Image simulation (#16)

* Added dark frame generation to Camera, moved other astroimsim code

* Initial implementations of image simulation methods

* Docs build fix

* Remove now redundant astroimsim.py

* Memory use reduction (no longer creates huge temporary arrays)

* Fix off-by-one, array vs Quantity & floating point stopping bugs

* Fix axis 18 (#20)

* Axis order changed

* Camera.py docstring improved

* clipping below zero pixel values

* Correcting test_psf.py

* camera.py docstring improved

* below zero assert added

* below zero and infinit asserts added

* combining pairs

* `@pytest.mark.parameterize` implemented

* Some problems with ...

* something that works for now

* Crval not set as per Issue #17 (#25)

* use centre to always set CRVAL first thing

See issue: #17

* created get_pixel_coords method for Imager

* remove centre for get_pixel_coords & check for CRVAL

* add :skip: InvalidTransformError to docs/index.rst

* added test of get_pixel_coords

* fix unit=deg problems in SkyCoord

* also unit=deg fix

* another unit=deg fix

* split test and make scope function

* make_noiseless_image unit=deg

* kwargs docstrings & split star_ & centre_ kwargs

* @bazkiaei
trying to parametrize as it has been advised

* @bazkiaei
trying to parametrize as it has been advised

* Revert "Merge remote-tracking branch 'upstream/image_sim' into improve-pytest-#26"

This reverts commit 308168f.

* Revert "Merge remote-tracking branch 'upstream/image_sim' into improve-pytest-#26"

This reverts commit 4b4bc04.

* Revert "Revert "Merge remote-tracking branch 'upstream/image_sim' into improve-pytest-#26""

This reverts commit 25a4c04.

* Revert "@bazkiaei"

This reverts commit 94273a2.

* Revert "@bazkiaei"

This reverts commit c811d41.

* Revert "Merge remote-tracking branch 'upstream/image_sim' into improve-pytest-#26"

This reverts commit 308168f.

* Revert "Revert "Merge remote-tracking branch 'upstream/image_sim' into improve-pytest-#26""

This reverts commit 9eb810c.

* Improving psf_pytest.py  #26 (#28)

The `test_psf.py` parametrised and decorated.

* auto pep8

* fix pixellated call

* add notimplemented error for analytical psf

* fix real image generator bug

* rename ZWO QE

.travis.yml

@@ -88,8 +88,8 @@ matrix:
                EVENT_TYPE='pull_request push cron'
         #- os: linux
         #  env: PYTHON_VERSION=2.7 ASTROPY_VERSION=lts
-        - os: linux
-          env: ASTROPY_VERSION=lts
+        # - os: linux
+        #   env: ASTROPY_VERSION=lts
 
         # Try all python versions and Numpy versions. Since we can assume that
         # the Numpy developers have taken care of testing Numpy with different

docs/index.rst

@@ -123,11 +123,13 @@ Reference/API
   :skip: PSF
   :skip: Sky
   :skip: Simple
-  :skip: Table
   :skip: MoffatPSF
   :skip: ZodiacalLight
   :skip: WCS
+  :skip: SkyCoord
+  :skip: CCDData
   :skip: interp1d
+  :skip: InvalidTransformError
   :no-inheritance-diagram:
 
 .. automodapi:: gunagala.optic

gunagala/camera.py

@@ -2,6 +2,7 @@
 Cameras (stricly the image sensor subsystem, not including optics, optical filters, etc)
 """
 import os
+import numpy as np
 
