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ixstools
xrstools
Commits
36a80a7d
Commit
36a80a7d
authored
Dec 04, 2020
by
myron
Browse files
finished with the ant in interpolation
parent
bb162b0b
Changes
5
Hide whitespace changes
Inline
Side-by-side
XRStools/XRS_swissknife.py
View file @
36a80a7d
...
...
@@ -2849,9 +2849,12 @@ def superR_scal_deltaXimages(mydata):
solution
=
None
else
:
solution_filename
,
solution_groupname
=
split_hdf5_address
(
solution_address
)
solution
=
h5py
.
File
(
solution_filename
,
"r"
)
solution
=
solution
[
solution_groupname
][:]
try
:
solution
=
h5py
.
File
(
solution_filename
,
"r"
)
solution
=
solution
[
solution_groupname
][:]
except
:
raise
ValueError
(
"You asked for the utilisation of the optional solution to fix factors but could not read file %s groupname %s "
%
(
solution_filename
,
solution_groupname
)
)
roi_keys
=
filterRoiList
(
h5
.
keys
(),
prefix
=
""
)
...
...
@@ -3905,14 +3908,16 @@ def superR_recreate_rois(mydata):
# not necessary of old_scan_address contains also the ROI
original_roi_path : None
resynth_z_square : None
"""
allowed_keys
=
[
"old_scan_address"
,
"original_roi_path"
,
"responsefilename"
,
"nex"
,
"target_filename"
,
"filter_rois"
,
"recenterings_refined"
,
"filter_path"
,]
allowed_keys
=
[
"old_scan_address"
,
"original_roi_path"
,
"responsefilename"
,
"nex"
,
"target_filename"
,
"filter_rois"
,
"recenterings_refined"
,
"filter_path"
,
"resynth_z_square"
]
check_allowed_keys
(
mydata
,
allowed_keys
)
foil_scan_address
=
mydata
[
"old_scan_address"
]
foil_filename
,
foil_groupname
=
split_hdf5_address
(
foil_scan_address
)
tmp_groupname
=
foil_groupname
newscanstarget
=
""
for
i
in
range
(
2
):
...
...
@@ -3927,11 +3932,6 @@ def superR_recreate_rois(mydata):
else
:
roi_filename
,
roisgroupname
=
split_hdf5_address
(
mydata
[
"original_roi_path"
])
responsefilename
=
mydata
[
"responsefilename"
]
responsefilename
,
responsepath
=
split_hdf5_address
(
responsefilename
)
...
...
@@ -3941,8 +3941,6 @@ def superR_recreate_rois(mydata):
newscanstarget
=
newscanstarget
[
1
:]
# if os.path.exists(target_filename):
# sys.stdout.write("Error : file %s exists already. Remove it yourself\n"%target_filename)
# sys.stderr.write("Error : file %s exists already. Remove it yourself\n"%target_filename)
...
...
@@ -3954,6 +3952,12 @@ def superR_recreate_rois(mydata):
filter_rois
=
1
if
(
"resynth_z_square"
in
mydata
and
mydata
[
"resynth_z_square"
]
!=
"None"
)
:
resynth_z_square
=
mydata
[
"resynth_z_square"
]
else
:
resynth_z_square
=
None
if
"recenterings_refined"
in
mydata
:
...
...
@@ -3991,6 +3995,7 @@ def superR_recreate_rois(mydata):
roisgroupname_target
=
roisgroupname_target
,
newscanstarget
=
newscanstarget
,
responsefilename
=
responsefilename
,
resynth_z_square
=
resynth_z_square
,
responsepath
=
responsepath
,
nex
=
nex
,
filter_rois
=
filter_rois
,
recenterings
=
recenterings
,
filterMask
=
filterMask
)
...
...
XRStools/reponse_percussionelle.py
View file @
36a80a7d
...
...
@@ -6,6 +6,7 @@ import math
import
scipy
import
scipy.stats
import
scipy.ndimage.filters
as
filt
from
scipy.ndimage
import
gaussian_filter
import
sys
import
pickle
import
os
...
...
