Initial commit adding documentation for semi-coherent glitch search

docs/fully_coherent_search_using_MCMC_on_glitching_data.md

@@ -54,8 +54,8 @@ Running this example, we obtain traces of the walkers like this:
 ![](img/fully_coherent_search_using_MCMC_on_glitching_data_walkers.png)
 
 Although it is not obvious at first, the large widths of these traces in fact
-show that the walkers are jumping between two bimodal peaks (for both `F0` and
-`F1): this is possible due to the tuning of the parallel tempering. To see this
+show that the walkers are jumping between multiple peaks (for both `F0` and
+`F1): this is possible, due to the tuning of the parallel tempering. To see this
 clearly, we also plot the corner plot:
 ![](img/fully_coherent_search_using_MCMC_on_glitching_data_corner.png)
 
@@ -71,7 +71,7 @@ see bimodality in `F1`, which did does not change during the glitch.
 
 ```
 >>> mcmc.print_summary()
-Max twoF: 1354.7
+Max twoF: 422.97
 ```
 That is, compared to the basic search (on a smooth signal) which had a twoF of
 `~1764` (in agreement with the predicted twoF), we have lost a large

docs/semi_coherent_glitch_search_using_MCMC_on_glitching_data.md

+# Semi-coherent glitch search on data with a single glitch using MCMC
+
+In this example, based on [this
+script](../examples/semi_coherent_glitch_search_using_MCMC.py), we show the
+basic setup for a single-glitch search. We begin, in the usual way, with
+defining some the prior
+
+```python
+import pyfstat
+
+F0 = 30.0
+F1 = -1e-10
+F2 = 0
+Alpha = 5e-3
+Delta = 6e-2
+tref = 362750407.0
+
+tstart = 1000000000
+duration = 100*86400
+tend = tstart + duration
+
+theta_prior = {'F0': {'type': 'norm', 'loc': F0, 'scale': abs(1e-6*F0)},
+               'F1': {'type': 'norm', 'loc': F1, 'scale': abs(1e-6*F1)},
+               'F2': F2,
+               'Alpha': Alpha,
+               'Delta': Delta,
+               'delta_F0': {'type': 'halfnorm', 'loc': 0,
+                            'scale': 1e-5*F0},
+               'delta_F1': 0,
+               'tglitch': {'type': 'unif',
+                           'lower': tstart+0.1*duration,
+                           'upper': tstart+0.9*duration},
+               }
+```
+
+For simplicity, we have chosen a prior based on the known inputs. The important
+steps here are the definition of `delta_F0`, `delta_F1` and `tglitch`, the
+prior densities for the glitch-parameters. We then use a parallel-tempered
+set-up, in addition to an initialisation step and run the search:
+```python
+ntemps = 4
+log10temperature_min = -1
+nwalkers = 100
+nsteps = [5000, 1000, 1000]
+
+mcmc = pyfstat.MCMCGlitchSearch(
+    'semi_coherent_glitch_search_using_MCMC', 'data',
+    sftfilepath='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)
+
+mcmc.run()
+mcmc.plot_corner(add_prior=True)
+mcmc.print_summary()
+```
+
+The posterior for this search demonstrates that we recover the input parameters:
+![](img/semi_coherent_search_using_MCMC_corner.png)

docs/semi_coherent_glitch_search_with_two_glitches_using_MCMC_on_glitching_data.md

+# Semi-coherent glitch search on data with two-glitches using MCMC
+
+![](img/semi_coherent_twoglitch_search_walkers.png)
+![](img/semi_coherent_twoglitch_search_corner.png)

examples/make_fake_data.py

@@ -36,7 +36,7 @@ delta_F1 = 0
 glitch_data = Writer(
     label='glitch', outdir='data', tref=tref, tstart=tstart, F0=F0, F1=F1,
     F2=F2, duration=duration, Alpha=Alpha, Delta=Delta, h0=h0, sqrtSX=sqrtSX,
-    dtglitch=dtglitch, delta_F0=delta_F0, delta_F1=delta_F1, detector='L1')
+    dtglitch=dtglitch, delta_F0=delta_F0, delta_F1=delta_F1)
 glitch_data.make_data()
 
 # Making data with two glitches

examples/semi_coherent_glitch_search.py → examples/semi_coherent_glitch_search_using_MCMC.py

@@ -24,13 +24,17 @@ theta_prior = {'F0': {'type': 'norm', 'loc': F0, 'scale': abs(1e-6*F0)},
                            'upper': tstart+0.9*duration},
                }
 
-nwalkers = 500
-nsteps = [1000, 1000, 1000]
+ntemps = 4
+log10temperature_min = -1
+nwalkers = 100
+nsteps = [5000, 1000, 1000]
 
 mcmc = pyfstat.MCMCGlitchSearch(
-    'semi_coherent_glitch_search', 'data', sftfilepath='data/*_glitch*sft',
-    theta_prior=theta_prior, tref=tref, tstart=tstart, tend=tend,
-    nsteps=nsteps, nwalkers=nwalkers, scatter_val=1e-10, nglitch=1)
+    'semi_coherent_glitch_search_using_MCMC', 'data',
+    sftfilepath='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)
 
 mcmc.run()
 mcmc.plot_corner(add_prior=True)

examples/semi_coherent_twoglitch_search.py

@@ -16,9 +16,12 @@ theta_prior = {'F0': {'type': 'norm', 'loc': F0, 'scale': abs(1e-6*F0)},
                'F2': F2,
                'Alpha': Alpha,
                'Delta': Delta,
-               'delta_F0': {'type': 'halfnorm', 'loc': 0,
+               'delta_F0_0': {'type': 'halfnorm', 'loc': 0,
                               'scale': 1e-7*F0},
-               'delta_F1': 0,
+               'delta_F0_1': {'type': 'halfnorm', 'loc': 0,
+                              'scale': 1e-7*F0},
+               'delta_F1_0': 0,
+               'delta_F1_1': 0,
                'tglitch_0': {'type': 'unif',
                              'lower': tstart+0.01*duration,
                              'upper': tstart+0.5*duration},
@@ -27,8 +30,8 @@ theta_prior = {'F0': {'type': 'norm', 'loc': F0, 'scale': abs(1e-6*F0)},
                              'upper': tstart+0.99*duration},
                }
 
-nwalkers = 50
-nsteps = [500, 500, 500]
+nwalkers = 100
+nsteps = [1000, 1000, 5000]
 
 mcmc = pyfstat.MCMCGlitchSearch(
     'semi_coherent_twoglitch_search', 'data', sftfilepath='data/*twoglitch*sft',