Merge pull request #7 from jzuhone/fix_thermal_models

MANIFEST.in

@@ -1,2 +1 @@
-include versioneer.py
-include acispy/_version.py
+include acispy/tests/*

acispy/__init__.py

@@ -11,6 +11,14 @@
     HistogramPlot, make_dateplots, DummyDatePlot
 from acispy.thermal_models import SimulateECSRun, \
     ThermalModelRunner, ThermalModelFromLoad, \
-    ThermalModelFromRun, SimulateSingleObs
+    ThermalModelFromRun, SimulateSingleState
 from acispy.load_review import ACISLoadReview
 
+
+def test(*args, **kwargs):
+    """
+    Run py.test unit tests.
+    """
+    import testr
+    return testr.test(*args, **kwargs)
+

acispy/dataset.py

@@ -69,29 +69,29 @@ def _determine_field(self, field):
         if field not in self._checked_fields:
             if isinstance(field, tuple):
                 if len(field) != 2:
-                    raise RuntimeError("Invalid field specification {}!".format(field))
+                    raise RuntimeError(f"Invalid field specification {format}!")
                 fd = (field[0].lower(), field[1].lower())
                 if fd in self.fields:
                     checked_field = fd
                 else:
-                    raise RuntimeError("Cannot find field {}!".format(field))
+                    raise RuntimeError(f"Cannot find field {field}!")
             elif isinstance(field, str):
                 fd = field.lower()
                 candidates = []
                 for ftype in self.fields.types:
                     if (ftype, fd) in self.fields:
                         candidates.append((ftype, fd))
                 if len(candidates) > 1:
-                    msg = "Multiple field types for field name %s!\n" % field
+                    msg = f"Multiple field types for field name {field}!\n"
                     for c in candidates:
-                        msg += "    {}\n".format(c)
+                        msg += f"    {c}\n"
                     raise RuntimeError(msg)
                 elif len(candidates) == 0:
-                    raise RuntimeError("Cannot find field {}!".format(field))
+                    raise RuntimeError(f"Cannot find field {field}!")
                 else:
                     checked_field = candidates[0]
             else:
-                raise RuntimeError("Invalid field specification {}!".format(field))
+                raise RuntimeError(f"Invalid field specification {field}!")
         else:
             checked_field = field
         return checked_field
@@ -132,7 +132,7 @@ def write_hdf5(self, filename, overwrite=True):
         import h5py
         import os
         if os.path.exists(filename) and not overwrite:
-            raise IOError("The file %s already exists and overwrite=False!!" % filename)
+            raise IOError(f"The file {filename} already exists and overwrite=False!!")
         f = h5py.File(filename, "w")
         if not self.msids._is_empty:
             gmsids = f.create_group("msids")
@@ -348,8 +348,8 @@ def write_msids(self, filename, fields, mask=None, overwrite=False):
                                        "but '%s', '%s' does not have the same " % field +
                                        "set of times as '%s', '%s'!" % (fields[0][0], fields[0][1]))
         data = dict(("_".join(k), self[k].value[mask]) for k in fields)
-        data["times"] = self.times(*fields[0]).value[mask]
-        data["dates"] = self.dates(*fields[0])[mask]
+        data["time"] = self.times(*fields[0]).value[mask]
+        data["date"] = self.dates(*fields[0])[mask]
         Table(data).write(filename, format='ascii', overwrite=overwrite)
 
     def write_states(self, filename, overwrite=False):

acispy/fields.py

@@ -31,8 +31,8 @@ def __init__(self, dfield, ofields):
         self.ofields = ofields
 
     def __str__(self):
-        return ("Derived field {} depends on the following ".format(self.dfield) +
-                "fields which are not found in this Dataset: {} ".format(self.ofields))
+        return (f"Derived field {self.dfield} depends on the following "
+                f"fields which are not found in this Dataset: {self.ofields} ")
 
