Merge 3a31029 into 5901d17

.travis.yml

@@ -1,69 +1,47 @@
-language:
-#  - objective-c  # Used for OSX tests
-  - python        # Used for linux tests
-#  - c
-
-os:
-  - linux
-#  - osx
-
-env:
-  - python=2.7
-  - python=3.4
-
-#matrix:
-#
-#  # Don't wait for allowed failures
-#  fast_finish: true
-#
-#  include:
-#
-#    # Try MacOS X
-#    - os: osx
-#      env: PYTHON_VERSION=2.7 SETUP_CMD='test' OPTIONAL_DEPS=true
-#
-#    - os: linux
-#      env: PYTHON_VERSION=2.7 SETUP_CMD='test --open-files'
-#    - os: linux
-#      env: PYTHON_VERSION=3.4 SETUP_CMD='test --open-files'
-
-
+language: python
+sudo: false
+
+matrix:
+  include:
+    - python: "2.7"
+      env: DEPS="numpy=1.9 scipy=0.15 astropy=1.0" COVERAGE=true
+    - python: "3.4"
+      env: DEPS="numpy=1.9 scipy=0.15 astropy=1.0"
+
+cache:
+  apt: true
+  pip: true
+  directories:
+    - $HOME/.cache/pip
+    - $HOME/.local
 
 before_install:
-  - echo $TRAVIS_OS_NAME
-  - echo ${TRAVIS_PYTHON_VERSION:0:1}
-  - echo $TRAVIS_PYTHON_VERSION
-  - echo $python
-#  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-get update; fi
-#  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-get install libsdl1.2-dev; fi
-  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then if [ $python == "2.7" ]; then wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; fi ; fi
-  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then chmod +x miniconda.sh; fi
-  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then ./miniconda.sh -b -p /home/travis/mc; fi
-  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then export PATH=/home/travis/mc/bin:$PATH; fi
-  - if [ "$TRAVIS_OS_NAME" = "osx" ]; then brew update; fi
-  - if [ "$TRAVIS_OS_NAME" = "osx" ]; then if [ $python == "2.7" ]; then wget http://repo.continuum.io/miniconda/Miniconda-latest-MacOSX-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh; fi ; fi
-  - if [ "$TRAVIS_OS_NAME" = "osx" ]; then chmod +x miniconda.sh; fi
-  - if [ "$TRAVIS_OS_NAME" = "osx" ]; then ./miniconda.sh -b; fi
-  - if [ "$TRAVIS_OS_NAME" = "osx" ]; then if [ $python == "2.7" ]; then export PATH=/Users/travis/miniconda/bin:$PATH; else export PATH=/Users/travis/miniconda3/bin:$PATH; fi ; fi
+  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-3.5.5-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.5.5-Linux-x86_64.sh -O miniconda.sh; fi
+  - chmod +x miniconda.sh
+  - ./miniconda.sh -b -p /home/travis/mc
+  - export PATH=/home/travis/mc/bin:$PATH
+
 
 install:
   # See:
   # https://groups.google.com/a/continuum.io/forum/#!topic/conda/RSFENqovnro
+  # - conda update --yes --no-deps conda
+  # OK, this used to *fix* the build, but now it *breaks* the build.
+  # If you're reading this, good luck out there. I'm not sure what to tell you.
   - conda update --yes conda
-  - conda list
-  - conda install --yes numpy
   - conda create -n testenv --yes --file requirements.txt
-  - conda list
   - source activate testenv
+  - pip install pytest-benchmark pytest-cov
+  - pip install setuptools
   - pip install -e git+git://github.com/guaix-ucm/numina.git#egg=numina
-  - echo $PATH
-  - which python
-  - conda info
-  - conda list
-  - python setup.py install
+  - if [[ $COVERAGE == true ]]; then pip install coveralls; fi
   # Build in place so we can run tests
   - python setup.py build_ext --inplace
-  - pwd
+
 
 script:
-  - py.test -s -v megaradrp
+  - py.test -s -v megaradrp
+  - if [[ $COVERAGE == true ]]; then py.test megaradrp --cov=megaradrp; fi
+
+after_success:
+  - if [[ $COVERAGE == true ]]; then coveralls; fi

megaradrp/core.py

@@ -22,9 +22,7 @@
 from astropy.io import fits
 import numpy as np
 
-from numina.core import BaseRecipeAutoQC as MegaraBaseRecipe  # @UnusedImport
-from megaradrp.products import TraceMap
-from megaradrp.trace.peakdetection import peakdet
+from numina.core import BaseRecipeAutoQC as MegaraBaseRecipe
 from numina.array.trace.extract import extract_simple_rss
 from numina.array.utils import wc_to_pix_1d as wcs_to_pix_1d
 
