[yt-svn] commit/yt: 3 new changesets

[commits-noreply at bitbucket.org]

3 new commits in yt:

https://bitbucket.org/yt_analysis/yt/commits/f907a339e78e/
Changeset:   f907a339e78e
Branch:      yt
User:        hegan
Date:        2013-10-19 00:24:26
Summary:     Fixed OOB errors for windowed spectra and bug with single wavelength partner checking
Affected #:  1 file

diff -r c2b8455b43a67b78aa01953daf000dcca10aa8cb -r f907a339e78e7363c74d2b17ed7a6ac01ffd863f yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
--- a/yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
+++ b/yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
@@ -86,6 +86,10 @@
     #Empty fit without any lines
     yFit = na.ones(len(fluxData))
 
+    #Force the first and last flux pixel to be 1 to prevent OOB
+    fluxData[0]=1
+    fluxData[-1]=1
+
     #Find all regions where lines/groups of lines are present
     cBounds = _find_complexes(x, fluxData, fitLim=fitLim,
             complexLim=complexLim, minLength=minLength,
@@ -103,6 +107,7 @@
         initWl = speciesDict['wavelength'][0]
 
         for b_i,b in enumerate(cBounds):
+            print b
             xBounded=x[b[1]:b[2]]
             yDatBounded=fluxData[b[1]:b[2]]
             yFitBounded=yFit[b[1]:b[2]]
@@ -120,9 +125,10 @@
                     z,fitLim,minError*(b[2]-b[1]),speciesDict)
 
             #Check existence of partner lines if applicable
-            newLinesP = _remove_unaccepted_partners(newLinesP, x, fluxData, 
-                    b, minError*(b[2]-b[1]),
-                    x0, xRes, speciesDict)
+            if len(speciesDict['wavelength']) != 1:
+                newLinesP = _remove_unaccepted_partners(newLinesP, x, fluxData, 
+                        b, minError*(b[2]-b[1]),
+                        x0, xRes, speciesDict)
 
             #If flagged as a bad fit, species is lyman alpha,
             #   and it may be a saturated line, use special tools
@@ -548,6 +554,10 @@
         #Index of the redshifted wavelength
         indexRedWl = (redWl-x0)/xRes
 
+        #Check to see if even in flux range
+        if indexRedWl > len(y):
+            return False
+
         #Check if surpasses minimum absorption bound
         if y[int(indexRedWl)]>fluxMin:
             return False


https://bitbucket.org/yt_analysis/yt/commits/0a55ec8da822/
Changeset:   0a55ec8da822
Branch:      yt
User:        hegan
Date:        2013-10-19 00:27:50
Summary:     got rid of accidental print statement
Affected #:  1 file

diff -r f907a339e78e7363c74d2b17ed7a6ac01ffd863f -r 0a55ec8da8220b26b8215884bdef52ec34ab5f78 yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
--- a/yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
+++ b/yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
@@ -107,7 +107,6 @@
         initWl = speciesDict['wavelength'][0]
 
         for b_i,b in enumerate(cBounds):
-            print b
             xBounded=x[b[1]:b[2]]
             yDatBounded=fluxData[b[1]:b[2]]
             yFitBounded=yFit[b[1]:b[2]]


https://bitbucket.org/yt_analysis/yt/commits/7b1622244f87/
Changeset:   7b1622244f87
Branch:      yt
User:        brittonsmith
Date:        2013-10-22 07:52:48
Summary:     Merged in hegan/yt (pull request #617)

Absorption spectrum fitting tweaks
Affected #:  1 file

diff -r 0969081e02f4b595a6b60473d7582ab7b3f195c4 -r 7b1622244f87f663d42f3f6e8e70d8c5eacc15b2 yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
--- a/yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
+++ b/yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
@@ -86,6 +86,10 @@
     #Empty fit without any lines
     yFit = na.ones(len(fluxData))
 
+    #Force the first and last flux pixel to be 1 to prevent OOB
+    fluxData[0]=1
+    fluxData[-1]=1
+
     #Find all regions where lines/groups of lines are present
     cBounds = _find_complexes(x, fluxData, fitLim=fitLim,
             complexLim=complexLim, minLength=minLength,
@@ -120,9 +124,10 @@
                     z,fitLim,minError*(b[2]-b[1]),speciesDict)
 
             #Check existence of partner lines if applicable
-            newLinesP = _remove_unaccepted_partners(newLinesP, x, fluxData, 
-                    b, minError*(b[2]-b[1]),
-                    x0, xRes, speciesDict)
+            if len(speciesDict['wavelength']) != 1:
+                newLinesP = _remove_unaccepted_partners(newLinesP, x, fluxData, 
+                        b, minError*(b[2]-b[1]),
+                        x0, xRes, speciesDict)
 
             #If flagged as a bad fit, species is lyman alpha,
             #   and it may be a saturated line, use special tools
@@ -548,6 +553,10 @@
         #Index of the redshifted wavelength
         indexRedWl = (redWl-x0)/xRes
 
+        #Check to see if even in flux range
+        if indexRedWl > len(y):
+            return False
+
         #Check if surpasses minimum absorption bound
         if y[int(indexRedWl)]>fluxMin:
             return False

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

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