def move_peak_start(self, x_axis_time, peak_index):
"""
Moves the peak window start point to where ever the user clicked on the screen
:param x_axis_time:
:param peak_index:
:return:
"""
picked_peak_start = int(
self.slk_data.peak_starts[self.current_nutrient][peak_index])
win_start = int(
self.processing_parameters['nutrientprocessing']['processingpars'][
self.current_nutrient]['windowStart'])
win_length = int(
self.processing_parameters['nutrientprocessing']['processingpars'][
self.current_nutrient]['windowSize'])
# If picked point is less than the end of the peak window i.e. valid
if x_axis_time < (picked_peak_start + win_start + win_length):
# If picked point is further along than the current peak window
if x_axis_time > (picked_peak_start + win_start):
window_start_time = x_axis_time - picked_peak_start
new_window_length = win_length - (
x_axis_time - (picked_peak_start + win_start))
self.processing_parameters['nutrientprocessing'][
'processingpars'][self.current_nutrient][
'windowStart'] = window_start_time
self.processing_parameters['nutrientprocessing'][
'processingpars'][self.current_nutrient][
'windowSize'] = new_window_length
# If picked point is less than the start of the peak window
if x_axis_time < (picked_peak_start + win_start):
window_start_time = x_axis_time - picked_peak_start
new_window_length = win_length + (
(picked_peak_start + win_start) - x_axis_time)
self.processing_parameters['nutrientprocessing'][
'processingpars'][self.current_nutrient][
'windowStart'] = window_start_time
self.processing_parameters['nutrientprocessing'][
'processingpars'][self.current_nutrient][
'windowSize'] = new_window_length
# If point is actually less than the value given of the peak starts...
if x_axis_time < picked_peak_start:
time_offset = picked_peak_start - x_axis_time
adjusted_peak_starts = [
p_s - time_offset for p_s in self.slk_data.peak_starts
]
self.slk_data.peak_starts = adjusted_peak_starts
self.w_d = psn.processing_routine(self.slk_data, self.chd_data,
self.w_d,
self.processing_parameters,
self.current_nutrient)
self.interactive_routine(trace_redraw=True)
def update_from_dialog(self, index):
self.slk_data.cup_types[index] = self.peak_display.peakcupline.text()
self.w_d.dilution_factor[index] = int(
self.peak_display.dilutionline.text())
# TODO: Add validation check to these user editable fields
rev_flag_convert = {x: y for y, x in self.FLAG_CONVERTER.items()}
self.w_d.quality_flag[index] = rev_flag_convert[
self.peak_display.flagbox.currentText()]
self.w_d = psn.processing_routine(self.slk_data, self.chd_data,
self.w_d, self.processing_parameters,
self.current_nutrient)
self.interactive_routine(trace_redraw=True)
def shift_trace(self, x_axis_time, direction):
"""
Function for physically shifting the whole trace by 3 time points. Used to realign the trace if necessary
:param x_axis_time:
:param direction:
:return:
"""
if direction == 'right':
for i in range(3):
self.chd_data.ad_data[self.current_nutrient].insert(
int(x_axis_time), 100)
elif direction == 'left':
for i in range(3):
self.chd_data.ad_data[self.current_nutrient].pop(
int(x_axis_time))
self.w_d = psn.processing_routine(self.slk_data, self.chd_data,
self.w_d, self.processing_parameters,
self.current_nutrient)
self.interactive_routine(trace_redraw=True)
def move_peak_end(self, x_axis_time, peak_index):
"""
Moves the peak end after a user has clicked into a spot on the trace and pressed move end
:param x_axis_time:
:param peak_index:
:return:
"""
picked_peak_start = int(
self.slk_data.peak_starts[self.current_nutrient][peak_index])
win_start = int(
self.processing_parameters['nutrientprocessing']['processingpars'][
self.current_nutrient]['windowStart'])
win_length = int(
self.processing_parameters['nutrientprocessing']['processingpars'][
