restructuring all teh non regression tests

.gitlab-ci.yml

@@ -30,7 +30,7 @@ test:
     - pip install .
 
   script:
-    - cd nonregressions
+    - cd nonregressions/xrs_raman
     - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python non_reg_testing_XRS.py
     - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python non_reg_testing_XRS_small.py
     - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python non_reg_testing_XRS_raman_extraction.py

XRStools/XRS_swissknife.py

@@ -1452,8 +1452,6 @@ def extract_spectra(mydata):
         print("CONFRONTO roiskeys ", rois_keys, rois_keys_orig)
         rois_keys = list(set.intersection(  set(rois_keys), set(rois_keys_orig)       ) )
         
-
-        
         incidentE = None
         if "motorDict/energy" in h5:
             incidentE =  h5["motorDict/energy"][()]

nonregressions/conf_raman_nonreg.yaml

-selected_scans :
-    elastic : [611, 615, 619, 623]
-    ok0 : [628]
-    ok1 : [612, 616, 620, 624]
-    ok2 : [613, 617, 621, 625]
-    ok3 : [614, 618, 622, 626]
-selected_subsets :
-    lowq : [1.0, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]
-    mediumq : [1.0, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]
-    highq : [1.0, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]
-selected_acquisition :
-    method : sum
-    refscan : 611
-    include_elastic : True
-    output_prefix : non_reg_output_gui_raman
-selected_experiment :
-    specfile_name : /data/id20/inhouse/data/run5_17/run7_ihr/hydra
-    roifile_address : sp_roi.h5:/spectral_roi_from_selector/
-selected_edges :
-     formula : [['H2O', '1.0']]
-     edges : {'O': ['K']}
-plots :
-    lowq   :
-        hfcore_shift : -5.0
-        pea_center : 7.526853e+01
-        pea_width : 6.523245e+01
-        pea_shape : 1.119493e+00
-        pea_height : 1.755123e+09
-        lin_back0 : 3.382474e-14
-        lin_back1 : 8.366045e+05
-        hf_factor : 1.990498e+09
-        ICR :   [-6.556967e+01,7.814317e+02]
-        range1 :   [1.000000e+02,5.000000e+02]
-        range2 :   [5.500000e+02,5.940000e+02]
-        Output :   [4.570000e+02,5.770000e+02]
-        Norm :   [5.160000e+02,5.530000e+02]
-    mediumq   :
-        hfcore_shift : -5.0
-        pea_center : 9.391416e+01
-        pea_width : 1.632100e+02
-        pea_shape : 2.607944e+00
-        pea_height : 2.924899e+09
-        lin_back0 : 7.168805e-16
-        lin_back1 : 1.286811e+07
-        hf_factor : 2.263246e+09
-        ICR :   [-6.556967e+01,7.814317e+02]
-        range1 :   [1.000000e+02,5.000000e+02]
-        range2 :   [5.500000e+02,5.940000e+02]
-        Output :   [4.570000e+02,5.770000e+02]
-        Norm :   [5.160000e+02,5.530000e+02]
-    highq   :
-        hfcore_shift : -5.0
-        pea_center : 3.422024e+02
-        pea_width : 2.487023e+02
-        pea_shape : 1.559654e+01
-        pea_height : 3.424977e+09
-        lin_back0 : 1.361906e-08
-        lin_back1 : 1.958734e+08
-        hf_factor : 4.059763e+09
-        ICR :   [-6.556967e+01,7.814317e+02]
-        range1 :   [1.000000e+02,5.000000e+02]
-        range2 :   [5.500000e+02,5.940000e+02]
-        Output :   [4.570000e+02,5.770000e+02]
-        Norm :   [5.160000e+02,5.530000e+02]