 
 class OutputFieldFunction(object):
@@ -162,9 +162,9 @@ def _simpos(ds):
     if "earth_solid_angle" in dset.msids.derived_msids:
         def _earth_solid_angle(ds):
             # Collect individual MSIDs for use in calc_earth_vis()
-            ephem_xyzs = [ds["msids", "orbitephem0_{}".format(x)]
+            ephem_xyzs = [ds["msids", f"orbitephem0_{x}"]
                           for x in "xyz"]
-            aoattqt_1234s = [ds["msids","aoattqt{}".format(x)]
+            aoattqt_1234s = [ds["msids",f"aoattqt{x}"]
                              for x in range(1, 5)]
             ephems = np.array([x.value for x in ephem_xyzs]).transpose()
             q_atts = np.array([x.value for x in aoattqt_1234s]).transpose()

acispy/load_review.py

@@ -91,10 +91,10 @@ def __init__(self, load_name, get_msids=True, tl_file=None):
         self.load_name = find_load(load_name)
         self.load_letter = self.load_name[-1]
         self.load_week = self.load_name[:7]
-        self.load_year = "20%s" % self.load_week[5:7]
+        self.load_year = f"20{self.load_week[5:7]}"
         self.next_year = str(int(self.load_year)+1)
         loaddir = os.path.join(lr_root, self.load_year, self.load_week)
-        oflsdir = os.path.join(loaddir, "ofls%s" % self.load_letter.lower())
+        oflsdir = os.path.join(loaddir, f"ofls{self.load_letter.lower()}")
         self.load_file = os.path.join(oflsdir, lr_file)
         self.events = defaultdict(dict)
         self.start_status = self._get_start_status()
@@ -290,7 +290,7 @@ def __getattr__(self, item):
         if item in self.events:
             return LoadReviewEvent(item, self.events[item])
         else:
-            raise AttributeError("'LoadReview' object has no attribute '%s'" % item)
+            raise AttributeError(f"'LoadReview' object has no attribute '{item}'")
 
     def _add_annotations(self, plot, annotations, tbegin, tend):
         for i, line in enumerate(plot.ax.lines):

acispy/model.py

@@ -67,27 +67,27 @@ def from_xija(cls, model, components, interp_times=None, masks=None):
     def from_load_page(cls, load, components, time_range=None):
         components = [comp.lower() for comp in components]
         load = find_load(load)
-        mylog.info("Reading model data from the %s load." % load)
+        mylog.info(f"Reading model data from the {load} load.")
         components = ensure_list(components)
         if "fptemp_11" in components:
             components.append("earth_solid_angle")
         data = {}
         for comp in components:
             if comp == "earth_solid_angle":
                 url = "http://cxc.cfa.harvard.edu/acis/FP_thermPredic/"
-                url += "%s/ofls%s/earth_solid_angles.dat" % (load[:-1].upper(), load[-1].lower())
+                url += f"{load[:-1].upper()}/ofls{load[-1].lower()}/earth_solid_angles.dat"
                 table_key = comp
             else:
                 c = comp_map[comp].upper()
                 table_key = "fptemp" if comp == "fptemp_11" else comp
-                url = "http://cxc.cfa.harvard.edu/acis/%s_thermPredic/" % c
-                url += "%s/ofls%s/temperatures.dat" % (load[:-1].upper(), load[-1].lower())
+                url = f"http://cxc.cfa.harvard.edu/acis/{c}_thermPredic/"
+                url += f"{load[:-1].upper()}/ofls{load[-1].lower()}/temperatures.dat"
             u = requests.get(url)
             if not u.ok:
                 if table_key == "earth_solid_angle":
                     mylog.warning("Could not find the earth solid angles file. Skipping.")
                 else:
-                    mylog.warning("Could not find the model page for '%s'. Skipping." % comp)
+                    mylog.warning(f"Could not find the model page for '{comp}'. Skipping.")
                 continue
             table = ascii.read(u.text)
             if time_range is None:

acispy/msids.py

@@ -118,7 +118,7 @@ def from_mit_file(cls, filename, tbegin=None, tend=None):
         bmask = masks["bilevels"]
         bilevels = np.char.strip(table["bilevels"], "b")[bmask]
         for i in range(8):
-            key = "1stat%dst" % (7-i)
+            key = f"1stat{7-i}dst"
             table[key] = np.array(["BAD"]*bmask.size)
             table[key][bmask] = np.array([b[i] for b in bilevels])
             times[key] = times["bilevels"]

