tidy up main script making use of new query library

src/lib/background.py

@@ -10,6 +10,7 @@ prototypes :
         Compute the error (noise) of the input array by looking at the sub-region of minimal flux in every image and of shape sub_shape.
 """
 import sys
+from os.path import join as path_join
 from copy import deepcopy
 import numpy as np
 import matplotlib.pyplot as plt
@@ -59,7 +60,7 @@ def display_bkg(data, background, std_bkg, headers, histograms=None, binning=Non
     ax.set_ylabel(r"Flux [$ergs \cdot cm^{-2} \cdot s^{-1} \cdot \AA^{-1}$]")
     plt.legend()
     if not(savename is None):
-        fig.savefig(plots_folder+savename+"_background_flux.png", bbox_inches='tight')
+        fig.savefig(path_join(plots_folder,savename+"_background_flux.png"), bbox_inches='tight')
 
     if not(histograms is None):
         filt_obs = {"POL0":0, "POL60":0, "POL120":0}
@@ -78,7 +79,7 @@ def display_bkg(data, background, std_bkg, headers, histograms=None, binning=Non
         ax_h.set_title("Histogram for each observation")
         plt.legend()
         if not(savename is None):
-            fig_h.savefig(plots_folder+savename+'_histograms.png', bbox_inches='tight')
+            fig_h.savefig(path_join(plots_folder,savename+'_histograms.png'), bbox_inches='tight')
 
     fig2, ax2 = plt.subplots(figsize=(10,10))
     data0 = data[0]*convert_flux[0]
@@ -103,7 +104,7 @@ def display_bkg(data, background, std_bkg, headers, histograms=None, binning=Non
     fig2.colorbar(im, cax=cbar_ax, label=r"Flux [$ergs \cdot cm^{-2} \cdot s^{-1} \cdot \AA^{-1}$]")
 
     if not(savename is None):
-        fig2.savefig(plots_folder+savename+'_'+filt+'_background_location.png', bbox_inches='tight')
+        fig2.savefig(path_join(plots_folder,savename+'_'+filt+'_background_location.png'), bbox_inches='tight')
         if not(rectangle is None):
             plot_obs(data, headers, vmin=data[data > 0.].min()*convert_flux.mean(), vmax=data[data > 0.].max()*convert_flux.mean(), rectangle=rectangle,
                     savename=savename+"_background_location",plots_folder=plots_folder)

src/lib/fits.py

@@ -10,6 +10,7 @@ prototypes :
 """
 
 import numpy as np
+from os.path import join as path_join
 from astropy.io import fits
 from astropy import wcs
 from lib.convex_hull import image_hull, clean_ROI
@@ -39,7 +40,7 @@ def get_obs_data(infiles, data_folder="", compute_flux=False):
     """
     data_array, headers = [], []
     for i in range(len(infiles)):
-        with fits.open(data_folder+infiles[i]) as f:
+        with fits.open(path_join(data_folder,infiles[i])) as f:
             headers.append(f[0].header)
             data_array.append(f[0].data)
     data_array = np.array(data_array,dtype=np.double)
@@ -188,7 +189,7 @@ def save_Stokes(I_stokes, Q_stokes, U_stokes, Stokes_cov, P, debiased_P, s_P,
         hdul.append(hdu)
 
     #Save fits file to designated filepath
-    hdul.writeto(data_folder+filename+".fits", overwrite=True)
+    hdul.writeto(path_join(data_folder,filename+".fits"), overwrite=True)
 
     if return_hdul:
         return hdul

src/lib/plots.py

@@ -38,6 +38,7 @@ prototypes :
 
 from copy import deepcopy
 import numpy as np
+from os.path import join as path_join
 import matplotlib.pyplot as plt
 from matplotlib.patches import Rectangle, Circle
 from matplotlib.path import Path
@@ -161,7 +162,7 @@ def plot_obs(data_array, headers, shape=None, vmin=None, vmax=None, rectangle=No
 
     if not (savename is None):
         #fig.suptitle(savename)
-        fig.savefig(plots_folder+savename+".png",bbox_inches='tight')
+        fig.savefig(path_join(plots_folder,savename+".png"),bbox_inches='tight')
     plt.show()
     return 0
 
@@ -211,7 +212,7 @@ def plot_Stokes(Stokes, savename=None, plots_folder=""):
 
     if not (savename is None):
         #fig.suptitle(savename+"_IQU")
-        fig.savefig(plots_folder+savename+"_IQU.png",bbox_inches='tight')
+        fig.savefig(path_join(plots_folder,savename+"_IQU.png"),bbox_inches='tight')
     plt.show()
     return 0
 
