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Commit 6d9a61cf authored by myron's avatar myron
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small cleaning

parent 35220b5a
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XRStools/XRS_swissknife.py
View file @ 6d9a61cf
......@@ -237,7 +237,6 @@ class Loader_map_as_anydict( object):
class myOrderedDict (collections.OrderedDict):
def __setitem__(self,a,b):
## print "cucu",a,b
if type(a)==type("") and a in self:
self[a+"_tagkajs"]=b
else:
......@@ -307,7 +306,6 @@ def main():
mydata = yamlData[key]
if isinstance(mydata,dict) and "active" in mydata :
if mydata["active"]==0:
# print " continuo "
continue
if key != "help":
......@@ -582,7 +580,7 @@ def calculate_recenterings(mydata):
target_filename, target_groupname = split_hdf5_address( target )
print( bariA_filename, bariA_groupname)
print( " OPENIN FILE FOR RECENTERING ")
print( " OPENIN FILE ", bariA_filename , " FOR RECENTERING ")
h5A_f = h5py.File(bariA_filename,"r")
h5A = h5A_f [bariA_groupname]
if bariB_filename == bariA_filename :
......@@ -956,8 +954,6 @@ def loadscan_2Dimages(mydata):
else:
isolateSpot = 0
print( " creo oggetto ", energycolumn)
print( " DIVIDER ", monitor_divider)
reader = xrs_imaging.oneD_imaging( mydata["expdata"] ,monitorcolumn = monitorcolumn , monitor_divider=monitor_divider,
energycolumn = energycolumn , edfName = edfName, sumto1D = sumto1D,
......@@ -978,12 +974,8 @@ def loadscan_2Dimages(mydata):
mytodo = np.array_split(todo_list, nprocs) [myrank]
print( mytodo)
print( " Process ", myrank, " is going to read the following scans ", mytodo)
maxvalue=0.0
if(len(mytodo)):
maxvalue = reader.loadscan_2Dimages( list(mytodo) ,scantype=energycolumn, isolateSpot = isolateSpot)
......@@ -995,7 +987,7 @@ def loadscan_2Dimages(mydata):
raise Exception("When using recentering with refinement parallelism cannote be used")
if os.path.exists(recenterings_confirmed_filename):
check_libre( recenterings_confirmed_filename , recenterings_confirmed_groupname )
print( " APRO IN MODO a ", recenterings_confirmed_filename)
h5f = h5py.File(recenterings_confirmed_filename,"a")
else:
h5f = h5py.File(recenterings_confirmed_filename,"w")
......@@ -1031,7 +1023,7 @@ def loadscan_2Dimages(mydata):
comm.Barrier()
if myrank==0:
print(" TRASCRIVO ")
if save_also_roi == "for_resynth":
myfile = h5py.File(filename,'r+')
myfile[os.path.join( groupname,"image")] = h5py.SoftLink( os.path.join( os.path.dirname( groupname[:-1]) , "rois_definition/image" ) )
......@@ -1078,7 +1070,6 @@ def loadscan_2Dimages_galaxies(mydata):
shape, image=xrs_rois.load_rois_fromh5(file[groupname],rois, retrieveImage = True)
file.close()
print( " carico maschere ")
roiob = xrs_rois.roi_object()
roiob.load_rois_fromMasksDict(rois , newshape = shape, kind="zoom")
roiob.input_image = image
......@@ -1127,14 +1118,13 @@ def loadscan_2Dimages_galaxies(mydata):
averaged_monitor += monitor
averaged_monitor = averaged_monitor / len(todo_list)
for iscan in todo_list:
iZ = (iscan-scan_interval[0]) % Zdim
iY = (iscan-scan_interval[0]) // Zdim
filename, dataname = split_hdf5_address( mydata["expdata"] % iscan )
print(" working on ", filename, dataname )
data = np.array(h5py.File(filename,"r")[dataname][:])
......@@ -1157,7 +1147,7 @@ def loadscan_2Dimages_galaxies(mydata):
for iE in range(Edim):
egroup = "E%d/"%iE
scangroup = "Scan%d/"% iZ
print ( " iE iY, shape", iE, iY, sliced.shape, hf[ egroup+scangroup+roigroup+"matrix" ].shape )
hf[ egroup+scangroup+roigroup+"matrix" ][ iY ] = sliced[iE]
hf.close()