self.current_nutrient]['windowSize'])
peak_window_start = picked_peak_start + win_start
if x_axis_time > (picked_peak_start + win_start):
window_end = picked_peak_start + win_start + win_length
if x_axis_time > window_end:
window_end_increase = x_axis_time - window_end
print(window_end_increase)
self.processing_parameters['nutrientprocessing'][
'processingpars'][self.current_nutrient][
'windowSize'] = win_length + window_end_increase
if window_end > x_axis_time:
window_end_decrease = window_end - x_axis_time
self.processing_parameters['nutrientprocessing'][
'processingpars'][self.current_nutrient][
'windowSize'] = win_length - window_end_decrease
self.w_d = psn.processing_routine(self.slk_data, self.chd_data,
self.w_d,
self.processing_parameters,
self.current_nutrient)
self.interactive_routine(trace_redraw=True)
def proceed(self):
#self.main_trace.cla()
#self.tracecanvas.draw()
self.store_data()
# If the matching lat/lons check box is active assume the file is a underway one. Pull out samples and
# find the latitude and longitudes that correspond
if self.find_lat_lons.isChecked():
print('Checked')
try:
complete = psn.match_lat_lons_routine(
self.path, self.project, self.database,
self.current_nutrient, self.processing_parameters,
self.w_d, self.slk_data)
except Exception:
print(traceback.print_exc())
index = self.slk_data.active_nutrients.index(self.current_nutrient)
try:
self.current_nutrient = self.slk_data.active_nutrients[index + 1]
except IndexError:
print('Processing completed')
logging.info(
f'Processing successfully completed for nutrient file - {self.file}'
)
#plt.close('all')
self.close()
self.analysistraceLabel.setText(
'<b>Processing file: </b>' + str(self.file) +
' | <b>Analysis Trace: </b>' +
str(self.current_nutrient).capitalize())
self.w_d.analyte = self.current_nutrient
self.w_d = psn.processing_routine(self.slk_data, self.chd_data,
self.w_d, self.processing_parameters,
self.current_nutrient)
self.interactive_routine()
def keyPressEvent(self, event):
"""
Handles keyboard button presses and completes functions accordingly
:param event:
:return:
"""
print(event.key())
if event.key() == 65: # Assign A to move left
self.move_camera_left()
elif event.key() == 68: # Assign D to move right
self.move_camera_right()
elif event.key() == 87: # Assign W to zoom in
self.zoom_in()
elif event.key() == 88: # Assign X to zoom out
self.zoom_out()
elif event.key() == 83: # Assign S to zoom fit
self.zoom_fit()
elif event.key() == 81: # Assign Q to auto zoom toggle
if self.auto_size.isChecked():
self.auto_size.setChecked(False)
else:
self.auto_size.setChecked(True)
elif event.key() == 78: # Assign N to iterate through tabs
curr_tab = self.qctabs.currentIndex()
if curr_tab == (len(self.qctabs) - 1):
self.qctabs.setCurrentIndex(0)
else:
self.qctabs.setCurrentIndex(curr_tab + 1)
elif event.key() == 90: # Assign Z to shift peak window left
ws = int(self.processing_parameters['nutrientprocessing']
['processingpars'][self.current_nutrient]['windowStart'])
ws = ws - 2
self.processing_parameters['nutrientprocessing']['processingpars'][
self.current_nutrient]['windowStart'] = ws
self.w_d = psn.processing_routine(self.slk_data, self.chd_data,
self.w_d,
self.processing_parameters,
self.current_nutrient)
self.interactive_routine(trace_redraw=True)
elif event.key() == 67: # Assign C to shift peak window right
ws = int(self.processing_parameters['nutrientprocessing']
['processingpars'][self.current_nutrient]['windowStart'])
ws = ws + 2
self.processing_parameters['nutrientprocessing']['processingpars'][
self.current_nutrient]['windowStart'] = ws
self.w_d = psn.processing_routine(self.slk_data, self.chd_data,
self.w_d,
self.processing_parameters,
self.current_nutrient)
self.interactive_routine(trace_redraw=True)
