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Commit 4e823e2b authored by myron's avatar myron
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finished with the Raffaela dataset and the new scheme

parent 85697144
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XRStools/XRS_swissknife.py
View file @ 4e823e2b
......@@ -374,7 +374,6 @@ but : was not found
filename, groupname = dataadress[:pos], dataadress[pos+1:]
if( len(groupname) and groupname[0:1] !="/" ):
groupname = "/"+groupname
print(" RITORNO ", groupname, (groupname[0:1] !="/" ), len(groupname) )
return filename, groupname
......@@ -2836,7 +2835,6 @@ def superR_scal_deltaXimages(mydata):
"""
allowed_keys = [ "delta_address",'orig_delta_address','nbin','optional_solution' ,'roi_keys',"sample_address",'scan_interval',"load_factors_from","save_factors_on","target_address", ]
check_allowed_keys(mydata, allowed_keys)
......@@ -2880,8 +2878,8 @@ def superR_scal_deltaXimages(mydata):
if ('roi_keys' in mydata) :
u_roi_keys = mydata['roi_keys']
u_roi_keys = [str(t) for t in u_roi_keys]
roi_keys = [ t for t in u_roi_keys if t in roi_keys]
u_roi_keys = [int(t) for t in u_roi_keys]
roi_keys = [ t for t in roi_keys if int(t) in u_roi_keys]
roi_keys = [str(t) for t in roi_keys]
......
nonregressions/volumes/test3/batch_extraction_esynth1.py → XRStools/tools_sequencer_esynth_galaxies.py
View file @ 4e823e2b
# newfactors e' gia pronto , dopo verifica fuzionalita di roi_sel in ximages
import numpy as np
import h5py
import glob
import json
import sys
BATCH_PARALLELISM = 1
import os
def main():
os.system("mkdir results")
peaks_shifts = np.array(
[ 0.0,
0.0,
0.0,
0.0,
]) - 0.0
dataprefix = "/data/raffaela/"
datadir = dataprefix + "GS9_dataGalaxies/"
filter_path = dataprefix + "mymask.h5:/mymask"
filename_template = "GS9_%05d_01"
data_path_template = datadir + filename_template + ".nxs:/root_spyc_config1d_RIXS_00001/scan_data/data_07"
reference_data_path_template = dataprefix + "kapton_%05d_01" + ".nxs:/root_spyc_config1d_RIXS_00001/scan_data/data_07"
monitor_path_template = None
# monitor_path_template = datadir + filename_template +"_monitor.hd5:/monitor"
print( datadir +(filename_template%1)+".nxs" )
energy_exp_grid = h5py.File( datadir +(filename_template%1)+".nxs" ,"r")["/root_spyc_config1d_RIXS_00001/scan_data/actuator_1_1"][()]
energy_custom_grid = np.array( energy_exp_grid )
energy_custom_grid [ 0 ] -= 0.1
energy_custom_grid [+1 ] -= 0.1
scan_interval = [1,257] # from 1 to 475 included
Ydim = 16
Zdim = 16
Edim = 19
reference_scan_list = [1]
custom_components_file = None
# custom_components_file = "components.h5"
roi_scan_num = list(range(1,3))
reference_clip = None
reference_clip = [ 0, 200 ]
## in the reference scan for each position there is a spot with a maximum. We set zero the background which is further than
## such radius from the maximum
isolate_spot_by = 7
#### For the fit of the response function based on reference scans
response_fit_options = dict( [
["niter_optical" , 40],
["beta_optical" , 0.1],
["niter_global" , 1 ]
])
resynth_z_square = 0
selected_rois = list(range(0,4) )
steps_to_do = {
"do_step_make_roi": False,
"do_step_sample_extraction": False,
"do_step_extract_reference_scan": False,
"do_step_fit_reference_response": False,
"do_step_resynthetise_reference": False,
"do_step_scalar": False,
"do_step_interpolation_coefficients": False,
"do_step_finalise_for_fit": True
}
scalar_products_target_file = "results/scalar_prods.h5"
roi_target_path = "results/myrois.h5:/ROIS"
reference_target_file = "results/response.h5"
signals_target_file = "results/extracted.h5"
extracted_reference_target_file = "results/reference.h5"
response_target_file = "results/response.h5"
interpolation_infos_file = "interpolation_infos.json"
resynthetised_reference_and_roi_target_file = "results/resynthetised_roi_and_scan.h5"
tools_sequencer( peaks_shifts = peaks_shifts ,
datadir = datadir ,
filter_path = filter_path ,
roi_scan_num = roi_scan_num ,
roi_target_path = roi_target_path ,
data_path_template = data_path_template ,
reference_data_path_template = reference_data_path_template,
steps_to_do = steps_to_do,
scan_interval = scan_interval ,
Ydim = Ydim ,
Zdim = Zdim ,
Edim = Edim ,
monitor_path_template = monitor_path_template ,
signals_target_file = signals_target_file,
reference_scan_list = reference_scan_list,
reference_clip = reference_clip,
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,
