Merge pull request #91 from sot/shiny

Shiny

pytest.ini

@@ -0,0 +1,7 @@
+[pytest]
+filterwarnings =
+    # See https://github.com/numpy/numpy/issues/11788 for why this is benign
+    ignore:numpy.ufunc size changed:RuntimeWarning
+    ignore:the imp module is deprecated in favour of importlib:DeprecationWarning
+    ignore:parse functions are required to provide a named argument:PendingDeprecationWarning
+norecursedirs = .* alt_core build ctypes_example dist doc examples GUI_play ipynb models* nmass* pyside tests_no_pytest tmp twodof www

xija/component/experimental.py

@@ -95,7 +95,7 @@ class SolarHeatSimZ(SolarHeat):
     """Solar heating (pitch and SimZ dependent)"""
     def __init__(self, model, node, simz_comp, pitch_comp, eclipse_comp=None,
                  P_pitches=None, Ps=None, dPs=None, var_func='exp',
-                 tau=1732.0, ampl=0.05, bias=0.0, epoch='2010:001',
+                 tau=1732.0, ampl=0.05, bias=0.0, epoch='2010:001:12:00:00',
                  hrci_bias=0.0, hrcs_bias=0.0, acisi_bias=0.0):
         SolarHeat.__init__(self, model, node, pitch_comp, eclipse_comp,
                            P_pitches, Ps, dPs, var_func, tau, ampl, bias,

xija/component/heat.py

@@ -117,7 +117,7 @@ class SolarHeat(PrecomputedHeatPower):
     """
     def __init__(self, model, node, pitch_comp, eclipse_comp=None,
                  P_pitches=None, Ps=None, dPs=None, var_func='exp',
-                 tau=1732.0, ampl=0.05, bias=0.0, epoch='2010:001'):
+                 tau=1732.0, ampl=0.05, bias=0.0, epoch='2010:001:12:00:00'):
         ModelComponent.__init__(self, model)
         self.node = self.model.get_comp(node)
         self.pitch_comp = self.model.get_comp(pitch_comp)
@@ -283,10 +283,10 @@ def plot_solar_heat__pitch(self, fig, ax):
 class SolarHeatMulplicative(SolarHeat):
     def __init__(self, model, node, pitch_comp, eclipse_comp=None,
                  P_pitches=None, Ps=None, dPs=None, var_func='exp',
-                 tau=1732.0, ampl=0.0334, bias=0.0, epoch='2010:001'):
+                 tau=1732.0, ampl=0.0334, bias=0.0, epoch='2010:001:12:00:00'):
         super(SolarHeatMulplicative, self).__init__(
             model, node, pitch_comp, eclipse_comp=eclipse_comp,
-            P_pitches=P_pitches, Ps=Ps, dPs=dPs, var_func=var_func, 
+            P_pitches=P_pitches, Ps=Ps, dPs=dPs, var_func=var_func,
             tau=tau, ampl=ampl, bias=bias, epoch=epoch)
 
     def _compute_dvals(self):
@@ -316,7 +316,7 @@ class SolarHeatAcisCameraBody(SolarHeat):
     """
     def __init__(self, model, node, pitch_comp, eclipse_comp=None,
                  P_pitches=None, Ps=None, dPs=None, var_func='exp',
-                 tau=1732.0, ampl=0.05, bias=0.0, epoch='2010:001',
+                 tau=1732.0, ampl=0.05, bias=0.0, epoch='2010:001:12:00:00',
                  dh_heater_comp=None, dh_heater_bias=0.0):
 
