PyCBC 2.1.3__tar.gz → 2.1.4__tar.gz

{PyCBC-2.1.3 → PyCBC-2.1.4}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.1
 Name: PyCBC
-Version: 2.1.3
+Version: 2.1.4
 Summary: Core library to analyze gravitational-wave data, find signals, and study their parameters.
 Home-page: http://www.pycbc.org/
 Author: The PyCBC team
 Author-email: alex.nitz@gmail.org
 License: UNKNOWN
-Download-URL: https://github.com/gwastro/pycbc/tarball/v2.1.3
+Download-URL: https://github.com/gwastro/pycbc/tarball/v2.1.4
 Description: ![GW150914](https://raw.githubusercontent.com/gwastro/pycbc-logo/master/pycbc_logo_name.png)
         
         [PyCBC](http://pycbc.org) is a software package used to explore astrophysical sources of gravitational waves.

{PyCBC-2.1.3 → PyCBC-2.1.4}/PyCBC.egg-info/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.1
 Name: PyCBC
-Version: 2.1.3
+Version: 2.1.4
 Summary: Core library to analyze gravitational-wave data, find signals, and study their parameters.
 Home-page: http://www.pycbc.org/
 Author: The PyCBC team
 Author-email: alex.nitz@gmail.org
 License: UNKNOWN
-Download-URL: https://github.com/gwastro/pycbc/tarball/v2.1.3
+Download-URL: https://github.com/gwastro/pycbc/tarball/v2.1.4
 Description: ![GW150914](https://raw.githubusercontent.com/gwastro/pycbc-logo/master/pycbc_logo_name.png)
         
         [PyCBC](http://pycbc.org) is a software package used to explore astrophysical sources of gravitational waves.

{PyCBC-2.1.3 → PyCBC-2.1.4}/PyCBC.egg-info/SOURCES.txt

@@ -503,6 +503,8 @@ pycbc/io/hdf.py
 pycbc/io/ligolw.py
 pycbc/io/live.py
 pycbc/io/record.py
+pycbc/live/__init__.py
+pycbc/live/snr_optimizer.py
 pycbc/neutron_stars/__init__.py
 pycbc/neutron_stars/eos_utils.py
 pycbc/neutron_stars/pg_isso_solver.py

{PyCBC-2.1.3 → PyCBC-2.1.4}/bin/live/pycbc_live_combine_single_fits

@@ -15,8 +15,10 @@
 """Combine PyCBC Live single-detector trigger fitting parameters from several
 different files."""
 
-import h5py, numpy as np, argparse
+import argparse
 import logging
+import numpy as np
+import h5py
 import pycbc
 
 
@@ -45,66 +47,80 @@ if args.conservative_percentile < 50 or \
                  "otherwise it is either not a percentile, or not "
                  "conservative.")
 
-counts_all = {ifo: [] for ifo in args.ifos}
-alphas_all = {ifo: [] for ifo in args.ifos}
-analysis_dates = []
+logging.info("%d input files", len(args.trfits_files))
+
+# We only want to combine fit results if they were done with the same
+# configuration.  So start by finding the most recent fit file and reading its
+# configuration parameters.
 
-with h5py.File(args.trfits_files[0], 'r') as fit_f0:
-    # Store some attributes so we can check that all files are
-    # comparable
+logging.info("Determining the most recent configuration parameters")
 
-    # Keep the upper and lower bins
-    bl = fit_f0['bins_lower'][:]
-    bu = fit_f0['bins_upper'][:]
+latest_date = None
+for f in args.trfits_files:
+    with h5py.File(f, 'r') as fit_f:
+        if latest_date is None or fit_f.attrs['analysis_date'] > latest_date:
+            latest_date = fit_f.attrs['analysis_date']
+            bl = fit_f['bins_lower'][:]
+            bu = fit_f['bins_upper'][:]
+            sngl_rank = fit_f.attrs['sngl_ranking']
+            fit_thresh = fit_f.attrs['fit_threshold']
+            fit_func = fit_f.attrs['fit_function']
 
-    sngl_rank = fit_f0.attrs['sngl_ranking']
-    fit_thresh = fit_f0.attrs['fit_threshold']
-    fit_func = fit_f0.attrs['fit_function']
+# Now go back through the fit files and read the actual information.  Skip the
+# files that have fit parameters inconsistent with what we found earlier.
 