......@@ -1195,7 +1185,6 @@ def loadscan_2Dimages_galaxies_foilscan(mydata):
shape, image=xrs_rois.load_rois_fromh5(file[groupname],rois,retrieveImage = True)
file.close()
print( " carico maschere ")
roiob = xrs_rois.roi_object()
roiob.load_rois_fromMasksDict(rois , newshape = shape, kind="zoom")
roiob.input_image = image
......@@ -1391,11 +1380,11 @@ def extract_spectra(mydata):
raise ValueError("Key %s not present in file %s"%(reference_groupname, reference_file) )
h5 = h5f[reference_groupname]
print( " FILTRO ", list(h5.keys()) )
rois_keys = filterRoiList(h5.keys(),prefix="")
print(reference_file, reference_groupname, list(h5.keys() ) )
print("CONFRONTO roiskeys ", rois_keys, rois_keys_orig)
rois_keys = list(set.intersection( set(rois_keys), set(rois_keys_orig) ) )
printf(" After filtering the list of rois to be used is ", rois_keys )
incidentE = None
if "motorDict/energy" in h5:
......@@ -1407,7 +1396,7 @@ def extract_spectra(mydata):
else:
mm = None
print(reference_file, reference_groupname, list(h5[k].keys() ) )
zscale = h5[k]["xscale"][()]*1000.0
mask = h5rois["ROI%02d"%int(k)]["mask"][:]
cummask = np.cumsum(mask,axis=0)
......@@ -1446,17 +1435,14 @@ def extract_spectra(mydata):
for scan_num, extra in zip(scans, extratags) :
sample = {}
scan_name = "scans/Scan%03d"%scan_num
print( " FILE was ", sample_file)
print( " sample_groupname " , sample_groupname)
print( " scan_name " , scan_name)
h5 = h5_sample_group[scan_name]
scan_energy_0 = h5["motorDict/energy"][()]
print(" ROISKEYS ", rois_keys )
denominator = h5[ rois_keys[0] ]["monitor"][()]/(float(h5[ rois_keys[0] ]["monitor_divider"][()]))
for k in rois_keys:
print( " KKKKK " , k)
mm = h5[k]["matrix"][:]
zscale = h5[k]["xscale"][:]*1000
......@@ -1722,8 +1708,7 @@ def create_rois(mydata):
w4r = roiSelectionWidget.mainwindow(layout=layout)
if image4roi is not None:
if filterMask is not None:
print( image4roi)
print( filterMask)
image4roi = image4roi * filterMask
w4r.showImage( image4roi , xrs_rois.get_geo_informations( image4roi.shape +(layout,) ))
......@@ -1736,7 +1721,7 @@ def create_rois(mydata):
w4r.show()
app.exec_()
print(" USCITA ", w4r.isOK)
if not w4r.isOK:
sys.stderr.write('ROI CREATION SEEMS TO HAVE BEEN STOPPED BY USER')
sys.exit(1)
......@@ -1860,7 +1845,7 @@ def create_rois_galaxies(mydata):
w4r.show()
app.exec_()
print(" USCITA ", w4r.isOK)
if not w4r.isOK:
sys.stderr.write('ROI CREATION SEEMS TO HAVE BEEN STOPPED BY USER')
sys.exit(1)
......@@ -2376,7 +2361,7 @@ def superR_getVolume_fullfit(mydata):
solution = None
else:
solution_address = str(mydata["optional_solution"])
print( "solution_address " , solution_address)
if solution_address=="None" or solution_address is None or solution_address.strip()=="":
solution = None
else:
......@@ -2406,7 +2391,7 @@ def superR_getVolume_fullfit(mydata):
if XDIM is None:
XDIM = m.shape[0]
else:
assert(XDIM==m.shape[0])
assert (XDIM==m.shape[0]), "The probes ( references) dont have the same X lenght ( scan lenght). One is %s, anoter other %s "%(XDIM, m.shape[0] )
## DELTA <<<<<<<<<<<<<<<<<<<<<
## #############################
h5f.close()
......@@ -2437,7 +2422,9 @@ def superR_getVolume_fullfit(mydata):
if ro in h5[zscan_keys[0]]:
m = h5[zscan_keys[0]][ro]["matrix"][:]
if YDIM is not None:
assert(YDIM == m.shape[0]) ## we take the Y lenght from the first roi of the first scan :
assert (YDIM == m.shape[0]), "The probes ( references) dont have the same X lenght ( scan lenght). One is %s, anoter other %s "%(XDIM, m.shape[0] )
## we take the Y lenght from the first roi of the first scan :
## this lenght is supposed to be the same are supposed to be the same for all scans
else:
