def navigation_sliders(data_axes, title=None):
"""Raises a windows with sliders to control the index of DataAxis
Parameters
----------
data_axes : list of DataAxis instances
"""
class NavigationSliders(t.HasTraits):
pass
nav = NavigationSliders()
view_tuple = ()
for axis in data_axes:
name = str(axis).replace(" ", "_")
nav.add_class_trait(name, axis)
nav.trait_set([name, axis])
view_tuple += (
tui.Item(name,
style = "custom",
editor = tui.InstanceEditor(
view=tui.View(
tui.Item(
"index",
show_label=False,
# The following is commented out
# due to a traits ui bug
#editor=tui.RangeEditor(mode="slider"),
),
),
),
),
)
view = tui.View(tui.VSplit(view_tuple), title="Navigation sliders"
if title is None
else title)
nav.edit_traits(view=view)
class ADC(traits.HasTraits):
refreshTime = traits.Float(
0.1, desc="how often to update the frequencies in seconds")
logFile = traits.File
rpiADCLogFolder = traits.String
averageN = traits.Int(100)
VMax = traits.Enum(3.3, 5.0)
channelList = traits.List(
[1, 3, 5, 6],
desc="list of channels to show frequencies for and query")
channelValues = [(0, 'Ch 0'), (1, 'Ch 1'), (2, 'Ch 2'), (3, 'Ch 3'),
(4, 'Ch 4'), (5, 'Ch 5'), (6, 'Ch 6'), (7, 'Ch 7')]
#THIS ONLY WORKS IF PyHWI can be found! it is in the python path manager for lab-Monitoring-0
connection = rpiADCClient.Connection()
#if there are problems check the server is running on 192.168.0.111
icon_trait = pyface.image_resource.ImageResource('icons/wavemeter.png')
#oscilloscope = None
currentLocalTime = time.localtime()
currentYear = currentLocalTime.tm_year
currentMonth = currentLocalTime.tm_mon
currentDay = currentLocalTime.tm_mday
channel0 = ADCChannel(channelNumber=0,
connection=connection,
channelName="Na Cavity Lock",
channelMessageHigh="Na Cavity Locked",
channelMessageLow="Na Cavity Out of Lock",
criticalValue=1.5,
highIsGood=True,
highSoundFile="NaLocked.wav",
lowSoundFile="NaOutOfLock.wav")
channel1 = ADCChannel(channelNumber=1,
connection=connection,
channelName="Li MOT Fluorescence",
channelMessageHigh="MOT Loading",
channelMessageLow="No MOT",
criticalValue=0.1)
channel2 = ADCChannel(
channelNumber=2,
connection=connection,
channelName="Li MOT Power (stable)") #changed by Martin
channel3 = ADCChannel(channelNumber=3,
connection=connection,
channelName="Li MOT (unstable)")
channel4 = ADCChannel(channelNumber=4,
connection=connection,
channelName="Na MOT Power (stable)")
channel5 = ADCChannel(channelNumber=5,
connection=connection,
channelName="Na MOT Flourescence")
channel6 = ADCChannel(channelNumber=6,
connection=connection,
channelName="ZS light Power")
channel7 = ADCChannel(channelNumber=7,
connection=connection,
channelName="disconnected")
channels = {
0: channel0,
1: channel1,
2: channel2,
3: channel3,
4: channel4,
5: channel5,
6: channel6,
7: channel7
}
def __init__(self, **traitsDict):
"""Called when object initialises. Starts timer etc. """
print "Instantiating GUI.."
super(ADC, self).__init__(**traitsDict)
self.connection.connect()
self.oscilloscope = Oscilloscope(connection=self.connection,
resolution=self.refreshTime,
visibleChannels=self.channelList)
self.start_timer()
def start_timer(self):
"""Called in init if user selected live update mode, otherwise called from menu action.
Every self.wizard.updateRateSeconds, self._refresh_data_action will be called"""
print "Timer Object Started. Will update ADC Information every %s seconds" % self.refreshTime
self.timer = Timer(
float(self.refreshTime) * 1000, self._refresh_Visible_channels)
def _refreshTime_changed(self):
self.timer.setInterval(float(self.refreshTime) * 1000)
print "will update ADC every %s seconds" % (float(self.refreshTime))
self.oscilloscope.resolution = self.refreshTime #use refresh time to set resolution of oscilloscope
def _logFile_changed(self):
self._create_log_file()
def _channelList_changed(self):
"""push changes to visible channels in oscilloscope """
self.oscilloscope.visibleChannels = self.channelList
def _logFile_default(self):
"""default log file has date stamp. log file is changed once a day """
print "choosing default log file"
return os.path.join(
self.rpiADCLogFolder,
time.strftime("rpiADC-%Y-%m-%d.csv", self.currentLocalTime))
def getGroupFolder(self):
"""returns the location of the group folder. supports both
linux and windows. assumes it is mounted to /media/ursa/AQOGroupFolder
for linux"""
if platform.system() == "Windows":
groupFolder = os.path.join("\\\\ursa", "AQOGroupFolder")
if platform.system() == "Linux":
groupFolder = os.path.join("/media", "ursa", "AQOGroupFolder")
return groupFolder
def _rpiADCLogFolder_default(self):
return os.path.join(self.getGroupFolder(), "Experiment Humphry",
"Experiment Control And Software", "rpiADC",
"data")
def _create_log_file(self):
if not os.path.exists(os.path.join(self.rpiADCLogFolder,
self.logFile)):
with open(self.logFile, 'a+') as csvFile:
csvWriter = csv.writer(csvFile)
csvWriter.writerow([
"epochSeconds", "Channel 0", "Channel 1", "Channel 2",
"Channel 3", "Channel 4", "Channel 5", "Channel 6",
"Channel 7"
])
def checkDateForFileName(self):
"""gets current date and time and checks if we should change file name
if we should it creates the new file and the name"""
#self.currentLocalTime was already changed in log Temperatures
if self.currentLocalTime.tm_mday != self.currentDay:
#the day has changed we should start a new log file!
self.logFile = self._logFile_default()
self._create_log_file()
def _log_channels(self):
self.currentLocalTime = time.localtime()
self.checkDateForFileName()
self.currentMonth = self.currentLocalTime.tm_mon
self.currentDay = self.currentLocalTime.tm_mday
if not os.path.exists(os.path.join(self.rpiADCLogFolder,
self.logFile)):
self._create_log_file()
voltages = [self.channels[i]._voltage_get() for i in range(0, 8)]
with open(self.logFile, 'a+') as csvFile:
csvWriter = csv.writer(csvFile)
csvWriter.writerow([time.time()] + voltages)
def _refresh_Visible_channels(self):
self.connection.getResults() #updates dictionary in connection object
for channelNumber in self.channelList:
channel = self.channels[channelNumber]
channel._voltage_update()
self.oscilloscope.updateArrays()
self.oscilloscope.updateArrayPlotData()
self._log_channels()
settingsGroup = traitsui.VGroup(
traitsui.Item("logFile", label="Log File"),
traitsui.HGroup(
traitsui.Item('refreshTime', label='refreshTime'),
traitsui.Item(
'averageN',
label='averaging Number',
tooltip=
"Number of measurements taken and averaged for value shown"),
traitsui.Item('VMax',
label='Maximum Voltage Setting',
tooltip="Whether the box is set to 3.3V or 5V max")),
)
selectionGroup = traitsui.Group(
traitsui.Item('channelList',
editor=traitsui.CheckListEditor(values=channelValues,
cols=4),
style='custom',
label='Show'))
groupLeft = traitsui.VGroup(
traitsui.Item('channel0',
editor=traitsui.InstanceEditor(),
style='custom',
show_label=False,
visible_when="(0 in channelList)"),
traitsui.Item('channel1',
editor=traitsui.InstanceEditor(),
style='custom',
show_label=False,
visible_when="(1 in channelList)"),
traitsui.Item('channel2',
editor=traitsui.InstanceEditor(),
style='custom',
show_label=False,
visible_when="(2 in channelList)"),
traitsui.Item('channel3',
editor=traitsui.InstanceEditor(),
style='custom',
show_label=False,
visible_when="(3 in channelList)"))
groupRight = traitsui.VGroup(
traitsui.Item('channel4',
editor=traitsui.InstanceEditor(),
style='custom',
show_label=False,
visible_when="(4 in channelList)"),
traitsui.Item('channel5',
editor=traitsui.InstanceEditor(),
style='custom',
show_label=False,
visible_when="(5 in channelList)"),
traitsui.Item('channel6',
editor=traitsui.InstanceEditor(),
style='custom',
show_label=False,
visible_when="(6 in channelList)"),
traitsui.Item('channel7',
editor=traitsui.InstanceEditor(),
style='custom',
show_label=False,
visible_when="(7 in channelList)"))
groupOscilloscope = traitsui.Group(
traitsui.Item('oscilloscope',
editor=traitsui.InstanceEditor(),
style='custom',
show_label=False))
groupAll = traitsui.VGroup(
settingsGroup, selectionGroup,
traitsui.VSplit(traitsui.HGroup(groupLeft, groupRight),
groupOscilloscope))
traits_view = traitsui.View(groupAll,
resizable=True,
title="ADC Monitor",
handler=ADCHandler(),
icon=icon_trait)
class CSVFile(tr.HasStrictTraits):
path = tr.Str
count_lines = tr.Button
_lines_number = tr.Int # _ is the private field convention
show_lines_number = tr.Bool
num_of_first_lines_to_show = tr.Int(10)
num_of_last_lines_to_show = tr.Int(10)
first_lines = tr.Property(
depends_on='path, num_of_first_lines_to_show, first_lines_to_skip')
last_lines = tr.Property(
depends_on='path, num_of_last_lines_to_show, last_lines_to_skip')
first_lines_to_skip = tr.Range(low=0, high=10**9, mode='spinner')
last_lines_to_skip = tr.Range(low=0, high=10**9, mode='spinner')
def _count_lines_fired(self):
# return sum(1 for line in open(self.path))
self.show_lines_number = True
self._lines_number = self._count_lines_in_file(self.path)
def get_lines_number(self):
# If it was not yet calculated, calc it first
if self._lines_number == 0:
self._lines_number = self._count_lines_in_file(self.path)
return self._lines_number
def _count_lines_in_file(self, file_name):
''' This method will count the number of lines in a huge file pretty
quickly using custom buffering'''
f = open(file_name, 'rb')
bufgen = takewhile(lambda x: x,
(f.raw.read(1024 * 1024) for i in repeat(None)))
return sum(buf.count(b'\n') for buf in bufgen) + 1
@tr.cached_property
def _get_first_lines(self):
first_lines_list = []
with open(self.path) as myfile:
for i in range(self.num_of_first_lines_to_show):
try:
