Merge remote-tracking branch 'origin/master'

# Conflicts:
#	pampelmuse/graphics/pampelmuse_gui.py

pampelmuse/core/fit_layer.py

@@ -1160,10 +1160,14 @@ class FitLayer(object):
             else:
                 background_x0 = None
 
-            result = psf.fitter(psf=data, weights=weights, parameters=psf_parameters if is_psf_source[i] else [],
-                                fit_positions=fit_positions, fit_background=local_background,
-                                flux_x0=self.fluxes[self.catalog.at[i, 'component']], background_x0=background_x0,
-                                psf_padding=int(round(self.psf_radius-psf.maxrad)) if is_psf_source[i] else 0)
+            try:
+                result = psf.fitter(psf=data, weights=weights, parameters=psf_parameters if is_psf_source[i] else [],
+                                    fit_positions=fit_positions, fit_background=local_background,
+                                    flux_x0=self.fluxes[self.catalog.at[i, 'component']], background_x0=background_x0,
+                                    psf_padding=int(round(self.psf_radius-psf.maxrad)) if is_psf_source[i] else 0)
+            except ValueError as msg:
+                logger.error("Unexpected fit problem for sources #{0}: {1}".format(i, msg))
+                continue
 
             # check if result of a successful fit makes any sense:
             if not result.success:

pampelmuse/core/parameters.py

@@ -457,7 +457,7 @@ class Parameters(object):
 
             logger.info(log_string)
 
-    def polynomial_fit(self, name, order, mask=None, polynom="plain"):
+    def polynomial_fit(self, name, order, mask=None, polynom="plain", bounds=None):
         """
         Fit a parameter using a polynomial.
         
@@ -478,6 +478,13 @@ class Parameters(object):
         polynom : str, optional
             The function used in the fitting. May be either 'plain',
             'legendre', 'hermite', or 'chebyshev'.
+        bounds : tuple
+            In case the polynomial fit should be
+
+        Returns
+        -------
+        success : bool
+            Flag indicating if the fit has been successful.
         """
         # sanity check on provided parameter
         if name not in self.names:
@@ -503,8 +510,11 @@ class Parameters(object):
             mask = self.mask[(name, 'value')]
 
         # carry out fit
-        fit = fit_function.fit(abscissa[~mask], self.data.loc[~mask, (name, 'value')], order)
-        self.data[(name, 'fit')] = fit(abscissa)
+        f = fit_function.fit(abscissa[~mask], self.data.loc[~mask, (name, 'value')], order)
+
+        fitted_values = f(abscissa)
+
+        self.data[(name, 'fit')] = fitted_values
 
     def make_hdu(self, include_fit=True, header_keys=None):
         """

pampelmuse/core/sources.py

@@ -774,9 +774,9 @@ class Sources(object):
         """
         logger.info("Current status of catalogue of sources:")
         logger.info("   no. of PSF sources: {0}".format(self.psf_indices.size))
-        logger.info("   no. of resolved sources: {0}".format(self.is_resolved.sum()))
+        logger.info("   no. of resolved sources: {0}".format(np.sum(self.status == 2)))
         logger.info("   no. of nearby sources: {0}".format(np.sum(self.status == 1)))
-        logger.info("   no. of unresolved sources: {0}".format(self.is_unresolved.sum()))
+        logger.info("   no. of unresolved sources: {0}".format(np.sum(self.status ==0)))
         logger.info("   no. of background components: {0}".format(self.n_background))
 
         logger.debug("Overview of all components used in fit:")

pampelmuse/graphics/pampelmuse_gui.py

@@ -52,7 +52,7 @@ from astropy import wcs
 from astropy.io import fits
 from PyQt5.QtCore import pyqtSignal, pyqtSlot, Qt
 from PyQt5.QtGui import QDoubleValidator
-from PyQt5.QtWidgets import QMainWindow, QHBoxLayout, QVBoxLayout, QFileDialog
+from PyQt5.QtWidgets import QAction, QMainWindow, QHBoxLayout, QVBoxLayout, QFileDialog
 from .dynamic_plot_canvas import DynamicPlotCanvas
 from .dynamic_ima_canvas import DynamicImaCanvas
 from .Ui_pampelmuse_gui import Ui_PampelMuseGui
@@ -71,12 +71,27 @@ class ToolbarWithoutMessage(NavigationToolbar):
     """
     A small subclass of the navigation toolbar that does not display the
     coordinates under the mouse pointer. This is used for the reference
-    image and IFS data because to save space and because this information
+    image and IFS data in order to save space and because this information
     is already displayed in the status bar.
+
+    The class also keeps track of the status of the toolbar buttons (checked
+    or unchecked), as this information is used to determine the interaction
+    status of the GUI.
     """
+    def __init__(self, canvas, parent, coordinates=True):
+
+        super(ToolbarWithoutMessage, self).__init__(canvas=canvas, parent=parent, coordinates=coordinates)
+
+        self.actionTriggered.connect(self.on_actionTriggered)
+        self.in_navigation_mode = False
+
     def set_message(self, msg):
         pass
 
