Merge branch 'develop' of gitlab.oamp.dev:yannick/pcigale into develop

pcigale/analysis_modules/savefluxes/__init__.py

@@ -51,6 +51,11 @@ class SaveFluxes(AnalysisModule):
             "Name of the output file.",
             "computed_fluxes.txt"
         )),
+        ("save_sed", (
+            "boolean",
+            "If True, save the generated SED.",
+            "False"
+        )),
         ("output_format", (
             "string",
             "Format of the output file. Any format supported by astropy.table "
@@ -90,7 +95,7 @@ class SaveFluxes(AnalysisModule):
 
         out_file = parameters["output_file"]
         out_format = parameters["output_format"]
-
+        save_sed = parameters["save_sed"].lower() == "true"
 
         # Get the needed filters in the pcigale database. We use an ordered
         # dictionary because we need the keys to always be returned in the
@@ -132,8 +137,8 @@ class SaveFluxes(AnalysisModule):
                                      n_params * n_info),
                         (n_params, n_info))
 
-        initargs = (params, filters,  model_fluxes, model_parameters,
-                    time.time(), mp.Value('i', 0))
+        initargs = (params, filters, save_sed, model_fluxes,
+                    model_parameters, time.time(), mp.Value('i', 0))
         if cores == 1:  # Do not create a new process
             init_worker_fluxes(*initargs)
             for idx in range(n_params):

pcigale/analysis_modules/savefluxes/workers.py

@@ -11,8 +11,9 @@ import numpy as np
 
 from ...warehouse import SedWarehouse
 
+from ..utils import OUT_DIR
 
-def init_fluxes(params, filters, fluxes, info, t_begin, n_computed):
+def init_fluxes(params, filters, save_sed, fluxes, info, t_begin, n_computed):
     """Initializer of the pool of processes. It is mostly used to convert
     RawArrays into numpy arrays. The latter are defined as global variables to
     be accessible from the workers.
@@ -23,6 +24,8 @@ def init_fluxes(params, filters, fluxes, info, t_begin, n_computed):
         Handles the parameters from a 1D index.
     filters: OrderedDict
         Contains filters to compute the fluxes.
+    save_sed: boolean
+        Indicates whether the SED should be saved.
     fluxes: RawArray and tuple containing the shape
         Fluxes of individual models. Shared among workers.
     n_computed: Value
@@ -32,7 +35,8 @@ def init_fluxes(params, filters, fluxes, info, t_begin, n_computed):
 
     """
     global gbl_model_fluxes, gbl_model_info, gbl_n_computed, gbl_t_begin
-    global gbl_params, gbl_previous_idx, gbl_filters, gbl_warehouse
+    global gbl_params, gbl_previous_idx, gbl_filters, gbl_save_sed
+    global gbl_warehouse
 
     gbl_model_fluxes = np.ctypeslib.as_array(fluxes[0])
     gbl_model_fluxes = gbl_model_fluxes.reshape(fluxes[1])
@@ -49,6 +53,8 @@ def init_fluxes(params, filters, fluxes, info, t_begin, n_computed):
 
     gbl_filters = filters
 
+    gbl_save_sed = save_sed
+
     gbl_warehouse = SedWarehouse()
 
 
@@ -72,6 +78,9 @@ def fluxes(idx):
     sed = gbl_warehouse.get_sed(gbl_params.modules,
                                 gbl_params.from_index(idx))
 
+    if gbl_save_sed == True:
+        sed.to_votable(OUT_DIR + "{}_best_model.xml".format(idx))
+
     if 'age' in sed.info and sed.info['age'] > sed.info['universe.age']:
         model_fluxes = -99. * np.ones(len(gbl_filters))
     else:

pcigale/analysis_modules/utils.py

@@ -171,4 +171,7 @@ def save_fluxes(model_fluxes, model_parameters, filters, names, filename,
     out_table = Table(np.hstack((out_fluxes, out_params)),
                       names=list(filters.keys()) + list(names))
 
+    out_table.add_column(Column(np.arange(model_fluxes[1][0]), name='id'),
+                         index=0)
+
     out_table.write("{}/{}".format(directory, filename), format=out_format)