# Get next line if it exists!
line = next(myfile)
# The following will not executed if an exception was thrown
first_lines_list.append(line)
except StopIteration:
# If last line ends with \n then a new empty line is
# actually there
if len(first_lines_list) != 0:
if first_lines_list[-1].endswith('\n'):
first_lines_list.append('')
break
first_lines_list = self.add_line_numbers(first_lines_list)
first_lines_list = first_lines_list[self.first_lines_to_skip:]
first_lines_str = ''.join(first_lines_list)
return first_lines_str
def add_line_numbers(self, lines_list):
new_list = []
for line_num, line in zip(range(1, len(lines_list) + 1), lines_list):
new_list.append('(' + str(line_num) + ')--> ' + str(line))
return new_list
def add_reverse_line_numbers(self, lines_list):
new_list = []
for line_num, line in zip(range(len(lines_list), 0, -1), lines_list):
new_list.append('(' + str(line_num) + ')--> ' + str(line))
return new_list
@tr.cached_property
def _get_last_lines(self):
last_lines_list = self.get_last_n_lines(self.path,
self.num_of_last_lines_to_show,
False)
last_lines_list = self.add_reverse_line_numbers(last_lines_list)
last_lines_list = last_lines_list[0:len(last_lines_list) -
self.last_lines_to_skip]
last_lines_str = ''.join(last_lines_list)
return last_lines_str
def get_last_n_lines(self, file_name, N, skip_empty_lines=False):
# Create an empty list to keep the track of last N lines
list_of_lines = []
# Open file for reading in binary mode
with open(file_name, 'rb') as read_obj:
# Move the cursor to the end of the file
read_obj.seek(0, os.SEEK_END)
# Create a buffer to keep the last read line
buffer = bytearray()
# Get the current position of pointer i.e eof
pointer_location = read_obj.tell()
# Loop till pointer reaches the top of the file
while pointer_location >= 0:
# Move the file pointer to the location pointed by pointer_location
read_obj.seek(pointer_location)
# Shift pointer location by -1
pointer_location = pointer_location - 1
# read that byte / character
new_byte = read_obj.read(1)
# If the read byte is new line character then it means one line is read
if new_byte == b'\n':
# Save the line in list of lines
line = buffer.decode()[::-1]
if (skip_empty_lines):
line_is_empty = line.isspace()
if (line_is_empty == False):
list_of_lines.append(line)
else:
list_of_lines.append(line)
# If the size of list reaches N, then return the reversed list
if len(list_of_lines) == N:
return list(reversed(list_of_lines))
# Reinitialize the byte array to save next line
buffer = bytearray()
else:
# If last read character is not eol then add it in buffer
buffer.extend(new_byte)
# As file is read completely, if there is still data in buffer, then its first line.
if len(buffer) > 0:
list_of_lines.append(buffer.decode()[::-1])
# return the reversed list
return list(reversed(list_of_lines))
traits_view = ui.View(
ui.Item('path', style='readonly', label='File'),
ui.HGroup(
ui.UItem('count_lines'),
ui.Item('_lines_number',
style='readonly',
visible_when='show_lines_number == True')),
ui.VSplit(
ui.HGroup(ui.Item('first_lines', style='custom'),
'first_lines_to_skip',
label='First lines in the file'),
ui.HGroup(ui.Item('last_lines', style='custom'),
'last_lines_to_skip',
label='Last lines in the file')))
class HCFF(tr.HasStrictTraits):
'''High-Cycle Fatigue Filter
'''
#=========================================================================
# Traits definitions
#=========================================================================
decimal = tr.Enum(',', '.')
delimiter = tr.Str(';')
file_csv = tr.File
open_file_csv = tr.Button('Input file')
skip_rows = tr.Int(4, auto_set=False, enter_set=True)
columns_headers_list = tr.List([])
x_axis = tr.Enum(values='columns_headers_list')
y_axis = tr.Enum(values='columns_headers_list')
x_axis_multiplier = tr.Enum(1, -1)
y_axis_multiplier = tr.Enum(-1, 1)
npy_folder_path = tr.Str
file_name = tr.Str
apply_filters = tr.Bool
force_name = tr.Str('Kraft')
peak_force_before_cycles = tr.Float(30)
plots_num = tr.Enum(1, 2, 3, 4, 6, 9)
plot_list = tr.List()
plot = tr.Button
add_plot = tr.Button
add_creep_plot = tr.Button
parse_csv_to_npy = tr.Button
generate_filtered_npy = tr.Button
add_columns_average = tr.Button
force_max = tr.Float(100)
force_min = tr.Float(40)
figure = tr.Instance(Figure)
# plots_list = tr.List(editor=ui.SetEditor(
# values=['kumquats', 'pomegranates', 'kiwi'],
# can_move_all=False,
# left_column_title='List'))
#=========================================================================
# File management
#=========================================================================
def _open_file_csv_fired(self):
""" Handles the user clicking the 'Open...' button.
"""
extns = ['*.csv', ] # seems to handle only one extension...
wildcard = '|'.join(extns)
dialog = FileDialog(title='Select text file',
action='open', wildcard=wildcard,
default_path=self.file_csv)
dialog.open()
self.file_csv = dialog.path
""" Filling x_axis and y_axis with values """
headers_array = np.array(
pd.read_csv(
self.file_csv, delimiter=self.delimiter, decimal=self.decimal,
nrows=1, header=None
)
)[0]
for i in range(len(headers_array)):
headers_array[i] = self.get_valid_file_name(headers_array[i])
self.columns_headers_list = list(headers_array)
""" Saving file name and path and creating NPY folder """
dir_path = os.path.dirname(self.file_csv)
self.npy_folder_path = os.path.join(dir_path, 'NPY')
if os.path.exists(self.npy_folder_path) == False:
os.makedirs(self.npy_folder_path)
self.file_name = os.path.splitext(os.path.basename(self.file_csv))[0]
#=========================================================================
# Parameters of the filter algorithm
#=========================================================================
def _figure_default(self):
figure = Figure(facecolor='white')
figure.set_tight_layout(True)
return figure
def _parse_csv_to_npy_fired(self):
print('Parsing csv into npy files...')
for i in range(len(self.columns_headers_list)):
column_array = np.array(pd.read_csv(
self.file_csv, delimiter=self.delimiter, decimal=self.decimal, skiprows=self.skip_rows, usecols=[i]))
np.save(os.path.join(self.npy_folder_path, self.file_name +
'_' + self.columns_headers_list[i] + '.npy'), column_array)
print('Finsihed parsing csv into npy files.')