-live_times = {ifo: [] for ifo in args.ifos}
+logging.info("Reading individual fit results")
 
+live_times = {ifo: [] for ifo in args.ifos}
 trigger_file_starts = []
 trigger_file_ends = []
-
-n_files = len(args.trfits_files)
-logging.info("Checking through %d files", n_files)
+counts_all = {ifo: [] for ifo in args.ifos}
+alphas_all = {ifo: [] for ifo in args.ifos}
 
 for f in args.trfits_files:
-    fits_f = h5py.File(f, 'r')
-    # Check that the file uses the same setup as file 0, to make sure
-    # all coefficients are comparable
-
-    assert fits_f.attrs['sngl_ranking'] == sngl_rank
-    assert fits_f.attrs['fit_threshold'] == fit_thresh
-    assert fits_f.attrs['fit_function'] == fit_func
-    assert all(fits_f['bins_lower'][:] == bl)
-    assert all(fits_f['bins_upper'][:] == bu)
-
-    # Get the time of the first/last triggers in the trigger_fits file
-    gps_last = 0
-    gps_first = np.inf
-    for ifo in args.ifos:
-        if ifo not in fits_f:
+    with h5py.File(f, 'r') as fits_f:
+        # Check that the file uses the same setup as file 0, to make sure
+        # all coefficients are comparable
+        same_conf = (fits_f.attrs['sngl_ranking'] == sngl_rank
+                     and fits_f.attrs['fit_threshold'] == fit_thresh
+                     and fits_f.attrs['fit_function'] == fit_func
+                     and all(fits_f['bins_lower'][:] == bl)
+                     and all(fits_f['bins_upper'][:] == bu))
+        if not same_conf:
+            logging.warn(
+                "Found a change in the fit configuration, skipping %s",
+                f
+            )
             continue
-        trig_times = fits_f[ifo]['triggers']['end_time'][:]
-        gps_last = max(gps_last, trig_times.max())
-        gps_first = min(gps_first, trig_times.min())
-    trigger_file_starts.append(gps_first)
-    trigger_file_ends.append(gps_last)
-
-    for ifo in args.ifos:
-        if ifo not in fits_f:
-            live_times[ifo].append(0)
-            counts_all[ifo].append(-1 * np.ones_like(bl))
-            alphas_all[ifo].append(-1 * np.ones_like(bl))
-        else:
-            live_times[ifo].append(fits_f[ifo].attrs['live_time'])
-            counts_all[ifo].append(fits_f[ifo + '/counts'][:])
-            alphas_all[ifo].append(fits_f[ifo + '/fit_coeff'][:])
-            if any(np.isnan(fits_f[ifo + '/fit_coeff'][:])):
-                logging.info("nan in %s, %s", f, ifo)
-                logging.info(fits_f[ifo + '/fit_coeff'][:])
-    fits_f.close()
+
+        # We now determine the (approximate) start/end times of the
+        # trigger_fits file via the time of the first/last triggers in it.
+        # Ideally this would be recorded exactly in the file.
+        gps_last = 0
+        gps_first = np.inf
+        for ifo in args.ifos:
+            if ifo not in fits_f:
+                continue
+            trig_times = fits_f[ifo]['triggers']['end_time'][:]
+            gps_last = max(gps_last, trig_times.max())
+            gps_first = min(gps_first, trig_times.min())
+        trigger_file_starts.append(gps_first)
+        trigger_file_ends.append(gps_last)
+
+        # Read the fitting parameters
+        for ifo in args.ifos:
+            if ifo not in fits_f:
+                live_times[ifo].append(0)
+                counts_all[ifo].append(-1 * np.ones_like(bl))
+                alphas_all[ifo].append(-1 * np.ones_like(bl))
+            else:
+                ffi = fits_f[ifo]
+                live_times[ifo].append(ffi.attrs['live_time'])
+                counts_all[ifo].append(ffi['counts'][:])
+                alphas_all[ifo].append(ffi['fit_coeff'][:])
+                if any(np.isnan(ffi['fit_coeff'][:])):
+                    logging.warn("nan in %s, %s", f, ifo)
+                    logging.warn(ffi['fit_coeff'][:])
 
