reorganised volume fit

XRStools/XRS_swissknife.py

@@ -2333,7 +2333,7 @@ def superR_getVolume_fullfit(mydata):
 
          niter                     :  20
          beta                      :  1.0e-8
-         eps                       : 0.000002
+         eps                       :  0.000002
 
          ###################################
          # optional
@@ -3929,6 +3929,9 @@ def superR_recreate_rois(mydata):
          original_roi_path : None
 
     """
+    allowed_keys = ["old_scan_address","original_roi_path","responsefilename","nex","target_filename","filter_rois","recenterings_refined","filter_path",]
+    check_allowed_keys(mydata, allowed_keys)
+
     foil_scan_address = mydata["old_scan_address"]
     foil_filename ,foil_groupname   = split_hdf5_address(foil_scan_address)
 
@@ -4081,6 +4084,10 @@ def superR_fit_responses(mydata):
 
     """ 
 
+    allowed_keys = ["foil_scan_address","ref_scan_number","response_scan_address","nref","niter_optical","beta_optical","beta_pixel","niter_pixel","niter_global","pixel_dim","simmetrizza","do_refine_trajectory","target_file","trajectory_reference_scansequence_address","trajectory_threshold","reload_trajectories_file","filter_rois","fit_lines",]
+    check_allowed_keys(mydata, allowed_keys)
+
+        
     if "foil_scan_address" in mydata:
         foil_scan_address = mydata["foil_scan_address"]
     else:

nonregressions/volumes/interpola_1/batch_extraction_esynth1.py

@@ -4,6 +4,7 @@ import glob
 import json
 import os
 import h5py
+import math
 
 BATCH_PARALLELISM = 4
 
@@ -57,9 +58,11 @@ def main():
     selected_rois = list(range(0,24)) + list( range(36,60) ) 
 
 
-    scal_prod_use_optional_solution = False 
-    scal_prod_load_factors          =   False 
-    scal_prod_load_factors_from     = "factors.json"  
+    scal_prod_use_optional_solution = True 
+
+
+    volume_retrieval_beta  = 6.0e-20
+    volume_retrieval_niter = 100 
     
     scalar_products_and_volume_target_file  = "results/scalar_products_and_volume.h5"
 
@@ -72,7 +75,8 @@ def main():
                 
         "do_step_fit_reference_response":               False,
         "do_step_resynthetise_reference":               False,
-        "do_step_scalars"               :    True
+        "do_step_scalars"               :    True,
+        "do_step_volume_retrieval"      :    False,
     }
 
     
@@ -120,9 +124,12 @@ def main():
                       selected_rois = selected_rois,
                       
                       scal_prod_use_optional_solution = scal_prod_use_optional_solution ,
-                      scal_prod_load_factors          = scal_prod_load_factors   ,
-                      scal_prod_load_factors_from     = scal_prod_load_factors_from  ,
-                      scalar_products_and_volume_target_file      = scalar_products_and_volume_target_file 
+                      scalar_products_and_volume_target_file      = scalar_products_and_volume_target_file ,
+
+                      volume_retrieval_beta  = volume_retrieval_beta ,
+                      volume_retrieval_niter = volume_retrieval_niter 
+
+                      
     )
     
     
@@ -470,7 +477,7 @@ def get_scalars(  Start = None,  Thickness = None ,
     """
     if scal_prod_use_optional_solution:
         input_string = input_string+"""
-        optional_solution : {target_file}:/_{start}_{end}/volume
+       optional_solution : {target_file}:/_{start}_{end}/volume
         """
 
     if True:
@@ -479,7 +486,7 @@ def get_scalars(  Start = None,  Thickness = None ,
         """
     if scal_prod_load_factors :
         input_string = input_string+"""
-        load_factors_from : %s
+       load_factors_from : %s
         """ % scal_prod_load_factors_from
 
 
@@ -494,6 +501,57 @@ def get_scalars(  Start = None,  Thickness = None ,
     process_input( input_string, exploit_slurm_mpi = 0)    
    
