Various tweaks to plots and scripts

- Logging: Using loguru, but removing the pint.logging dependency (I copied the pint.logging format, but not the custom filters). #84
- ENG plots:  changed name of reset rate issue #89
- SCI plots:  small changes to displayed information #88 and #14
- BKG plots: small changes (marker size, grid lines, etc) #90
- GTI sorting script:  dumps the optimal profile to a text file with option --save_profile

nicer/eng_plots.py

@@ -29,7 +29,7 @@ def eng_plots(etable, args, mktable, filttable, gtitable):
 
     # RESET RATE PER DETECTOR
     if mktable is not None:
-        log.info("Computing reset rates")
+        log.info("Computing undershoot-only reset rate")
         plot.subplot(sci_grid[:2, 2:4])
         reset_rates = calc_nresets(mktable, IDS) / etable.meta["EXPOSURE"]
         if reset_rates is not None:

nicer/plotutils.py

@@ -881,16 +881,18 @@ def plot_angles(mktable, gtitable):
     goodtime, moonangle, cc = convert_to_elapsed_goodtime(met, moon, gtitable)
     goodtime, elvangle, cc = convert_to_elapsed_goodtime(met, elv, gtitable)
 
-    plot.scatter(goodtime, sunangle, marker=".", color="y", alpha=0.5, label="Sun")
+    plot.scatter(goodtime, sunangle, marker=".", s=3, color="y", alpha=0.5, label="Sun")
     plot.scatter(
-        goodtime, earthangle, marker=".", color="b", alpha=0.5, label="Bright Earth"
+        goodtime, earthangle, marker=".", s=3, color="b", alpha=0.5, label="Bright Earth"
     )
-    plot.scatter(goodtime, moonangle, marker=".", color="grey", alpha=0.5, label="Moon")
-    plot.scatter(goodtime, elvangle, marker=".", color="m", alpha=0.5, label="ELV")
+    plot.scatter(goodtime, moonangle, marker=".", s=3, color="grey", alpha=0.5, label="Moon")
+    plot.scatter(goodtime, elvangle, marker=".", s=3, color="m", alpha=0.5, label="ELV")
     plot.legend(loc=2)
     plot.ylim((0.0, 180.0))
     plot.grid(True)
     plot.yticks([0.0, 45.0, 90.0, 135.0, 180.0])
+    plot.minorticks_on()
+    plot.grid(which='minor', axis='y', linewidth=0.5, alpha=0.4)
     plot.ylabel("Angle (deg)")
 
     return
@@ -963,15 +965,18 @@ def plot_cor(mktable, gtitable):
         c=np.fmod(cc, len(colornames)),
         norm=norm,
         cmap=cmap,
-        marker="^",
+        marker=".",
+        s=3,
         label="COR_SAX",
     )
     # plot.scatter(time, lon, c = colors, cmap = cmap, marker = '_', label = 'Longitude')
     plot.legend(loc=2)
     plot.ylim((0.0, 20.0))
-    plot.axhline(5.0, linestyle="--", color="r")
+    plot.axhline(1.5, linestyle="--", color="r")
     plot.xlabel("Elapsed Time (s)", labelpad=1)
     plot.grid(True)
+    plot.minorticks_on()
+    plot.grid(which='minor', axis='y', linewidth=0.5, alpha=0.3)
     plot.ylabel("GeV")
     return
 
@@ -1004,7 +1009,7 @@ def calc_nresets(mktable, IDS):
 def plot_resetrate(IDS, reset_rates):
     "Plots reset rates"
     reset = plot.bar(IDS, reset_rates, width=0.85)
-    plot.title("Reset Rate by Detector")
+    plot.title("Undershoot-only reset rate by Detector")
     plot.ylabel("Reset Rate [Hz]")
     plot.xlabel("DET_ID")
     # plot.ylim([0, np.max(reset_rates)+2])

