Merge changes from May Huntsman commissioning run

conf_files/peas.yaml

@@ -14,7 +14,8 @@ environment:
 weather:
     station: mongo
     aag_cloud:
-        serial_port: '/dev/ttyUSB1'
+      #        serial_port: '/dev/ttyUSB1'
+        serial_port: '/dev/tty.USA19H2P1.1'
         threshold_cloudy: -25
         threshold_very_cloudy: -15.
         threshold_windy: 50.

pocs/camera/camera.py

@@ -249,6 +249,10 @@ def process_exposure(self, info, observation_event, exposure_event=None):
             self.logger.warning('Problem with extracting pretty image: {}'.format(e))
 
         file_path = self._process_fits(file_path, info)
+        try:
+            info['exp_time'] = info['exp_time'].value
+        except Exception:
+            pass
 
         if info['is_primary']:
             self.logger.debug("Adding current observation to db: {}".format(image_id))
@@ -261,6 +265,7 @@ def process_exposure(self, info, observation_event, exposure_event=None):
             fits_utils.fpack(file_path)
 
         self.logger.debug("Adding image metadata to db: {}".format(image_id))
+
         self.db.insert('observations', {
             'data': info,
             'date': current_time(datetime=True),

pocs/camera/sbigudrv.py

@@ -11,6 +11,7 @@
 import platform
 import ctypes
 from ctypes.util import find_library
+from warnings import warn
 import _ctypes
 import os
 import time

pocs/core.py

@@ -121,7 +121,6 @@ def has_messaging(self, value):
     def should_retry(self):
         return self._obs_run_retries >= 0
 
-
 ##################################################################################################
 # Methods
 ##################################################################################################
@@ -396,7 +395,6 @@ def has_free_space(self, required_space=0.25 * u.gigabyte):
         free_space = get_free_space()
         return free_space.value >= required_space.to(u.gigabyte).value
 
-
 ##################################################################################################
 # Convenience Methods
 ##################################################################################################
@@ -442,7 +440,6 @@ def wait_until_safe(self):
         while not self.is_safe(no_warning=True):
             self.sleep(delay=self._safe_delay)
 
-
 ##################################################################################################
 # Class Methods
 ##################################################################################################

pocs/dome/bisque.py

@@ -25,6 +25,7 @@ def __init__(self, *args, **kwargs):
             "Bisque Mounts required a template directory")
 
         self.template_dir = template_dir
+        self._is_parked = True
 
     @property
     def is_connected(self):
@@ -57,7 +58,17 @@ def read_slit_state(self):
 
     @property
     def status(self):
-        return self.read_slit_state()
+        self.write(self._get_command('dome/status.js'))
+        return self.read()
+
+    @property
+    def position(self):
+        self.write(self._get_command('dome/position.js'))
+        return self.read()
+
+    @property
+    def is_parked(self):
+        return self._is_parked
 
     def connect(self):
         if not self.is_connected:
@@ -105,6 +116,33 @@ def close(self):
 
         return self.is_closed
 
+    def park(self):
+        if self.is_connected:
+            self.write(self._get_command('dome/park.js'))
+            response = self.read()
+
+            self._is_parked = response['success']
+
+        return self.is_parked
+
+    def unpark(self):
+        if self.is_connected:
+            self.write(self._get_command('dome/unpark.js'))
+            response = self.read()
+
+            self._is_parked = not response['success']
+
+        return not self.is_parked
+
+    def find_home(self):
+        if self.is_connected:
+            self.write(self._get_command('dome/home.js'))
+            response = self.read()
+
+            self._is_parked = response['success']
+
+        return self.is_parked
+
 ##################################################################################################
 # Communication Methods
 ##################################################################################################
@@ -133,7 +171,6 @@ def read(self, timeout=5):
 
         return response_obj
 
-
 ##################################################################################################
 # Private Methods
 ##################################################################################################

pocs/focuser/focuser.py

@@ -1,7 +1,7 @@
 import matplotlib.colors as colours
 import matplotlib.pyplot as plt
 