 
+def get_volume(  Start = None,
+                 Thickness = None,
+                 volumes_file= None,
+                 niter =  None,
+                 beta  = None,
+                 
+
+):
+    inputstring = """    
+     superR_getVolume :
+        scalprods_address : {volumes_file}:/_{start}_{end}/scal_prods
+        target_address :  {volumes_file}:/_{start}_{end}/volume
+        niter : {niter}
+        beta : {beta}
+        eps : 2e-07
+        debin : [1, 1]
+    """
+    s=inputstring.format(start=Start, end=Start+Thickness,   
+                         volumes_file = volumes_file, niter = niter, beta = beta )
+    process_input(s, exploit_slurm_mpi = 0  )
+
+
+
+    
+def collect_factors(pattern="factors_*_*", newfile="newfactors.json"):
+
+    files = glob.glob(pattern)
+    indexes = [ int(s.split("_")[1]) for s in files ]
+    order = np.argsort(indexes)
+    files = [files[i] for i in order]
+    print( files)
+    files  = files[1:-1]
+    result  = {}
+    result2 = {}
+    Nkeys = None
+    for f in files:
+        factors = json.load(open(f,"r"))
+        if Nkeys is None:
+            Nkeys = len(list(factors.keys()))
+        assert(Nkeys == len(list(factors.keys())) )
+        for k,val in factors.items():
+            if k not in result:
+                result[k] = 0.0
+                result2[k] = 0.0
+            result[k] += factors[k]/ len(files)
+            result2[k] += (factors[k]*factors[k])/ len(files)
+    json.dump(result,open(newfile,"w") )     
+    keys = list(result.keys() )
+    keys.sort(key=int)
+    for k  in keys:
+        print( k , " ",   result[k] , " " , math.sqrt( result2[k] - result[k]*result[k]    ) / result[k]  )
 
     
     
@@ -530,9 +588,10 @@ def tools_sequencer(  peaks_shifts = None,
 
                       selected_rois = None, 
                       scal_prod_use_optional_solution= False,
-                      scal_prod_load_factors         = False,
-                      scal_prod_load_factors_from    = None,
-                      scalar_products_and_volume_target_file     = None
+                      scalar_products_and_volume_target_file     = None,
+
+                      volume_retrieval_beta  = None,
+                      volume_retrieval_niter = None 
 ) :
 
     if roi_path is None:
@@ -631,13 +690,39 @@ def tools_sequencer(  peaks_shifts = None,
                          signals_file  = interpolated_signals_file ,
                          target_file   = scalar_products_and_volume_target_file,
                          selected_rois = selected_rois                , 
-                         scal_prod_use_optional_solution= False,
+                         scal_prod_use_optional_solution= scal_prod_use_optional_solution,
                          scal_prod_load_factors         = False,
                          scal_prod_load_factors_from    = None
             )
 
+            
+        if(scal_prod_use_optional_solution):
+            collect_factors(pattern="factors_*_*.json", newfile="newfactors.json")
+        
+            for start in range( first_scan_num , ( first_scan_num + Edim * Zdim ), Zdim ):            
+                get_scalars( Start = start,  Thickness = Zdim , 
+                             reference_address = resynthetised_reference_and_roi_target_file +  ":/rois_and_reference/scans/ScansSum" ,
+                             signals_file  = interpolated_signals_file ,
+                             target_file   = scalar_products_and_volume_target_file,
+                             selected_rois = selected_rois                , 
+                             scal_prod_use_optional_solution= False,
+                             scal_prod_load_factors         = False,
+                             scal_prod_load_factors_from    = "newfactors.json"
+                )
+
 
             
+    if(steps_to_do["do_step_volume_retrieval"]):          
+        for start in range( first_scan_num , ( first_scan_num + Edim * Zdim ), Zdim ):            
+            get_volume(  Start = start,
+                         Thickness = Zdim,
+                         volumes_file = scalar_products_and_volume_target_file,
+                         beta  = volume_retrieval_beta ,
+                         niter = volume_retrieval_niter,
+            )
+
+            
+            
 main()