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Commit 734f930a authored by myron's avatar myron
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a forgotten check on input variables

parent 5f43930b
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XRStools/XRS_swissknife.py
View file @ 734f930a
......@@ -1063,7 +1063,7 @@ def loadscan_2Dimages_galaxies(mydata):
#
"""
allowed_keys = [ "roiaddress",'Ydim','Zdim','Edim',"signalfile","monitor_address","expdata", ]
allowed_keys = [ "roiaddress",'Ydim','Zdim','Edim',"signalfile","monitor_address","expdata", "scan_interval" ]
check_allowed_keys(mydata, allowed_keys)
roiaddress=None
......
nonregressions/volumes/test3/batch_extraction_esynth1.py
View file @ 734f930a
g# newfactors e' gia pronto , dopo verifica fuzionalita di roi_sel in ximages
# newfactors e' gia pronto , dopo verifica fuzionalita di roi_sel in ximages
import numpy as np
import h5py
import glob
......@@ -8,6 +8,10 @@ BATCH_PARALLELISM = 1
import os
def main():
os.system("mkdir results")
peaks_shifts = np.array(
[ 0.0,
0.0,
......@@ -15,21 +19,23 @@ def main():
0.0,
]) - 0.0
datadir = "/data/raffaela/GS9_dataGalaxies/"
filter_path = datadir + "mymask.h5:/mymask"
filename_template = "GS9_%05d_01.nxs"
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"
monitor_path_template = None
# monitor_path_template = datadir + filename_template +"_monitor.hd5:/monitor"
energy_exp_grid = h5py.File( datadir +(filename_template%1)+".nxs" ,"r")["/root_spyc_config1d_RIXS_00001/actuator_1_1"][()]
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
energy_custom_grid [+1 ] -= 0.1
scan_interval = [1,257] # from 1 to 475 included
......@@ -37,15 +43,12 @@ def main():
Zdim = 16
Edim = 19
reference_scan_list = list(range(1,20))
custom_components_file = None
# custom_components_file = "components.h5"
roi_scan_num = list(range(1,20))
reference_clip = None
# reference_clip = [ 90, 180 ]
......@@ -60,18 +63,17 @@ def main():
["niter_global" , 1 ]
])
resynth_z_square = 0
selected_rois = list(range(0,4)) )
selected_rois = list(range(0,4) )
steps_to_do = {
"do_step_make_roi": False,
"do_step_sample_extraction": False,
"do_step_sample_extraction": True,
"do_step_extract_reference_scan": False,
"do_step_fit_reference_response": False,
"do_step_resynthetise_reference": False,
"do_step_scalar": True,
"do_step_scalar": False,
"do_step_interpolation_coefficients": False,
"do_step_finalise_for_fit": False
}
......@@ -125,7 +127,7 @@ def main():
energy_custom_grid = energy_custom_grid ,
custom_components_file = use_custom_components_file,
custom_components_file = custom_components_file,
interpolation_infos_file = interpolation_infos_file
)
......@@ -402,7 +404,6 @@ def get_scalars( iE = None,
def get_volume_Esynt( scalarprods_file = None, interpolation_file = None):
os.system("mkdir DATASFORCC")
os.system("mkdir results")
inputstring = """
superR_getVolume_Esynt :
......@@ -449,66 +450,48 @@ def reshuffle( volumefile = "volumes.h5", nick = None ):
## THE FOLLOWING PART IS THE RELEVANT ONE
tools_sequencer( peaks_shifts = None,
datadir = None,
filter_path = None,
roi_scan_num = None,
roi_target_path = None,
data_path_template = None,
def tools_sequencer( peaks_shifts = None,
datadir = None,
filter_path = None,
roi_scan_num = None,
roi_target_path = None,
data_path_template = None,
steps_to_do = None,
scan_interval = None,
Ydim = None,
Zdim = None,
Edim = None,
scan_interval = None,
Ydim = None,
Zdim = None,
Edim = None,
monitor_path_template = None,
signals_target_file = None,
monitor_path_template = None,
signals_target_file = None,
reference_scan_list = None,
reference_clip = None,
extracted_reference_target_file = None,
extracted_reference_target_file = None ,
isolate_spot_by = None,
isolate_spot_by = None,
response_target_file = None,
response_fit_options = None,
resynthetised_reference_and_roi_target_file = None,
resynthetised_reference_and_roi_target_file = None ,
resynth_z_square = None,
selected_rois = None,
scalar_products_target_file = None,
energy_custom_grid = None,
energy_custom_grid = None ,
custom_components_file = None,
interpolation_infos_file = None
)
interpolation_infos_file = None,
def tools_sequencer( peaks_shifts = None,
datadir = None,
filter_path = None,
data_path_template = None,
energy_custom_grid = None,
energy_exp_grid = None,
monitor_path_template = None,
scan_interval = None,
scans_to_use_for_roi = None,
Ydim = None,
Zdim = None,
Edim = None,
roi_target_path = None,
reference_target_file = None,
signals_target_file = None,
scalarprods_target_file = None,
steps_to_do = None,
use_custom_components = None
custom_components = None
) :
......@@ -518,7 +501,7 @@ def tools_sequencer( peaks_shifts = None,
roi_path = roi_target_path
if(steps_to_do["do_step_make_reference"]):
if("do_step_make_reference" in steps_to_do and steps_to_do["do_step_make_reference"]):
get_reference( roi_path = roi_path , reference_target_file = reference_target_file )
reference_file = reference_target_file
......@@ -541,7 +524,7 @@ def tools_sequencer( peaks_shifts = None,
if(steps_to_do["do_step_scalar_products"]):
if(steps_to_do["do_step_scalar"]):
os.system("rm %s"%scalarprods_target_file)
for iE in range(Edim) :
get_scalars( iE = iE,
......
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