def get_data(datdir, prefd, sufd, nf1, nf2):
# read Maxipix, Eiger edf images ####
t0 = time.time()
swrite = stdout.write
sflush = stdout.flush
print("start reading the files")
# creating filenames
filenames = nfiles.filename(datdir + prefd, sufd, nf1, nf2)
lfilenames = len(filenames)
# reading first image to get dimenstions of the matrix
headers = EdfMethods.headeredf(filenames[0])
dim1 = np.intc(headers['Dim_1'])
dim2 = np.intc(headers['Dim_2'])
nx = dim2
ny = dim1
data = np.zeros((lfilenames, nx, ny), np.uint16)
i = 0
for mfile in filenames:
data[i, :, :] = EdfMethods.loadedf(mfile)
i += 1
swrite(4 * '\x08')
swrite(str(int(i * 100. / lfilenames)) + '%')
sflush()
print("\n")
print("Reading time %3.3f sec" % (time.time() - t0))
return data
def get_delta(datdir, prefd, sufd, nf1, nf2, scan="1"):
if sufd == ".edf":
filenames = nfiles.filename(datdir + prefd, sufd, nf1, nf2)
h = EdfMethods.headeredf(filenames[10])
delta = float(
h['motor_pos'].split(" ")[h['motor_mne'].split(" ").index('del')])
if sufd == ".h5":
filename = datdir + prefd + sufd
with h5py.File(filename, mode="r") as h5:
delta = h5['/' + scan + '.1/instrument/positioners/delta'][()]
return delta
def get_ccd_event_datan(datdir,
prefd,
sufd,
nf1,
nf2,
darkdir,
df1,
df2,
sname,
lth,
bADU,
tADU,
mNp,
aduph,
savdir,
mask_file,
thr=20,
frc=0.15):
### read ccd edf images and convert for Pierre's event correlator using numba ####
t0 = time.time()
swrite = stdout.write
sflush = stdout.flush
print("start reading the files")
# creating filenames
filenames = nfiles.filename(datdir + prefd, sufd, nf1, nf2)
lfilenames = len(filenames) # -1
# reading first image to get dimenstions of the matrix
headers = EdfMethods.headeredf(filenames[0])
dim1 = np.intc(headers['Dim_1'])
dim2 = np.intc(headers['Dim_2'])
nx = dim2
ny = dim1
############reading mask##########
try:
mask_data = EdfMethods.loadedf(mask_file)
print("use mask file " + mask_file)
ind = np.where(mask_data > 0)
for_norm = dim1 * dim2 - len(mask_data[ind])
except:
mask_data = np.zeros((dim2, dim1), np.uint8)
print("no mask applied")
for_norm = dim1 * dim2 # 1024**2
pass
print("Numebr of pixels used " + str(for_norm))
########reading dark##########
darkfilenames = nfiles.filename(darkdir + prefd, sufd, df1, df2)
ndarks = 0
for dfile in darkfilenames:
if ndarks == 0:
darkimg = np.asfarray(EdfMethods.loadedf(dfile), dtype=np.float32)
else:
darkimg += np.asfarray(EdfMethods.loadedf(dfile), dtype=np.float32)
ndarks += 1
darkimg = darkimg / ndarks
n_frames = len(filenames)
ll = nx * ny # total number of pixels
lp = int(n_frames * frc) # total number of frames with events 15%
mask = np.array(np.ravel(mask_data), np.uint8)
evs = np.zeros((ll, lp), np.uint8)
tms = np.zeros((ll, lp), np.uint16)
cnt = np.ravel(np.zeros((ll, ), np.uint16))
afr = np.ravel(np.zeros((ll, ), np.uint32))
tr = 0
trace = np.zeros((n_frames, ), np.uint32)
it = 0
print("Number of frames %d" % n_frames)
###########reading and summing files###########
for i in range(lfilenames):
swrite(4 * '\x08')
swrite(str(int(i * 100. / lfilenames)) + '%')
sflush()
matr = np.asfarray(EdfMethods.loadedf(filenames[i]), dtype=np.float32)
try:
matr[ind] = 0