nonregressions/input2.yaml

-help:
-   "load_scans"
-
-create_rois:
-    active : 1
-    expdata :  "/scisoft/users/mirone/WORKS/Christoph/for_alessandro/hydra" 
-    scans   : [623]                  
-    roiaddress : "test.hdf5:/ROI_C"
-
-load_scans :
-    active : 0
-    roiaddress :  "test.hdf5:/ROI_A"  
-    expdata    :  "/scisoft/users/mirone/WORKS/Christoph/for_alessandro/hydra"  
-    elastic_scans    : [623]
-    fine_scans       : [625,629,633,637,641]
-    n_loop           : 1
-    long_scan        : 624
-    order : [0,1,2,3,4,5]
-    signaladdress : "loaded_datas"  
-
-
-    rvd : -41              # mean tth angle of HL module (default is 0.0)
-    rvu : 85               # mean tth angle of HR module (default is 0.0)
-    rvb : 121.8            # mean tth angle of HB module (default is 0.0)
-    rhl : 41.0             # mean tth angle of VD module (default is 0.0)
-    rhr : 41.0             # mean tth angle of VU module (default is 0.0)
-    rhb : 121.8            # mean tth angle of VB module (default is 0.0)
-    #
-
-
-HFspectrum :
-    active : 0
-    dataadress : "test.hdf5:/ROI_A/loaded_datas"   # where load_scans wrote data
-    formulas   :  ['O']     # list of strings of chemical sum formulas of which the sample is made up
-    concentrations : [1.0]  # list of concentrations of how the different chemical formulas are mixed (sum should be 1)
-    correctasym    : [[0.0,0.0,0.0]]  #  single value or list of scaling values for the HR-correction to 
-                                      # the 1s, 2s, and 2p shells. one value per element in the list of formulas
-    hfspectrum_address : "HF_O" # Target group for writing Relative to dataadress (and in the same file)!!!!
-
-
-Extraction :
-    active : 0
-
-    dataadress   : "test.hdf5:/ROI_A/loaded_datas"   # where load_scans wrote data
-    hfspectrum_address    : "test.hdf5:/ROI_A/loaded_datas/HF_O"
-    # prenormrange : [ 5 , .inf ]		
-
-    analyzerAverage :
-        active : 1
-        which : [0,11  , 36,59   ]
-        errorweighing  : False
-
-    removeLinearAv :
-        active  : 1
-        region1 :  [520.0,532.0]   
-        region2 :  None 
-        ewindow : 100 
-        scale : 1
-
-    removePearsonAv:
-        active  : 0
-        region1 :  [520.0,532.0]   
-        region2 :  None  
-        guess :
-            Peak_position : 600.0
-            FWHM          :  10
-            Shape         : "Lorentzian" 
-            Peak_intensity: 100.0
-            linear_slope  : 1
-            linear_background : 0
-            scaling_factor : 1
-            
-    view : True
-   
-
-    target :   "myextraction"