def get_valid_file_name(self, original_file_name):
valid_chars = "-_.() %s%s" % (string.ascii_letters, string.digits)
new_valid_file_name = ''.join(
c for c in original_file_name if c in valid_chars)
return new_valid_file_name
# def _add_columns_average_fired(self):
# columns_average = ColumnsAverage(
# columns_names=self.columns_headers_list)
# # columns_average.set_columns_headers_list(self.columns_headers_list)
# columns_average.configure_traits()
def _generate_filtered_npy_fired(self):
# 1- Export filtered force
force = np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.force_name + '.npy')).flatten()
peak_force_before_cycles_index = np.where(
abs((force)) > abs(self.peak_force_before_cycles))[0][0]
force_ascending = force[0:peak_force_before_cycles_index]
force_rest = force[peak_force_before_cycles_index:]
force_max_indices, force_min_indices = self.get_array_max_and_min_indices(
force_rest)
force_max_min_indices = np.concatenate(
(force_min_indices, force_max_indices))
force_max_min_indices.sort()
force_rest_filtered = force_rest[force_max_min_indices]
force_filtered = np.concatenate((force_ascending, force_rest_filtered))
np.save(os.path.join(self.npy_folder_path, self.file_name +
'_' + self.force_name + '_filtered.npy'), force_filtered)
# 2- Export filtered displacements
# TODO I skipped time with presuming it's the first column
for i in range(1, len(self.columns_headers_list)):
if self.columns_headers_list[i] != str(self.force_name):
disp = np.load(os.path.join(self.npy_folder_path, self.file_name +
'_' + self.columns_headers_list[i] + '.npy')).flatten()
disp_ascending = disp[0:peak_force_before_cycles_index]
disp_rest = disp[peak_force_before_cycles_index:]
disp_ascending = savgol_filter(
disp_ascending, window_length=51, polyorder=2)
disp_rest = disp_rest[force_max_min_indices]
filtered_disp = np.concatenate((disp_ascending, disp_rest))
np.save(os.path.join(self.npy_folder_path, self.file_name + '_' +
self.columns_headers_list[i] + '_filtered.npy'), filtered_disp)
# 3- Export creep for displacements
# Cutting unwanted max min values to get correct full cycles and remove
# false min/max values caused by noise
force_max_indices_cutted, force_min_indices_cutted = self.cut_indices_in_range(force_rest,
force_max_indices,
force_min_indices,
self.force_max,
self.force_min)
print("Cycles number= ", len(force_min_indices))
print("Cycles number after cutting unwanted max-min range= ",
len(force_min_indices_cutted))
# TODO I skipped time with presuming it's the first column
for i in range(1, len(self.columns_headers_list)):
if self.columns_headers_list[i] != str(self.force_name):
disp_rest_maxima = disp_rest[force_max_indices_cutted]
disp_rest_minima = disp_rest[force_min_indices_cutted]
np.save(os.path.join(self.npy_folder_path, self.file_name + '_' +
self.columns_headers_list[i] + '_max.npy'), disp_rest_maxima)
np.save(os.path.join(self.npy_folder_path, self.file_name + '_' +
self.columns_headers_list[i] + '_min.npy'), disp_rest_minima)
print('Filtered npy files are generated.')
def cut_indices_in_range(self, array, max_indices, min_indices, range_upper_value, range_lower_value):
cutted_max_indices = []
cutted_min_indices = []
for max_index in max_indices:
if abs(array[max_index]) > abs(range_upper_value):
cutted_max_indices.append(max_index)
for min_index in min_indices:
if abs(array[min_index]) < abs(range_lower_value):
cutted_min_indices.append(min_index)
return cutted_max_indices, cutted_min_indices
def get_array_max_and_min_indices(self, input_array):
# Checking dominant sign
positive_values_count = np.sum(np.array(input_array) >= 0)
negative_values_count = input_array.size - positive_values_count
# Getting max and min indices
if (positive_values_count > negative_values_count):
force_max_indices = argrelextrema(input_array, np.greater_equal)[0]
force_min_indices = argrelextrema(input_array, np.less_equal)[0]
else:
force_max_indices = argrelextrema(input_array, np.less_equal)[0]
force_min_indices = argrelextrema(input_array, np.greater_equal)[0]
# Remove subsequent max/min indices (np.greater_equal will give 1,2 for
# [4, 8, 8, 1])
force_max_indices = self.remove_subsequent_max_values(
force_max_indices)
force_min_indices = self.remove_subsequent_min_values(
force_min_indices)
# If size is not equal remove the last element from the big one
if force_max_indices.size > force_min_indices.size:
force_max_indices = force_max_indices[:-1]
elif force_max_indices.size < force_min_indices.size:
force_min_indices = force_min_indices[:-1]
return force_max_indices, force_min_indices
def remove_subsequent_max_values(self, force_max_indices):
to_delete_from_maxima = []
for i in range(force_max_indices.size - 1):
if force_max_indices[i + 1] - force_max_indices[i] == 1:
to_delete_from_maxima.append(i)
force_max_indices = np.delete(force_max_indices, to_delete_from_maxima)
return force_max_indices
def remove_subsequent_min_values(self, force_min_indices):
to_delete_from_minima = []
for i in range(force_min_indices.size - 1):
if force_min_indices[i + 1] - force_min_indices[i] == 1:
to_delete_from_minima.append(i)
force_min_indices = np.delete(force_min_indices, to_delete_from_minima)
return force_min_indices
#=========================================================================
# Plotting
#=========================================================================
plot_figure_num = tr.Int(0)
def _plot_fired(self):
ax = self.figure.add_subplot()
def x_plot_fired(self):
self.plot_figure_num += 1
plt.draw()
plt.show()
data_changed = tr.Event
def _add_plot_fired(self):
if False: # (len(self.plot_list) >= self.plots_num):
dialog = MessageDialog(
title='Attention!', message='Max plots number is {}'.format(self.plots_num))
dialog.open()
return
print('Loading npy files...')
if self.apply_filters:
x_axis_name = self.x_axis + '_filtered'
y_axis_name = self.y_axis + '_filtered'
x_axis_array = self.x_axis_multiplier * \
np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.x_axis + '_filtered.npy'))
y_axis_array = self.y_axis_multiplier * \
np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.y_axis + '_filtered.npy'))
else:
x_axis_name = self.x_axis
y_axis_name = self.y_axis
x_axis_array = self.x_axis_multiplier * \
np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.x_axis + '.npy'))
y_axis_array = self.y_axis_multiplier * \
np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.y_axis + '.npy'))
print('Adding Plot...')
mpl.rcParams['agg.path.chunksize'] = 50000
# plt.figure(self.plot_figure_num)
ax = self.figure.add_subplot(1, 1, 1)
ax.set_xlabel('Displacement [mm]')
ax.set_ylabel('kN')
ax.set_title('Original data', fontsize=20)
ax.plot(x_axis_array, y_axis_array, 'k', linewidth=0.8)
self.plot_list.append('{}, {}'.format(x_axis_name, y_axis_name))
self.data_changed = True
print('Finished adding plot!')
def apply_new_subplot(self):
plt = self.figure
if (self.plots_num == 1):
plt.add_subplot(1, 1, 1)
elif (self.plots_num == 2):
plot_location = int('12' + str(len(self.plot_list) + 1))
plt.add_subplot(plot_location)
elif (self.plots_num == 3):
plot_location = int('13' + str(len(self.plot_list) + 1))
plt.add_subplot(plot_location)
elif (self.plots_num == 4):
plot_location = int('22' + str(len(self.plot_list) + 1))
plt.add_subplot(plot_location)
elif (self.plots_num == 6):
plot_location = int('23' + str(len(self.plot_list) + 1))
plt.add_subplot(plot_location)
elif (self.plots_num == 9):
plot_location = int('33' + str(len(self.plot_list) + 1))
plt.add_subplot(plot_location)
def _add_creep_plot_fired(self):
plt = self.figure
if (len(self.plot_list) >= self.plots_num):
dialog = MessageDialog(
title='Attention!', message='Max plots number is {}'.format(self.plots_num))
dialog.open()
return
disp_max = self.x_axis_multiplier * \
np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.x_axis + '_max.npy'))
disp_min = self.x_axis_multiplier * \
np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.x_axis + '_min.npy'))
print('Adding creep plot...')
mpl.rcParams['agg.path.chunksize'] = 50000
self.apply_new_subplot()
plt.xlabel('Cycles number')
plt.ylabel('mm')
plt.title('Fatigue creep curve', fontsize=20)
plt.plot(np.arange(0, disp_max.size), disp_max,
'k', linewidth=0.8, color='red')
plt.plot(np.arange(0, disp_min.size), disp_min,
'k', linewidth=0.8, color='green')
self.plot_list.append('Plot {}'.format(len(self.plot_list) + 1))
print('Finished adding creep plot!')
#=========================================================================
# Configuration of the view
#=========================================================================
traits_view = ui.View(
ui.HSplit(
ui.VSplit(
ui.HGroup(
ui.UItem('open_file_csv'),
ui.UItem('file_csv', style='readonly'),
label='Input data'
),
ui.Item('add_columns_average', show_label=False),
ui.VGroup(
ui.Item('skip_rows'),
ui.Item('decimal'),
ui.Item('delimiter'),
ui.Item('parse_csv_to_npy', show_label=False),
label='Filter parameters'
),
ui.VGroup(
ui.Item('plots_num'),
ui.HGroup(ui.Item('x_axis'), ui.Item('x_axis_multiplier')),
ui.HGroup(ui.Item('y_axis'), ui.Item('y_axis_multiplier')),
ui.HGroup(ui.Item('add_plot', show_label=False),
ui.Item('apply_filters')),
ui.HGroup(ui.Item('add_creep_plot', show_label=False)),
ui.Item('plot_list'),
ui.Item('plot', show_label=False),
show_border=True,
label='Plotting settings'),
),
ui.VGroup(
ui.Item('force_name'),
ui.HGroup(ui.Item('peak_force_before_cycles'),
show_border=True, label='Skip noise of ascending branch:'),
# ui.Item('plots_list'),
ui.VGroup(ui.Item('force_max'),
ui.Item('force_min'),
show_border=True,
label='Cut fake cycles for creep:'),
ui.Item('generate_filtered_npy', show_label=False),
show_border=True,
label='Filters'
),
ui.UItem('figure', editor=MPLFigureEditor(),
resizable=True,
springy=True,
width=0.3,
label='2d plots'),
),
title='HCFF Filter',
resizable=True,
width=0.6,
height=0.6
)
class HCFF(tr.HasStrictTraits):
'''High-Cycle Fatigue Filter
'''
#=========================================================================
# Traits definitions
#=========================================================================
decimal = tr.Enum(',', '.')