except:
pass
msumpix, mpix, fr = dropimgood(matr, darkimg, lth, bADU, tADU, mNp,
aduph, nx, ny) # dropletize CCD frames
fr = np.ravel(fr)
evs, tms, cnt, afr, mask, tr = neigercompress(evs, tms, cnt, afr, mask,
tr, fr, thr, it, ll, lp)
trace[i] = tr
it += 1
if not os.path.exists(savdir):
answ = input("create a director (y)/n").lower()
if answ == "n":
print("exit")
exit()
else:
os.makedirs(savdir)
print("directory " + savdir + " has been created")
afr = afr / n_frames
afr = np.reshape(afr, (nx, ny))
mask = np.reshape(mask, (nx, ny))
evs, tms, c = nprepare(np.ravel(evs), np.ravel(tms))
evs = np.array(evs[:c], np.int8)
tms = tms[:c]
print("Reading time %3.3f sec" % (time.time() - t0))
return evs, tms, cnt, afr, n_frames, mask, trace
def get_ccd_event_data(datdir, prefd, sufd, nf1, nf2, darkdir, df1, df2, sname,
lth, bADU, tADU, mNp, aduph, savdir, mask_file):
### read ccd edf images and convert for event correlator ####
time0 = time.time()
swrite = stdout.write
sflush = stdout.flush
print("start reading the files")
# creating filenames
filenames = nfiles.filename(datdir + prefd, sufd, nf1, nf2)
lfilenames = len(filenames) # -1
# reading first image to get dimenstions of the matrix
headers = EdfMethods.headeredf(filenames[0])
dim1 = np.intc(headers['Dim_1'])
dim2 = np.intc(headers['Dim_2'])
nx = dim2
ny = dim1
############reading mask##########
try:
mask_data = EdfMethods.loadedf(mask_file)
print("use mask file " + mask_file)
ind = np.where(mask_data > 0)
for_norm = dim1 * dim2 - len(mask_data[ind])
except:
print("no mask applied")
for_norm = dim1 * dim2 # 1024**2
pass
print("Numebr of pixels used " + str(for_norm))
########creating image matrix of zeros############
img = np.zeros((dim2, dim1))
########reading dark##########
darkfilenames = nfiles.filename(darkdir + prefd, sufd, df1, df2)
ndarks = 0
for dfile in darkfilenames:
if ndarks == 0:
darkimg = np.asfarray(EdfMethods.loadedf(dfile), dtype=np.float32)
else:
darkimg += np.asfarray(EdfMethods.loadedf(dfile), dtype=np.float32)
ndarks += 1
darkimg = darkimg / ndarks
pixels = []
s = []
data = []
pread = []
for i in range(2):
data.append(Queue(2))
# pread.append(Process(target=mread_ccd, args=(filenames[i:-1:2],data[i],darkimg,lth,bADU,tADU,mNp,aduph,nx,ny)))
pread.append(
Process(target=mread_ccd,
args=(filenames[:-1:2], data[0], darkimg, lth, bADU, tADU, mNp,
aduph, nx, ny)))
pread.append(
Process(target=mread_ccd,
args=(filenames[1::2], data[1], darkimg, lth, bADU, tADU, mNp,
aduph, nx, ny)))
for i in range(2):
pread[i].start()
ii = 0
###########reading and summing files###########
for i in range(lfilenames):
swrite(4 * '\x08')
swrite(str(int(i * 100. / lfilenames)) + '%')
sflush()
fromproc = data[ii].get()
pixels.append(fromproc[0])
s.append(fromproc[1])
img += fromproc[2]
ii += 1
if ii == 2:
ii = 0
for i in range(2):
pread[i].join()
data[i].close()
dtime = time.time() - time0
print('reading of %d files took %5.2f sec' % (lfilenames, dtime))
if not os.path.exists(savdir):
answ = input("create a director (y)/n")
if answ == "n":
print("exit")
exit()
else:
os.makedirs(savdir)
print("directory " + savdir + " has been created")
return pixels, s, for_norm, img