+    @pyqtSlot(QAction)
+    def on_actionTriggered(self, action):
+        self.in_navigation_mode = action.isChecked()
+
 
 class PampelMuseGui(QMainWindow, Ui_PampelMuseGui):
     """
@@ -767,7 +782,7 @@ class PampelMuseGui(QMainWindow, Ui_PampelMuseGui):
         """
 
         # do nothing if event happened outside axes
-        if event.inaxes != self.ifsPlot.axes or self.ifsInteractMode != 'grab' or self.ifsToolbar._active is not None:
+        if event.inaxes != self.ifsPlot.axes or self.ifsInteractMode != 'grab' or self.ifsToolbar.in_navigation_mode:
             return
 
         # check if click was inside field of view of IFU
@@ -791,7 +806,7 @@ class PampelMuseGui(QMainWindow, Ui_PampelMuseGui):
         event : a matplotlib.backend_bases.PickEvent instance
             The mouse event that triggered the method call.
         """
-        if self.ifsInteractMode != 'pick' or self.ifsToolbar._active is not None:
+        if self.ifsInteractMode != 'pick' or self.ifsToolbar.in_navigation_mode:
             return
         if len(event.ind) != 1:
             self.statusBar.showMessage("Multiple sources selected", 5000)
@@ -812,7 +827,7 @@ class PampelMuseGui(QMainWindow, Ui_PampelMuseGui):
         event : a matplotlib.backend_bases.PickEvent instance
             The mouse event that triggered the method call.
         """
-        if self.refInteractMode != 'pick' or self.refToolbar._active is not None:
+        if self.refInteractMode != 'pick' or self.refToolbar.in_navigation_mode:
             return
 
         # do nothing if more than one source selected
@@ -1406,7 +1421,7 @@ class PampelMuseGui(QMainWindow, Ui_PampelMuseGui):
         self.ifsPlot.loadLayer(self.ifuLayerSelectSlider.value(), residuals=False)
 
         # change cuts unless absolute values were set by the user:
-        if self.ifuCutsComboBox.currentText() is not "User":
+        if self.ifuCutsComboBox.currentText() != "User":
             self.on_ifuCutsComboBox_currentIndexChanged(self.ifuCutsComboBox.currentText())
 
     @pyqtSlot(bool)
@@ -1423,7 +1438,7 @@ class PampelMuseGui(QMainWindow, Ui_PampelMuseGui):
         self.ifsPlot.loadLayer(self.ifuLayerSelectSlider.value(), residuals=True)
 
         # change cuts unless absolute values were set by the user:
-        if self.ifuCutsComboBox.currentText() is not "User":
+        if self.ifuCutsComboBox.currentText() != "User":
             self.on_ifuCutsComboBox_currentIndexChanged(self.ifuCutsComboBox.currentText())
 
     def plot_sources_on_ref(self):

pampelmuse/psf/profiles/maoppy.py

@@ -35,12 +35,13 @@ import io
 import logging
 import numpy as np
 from contextlib import redirect_stdout
-from scipy.interpolate import RectBivariateSpline, interp2d
+from scipy.interpolate import RectBivariateSpline, InterpolatedUnivariateSpline, interp2d
 from .profile import Profile, FitResult
 
 if importlib.util.find_spec('maoppy') is not None:
     from maoppy.psfmodel import Psfao, psffit, oversample
     from maoppy.instrument import muse_nfm
+    from maoppy.utils import circavgplt
 else:
     logging.error('Package "maoppy" is not installed. Cannot use MAOPPY PSF model.')
 
@@ -424,7 +425,6 @@ class Maoppy(Profile):
         centre : tuple of 2 floats
             The central coordinates of the PSF along the y- and x-axes.
         """
-
         if shape is None:
             shape = self.maoppy_shape
         return shape[0]/2 - (k - 1.)/(2.*k), shape[1]/2 - (k - 1.)/(2.*k)
@@ -432,9 +432,14 @@ class Maoppy(Profile):
     @classmethod
     def calculate_fwhm(cls, r0, bck, amp, alpha, e, beta, wvl=6e-7, **kwargs):
         """
-        Calculate and return the FWHM of the MAOPPY PSF profile for a given
+        Estimate and return the FWHM of the MAOPPY PSF profile for a given
         set of parameters.
 