 # Set up the date array, this is stored as an offset from the first trigger time of
 # the first file to the last trigger of the file
@@ -115,7 +131,7 @@ ad_order = np.argsort(trigger_file_starts)
 start_time_n = trigger_file_starts[ad_order[0]]
 ad = trigger_file_ends[ad_order] - start_time_n
 
-# Get the counts and alphas
+# Swap the time and bin dimensions for counts and alphas
 counts_bin = {ifo: [c for c in zip(*counts_all[ifo])] for ifo in args.ifos}
 alphas_bin = {ifo: [a for a in zip(*alphas_all[ifo])] for ifo in args.ifos}
 
@@ -125,6 +141,7 @@ cons_alphas_out = {ifo: np.zeros(len(alphas_bin[ifo])) for ifo in args.ifos}
 cons_counts_out = {ifo: np.inf * np.ones(len(alphas_bin[ifo])) for ifo in args.ifos}
 
 logging.info("Writing results")
+
 fout = h5py.File(args.output, 'w')
 fout.attrs['fit_threshold'] = fit_thresh
 fout.attrs['conservative_percentile'] = args.conservative_percentile

{PyCBC-2.1.3 → PyCBC-2.1.4}/bin/live/pycbc_live_plot_combined_single_fits

@@ -12,18 +12,23 @@
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
 # Public License for more details.
 
-import h5py, numpy as np, argparse
+"""Plot the time evolution of fit parameters of PyCBC Live triggers.
+"""
+
+import argparse
+import logging
+import numpy as np
+import h5py
 import matplotlib
 matplotlib.use('agg')
 from matplotlib import pyplot as plt
-import logging
+
 from lal import gpstime
-import pycbc
 
+import pycbc
 
 
-parser = argparse.ArgumentParser(usage="",
-    description="Combine fitting parameters from several different files")
+parser = argparse.ArgumentParser(description=__doc__)
 parser.add_argument("--verbose", action="store_true",
                     help="Print extra debugging information", default=False)
 parser.add_argument("--combined-fits-file", required=True,
@@ -45,7 +50,7 @@ parser.add_argument("--colormap", default="rainbow_r", choices=plt.colormaps(),
 parser.add_argument("--log-colormap", action='store_true',
                     help="Use log spacing for choosing colormap values "
                          "based on duration bins.")
-args=parser.parse_args()
+args = parser.parse_args()
 
 if '{ifo}' not in args.output_plot_name_format or \
     '{type}' not in args.output_plot_name_format:
@@ -94,21 +99,6 @@ with h5py.File(args.combined_fits_file, 'r') as cff:
 bin_starts = bins_edges[:-1]
 bin_ends = bins_edges[1:]
 
-bin_max = max(bin_ends)
-bin_min = min(bin_starts)
-
-def bin_proportion(upper, lower, log_spacing=False):
-    if log_spacing:
-        ll = np.log(lower)
-        ul = np.log(lower)
-        centl = (ll + ul) / 2.
-        minl = np.log(bin_min)
-        maxl = np.log(bin_max)
-        return (centl - minl) / (maxl - minl)
-
-    else:
-        return ((lower + upper) / 2. - bin_min) / (bin_max - bin_min)
-
 # Set up the x ticks - note that these are rounded to the nearest
 # midnight, so may not line up exactly with the data
 min_start = min([separate_starts[ifo].min() for ifo in ifos])
@@ -157,8 +147,7 @@ for ifo in ifos:
         mr = mean_count[ifo][i] / live_total[ifo]
         cr = cons_count[ifo][i] / live_total[ifo]
 
-        bin_prop = bin_proportion(bu, bl,
-                                  log_spacing=args.log_colormap)
+        bin_prop = i / len(bin_starts)
         bin_colour = plt.get_cmap(args.colormap)(bin_prop)
         bin_label = f"duration {bl:.2f}-{bu:.2f}"
         alpha_lines += ax_alpha.plot(separate_starts[ifo], alphas, c=bin_colour,
@@ -199,6 +188,12 @@ for ifo in ifos:
         ax.grid(zorder=-30)
 
     fig_count.tight_layout()
-    fig_count.savefig(args.output_plot_name_format.format(ifo=ifo, type='counts'))
+    fig_count.savefig(
+        args.output_plot_name_format.format(ifo=ifo, type='counts')
+    )
     fig_alpha.tight_layout()
-    fig_alpha.savefig(args.output_plot_name_format.format(ifo=ifo, type='fit_coeffs'))
+    fig_alpha.savefig(
+        args.output_plot_name_format.format(ifo=ifo, type='fit_coeffs')
+    )
+
+logging.info("Done")