@@ -1217,6 +1218,7 @@ def DOROIS(filename = "../nonregressions/demo_imaging.hdf5" , groupname = "ROI_B
roisgroupname_target
=
"ROI_B_FIT8/"
,
newscanstarget
=
"scanXX/scans/Scan273"
,
responsefilename
=
"responses.h5"
,
resynth_z_square
=
None
,
responsepath
=
"fit"
,
nex
=
3
,
filter_rois
=
1
,
...
...
@@ -1244,13 +1246,16 @@ def DOROIS(filename = "../nonregressions/demo_imaging.hdf5" , groupname = "ROI_B
h5group
=
h5
[
name
]
print
(
name
,
"data"
)
solution
=
h5group
[
"data"
][
:
]
solution
=
h5group
[
"data"
][
()
]
trajectory
=
Trajectory
()
trajectory
.
X
.
intercept
=
h5group
[
"Xintercept"
][()]
trajectory
.
X
.
slope
=
h5group
[
"Xslope"
][()]
trajectory
.
Y
.
intercept
=
h5group
[
"Yintercept"
][()]
trajectory
.
Y
.
slope
=
h5group
[
"Yslope"
][()]
nref
=
h5group
[
"nref"
][()]
if
resynth_z_square
is
not
None
:
solution
=
gaussian_filter
(
solution
,
[
nref
*
resynth_z_square
,
0
])
trajectory
.
N
=
O_spots
.
shape
[
0
]
if
recenterings
is
not
None
:
...
...
XRStools/tools_sequencer_esynth.py
View file @
36a80a7d
...
...
@@ -194,7 +194,8 @@ def resynthetise_scan(
old_scan_address
=
None
,
response_file
=
None
,
target_address
=
None
,
original_roi_path
=
None
original_roi_path
=
None
,
resynth_z_square
=
None
):
...
...
@@ -216,8 +217,16 @@ def resynthetise_scan(
filter_rois : 0
original_roi_path : {original_roi_path}
resynth_z_square : {resynth_z_square}
"""
s
=
input_string
.
format
(
response_file
=
response_file
,
target_address
=
target_address
,
old_scan_address
=
old_scan_address
,
original_roi_path
=
original_roi_path
+
"/rois_definition"
)
s
=
input_string
.
format
(
response_file
=
response_file
,
target_address
=
target_address
,
old_scan_address
=
old_scan_address
,
original_roi_path
=
original_roi_path
+
"/rois_definition"
,
resynth_z_square
=
resynth_z_square
)
process_input
(
s
,
exploit_slurm_mpi
=
0
,
stop_omp
=
True
)
...
...
@@ -384,7 +393,8 @@ def tools_sequencer( peaks_shifts = None,
energy_custom_grid
=
None
,
custom_components_file
=
None
,
interpolation_infos_file
=
None
interpolation_infos_file
=
None
,
resynth_z_square
=
None
)
:
...
...
@@ -467,7 +477,8 @@ def tools_sequencer( peaks_shifts = None,
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
original_roi_path
=
roi_path
,
resynth_z_square
=
resynth_z_square
)
...
...
XRStools/tools_sequencer_interp.py
View file @
36a80a7d
...
...
@@ -293,13 +293,13 @@ def synthetise_response(scan_address=None, target_address=None, resp
process_input
(
s
,
exploit_slurm_mpi
=
1
,
stop_omp
=
True
)
def
resynthetise_scan
(
def
resynthetise_scan
(
old_scan_address
=
None
,
response_file
=
None
,
target_address
=
None
,
original_roi_path
=
None
):
original_roi_path
=
None
,
resynth_z_square
=
None
):
input_string
=
"""
superR_recreate_rois :
...
...
@@ -319,8 +319,15 @@ def resynthetise_scan(
filter_rois : 0
original_roi_path : {original_roi_path}
resynth_z_square : {resynth_z_square}
"""
s
=
input_string
.
format
(
response_file
=
response_file
,
target_address
=
target_address
,
old_scan_address
=
old_scan_address
,
original_roi_path
=
original_roi_path
+
"/rois_definition"
)
s
=
input_string
.
format
(
response_file
=
response_file
,
target_address
=
target_address
,
old_scan_address
=
old_scan_address
,
original_roi_path
=
original_roi_path
+
"/rois_definition"
,
resynth_z_square
=
resynth_z_square
)
process_input
(
s
,
exploit_slurm_mpi
=
0
,
stop_omp
=
True
)
...