         super(SolarHeatAcisCameraBody, self).__init__(
@@ -353,7 +353,7 @@ class SolarHeatHrc(SolarHeat):
     """
     def __init__(self, model, node, simz_comp, pitch_comp, eclipse_comp=None,
                  P_pitches=None, Ps=None, dPs=None, var_func='exp',
-                 tau=1732.0, ampl=0.05, bias=0.0, epoch='2010:001',
+                 tau=1732.0, ampl=0.05, bias=0.0, epoch='2010:001:12:00:00',
                  hrc_bias=0.0):
         SolarHeat.__init__(self, model, node, pitch_comp, eclipse_comp,
                            P_pitches, Ps, dPs, var_func, tau, ampl, bias,
@@ -391,7 +391,7 @@ class SolarHeatHrcOpts(SolarHeat):
     """
     def __init__(self, model, node, simz_comp, pitch_comp, eclipse_comp=None,
                  P_pitches=None, Ps=None, dPs=None, var_func='exp',
-                 tau=1732.0, ampl=0.05, bias=0.0, epoch='2010:001',
+                 tau=1732.0, ampl=0.05, bias=0.0, epoch='2010:001:12:00:00',
                  hrci_bias=0.0, hrcs_bias=0.0):
         SolarHeat.__init__(self, model, node, pitch_comp, eclipse_comp,
                            P_pitches, Ps, dPs, var_func, tau, ampl, bias,
@@ -415,12 +415,12 @@ def dvals_post_hook(self):
 class SolarHeatHrcMult(SolarHeatHrcOpts, SolarHeatMulplicative):
     def __init__(self, model, node, simz_comp, pitch_comp, eclipse_comp=None,
                  P_pitches=None, Ps=None, dPs=None, var_func='exp',
-                 tau=1732.0, ampl=0.0334, bias=0.0, epoch='2010:001',
+                 tau=1732.0, ampl=0.0334, bias=0.0, epoch='2010:001:12:00:00',
                  hrci_bias=0.0, hrcs_bias=0.0):
         super(SolarHeatHrcMult, self).__init__(
             model, node, simz_comp, pitch_comp, eclipse_comp=eclipse_comp,
             P_pitches=P_pitches, Ps=Ps, dPs=dPs, var_func=var_func, tau=tau,
-            ampl=ampl, bias=bias, epoch=epoch, hrci_bias=hrci_bias, 
+            ampl=ampl, bias=bias, epoch=epoch, hrci_bias=hrci_bias,
             hrcs_bias=hrcs_bias)
 
 # For back compatibility prior to Xija 0.2
@@ -506,7 +506,10 @@ def dvals(self):
                           for x in ('x', 'y', 'z')]
             aoattqt_1234s = [getattr(self, 'aoattqt{}'.format(x))
                              for x in range(1, 5)]
-            ephems = np.array([x.dvals for x in ephem_xyzs]).transpose()
+            # Note: the copy() here is so that the array becomes contiguous in
+            # memory and allows numba to run faster (and avoids NumbaPerformanceWarning:
+            # np.dot() is faster on contiguous arrays).
+            ephems = np.array([x.dvals for x in ephem_xyzs]).transpose().copy()
             q_atts = np.array([x.dvals for x in aoattqt_1234s]).transpose()
 
             # Q_atts can have occasional bad values, maybe because the
@@ -608,7 +611,7 @@ class AcisPsmcSolarHeat(PrecomputedHeatPower):
     """Solar heating of PSMC box.  This is dependent on SIM-Z"""
     def __init__(self, model, node, pitch_comp, simz_comp, dh_heater_comp, P_pitches=None,
                  P_vals=None, dPs=None, var_func='linear',
-                 tau=1732.0, ampl=0.05, epoch='2013:001', dh_heater=0.05):
+                 tau=1732.0, ampl=0.05, epoch='2013:001:12:00:00', dh_heater=0.05):
         ModelComponent.__init__(self, model)
         self.n_mvals = 1
         self.node = self.model.get_comp(node)
@@ -833,7 +836,7 @@ class AcisDpaStatePower(PrecomputedHeatPower):
     state.  See dpa/NOTES.power.
     """
     def __init__(self, model, node, mult=1.0,
-                 fep_count=None, ccd_count=None, 
+                 fep_count=None, ccd_count=None,
                  vid_board=None, clocking=None,
                  pow_states=None):
         super(AcisDpaStatePower, self).__init__(model)
@@ -927,7 +930,7 @@ def plot_data__time(self, fig, ax):
         else:
             plot_cxctime(self.model.times, powers, ls='-',
                          color='#d92121', fig=fig, ax=ax)
-            plot_cxctime(self.model.times, self.dvals, 
+            plot_cxctime(self.model.times, self.dvals,
                          color='#386cb0', ls='-', fig=fig, ax=ax)
             ax.grid()
             ax.set_title('{}: model (red) and data (blue)'.format(self.name))

xija/model.py

@@ -18,15 +18,11 @@
 from . import component
 from . import tmal
 
-try:
-    # Optional packages for model fitting or use on HEAD LAN
-    from Chandra.Time import DateTime, date2secs
-    from astropy.io import ascii
-    import Ska.Numpy
-    import Chandra.cmd_states
-    import Ska.DBI
-except ImportError:
-    pass
+# Optional packages for model fitting or use on HEAD LAN
+from Chandra.Time import DateTime, date2secs
+from astropy.io import ascii
+import Ska.Numpy
+import Ska.DBI
 
