getrawfitspath() will return url; TODO listed.

SpectrumViewer - Copy/.ipynb_checkpoints/demo 1-checkpoint.ipynb

@@ -0,0 +1,6 @@
+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

SpectrumViewer - Copy/.ipynb_checkpoints/demo 2-checkpoint.ipynb

@@ -0,0 +1,62 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "ename": "ModuleNotFoundError",
+     "evalue": "No module named 'SpectrumViewer'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[1;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
+      "\u001b[1;32m<ipython-input-6-5fc1ec971204>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[1;32mimport\u001b[0m \u001b[0mInlineViewer\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m      2\u001b[0m \u001b[0mget_ipython\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mmagic\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'matplotlib notebook'\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      3\u001b[0m \u001b[0mfileName\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;34m'example_lite.fits'\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      4\u001b[0m \u001b[0mfileSource\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;34m'SDSS'\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      5\u001b[0m \u001b[0mInlineViewer\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mview\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfileName\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mfileSource\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
+      "\u001b[1;32mC:\\Users\\wzuo\\Developer\\Spectrum Viewer\\SpectrumViewer\\InlineViewer.py\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[1;32mimport\u001b[0m \u001b[0mSpectrumViewer\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mSpecUtil_inline\u001b[0m \u001b[1;32mas\u001b[0m \u001b[0minline\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m      2\u001b[0m \u001b[1;32mimport\u001b[0m \u001b[0mSpectrumViewer\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mSDSSDriver\u001b[0m \u001b[1;32mas\u001b[0m \u001b[0mdriver\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      3\u001b[0m \u001b[1;32mdef\u001b[0m \u001b[0mview\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfilename\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mfilesource\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      4\u001b[0m     \u001b[0mcoaddObj\u001b[0m\u001b[1;33m,\u001b[0m\u001b[0mzObj\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mdriver\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mloadFITS\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfilename\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mfilesource\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      5\u001b[0m     \u001b[0mspec\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0minline\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mSpecUtil\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfilename\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mcoaddObj\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mzObj\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
+      "\u001b[1;31mModuleNotFoundError\u001b[0m: No module named 'SpectrumViewer'"
+     ]
+    }
+   ],
+   "source": [
+    "import InlineViewer\n",
+    "%matplotlib notebook\n",
+    "fileName = 'example_lite.fits'\n",
+    "fileSource = 'SDSS'\n",
+    "InlineViewer.view(fileName, fileSource)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 1
+}

SpectrumViewer - Copy/CoaddObj.py

@@ -0,0 +1,17 @@
+# This class init with a fits file in the directory and store all the data in the RAM
+import numpy as np
+class CoaddObj:
+    def __init__(self,flux,loglam=None,ivar=None,andMask=None,orMask=None
+                 ,wdisp=None,sky=None,model=None):#type can be pfs
+        self.flux = flux
+        self.loglam = loglam
+        self.ivar =ivar
+        self.andMask =andMask
+        self.orMask = orMask
+        self.wdisp = wdisp
+        self.sky =sky
+        self.model = model
+        self.lam = np.power(10,self.loglam)
+
+
+

SpectrumViewer - Copy/InlineViewer.py

@@ -0,0 +1,6 @@
+import SpectrumViewer.SpecUtil_inline as inline
+import SpectrumViewer.SDSSDriver as driver
+def view(filename, filesource):
+    coaddObj,zObj=driver.loadFITS(filename, filesource)
+    spec = inline.SpecUtil(filename, coaddObj, zObj)
+    spec.showfig()

SpectrumViewer - Copy/SDSSDriver.py

@@ -0,0 +1,52 @@
+#load SDSS into workable object
+from astropy.io import fits
+#from py3.SciServer import Authentication, Config
+#from py3.SciServer import CasJobs
+from urllib.parse import urlparse
+import SpectrumViewer.CoaddObj as Coadd
+import SpectrumViewer.ZObj as Z
+# def getSpecObjID(ra, dec, width, height, context=None, URL=True):
+#     leftBoundry = ra - width / 2
+#     rightBoundry = ra + width / 2
+#     upperBoundry = dec + height / 2
+#     lowerBoundry = dec - height / 2
+#     sqlQuery = 'select specObjID from dr7.specobjall Where (ra >' + str(leftBoundry) + ' and ra<' + str(
+#         rightBoundry) + ') and (dec>' + str(lowerBoundry) + ' and dec<' + str(upperBoundry) + ')'
+#     return CasJobs.executeQuery(sqlQuery, context='dr7', format='pandas')
+# def getRawFITSPathInDAS(SpecObjID):
+#     sqlQuery = 'select dr7.fGetUrlFitsSpectrum('+SpecObjID+')'
+#     response = CasJobs.executeQuery(sqlQuery, context='dr7', format='pandas')
+#     url= response['Column1'][0]
+#     parseResult = urlparse(url)
+#     prefix = '/home/idies/workspace/sdss_das/das2'
+#     path = prefix+parseResult.path
+#     return path
+
+def loadFITS(filename,fileSource):
+
+    if fileSource=='SDSS':
+        coaddData =1
+        zData =3
+        hdulist = fits.open(filename)
+        c=hdulist[coaddData].data
+        z=hdulist[zData].data
+        coaddObj = Coadd.CoaddObj(
+            flux=c['flux'],
+            loglam=c['loglam'],
+            ivar=c['ivar'],
+            andMask=c['and_Mask'],
+            orMask=c['or_Mask'],
+            wdisp=c['wdisp'],
+            sky = c['sky'],
+            model=c['model'])
+        zObj = Z.ZObj(
+            LINENAME=z['LINENAME'],
+            LINEWAVE=z['LINEWAVE'],
+            LINEZ=z['LINEZ'],
+            LINEEW=z['LINEEW'],
+            LINEZ_ERR=z['LINEZ_ERR'],
+            LINEEW_ERR=z['LINEEW_ERR'])
+        return coaddObj,zObj
+
+    else:
+        print('Sorry, we are loyal to SDSS ONLY, for the time being. ')