+        To estimate the FWHM, the method creates the MAOPPY PSF on a 2dim.
+        grid, then determines the symmetric radial profile, and tries to
+        obtain the radii where the intensity drops to half its central value
+        using univariate spline interpolation.
+
         Parameters
         ----------
         r0 : float
@@ -469,11 +474,18 @@ class Maoppy(Profile):
             raise IOError('Unknown argument(s) to call of Maoppy.fwhm: {0}'.format(kwargs))
 
         psf = Psfao(Npix=(30, 30), system=muse_nfm, samp=muse_nfm.samp(wvl))
-
         theta = 0.
-        f = psf((r0, bck, amp, alpha, 1-e, theta, beta))[:15]
+        f = psf((r0, bck, amp, alpha, 1 - e, theta, beta))
 
-        return 2.*np.sqrt(np.sum(f > (0.5*f.max()))/np.pi)
+        r, fr = circavgplt(f)
+        f = InterpolatedUnivariateSpline(r, fr - f.max() / 2.)
+        roots = f.roots()
+
+        if len(roots) != 2:
+            logger.error("Could not estimate FWHM of MAOPPY profile.")
+            return np.nan
+        else:
+            return roots.max() - roots.min()
 
     @property
     def fwhm(self):
@@ -483,26 +495,24 @@ class Maoppy(Profile):
         fwhm : float
             The FWHM of the MAOPPY PSF profile with the given parameters.
         """
-        from scipy.stats import binned_statistic
-
-        # get mean radii for fluxes for annuli of widths ~1 pixel
-        bstat = binned_statistic(self.r, [self.r, self.f], bins=self.maxrad)
-        r_bin, f_bin = bstat.statistic
-
-        # interpolate along flux axis to get FWHM. Note that flux values must  be monotonically INCREASING
-        fwhm = 2.*np.interp(0.5*self.f.max(), f_bin[::-1], r_bin[::-1])
-
-        return fwhm
+        return Maoppy.calculate_fwhm(r0=self.r0, bck=self.bck, amp=self.amp, alpha=self.alpha, e=self.e,
+                                     beta=self.beta, wvl=self.wvl)
 
     @property
     def strehl(self):
         """
-        Returns the Strehl ratio for the current set of parameters. The Strehl
-        ratio is calculated using eq. 14 from Fetick et al. (2019).
+        Returns
+        -------
+        strehl : float
+            The Strehl ratio for the current set of parameters.
         """
-        f_ao = muse_nfm.Nact/(2.*muse_nfm.D)
+        psf = Psfao(Npix=(30, 30), system=muse_nfm, samp=muse_nfm.samp(self.wvl))
+        return psf.strehlOTF((self.r0, self.bck, self.amp, self.alpha, 1 - self.e, self.theta, self.beta))
 
-        return np.exp(-self.amp - self.bck*np.pi*(f_ao**2) - (0.023*6.*np.pi*(self.r0*f_ao)**(-5./3.))/5.)
+        # Analyytical calculation based on eq. 14 from the paper by Fetick et al. (2019). This seems to underestimate
+        # the Strehl significantly for NFM data.
+        # f_ao = muse_nfm.Nact/(2.*muse_nfm.D)
+        # return np.exp(-self.amp - self.bck*np.pi*(f_ao**2) - (0.023*6.*np.pi*(self.r0*f_ao)**(-5./3.))/5.)
 
     def fitter(self, psf, weights, parameters, fit_positions=True, fit_background=False, psf_padding=0, **kwargs):
         """

pampelmuse/psf/profiles/profile.py

@@ -1433,6 +1433,14 @@ class Profile(Canvas):
 
         return radii, np.cumsum(cog_flux)
 
+    @classmethod
+    def calculate_fwhm(cls, **kwargs):
+        """
+        Calculate FWHM for a given set of parameters. Must be overwritten by
+        classes inheriting from Profile().
+        """
+        raise NotImplementedError
+
     @property
     def fwhm(self):
         """

pampelmuse/psf/variables.py

@@ -263,7 +263,8 @@ class Variables(Parameters):
                 self.lut.index = index
             else:
                 if not self.lut.index.isin(index).all():
-                    logger.warning('Changing dispersion axis as requested will alter existing values of look-up table.')
+                    logger.warning(
+                        'Changing dispersion axis as requested will alter existing values of look-up table.')
                 self.lut = self.lut.reindex(index=index, method='nearest')
 
     def fit_lut(self, order, mask=None):