def set_energy(self):
energy = self.hhm.energy.read()['hhm_energy']['value']
dlg = SetEnergy.SetEnergy(round(energy), parent=self)
if dlg.exec_():
try:
new_energy=float(dlg.getValues())
print(new_energy)
if (new_energy > 4700) and (new_energy < 32000):
self.RE(bps.mv(self.hhm.energy, new_energy))
else:
raise ValueError
except Exception as exc:
message_box('Incorrect energy','Energy should be within 4700-32000 eV range')
def _check_entry(el, edge, energy, name, row):
info = f'Proposal: {name}, row: {row+1}, element: {el}, edge: {edge}, energy: {energy}'
if el in element_dict.keys():
if edge in element_dict[el].keys():
if abs(
energy - float(element_dict[el][edge])
) < 10: # provided energy must be within 10 eV from the xray DB
if (energy > 4900) and (energy < 32000):
return True
else:
message_box('Energy outside of feasible range', (
'Warning\nAn entry with energy outside of feasible range found!\n'
+ 'This measurement will be skipped.\n' + info))
else:
message_box(
'Invalid energy',
('Warning\nAn entry with invalid energy was found!\n' +
'This measurement will be skipped.\n' + info))
else:
message_box('Edge not found',
('Warning\nAn entry with invalid edge was found!\n' +
'This measurement will be skipped.\n' + info))
else:
message_box('Element not found',
('Warning\nAn entry with invalid element was found!\n' +
'This measurement will be skipped.\n' + info))
return False
def send_results(self):
dlg = GetEmailAddress.GetEmailAddress('', parent=self)
if dlg.exec_():
email_address = dlg.getValue()
regex = '^\w+([\.-]?\w+)*@\w+([\.-]?\w+)*(\.\w{2,3})+$'
if re.search(regex, email_address):
#print(f'email {email_address}')
pass
else:
message_box('Error', 'Invaild email')
return 0
year = self.RE.md['year']
cycle = self.RE.md['cycle']
proposal = self.RE.md['PROPOSAL']
PI = self.RE.md['PI']
working_directory = f'/nsls2/xf08id/users/{year}/{cycle}/{proposal}'
zip_file = f'{working_directory}/{proposal}.zip'
id = str(uuid.uuid4())[0:5]
zip_id_file = f'{proposal}-{id}.zip'
if os.path.exists(zip_file):
os.remove(zip_file)
os.system(f'zip {zip_file} {working_directory}/*.dat ')
dropbox_service = get_dropbox_service()
with open(zip_file, "rb") as f:
file_id = dropbox_service.files_upload(
f.read(), f'/{year}/{cycle}/{zip_id_file}')
file_link = dropbox_service.sharing_create_shared_link(
f'/{year}/{cycle}/{zip_id_file}')
link_url = file_link.url
print('Upload succesful')
gmail_service = get_gmail_service()
message = create_html_message(
'*****@*****.**', email_address,
f'ISS beamline results Proposal {proposal}',
f' <p> Dear {PI},</p> <p>You can download the result of your experiment at ISS under proposal {proposal} here,</p> <p> {link_url} </p> <p> Sincerely, </p> <p> ISS Staff </p>'
)
draft = upload_draft(gmail_service, message)
sent = send_draft(gmail_service, draft)
print('Email sent')
def plot_xas_data(self):
selected_items = (self.list_data.selectedItems())
update_figure([self.figure_data.ax], self.toolbar, self.canvas)
if self.comboBox_data_numerator.currentText() == -1 or self.comboBox_data_denominator.currentText() == -1:
message_box('Warning','Please select numerator and denominator')
return
self.last_numerator = self.comboBox_data_numerator.currentText()
self.last_denominator = self.comboBox_data_denominator.currentText()
energy_key = 'energy'
handles = []
for i in selected_items:
path = f'{self.working_folder}/{i.text()}'
print(path)
df, header = load_binned_df_from_file(path)
numer = np.array(df[self.comboBox_data_numerator.currentText()])
denom = np.array(df[self.comboBox_data_denominator.currentText()])