nonregressions/input_imaging.yaml

-help:
-#  superR_scal_deltaXimages
-#    create_rois
-#    "load_scans"
-
-create_rois:
-    active : 0
-    expdata :  "/data/id20/inhouse/data/run3_15/run6_ihr/hydra" 
-    scans   : [372]                  
-    roiaddress : "oggetto_imaging.hdf5:/ROI_F"
-    
-create_rois:
-    active : 0
-    expdata :  "/data/id20/inhouse/data/run3_15/run6_ihr/hydra" 
-    scans   : [273]                  
-    roiaddress : "demo_imaging.hdf5:/ROI_D"
-
-loadscan_2Dimages :
-     active : 0
-     roiaddress :  "demo_imaging.hdf5:/ROI_B_FIT8"                               # the same given in create_rois
-     expdata    :   '/data/id20/inhouse/data/run3_15/run6_ihr/hydra'        # this points to a spec file
-     scan_interval    :  [322,423]
-     # scan_interval    :  [372,373]
-     signaladdress : "images"                                               # Target group for writing Relative
-                                                                            #  to nameofroigroup/2Dimages (and in the same file)!!!!
-     sumto1D  : 0
-
-
-superR_scal_deltaXimages :
-  active : 0
-  sample_address : "demo_imaging.hdf5:ROI_B_FIT8/images/scans/"
-  delta_address  : "demo_imaging.hdf5:ROI_B_FIT8/scanXX/scans/Scan273/"
-  target_address         : "scalprods.hdf5:scal_prods/"
-  orig_delta_address  : "demo_imaging.hdf5:ROI_B/foil_scanXX/scans/Scan273/"
-
-  nbin           : 5                                # defaults to 1
-  # scan_interval    :  [322,423]
-  scan_interval    :  [322,354]
-  ## roi_keys       :  [60, 64, 35, 69, 34, 24, 5, 6, 71, 70, 39, 58, 56, 33]
-
-
-
-loadscan_2Dimages :
-     active : 0
-     roiaddress :  "demo.hdf5:/ROI_B_FIT8"                               # the same given in create_rois
-     expdata    :   '/data/id20/inhouse/data/run3_15/run6_ihr/hydra'        # this points to a spec file
-     scan_interval    :  [276,315]
-     signaladdress : "imagesalter"                                               # Target group for writing Relative
-                                                                            #  to nameofroigroup/2Dimages (and in the same file)!!!!
-     sumto1D  : 0
-
-loadscan_2Dimages :
-     active : 0
-     roiaddress :  "demo.hdf5:/ROI_B_FIT8"                               # the same given in create_rois
-     expdata    :   '/data/id20/inhouse/data/run3_15/run6_ihr/hydra'        # this points to a spec file
-     scan_interval    :  [273,274]
-     # scan_interval    :  [372,375]
-     signaladdress : "diracs"                                               # Target group for writing Relative
-                                                                            #  to nameofroigroup/2Dimages (and in the same file)!!!!
-     sumto1D  : 0
-     energycolumn : 'stx'
-
-
-loadscan_2Dimages :
-     active : 0
-     roiaddress :  "test_imaging.hdf5:/ROI_A"                               # the same given in create_rois
-     expdata    :   '/data/id20/inhouse/data/run3_15/run6_ihr/hydra'        # this points to a spec file
-     # scan_interval    :  [273,274]
-     scan_interval    :  [372,423]
-     signaladdress : "imagesd"                                               # Target group for writing Relative
-                                                                            #  to nameofroigroup/2Dimages (and in the same file)!!!!
-     sumto1D  : 1
-     energycolumn : 'sty'
-
-
-volume_from_2Dimages :
-     active : 0
-     imagesaddress :  "test_imaging.hdf5:/ROI_A/imagesd"  # where the data have been extracted
-     scan_interval    :  [372,423]                    # optional : can be shorter
-     # roi_n            : 0           # OPTIONAL. if not given, the first non empty found roi. Starts from 0
-     volumeaddress : "volume_file.hdf5:/volume/data2"  # OPTIONAL. the target destination for volume. if not given mayavi is launched on the fly.
-
-view_Volume_myavi:
-    active : 1
-    # volumeaddress : "volume_file.hdf5:/volume/data2"  # the target destination for volume. 
-    volumeaddress : "/scisoft/users/mirone/Volume.h5:/Volume_allgoods_15iters_beta1.0em8"
-
-loadscan_2Dimages :
-     active : 0
-     roiaddress :  "demo_imaging.hdf5:/ROI_B"                               # the same given in create_rois
-     expdata    :   '/data/id20/inhouse/data/run3_15/run6_ihr/hydra'        # this points to a spec file
-     scan_interval    :  [270,271]
-     signaladdress : "foil_scanY"                                               # Target group for writing Relative
-                                                                               #  to nameofroigroup/2Dimages (and in the same file)!!!!
-     sumto1D  : 0
-
-loadscan_2Dimages :
-     active : 0
-     roiaddress :  "demo_imaging.hdf5:/ROI_B"   # "demo_imaging.hdf5:/ROI_A"                               # the same given in create_rois
-     expdata    :   '/data/id20/inhouse/data/run3_15/run6_ihr/hydra'        # this points to a spec file
-     scan_interval    :  [273,274]
-     signaladdress : "foil_scanXX"                                               # Target group for writing Relative
-                                                                                #  to nameofroigroup/2Dimages (and in the same file)!!!!
-
-     monitorcolumn  :  "nessuno"
-     sumto1D  : 0
-     energycolumn : 'stx'
-     

nonregressions/compton_profiles_test.py → nonregressions/oldstuff/compton_profiles_test.py

 from __future__ import absolute_import
 from __future__ import division
 from __future__ import print_function
-from .XRStools import xrs_ComptonProfiles as CP
+from XRStools import xrs_ComptonProfiles as CP
 import numpy as np
 
 from pylab import *