Magnetic field directory specification

README.md

@@ -21,10 +21,10 @@ A previous incarnation of this code, GACHD ([Lowder et al. 2014](http://adsabs.h
 import numpy as np
 from chortle import chortle, genprof
 
-crlist = np.arange(2193,2200)
+crlist = np.arange(2193,2269)
 
 for cr in crlist:
-    chortle(crlist)
+    chortle(cr)
 
 genprof(crlist[0], crlist[-1])
 ```

chortle.py

@@ -83,9 +83,11 @@ def chortle(cr, plot=False):
         nsday * u.day) & a.Time(t0, t1))
     res_stb = Fido.search(a.Wavelength(19.5 * u.nm), search_stb)
 
-    search_hmi = Fido.search(a.jsoc.Series('hmi.Synoptic_Mr_polfil_720s'), 
-                             a.jsoc.PrimeKey('CAR_ROT', str(cr)), 
-                             a.jsoc.Notify(os.environ["JSOC_EMAIL"]))
+    if not os.path.exists(magdir + 'hmi.synoptic_mr_polfil_720s.' + str(cr) + '.Mr_polfil.fits'):
+        search_hmi = Fido.search(a.jsoc.Series('hmi.Synoptic_Mr_polfil_720s'), 
+                                a.jsoc.PrimeKey('CAR_ROT', str(cr)), 
+                                a.jsoc.Notify(os.environ["JSOC_EMAIL"]))
+        files_hmi = Fido.fetch(search_hmi, path=magdir)
 
     files_aia = Fido.fetch(res_aia, path=datdir + 'aia/')
     files_aia.sort()
@@ -98,8 +100,6 @@ def chortle(cr, plot=False):
 
     skip_aia = skip_sta = skip_stb = False
 
-    files_hmi = Fido.fetch(search_hmi, path=magdir)
-
     if len(files_aia) == 0:
         skip_aia = True
     if len(files_sta) == 0:
@@ -437,11 +437,15 @@ def chortle(cr, plot=False):
 
 def grab_data():
 
-    # Specify any directories
-    hmidat = os.path.expanduser('~/data/hmi.Synoptic_Mr.polfil/')
+    # Read configuration file
+    config = configparser.ConfigParser()
+    config.read('config.cfg')
+
+    # Specify directory structures from configuration file    
+    magdir = config['paths']['magdir']
 
     # Sort out the last downloaded rotation
-    crfiles = glob.glob(hmidat+'*.fits')
+    crfiles = glob.glob(magdir+'*.fits')
     crfiles.sort()
     crlist = [int(i[-19:-15]) for i in crfiles]
 
@@ -463,7 +467,7 @@ def grab_data():
     res = Fido.search(a.jsoc.Series('hmi.Synoptic_Mr_polfil_720s'), crots, a.jsoc.Notify(os.environ["JSOC_EMAIL"]))
 
     # Once the query is made and trimmed down...
-    download = Fido.fetch(res, path=hmidat+'{file}.fits')
+    download = Fido.fetch(res, path=magdir+'{file}.fits')
 
 
 def genprof(cr0, cr1):
@@ -572,7 +576,7 @@ def chortle_eit(cr, plot=False):
 
     # Specify directory structures from configuration file
     datdir = config['paths']['datdir']
-    magdir = config['paths']['magdir']
+    magdir_mdi = config['paths']['magdir_mdi']
     outdir = config['paths']['outdir']
 
     # Specify timing parameters
@@ -602,7 +606,7 @@ def chortle_eit(cr, plot=False):
     files_eit.sort()
 
     ## Grab a synoptic magnetogram
-    with astropy.io.fits.open(magdir + 'mdi.synoptic_mr_polfil_720s.' + str(cr) + '.Mr_polfil.fits') as hdul:
+    with astropy.io.fits.open(magdir_mdi + 'mdi.synoptic_mr_polfil_720s.' + str(cr) + '.Mr_polfil.fits') as hdul:
         br = hdul[0].data
 
     ## Generate some blank storage arrays

config.cfg

@@ -4,6 +4,7 @@
 # Input data directory
 datdir = /Users/clowder/data/chortle/
 # Magnetic field data directory
-magdir =/Users/clowder/data/hmi.Synoptic_Mr.polfil/ 
+magdir = /Users/clowder/data/hmi.Synoptic_Mr.polfil/ 
+magdir_mdi = /Users/clowder/data/mdi.Synoptic_Mr.polfil/ 
 # Output data directory
 outdir = /Users/clowder/data/chortle/