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ixstools
xrstools
Commits
3326acdd
Commit
3326acdd
authored
Dec 01, 2020
by
myron
Browse files
restructured the reference resynthesis
parent
3a7e1658
Changes
3
Hide whitespace changes
Inline
Side-by-side
XRStools/XRS_swissknife.py
View file @
3326acdd
...
...
@@ -3923,17 +3923,35 @@ def superR_recreate_rois(mydata):
## simple statistical criteria which is har coded in file reponse_percussionelle.py
## routine get_spots_list
filter_rois : 1
# not necessary of old_scan_address contains also the ROI
original_roi_path : None
"""
foil_scan_address
=
mydata
[
"old_scan_address"
]
foil_filename
,
foil_groupname
=
split_hdf5_address
(
foil_scan_address
)
roisgroupname
=
foil_groupname
tmp_groupname
=
foil_groupname
newscanstarget
=
""
for
i
in
range
(
2
):
pos
=
roisgroupname
.
rfind
(
"/"
)
newscanstarget
=
roisgroupname
[
pos
:]
+
newscanstarget
roisgroupname
=
roisgroupname
[:
pos
]
pos
=
tmp_groupname
.
rfind
(
"/"
)
newscanstarget
=
tmp_groupname
[
pos
:]
+
newscanstarget
tmp_groupname
=
tmp_groupname
[:
pos
]
if
"original_roi_path"
not
in
mydata
or
mydata
[
"original_roi_path"
]
in
[
"None"
,
None
]:
roisgroupname
=
tmp_groupname
roi_filename
=
foil_filename
else
:
roi_filename
,
roisgroupname
=
split_hdf5_address
(
mydata
[
"original_roi_path"
])
responsefilename
=
mydata
[
"responsefilename"
]
responsefilename
,
responsepath
=
split_hdf5_address
(
responsefilename
)
...
...
@@ -3957,16 +3975,6 @@ def superR_recreate_rois(mydata):
print
(
"LANCIO "
)
dic
=
{
"filename"
:
foil_filename
,
"groupname"
:
foil_groupname
,
"roisgroupname"
:
roisgroupname
,
"target_filename"
:
target_filename
,
"roisgroupname_target"
:
roisgroupname_target
,
"newscanstarget"
:
newscanstarget
,
"responsefilename"
:
responsefilename
,
"responsepath"
:
responsepath
,
"nex"
:
nex
,
"filter_rois"
:
filter_rois
}
print
(
dic
)
if
"recenterings_refined"
in
mydata
:
recenterings_refined
=
mydata
[
"recenterings_refined"
]
...
...
@@ -3994,9 +4002,10 @@ def superR_recreate_rois(mydata):
filterMask
=
h5f
[
dataname
][:]
reponse_percussionelle
.
DOROIS
(
filename
=
foil_filename
,
groupname
=
foil_groupname
,
reponse_percussionelle
.
DOROIS
(
filename
=
foil_filename
,
groupname
=
foil_groupname
,
roi_filename
=
roi_filename
,
roisgroupname
=
roisgroupname
,
target_filename
=
target_filename
,
roisgroupname_target
=
roisgroupname_target
,
...
...
XRStools/reponse_percussionelle.py
View file @
3326acdd
...
...
@@ -1211,6 +1211,7 @@ def reload_trajectories(trajectory_file, nomi_rois) : ### , trajectory_file_grou
def
DOROIS
(
filename
=
"../nonregressions/demo_imaging.hdf5"
,
groupname
=
"ROI_B/foil_scanXX/scans/Scan273/"
,
roi_filename
=
None
,
roisgroupname
=
"ROI_B/"
,
target_filename
=
"newscan.h5"
,
roisgroupname_target
=
"ROI_B_FIT8/"
,
...
...
@@ -1221,7 +1222,10 @@ def DOROIS(filename = "../nonregressions/demo_imaging.hdf5" , groupname = "ROI_B
filter_rois
=
1
,
recenterings
=
None
,
filterMask
=
None
):
if
roi_filename
is
None
:
roi_filename
=
filename
O_spots_list
,
nomi_rois
,
stats
,
origini
,
rois
,
xscales
,
energy
=
get_spots_list
(
filename
,
groupname
,
filter_rois
=
filter_rois
)
trajectory_list
=
[]
...
...
@@ -1305,10 +1309,10 @@ def DOROIS(filename = "../nonregressions/demo_imaging.hdf5" , groupname = "ROI_B
# print( filename)
# print( roisgroupname+ "/rois_definition/image")
h5f
=
h5py
.
File
(
filename
,
"r"
)
h5f
=
h5py
.
File
(
roi_
filename
,
"r"
)
# imagealldect = h5f [roisgroupname+ "/rois_definition/image"][:]
print
(
filename
)
print
(
roi_
filename
)
print
(
roisgroupname
+
"/image"
)
imagealldect
=
h5f
[
roisgroupname
+
"/image"
][:]
...
