Misc updates

.travis.yml

@@ -54,7 +54,6 @@ env:
     matrix:
         # Make sure that egg_info works without dependencies
         - PYTHON_VERSION=2.7 SETUP_CMD='egg_info'
-        - PYTHON_VERSION=3.4 SETUP_CMD='egg_info'
         - PYTHON_VERSION=3.5 SETUP_CMD='egg_info'
         - PYTHON_VERSION=3.6 SETUP_CMD='egg_info'
 
@@ -86,17 +85,15 @@ matrix:
         - os: linux
           env: ASTROPY_VERSION=lts
 
-        # Try all python versions and Numpy versions. Since we can assume that
+        # Try various python and numpy combinations. Since we can assume that
         # the Numpy developers have taken care of testing Numpy with different
         # versions of Python, we can vary Python and Numpy versions at the same
         # time.
 
         - os: linux
-          env: PYTHON_VERSION=3.5 NUMPY_VERSION=1.10
+          env: PYTHON_VERSION=3.5 NUMPY_VERSION=1.13
         - os: linux
-          env: PYTHON_VERSION=3.5 NUMPY_VERSION=1.11
-        - os: linux
-          env: NUMPY_VERSION=1.12
+          env: PYTHON_VERSION=3.5 NUMPY_VERSION=1.14
 
         # Try numpy pre-release
         - os: linux

CHANGES.rst

@@ -5,7 +5,13 @@ specsim Change Log
 0.13 (unreleased)
 -----------------
 
-- No changes yet.
+- Changes to SimulationExamples notebook:
+   - Change median LRG minor/major axis ratio from 0.16 to 0.5.
+   - Add quantitative comparison of galsim and fastsim fiberloss modes.
+- Streamline array indexing for downsampling and convolution operations.
+- Do not require fastsim file to be present (fixes #90).
+- Update to astropy_helpers v2.0.6 (merges #85).
+- Remove python 3.4 from travis test matrix and update "old" numpy versions used (fixes #93).
 
 0.12 (2018-07-26)
 -----------------

docs/fiberloss.rst

@@ -48,8 +48,16 @@ methods selected by the value of ``instrument.fiberloss.method``:
   atmospheric models.  This mode is the most flexible and slowest, and uses
   all of the relevant configuration parameters.
 * The ``fastsim`` method is based on an interpolation of fiber acceptance values
-  pre-computed with ``galsim`` using the script ``fitgalsim``.
-  The interpolation parameters/axis are source profile (point source, exponential disk, De Vaucouleurs bulge), sigma (atmosphere+telescope blur, in um on focal surface), fiber offset from source (in um on focal surface), and half light radius (in arcsec) from extended source. This interpolation is performed with the class ``fastfiberacceptance.FastFiberAcceptance``. The accuracy is about 1 percent, which is sufficient for simulations.
+  pre-computed with ``galsim`` using the script ``fitgalsim``, which assumes
+  a fixed axis ratio of 0.7 (for extended objects), a fixed Moffat PSF
+  model with beta=3.5 (but variable FWHM) for the atmosphere, and a fixed
+  fiber diameter of 107um.
+  The interpolation parameters/axis are source profile (point source,
+  exponential disk, De Vaucouleurs bulge), sigma (atmosphere+telescope blur,
+  in um on focal surface), fiber offset from source (in um on focal surface),
+  and half light radius (in arcsec) from extended source. This interpolation
+  is performed with the class ``fastfiberacceptance.FastFiberAcceptance``.
+  The accuracy is about 1 percent when the assumptions above are valid.
 
 Refer to the comments in the sample configuration files for more information
 about the available parameters.
@@ -58,6 +66,9 @@ GalSim Dependency
 -----------------
 
 The GalSim package is only required when the ``galsim`` method is selected.
+As of GalSim version 2.0, this package can be easily install using either
+conda or pip.
+
 Fiberloss arrays calculated with GalSim can be saved for later table-based
 simulations.  For example, first run the :ref:`quickspecsim` script to
 use GalSim to calculate and save the fiberloss for a specific configuration

specsim/camera.py

@@ -338,13 +338,13 @@ def downsample(self, data, method=np.sum):
         if not self.allow_convolution:
             raise RuntimeError('Camera created with allow_convolution False.')
         data = np.asanyarray(data)
-        if data.shape[-1] != len(self._wavelength):
+        if data.shape[0] != len(self._wavelength):
             raise ValueError(
                 'Invalid data shape for downsampling: {0}.'.format(data.shape))
 
-        output = data[..., self._output_slice]
-        new_shape = output.shape[:-1] + self._downsampled_shape
-        return method(output.reshape(new_shape), axis=-1)
+        output = data[self._output_slice]
+        new_shape = self._downsampled_shape + output.shape[1:]
+        return method(output.reshape(new_shape), axis=1)
 
     def apply_resolution(self, flux):
         """
@@ -357,8 +357,8 @@ def apply_resolution(self, flux):
         flux = np.asarray(flux)
         dispersed = np.zeros_like(flux)
 