YDIM = m.shape[0]
......@@ -2446,7 +2433,7 @@ def superR_getVolume_fullfit(mydata):
del sonde[ro]
del integrated_images[ro]
for ro in rois_to_be_removed:
print ( " RIMUOVO ", ro )
roi_keys.remove(ro)
if YDIM is None:
......@@ -2531,9 +2518,6 @@ def superR_getVolume_fullfit(mydata):
else:
h5 = h5py.File(target_filename,"w")
print( h5.keys())
print( target_groupname)
print( target_groupname in h5)
if target_groupname in h5:
del h5[target_groupname]
......@@ -2568,7 +2552,6 @@ def superR_getVolume_Esynt(mydata):
scalprods_filename, scalprods_groupname = split_hdf5_address(scalprods_address)
print(" GROUPNAME ", scalprods_groupname)
output_prefix = mydata["output_prefix"]
......@@ -2579,8 +2562,7 @@ def superR_getVolume_Esynt(mydata):
vkeys = list(h5.keys())
vkeys.sort()
print(vkeys)
print(h5[vkeys[0]]["scal_prods"].keys())
DS=[]
DD=[]
......@@ -2596,17 +2578,16 @@ def superR_getVolume_Esynt(mydata):
roi_keys = h5[k]["scal_prods"]["roi_keys"][()]
else:
tmp = h5[k]["scal_prods"]["roi_keys"][()]
assert abs((tmp-roi_keys)).sum()==0
assert abs((tmp-roi_keys)).sum()==0
DS = np.array(DS,"f")
DD = np.array(DD,"f")
SS = np.array(SS,"f")
print(" ROI_keys " , roi_keys)
h5f.close()
NV, NROI, DIMZ,DIMY,DIMX = DS.shape
print( NV, NROI, DIMZ,DIMY,DIMX )
print(" NV, NROI, DIMZ,DIMY,DIMX " , NV, NROI, DIMZ,DIMY,DIMX )
print( " DS SHAPE ", DS.shape)
print( " DD SHAPE ", DD.shape)
......@@ -2626,15 +2607,13 @@ def superR_getVolume_Esynt(mydata):
roi_map[str(k)]=i
print(" ROIMAP ", roi_map )
id = interpolation_dict
for iE in range(NE):
ide = id[str(iE)]["coefficients"]
for iv,vk in enumerate(vkeys):
idev=ide[vk]
used_rois = list(idev.keys())
print("used rois ",used_rois)
for rk,c in idev.items():
if(rk in roi_map):
coefficients[iE, iv, roi_map[rk]] = c
......@@ -2746,9 +2725,7 @@ def superR_getVolume(mydata):
else:
h5 = h5py.File(target_filename,"w")
print( h5.keys())
print( target_groupname)
print( target_groupname in h5)
if target_groupname in h5:
del h5[target_groupname]
......@@ -2867,7 +2844,7 @@ def superR_scal_deltaXimages(mydata):
solution = None
else:
solution_address = str(mydata["optional_solution"])
print( "solution_address " , solution_address)
if solution_address=="None" or solution_address is None or solution_address.strip()=="":
solution = None
else:
......@@ -2916,7 +2893,7 @@ def superR_scal_deltaXimages(mydata):
if XDIM is None:
XDIM = m.shape[0]
else:
assert(XDIM==m.shape[0])
assert(XDIM==m.shape[0]), "The probes ( references) dont have the same X lenght ( scan lenght). One is %s, anoter other %s "%(XDIM, m.shape[0] )
## DELTA <<<<<<<<<<<<<<<<<<<<<
## #############################
h5f.close()
......@@ -2970,8 +2947,8 @@ def superR_scal_deltaXimages(mydata):
m = h5[zscan_keys[0]][ro]["matrix"][:]
if YDIM is not None:
assert(YDIM == m.shape[0]) ## we take the Y lenght from the first roi of the first scan :
## this lenght is supposed to be the same are supposed to be the same for all scans
assert(YDIM == m.shape[0]) , " "
else:
YDIM = m.shape[0]
else:
......@@ -2981,7 +2958,7 @@ def superR_scal_deltaXimages(mydata):
for ro in rois_to_be_removed:
print ( " RIMUOVO ", ro )
roi_keys.remove(ro)
if YDIM is None:
......@@ -3087,7 +3064,7 @@ def superR_scal_deltaXimages(mydata):
new_roi_keys=[]
for ok in roi_keys:
if ok not in my_roi_keys:
print(" MANCA ", ok , end= {False:"", True:"\n"} [ok==roi_keys[-1]] )
del integrated_images[ok]
else:
new_roi_keys.append(ok)
......@@ -3143,14 +3120,14 @@ def superR_scal_deltaXimages(mydata):
if nprocs>1:
for n in list(integrated_images.keys()):