 from astropy import units as u
 from astropy.table import Table
@@ -37,7 +38,8 @@ class Camera:
         Pixel pitch. Square pixels are assumed.
     Resolution : astropy.units.Quantity
         Two element Quantity containing the number of pixels across
-        the image sensor in both horizontal & vertical directions.
+        the image sensor in both vertical & horizontal directions.
+        (y, x)
     read_noise astropy.units.Quantity
         Intrinsic noise of image sensor and readout electronics, in
         electrons/pixel units.
@@ -55,6 +57,13 @@ class Camera:
     minimum_exposure : astropy.units.Quantity
         Length of the shortest exposure that the camera is able to
         take.
+    dark_current_dist : scipy.stats.rv_continuous, optional
+        A 'frozen' continuous random variable object that describes the distribution
+        of dark currents for the pixels in the image sensor. Used to create a `dark frame`
+        of uncorrelated dark current values. If not given no dark frame is created.
+    dark_current_seed: int, optional
+        Seed used to initialise the random number generator before creating the dark
+        frame. Set to a fixed value if you need to repeatedly generate the same dark frame.
 
     Attributes
     ----------
@@ -86,9 +95,23 @@ class Camera:
         Sequence of wavelengths from the QE data
     QE : astropy.units.Quantity
         Sequence of quantum efficiency values from the QE data.
+    dark_frame: astropy.units.Quantity or None
+        Array containing the dark current values for the pixels of the image sensor
     """
-    def __init__(self, bit_depth, full_well, gain, bias, readout_time, pixel_size, resolution,
-                 read_noise, dark_current, QE, minimum_exposure):
+    def __init__(self,
+                 bit_depth,
+                 full_well,
+                 gain,
+                 bias,
+                 readout_time,
+                 pixel_size,
+                 resolution,
+                 read_noise,
+                 dark_current,
+                 QE,
+                 minimum_exposure,
+                 dark_current_dist=None,
+                 dark_current_seed=None):
 
         self.bit_depth = int(bit_depth)
         self.full_well = ensure_unit(full_well, u.electron / u.pixel)
@@ -112,3 +135,44 @@ def __init__(self, bit_depth, full_well, gain, bias, readout_time, pixel_size, r
         self.wavelengths, self.QE = get_table_data(QE,
                                                    column_names=('Wavelength', 'QE'),
                                                    column_units=(u.nm, u.electron / u.photon))
+
+        # Generate dark frame
+        if dark_current_dist is not None:
+            try:
+                dark_current_dist.rvs
+            except AttributeError:
+                raise ValueError("dark_current_dist ({}) has no rvs() method!".format(dark_current_dist))
+            self.dark_frame = self._make_dark_frame(dark_current_dist, dark_current_seed)
+        else:
+            self.dark_frame = None
+
+    def _make_dark_frame(self, distribution, seed=None):
+        """
+        Function to create a dark current 'image' in electrons per second per pixel.
+
+        Creates an array of random, uncorrelated dark current values drawn from the
+        statistical distribution defined by the `distribution` parameter and returns
+        it as an astropy.units.Quantity.
+
+        Parameters
+        ----------
+        distribution : scipy.stats.rv_continuous
+            A 'frozen' continuous random variable object that describes the distribution
+            of dark current values for the pixels in the image sensor.
+        seed: int
+            Seed used to initialise the random number generator before creating the dark
+            frame. Set to a fixed value if you need to repeatedly generate the same dark
+            frame.
+        """
+        if seed is not None:
+            # Initialise RNG
+            np.random.seed(seed)
+
+        dark_frame = distribution.rvs(size=self.resolution.value.astype(int))
+        dark_frame = dark_frame * u.electron / (u.second * u.pixel)\
+
+        if seed is not None:
+            # Re-initialise RNG with random seed
+            np.random.seed()
+
+        return dark_frame

gunagala/data/performance.yaml

@@ -57,7 +57,7 @@ cameras:
         resolution: 4656, 3520 # pixel
         read_noise: 2.5 # electron / pixel
         dark_current: 0.008 # electron / (second * pixel)
-        QE: ZWO_QE.csv
+        QE: ZWO_QE_asi1600.csv
         minimum_exposure: 0.000032 # second
 
     cis115: # e2v CIS115 'Sirius' back side illuminated CMOS image sensor