...
@@ -462,7 +469,9 @@ def tools_sequencer( peaks_shifts = None,
response_target_file
=
None
,
response_fit_options
=
None
,
resynthetised_reference_and_roi_target_file
=
None
,
resynth_z_square
=
None
,
selected_rois
=
None
,
scal_prod_use_optional_solution
=
False
,
scalar_products_and_volume_target_file
=
None
,
...
...
@@ -556,7 +565,8 @@ def tools_sequencer( peaks_shifts = None,
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
original_roi_path
=
roi_path
,
resynth_z_square
=
resynth_z_square
)
...
...
nonregressions/volumes/esrf_scans/fourmis/interp/batch_extraction_interp.py
View file @
36a80a7d
...
...
@@ -48,19 +48,20 @@ def main():
#### For the fit of the response function based on reference scans
response_fit_options
=
dict
(
[
[
"niter_optical"
,
10
0
],
[
"niter_optical"
,
4
0
],
[
"beta_optical"
,
0.1
],
[
"niter_global"
,
3
]
[
"niter_global"
,
1
]
])
resynth_z_square
=
8
selected_rois
=
list
(
range
(
0
,
24
))
+
list
(
range
(
36
,
60
)
)
scal_prod_use_optional_solution
=
True
scal_prod_use_optional_solution
=
False
volume_retrieval_beta
=
6.0e-20
volume_retrieval_beta
=
0.12
volume_retrieval_niter
=
100
...
...
@@ -70,10 +71,11 @@ def main():
"do_step_interpolation"
:
False
,
"do_step_extract_reference_scan"
:
False
,
"do_step_fit_reference_response"
:
Tru
e
,
"do_step_fit_reference_response"
:
Fals
e
,
"do_step_resynthetise_reference"
:
False
,
"do_step_scalars"
:
False
,
"do_step_volume_retrieval"
:
False
,
"do_step_put_all_in_one_stack"
:
True
}
...
...
@@ -99,7 +101,7 @@ def main():
###### peaks_shifts = h5py.File("../peaks_positions_for_analysers.h5","r")["peaks_positions"][()]
###### assert( len(peaks_shifts) == 72)
if
rois_are_ready
:
if
steps_to_do
[
"do_step_interpolation"
]
:
roiob
=
xrs_rois
.
roi_object
()
roiob
.
loadH5
(
roi_target_path
)
elastic
=
xrs_read
.
Hydra
(
datadir
)
...
...
@@ -143,7 +145,8 @@ def main():
response_fit_options
=
response_fit_options
,
resynthetised_reference_and_roi_target_file
=
resynthetised_reference_and_roi_target_file
,
resynth_z_square
=
resynth_z_square
,
selected_rois
=
selected_rois
,
scal_prod_use_optional_solution
=
scal_prod_use_optional_solution
,
...
...
@@ -153,7 +156,27 @@ def main():
volume_retrieval_niter
=
volume_retrieval_niter
)
if
steps_to_do
[
"do_step_put_all_in_one_stack"
]
:
volumefile
=
scalar_products_and_volume_target_file
h5file_root
=
h5py
.
File
(
volumefile
,
"r+"
)
scankeys
=
list
(
h5file_root
.
keys
())
scankeys
.
sort
()
volumes
=
[]
for
k
in
scankeys
:
if
k
[:
1
]
!=
"_"
:
continue
print
(
k
)
if
"volume"
in
h5file_root
[
k
]:
volumes
.
append
(
h5file_root
[
k
][
"volume"
]
)
# volume = np.concatenate(volumes,axis=0)
volume
=
np
.
array
(
volumes
)
h5py
.
File
(
"concatenated_volume.h5"
,
"w"
)[
"volume"
]
=
volume
h5file_root
.
close
()
...
...
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