SpectrumViewer - Copy/SpecUtil.py

@@ -0,0 +1,131 @@
+# this file hold utility functions that generate the plot and actual data
+import matplotlib.pyplot as plt
+from matplotlib.figure import Figure
+import numpy as np
+class SpecUtil:
+    def __init__(self,coaddObj,zObj):
+        self.coaddObj = coaddObj
+        self.zObj=zObj
+        # self.totalFig = plt.figure()
+        # self.shownFig = plt.figure()
+        #self.totalFig = Figure(figsize=(5, 4), dpi=100)
+        self.shownFig = Figure(figsize=(5, 4), dpi=100)
+        self.shownFig = plt.figure()
+        self.plotDict = {0: True,
+                         1: True,
+                         2: True,
+                         3: True,
+                         4: True}
+        #0 flux 1 skyline 2 emission 3 absorb 4 model
+        #self.totalAx = self.totalFig.add_subplot(111)
+        #fluxLine,=self.totalAx.plot(self.coaddObj.lam,self.coaddObj.flux)
+        #skyLine, = self.totalAx.plot(self.coaddObj.lam,self.coaddObj.sky)
+
+        self.shownAx = self.shownFig.add_subplot(111)
+        self.shownAx.set_xlabel('lambda/Å')
+        self.shownAx.set_ylabel('10-17 ergs/s/cm2/Å')
+
+        for key in self.plotDict.keys():
+            if self.plotDict[key]:
+                try:
+                    self.plotLines(self.shownAx, key)
+                except IndexError: # dict is longer than plot numbers in totalax
+                    pass
+        self.shownAx.legend()
+        #self.shownAx = self.totalAx
+    def updateFig(self):
+        #self.shownAx.lines=[]
+        self.shownAx.clear()
+        self.shownAx.set_xlabel('lambda/Å')
+        self.shownAx.set_ylabel('10-17 ergs/s/cm2/Å')
+        for key in self.plotDict.keys():
+            if self.plotDict[key]:
+                try:
+                    self.plotLines(self.shownAx,key)
+                except IndexError:
+                    pass
+        #line1, = ax.plot(x, y, 'b-')
+        self.shownAx.legend()
+        #for phase in np.linspace(0, 10 * np.pi, 100):
+         #   line1.set_ydata(np.sin(0.5 * x + phase))
+          #  fig.canvas.draw()
+    def addFlux(self):
+        self.plotDict[0]=True
+        self.updateFig()
+    def removeFlux(self):
+        self.plotDict[0] = False
+        self.updateFig()
+
+    def addSkyline(self):
+        self.plotDict[1] = True
+        self.updateFig()
+    def removeSkyline(self):
+        self.plotDict[1] = False
+        self.updateFig()
+    def addEmissionLine(self):
+        self.plotDict[2] = True
+        self.updateFig()
+    def removeEmissionLine(self):
+        self.plotDict[2] = False
+        self.updateFig()
+    def addAbsorbLine(self):
+        self.plotDict[3] = True
+        self.updateFig()
+    def removeAbsorbLine(self):
+        self.plotDict[3] = False
+        self.updateFig()
+    def addModel(self):
+        self.plotDict[4] = True
+        self.updateFig()
+    def removeModel(self):
+        self.plotDict[4] = False
+        self.updateFig()
+    def plotLines(self,axes,actionIndex):
+        if actionIndex==0:
+            axes.plot(self.coaddObj.lam, self.coaddObj.flux,'C0',label='flux')
+        elif actionIndex==1:
+            axes.plot(self.coaddObj.lam, self.coaddObj.sky,'C1',label='skyline')
+        elif actionIndex==2:
+            #plot emission line
+            self.plotSegment(axes,actionIndex)
+
+        elif actionIndex ==3:
+            #plot absorption line
+            self.plotSegment(axes,actionIndex)
+
+
+        elif actionIndex ==4:
+
+            #plot best fit model
+            axes.plot(self.coaddObj.lam, self.coaddObj.model, 'C3', label='best fit model')
+        else:
+
+            pass
+    def plotSegment(self,axes,actionIndex):
+
+        # read e/a line from zobj and plot it on axes with function from axhspan
+        if actionIndex==2:#emissiaon line
+            for lineIndex in range(0,len(self.zObj.LINENAME)):
+
+                width = self.zObj.LINEEW[lineIndex]
+                if width >0:
+                    #print(width)
+                    position = self.zObj.LINEWAVE[lineIndex]
+                    startPostition = position-width/2
+                    endPostition = position + width / 2
+                    name= self.zObj.LINENAME[lineIndex]
+                    #print(name)
+                    axes.axvspan(xmin=startPostition,xmax=endPostition, facecolor='C4')
+                    axes.text(position,0,name , rotation=90)
+        elif actionIndex==3:#absorption line
+            for lineIndex in range(0,len(self.zObj.LINENAME)):
+                width = self.zObj.LINEEW[lineIndex]
+                if width >0:
+                    #print(width)
+                    position = self.zObj.LINEWAVE[lineIndex]
+                    startPostition = position-width/2
+                    endPostition = position + width / 2
+                    name= self.zObj.LINENAME[lineIndex]
+                    #print(name)
+                    axes.axvspan(xmin=startPostition,xmax=endPostition, facecolor='C4')
+                    axes.text(position,0,name , rotation=90)