@@ -320,7 +321,7 @@ def polarization_map(Stokes, data_mask=None, rectangle=None, SNRp_cut=3., SNRi_c
     if display.lower() in ['intensity']:
         # If no display selected, show intensity map
         display='i'
-        vmin, vmax = 1.*np.mean(np.sqrt(stk_cov.data[0,0][mask])*convert_flux), np.max(stkI.data[stkI.data > 0.]*convert_flux)
+        vmin, vmax = 1/5.0*np.mean(np.sqrt(stk_cov.data[0,0][mask])*convert_flux), np.max(stkI.data[stkI.data > 0.]*convert_flux)
         im = ax.imshow(stkI.data*convert_flux, norm=LogNorm(vmin,vmax), aspect='equal', cmap='inferno', alpha=1.)
         cbar = plt.colorbar(im, cax=cbar_ax, label=r"$F_{\lambda}$ [$ergs \cdot cm^{-2} \cdot s^{-1} \cdot \AA^{-1}$]")
         levelsI = np.linspace(vmax*0.01, vmax*0.99, 10)
@@ -446,7 +447,7 @@ def polarization_map(Stokes, data_mask=None, rectangle=None, SNRp_cut=3., SNRi_c
 
     if not savename is None:
         #fig.suptitle(savename)
-        fig.savefig(plots_folder+savename+".png",bbox_inches='tight',dpi=300)
+        fig.savefig(path_join(plots_folder,savename+".png"),bbox_inches='tight',dpi=300)
 
     plt.show()
     return fig, ax
@@ -1766,7 +1767,7 @@ class pol_map(object):
             self.display_selection = "total_flux"
         if self.display_selection.lower() in ['total_flux']:
             self.data = self.I*self.convert_flux
-            vmin, vmax = 1/2.0*np.median(self.data[self.data > 0.]), np.max(self.data[self.data > 0.])
+            vmin, vmax = 1/5.0*np.median(self.data[self.data > 0.]), np.max(self.data[self.data > 0.])
             norm = LogNorm(vmin, vmax)
             label = r"$F_{\lambda}$ [$ergs \cdot cm^{-2} \cdot s^{-1} \cdot \AA^{-1}$]"
         elif self.display_selection.lower() in ['pol_flux']:

src/lib/query.py

@@ -1,5 +1,3 @@
-from sys import exit as sys_exit, argv as sys_argv
-from getopt import getopt, error as geterr
 from os import system
 from os.path import join as path_join, exists as path_exists
 from astroquery.mast import MastMissions, Observations
@@ -102,10 +100,11 @@ def get_product_list(target, proposal_id=None):
     return products
 
 
-def retrieve_products(target, products):
+def retrieve_products(target, proposal_id=None):
     """
-    Given a target name and a products list, create the local directories and retrieve the fits files from the MAST Archive
+    Given a target name and a proposal_id, create the local directories and retrieve the fits files from the MAST Archive
     """
+    products = get_product_list(target=target,proposal_id=proposal_id)
     prodpaths = []
     data_dir = path_join("../data", target)
     out = ""
@@ -113,7 +112,7 @@ def retrieve_products(target, products):
         filepaths = []
         obs_dir = path_join(data_dir, obs_id)
         if not path_exists(obs_dir):
-            system("mkdir -p "+obs_dir)
+            system("mkdir -p {0:s} {1:s}".format(obs_dir,path_join("../plots",target,obs_id)))
         for file in products['productFilename'][products['proposal_id'] == obs_id]:
             fpath = path_join(obs_dir, file)
             if not path_exists(fpath):
@@ -121,37 +120,20 @@ def retrieve_products(target, products):
                     products['dataURI'][products['productFilename'] == file][0], local_path=fpath)[0])
             else:
                 out += "{0:s} : Exists\n".format(file)
-            filepaths.append(fpath)
-        prodpaths.append(filepaths)
+            filepaths.append([obs_dir,file])
+        prodpaths.append(np.array(filepaths,dtype=str))
 
     return prodpaths
 
 
-def main():
-    
-    target, proposal_id = None, None
-    try:
-        arg, _ = getopt(sys_argv[1:], "ht:p:", ["help", "target=", "proposal_id="])
-        for curr_arg, curr_val in arg:
-            if curr_arg in ("-h", "--help"):
-                print("python3 query.py -t <target_name> -p <proposal_id>")
-            elif curr_arg in ("-t", "--target"):
-                target = str(curr_val)
-            elif curr_arg in ("-p", "--proposal_id"):
-                proposal_id = int(curr_val)
-    except geterr:
-        print(str(geterr))
-    
-    if target is None:
-        target = input("Target name\n>")
-
-    products = get_product_list(target=target,proposal_id=proposal_id)
-    products_paths = retrieve_products(target=target, products=products)
-
-    print(products_paths)
-
-    return 0
-
-
 if __name__ == "__main__":
-    sys_exit(main())
+    import argparse
+
+    parser = argparse.ArgumentParser(description='Query MAST for target products')
+    parser.add_argument('-t','--target', metavar='targetname', required=False,
+                        help='the name of the target', type=str, default=None)
+    parser.add_argument('-p','--proposal_id', metavar='proposal_id', required=False,
+                        help='the proposal id of the data products', type=int, default=None)
+    args = parser.parse_args()
+    prodpaths = retrieve_products(target=args.target, proposal_id=args.proposal_id)
+    print(prodpaths)