acispy/plots.py

@@ -15,6 +15,8 @@
 import numpy as np
 from astropy.units import Quantity
 
+datefmt = "%Y-%m-%d %H:%M:%S.%f"
+
 drawstyles = {"simpos": "steps",
               "pitch": "steps",
               "ccd_count": "steps",
@@ -195,6 +197,8 @@ def get_figure(plot, fig, subplot, figsize):
         if hasattr(plot, "ax2"):
             ax2 = plot.ax2
             lines2 = plot.lines2
+    for axis in ['top', 'bottom', 'left', 'right']:
+        ax.spines[axis].set_linewidth(2)
     return fig, ax, lines, ax2, lines2
 
 
@@ -235,10 +239,12 @@ def __init__(self, dates, values, fmt='-b', lw=2, fontsize=18, ls='-',
             x = np.asarray(dates)
             y = np.asarray(values)
         if color is None:
-            color = "C{}".format(len(lines))
+            color = f"C{len(lines)}"
         ticklocs, fig, ax = plot_cxctime(x, y, fmt=fmt, fig=fig, ax=ax, 
                                          lw=lw, ls=ls, color=color, **kwargs)
         super(CustomDatePlot, self).__init__(fig, ax, lines, ax2, lines2)
+        self.ax.tick_params(which="major", width=2, length=6)
+        self.ax.tick_params(which="minor", width=2, length=3)
         self.lines.append(ax.lines[-1])
         self.ax.set_xlabel("Date", fontdict={"size": fontsize})
         fontProperties = font_manager.FontProperties(size=fontsize)
@@ -287,6 +293,8 @@ def plot_right(self, dates, values, fmt='-b', lw=2, fontsize=18,
             y = np.asarray(values)
         plot_cxctime(x, y, fmt=fmt, fig=self.fig,
                      ax=self.ax2, ls=ls, color=color, lw=lw, **kwargs)
+        self.ax2.tick_params(which="major", width=2, length=6)
+        self.ax2.tick_params(which="minor", width=2, length=3)
         fontProperties = font_manager.FontProperties(size=fontsize)
         for label in self.ax2.get_xticklabels():
             label.set_fontproperties(fontProperties)
@@ -303,9 +311,9 @@ def set_xlim(self, xmin, xmax):
         >>> p.set_xlim("2016:050:12:45:47.324", "2016:056:22:32:01.123")
         """
         if not isinstance(xmin, datetime):
-            xmin = datetime.strptime(DateTime(xmin).iso, "%Y-%m-%d %H:%M:%S.%f")
+            xmin = datetime.strptime(DateTime(xmin).iso, datefmt)
         if not isinstance(xmax, datetime):
-            xmax = datetime.strptime(DateTime(xmax).iso, "%Y-%m-%d %H:%M:%S.%f")
+            xmax = datetime.strptime(DateTime(xmax).iso, datefmt)
         self.ax.set_xlim(xmin, xmax)
 
     def add_hline(self, y, lw=2, ls='-', color='green', 
@@ -333,11 +341,11 @@ def add_hline(self, y, lw=2, ls='-', color='green',
         if xmin is None:
             xmin = 0
         else:
-            xmin = datetime.strptime(DateTime(xmin).iso, "%Y-%m-%d %H:%M:%S.%f")
+            xmin = datetime.strptime(DateTime(xmin).iso, datefmt)
         if xmax is None:
             xmax = 1
         else:
-            xmax = datetime.strptime(DateTime(xmax).iso, "%Y-%m-%d %H:%M:%S.%f")
+            xmax = datetime.strptime(DateTime(xmax).iso, datefmt)
         self.ax.axhline(y=y, lw=lw, ls=ls, color=color, xmin=xmin,
                         xmax=xmax, label='_nolegend_', **kwargs)
 