delimiter = tr.Str(';')
records_per_second = tr.Float(100)
take_time_from_first_column = tr.Bool
file_csv = tr.File
open_file_csv = tr.Button('Input file')
skip_first_rows = tr.Int(3, auto_set=False, enter_set=True)
columns_headers_list = tr.List([])
x_axis = tr.Enum(values='columns_headers_list')
y_axis = tr.Enum(values='columns_headers_list')
x_axis_multiplier = tr.Enum(1, -1)
y_axis_multiplier = tr.Enum(-1, 1)
npy_folder_path = tr.Str
file_name = tr.Str
apply_filters = tr.Bool
normalize_cycles = tr.Bool
smooth = tr.Bool
plot_every_nth_point = tr.Range(low=1, high=1000000, mode='spinner')
force_name = tr.Str('Kraft')
old_peak_force_before_cycles = tr.Float
peak_force_before_cycles = tr.Float
window_length = tr.Int(31)
polynomial_order = tr.Int(2)
activate = tr.Bool(False)
plots_num = tr.Enum(1, 2, 3, 4, 6, 9)
plot_list = tr.List()
add_plot = tr.Button
add_creep_plot = tr.Button(desc='Creep plot of X axis array')
clear_plot = tr.Button
parse_csv_to_npy = tr.Button
generate_filtered_and_creep_npy = tr.Button
add_columns_average = tr.Button
force_max = tr.Float(100)
force_min = tr.Float(40)
min_cycle_force_range = tr.Float(50)
cutting_method = tr.Enum('Define min cycle range(force difference)',
'Define Max, Min')
columns_to_be_averaged = tr.List
figure = tr.Instance(Figure)
def _figure_default(self):
figure = Figure(facecolor='white')
figure.set_tight_layout(True)
return figure
#=========================================================================
# File management
#=========================================================================
def _open_file_csv_fired(self):
self.reset()
""" Handles the user clicking the 'Open...' button.
"""
extns = [
'*.csv',
] # seems to handle only one extension...
wildcard = '|'.join(extns)
dialog = FileDialog(title='Select text file',
action='open',
wildcard=wildcard,
default_path=self.file_csv)
result = dialog.open()
""" Test if the user opened a file to avoid throwing an exception if he
doesn't """
if result == OK:
self.file_csv = dialog.path
else:
return
""" Filling x_axis and y_axis with values """
headers_array = np.array(
pd.read_csv(self.file_csv,
delimiter=self.delimiter,
decimal=self.decimal,
nrows=1,
header=None))[0]
for i in range(len(headers_array)):
headers_array[i] = self.get_valid_file_name(headers_array[i])
self.columns_headers_list = list(headers_array)
""" Saving file name and path and creating NPY folder """
dir_path = os.path.dirname(self.file_csv)
self.npy_folder_path = os.path.join(dir_path, 'NPY')
if os.path.exists(self.npy_folder_path) == False:
os.makedirs(self.npy_folder_path)
self.file_name = os.path.splitext(os.path.basename(self.file_csv))[0]
def _parse_csv_to_npy_fired(self):
print('Parsing csv into npy files...')
for i in range(
len(self.columns_headers_list) -
len(self.columns_to_be_averaged)):
column_array = np.array(
pd.read_csv(self.file_csv,
delimiter=self.delimiter,
decimal=self.decimal,
skiprows=self.skip_first_rows,
usecols=[i]))
""" TODO! Create time array supposing it's column is the
first one in the file and that we have 100 reads in 1 second """
if i == 0 and self.take_time_from_first_column == False:
column_array = np.arange(start=0.0,
stop=len(column_array) /
self.records_per_second,
step=1.0 / self.records_per_second)
np.save(
os.path.join(
self.npy_folder_path, self.file_name + '_' +
self.columns_headers_list[i] + '.npy'), column_array)
""" Exporting npy arrays of averaged columns """
for columns_names in self.columns_to_be_averaged:
temp = np.zeros((1))
for column_name in columns_names:
temp = temp + np.load(
os.path.join(self.npy_folder_path, self.file_name + '_' +
column_name + '.npy')).flatten()
avg = temp / len(columns_names)
avg_file_suffex = self.get_suffex_for_columns_to_be_averaged(
columns_names)
np.save(
os.path.join(self.npy_folder_path,
self.file_name + '_' + avg_file_suffex + '.npy'),
avg)
print('Finsihed parsing csv into npy files.')
def get_suffex_for_columns_to_be_averaged(self, columns_names):
suffex_for_saved_file_name = 'avg_' + '_'.join(columns_names)
return suffex_for_saved_file_name
def get_valid_file_name(self, original_file_name):
valid_chars = "-_.() %s%s" % (string.ascii_letters, string.digits)
new_valid_file_name = ''.join(c for c in original_file_name
if c in valid_chars)
return new_valid_file_name
def _clear_plot_fired(self):
self.figure.clear()
self.plot_list = []
self.data_changed = True
def _add_columns_average_fired(self):
columns_average = ColumnsAverage()
for name in self.columns_headers_list:
columns_average.columns.append(Column(column_name=name))
# kind='modal' pauses the implementation until the window is closed
columns_average.configure_traits(kind='modal')
columns_to_be_averaged_temp = []
for i in columns_average.columns:
if i.selected:
columns_to_be_averaged_temp.append(i.column_name)
if columns_to_be_averaged_temp: # If it's not empty
self.columns_to_be_averaged.append(columns_to_be_averaged_temp)
avg_file_suffex = self.get_suffex_for_columns_to_be_averaged(
columns_to_be_averaged_temp)
self.columns_headers_list.append(avg_file_suffex)
def _generate_filtered_and_creep_npy_fired(self):
if self.npy_files_exist(
os.path.join(self.npy_folder_path, self.file_name + '_' +
self.force_name + '.npy')) == False:
return
# 1- Export filtered force
force = np.load(
os.path.join(self.npy_folder_path, self.file_name + '_' +
self.force_name + '.npy')).flatten()
peak_force_before_cycles_index = np.where(
abs((force)) > abs(self.peak_force_before_cycles))[0][0]
force_ascending = force[0:peak_force_before_cycles_index]
force_rest = force[peak_force_before_cycles_index:]
force_max_indices, force_min_indices = self.get_array_max_and_min_indices(
force_rest)
force_max_min_indices = np.concatenate(
(force_min_indices, force_max_indices))
force_max_min_indices.sort()
force_rest_filtered = force_rest[force_max_min_indices]
force_filtered = np.concatenate((force_ascending, force_rest_filtered))
np.save(
os.path.join(
self.npy_folder_path,
self.file_name + '_' + self.force_name + '_filtered.npy'),
force_filtered)
# 2- Export filtered displacements
# TODO I skipped time presuming it's the first column
for i in range(1, len(self.columns_headers_list)):
if self.columns_headers_list[i] != str(self.force_name):
disp = np.load(
os.path.join(
self.npy_folder_path, self.file_name + '_' +
self.columns_headers_list[i] + '.npy')).flatten()
disp_ascending = disp[0:peak_force_before_cycles_index]
disp_rest = disp[peak_force_before_cycles_index:]
if self.activate == True:
disp_ascending = savgol_filter(
disp_ascending,
window_length=self.window_length,
polyorder=self.polynomial_order)
disp_rest_filtered = disp_rest[force_max_min_indices]
filtered_disp = np.concatenate(
(disp_ascending, disp_rest_filtered))
np.save(
os.path.join(
self.npy_folder_path, self.file_name + '_' +
self.columns_headers_list[i] + '_filtered.npy'),
filtered_disp)
# 3- Export creep for displacements
# Cutting unwanted max min values to get correct full cycles and remove
# false min/max values caused by noise
if self.cutting_method == "Define Max, Min":
force_max_indices_cutted, force_min_indices_cutted = \
self.cut_indices_of_min_max_range(force_rest,
force_max_indices,
force_min_indices,
self.force_max,
self.force_min)
elif self.cutting_method == "Define min cycle range(force difference)":
force_max_indices_cutted, force_min_indices_cutted = \
self.cut_indices_of_defined_range(force_rest,
force_max_indices,
force_min_indices,
self.min_cycle_force_range)
print("Cycles number= ", len(force_min_indices))
print("Cycles number after cutting fake cycles because of noise= ",
len(force_min_indices_cutted))
# TODO I skipped time with presuming it's the first column
for i in range(1, len(self.columns_headers_list)):
array = np.load(
os.path.join(
self.npy_folder_path, self.file_name + '_' +
self.columns_headers_list[i] + '.npy')).flatten()
array_rest = array[peak_force_before_cycles_index:]
array_rest_maxima = array_rest[force_max_indices_cutted]
array_rest_minima = array_rest[force_min_indices_cutted]
np.save(
os.path.join(
self.npy_folder_path, self.file_name + '_' +
self.columns_headers_list[i] + '_max.npy'),
array_rest_maxima)
np.save(
os.path.join(
self.npy_folder_path, self.file_name + '_' +
self.columns_headers_list[i] + '_min.npy'),
array_rest_minima)
print('Filtered and creep npy files are generated.')