 import pyyaks.context as pyc
 from .files import files as xija_files
@@ -73,9 +69,9 @@ class XijaModel(object):
     - ``evolve_method = 1`` uses the original ODE solver which treats every
       two steps as a full RK2 step.
     - ``evolve_method = 2`` uses the new ODE solver which treats every step
-      as a full RK2 step, and optionally allows for RK4 if ``rk4 = 1``.  
+      as a full RK2 step, and optionally allows for RK4 if ``rk4 = 1``.
     - Otherwise defaults are: ``name='xijamodel'``, ``start = stop - 45 days``,
-      ``stop = NOW - 30 days``, ``dt = 328 secs``, ``evolve_method = 1``, 
+      ``stop = NOW - 30 days``, ``dt = 328 secs``, ``evolve_method = 1``,
       ``rk4 = 0``
 
     :param name: model name
@@ -158,7 +154,7 @@ def _get_allowed_timestep(self, dt):
         """
         This method ensures that only certain timesteps are chosen,
         which are integer multiples of 8.2 and where 328.0/dt is an
-        integer. 
+        integer.
         """
         if dt > DEFAULT_DT:
             logger.warning("dt = %g s greater than upper "
@@ -218,23 +214,11 @@ def _eng_match_times(self, start, stop):
 
     def _get_cmd_states(self):
         if not hasattr(self, '_cmd_states'):
-            logger.info('Reading commanded states DB over %s to %s' %
+            import kadi.commands.states as kadi_states
+            logger.info('Getting kadi commanded states over %s to %s' %
                         (self.datestart, self.datestop))
-            for dbi in ('hdf5', 'sybase'):
-                try:
-                    states = Chandra.cmd_states.fetch_states(
-                        self.datestart, self.datestop, dbi=dbi)
-                    break
-                except IOError as err:
-                    logger.info('Warning: ' + str(err))
-                    pass
-            else:
-                # Both hdf5 and sybase failed
-                raise IOError('Could not read commanded states from '
-                              'HDF5 or sybase tables')
-
-            self._cmd_states = Chandra.cmd_states.interpolate_states(
-                states, self.times)
+            states = kadi_states.get_states(self.datestart, self.datestop)
+            self._cmd_states = kadi_states.interpolate_states(states, self.times).as_array()
 
         return self._cmd_states
 
@@ -591,7 +575,7 @@ def core_2(self):
             _core_2 = np.ctypeslib.load_library('core_2', loader_path)
             _core_2.calc_model_2.restype = ctypes.c_int
             _core_2.calc_model_2.argtypes = [
-                ctypes.c_int, ctypes.c_int, ctypes.c_int, 
+                ctypes.c_int, ctypes.c_int, ctypes.c_int,
                 ctypes.c_int, ctypes.c_double,
                 ctypes.POINTER(ctypes.POINTER(ctypes.c_double)),
                 ctypes.POINTER(ctypes.POINTER(ctypes.c_int)),

xija/tests/test_models.py

@@ -26,15 +26,9 @@ def abs_path(spec):
 
 
 def test_dpa_real():
-    mdl = ThermalModel('dpa', start='2012:001', stop='2012:007',
+    mdl = ThermalModel('dpa', start='2020:001:12:00:00', stop='2020:007:12:00:00',
                        model_spec=abs_path('dpa.json'))
-    # Check that cmd_states database can be read.  Skip if not, probably
-    # running test on a platform without access.
-    try:
-        mdl._get_cmd_states()
-    except:
-        pytest.skip('No commanded states access - '
-                    'cannot run DPA model with real states')
+    mdl._get_cmd_states()
 
     mdl.make()
     mdl.calc()
@@ -57,13 +51,9 @@ def test_pitch_clip():
     has been modified so the solarheat pitch range is from 55 .. 153.
     Make sure the model still runs with no interpolation error.
     """
-    mdl = ThermalModel('dpa', start='2012:001', stop='2012:007',
+    mdl = ThermalModel('dpa', start='2012:001:12:00:00', stop='2012:007:12:00:00',
                        model_spec=abs_path('dpa_clip.json'))
-    try:
-        mdl._get_cmd_states()
-    except:
-        pytest.skip('No commanded states access - '
-                    'cannot run DPA model with real states')
+    mdl._get_cmd_states()
 
     mdl.make()
     mdl.calc()
@@ -78,7 +68,7 @@ def test_pitch_range_clip():
     Make sure the pitch range stored does not include values outside of the 45
     to 180 degree range.
     """
-    mdl = ThermalModel('tank', start='2019:120', stop='2019:122',
+    mdl = ThermalModel('tank', start='2019:120:12:00:00', stop='2019:122:12:00:00',
                        model_spec=abs_path('pftank2t.json'))
 