resynthetised_reference_and_roi_target_file = resynthetised_reference_and_roi_target_file,
resynth_z_square = resynth_z_square,
selected_rois = selected_rois,
scalar_products_target_file = scalar_products_target_file ,
energy_custom_grid = energy_custom_grid ,
custom_components_file = custom_components_file,
interpolation_infos_file = interpolation_infos_file,
energy_exp_grid = energy_exp_grid
)
def synthetise_response(scan_address=None, target_address=None, response_fit_options = None
):
......@@ -586,7 +459,6 @@ def reshuffle( volumefile = "volumes.h5", nick = None ):
## THE FOLLOWING PART IS THE RELEVANT ONE
def tools_sequencer( peaks_shifts = None,
datadir = None,
filter_path = None,
roi_scan_num = None,
roi_target_path = None,
......@@ -678,7 +550,7 @@ def tools_sequencer( peaks_shifts = None,
if(steps_to_do["do_step_fit_reference_response"]):
synthetise_response(
scan_address= extracted_reference_target_file +":Scan0" ,
target_address = +":/FIT",
target_address = response_target_file +":/FIT",
response_fit_options = response_fit_options
)
......@@ -733,6 +605,3 @@ def tools_sequencer( peaks_shifts = None,
get_volume_Esynt( scalarprods_file = scalarprods_file,
interpolation_file = interpolation_infos_file)
main()
XRStools/tools_sequencer_esynth_galaxies.py~ 0 → 100644
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XRStools/tools_sequencer_interp.py~ 0 → 100644
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XRStools/tools_sequencer_interp_galaxies.py 0 → 100644
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XRStools/tools_sequencer_interp_galaxies.py~ 0 → 100644
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nonregressions/volumes/test3/esynth/batch_extraction_esynth1.py 0 → 100644
View file @ 4e823e2b
import numpy as np
import h5py
import glob
import json
import os
import h5py
import math
from XRStools import tools_sequencer_esynth_galaxies
from XRStools import xrs_read, xrs_rois
import os
def main():
os.system("mkdir results")
peaks_shifts = np.array(
[ 0.0,
0.0,
0.0,
0.0,
]) - 0.0
dataprefix = "/data/raffaela/"
datadir = dataprefix + "GS9_dataGalaxies/"
filter_path = dataprefix + "mymask.h5:/mymask"
filename_template = "GS9_%05d_01"
data_path_template = datadir + filename_template + ".nxs:/root_spyc_config1d_RIXS_00001/scan_data/data_07"
reference_data_path_template = dataprefix + "kapton_%05d_01" + ".nxs:/root_spyc_config1d_RIXS_00001/scan_data/data_07"
monitor_path_template = None
# monitor_path_template = datadir + filename_template +"_monitor.hd5:/monitor"
print( datadir +(filename_template%1)+".nxs" )
energy_exp_grid = h5py.File( datadir +(filename_template%1)+".nxs" ,"r")["/root_spyc_config1d_RIXS_00001/scan_data/actuator_1_1"][()]
energy_custom_grid = np.array( energy_exp_grid )
energy_custom_grid [ 0 ] -= 0.1
energy_custom_grid [+1 ] -= 0.1
scan_interval = [1,257] # from 1 to 475 included
Ydim = 16
Zdim = 16
Edim = 19
reference_scan_list = [1]
custom_components_file = None
# custom_components_file = "components.h5"
roi_scan_num = list(range(1,3))
reference_clip = None
reference_clip = [ 0, 200 ]
## in the reference scan for each position there is a spot with a maximum. We set zero the background which is further than
## such radius from the maximum
isolate_spot_by = 7
#### For the fit of the response function based on reference scans
response_fit_options = dict( [
["niter_optical" , 40],
["beta_optical" , 0.1],
["niter_global" , 1 ]
])
resynth_z_square = 0
selected_rois = list(range(0,4) )
steps_to_do = {
"do_step_make_roi": False,
"do_step_sample_extraction": False,
"do_step_extract_reference_scan": False,
"do_step_fit_reference_response": False,
"do_step_resynthetise_reference": False,
"do_step_scalar": False,
"do_step_interpolation_coefficients": False,
"do_step_finalise_for_fit": True
}
scalar_products_target_file = "results/scalar_prods.h5"
roi_target_path = "results/myrois.h5:/ROIS"
reference_target_file = "results/response.h5"
signals_target_file = "results/extracted.h5"
extracted_reference_target_file = "results/reference.h5"
response_target_file = "results/response.h5"
interpolation_infos_file = "interpolation_infos.json"
resynthetised_reference_and_roi_target_file = "results/resynthetised_roi_and_scan.h5"
tools_sequencer_esynth_galaxies.tools_sequencer( peaks_shifts = peaks_shifts ,
filter_path = filter_path ,
roi_scan_num = roi_scan_num ,
roi_target_path = roi_target_path ,
data_path_template = data_path_template ,
reference_data_path_template = reference_data_path_template,