if self.checkBox_ratio.checkState():
y_label = (f'{self.comboBox_data_numerator.currentText()} / '
f'{self.comboBox_data_denominator.currentText()}')
spectrum = numer/denom
else:
y_label = (f'{self.comboBox_data_numerator.currentText()}')
spectrum = numer
if self.checkBox_log_bin.checkState():
spectrum = np.log(spectrum)
y_label = f'ln ({y_label})'
if self.checkBox_inv_bin.checkState():
spectrum = -spectrum
y_label = f'- {y_label}'
self.figure_data.ax.plot(df[energy_key], spectrum)
self.parent.set_figure(self.figure_data.ax,self.canvas,label_x='Energy (eV)', label_y=y_label)
self.figure_data.ax.set_xlabel('Energy (eV)')
self.figure_data.ax.set_ylabel(y_label)
last_trace = self.figure_data.ax.get_lines()[len(self.figure_data.ax.get_lines()) - 1]
patch = mpatches.Patch(color=last_trace.get_color(), label=i.text())
handles.append(patch)
self.figure_data.ax.legend(handles=handles)
self.figure_data.tight_layout()
self.canvas.draw_idle()
def set_energy(self):
energy = self.hhm.energy.read()['hhm_energy']['value']
dlg = SetEnergy.SetEnergy(round(energy), parent=self)
if dlg.exec_():
try:
new_energy = float(dlg.getValues())
print(new_energy)
except Exception as exc:
message_box('Incorrect energy', 'Energy should be numerical')
if (new_energy > 4700) and (new_energy < 32000):
self.plan_processor.add_plan_and_run_if_idle(
'move_mono_energy', {'energy': new_energy})
# self.plan_processor.add_execute_pause_plan_at_head('move_mono_energy', {'energy': new_energy})
# self.RE(bps.mv(self.hhm.energy, new_energy))
else:
message_box('Incorrect energy',
'Energy should be within 4700-32000 eV range')
def set_emission_energy(self):
energy = np.round(self.motor_emission.energy.position, 2)
limits = self.motor_emission.energy.limits
dlg = SetEnergy.SetEnergy(energy, parent=self)
if dlg.exec_():
try:
new_energy = float(dlg.getValues())
print(new_energy)
except Exception as exc:
message_box('Incorrect energy', 'Energy should be numerical')
if (new_energy > 4700) and (new_energy < 32000):
self.plan_processor.add_plan_and_run_if_idle(
'move_johann_spectrometer_energy', {'energy': new_energy})
# self.plan_processor.add_execute_pause_plan_at_head('move_johann_spectrometer_energy', {'energy': new_energy})
# self.RE(bps.mv(self.hhm.energy, new_energy))
else:
message_box(
'Incorrect energy',
f'Energy should be within {limits[0]}-{limits[1]} eV range'
)
def add_data_to_project(self):
if self.comboBox_data_numerator.currentText(
) != -1 and self.comboBox_data_denominator.currentText() != -1:
for item in self.list_data.selectedItems():
filepath = str(Path(self.working_folder) / Path(item.text()))
name = Path(filepath).resolve().stem
df, header = load_binned_df_from_file(filepath)
uid = header[header.find('UID:') +
5:header.find('\n', header.find('UID:'))]
try:
md = self.db[uid]['start']
except:
print('Metadata not found')
md = {}
df = df.sort_values('energy')
num_key = self.comboBox_data_numerator.currentText()
den_key = self.comboBox_data_denominator.currentText()
mu = df[num_key] / df[den_key]
if self.checkBox_log_bin.checkState():
mu = np.log(mu)
if self.checkBox_inv_bin.checkState():
mu = -mu
mu = np.array(mu)
ds = XASDataSet(name=name,
md=md,
energy=df['energy'],
mu=mu,
filename=filepath,
datatype='experiment')
ds.header = header
self.parent.project.append(ds)
self.parent.statusBar().showMessage(
'Scans added to the project successfully')
else:
message_box('Error', 'Select numerator and denominator columns')
def calibrate_offset(self):
ret = question_message_box(
self, 'Confirmation',
'Are you sure you would like to calibrate it?')