nicer/sci_plots.py

@@ -85,23 +85,50 @@ def sci_plots(etable, gtitable, args):
     plt.figtext(
         0.07,
         0.93,
-        "Start time is {0}, End time is {1}".format(tstart.iso, tend.iso),
+        "Start time: {0} - End time: {1}".format(tstart.iso, tend.iso),
         fontsize=10,
     )
     plt.figtext(
         0.07,
         0.90,
-        "Exposure is {0:.1f} s, Good time fraction is {1:.3f}".format(
+        "Total clock time between start and stop: {0:.1f} s".format(
+            float(etable.meta["TSTOP"]) - float(etable.meta["TSTART"])
+        ),
+        fontsize=10,
+    )
+    plt.figtext(
+        0.07,
+        0.87,
+        "Exposure: {0:.1f} s   -->   Coverage fraction is {1:.3f}".format(
             exposure, fraction
         ),
         fontsize=10,
     )
-    plt.figtext(0.07, 0.87, "Mean count rate {0:.3f} c/s".format(meanrate), fontsize=10)
+    plt.figtext(0.07, 0.84, "Mean count rate:  {0:.3f} c/s".format(meanrate), fontsize=10)
     # plt.figtext(.07, .84, etable.meta['FILT_STR'], fontsize=10)
     if args.mask:
         plt.figtext(0.07, 0.81, "IDS {0} are masked".format(args.mask), fontsize=10)
-    plt.figtext(0.5, 0.77, str(gtitable["START"][:]), fontsize=9)
-    plt.figtext(0.58, 0.77, str(gtitable["STOP"][:]), fontsize=9)
-    plt.figtext(0.66, 0.77, str(gtitable["DURATION"][:]), fontsize=9)
+
+    stringtable_start = str(gtitable["START"][:]).split('\n')
+    stringtable_stop = str(gtitable["STOP"][:]).split('\n')
+    stringtable_duration = str(gtitable["DURATION"][:]).split('\n')
+
+    # Bit of formatting of the duration table
+    stringtable_duration[0:2] = ["  {}".format(i) for i in stringtable_duration[0:2]]
+    stringtable_duration[2] = "---{}".format(stringtable_duration[2])
+    stringtable_duration[3:] = ["  {}".format(i) for i in stringtable_duration[3:]]
+
+    # omits GTIs in the display table if there are more than 7 (the first 3 lines are for the table header)
+    if len(stringtable_start)> 10:
+        stringtable_start = stringtable_start[0:6] + ['...'] + stringtable_start[-3:]
+        stringtable_stop = stringtable_stop[0:6] + ['...'] + stringtable_stop[-3:]
+        stringtable_duration = stringtable_duration[0:6] + ['({:9.1f})'.format(np.sum(list(map(float, stringtable_duration[7:-3]))))] + stringtable_duration[-3:]
+    stringtable_start ='\n'.join(stringtable_start)
+    stringtable_stop ='\n'.join(stringtable_stop)
+    stringtable_duration ='\n'.join(stringtable_duration)
+
+    plt.figtext(0.5, 0.77, stringtable_start, fontsize=10, fontname='Courier')
+    plt.figtext(0.58, 0.77, stringtable_stop, fontsize=10, fontname='Courier')
+    plt.figtext(0.66, 0.77, stringtable_duration, fontsize=10, fontname='Courier')
 
     return figure2

scripts/ni_Htest_sortgti.py

@@ -123,6 +123,13 @@
     action="store_true",
     default=False,
 )
+
+parser.add_argument(
+    "--save_profile",
+    help="export optimal profile as ascii file",
+    action="store_true",
+    default=False,
+)
 parser.add_argument(
     "--usez",
     help="Use Z^2_2 test instead of H test.",
@@ -811,6 +818,12 @@ def make_sn(data, rate=0.1, usez=False, snonly=False, minexp=None):
     )
     log.info("   for {} events".format(len(select_ph)))
 
+if args.save_profile:
+    output_data = np.array([bbins - (0.5 / nbins), fullprof, fullprof**0.5]).T
+    np.savetxt("{}_profile.txt".format(args.outfile),
+               output_data,
+               header='Phase      Counts     ErrorBar')
+
 # output summary results to text file
 a50 = int(round(len(gti_rts_s) * 0.5))
 a90 = int(round(len(gti_rts_s) * 0.9))

scripts/nicerql.py

@@ -1,9 +1,9 @@
 #!/usr/bin/env python
 import os, sys
-import pint.logging
+#import pint.logging
 from loguru import logger as log
 
-pint.logging.setup(level=pint.logging.script_level)
+#pint.logging.setup(level=pint.logging.script_level)
 
 
 # Hack to add this to pythonpath
@@ -165,8 +165,8 @@
     sys.stderr,
     level=args.loglevel,
     colorize=True,
-    format=pint.logging.format,
-    filter=pint.logging.LogFilter(),
+    format='<level>{level: <8}</level> ({name: <30}): <level>{message}</level>'
+    #filter=pint.logging.LogFilter(),
 )
 
 # ------------------------------Getting the data and concatenating------------------------------
@@ -534,7 +534,7 @@
 
 # Map plot is overshoot and undershoot rates on maps
 if args.map:
-    log.info("I'M THE MAP I'M THE MAP I'M THE MAAAAP")
+    #log.info("I'M THE MAP I'M THE MAP I'M THE MAAAAP")
     # if eventovershoots is not None:
     #     figure3 = cartography(hkmet, eventovershoots, args, eventundershoots,
     #         filttable, mktable, gtitable)

scripts/photon_toa.py

@@ -34,10 +34,10 @@
 from pint.observatory import get_observatory
 from pint.observatory.special_locations import T2SpacecraftObs
 
-import pint.logging
+#import pint.logging
 from loguru import logger as log
 
-pint.logging.setup(level=pint.logging.script_level)
+#pint.logging.setup(level=pint.logging.script_level)
 
 
 def local_load_NICER_TOAs(eventname):

scripts/psrpipe.py

@@ -1,9 +1,9 @@
 #!/usr/bin/env python
 import os, sys
-import pint.logging
+#import pint.logging
 from loguru import logger as log
 
-pint.logging.setup(level=pint.logging.script_level)
+#pint.logging.setup(level=pint.logging.script_level)
 
 import numpy as np
 import argparse
@@ -182,8 +182,8 @@
     sys.stderr,
     level=args.loglevel,
     colorize=True,
-    format=pint.logging.format,
-    filter=pint.logging.LogFilter(),
+    format='<level>{level: <8}</level> ({name: <30}): <level>{message}</level>'
+    #filter=pint.logging.LogFilter(),
 )