-from scipy.interpolate import UnivariateSpline
+from astropy.modeling import models, fitting
 from scipy.ndimage import binary_dilation
 
 import numpy as np
@@ -437,22 +437,38 @@ def _autofocus(self,
             best_focus = focus_positions[imax]
 
         elif not coarse:
-            # Crude guess at a standard deviation for focus metric, 40% of the maximum value
-            weights = np.ones(len(focus_positions)) / (spline_smoothing * metric.max())
-
-            # Fit smoothing spline to focus metric data
-            fit = UnivariateSpline(focus_positions, metric, w=weights, k=4, ext='raise')
-
-            try:
-                stationary_points = fit.derivative().roots()
-            except ValueError as err:
-                self.logger.warning('Error finding extrema of spline fit: {}'.format(err))
-                best_focus = focus_positions[imax]
-            else:
-                extrema = fit(stationary_points)
-                if len(extrema) > 0:
-                    best_focus = stationary_points[extrema.argmax()]
-                    fitted = True
+            # Fit data around the maximum value to determine best focus position.
+            # Initialise models
+            shift = models.Shift(offset=-focus_positions[imax])
+            poly = models.Polynomial1D(degree=4, c0=1, c1=0, c2=-1e-2, c3=0, c4=-1e-4,
+                                       fixed={'c0': True, 'c1': True, 'c3': True})
+            scale = models.Scale(factor=metric[imax])
+            reparameterised_polynomial = shift | poly | scale
+
+            # Initialise fitter
+            fitter = fitting.LevMarLSQFitter()
+
+            # Select data range for fitting. Tries to use 2 points either side of max, if in range.
+            fitting_indices = (max(imax - 2, 0), min(imax + 2, n_positions - 1))
+
+            # Fit models to data
+            fit = fitter(reparameterised_polynomial,
+                         focus_positions[fitting_indices[0]:fitting_indices[1] + 1],
+                         metric[fitting_indices[0]:fitting_indices[1] + 1])
+
+            best_focus = -fit.offset_0
+            fitted = True
+
+            # Guard against fitting failures, force best focus to stay within sweep range
+            if best_focus < focus_positions[0]:
+                self.logger.warning("Fitting failure: best focus {} below sweep limit {}".format(best_focus,
+                                                                                                 focus_positions[0]))
+                best_focus = focus_positions[1]
+
+            if best_focus > focus_positions[-1]:
+                self.logger.warning("Fitting failure: best focus {} above sweep limit {}".format(best_focus,
+                                                                                                 focus_positions[-1]))
+                best_focus = focus_positions[-2]
 
         else:
             # Coarse focus, just use max value.
@@ -462,8 +478,9 @@ def _autofocus(self,
             ax2 = fig.add_subplot(3, 1, 2)
             ax2.plot(focus_positions, metric, 'bo', label='{}'.format(merit_function))
             if fitted:
-                fs = np.arange(focus_positions[0], focus_positions[-1] + 1)
-                ax2.plot(fs, fit(fs), 'b-', label='Smoothing spline fit')
+                fs = np.arange(focus_positions[fitting_indices[0]],
+                               focus_positions[fitting_indices[1]] + 1)
+                ax2.plot(fs, fit(fs), 'b-', label='Polynomial fit')
 
             ax2.set_xlim(focus_positions[0] - focus_step / 2, focus_positions[-1] + focus_step / 2)
             u_limit = 1.10 * metric.max()

pocs/observatory.py

@@ -455,7 +455,7 @@ def get_standard_headers(self, observation=None):
 
         return headers
 
-    def autofocus_cameras(self, camera_list=None, coarse=False):
+    def autofocus_cameras(self, camera_list=None, coarse=None):
         """
         Perform autofocus on all cameras with focus capability, or a named subset
         of these. Optionally will perform a coarse autofocus first, otherwise will

pocs/utils/images/__init__.py

@@ -113,7 +113,7 @@ def _make_pretty_from_fits(
     title = '{} ({}s {}) {}'.format(title, exp_time, filter_type, date_time)
     norm = ImageNormalize(interval=PercentileInterval(percent_value), stretch=LogStretch())
 
-    plt.figure(figsize=figsize, dpi=dpi)
+    fig = plt.figure(figsize=figsize, dpi=dpi)
 
     if wcs.is_celestial:
         ax = plt.subplot(projection=wcs)
@@ -143,7 +143,8 @@ def _make_pretty_from_fits(
         ax.set_xlabel('X / pixels')
         ax.set_ylabel('Y / pixels')
 
-    ax.imshow(data, norm=norm, cmap=palette, origin='lower')
+    im = ax.imshow(data, norm=norm, cmap=palette, origin='lower')
+    fig.colorbar(im)
     plt.title(title)
 
     new_filename = fname.replace('.fits', '.jpg')

resources/bisque/dome/park.js

@@ -3,5 +3,12 @@ sky6Dome.Connect();
 if (sky6Dome.IsConnected == 0) {
     Out = "Not connected"
 } else {
-    Out = sky6Dome.Park();
+	sky6Dome.Park();
+    while (!sky6Dome.IsParkComplete) {
+	    sky6Web.Sleep(1000);
+	}
+
+	Out = JSON.stringify({
+	    "success": sky6Dome.IsParkComplete
+	});
 };