# Below is only meant to be used for DEVELOPMENT PURPOSES, used to inject random values into peak picking
# to check how the software responds, used to check speed of processing and robustness
elif event.key(
) == 82: # R Imitates changing peak windows etc, for testing optimisation of processing and draw
random_modifier = np.random.randint(low=15, high=45)
random_modifier2 = np.random.randint(low=2, high=30)
print(random_modifier)
print(random_modifier2)
self.processing_parameters['nutrientprocessing']['processingpars'][
self.current_nutrient]['windowStart'] = random_modifier
self.processing_parameters['nutrientprocessing']['processingpars'][
self.current_nutrient]['windowSize'] = random_modifier
self.w_d.quality_flag = [
self.w_d.quality_flag[i] if x not in [4, 5] else 1
for i, x in enumerate(self.w_d.quality_flag)
]
self.w_d = psn.processing_routine(self.slk_data, self.chd_data,
self.w_d,
self.processing_parameters,
self.current_nutrient)
self.draw_data(self.chd_data, self.w_d, self.current_nutrient,
False)
self.interactive_routine(trace_redraw=True)
def __init__(self,
file,
database,
path,
project,
interactive=True,
rereading=False,
perf_mode=False,
ultra_perf_mode=False):
screenwidth = QDesktopWidget().availableGeometry().width()
screenheight = QDesktopWidget().availableGeometry().height()
super().__init__((screenwidth * 0.85), (screenheight * 0.85),
'HyPro - Process Nutrient Analysis')
# Set flagging colours
self.FLAG_COLORS = {
1: '#68C968',
2: '#45D4E8',
3: '#C92724',
4: '#3CB6C9',
5: '#C92724',
6: '#DC9530',
91: '#9CCDD6',
92: '#F442D9',
8: '#3CB6C9'
}
self.FLAG_CONVERTER = {
1: 'Good',
2: 'Suspect',
3: 'Bad',
4: 'Shape Sus',
5: 'Shape Bad',
91: 'CalError Sus',
92: 'CalError Bad',
8: 'Dup Diff'
}
# Load in the processing parameters
self.processing_parameters = load_proc_settings(path, project)
self.file_path = path + '/' + 'Nutrients' + '/' + file
self.file = file
self.path = path
self.project = project
self.database = database
self.interactive = interactive
self.rereading = rereading
self.perf_mode = perf_mode
self.ultra_perf_mode = ultra_perf_mode
# General HyPro settings, use for setting theme of window
with open('C:/HyPro/hyprosettings.json', 'r') as temp:
params = json.loads(temp.read())
# Load up theme for window
if params['theme'] == 'normal':
plt.style.use(style.mplstyle['normal'])
self.theme = 'normal'
else:
plt.style.use(style.mplstyle['dark'])
self.theme = 'dark'
# Holds all the calculation data
self.w_d = WorkingData(file)
# Pull out the data from the files in the directory
try:
self.slk_data, self.chd_data, self.w_d, self.current_nutrient = rsn.get_data_routine(
self.file_path, self.w_d, self.processing_parameters,
self.database)
self.slk_data.run_number = int(
file[len(self.processing_parameters['analysisparams']['seal']
['filePrefix']):-4])
# Process the data and return calculated values
self.w_d = psn.processing_routine(self.slk_data, self.chd_data,
self.w_d,
self.processing_parameters,
self.current_nutrient)
# If interactive processing is activated on the Processing Menu window, then continue to plot everything up
# Otherwise store data and exit without drawing or creating any UI elements
if self.interactive:
self.init_ui()
self.create_standard_qc_tabs()
qc_cups = self.processing_parameters['nutrientprocessing'][
'qcsamplenames']
self.create_custom_qc_tabs(self.slk_data.sample_ids, qc_cups)
self.interactive_routine()
else:
# TODO: Store data if not interactive processing
sys.exit()
except TypeError:
logging.error(
f'Formatting error in .SLK file. Processing aborted.')
traceback.print_exc()
except FileNotFoundError:
logging.error(
'Could not find the nutrient file, is it in the right spot? Does a Nutrient folder exist?'
)
except IndexError:
logging.error(
'HyPro could not find any nutrients! Please check the spelling of your analyte names'
)
