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ixstools
xrstools
Commits
55940064
Commit
55940064
authored
Dec 07, 2020
by
myron
Browse files
all non regression tests pass
parent
a79301c5
Changes
7
Expand all
Hide whitespace changes
Inline
Side-by-side
XRStools/XES_spectra_extraction.py
View file @
55940064
...
...
@@ -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_refine
s
: recentering.h5:/confirmed_shift
recenterings_refine
d
: 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
View file @
55940064
...
...
@@ -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
[
-
2
8
:]
==
"_
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
)
)
)
print
f
(
" 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/results/spectra_ref.txt
View file @
55940064
This diff is collapsed.
Click to expand it.
nonregressions/xes/xes_analysis.py
View file @
55940064
...
...
@@ -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
View file @
55940064
...
...
@@ -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
View file @
55940064
...
...
@@ -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
View file @
55940064
...
...
@@ -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
)
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