@@ -153,7 +151,6 @@ def trim_and_o_array(array, direction='normal', bins='11'):
     nc2 = H_X_DIM * 2 / bng[1]
 
     nr = H_Y_DIM / bng[0]
-    nc = H_X_DIM / bng[1]
 
     oscan2 = OSCANW / bng[0]
     psc1 = PSCANW / bng[0]
@@ -228,8 +225,6 @@ def apextract_tracemap(data, tracemap):
     pix_12 = 2 * pix_1 - pix_01
     borders.append((pix_01, pix_12))
 
-    rss = np.empty((len(pols), data.shape[1]))
-
     rss = extract_simple_rss(data, borders)
 
 

megaradrp/recipes/calibration/arc.py

@@ -26,7 +26,6 @@
 import numpy
 from astropy.io import fits
 
-from numina.core import Product
 from numina.core import Requirement, Product, Parameter
 from numina.core import DataFrameType
 from numina.core.products import ArrayType
@@ -40,15 +39,16 @@
 from numina.core.products import LinesCatalog
 from scipy.interpolate import interp1d
 import matplotlib.pyplot as plt
-from numina.array.wavecal.arccalibration import arccalibration_direct, fit_solution, gen_triplets_master
+from numina.array.wavecal.arccalibration import arccalibration_direct
+from numina.array.wavecal.arccalibration import fit_solution
+from numina.array.wavecal.arccalibration import gen_triplets_master
 from numina.array.wavecal.statsummary import sigmaG
-from numina.array.wavecal.findpeaks1D import findPeaks_spectrum, refinePeaks_spectrum
+from numina.array.peaks.findpeaks1D import findPeaks_spectrum
+from numina.array.peaks.findpeaks1D import refinePeaks_spectrum
 
 from megaradrp.core import MegaraBaseRecipe
 from megaradrp.processing import OverscanCorrector, TrimImage
-# from numina.logger import log_to_history
 
-from megaradrp.products import MasterFiberFlat
 from megaradrp.products import TraceMap
 from megaradrp.requirements import MasterBiasRequirement
 
@@ -65,7 +65,7 @@ class ArcCalibrationRecipe(MegaraBaseRecipe):
     master_bias = MasterBiasRequirement()
     tracemap = Requirement(TraceMap, 'Trace information of the Apertures')
     lines_catalog = Requirement(LinesCatalog, 'Catalog of lines')
-    polynomial_degree = Parameter(2, 'Polynomial degree of the arc calibration')
+    polynomial_degree = Parameter(2, 'Polynomial degree of arc calibration')
     # Products
     arc_image = Product(DataFrameType)
     arc_rss = Product(DataFrameType)
@@ -86,7 +86,8 @@ def run(self, rinput):
         rss = fits.HDUList([rsshdu])
 
         # Skip any other inputs for the moment
-        coeff_table = self.calibrate_wl(rssdata, rinput.lines_catalog, rinput.polynomial_degree)
+        coeff_table = self.calibrate_wl(rssdata, rinput.lines_catalog,
+                                        rinput.polynomial_degree)
 
         # WL calibration goes here
         return self.create_result(arc_image=reduced, arc_rss=rss,
@@ -98,7 +99,7 @@ def calibrate_wl(self, rss, lines_catalog, poldeg, times_sigma=50.0):
         # all the slits) for the wavelength calibration
         wv_master = lines_catalog[:,0]
         ntriplets_master, ratios_master_sorted, triplets_master_sorted_list = \
-                  gen_triplets_master(wv_master, LDEBUG=True)
+                  gen_triplets_master(wv_master)
         # FIXME: this depends on the spectral and dispersion axes
         nspec = rss.shape[0]
         coeff_table = numpy.zeros((nspec, poldeg + 1))
@@ -109,12 +110,11 @@ def calibrate_wl(self, rss, lines_catalog, poldeg, times_sigma=50.0):
             # find peaks (initial search providing integer numbers)
             threshold = numpy.median(row)+times_sigma*sigmaG(row)
             ipeaks_int = findPeaks_spectrum(row, nwinwidth=nwinwidth, 
-                                                 data_threshold=threshold,
-                                                 LDEBUG=False, LPLOT=False)
+                                                 data_threshold=threshold)
             # refine peaks fitting an appropriate function (providing float 
             # numbers)
             ipeaks_float = refinePeaks_spectrum(row, ipeaks_int, nwinwidth, 
-                                                method=2, LDEBUG=False)
+                                                method=2)
 
