all non regression tests pass

XRStools/XES_spectra_extraction.py

@@ -104,25 +104,21 @@ def prepare(
         runit( s , work_dir, "05_setup_recentering.yaml" ) 
         
 
-
         s="""
         loadscan_2Dimages :
           expdata : {data_file}
           roiaddress : roi.h5:/ROI_AS_SELECTED 
           scan_interval : [{scan_for_roi},{scan_for_roi_P1}] 
-          monitor_column : {monitorcolumn}
+          monitorcolumn : {monitorcolumn}
           recenterings  : recentering.h5:/recentering
           recenterings_confirmed : recentering.h5:/confirmed_shift 
           signaladdress : Centered_sample_scans 
 
           sumto1D  : 0
           energycolumn : 'Anal Energy'
-          monitorcolumn : izero
         """.format( data_file = data,  scan_for_roi = scan_for_sample_roi , scan_for_roi_P1 = scan_for_sample_roi +1 , monitorcolumn = monitorcolumn )
         runit( s , work_dir, "06_calculate_recentering.yaml" ) 
 
-
-
         s="""
         superR_fit_responses:
            foil_scan_address : roi.h5:/ROI_AS_SELECTED/calibration_scan/scans/Scan%03d
@@ -137,7 +133,6 @@ def prepare(
            simmetrizza : 1
            filter_rois : 0
            target_file : fitted_response.h5:/ScanFittedResponse_%03d
-           MPI_N_PROCS : 1 
            fit_lines   : 1 
         """%( reference_scan, beta_response, reference_scan ) 
         runit( s , work_dir, "07_fit.yaml" ) 
@@ -149,7 +144,7 @@ def prepare(
            nex : 0 
            old_scan_address : roi.h5:/ROI_AS_SELECTED/calibration_scan/scans/Scan%03d
            filter_rois : 0
-           recenterings_refines : recentering.h5:/confirmed_shift
+           recenterings_refined : recentering.h5:/confirmed_shift
            target_filename : newscan.h5:/ROI_AS_SELECTED/calibration_scan/scans/ScanReSynth_%03d
         """%( reference_scan,  reference_scan,  reference_scan ) 
         runit( s , work_dir, "08_resynth.yaml" ) 
@@ -202,7 +197,7 @@ def extract(
      scan_interval : [{start}, {end}]
      zmargin : 0
      target : ../{result_file}:/fromscans_{start}_{end}
-     final_plot : PLOT
+     # final_plot : PLOT
      DE : 0.0
      niterLip : {niterLip}
      niter : {niter}

XRStools/XRS_swissknife.py

@@ -244,14 +244,14 @@ class Loader_map_as_anydict( object):
 class myOrderedDict (collections.OrderedDict):
     def __setitem__(self,a,b):
         if type(a)==type("") and a in self:
-            self[a+"_tagkajs"]=b 
+            self[a+"_TAG_this_key_is_given_twice"]=b 
         else:
             ## print super(myOrderedDict, self)
             super(myOrderedDict, self).__setitem__(a,b )
 
 
 def cleaned(key):
-    while key[-8:]=="_tagkajs":
+    while key[-28:]=="_TAG_this_key_is_given_twice":
         key=key[:-8]
     return key
   
@@ -1281,7 +1281,7 @@ def extract_spectra(mydata):
         final_plot        : "PLOT"  # or "NOPLOT"
     """
 
-    allowed_keys = [ "target","sample_address","scan_interval","roiaddress","DE","discard_threshold","threshold_fraction","zmargin", "flatTriggerer","slope","fitted_response","niter","niterLip","beta","weight_by_response","reference_scan", ]
+    allowed_keys = [ "target","sample_address","scan_interval","roiaddress","DE","discard_threshold","threshold_fraction","zmargin", "flatTriggerer","slope","fitted_response","niter","niterLip","beta","weight_by_response","reference_scan","reference_address" ]
     check_allowed_keys(mydata, allowed_keys)
     
     target_filename , target_groupname  = split_hdf5_address( mydata["target"])    
@@ -1390,7 +1390,7 @@ def extract_spectra(mydata):
         rois_keys = list(set.intersection(  set(rois_keys), set(rois_keys_orig)       ) )
 
