def load_tab(self, load_item):
"""
It verifies given configuration file, reads the parameters, and fills out the window.
Parameters
----------
conf : str
configuration file (config_disp)
Returns
-------
nothing
"""
if os.path.isfile(load_item):
conf = load_item
else:
conf = os.path.join(load_item, 'conf', 'config_disp')
if not os.path.isfile(conf):
msg_window(
'info: the load directory does not contain config_disp file'
)
return
if not ver.ver_config_data(conf):
msg_window('please check configuration file ' + conf +
'. Cannot parse, ')
return
try:
conf_map = ut.read_config(conf)
except Exception as e:
msg_window('please check configuration file ' + conf +
'. Cannot parse, ' + str(e))
return
self.parse_spec()
try:
self.results_dir = str(conf_map.results_dir).replace(" ", "")
except AttributeError:
if self.results_dir is None:
self.results_dir = self.main_win.experiment_dir
self.result_dir_button.setStyleSheet("Text-align:left")
self.result_dir_button.setText(self.results_dir)
# if parameters are configured, override the readings from spec file
try:
self.diffractometer.setText(
str(conf_map.diffractometer).replace(" ", ""))
except AttributeError:
pass
try:
self.crop.setText(str(conf_map.crop).replace(" ", ""))
except AttributeError:
pass
try:
self.rampups.setText(str(conf_map.rampups).replace(" ", ""))
except AttributeError:
pass
try:
self.energy.setText(str(conf_map.energy).replace(" ", ""))
self.energy.setStyleSheet('color: black')
except AttributeError:
pass
try:
self.delta.setText(str(conf_map.delta).replace(" ", ""))
self.delta.setStyleSheet('color: black')
except AttributeError:
pass
try:
self.gamma.setText(str(conf_map.gamma).replace(" ", ""))
self.gamma.setStyleSheet('color: black')
except AttributeError:
pass
try:
self.detdist.setText(str(conf_map.detdist).replace(" ", ""))
self.detdist.setStyleSheet('color: black')
except AttributeError:
pass
try:
self.theta.setText(str(conf_map.theta).replace(" ", ""))
self.theta.setStyleSheet('color: black')
except AttributeError:
pass
try:
self.chi.setText(str(conf_map.chi).replace(" ", ""))
self.chi.setStyleSheet('color: black')
except AttributeError:
pass
try:
self.phi.setText(str(conf_map.phi).replace(" ", ""))
self.phi.setStyleSheet('color: black')
except AttributeError:
pass
try:
self.scanmot.setText(str(conf_map.scanmot).replace(" ", ""))
self.scanmot.setStyleSheet('color: black')
except AttributeError:
pass
try:
self.scanmot_del.setText(
str(conf_map.scanmot_del).replace(" ", ""))
self.scanmot_del.setStyleSheet('color: black')
except AttributeError:
pass
try:
self.detector.setText(str(conf_map.detector).replace(" ", ""))
self.detector.setStyleSheet('color: black')
except AttributeError:
pass
def prep(fname, conf_info):
"""
This function formats data for reconstruction. It uses configured parameters. The preparation consists of the following steps:
1. removing the "aliens" - aliens are areas that are effect of interference. The area is manually set in a configuration file after inspecting the data. It could be also a mask file of the same dimensions that data.
2. clearing the noise - the values below an amplitude threshold are set to zero
3. amplitudes are set to sqrt
4. cropping and padding. If the adjust_dimention is negative in any dimension, the array is cropped in this dimension.
The cropping is followed by padding in the dimensions that have positive adjust dimension. After adjusting, the dimensions
are adjusted further to find the smallest dimension that is supported by opencl library (multiplier of 2, 3, and 5).
5. centering - finding the greatest amplitude and locating it at a center of new array. If shift center is defined, the center will be shifted accordingly.
6. binning - adding amplitudes of several consecutive points. Binning can be done in any dimension.
The modified data is then saved in data directory as data.tif.