 
             # define interpolation function and interpolate the refined peak 
@@ -132,24 +132,7 @@ def calibrate_wl(self, rss, lines_catalog, poldeg, times_sigma=50.0):
             finterp_channel = interp1d(range(xchannel.size), xchannel, 
                                        kind='linear')
             xpeaks_refined = finterp_channel(ipeaks_float)
-
-            if False: # TBR (to be removed in the future)
-                # plot extracted spectrum
-                fig = plt.figure()
-                ax = fig.add_subplot(111)
-                ax.set_title('row %d' % idx)
-                ax.set_xlim([1,naxis1])
-                ax.plot(xchannel,row,'k-')
-                ax.plot(xchannel[ipeaks_int], row[ipeaks_int], 'ro')
-                ax.plot([1,naxis1],[threshold, threshold], linestyle='dashed')
-                ylim = ax.get_ylim()
-                for xdum in zip(xpeaks_refined,xpeaks_refined):
-                    ax.plot(xdum, ylim, linestyle='dotted', color='magenta')
-                plt.show()
-                #plt.show(block=False)
-                #input('press <RETURN> to continue...')
-
-           # wavelength calibration
+
             try:
                 solution = arccalibration_direct(wv_master,
                                                  ntriplets_master,
@@ -162,25 +145,21 @@ def calibrate_wl(self, rss, lines_catalog, poldeg, times_sigma=50.0):
                                                  error_xpos_arc=2.0,
                                                  times_sigma_r=3.0,
                                                  frac_triplets_for_sum=0.50,
-                                                 times_sigma_TheilSen=10.0,
-                                                 poly_degree=2,
+                                                 times_sigma_theil_sen=10.0,
+                                                 poly_degree_wfit=2,
                                                  times_sigma_polfilt=10.0,
-                                                 times_sigma_inclusion=5.0,
-                                                 LDEBUG=False,
-                                                 LPLOT=False)
+                                                 times_sigma_inclusion=5.0)
                 _logger.info('Solution for row %d completed', idx)
                 _logger.info('Fitting solution for row %d', idx)
                 numpy_array_with_coeff, crval1_approx, cdelt1_approx = \
                   fit_solution(wv_master,
                                xpeaks_refined,
                                solution,
-                               naxis1,
-                               poly_degree=2,
-                               weighted=False,
-                               LDEBUG=False,
-                               LPLOT=False)
+                               poly_degree_wfit=2,
+                               weighted=False)
 
-                _logger.info('approximate crval1, cdelt1: %f %f',crval1_approx,cdelt1_approx)
+                _logger.info('approximate crval1, cdelt1: %f %f',
+                             crval1_approx,cdelt1_approx)
                 _logger.info('fitted coefficients %s',numpy_array_with_coeff)
                 coeff_table[idx] = numpy_array_with_coeff
             except TypeError as error:

megaradrp/recipes/calibration/base.py

@@ -40,7 +40,6 @@
 from megaradrp.core import MegaraBaseRecipe
 from megaradrp.processing import OverscanCorrector, TrimImage
 from megaradrp.processing import ApertureExtractor, FiberFlatCorrector
-from megaradrp.core import peakdet
 # from numina.logger import log_to_history
 from megaradrp.requirements import MasterBiasRequirement
 from megaradrp.requirements import MasterFiberFlatRequirement

megaradrp/recipes/calibration/tests/test_arc.py

@@ -41,4 +41,4 @@ def test_mode_arc_calibration_set0(drpmocker):
     drpmocker.add_drp('MEGARA', megara_drp_load)
     load_cli_storage()
 
-    run_recipe()
+    run_recipe()