 
-        printf(" After filtering the list of rois to be used is ",  rois_keys ) 
+        print(" After filtering the list of rois to be used is ",  rois_keys ) 
         
         incidentE = None
         if "motorDict/energy" in h5:
@@ -3975,7 +3975,10 @@ def superR_recreate_rois(mydata):
         h5f = h5py.File(recenterings_filename,"r")
         h5 = h5f[recenterings_groupname]
         recenterings= {}
-        chiavi = filterRoiList(h5.keys())
+
+        chiavi = filterRoiList(h5.keys(), prefix="")
+
+
         for c in chiavi:
             recenterings[int(c)]= h5[c][:]
             assert(recenterings[int(c)].shape == (2,))

nonregressions/xes/xes_analysis.py

@@ -9,8 +9,8 @@ if(1):
     os.system("xz -d --keep  preparation_run4_16/ROI.xz ; mv  preparation_run4_16/ROI   preparation_run4_16/roi.h5" ) 
     os.system("xz -d --keep  preparation_run4_16/roi_sample.h5.xz" ) 
 
-    
-    spectra_extraction.prepare(
+    if 1:
+        spectra_extraction.prepare(
         work_dir="preparation_run4_16",
         data = "/data/id20/inhouse/data/run4_16/run6_ihr/rixs" ,
         scan_for_roi= 66            ,           
@@ -27,7 +27,7 @@ if(1):
         do_recentering= True,
         
         beta_response = 1.0
-    ) 
+        ) 
 
 spectra_extraction.extract(
     work_dir="preparation_run4_16",
@@ -51,5 +51,5 @@ ref = np.loadtxt( "results/spectra_ref.txt")
 
 assert( abs(ref-results).max( )< 1.0e-7) 
 
-if os.environ["CLEAN_RESULTS"] == "true" :
+if   "CLEAN_RESULTS" in os.environ and   os.environ["CLEAN_RESULTS"] == "true" :
     os.system("rm results/*")

nonregressions/xrs_raman/non_reg_testing_XRS.py

@@ -280,5 +280,5 @@ lw_ex.save_average_Sqw(save_path+'/h2o_pixel_hq.dat', emin=0.0, emax=600.0, norm
 
 check_results( os.path.join(save_path,'h2o_pixel_hq.dat') , os.path.join(save_path,"h2o_pixel_hq_ref.dat")   )
 
-if os.environ["CLEAN_RESULTS"] == "true" :
+if  "CLEAN_RESULTS" in os.environ and  os.environ["CLEAN_RESULTS"] == "true" :
     os.system("rm %s/*" % save_path)

nonregressions/xrs_raman/non_reg_testing_XRS_raman_extraction.py

@@ -387,5 +387,5 @@ check_results(tosavepath("non_reg_output_gui_raman_mediumq.txt"),tosavepath("non
 check_results(tosavepath("non_reg_output_gui_raman_highq.txt"),tosavepath("non_reg_output_gui_raman_reference_highq.txt"))
 print(" OK " )
 
-if os.environ["CLEAN_RESULTS"] == "true" :
+if "CLEAN_RESULTS" in os.environ and  os.environ["CLEAN_RESULTS"] == "true" :
     os.system("rm %s/*" % save_path)

nonregressions/xrs_raman/non_reg_testing_XRS_small.py

@@ -282,5 +282,5 @@ lw_ex.save_average_Sqw(save_path+'/h2o_pixel_hq_small.dat', emin=0.0, emax=600.0
 
 check_results( os.path.join(save_path,'h2o_pixel_hq_small.dat') , os.path.join(save_path,"h2o_pixel_hq_small.dat.ref")   )
 
-if os.environ["CLEAN_RESULTS"] == "true" :
+if "CLEAN_RESULTS" in os.environ and os.environ["CLEAN_RESULTS"] == "true" :
     os.system("rm %s/*" % save_path)