if not ret:
print('[E0 Calibration] Aborted!')
return False
new_value = str(
self.hhm.angle_offset.value -
(xray.energy2encoder(float(self.edit_E0.text(
)), self.hhm.pulses_per_deg) - xray.energy2encoder(
float(self.edit_ECal.text()), self.hhm.pulses_per_deg)) /
self.hhm.pulses_per_deg)
if self.set_new_angle_offset(new_value):
return
print('[E0 Calibration] New value: {}\n[E0 Calibration] Completed!'.
format(new_value))
message_box(
'Reload trajectory',
'Switch to Trajectory tab and re-load and re-initialize the trajectory'
)
def update_offset(self):
offset = float(self.label_angle_offset.text())
energy = float(self.widget_energy_selector.edit_E0.text())
dlg = UpdateAngleOffset.UpdateAngleOffset(offset, energy, parent=self)
if dlg.exec_():
try:
values = dlg.getValues()
if len(values) == 1:
offset = values[0]
self.hhm.angle_offset.put(float(offset))
self.update_angle_offset_label(value=float(dlg.getValues()))
elif len(values) == 2:
old_energy_str, new_energy_str = values
# self.hhm.calibrate(float(old_energy_str), float(new_energy_str))
self.hhm.calibrate(float(new_energy_str), float(old_energy_str))
self.update_angle_offset_label(value=self.hhm.angle_offset.get())
message_box('Warning', 'The new calibration will be applied only to new scans.\nIf you want new calibration to apply to old scans, you will have to redefine/recreate them.')
except Exception as exc:
if type(exc) == ophyd_utils.errors.LimitError:
print('[New offset] {}. No reason to be desperate, though.'.format(exc))
else:
print('[New offset] Something went wrong, not the limit: {}'.format(exc))
def create_new_sample(self):
if self.lineEdit_sample_name.text():
x = self.spinBox_sample_x.value()
y = self.spinBox_sample_y.value()
name = self.lineEdit_sample_name.text()
comment = self.lineEdit_sample_comment.text()
item = QtGui.QStandardItem(f'{name} at X {x} Y {y}')
item.setDropEnabled(False)
item.item_type = 'sample'
item.setCheckable(True)
item.setEditable(False)
item.x = x
item.y = y
item.name = name
item.comment = comment
item.setIcon(icon_sample)
parent = self.model_samples.invisibleRootItem()
parent.appendRow(item)
self.listView_samples.setModel(self.model_samples)
else:
message_box('Warning', 'Sample name is empty')
def create_map(self):
if self.treeView_batch.model().rowCount(
) and self.treeView_batch.selectedIndexes():
parent = self.model_batch.itemFromIndex(
self.treeView_batch.selectedIndexes()[0])
if (parent.item_type
== 'experiment') and (self.listView_scans.model()
is not None):
for index in range(self.listView_scans.model().rowCount()):
item_scan = self.listView_scans.model().item(index)
if item_scan.checkState():
new_item_scan = self.clone_scan_item(item_scan)
#calculate_map
if self.radioButton_sample_map_1D.isChecked():
x_coord = np.linspace(
self.spinBox_sample_x_map_start.value(),
self.spinBox_sample_x_map_end.value(),
self.spinBox_sample_x_map_steps.value())
y_coord = np.linspace(
self.spinBox_sample_y_map_start.value(),
self.spinBox_sample_y_map_end.value(),
self.spinBox_sample_x_map_steps.value())
xy_coord = np.column_stack((x_coord, y_coord))
elif self.radioButton_sample_map_2D.isChecked():
x_coord = np.ndarray(0)
y_coord = np.ndarray(0)
y_points = np.linspace(
self.spinBox_sample_y_map_start.value(),
self.spinBox_sample_y_map_end.value(),
self.spinBox_sample_y_map_steps.value())
if int(self.spinBox_sample_y_map_steps.value()
) == 0:
message_box('Warning',
'Select nonzero number of steps ')
return
for i in range(
int(self.spinBox_sample_y_map_steps.value(
))):
x_line = np.linspace(
self.spinBox_sample_x_map_start.value(),
self.spinBox_sample_x_map_end.value(),
self.spinBox_sample_x_map_steps.value())
y_line = np.ones(len(x_line)) * (y_points[i])