-        dispersed[..., self.ccd_slice] = self._resolution_matrix.dot(
-            flux[..., self.response_slice].T).T
+        dispersed[self.ccd_slice] = self._resolution_matrix.dot(
+            flux[self.response_slice])
 
         return dispersed
 

specsim/data/config/desi.yaml

@@ -143,9 +143,12 @@ instrument:
             columns:
                 wavelength: { index: 0, unit: Angstrom }
                 fiber_acceptance: { index: 1 }
-        # Fits file of precomputed galsim fiber acceptance 
-        # the fits file is created with specsim/fitgalsim.py
-        # the fits file is read with specsim/fastfiberacceptance.py
+        # Fits file of precomputed galsim fiber acceptances.
+        # Ignored unless method is fastsim.
+        # The fits file is created with specsim/fitgalsim.py
+        # and used by specsim/fastfiberacceptance.py
+        # Comment out this line to disable the "fastsim" mode (e.g., if
+        # this file is not available or describes a different config).
         fast_fiber_acceptance_path: throughput/galsim-fiber-acceptance.fits
     blur:
         # Read RMS blur values tabulated as a function of field angle and

specsim/instrument.py

@@ -55,6 +55,9 @@ class Instrument(object):
         Dictionary of fiber acceptance fractions tabulated for different
         source models, with keys corresponding to source model names.
         Ignored when fiberloss_method is "galsim".
+    fast_fiber_acceptance : specsim.fastfiberacceptance.FastFiberAcceptance or None
+        Initialized instance to use when fiberloss_method is "fastsim".
+        Ignored for other values of fiberloss_method.
     fiberloss_num_wlen : int
         Number of wavelengths where the fiberloss fraction should be tabulated
         for interpolation.  Ignored when fiberloss_method is not "galsim".
@@ -103,6 +106,8 @@ def __init__(self, name, wavelength, fiberloss_method,
         self._wavelength = wavelength
         self.fiber_acceptance_dict = fiber_acceptance_dict
         self.fast_fiber_acceptance = fast_fiber_acceptance
+        # Both fiber_acceptance_dict and fast_fiber_acceptance must be initialized
+        # before assigning to fiberloss_method (since its setter checks their values).
         self.fiberloss_method = fiberloss_method
         self.fiberloss_num_wlen = fiberloss_num_wlen
         self.fiberloss_num_pixels = fiberloss_num_pixels
@@ -186,9 +191,13 @@ def fiberloss_method(self, fiberloss_method):
         Must be one of "table" or "galsim" or "fastsim".
         """
         if fiberloss_method not in ('table', 'galsim', 'fastsim' ):
-            raise ValueError('fiberloss_method must be "table" or "galsim" or "fastsim".')
+            raise ValueError(
+                'fiberloss_method must be "table" or "galsim" or "fastsim".')
         if fiberloss_method == 'table' and self.fiber_acceptance_dict is None:
             raise ValueError('Missing required instrument.fiberloss.table.')
+        if fiberloss_method == 'fastsim' and self.fast_fiber_acceptance is None:
+            raise ValueError(
+                'Missing required instrument.fiberloss.fast_fiber_acceptance_path.')
         if fiberloss_method == 'galsim':
             try:
                 import galsim

specsim/observation.py

@@ -251,7 +251,7 @@ def initialize(config):
             print('Adjusted by {0:+.3f} for HA {1}.'
                   .format(dt.to(u.hour), hour_angle))
         cond = obs.observing_model
-        print('Conditions: pressure {0:.1f}, temperature {1:.1f}, RH {2:.3f}.'
+        print('Conditions: pressure {0:.1f}, temperature {1:.1f}, RH {2}.'
               .format(cond.pressure, cond.temperature, cond.relative_humidity))
         altaz = obs.boresight_altaz
         print('Boresight (alt, az) = ({0:.1f}, {1:.1f}).'

specsim/simulator.py

@@ -525,19 +525,19 @@ def simulate(self, sky_positions=None, focal_positions=None,
             # Apply resolution to the source and sky detected electrons on
             # the high-resolution grid.
             num_source_electrons[:] = camera.apply_resolution(
-                num_source_electrons.T).T
+                num_source_electrons)
             num_sky_electrons[:] = camera.apply_resolution(
-                num_sky_electrons.T).T
+                num_sky_electrons)
 
             # Calculate the corresponding downsampled output quantities.
             output['num_source_electrons'][:] = (
-                camera.downsample(num_source_electrons.T)).T
+                camera.downsample(num_source_electrons))
             output['num_sky_electrons'][:] = (
-                camera.downsample(num_sky_electrons.T)).T
+                camera.downsample(num_sky_electrons))
             output['num_dark_electrons'][:] = (
-                camera.downsample(num_dark_electrons.T)).T
+                camera.downsample(num_dark_electrons))
             output['read_noise_electrons'][:] = np.sqrt(
-                camera.downsample(read_noise_electrons.T ** 2)).T
+                camera.downsample(read_noise_electrons ** 2))
             output['variance_electrons'][:] = (
                 output['num_source_electrons'] +
                 output['num_sky_electrons'] +
@@ -548,7 +548,7 @@ def simulate(self, sky_positions=None, focal_positions=None,
             # source flux above the atmosphere, downsampled to output pixels.
             output['flux_calibration'][:] = 1.0 / camera.downsample(
                 camera.apply_resolution(
-                    source_flux_to_photons.T * camera.throughput)).T
+                    source_flux_to_photons * camera.throughput.reshape(-1, 1)))
 
             # Calculate the calibrated flux in this camera.
             output['observed_flux'][:] = (