Merge pull request #25 from jbkalmbach/issue/12/create_notebook_for_p…

…aper

Issue/12/create notebook for paper

esp/__init__.py

@@ -1,5 +1,9 @@
-from .esp import *
-from .pca import *
-from .plot_utils import *
-from .spec_utils import *
-from .gp_utils import *
+__all__ = ["estimateBase", "NearestNeighborEstimate",
+           "gaussianProcessEstimate"]
+
+from .esp import estimateBase, nearestNeighborEstimate, gaussianProcessEstimate
+from .pca import pcaSED
+from .plot_utils import plotUtils
+from .spec_utils import specUtils
+from .lsst_utils import Bandpass, BandpassDict, Sed, PhysicalParameters
+from .gp_utils import optimize

esp/esp.py

@@ -5,6 +5,9 @@
 from .gp_utils import optimize
 from sklearn.neighbors import KNeighborsRegressor as knr
 
+__all__ = ["estimateBase", "NearestNeighborEstimate",
+           "gaussianProcessEstimate"]
+
 
 class estimateBase(object):
 

esp/gp_utils.py

@@ -1,6 +1,8 @@
 import numpy as np
 import scipy.optimize as op
 
+__all__ = ["optimize"]
+
 
 def optimize(gp_obj, x, y, **kwargs):
 

esp/lsst_utils/__init__.py

@@ -1,4 +1,6 @@
-from .Bandpass import *
-from .BandpassDict import *
-from .PhysicalParameters import *
-from .Sed import *
+__all__ = ["Bandpass", "BandpassDict", "PhysicalParameters", "Sed"]
+
+from .Bandpass import Bandpass
+from .BandpassDict import BandpassDict
+from .PhysicalParameters import PhysicalParameters
+from .Sed import Sed

esp/pca.py

@@ -3,7 +3,9 @@
 import numpy as np
 from .spec_utils import specUtils
 from sklearn.decomposition import PCA as sklPCA
-from .lsst_utils.Sed import Sed
+from .lsst_utils import Sed
+
+__all__ = ["pcaSED"]
 
 
 class pcaSED(specUtils):
@@ -150,6 +152,10 @@ def reconstruct_spectra(self, num_comps):
             np.dot(self.coeffs[:, :num_comps],
                    self.eigenspectra[:num_comps])
 
+        for spec_num in range(len(reconstructed_specs)):		
+            neg_idx = np.where(reconstructed_specs[spec_num] < 0.)[0]		
+            reconstructed_specs[spec_num][neg_idx] = 0.
+
         return reconstructed_specs
 
     def calc_colors(self, bandpass_dict, num_comps):

esp/plot_utils.py

@@ -3,6 +3,8 @@
 import matplotlib.pyplot as plt
 plt.style.use('ggplot')
 
+__all__ = ["plotUtils"]
+
 
 class plotUtils(object):
     """

esp/spec_utils.py

@@ -3,7 +3,9 @@
 import os
 import math
 import numpy as np
-from .lsst_utils.Sed import Sed
+from .lsst_utils import Sed
+
+__all__ = ["specUtils"]
 
 
 class specUtils(object):
@@ -28,7 +30,7 @@ def load_spectra(self, directory):
         for root, dirs, files in os.walk(directory):
             file_total = len(files)
             file_on = 1
-            for name in files:
+            for name in sorted(files):
                 if file_on % 100 == 0:
                     print(str("File On " + str(file_on) + " out of " +
                               str(file_total)))