir=outdir, theta_prior=theta, tref=tref,
-            sftfilepath='{}/*{}*sft'.format(Writer.outdir, Writer.label),
+            sftfilepattern='{}/*{}*sft'.format(Writer.outdir, Writer.label),
             minStartTime=minStartTime, maxStartTime=maxStartTime,
             nsteps=[100, 100], nwalkers=100, ntemps=2, log10temperature_min=-1)
         search.setup_convergence_testing()