...
nonregressions/volumes/interpola_1/batch_extraction_esynth1.py
View file @
3326acdd
...
...
@@ -58,10 +58,10 @@ def main():
"do_step_make_roi"
:
False
,
"do_step_sample_extraction"
:
False
,
"do_step_interpolation"
:
False
,
"do_extract_reference_scan"
:
False
,
"do_
step_
extract_reference_scan"
:
False
,
"do_fit_reference_response"
:
False
,
"do_resynthetise_reference"
:
Fals
e
,
"do_
step_
fit_reference_response"
:
False
,
"do_
step_
resynthetise_reference"
:
Tru
e
,
"do_step_finalise_for_fit"
:
False
}
...
...
@@ -78,7 +78,7 @@ def main():
response_target_file
=
"results/response.h5"
resynthetised_reference_and_roi_target_file
=
"results/resyntetised_roi_and_scan.h5"
tools_sequencer
(
peaks_shifts
=
peaks_shifts
,
datadir
=
datadir
,
...
...
@@ -102,8 +102,9 @@ def main():
extracted_reference_target_file
=
extracted_reference_target_file
,
isolate_spot_by
=
isolate_spot_by
,
response_target_file
=
response_target_file
,
response_fit_options
=
response_fit_options
response_fit_options
=
response_fit_options
,
resynthetised_reference_and_roi_target_file
=
resynthetised_reference_and_roi_target_file
)
...
...
@@ -389,7 +390,40 @@ def synthetise_response(scan_address=None, target_address=None, resp
niter_global
=
response_fit_options
[
"niter_global"
]
)
process_input
(
s
,
exploit_slurm_mpi
=
1
,
stop_omp
=
True
)
def
resynthetise_scan
(
old_scan_address
=
None
,
response_file
=
None
,
target_address
=
None
,
original_roi_path
=
None
):
inputstring
=
"""
superR_recreate_rois :
### we have calculated the responses in responsefilename
### and we want to enlarge the scan by a margin of 3 times
### the original scan on the right and on the left
### ( so for a total of a 7 expansion factor )
responsefilename : {response_file}
nex : 0
## the old scan covered by the old rois
old_scan_address : {old_scan_address}
## where new rois and bnew scan are written
target_filename : {target_address}
filter_rois : 0
original_roi_path : {original_roi_path}
"""
s
=
inputstring
.
format
(
response_file
=
response_file
,
target_address
=
target_address
,
old_scan_address
=
old_scan_address
,
original_roi_path
=
original_roi_path
+
"/rois_definition"
)
process_input
(
s
,
exploit_slurm_mpi
=
0
,
stop_omp
=
True
)
def
tools_sequencer
(
peaks_shifts
=
None
,
datadir
=
None
,
filter_path
=
None
,
...
...
@@ -418,8 +452,8 @@ def tools_sequencer( peaks_shifts = None,
reference_scan_list
=
None
,
extracted_reference_target_file
=
None
,
response_target_file
=
None
,
response_fit_options
=
None
response_fit_options
=
None
,
resynthetised_reference_and_roi_target_file
=
None
)
:
if
roi_path
is
None
:
...
...
@@ -452,7 +486,7 @@ def tools_sequencer( peaks_shifts = None,
interpolate
(
peaks_shifts
,
signals_file
,
interpolated_signals_target_file
)
if
(
steps_to_do
[
"do_extract_reference_scan"
]):
# of course we need the REFERENCE SCAN
if
(
steps_to_do
[
"do_
step_
extract_reference_scan"
]):
# of course we need the REFERENCE SCAN
get_reference
(
datadir
=
datadir
,
roi_path
=
roi_path
,
...
...
@@ -494,7 +528,7 @@ def tools_sequencer( peaks_shifts = None,
ftarget
.
close
()
if
(
steps_to_do
[
"do_fit_reference_response"
]):
# of course we need the REFERENCE SCAN
if
(
steps_to_do
[
"do_
step_
fit_reference_response"
]):
synthetise_response
(
scan_address
=
extracted_reference_target_file
+
":references/scans/ScansSum"
,
target_address
=
response_target_file
+
":/FIT"
,
...
...
@@ -502,8 +536,13 @@ def tools_sequencer( peaks_shifts = None,
)
if
(
steps_to_do
[
"do_step_resynthetise_reference"
]):
resynthetise_scan
(
old_scan_address
=
extracted_reference_target_file
+
":references/scans/ScansSum"
,
response_file
=
response_target_file
+
":/FIT"
,
target_address
=
resynthetised_reference_and_roi_target_file
+
":/rois_and_reference"
,
original_roi_path
=
roi_path
)
...
...
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