Commit c3c369fb authored by myron's avatar myron
Browse files

restructuring all teh non regression tests

parent f29c585e
......@@ -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
......
......@@ -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"][()]
......
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]
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"
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'
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 *
......
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