     mdl.comp['pf0tank2t'].set_data(20.0)
@@ -91,15 +81,9 @@ def test_pitch_range_clip():
 
 
 def test_dpa_remove_pow():
-    mdl = ThermalModel('dpa', start='2012:001', stop='2012:007',
+    mdl = ThermalModel('dpa', start='2019:001:12:00:00', stop='2019:007:12:00:00',
                        model_spec=abs_path('dpa_remove_pow.json'))
-    # Check that cmd_states database can be read.  Skip if not, probably
-    # running test on a platform without access.
-    try:
-        mdl._get_cmd_states()
-    except:
-        pytest.skip('No commanded states access - '
-                    'cannot run DPA model with real states')
+    mdl._get_cmd_states()
 
     mdl.make()
     mdl.calc()
@@ -116,7 +100,7 @@ def test_dpa_remove_pow():
     assert np.allclose(dpa.mvals, regr['mvals'])
 
 def get_dpa_model():
-    mdl = ThermalModel('dpa', start='2012:001', stop='2012:007',
+    mdl = ThermalModel('dpa', start='2012:001:12:00:00', stop='2012:007:12:00:00',
                             model_spec=abs_path('dpa.json'))
     times = (mdl.times - mdl.times[0]) / 10000.0
     mdl.comp['1dpamzt'].set_data(30.0)
@@ -148,7 +132,7 @@ def test_dpa():
                  mvals=dpa.mvals)
 
     regr = np.load(reffile)
-    assert np.allclose(mdl.times, regr['times'])
+    assert np.allclose(mdl.times, regr['times'], rtol=0, atol=1e-3)
     assert np.allclose(dpa.dvals, regr['dvals'])
     assert np.allclose(dpa.mvals, regr['mvals'])
 
@@ -162,7 +146,7 @@ def test_plotdate():
 
 def test_data_types():
     for data_type in (int, float, np.float32, np.float64, np.int32, np.int64, np.complex64):
-        mdl = ThermalModel('dpa', start='2012:001', stop='2012:007',
+        mdl = ThermalModel('dpa', start='2012:001:12:00:00', stop='2012:007:12:00:00',
                            model_spec=abs_path('dpa.json'))
         dpa = mdl.comp['1dpamzt']
         dpa.set_data(data_type(30.0))
@@ -174,7 +158,7 @@ def test_data_types():
 
 
 def test_minusz():
-    mdl = ThermalModel('minusz', start='2012:001', stop='2012:004',
+    mdl = ThermalModel('minusz', start='2012:001:12:00:00', stop='2012:004:12:00:00',
                        model_spec=abs_path('minusz.json'))
     times = (mdl.times - mdl.times[0]) / 10000.0
     msids = ('tephin', 'tcylaft6', 'tcylfmzm', 'tmzp_my', 'tfssbkt1')
@@ -199,7 +183,7 @@ def test_minusz():
 
 
 def test_pftank2t():
-    mdl = ThermalModel('pftank2t', start='2012:001', stop='2012:004',
+    mdl = ThermalModel('pftank2t', start='2012:001:12:00:00', stop='2012:004:12:00:00',
                        model_spec=abs_path('pftank2t.json'))
     times = (mdl.times - mdl.times[0]) / 10000.0
     msids = ('pftank2t', 'pf0tank2t')
@@ -237,7 +221,7 @@ def test_multi_solar_heat_values():
     P_pitches2 = [45, 65, 90, 140, 180]
     P_vals2 = [1.0, 1.0, 0.0, 1.0, 1.0]
 
-    model = ThermalModel('test', start='2011:001', stop='2011:005')
+    model = ThermalModel('test', start='2011:001:12:00:00', stop='2011:005:12:00:00')
     tephin = model.add(Node, 'tephin')
     tcylaft6 = model.add(Node, 'tcylaft6')
     pitch = model.add(Pitch)
@@ -273,7 +257,7 @@ def test_multi_solar_heat_values():
     temp_name = tempfile.NamedTemporaryFile(delete=False).name
     model.write(temp_name)
     model2 = ThermalModel('test', model_spec=temp_name,
-                          start='2011:001', stop='2011:005')
+                          start='2011:001:12:00:00', stop='2011:005:12:00:00')
     os.unlink(temp_name)
     model2.get_comp('tephin').set_data(30.0)
     model2.get_comp('tcylaft6').set_data(30.0)