{PyCBC-2.1.3 → PyCBC-2.1.4}/bin/live/pycbc_live_plot_single_trigger_fits

@@ -12,17 +12,24 @@
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
 # Public License for more details.
 
+"""Plot histograms of PyCBC Live triggers split over various parameters, and
+the corresponding fits.
+"""
+
+import argparse
+import logging
 import numpy as np
-import pycbc
-from pycbc import bin_utils
-from pycbc.events import trigger_fits as trstats
+import h5py
 import matplotlib
 matplotlib.use('agg')
 from matplotlib import pyplot as plt
-import argparse, logging, h5py
 
-parser = argparse.ArgumentParser(usage="",
-    description="Plot histograms of triggers split over various parameters")
+import pycbc
+from pycbc.bin_utils import IrregularBins
+from pycbc.events.trigger_fits import cum_fit as eval_cum_fit
+
+
+parser = argparse.ArgumentParser(description=__doc__)
 parser.add_argument("--verbose", action="store_true",
                     help="Print extra debugging information", default=False)
 parser.add_argument("--trigger-fits-file", required=True,
@@ -39,11 +46,14 @@ parser.add_argument("--colormap", default="rainbow_r", choices=plt.colormaps(),
 parser.add_argument("--log-colormap", action='store_true',
                     help="Use log spacing for choosing colormap values "
                          "based on duration bins.")
+parser.add_argument("--x-lim-lower", type=float,
+                    help="Add a lower limit to the x-axis of the plot")
 parser.add_argument("--x-lim-upper", type=float,
                     help="Add an upper limit to the x-axis of the plot")
+parser.add_argument("--y-lim-lower", type=float,
+                    help="Add a lower limit to the y-axis of the plot")
 parser.add_argument("--y-lim-upper", type=float,
                     help="Add an upper limit to the y-axis of the plot")
-#parser.add_argument("--", default="", help="")
 
 #Add some input sanitisation
 args = parser.parse_args()
@@ -58,6 +68,7 @@ logging.info("Getting trigger fits file information")
 with h5py.File(args.trigger_fits_file, 'r') as trfit_f:
     # Get the ifos to plot from the file
     # Check that all the ifos we want to plot are in the file
+    all_ifos = trfit_f.attrs['ifos'].split(',')
     ifos = [k for k in trfit_f.keys() if not k.startswith('bins')]
 
     # Grab some info from the attributes
@@ -79,54 +90,54 @@ with h5py.File(args.trigger_fits_file, 'r') as trfit_f:
     bu = trfit_f['bins_upper'][:]
     bl = trfit_f['bins_lower'][:]
 
-bin_max = max(bu)
-bin_min = min(bl)
-
-def bin_proportion(upper, lower, log_spacing=False):
-    if log_spacing:
-        ll = np.log(lower)
-        ul = np.log(lower)
-        centl = (ll + ul) / 2.
-        minl = np.log(bin_min)
-        maxl = np.log(bin_max)
-        return (centl - minl) / (maxl - minl)
-
-    else:
-        return ((lower + upper) / 2. - bin_min) / (bin_max - bin_min)
-
-
 duration_bin_edges = list(bl) + [bu[-1]]
-
-tbins = bin_utils.IrregularBins(duration_bin_edges)
+tbins = IrregularBins(duration_bin_edges)
 
 logger = logging.getLogger()
 init_level = logger.level
 
 logging.info("Plotting fits")
 