@@ -363,7 +371,7 @@ def add_vline(self, time, lw=2, ls='solid', color='green', **kwargs):
         --------
         >>> p.add_vline("2016:101:12:36:10.102", lw=3, ls='dashed', color='red')
         """
-        time = datetime.strptime(DateTime(time).iso, "%Y-%m-%d %H:%M:%S.%f")
+        time = datetime.strptime(DateTime(time).iso, datefmt)
         self.ax.axvline(x=time, lw=lw, ls=ls, color=color, **kwargs, 
                         label='_nolegend_')
 
@@ -393,7 +401,7 @@ def add_text(self, time, y, text, fontsize=18, color='black',
         >>> dp.add_text("2016:101:12:36:10.102", 35., "Something happened here!",
         ...             fontsize=15, color='magenta')
         """
-        time = datetime.strptime(DateTime(time).iso, "%Y-%m-%d %H:%M:%S.%f")
+        time = datetime.strptime(DateTime(time).iso, datefmt)
         self.ax.text(time, y, text, fontsize=fontsize, color=color,
                      rotation=rotation, **kwargs)
 
@@ -701,17 +709,20 @@ def __init__(self, ds, fields, field2=None, fmt='-b', lw=2, ls='-',
         self.ax.set_ylim(ymin, ymax)
         if self.num_fields > 0:
             units = ds.fields[self.fields[0]].units
+            ulabel = unit_labels.get(units, units)
             if self.num_fields > 1:
                 if units == '':
                     ylabel = ''
                 else:
-                    ylabel = '%s (%s)' % (units_map[units], unit_labels.get(units, units))
+                    ylabel = f"{units_map[units]} ({ulabel})"
                 self.set_ylabel(ylabel)
             else:
                 ylabel = ds.fields[self.fields[0]].display_name
                 if units != '':
-                    ylabel += ' (%s)' % unit_labels.get(units, units)
+                    ylabel += f" ({ulabel})"
                 self.set_ylabel(ylabel)
+        self.ax.tick_params(which="major", width=2, length=6)
+        self.ax.tick_params(which="minor", width=2, length=3)
         if field2 is not None:
             field2 = ds._determine_field(field2)
             self.field2 = field2
@@ -720,6 +731,8 @@ def __init__(self, ds, fields, field2=None, fmt='-b', lw=2, ls='-',
                 self.ax2 = self.ax.twinx()
                 self.ax2.set_zorder(-10)
                 self.ax.patch.set_visible(False)
+            self.ax2.tick_params(which="major", width=2, length=6)
+            self.ax2.tick_params(which="minor", width=2, length=3)
             drawstyle = drawstyles.get(fd2, None)
             state_codes = ds.state_codes.get(field2, None)
             if not plot_bad:
@@ -759,8 +772,9 @@ def __init__(self, ds, fields, field2=None, fmt='-b', lw=2, ls='-',
             self.ax2.set_ylim(ymin2, ymax2)
             units2 = ds.fields[field2].units
             ylabel2 = ds.fields[field2].display_name
+            ulabel2 = unit_labels.get(units2, units2)
             if units2 != '':
-                ylabel2 += ' (%s)' % unit_labels.get(units2, units2)
+                ylabel2 += f" ({ulabel2})"
             self.set_ylabel2(ylabel2)
         else:
             self.field2 = None
@@ -1087,8 +1101,9 @@ def _annotate_plot(self, fontsize, density, cumulative):
             label.set_fontproperties(fontProperties)
         for label in self.ax.get_yticklabels():
             label.set_fontproperties(fontProperties)
+        ulabel = unit_labels.get(self.unit, self.unit)
         if self.unit != '':
-            self.xlabel += ' (%s)' % unit_labels.get(self.unit, self.unit)
+            self.xlabel += f" ({ulabel})" 
         self.ax.set_xlabel(self.xlabel, fontsize=18)
         if density:
             self.ylabel = "Fraction of Time"
@@ -1128,10 +1143,12 @@ def _annotate_plot(self, fontsize):
             label.set_fontproperties(fontProperties)
         for label in self.ax.get_yticklabels():
             label.set_fontproperties(fontProperties)
+        uxlabel = unit_labels.get(self.xunit, self.xunit)
+        uylabel = unit_labels.get(self.yunit, self.yunit)
         if self.xunit != '':
-            self.xlabel += ' (%s)' % unit_labels.get(self.xunit, self.xunit)
+            self.xlabel += f" ({uxlabel})"
         if self.yunit != '':
-            self.ylabel += ' (%s)' % unit_labels.get(self.yunit, self.yunit)
+            self.ylabel += f" ({uylabel})"
         self.set_xlabel(self.xlabel)
         self.set_ylabel(self.ylabel)
         return fontProperties
@@ -1302,7 +1319,8 @@ def __init__(self, ds, x_field, y_field, c_field=None,
             clabel = self.ds.fields[c_field].display_name
             cunit = self.ds.fields[c_field].units
             if cunit != '':
-                clabel += ' (%s)' % unit_labels.get(cunit, cunit)
+                uclabel = unit_labels.get(cunit, cunit)
+                clabel += f" ({uclabel})"
             divider = make_axes_locatable(self.ax)
             cax = divider.append_axes("right", size="5%", pad=0.05)
             cb = plt.colorbar(self.pp, cax=cax)

