[yt-svn] commit/yt: ngoldbaum: Merged in jzuhone/yt (pull request #2210)

commits-noreply at bitbucket.org commits-noreply at bitbucket.org
Wed Jun 15 11:06:32 PDT 2016


1 new commit in yt:

https://bitbucket.org/yt_analysis/yt/commits/e0b1c973fefe/
Changeset:   e0b1c973fefe
Branch:      yt
User:        ngoldbaum
Date:        2016-06-15 18:06:25+00:00
Summary:     Merged in jzuhone/yt (pull request #2210)

Three fixes for photon_simulator
Affected #:  3 files

diff -r 3cc3e0d5b293914e592976c9c87e66e1a5b47154 -r e0b1c973fefe530286e6589ef119dce4e4fe09e4 yt/analysis_modules/photon_simulator/photon_simulator.py
--- a/yt/analysis_modules/photon_simulator/photon_simulator.py
+++ b/yt/analysis_modules/photon_simulator/photon_simulator.py
@@ -1194,8 +1194,9 @@
         col6 = pyfits.Column(name='FLUX', format='D', array=np.array([flux.value]))
         col7 = pyfits.Column(name='SPECTRUM', format='80A', array=np.array([phfile+"[PHLIST,1]"]))
         col8 = pyfits.Column(name='IMAGE', format='80A', array=np.array([phfile+"[PHLIST,1]"]))
+        col9 = pyfits.Column(name='SRC_NAME', format='80A', array=np.array(["yt_src"]))
 
-        coldefs = pyfits.ColDefs([col1, col2, col3, col4, col5, col6, col7, col8])
+        coldefs = pyfits.ColDefs([col1, col2, col3, col4, col5, col6, col7, col8, col9])
 
         wrhdu = pyfits.BinTableHDU.from_columns(coldefs)
         wrhdu.update_ext_name("SRC_CAT")
@@ -1350,13 +1351,17 @@
             f = pyfits.open(self.parameters["RMF"])
             nchan = int(f["EBOUNDS"].header["DETCHANS"])
             num = 0
-            for i in range(1,len(f["EBOUNDS"].columns)+1):
-                if f["EBOUNDS"].header["TTYPE%d" % i] == "CHANNEL":
+            if "MATRIX" in f:
+                mat_key = "MATRIX"
+            elif "SPECRESP MATRIX" in f:
+                mat_key = "SPECRESP MATRIX"
+            for i in range(1,len(f[mat_key].columns)+1):
+                if f[mat_key].header["TTYPE%d" % i] == "F_CHAN":
                     num = i
                     break
             if num > 0:
                 tlmin = "TLMIN%d" % num
-                cmin = int(f["EBOUNDS"].header[tlmin])
+                cmin = int(f[mat_key].header[tlmin])
             else:
                 mylog.warning("Cannot determine minimum allowed value for channel. " +
                               "Setting to 0, which may be wrong.")

diff -r 3cc3e0d5b293914e592976c9c87e66e1a5b47154 -r e0b1c973fefe530286e6589ef119dce4e4fe09e4 yt/analysis_modules/photon_simulator/spectral_models.py
--- a/yt/analysis_modules/photon_simulator/spectral_models.py
+++ b/yt/analysis_modules/photon_simulator/spectral_models.py
@@ -264,7 +264,7 @@
         emid = self.emid.d
         if self.thermal_broad:
             sigma = E0*np.sqrt(2.*kT*erg_per_keV/(self.A[element]*amu_grams))/cl
-            vec = broaden_lines(E0, sigma, amp, emid)*de
+            vec = broaden_lines(E0, sigma, amp, ebins)
         else:
             vec = np.histogram(E0, ebins, weights=amp)[0]
         tmpspec += vec

diff -r 3cc3e0d5b293914e592976c9c87e66e1a5b47154 -r e0b1c973fefe530286e6589ef119dce4e4fe09e4 yt/analysis_modules/photon_simulator/utils.pyx
--- a/yt/analysis_modules/photon_simulator/utils.pyx
+++ b/yt/analysis_modules/photon_simulator/utils.pyx
@@ -1,31 +1,30 @@
 import numpy as np
 cimport numpy as np
 cimport cython
-from libc.math cimport exp
-
-cdef double gfac = 1.0/np.sqrt(np.pi)
-
+from libc.math cimport erf
+    
 @cython.cdivision(True)
 @cython.boundscheck(False)
 @cython.wraparound(False)
 def broaden_lines(np.ndarray[np.float64_t, ndim=1] E0,
                   np.ndarray[np.float64_t, ndim=1] sigma,
                   np.ndarray[np.float64_t, ndim=1] amp,
-                  np.ndarray[np.float64_t, ndim=1] E):
+                  np.ndarray[np.float64_t, ndim=1] ebins):
 
-    cdef int i, j, n
-    cdef double x, isigma, iamp
-    cdef np.ndarray[np.float64_t, ndim=1] lines
+    cdef int i, j, n, m
+    cdef double x, isigma
+    cdef np.ndarray[np.float64_t, ndim=1] cdf, vec
 
     n = E0.shape[0]
-    m = E.shape[0]
-    lines = np.zeros(m)
-
+    m = ebins.shape[0]
+    cdf = np.zeros(m)
+    vec = np.zeros(m-1)
+    
     for i in range(n):
         isigma = 1.0/sigma[i]
-        iamp = gfac*amp[i]*isigma
         for j in range(m):
-            x = (E[j]-E0[i])*isigma
-            lines[j] += iamp*exp(-x*x)
-
-    return lines
+            x = (ebins[j]-E0[i])*isigma
+            cdf[j] = 0.5*(1+erf(x))
+        for j in range(m-1):
+            vec[j] = vec[j] + (cdf[j+1] - cdf[j])*amp[i]
+    return vec

Repository URL: https://bitbucket.org/yt_analysis/yt/

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