adapt monitor for energy scans

.gitlab-ci.yml

@@ -6,7 +6,7 @@ variables:
   PROJECT_NAME: "xrstools"
   LOCAL_REPO: "/dev/shm/gitlab_ci/xrstools"
   VENV_DIR: /dev/shm/gitlab_ci/xrstools/venv
-  USE_CLEAN_VENV: "true"
+  USE_CLEAN_VENV: "false"
   CLEAN_RESULTS: "true"
 
 test:

XRStools/XRS_swissknife.py

@@ -1153,6 +1153,8 @@ def loadscan_2Dimages_galaxies(mydata):
      loadscan_2Dimages_galaxies :
          roiaddress :  "hdf5filename:nameofroigroup"  # the same given in create_rois
          expdata    :  "kapton_%05d_01.nxs:/root_spyc_config1d_RIXS_00001/scan_data/data_07"  
+         monitor_address : "kapton_%05d_01_monitor.nxs:/monitor"   # oppure None
+     
 
          scan_interval    :  [1,2]   # from 1 to 1 included ( kapton_00001_01.nxs)
 
@@ -1215,6 +1217,16 @@ def loadscan_2Dimages_galaxies(mydata):
                 hf.require_group(egroup+scangroup+roigroup)
                 hf.require_dataset(egroup+scangroup+roigroup+"matrix",  [Ydim, box.shape[0], box.shape[1]]    , "f",exact="True")
                 hf[egroup+scangroup+roigroup+"cornerpos"] = origin
+
+
+    if mydata["monitor_address"] not in  [None,"None"]  :
+        averaged_monitor = 0
+        for iscan in todo_list:
+            monitor_filename, monitor_dataname = split_hdf5_address(  mydata["monitor_address"]   % iscan      )
+            monitor = np.array(h5py.File(monitor_filename,"r")[monitor_dataname][:])
+            averaged_monitor += monitor
+        averaged_monitor = averaged_monitor / len(todo_list)
+                
            
     for iscan in todo_list:
         iZ = (iscan-scan_interval[0]) %  Zdim
@@ -1225,6 +1237,15 @@ def loadscan_2Dimages_galaxies(mydata):
 
         
         data =  np.array(h5py.File(filename,"r")[dataname][:])
+
+        
+        if mydata["monitor_address"] not in  [None,"None"]  :
+            monitor_filename, monitor_dataname = split_hdf5_address(  mydata["monitor_address"]   % iscan      )
+            monitor = np.array(h5py.File(monitor_filename,"r")[monitor_dataname][:])
+            monitor[:] = monitor / averaged_monitor
+
+            data[:] =   data / monitor[:, None, None] 
+            
         
         for roikey, (origin, box) in roiob.red_rois.items():
             

nonregressions/volumes/test1/01_create_rois_galaxies.yaml

 create_rois_galaxies :
-   expdata     :  "/data/scisofttmp/mirone/raffaela/kapton_00001_01.nxs:/root_spyc_config1d_RIXS_00001/scan_data/data_07"  ##-- this pointsto, inside a hdf5 file, a stack of images z,y,x
-   filter_path  :  "/data/scisofttmp/mirone/raffaela/mymask.h5:/mymask"       # the target destination for rois
+   expdata     :  "/data/scisofttmp/mirone/raffaela/kapton_00001_01.nxs:/root_spyc_config1d_RIXS_00001/scan_data/data_07"  ##-- this pointsto, inside a hdf5 file, a stack of images 
+   filter_path  :  "/data/scisofttmp/mirone/raffaela/mymask.h5:/mymask"    
    roiaddress : "results/myrois.h5:/ROIS"            # the target destination for rois
\ No newline at end of file

nonregressions/volumes/test1/05_loadscan_2Dimages_galaxies.yaml

@@ -5,6 +5,9 @@ loadscan_2Dimages_galaxies :
 
      expdata    :  "/data/scisofttmp/mirone/raffaela/GS9_dataGalaxies/GS9_%05d_01.nxs:/root_spyc_config1d_RIXS_00001/scan_data/data_07"  
 
+     monitor_address : None
+
+
      scan_interval    :  [1,257]   # from 1 to 256 included 
 
      Ydim : 16

nonregressions/volumes/test2/01_create_rois_galaxies.yaml

+create_rois_galaxies :
+   expdata     :  "/data/scisofttmp/mirone/Loic1/data/HC-D_2Dmap_0130.nxs:/root.spyc.config1d_RIXS_0024/scan_data/data_03"
+   filter_path  :  "/data/scisofttmp/mirone/Loic1/mask.h5:/filter"     
+   roiaddress : "results/myrois.h5:/ROIS"            # the target destination for rois
\ No newline at end of file