def cut_indices_of_min_max_range(self, array, max_indices, min_indices,
range_upper_value, range_lower_value):
cutted_max_indices = []
cutted_min_indices = []
for max_index in max_indices:
if abs(array[max_index]) > abs(range_upper_value):
cutted_max_indices.append(max_index)
for min_index in min_indices:
if abs(array[min_index]) < abs(range_lower_value):
cutted_min_indices.append(min_index)
return cutted_max_indices, cutted_min_indices
def cut_indices_of_defined_range(self, array, max_indices, min_indices,
range_):
cutted_max_indices = []
cutted_min_indices = []
for max_index, min_index in zip(max_indices, min_indices):
if abs(array[max_index] - array[min_index]) > range_:
cutted_max_indices.append(max_index)
cutted_min_indices.append(min_index)
return cutted_max_indices, cutted_min_indices
def get_array_max_and_min_indices(self, input_array):
# Checking dominant sign
positive_values_count = np.sum(np.array(input_array) >= 0)
negative_values_count = input_array.size - positive_values_count
# Getting max and min indices
if (positive_values_count > negative_values_count):
force_max_indices = argrelextrema(input_array, np.greater_equal)[0]
force_min_indices = argrelextrema(input_array, np.less_equal)[0]
else:
force_max_indices = argrelextrema(input_array, np.less_equal)[0]
force_min_indices = argrelextrema(input_array, np.greater_equal)[0]
# Remove subsequent max/min indices (np.greater_equal will give 1,2 for
# [4, 8, 8, 1])
force_max_indices = self.remove_subsequent_max_values(
force_max_indices)
force_min_indices = self.remove_subsequent_min_values(
force_min_indices)
# If size is not equal remove the last element from the big one
if force_max_indices.size > force_min_indices.size:
force_max_indices = force_max_indices[:-1]
elif force_max_indices.size < force_min_indices.size:
force_min_indices = force_min_indices[:-1]
return force_max_indices, force_min_indices
def remove_subsequent_max_values(self, force_max_indices):
to_delete_from_maxima = []
for i in range(force_max_indices.size - 1):
if force_max_indices[i + 1] - force_max_indices[i] == 1:
to_delete_from_maxima.append(i)
force_max_indices = np.delete(force_max_indices, to_delete_from_maxima)
return force_max_indices
def remove_subsequent_min_values(self, force_min_indices):
to_delete_from_minima = []
for i in range(force_min_indices.size - 1):
if force_min_indices[i + 1] - force_min_indices[i] == 1:
to_delete_from_minima.append(i)
force_min_indices = np.delete(force_min_indices, to_delete_from_minima)
return force_min_indices
def _activate_changed(self):
if self.activate == False:
self.old_peak_force_before_cycles = self.peak_force_before_cycles
self.peak_force_before_cycles = 0
else:
self.peak_force_before_cycles = self.old_peak_force_before_cycles
def _window_length_changed(self, new):
if new <= self.polynomial_order:
dialog = MessageDialog(
title='Attention!',
message='Window length must be bigger than polynomial order.')
dialog.open()
if new % 2 == 0 or new <= 0:
dialog = MessageDialog(
title='Attention!',
message='Window length must be odd positive integer.')
dialog.open()
def _polynomial_order_changed(self, new):
if new >= self.window_length:
dialog = MessageDialog(
title='Attention!',
message='Polynomial order must be less than window length.')
dialog.open()
#=========================================================================
# Plotting
#=========================================================================
plot_list_current_elements_num = tr.Int(0)
def npy_files_exist(self, path):
if os.path.exists(path) == True:
return True
else:
dialog = MessageDialog(
title='Attention!',
message='Please parse csv file to generate npy files first.'.
format(self.plots_num))
dialog.open()
return False
def filtered_and_creep_npy_files_exist(self, path):
if os.path.exists(path) == True:
return True
else:
dialog = MessageDialog(
title='Attention!',
message='Please generate filtered and creep npy files first.'.
format(self.plots_num))
dialog.open()
return False
def max_plots_number_is_reached(self):
if len(self.plot_list) >= self.plots_num:
dialog = MessageDialog(title='Attention!',
message='Max plots number is {}'.format(
self.plots_num))
dialog.open()
return True
else:
return False
def _plot_list_changed(self):
if len(self.plot_list) > self.plot_list_current_elements_num:
self.plot_list_current_elements_num = len(self.plot_list)
data_changed = tr.Event
def _add_plot_fired(self):
if self.max_plots_number_is_reached() == True:
return
if self.apply_filters:
if self.filtered_and_creep_npy_files_exist(
os.path.join(
self.npy_folder_path, self.file_name + '_' +
self.x_axis + '_filtered.npy')) == False:
return
x_axis_name = self.x_axis + '_filtered'
y_axis_name = self.y_axis + '_filtered'
print('Loading npy files...')
x_axis_array = self.x_axis_multiplier * \
np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.x_axis
+ '_filtered.npy'))
y_axis_array = self.y_axis_multiplier * \
np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.y_axis
+ '_filtered.npy'))
else:
if self.npy_files_exist(
os.path.join(self.npy_folder_path, self.file_name + '_' +
self.x_axis + '.npy')) == False:
return
x_axis_name = self.x_axis
y_axis_name = self.y_axis
print('Loading npy files...')
x_axis_array = self.x_axis_multiplier * \
np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.x_axis
+ '.npy'))
y_axis_array = self.y_axis_multiplier * \
np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.y_axis
+ '.npy'))
print('Adding Plot...')
mpl.rcParams['agg.path.chunksize'] = 50000
ax = self.apply_new_subplot()
ax.set_xlabel(x_axis_name)
ax.set_ylabel(y_axis_name)
ax.plot(x_axis_array,
y_axis_array,
'k',
linewidth=1.2,
color=np.random.rand(3, ),
label=self.file_name + ', ' + x_axis_name)
ax.legend()
self.plot_list.append('{}, {}'.format(x_axis_name, y_axis_name))
self.data_changed = True
print('Finished adding plot!')
def apply_new_subplot(self):
plt = self.figure
if (self.plots_num == 1):
return plt.add_subplot(1, 1, 1)
elif (self.plots_num == 2):
plot_location = int('12' + str(len(self.plot_list) + 1))
return plt.add_subplot(plot_location)
elif (self.plots_num == 3):
plot_location = int('13' + str(len(self.plot_list) + 1))
return plt.add_subplot(plot_location)
elif (self.plots_num == 4):
plot_location = int('22' + str(len(self.plot_list) + 1))
return plt.add_subplot(plot_location)
elif (self.plots_num == 6):
plot_location = int('23' + str(len(self.plot_list) + 1))
return plt.add_subplot(plot_location)
elif (self.plots_num == 9):
plot_location = int('33' + str(len(self.plot_list) + 1))
return plt.add_subplot(plot_location)
def _add_creep_plot_fired(self):
if self.filtered_and_creep_npy_files_exist(
os.path.join(self.npy_folder_path, self.file_name + '_' +
self.x_axis + '_max.npy')) == False:
return
if self.max_plots_number_is_reached() == True:
return
disp_max = self.x_axis_multiplier * \
np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.x_axis + '_max.npy'))
disp_min = self.x_axis_multiplier * \
np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.x_axis + '_min.npy'))
complete_cycles_number = disp_max.size
print('Adding creep-fatigue plot...')
mpl.rcParams['agg.path.chunksize'] = 50000
ax = self.apply_new_subplot()
ax.set_xlabel('Cycles number')
ax.set_ylabel(self.x_axis)
if self.plot_every_nth_point > 1:
disp_max = disp_max[0::self.plot_every_nth_point]
disp_min = disp_min[0::self.plot_every_nth_point]
if self.smooth:
# Keeping the first item of the array and filtering the rest
disp_max = np.concatenate(
(np.array([disp_max[0]]),
savgol_filter(disp_max[1:],
window_length=self.window_length,
polyorder=self.polynomial_order)))
disp_min = np.concatenate(
(np.array([disp_min[0]]),
savgol_filter(disp_min[1:],
window_length=self.window_length,
polyorder=self.polynomial_order)))
if self.normalize_cycles:
ax.plot(np.linspace(0, 1., disp_max.size),
disp_max,
'k',
linewidth=1.2,
color='red',
label='Max' + ', ' + self.file_name + ', ' + self.x_axis)
ax.plot(np.linspace(0, 1., disp_max.size),
disp_min,
'k',
linewidth=1.2,
color='green',
label='Min' + ', ' + self.file_name + ', ' + self.x_axis)
else:
ax.plot(np.linspace(0, complete_cycles_number, disp_max.size),
disp_max,
'k',
linewidth=1.2,
color='red',
label='Max' + ', ' + self.file_name + ', ' + self.x_axis)
ax.plot(np.linspace(0, complete_cycles_number, disp_max.size),
disp_min,
'k',
linewidth=1.2,
color='green',
label='Min' + ', ' + self.file_name + ', ' + self.x_axis)
ax.legend()
self.plot_list.append('Creep-fatigue: {}, {}'.format(
self.x_axis, self.y_axis))
self.data_changed = True
print('Finished adding creep-fatigue plot!')
