Merge pull request #45 from lsst/tickets/DM-40514

DM-40514: Integrate Spectractor speedups

README.md

@@ -40,6 +40,11 @@ conda install -c conda-forge astrometry
 and then download and move [index files](http://astrometry.net/doc/readme.html#getting-index-files) in the `$CONDA_PREFIX/data` folder.
 - compile it from [sources](https://astrometrynet.readthedocs.io/en/latest/): it needs the installation of [netpbm](https://netpbm.sourceforge.net/) and [wcslib](https://www.atnf.csiro.au/people/mcalabre/WCS/wcslib/); `solve-field` executable must in the user `$PATH` or the user has to set an environmental variable `$ASTROMETRYNET_DIR` pointing to the install directory.
 
+For faster matrix multiplications, if available for a given computer configuration, one can install [sparse_dot_mkl](https://anaconda.org/conda-forge/sparse_dot_mkl):
+```
+conda install -c conda-forge sparse_dot_mkl
+```
+
 Spectractor is able to perform parameter fits using the MCMC library [emcee](https://emcee.readthedocs.io/en/stable/) (optional) with [mpi4py](https://mpi4py.readthedocs.io/en/stable/) and [h5py](https://www.h5py.org/).  The latter might be better installed using `conda install ...` command to get their own dependencies (openmp and hdf5).
 
 ## Basic extraction

config/auxtel.ini

@@ -10,7 +10,7 @@ SPECTRACTOR_FIT_TARGET_CENTROID = fit
 # method to get image rotation angle: False, disperser, hessian
 SPECTRACTOR_COMPUTE_ROTATION_ANGLE = disperser
 # deconvolve spectrogram with simple 2D PSF analysis: False, True
-SPECTRACTOR_DECONVOLUTION_PSF2D = False
+SPECTRACTOR_DECONVOLUTION_PSF2D = True
 # deconvolve spectrogram with full forward model: False, True
 SPECTRACTOR_DECONVOLUTION_FFM = True
 # value of sigma clip parameter for the spectractor deconvolution process PSF2D and FFM
@@ -34,7 +34,7 @@ OBS_OBJECT_TYPE = STAR
 # telescope transmission file
 OBS_TELESCOPE_TRANSMISSION = multispectra_holo4_003_HD142331_AuxTel_throughput.txt
 # full instrument transmission file
-OBS_FULL_INSTRUMENT_TRANSMISSON = multispectra_holo4_003_HD142331_AuxTel_throughput.txt
+OBS_FULL_INSTRUMENT_TRANSMISSON = multispectra_holo4_003_multi_AuxTel_throughput.txt
 # quantum efficiency of the detector file
 OBS_QUANTUM_EFFICIENCY = multispectra_holo4_003_HD142331_AuxTel_throughput.txt
 # Camera (x,y) rotation angle with respect to (north-up, east-left) system

requirements.txt

@@ -13,7 +13,7 @@ h5py #==2.8.0
 emcee #==3.0rc2
 tqdm
 schwimmbad
-iminuit>=2
+# iminuit>=2
 coverage>=3.6 # <5
 configparser
 coveralls

setup.cfg

@@ -1,2 +1,5 @@
 [nosetests]
-exclude=test_(extractor_ctio_planetary_nebula|astrometry)
+exclude=test_(extractor_ctio_planetary_nebula|astrometry|mcmc|multispectra)
+
+[coverage:run]
+omit=spectractor/fit/mcmc.py

setup.py

@@ -44,7 +44,7 @@
     license='BSD',
     python_requires='>=3.7',
     author='J. Neveu, S. Dagoret-Campagne',
-    author_email='jneveu@lal.in2p3.fr',
+    author_email='jeremy.neveu@universite-paris-saclay.fr',
     description='',
     long_description=long_description,
 )

spectractor/_version.py

@@ -28,5 +28,5 @@
 # OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-__version__ = '2.5'
+__version__ = '3.0'
 __version_info__ = tuple(map(int, __version__.split('.')))

spectractor/extractor/background.py

@@ -135,7 +135,7 @@ def extract_spectrogram_background_fit1D(data, err, deg=1, ws=(20, 30), pixel_st
     >>> s0 = ChromaticPSF(psf, Nx=100, Ny=100, saturation=1000)
     >>> params = s0.generate_test_poly_params()
     >>> saturation = params[-1]
-    >>> data = s0.evaluate(params, mode="1D")
+    >>> data = s0.evaluate(s0.set_pixels(mode="1D"), params)
     >>> bgd = 10*np.ones_like(data)
     >>> data += bgd
     >>> data = np.random.poisson(data)
@@ -239,7 +239,7 @@ def extract_spectrogram_background_sextractor(data, err, ws=(20, 30), mask_signa
     >>> s0 = ChromaticPSF(psf, Nx=100, Ny=200, saturation=1000)
     >>> params = s0.generate_test_poly_params()
     >>> saturation = params[-1]
-    >>> data = s0.evaluate(params, mode="1D")
+    >>> data = s0.evaluate(s0.set_pixels(mode="1D"))
     >>> bgd = 10*np.ones_like(data)
     >>> data += bgd
     >>> data = np.random.poisson(data)
@@ -383,7 +383,7 @@ def extract_spectrogram_background_poly2D(data, deg=1, ws=(20, 30), pixel_step=1
     >>> s0 = ChromaticPSF(psf, Nx=100, Ny=100, saturation=1000)
     >>> params = s0.generate_test_poly_params()
     >>> saturation = params[-1]
-    >>> data = s0.evaluate(params, mode="1D")
+    >>> data = s0.evaluate(s0.set_pixels(mode="1D"), params)
     >>> bgd = 10.*np.ones_like(data)
     >>> xx, yy = np.meshgrid(np.arange(s0.Nx), np.arange(s0.Ny))
     >>> bgd += 1000*np.exp(-((xx-20)**2+(yy-10)**2)/(2*2))