def azimuthal_averaging(file, qgrid, n_proc=8, exp_folder = ""):
"""
azimuthal_averaging(masked_file, qgrid, n_proc=8)
"""
de = h5exp(exp_folder+"exp.h5")
dt = h5xs(file, [de.detectors, qgrid])
tic = time.perf_counter()
print(f'Circular averaging starts now ... ')
dt.load_data(N=n_proc)
print(f'{file} total 1-d averaging time {time.perf_counter() - tic} seconds')
def openFileNameDialog(self):
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
if self.name == 'exp':
filename, _ = QFileDialog.getOpenFileName(
self,
"Exp File",
"",
"All Files (*);;HDF Files (*.h5)",
options=options)
global dexp
dexp = h5exp(filename)
else:
filename, _ = QFileDialog.getOpenFileName(
self,
"Data File",
"",
"All Files (*);HDF Files (*.h5)",
options=options)
global data
data = h5xs(filename, [dexp.detectors, dexp.qgrid])
from py4xs.hdf import h5xs, h5exp, lsh5
from py4xs.data2d import Data2d
import numpy as np
import pylab as plt
import os, time
exp_file = '/home/bashit.a/July-2021/'
samples = '/home/bashit.a/July-2021/sample-4/'
os.chdir(samples)
de = h5exp(exp_file + "exp.h5")
#de.qgrid
print(de.detectors[1].extension)
qgrid2 = np.hstack([
np.arange(0.005, 0.0499, 0.001),
np.arange(0.05, 0.099, 0.002),
np.arange(0.1, 3.2, 0.005)
])
#print(qgrid2)
### load all files in a directory
def load_all_cwd():
for file in [
each for each in os.listdir(os.getcwd()) if each.endswith('.h5')
]:
try:
print(f'Loading file {file}')
dt = h5xs(file, [de.detectors, qgrid2])
def pack_and_move(data_type, uid, dest_dir):
# useful for moving files from RAM disk to GPFS during fly scans
#
# assume other type of data are saved on RAM disk as well (GPFS not working for WAXS2)
# these data must be moved manually to GPFS
global pilatus_trigger_mode #,CBF_replace_data_path
print(f"packing: {data_type}, {uid}, {dest_dir}")
print(f"data source: {PilatusCBFHandler.froot}")
t0 = time.time()
# if the dest_dir contains exp.h5, read detectors/qgrid from it
try:
dt_exp = h5exp(dest_dir + '/exp.h5')
except:
dt_exp = None
dir_name = None
if data_type in ["multi", "sol"]:
uids = uid.split('|')
if data_type == "sol":
sb_dict = json.loads(uids.pop())
pilatus_trigger_mode = triggerMode.fly_scan
else:
pilatus_trigger_mode = triggerMode.external_trigger
## assume that the meta data contains the holderName
if 'holderName' not in list(db[uids[0]].start.keys()):
print(
"cannot find holderName from the header, using tmp.h5 as filename ..."
)
fh5_name = "tmp.h5"
else:
dir_name = db[uids[0]].start['holderName']
fh5_name = dir_name + '.h5'
fn = pack_h5_with_lock(uids, dest_dir, fn="tmp.h5")
if fn is not None and dt_exp is not None:
print('processing ...')
if data_type == "sol":
dt = h5sol_HT(fn, [dt_exp.detectors, dt_exp.qgrid])
dt.assign_buffer(sb_dict)
dt.process(filter_data=True, sc_factor=0.998, debug='quiet')
dt.export_d1s(path=dest_dir + "/processed/")
else:
dt = h5xs(fn, [dt_exp.detectors, dt_exp.qgrid],
transField='em2_sum_all_mean_value')
dt.load_data(debug="quiet")
dt.fh5.close()
if fh5_name is not "tmp.h5": # temporary fix, for some reason other processes cannot open the packed file
os.system(f"cd {dest_dir} ; cp tmp.h5 {fh5_name} ; rm tmp.h5")
del dt, dt_exp
elif data_type == "HPLC":
uids = [uid]
if db[uid].start['plan_name'] == "hplc_scan":
# this was software_trigger_single_frame when using the flyer-based hplc_scan
pilatus_trigger_mode = triggerMode.software_trigger_single_frame
else:
# data collected using ct
pilatus_trigger_mode = triggerMode.software_trigger_multi_frame
fn = pack_h5_with_lock(uid, dest_dir=dest_dir, attach_uv_file=True)
if fn is not None and dt_exp is not None:
print('procesing ...')
dt = h5sol_HPLC(fn, [dt_exp.detectors, dt_exp.qgrid])
dt.process(debug='quiet')
dt.fh5.close()
del dt, dt_exp
elif data_type == "flyscan" or data_type == "scan":
if data_type == "flyscan":
pilatus_trigger_mode = triggerMode.fly_scan
else:
pilatus_trigger_mode = triggerMode.external_trigger
uids = [uid]
fn = pack_h5_with_lock(uid, dest_dir)
else:
print(f"invalid data type: {data_type} .")
return
if fn is None:
return # packing unsuccessful,
print(
f"{time.asctime()}: finished packing/processing, total time lapsed: {time.time()-t0:.1f} sec ..."
)
if PilatusCBFHandler.froot == data_file_path.gpfs:
return
for uid in uids:
print(f'moving files for {uid} from RAMDISK to GPFS ...')
h = db[uid]
p1 = h.start['data_path']
#p2 = p1.replace(default_data_path_root, '/ramdisk/')
p2 = p1.replace(data_file_path.gpfs.value, '/ramdisk')
sample_name = h.start['sample_name']
if dir_name is not None:
cmd = f"rsync -ahv --remove-source-files [email protected]:{p2}{dir_name} {p1}"
elif os.system(
f"ssh -q [email protected] [[ -d {p2}{sample_name} ]]") == 0:
# if sample name is a directory on the RAMDISK, move the entire directory
cmd = f"rsync -ahv --remove-source-files [email protected]:{p2}{sample_name} {p1}"
else:
cmd = f"rsync -ahv --remove-source-files [email protected]:{p2}{sample_name}_*.* {p1}"
#os.system(f"rsync -ahv --remove-source-files [email protected]:{p2}{h.start['sample_name']}_*.log {p1}")
print(cmd)
os.system(cmd)
#!/usr/bin/env python3
from py4xs.hdf import h5xs, h5exp, lsh5
from py4xs.data2d import Data2d
import numpy as np
import pylab as plt
import os, time
exp_folder = '/home/bashit.a/July-2021/'
samples = '/home/bashit.a/July-2021/sample-6/'
file = "2029_Dentate_gyrus-roi0.h5"
os.chdir(samples)
de = h5exp(exp_folder + "exp.h5")
#de.qgrid
print(de.detectors[1].extension)
qgrid2 = np.hstack([
np.arange(0.005, 0.0499, 0.001),
np.arange(0.05, 0.099, 0.002),
np.arange(0.1, 3.2, 0.005)
])
#print(qgrid2)
#load one file in a directory
dt = h5xs(file, [de.detectors, qgrid2])
tic = time.time()
print(f'Loading file at {tic}')
dt.load_data(N=8, debug=True)
tac = time.time()
print(f'total processing time {tac-tic} seconds')