def reset(self):
self.delimiter = ';'
self.skip_first_rows = 3
self.columns_headers_list = []
self.npy_folder_path = ''
self.file_name = ''
self.apply_filters = False
self.force_name = 'Kraft'
self.plot_list = []
self.columns_to_be_averaged = []
#=========================================================================
# Configuration of the view
#=========================================================================
traits_view = ui.View(ui.HSplit(
ui.VSplit(
ui.HGroup(ui.UItem('open_file_csv'),
ui.UItem('file_csv', style='readonly', width=0.1),
label='Input data'),
ui.Item('add_columns_average', show_label=False),
ui.VGroup(
ui.VGroup(ui.Item(
'records_per_second',
enabled_when='take_time_from_first_column == False'),
ui.Item('take_time_from_first_column'),
label='Time calculation',
show_border=True),
ui.VGroup(ui.Item('skip_first_rows'),
ui.Item('decimal'),
ui.Item('delimiter'),
ui.Item('parse_csv_to_npy', show_label=False),
label='Processing csv file',
show_border=True),
ui.VGroup(ui.HGroup(ui.Item('plots_num'),
ui.Item('clear_plot')),
ui.HGroup(ui.Item('x_axis'),
ui.Item('x_axis_multiplier')),
ui.HGroup(ui.Item('y_axis'),
ui.Item('y_axis_multiplier')),
ui.VGroup(ui.HGroup(
ui.Item('add_plot', show_label=False),
ui.Item('apply_filters')),
show_border=True,
label='Plotting X axis with Y axis'),
ui.VGroup(ui.HGroup(
ui.Item('add_creep_plot', show_label=False),
ui.VGroup(ui.Item('normalize_cycles'),
ui.Item('smooth'),
ui.Item('plot_every_nth_point'))),
show_border=True,
label='Plotting Creep-fatigue of x-axis'),
ui.Item('plot_list'),
show_border=True,
label='Plotting'))),
ui.VGroup(
ui.Item('force_name'),
ui.VGroup(ui.VGroup(
ui.Item('window_length'),
ui.Item('polynomial_order'),
enabled_when='activate == True or smooth == True'),
show_border=True,
label='Smoothing parameters (Savitzky-Golay filter):'),
ui.VGroup(ui.VGroup(
ui.Item('activate'),
ui.Item('peak_force_before_cycles',
enabled_when='activate == True')),
show_border=True,
label='Smooth ascending branch for all displacements:'),
ui.VGroup(
ui.Item('cutting_method'),
ui.VGroup(ui.Item('force_max'),
ui.Item('force_min'),
label='Max, Min:',
show_border=True,
enabled_when='cutting_method == "Define Max, Min"'),
ui.VGroup(
ui.Item('min_cycle_force_range'),
label='Min cycle force range:',
show_border=True,
enabled_when=
'cutting_method == "Define min cycle range(force difference)"'
),
show_border=True,
label='Cut fake cycles for creep:'),
ui.Item('generate_filtered_and_creep_npy', show_label=False),
show_border=True,
label='Filters'),
ui.UItem('figure',
editor=MPLFigureEditor(),
resizable=True,
springy=True,
width=0.8,
label='2d plots')),
title='HCFF Filter',
resizable=True,
width=0.85,
height=0.7)
class MATSXDEval(MATSEval):
'''Base class for elastic models.
'''
n_dims = Constant(Float)
'''Number of spatial dimensions of an integration
cell for the material model
'''
E = Float(34e+3,
label="E",
desc="Young's Modulus",
auto_set=False,
input=True)
nu = Float(0.2,
label='nu',
desc="Poison's ratio",
auto_set=False,
input=True)
def _get_lame_params(self):
# First Lame parameter (bulk modulus)
la = self.E * self.nu / ((1. + self.nu) * (1. - 2. * self.nu))
# second Lame parameter (shear modulus)
mu = self.E / (2. + 2. * self.nu)
return la, mu
D_abef = Property(Array, depends_on='+input')
'''Material stiffness - rank 4 tensor
'''
@cached_property
def _get_D_abef(self):
la, mu = self._get_lame_params()
delta = np.identity(self.n_dims)
return (np.einsum(',ij,kl->ijkl', la, delta, delta) +
np.einsum(',ik,jl->ijkl', mu, delta, delta) +
np.einsum(',il,jk->ijkl', mu, delta, delta))
def get_corr_pred(self, eps_Emab, tn1):
'''
Corrector predictor computation.
@param eps_Emab input variable - strain tensor
'''
sigma_Emab = np.einsum('abcd,...cd->...ab', self.D_abef, eps_Emab)
Em_len = len(eps_Emab.shape) - 2
new_shape = tuple([1 for _ in range(Em_len)]) + self.D_abef.shape
D_abef = self.D_abef.reshape(*new_shape)
return sigma_Emab, D_abef
#=========================================================================
# Response variables
#=========================================================================
def get_eps_ab(self, eps_ab, tn1, **state):
return eps_ab
def get_sig_ab(self, eps_ab, tn1, **state):
return self.get_sig(eps_ab, tn1, **state)
var_dict = Property(Dict(Str, Callable))
'''Dictionary of response variables
'''
@cached_property
def _get_var_dict(self):
return dict(eps_ab=self.get_eps_ab, sig_ab=self.get_sig_ab)
def x_var_dict_default(self):
return {
'sig_app': self.get_sig_ab,
'eps_app': self.get_eps_ab,
'max_principle_sig': self.get_max_principle_sig,
'strain_energy': self.get_strain_energy
}
view_traits = ui.View(ui.VSplit(ui.Group(
ui.Item('E'),
ui.Item('nu'),
), ),
resizable=True)
class Comparator(HasTraits):
""" The main application.
"""
#### Configuration traits ##################################################
# The root directory of the test suite.
suitedir = Str()
# Mapping of SVG basenames to their reference PNGs. Use None if there is no
# reference PNG.
svg_png = Dict()
# The list of SVG file names.
svg_files = List()
# The name of the default PNG file to display when no reference PNG exists.
default_png = Str(os.path.join(this_dir, 'images/default.png'))
#### State traits ##########################################################
# The currently selected SVG file.
current_file = Str()
abs_current_file = Property(depends_on=['current_file'])
# The current XML ElementTree root Element and its XMLTree view model.
current_xml = Any()
current_xml_view = Any()
# The profilers.
profile_this = Instance(ProfileThis, args=())
#### GUI traits ############################################################
# The text showing the current mouse coordinates over any of the components.
mouse_coords = Property(Str, depends_on=['ch_controller.svg_coords'])
# Move forward and backward through the list of SVG files.
move_forward = Button('>>')
move_backward = Button('<<')
# The description of the test.
description = HTML()
document = Instance(document.SVGDocument)
# The components to view.
kiva_component = ComponentTrait(klass=SVGComponent)
ref_component = ComponentTrait(klass=ImageComponent, args=())
ch_controller = Instance(MultiController)
# The profiler views.
parsing_sike = Instance(Sike, args=())
drawing_sike = Instance(Sike, args=())
wx_doc_sike = Instance(Sike, args=())
kiva_doc_sike = Instance(Sike, args=())
traits_view = tui.View(
tui.Tabbed(
tui.VGroup(
tui.HGroup(
tui.Item('current_file',
editor=tui.EnumEditor(name='svg_files'),
style='simple',
width=1.0,
show_label=False),
tui.Item(
'move_backward',
show_label=False,
enabled_when="svg_files.index(current_file) != 0"),
tui.Item(
'move_forward',
show_label=False,
enabled_when=
"svg_files.index(current_file) != len(svg_files)-1"),
),
tui.VSplit(
tui.HSplit(
tui.Item('description',
label='Description',
show_label=False),
tui.Item('current_xml_view',
editor=xml_tree_editor,
show_label=False),
),
tui.HSplit(
tui.Item('document',
editor=SVGEditor(),
show_label=False),
tui.Item('kiva_component', show_label=False),
tui.Item('ref_component', show_label=False),
# TODO: tui.Item('agg_component', show_label=False),
),
),
label='SVG',
),
tui.Item('parsing_sike',
style='custom',
show_label=False,
label='Parsing Profile'),
tui.Item('drawing_sike',
style='custom',
show_label=False,
label='Kiva Drawing Profile'),
tui.Item('wx_doc_sike',
style='custom',
show_label=False,
label='Creating WX document'),
tui.Item('kiva_doc_sike',
style='custom',
show_label=False,
label='Creating WX document'),
),
width=1280,
height=768,
resizable=True,
statusbar='mouse_coords',
title='SVG Comparator',
)
def __init__(self, **traits):
super(Comparator, self).__init__(**traits)
kiva_ch = activate_tool(self.kiva_component,
Crosshair(self.kiva_component))
ref_ch = activate_tool(self.ref_component,
Crosshair(self.ref_component))
self.ch_controller = MultiController(kiva_ch, ref_ch)
@classmethod
def fromsuitedir(cls, dirname, **traits):
""" Find all SVG files and their related reference PNG files under
a directory.