steps_to_do = steps_to_do,
scan_interval = scan_interval ,
Ydim = Ydim ,
Zdim = Zdim ,
Edim = Edim ,
monitor_path_template = monitor_path_template ,
signals_target_file = signals_target_file,
reference_scan_list = reference_scan_list,
reference_clip = reference_clip,
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,
resynthetised_reference_and_roi_target_file = resynthetised_reference_and_roi_target_file,
resynth_z_square = resynth_z_square,
selected_rois = selected_rois,
scalar_products_target_file = scalar_products_target_file ,
energy_custom_grid = energy_custom_grid ,
custom_components_file = custom_components_file,
interpolation_infos_file = interpolation_infos_file,
energy_exp_grid = energy_exp_grid
)
main()
nonregressions/volumes/test3/interp/batch_extraction_interp.py 0 → 100644
View file @ 4e823e2b
import numpy as np
import h5py
import glob
import json
import os
import h5py
import math
from XRStools import tools_sequencer_interp_galaxies
from XRStools import xrs_read, xrs_rois
import os
def main():
os.system("mkdir results")
peaks_shifts = np.array(
[ 0.0,
0.0,
0.0,
0.0,
]) - 0.0
dataprefix = "/data/raffaela/"
datadir = dataprefix + "GS9_dataGalaxies/"
filter_path = dataprefix + "mymask.h5:/mymask"
filename_template = "GS9_%05d_01"
data_path_template = datadir + filename_template + ".nxs:/root_spyc_config1d_RIXS_00001/scan_data/data_07"
reference_data_path_template = dataprefix + "kapton_%05d_01" + ".nxs:/root_spyc_config1d_RIXS_00001/scan_data/data_07"
monitor_path_template = None
# monitor_path_template = datadir + filename_template +"_monitor.hd5:/monitor"
print( datadir +(filename_template%1)+".nxs" )
energy_exp_grid = h5py.File( datadir +(filename_template%1)+".nxs" ,"r")["/root_spyc_config1d_RIXS_00001/scan_data/actuator_1_1"][()]
first_scan = 1
Ydim = 16
Zdim = 16
Edim = 19
reference_scan_list = [1]
roi_scan_num = list(range(1,3))
reference_clip = None
reference_clip = [ 0, 200 ]
## in the reference scan for each position there is a spot with a maximum. We set zero the background which is further than
## such radius from the maximum
isolate_spot_by = 7
#### For the fit of the response function based on reference scans
response_fit_options = dict( [
["niter_optical" , 40],
["beta_optical" , 0.1],
["niter_global" , 1 ]
])
resynth_z_square = 0
selected_rois = list(range(0,4) )
scal_prod_use_optional_solution = True
volume_retrieval_beta = 6.0e-1
volume_retrieval_niter = 100
steps_to_do = {
"do_step_make_roi": False,
"do_step_sample_extraction": False,
"do_step_interpolation": False,
"do_step_extract_reference_scan": False,
"do_step_fit_reference_response": False,
"do_step_resynthetise_reference": False,
"do_step_scalar": False,
"do_step_volume_retrieval" : False,
"do_step_put_all_in_one_stack" : True
}
scalar_products_and_volume_target_file = "results/scalar_prods_and_volume.h5"
roi_target_path = "results/myrois.h5:/ROIS"
reference_target_file = "results/response.h5"
signals_target_file = "results/extracted.h5"
interpolated_signals_target_file = "results/interpolated_signals.h5"
extracted_reference_target_file = "results/reference.h5"
response_target_file = "results/response.h5"
resynthetised_reference_and_roi_target_file = "results/resynthetised_roi_and_scan.h5"
tools_sequencer_interp_galaxies.tools_sequencer( peaks_shifts = peaks_shifts ,
data_path_template = data_path_template ,
filter_path = filter_path ,
roi_scan_num = roi_scan_num ,
roi_target_path = roi_target_path ,
first_scan = first_scan ,
Ydim = Ydim ,
Zdim = Zdim ,
Edim = Edim ,
monitor_path_template = monitor_path_template ,
signals_target_file = signals_target_file,
interpolated_signals_target_file = interpolated_signals_target_file,
steps_to_do = steps_to_do,
reference_clip = reference_clip,
isolate_spot_by = isolate_spot_by,
reference_scan_list = reference_scan_list,
reference_data_path_template = reference_data_path_template,
extracted_reference_target_file = extracted_reference_target_file ,
response_target_file = response_target_file,
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 ,
scalar_products_and_volume_target_file = scalar_products_and_volume_target_file ,
volume_retrieval_beta = volume_retrieval_beta ,
volume_retrieval_niter = volume_retrieval_niter ,
energy_exp_grid = energy_exp_grid
)
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]!="E":
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()
main()
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