x_coord = np.append(x_coord, x_line)
y_coord = np.append(y_coord, y_line)
xy_coord = np.column_stack((x_coord, y_coord))
print(xy_coord)
if self.lineEdit_map_name.text():
for index in range(len(xy_coord)):
x = xy_coord[index, 0]
y = xy_coord[index, 1]
name = f'{self.lineEdit_map_name.text()} at {x:.3f} {y:.3}'
item = QtGui.QStandardItem(name)
new_item_scan.appendRow(item)
item.setDropEnabled(False)
item.item_type = 'sample'
item.setEditable(False)
item.x = x
item.y = y
item.name = name
item.comment = self.lineEdit_map_comment.text()
item.setIcon(icon_sample)
else:
message_box('Warning',
'Select nonzero number of steps ')
parent.appendRow(new_item_scan)
new_item_scan.setCheckable(False)
new_item_scan.setEditable(False)
self.treeView_batch.expand(
self.model_batch.indexFromItem(parent))
for index in range(parent.rowCount()):
self.treeView_batch.expand(
self.model_batch.indexFromItem(parent.child(index)))
self.treeView_batch.setModel(self.model_batch)
else:
message_box('Warning', 'Select experiment before adding map')
def create_measurement(self):
if self.treeView_batch.model().rowCount():
if self.treeView_batch.selectedIndexes():
selected_index = self.treeView_batch.selectedIndexes()[0]
parent = self.model_batch.itemFromIndex(selected_index)
if parent.item_type == 'experiment':
if self.radioButton_priority_sample.isChecked():
if self.listView_samples.model() is not None:
for index in range(
self.listView_samples.model().rowCount()):
item_sample = self.listView_samples.model(
).item(index)
if item_sample.checkState():
new_item_sample = self.clone_sample_item(
item_sample)
if self.listView_scans.model() is not None:
scans_selected = 0
for index in range(self.listView_scans.
model().rowCount()):
item_scan = self.listView_scans.model(
).item(index)
if item_scan.checkState():
scans_selected = 1
new_item_scan = self.clone_scan_item(
item_scan)
new_item_sample.appendRow(
new_item_scan)
new_item_scan.setCheckable(
False)
new_item_scan.setEditable(
False)
new_item_scan.setIcon(
icon_scan)
if scans_selected:
parent.appendRow(new_item_sample)
new_item_sample.setCheckable(False)
new_item_sample.setEditable(False)
else:
if self.listView_scans.model() is not None:
for index in range(
self.listView_scans.model().rowCount()):
item_scan = self.listView_scans.model().item(
index)
if item_scan.checkState():
new_item_scan = self.clone_scan_item(
item_scan)
print(f' Repeat {new_item_scan.repeat}')
if self.listView_samples.model(
) is not None:
samples_selected = 0
for index in range(
self.listView_samples.model(
).rowCount()):
item_sample = self.listView_samples.model(
).item(index)
if item_sample.checkState():
samples_selected = 1
new_item_sample = self.clone_sample_item(
item_sample)
new_item_scan.appendRow(
new_item_sample)
new_item_scan.setCheckable(
False)
new_item_scan.setEditable(
False)
new_item_scan.setIcon(
icon_scan)
if samples_selected:
parent.appendRow(new_item_scan)
new_item_scan.setCheckable(False)
new_item_scan.setEditable(False)
self.treeView_batch.expand(
self.model_batch.indexFromItem(parent))
for index in range(parent.rowCount()):
self.treeView_batch.expand(
self.model_batch.indexFromItem(
parent.child(index)))
self.treeView_batch.setModel(self.model_batch)
else:
message_box(
'Warning',
'Select experiment before adding measurements')
def run_scan(self):
ignore_shutter = False
energy_grid = []
time_grid = []
for shutter in [
self.shutter_dictionary[shutter]
for shutter in self.shutter_dictionary
if self.shutter_dictionary[shutter].shutter_type != 'SP'
]:
if shutter.state.value:
ret = question_message_box(
self, 'Shutter closed',
'Would you like to run the scan with the shutter closed?')