-for ifo in ifos:
-    # Skip if no triggers in this IFO
-    if not len(stats[ifo]): continue
+for ifo in all_ifos:
+    fig, ax = plt.subplots(1)
+    oput_plot = args.output_plot_name_format.format(ifo=ifo)
+
+    if ifo not in ifos or not len(stats[ifo]):
+        # Plot a blank plot with a message to show it worked, but there
+        # weren't any triggers
+        plt.tick_params(labelcolor='none', top=False, bottom=False, left=False,
+                        right=False)
+        ax.text(
+            0.5, 0.5,
+            "No triggers above threshold in this detector",
+            horizontalalignment='center',
+            verticalalignment='center',
+        )
+        logging.info(f"Saving {oput_plot}")
+        # Save initial logging level
+        logger.setLevel(logging.WARNING)
+        fig.savefig(oput_plot)
+        logger.setLevel(init_level)
+
+        continue
 
     # Keep track of some maxima for use in setting the plot limits
     maxstat = stats[ifo].max()
     max_rate = 0
 
-    fig, ax = plt.subplots(1)
-
-    plotbins = np.linspace(fit_threshold, 1.05 * maxstat)
+    plotbins = np.linspace(fit_threshold, 1.05 * maxstat, 400)
 
     logging.info("Putting events into bins")
     event_bin = np.array([tbins[d] for d in durations[ifo]])
 
-    for bin_num, lower_upper in enumerate(zip(duration_bin_edges[:-1],
-                                              duration_bin_edges[1:])):
+    for bin_num, lower_upper in enumerate(zip(tbins.lower(), tbins.upper())):
         lower, upper = lower_upper
         binlabel = f"{lower:.3g} - {upper:.3g}"
 
         inbin = event_bin == bin_num
         # Skip if there are no triggers in this bin in this IFO
-        if not any(inbin): continue
+        if not any(inbin):
+            continue
         binned_sngl_stats = stats[ifo][event_bin == bin_num]
 
         # Histogram the triggers
@@ -136,34 +147,39 @@ for ifo in ifos:
 
         max_rate = max(max_rate, cum_rate[0])
 
-        cum_fit = counts[ifo][bin_num] / live_time[ifo] * \
-                      trstats.cum_fit(fit_function, plotbins,
-                                      alphas[ifo][bin_num], fit_threshold)
+        ecf = eval_cum_fit(
+            fit_function,
+            plotbins,
+            alphas[ifo][bin_num],
+            fit_threshold
+        )
+        cum_fit = counts[ifo][bin_num] / live_time[ifo] * ecf
 
-        # Get the colour from the centre of the bin vs the full range
-        # of all bins
-        bin_prop = bin_proportion(upper, lower,
-                                  log_spacing=args.log_colormap)
+        bin_prop = bin_num / len(tbins)
         bin_colour = plt.get_cmap(args.colormap)(bin_prop)
         ax.plot(edges[:-1], cum_rate, linewidth=2,
                 color=bin_colour, label=binlabel, alpha=0.6)
         ax.plot(plotbins, cum_fit, "--", color=bin_colour,
                 label=r"$\alpha = $%.2f" % alphas[ifo][bin_num])
-    oput_plot = args.output_plot_name_format.format(ifo=ifo)
     ax.semilogy()
     ax.grid()
-    x_upper = args.x_lim_upper or 1.05 * maxstat
-    y_upper = args.y_lim_upper or 1.5 * max_rate
-    ax.set_xlim(fit_threshold, x_upper)
-    ax.set_ylim(0.5 / live_time[ifo], y_upper)
+    ax.set_xlim(
+        fit_threshold if args.x_lim_lower is None else args.x_lim_lower,
+        1.05 * maxstat if args.x_lim_upper is None else args.x_lim_upper
+    )
+    ax.set_ylim(
+        0.5 / live_time[ifo] if args.y_lim_lower is None else args.y_lim_lower,
+        1.5 * max_rate if args.y_lim_upper is None else args.y_lim_upper
+    )
     ax.set_xlabel(sngl_ranking)
     ax.set_ylabel("Number of louder triggers per live time")
     title = f"{ifo} {analysis_date} trigger fits"
     ax.set_title(title)
-    ax.legend(loc='upper right')
+    ax.legend(loc='center left', bbox_to_anchor=(1.01, 0.5))
     logging.info(f"Saving {oput_plot}")
     # Save initial logging level
     logger.setLevel(logging.WARNING)
-    fig.savefig(oput_plot)
+    fig.savefig(oput_plot, bbox_inches="tight")
     logger.setLevel(init_level)
-    
+
+logging.info("Done")