acispy/states.py

@@ -33,6 +33,12 @@ def __init__(self, table):
         new_table = OrderedDict()
         if isinstance(table, np.ndarray):
             state_names = list(table.dtype.names)
+            if "date" in state_names:
+                table = rf.append_fields(
+                    table, ['time'],
+                    [date2secs(table["date"])],
+                    usemask=False
+                )
             if "tstart" not in state_names:
                 table = rf.append_fields(
                     table, ["tstart", "tstop"],
@@ -46,7 +52,10 @@ def __init__(self, table):
                 table["tstart"] = date2secs(table["datestart"])
                 table["tstop"] = date2secs(table["datestop"])
                 state_names += ["tstart", "tstop"]
-        times = Quantity([table["tstart"], table["tstop"]], "s")
+        if "tstart" in state_names:
+            times = Quantity([table["tstart"], table["tstop"]], "s")
+        else:
+            times = Quantity(table["time"], "s")
         for k in state_names:
             v = np.asarray(table[k])
             if k == "trans_keys" and v.dtype.char == "O":
@@ -78,21 +87,11 @@ def from_kadi_states(cls, tstart, tstop, state_keys=None):
                               merge_identical=True).as_array()
         return cls(t)
 
-    @classmethod
-    def from_database(cls, tstart, tstop, state_keys=None, server=None):
-        from Chandra.cmd_states import fetch_states
-        tstart = get_time(tstart)
-        tstop = get_time(tstop)
-        if state_keys is not None:
-            state_keys = ensure_list(state_keys)
-        t = fetch_states(tstart, tstop, vals=state_keys, server=server)
-        return cls(t)
-
     @classmethod
     def from_load_page(cls, load, comp="DPA"):
         load = find_load(load)
-        url = "http://cxc.cfa.harvard.edu/acis/%s_thermPredic/" % comp
-        url += "%s/ofls%s/states.dat" % (load[:-1].upper(), load[-1].lower())
+        url = f"http://cxc.cfa.harvard.edu/acis/{comp}_thermPredic/"
+        url += f"{load[:-1].upper()}/ofls{load[-1].lower()}/states.dat"
         u = requests.get(url)
         t = ascii.read(u.text)
         table = dict((k, t[k].data) for k in t.keys())
@@ -111,16 +110,9 @@ def from_load_file(cls, states_file):
         return cls(table)
 
     @classmethod
-    def from_commands(cls, tstart, tstop, cmds=None, state_keys=None):
-        from kadi import commands
+    def from_commands(cls, cmds, state_keys=None):
         from kadi.commands import states
-        tstart = get_time(tstart)
-        tstop = get_time(tstop)
-        if cmds is None:
-            cmds = commands.get_cmds(tstart, tstop)
-        continuity = states.get_continuity(tstart, state_keys)
-        t = states.get_states(cmds=cmds, continuity=continuity,
-                              state_keys=state_keys,
+        t = states.get_states(cmds=cmds, state_keys=state_keys,
                               merge_identical=True).as_array()
         return cls(t)