if not ret:
print('Aborted!')
return False
ignore_shutter = True
break
# Send sampling time to the pizzaboxes:
value = int(
round(
float(self.analog_samp_time) /
self.adc_list[0].sample_rate.get() * 100000))
for adc in self.adc_list:
adc.averaging_points.put(str(value))
for enc in self.enc_list:
enc.filter_dt.put(float(self.enc_samp_time) * 100000)
# not needed at QAS this is a detector
if self.xia is not None:
if self.xia.input_trigger is not None:
self.xia.input_trigger.unit_sel.put(1) # ms, not us
self.xia.input_trigger.period_sp.put(int(self.xia_samp_time))
name_provided = self.parameter_values[0].text()
if name_provided:
timenow = datetime.datetime.now()
print('\nStarting scan at {}'.format(timenow.strftime("%H:%M:%S"),
flush='true'))
start_scan_timer = timer()
# Get parameters from the widgets and organize them in a dictionary (run_params)
run_parameters = return_parameters_from_widget(
self.parameter_descriptions, self.parameter_values,
self.parameter_types)
# Run the scan using the dict created before
self.run_mode_uids = []
self.parent_gui.run_mode = 'run'
plan_key = self.comboBox_scan_type.currentText()
if plan_key == 'Step scan':
update_figure(
[self.figure.ax2, self.figure.ax1, self.figure.ax3],
self.toolbar, self.canvas)
energy_grid, time_grid = generate_energy_grid(
float(self.e0), float(self.edit_preedge_start.text()),
float(self.edit_xanes_start.text()),
float(self.edit_xanes_end.text()),
float(self.edit_exafs_end.text()),
float(self.edit_preedge_spacing.text()),
float(self.edit_xanes_spacing.text()),
float(self.edit_exafs_spacing.text()),
float(self.edit_preedge_dwell.text()),
float(self.edit_xanes_dwell.text()),
float(self.edit_exafs_dwell.text()),
int(self.comboBox_exafs_dwell_kpower.currentText()))
#print(energy_grid)
plan_func = self.plan_funcs[plan_key]
LivePlots = [
XASPlot(self.apb.ch1_mean.name,
self.apb.ch2_mean.name,
'Transmission',
self.hhm[0].energy.name,
log=True,
ax=self.figure.ax1,
color='b'),
XASPlot(self.apb.ch2_mean.name,
self.apb.ch3_mean.name,
'Reference',
self.hhm[0].energy.name,
log=True,
ax=self.figure.ax1,
color='r'),
XASPlot(self.apb.ch4_mean.name,
self.apb.ch1_mean.name,
'Fluorescence',
self.hhm[0].energy.name,
log=False,
ax=self.figure.ax1,
color='g'),
]
print(f'Edge at execution {self.edge}')
RE_args = [
plan_func(**run_parameters,
ignore_shutter=ignore_shutter,
energy_grid=energy_grid,
time_grid=time_grid,
element=self.element,
e0=self.e0,
edge=self.edge,
ax=self.figure.ax1,
stdout=self.parent_gui.emitstream_out)
]
if plan_key.lower() == 'step scan':
RE_args.append(LivePlots)
self.run_mode_uids = self.RE(*RE_args)
timenow = datetime.datetime.now()
print('Scan complete at {}'.format(timenow.strftime("%H:%M:%S")))
stop_scan_timer = timer()
print('Scan duration {} s'.format(stop_scan_timer -
start_scan_timer))
if self.rr_token is not None:
self.RE.unsubscribe(self.rr_token)
else:
message_box('Error', 'Please provide the name for the scan')