This assumes that the SVGs are located under <dirname>/svg/ and the
related PNGs under <dirname>/png/ and that there are no subdirectories.
"""
dirname = os.path.abspath(dirname)
svgs = glob.glob(os.path.join(dirname, 'svg', '*.svg'))
pngdir = os.path.join(dirname, 'png')
d = {}
for svg in svgs:
png = None
base = os.path.splitext(os.path.basename(svg))[0]
for prefix in ('full-', 'basic-', 'tiny-', ''):
fn = os.path.join(pngdir, prefix + base + '.png')
if os.path.exists(fn):
png = os.path.basename(fn)
break
d[os.path.basename(svg)] = png
svgs = sorted(d)
x = cls(suitedir=dirname, svg_png=d, svg_files=svgs, **traits)
x.current_file = svgs[0]
return x
def display_reference_png(self, filename):
""" Read the image file and shove its data into the display component.
"""
img = Image.open(filename)
arr = np.array(img)
self.ref_component.image = arr
def display_test_description(self):
""" Extract the test description for display.
"""
html = ET.Element('html')
title = self.current_xml.find('.//{http://www.w3.org/2000/svg}title')
if title is not None:
title_text = title.text
else:
title_text = os.path.splitext(self.current_file)[0]
p = ET.SubElement(html, 'p')
b = ET.SubElement(p, 'b')
b.text = 'Title: '
b.tail = title_text
desc_text = None
version_text = None
desc = self.current_xml.find('.//{http://www.w3.org/2000/svg}desc')
if desc is not None:
desc_text = desc.text
else:
testcase = self.current_xml.find(
'.//{http://www.w3.org/2000/02/svg/testsuite/description/}SVGTestCase'
)
if testcase is not None:
desc_text = testcase.get('desc', None)
version_text = testcase.get('version', None)
if desc_text is not None:
p = ET.SubElement(html, 'p')
b = ET.SubElement(p, 'b')
b.text = 'Description: '
b.tail = normalize_text(desc_text)
if version_text is None:
script = self.current_xml.find(
'.//{http://www.w3.org/2000/02/svg/testsuite/description/}OperatorScript'
)
if script is not None:
version_text = script.get('version', None)
if version_text is not None:
p = ET.SubElement(html, 'p')
b = ET.SubElement(p, 'b')
b.text = 'Version: '
b.tail = version_text
paras = self.current_xml.findall(
'.//{http://www.w3.org/2000/02/svg/testsuite/description/}Paragraph'
)
if len(paras) > 0:
div = ET.SubElement(html, 'div')
for para in paras:
p = ET.SubElement(div, 'p')
p.text = normalize_text(para.text)
# Copy over any children elements like <a>.
p[:] = para[:]
tree = ET.ElementTree(html)
f = StringIO()
tree.write(f)
text = f.getvalue()
self.description = text
def locate_file(self, name, kind):
""" Find the location of the given file in the suite.
Parameters
----------
name : str
Path of the file relative to the suitedir.
kind : either 'svg' or 'png'
The kind of file.
Returns
-------
path : str
The full path to the file.
"""
return os.path.join(self.suitedir, kind, name)
def _kiva_component_default(self):
return SVGComponent(profile_this=self.profile_this)
def _move_backward_fired(self):
idx = self.svg_files.index(self.current_file)
idx = max(idx - 1, 0)
self.current_file = self.svg_files[idx]
def _move_forward_fired(self):
idx = self.svg_files.index(self.current_file)
idx = min(idx + 1, len(self.svg_files) - 1)
self.current_file = self.svg_files[idx]
def _get_abs_current_file(self):
return self.locate_file(self.current_file, 'svg')
def _current_file_changed(self, new):
# Reset the warnings filters. While it's good to only get 1 warning per
# file, we want to get the same warning again if a new file issues it.
warnings.resetwarnings()
self.profile_this.start('Parsing')
self.current_xml = ET.parse(self.abs_current_file).getroot()
self.current_xml_view = xml_to_tree(self.current_xml)
resources = document.ResourceGetter.fromfilename(self.abs_current_file)
self.profile_this.stop()
try:
self.profile_this.start('Creating WX document')
self.document = document.SVGDocument(self.current_xml,
resources=resources,
renderer=WxRenderer)
except:
logger.exception('Error parsing document %s', new)
self.document = None
self.profile_this.stop()
try:
self.profile_this.start('Creating Kiva document')
self.kiva_component.document = document.SVGDocument(
self.current_xml, resources=resources, renderer=KivaRenderer)
except Exception as e:
logger.exception('Error parsing document %s', new)
self.kiva_component.document
self.profile_this.stop()
png_file = self.svg_png.get(new, None)
if png_file is None:
png_file = self.default_png
else:
png_file = self.locate_file(png_file, 'png')
self.display_test_description()
self.display_reference_png(png_file)
def _get_mouse_coords(self):
if self.ch_controller is None:
return ''
else:
return '%1.3g %1.3g' % self.ch_controller.svg_coords
@on_trait_change('profile_this:profile_ended')
def _update_profiling(self, new):
if new is not None:
name, p = new
stats = pstats.Stats(p)
if name == 'Parsing':
self.parsing_sike.stats = stats
elif name == 'Drawing':
self.drawing_sike.stats = stats
elif name == 'Creating WX document':
self.wx_doc_sike.stats = stats
elif name == 'Creating Kiva document':
self.kiva_doc_sike.stats = stats
class ExperimentSnake(traits.HasTraits):
"""Main Experiment Snake GUI that sends arbitrary actions based on the
experiment runner sequence and actions that have been set up."""
#mainLog = utilities.TextDisplay()
mainLog = outputStream.OutputStream()
statusString = traits.String("Press Start Snake to begin...")
isRunning = traits.Bool(False) # true when the snake is running
sequenceStarted = traits.Bool(
False) # flashes true for ~1ms when sequence starts
queue = traits.Int(0)
variables = traits.Dict(
key_trait=traits.Str, value_trait=traits.Float
) #dictionary mapping variable names in Exp control to their values in this sequence
timingEdges = traits.Dict(
key_trait=traits.Str, value_trait=traits.Float
) #dictionary mapping timing Edge names in Exp control to their values in this sequence
statusList = [
] #eventually will contain the information gathered from experiment Runner each time we poll
startAction = traitsui.Action(name='start',
action='_startSnake',
image=pyface.image_resource.ImageResource(
os.path.join('icons', 'start.png')))
stopAction = traitsui.Action(name='stop',
action='_stopSnakeToolbar',
image=pyface.image_resource.ImageResource(
os.path.join('icons', 'stop.png')))
reloadHWAsAction = traitsui.Action(
name='reload',
action='_reloadHWAsToolbar',
image=pyface.image_resource.ImageResource(
os.path.join('icons', 'reload.png')))
connectionTimer = traits.Instance(
Timer
) # polls the experiment runner and starts off callbacks at appropriate times
statusStringTimer = traits.Instance(
Timer) #updates status bar at regular times (less freque)
getCurrentTimer = traits.Instance(
Timer
) #waits for get current to return which marks the beginning of a sequence
getCurrentThread = traits.Instance(SocketThread)
connectionPollFrequency = traits.Float(
1000.0) #milliseconds defines accuracy you will perform callbacks at
statusStringFrequency = traits.Float(2000.0) #milliseconds
getCurrentFrequency = traits.Float(
1000.0) #milliseconds should be shorter than the sequence
timeRunning = traits.Float(0.0) #how long the sequence has been running
totalTime = traits.Float(0.0) # total length of sequence
runnerHalted = traits.Bool(True) # true if runner is halted
haltedCount = 0
progress = traits.Float(0.0) # % of cycle complete
#progressBar = ProgressDialog()
hardwareActions = traits.List(hardwareAction.hardwareAction.HardwareAction)
examineVariablesDictionary = traits.Instance(
variableDictionary.ExamineVariablesDictionary)
xmlString = "" # STRING that will contain entire XML File
menubar = traitsui.MenuBar(
traitsui.Menu(
traitsui.Action(name='Start Snake', action='_startSnake'),
traitsui.Action(name='Stop Snake', action='_stopSnake'),
traitsui.Action(name='Reload', action='_reloadHWAs'),
traitsui.Menu(traitsui.Action(name='DEBUG',
action='_changeLoggingLevelDebug'),
traitsui.Action(name='INFO',
action='_changeLoggingLevelInfo'),
traitsui.Action(name='WARNING',
action='_changeLoggingLevelWarning'),
traitsui.Action(name='ERROR',
action='_changeLoggingLevelError'),
name="Log Level"),
name='Menu'))
toolbar = traitsui.ToolBar(startAction, stopAction, reloadHWAsAction)
mainSnakeGroup = traitsui.VGroup(
traitsui.Item('statusString', show_label=False, style='readonly'),
traitsui.Item('mainLog',
show_label=False,
springy=True,
style='custom',
editor=traitsui.InstanceEditor()))
hardwareActionsGroup = traitsui.Group(traitsui.Item(
'hardwareActions',
show_label=False,
style='custom',
editor=traitsui.ListEditor(style="custom")),
label="Hardware Actions",
show_border=True)
variableExaminerGroup = traitsui.Group(traitsui.Item(
"examineVariablesDictionary",
editor=traitsui.InstanceEditor(),
style="custom",
show_label=False),
label="Variable Examiner")
sidePanelGroup = traitsui.VSplit(hardwareActionsGroup,
variableExaminerGroup)
traits_view = traitsui.View(traitsui.HSplit(sidePanelGroup,
mainSnakeGroup,
show_labels=True),
resizable=True,
menubar=menubar,
toolbar=toolbar,
width=0.5,
height=0.75,
title="Experiment Snake",
icon=pyface.image_resource.ImageResource(
os.path.join('icons', 'snakeIcon.ico')))
def __init__(self, **traits):
""" takes no arguments to construct the snake. Everything is done through GUI.