if myrank:
print( myrank, "A ", integrated_images[n][0].dtype, integrated_images[n][0].shape)
comm.Reduce([integrated_images[n][0], MPI.DOUBLE], None, op=MPI.SUM, root=0)
print( myrank, "B ", integrated_images[n][1].dtype, integrated_images[n][1].shape)
comm.Reduce([integrated_images[n][1], MPI.DOUBLE], None, op=MPI.SUM, root=0)
else:
print( myrank, " A " , integrated_images[n][0].dtype, integrated_images[n][0].shape)
comm.Reduce( [integrated_images[n][1], MPI.DOUBLE] , [integrated_images[n][0], MPI.DOUBLE], op=MPI.SUM, root=0)
print( myrank, " B " , integrated_images[n][1].dtype, integrated_images[n][1].shape)
comm.Reduce( [np.array(integrated_images[n][1]), MPI.DOUBLE], [integrated_images[n][1], MPI.DOUBLE], op=MPI.SUM, root=0)
......@@ -3181,13 +3158,13 @@ def superR_scal_deltaXimages(mydata):
h5["scalDD"][:]=0
for n in list(integrated_images.keys()):
print (" in key " , n)
B=integrated_images[n][1]
A=integrated_images[n][0]
# B=B.sum(axis=0)
pesiA = A.sum(axis=0)
pesiB = B.sum(axis=0)
## print(" pesi ", pesiA, pesiB)
medieA = (np.arange(A.shape[0])[:,None]*A).sum(axis=0)/pesiA
medieB = (np.arange(B.shape[0])[:,None]*B).sum(axis=0)/pesiB
......@@ -3441,7 +3418,7 @@ def superR_scal_deltaXimages_Esynt(mydata):
for ro in rois_to_be_removed:
print ( " RIMUOVO ", ro )
roi_keys.remove(ro)
if YDIM is None:
......@@ -3460,7 +3437,7 @@ def superR_scal_deltaXimages_Esynt(mydata):
new_roi_keys=[]
for ok in roi_keys:
if ok not in my_roi_keys:
print(" MANCA ", ok , end= {False:"", True:"\n"} [ok==roi_keys[-1]] )
del integrated_images[ok]
else:
new_roi_keys.append(ok)
......@@ -3480,7 +3457,7 @@ def superR_scal_deltaXimages_Esynt(mydata):
for i,rk in enumerate(roi_keys):
if rk in loaded_fattori:
print(" FATTORE ", rk , " ", loaded_fattori[rk] )
fattori[rk] *= loaded_fattori[rk]
else:
fattori[rk] = 0
......@@ -3497,7 +3474,7 @@ def superR_scal_deltaXimages_Esynt(mydata):
scalSS = np.zeros( [Nrois, XDIM,XDIM] ,"d" )
for i,rk in enumerate(roi_keys):
print( " ================= ", i, rk )
if i%nprocs == myrank:
probes = sonde [rk]
## Consider that, below, factor is a factor which is applied to the probe to better adapt it to the sample strenght
......@@ -3553,14 +3530,14 @@ def superR_scal_deltaXimages_Esynt(mydata):
if nprocs>1:
for n in list(integrated_images.keys()):
if myrank:
print( myrank, "A ", integrated_images[n][0].dtype, integrated_images[n][0].shape)
comm.Reduce([integrated_images[n][0], MPI.DOUBLE], None, op=MPI.SUM, root=0)
print( myrank, "B ", integrated_images[n][1].dtype, integrated_images[n][1].shape)
comm.Reduce([integrated_images[n][1], MPI.DOUBLE], None, op=MPI.SUM, root=0)
else:
print( myrank, " A " , integrated_images[n][0].dtype, integrated_images[n][0].shape)
comm.Reduce( [integrated_images[n][1], MPI.DOUBLE] , [integrated_images[n][0], MPI.DOUBLE], op=MPI.SUM, root=0)
print( myrank, " B " , integrated_images[n][1].dtype, integrated_images[n][1].shape)
comm.Reduce( [np.array(integrated_images[n][1]), MPI.DOUBLE], [integrated_images[n][1], MPI.DOUBLE], op=MPI.SUM, root=0)
......@@ -3592,7 +3569,7 @@ def superR_scal_deltaXimages_Esynt(mydata):
h5["scalSS"][:]=0
for n in list(integrated_images.keys()):
print (" in key " , n)
B=integrated_images[n][1]
A=integrated_images[n][0]
# B=B.sum(axis=0)
......@@ -3632,7 +3609,7 @@ def superR_scal_deltaXimages_Esynt(mydata):
h5f.require_group(target_groupname )
h5 = h5f[target_groupname]
print(" MY KEYS ", roi_keys)
if myrank == 0 :
h5["roi_keys"] = np.array(list( map(int,roi_keys)))
......
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