Parameters
----------
fname : str
tif file containing raw data
conf_info : str
experiment directory or configuration file. If it is directory, the "conf/config_data" will be
appended to determine configuration file
Returns
-------
nothing
"""
# The data has been transposed when saved in tif format for the ImageJ to show the right orientation
data = ut.read_tif(fname)
if os.path.isdir(conf_info):
experiment_dir = conf_info
conf = os.path.join(experiment_dir, 'conf', 'config_data')
# if the experiment contains separate scan directories
if not os.path.isfile(conf):
base_dir = os.path.abspath(os.path.join(experiment_dir, os.pardir))
conf = os.path.join(base_dir, 'conf', 'config_data')
else:
#assuming it's a file
conf = conf_info
experiment_dir = None
# verify the configuration file
if not ver.ver_config_data(conf):
return
try:
config_map = ut.read_config(conf)
if config_map is None:
print ("can't read configuration file")
return
except:
print ('Please check the configuration file ' + conf + '. Cannot parse')
return
try:
data_dir = config_map.data_dir
except AttributeError:
data_dir = 'data'
if experiment_dir is not None:
data_dir = os.path.join(experiment_dir, data_dir)
if not os.path.exists(data_dir):
os.makedirs(data_dir)
try:
data = at.remove_aliens(data, config_map, data_dir)
except AttributeError:
pass
except Exception as e:
print ('exiting, error in aliens removal ', str(e))
return
try:
amp_threshold = config_map.amp_threshold
except AttributeError:
print ('define amplitude threshold. Exiting')
return
# zero out the noise
prep_data = np.where(data <= amp_threshold, 0, data)
# square root data
prep_data = np.sqrt(prep_data)
try:
crops_pads = config_map.adjust_dimensions
# the adjust_dimension parameter list holds adjustment in each direction. Append 0s, if shorter
if len(crops_pads) < 6:
for _ in range (6 - len(crops_pads)):
crops_pads.append(0)
except AttributeError:
# the size still has to be adjusted to the opencl supported dimension
crops_pads = (0, 0, 0, 0, 0, 0)
# adjust the size, either pad with 0s or crop array
pairs = []
for i in range(int(len(crops_pads)/2)):
pair = crops_pads[2*i:2*i+2]
pairs.append(pair)
prep_data = ut.adjust_dimensions(prep_data, pairs)
if prep_data is None:
print('check "adjust_dimensions" configuration')
return
try:
center_shift = config_map.center_shift
print ('shift center')
prep_data = ut.get_centered(prep_data, center_shift)
except AttributeError:
prep_data = ut.get_centered(prep_data, [0,0,0])
try:
binsizes = config_map.binning
try:
bins = []
for binsize in binsizes:
bins.append(binsize)
filler = len(prep_data.shape) - len(bins)
for _ in range(filler):
bins.append(1)
prep_data = ut.binning(prep_data, bins)
except:
print ('check "binning" configuration')
except AttributeError:
pass
# save data
data_file = os.path.join(data_dir, 'data.tif')
ut.save_tif(prep_data, data_file)
print ('data ready for reconstruction, data dims:', prep_data.shape)
def write_conf(conf_map, dir, file):
"""
It creates configuration file from the parameters included in dictionary, verifies, and saves in the configuration directory.
Parameters
----------
conf_map : dict
dictionary containing configuration parameters
dir : str
a directory where the configuration file will be saved
file : str
name of the configuration file to save
Returns
-------
nothing
"""
# create "temp" file first, verify it, and if ok, copy to a configuration file
if not os.path.exists(dir):
os.makedirs(dir)
conf_file = os.path.join(dir, file)
temp_file = os.path.join(dir, 'temp')
if os.path.isfile(temp_file):
os.remove(temp_file)
with open(temp_file, 'a') as f:
for key in conf_map:
value = conf_map[key]
if len(value) > 0:
f.write(key + ' = ' + conf_map[key] + '\n')
f.close()
if file == 'config':
if not ver.ver_config(temp_file):
os.remove(temp_file)
msg_window(
'please check the entries in the main window. Cannot save this format'
)
return False
elif file == 'config_prep':
if not ver.ver_config_prep(temp_file):
os.remove(temp_file)
msg_window(
'please check the entries in the Data prep tab. Cannot save this format'
)
return False
elif file == 'config_data':
if not ver.ver_config_data(temp_file):
os.remove(temp_file)
msg_window(
'please check the entries in the Data tab. Cannot save this format'
)
return False
elif file.endswith('config_rec'):
if not ver.ver_config_rec(temp_file):
os.remove(temp_file)
msg_window(
'please check the entries in the Reconstruction tab. Cannot save this format'
)
return False
elif file == 'config_disp':
if not ver.ver_config_disp(temp_file):
os.remove(temp_file)
msg_window(
'please check the entries in the Display tab. Cannot save this format'
)
return False
# copy if verified
shutil.copy(temp_file, conf_file)
os.remove(temp_file)
return True