Snake construction makes a ExperimentSnakeConnection object and writes to the
main log window"""
super(ExperimentSnake, self).__init__(**traits)
self.connection = experimentRunnerConnection.Connection(
) #can override default ports and IP
self.hardwareActions = [
hardwareAction.sequenceLoggerHWA.SequenceLogger(
0.0, snakeReference=self),
hardwareAction.experimentTablesHWA.ExperimentTables(
0.0, snakeReference=self, enabled=False),
hardwareAction.dlicEvapHWA.EvaporationRamp(1.0,
snakeReference=self),
#hardwareAction.dlicRFSweepHWA.DLICRFSweep(1.0, snakeReference = self,enabled=False),
hardwareAction.dlicRFSweepLZHWA.DLICRFSweep(1.0,
snakeReference=self,
enabled=False),
hardwareAction.dlicRFSweepLZWithPowerCtrlHWA.DLICRFSweep(
1.0, snakeReference=self, enabled=False),
hardwareAction.dlicRFSweepLZWithPowerCtrl13PreparationHWA.
DLICRFSweep(1.0, snakeReference=self, enabled=True),
hardwareAction.dlicPiPulseHWA.DLICPiPulse(1.0,
snakeReference=self,
enabled=False),
hardwareAction.evapAttenuationHWA.EvapAttenuation(
1.0, snakeReference=self),
hardwareAction.greyMollassesOffsetFreqHWA.GreyMollassesOffset(
1.0, snakeReference=self, enabled=False),
hardwareAction.evapAttenuation2HWA.EvapAttenuation(
"EvapSnakeAttenuationTimeFinal",
snakeReference=self,
enabled=False),
hardwareAction.picomotorPlugHWA.PicomotorPlug(1.0,
snakeReference=self,
enabled=False),
hardwareAction.windFreakOffsetLockHWA.WindFreak(
0.0, snakeReference=self, enabled=False),
hardwareAction.windFreakOffsetLockHighFieldImagingHWA.WindFreak(
0.0, snakeReference=self, enabled=True),
hardwareAction.windFreakOffsetLock6ImagingHWA.WindFreak(
2.0, snakeReference=self, enabled=False),
hardwareAction.windFreak6To1HWA.WindFreak(2.0,
snakeReference=self,
enabled=False),
hardwareAction.windFreakOffsetLockLaser3.WindFreak(
3.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelNaZSFreq(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelNaZSAtten(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelNaZSEOMFreq(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelNaZSEOMAtten(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelNaSpecFreq(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelLiImaging(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelLiImagingDetuning(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelLiPushPulseAttenuation(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelLiPushPulseDetuning(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelNaDarkSpotAOMFreq(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelNaDarkSpotAOMAtten(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelNaMOTFreq(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelNaMOTAtten(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelNaMOTEOMAtten(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelNaImagingDP(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelLiMOTRep(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelLiMOTCool(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelLiOpticalPump(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelNa2to2OpticalPumpingFreq(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelNa2to2OpticalPumpingAtt(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelNaHighFieldImagingFreq(
1.0, snakeReference=self, enabled=False),
hardwareAction.AOMChannelHWAs.AOMChannelNaHighFieldImagingAtt(
1.0, snakeReference=self, enabled=False),
hardwareAction.digitalMultimeterCurrentMeasureHWA.
DigitalMultimeterMeasurement(1.0,
snakeReference=self,
enabled=True),
hardwareAction.MXGPiPulseHWA.PiPulse(1.0,
snakeReference=self,
enabled=False),
hardwareAction.variableExplorerHWA.VariableExplorer(
2.0, snakeReference=self, enabled=False),
hardwareAction.jds6600HWA.JDS6600HWA(1.0,
snakeReference=self,
enabled=False),
hardwareAction.watchdogHWA.WatchdogHWA(18.0,
snakeReference=self,
enabled=True)
]
introString = """Welcome to experiment snake."""
self.mainLog.addLine(introString, 1)
def initialiseHardwareActions(self):
for hdwAct in self.hardwareActions:
if hdwAct.enabled:
returnString = hdwAct.init()
hdwAct.variablesReference = self.variables
self.mainLog.addLine(returnString)
def closeHardwareActions(self):
""" this function is called when the user presses stop key. it should cleanly close or
shutdown all hardware. user must appropriately implement the hardware action close function"""
for hdwAct in self.hardwareActions:
if hdwAct.initialised:
returnString = hdwAct.close()
self.mainLog.addLine(returnString)
def _startSnake(self):
"""action call back from menu or toolbar. Simply starts the timer that
polls the runner and makes the isRunning bool true """
self.mainLog.addLine("Experiment Snake Started", 1)
self.isRunning = True
self.getCurrentBlocking()
self.initialiseHardwareActions()
self.startTimers()
def newSequenceStarted(self):
"""called by GetCurrent Thread at the beginning of every sequence """
if self.isRunning: #otherwise we have already stopped before new sequence began again
self.getStatusUpdate()
self.mainLog.addLine("New cycle started: %s" % self.statusList[0],
1)
self.refreshExamineVariablesDictionary(
) # update the examine variables dictionary to reflect the latest values
self.refreshVariableDependentCallbackTimes(
) # if a callback time is a timing edge name or variable name we must pull the value here
else:
self.mainLog.addLine("final connection closed")
for hdwAct in self.hardwareActions:
hdwAct.awaitingCallback = True
def _stopSnakeToolbar(self):
"""if snake is stopped, addLine to main log and then run stopSnake """
self.mainLog.addLine(
"Experiment Snake Stopped (you should still wait till the end of this sequence before continuing)",
1)
self._stopSnake()
def _reloadHWAsToolbar(self):
"""if snake is stopped, addLine to main log and then run stopSnake """
self.mainLog.addLine(
"Experiment Snake Stopped (you should still wait till the end of this sequence before continuing)",
1)
self._reloadHWAs()
def _reloadHWAs(self):
"""if snake is stopped, addLine to main log and then run stopSnake """
self.mainLog.addLine("Reloading hardware actions (advanced feature)",
3)
reload(hardwareAction.hardwareAction)
reload(hardwareAction.sequenceLoggerHWA)
reload(hardwareAction.dlicEvapHWA)
reload(hardwareAction.dlicRFSweepHWA)
reload(hardwareAction.dlicRFSweepHWA)
reload(hardwareAction.evapAttenuationHWA)
reload(hardwareAction.evapAttenuation2HWA)
reload(hardwareAction.picomotorPlugHWA)
reload(hardwareAction.windFreakOffsetLockHWA)
#reload( hardwareAction.AOMChannelHWAs)#CAUSES REFERENCING PROBLEMS!
reload(hardwareAction.experimentTablesHWA)
reload(hardwareAction.windFreakOffsetLockHighFieldImagingHWA)
reload(hardwareAction.greyMollassesOffsetFreqHWA)
reload(hardwareAction.dlicRFSweepLZHWA)
reload(hardwareAction.digitalMultimeterCurrentMeasureHWA)
self.__init__()
def stopTimers(self):
"""stops all timers with error catching """
try:
#stop any previous timer, should only have 1 timer at a time
if self.connectionTimer is not None:
self.connectionTimer.stop()
except Exception as e:
logger.error(
"couldn't stop current timer before starting new one: %s" %
e.message)
try:
#stop any previous timer, should only have 1 timer at a time
if self.statusStringTimer is not None:
self.statusStringTimer.stop()
except Exception as e:
logger.error(
"couldn't stop current timer before starting new one: %s" %
e.message)
try:
#stop any previous timer, should only have 1 timer at a time
if self.getCurrentTimer is not None:
self.getCurrentTimer.stop()
except Exception as e:
logger.error(
"couldn't stop current timer before starting new one: %s" %
e.message)
def _stopSnake(self):
"""Simply stops the timers, shuts down hardware and sets isRunning bool false """
self.stopTimers()
self.closeHardwareActions()
self.isRunning = False
def startTimers(self):
"""This timer object polls the experiment runner regularly polling at any time"""
#stop any previous timers
self.stopTimers()
#start timer
self.connectionTimer = Timer(self.connectionPollFrequency,
self.getStatus)
time.sleep(0.1)
self.statusStringTimer = Timer(self.statusStringFrequency,
self.updateStatusString)
time.sleep(0.1)
self.getCurrentTimer = Timer(self.getCurrentFrequency, self.getCurrent)
"""Menu action function to change logger level """
logger.info("timers started")
def getStatus(self):
"""calls the connection objects get status function and updates the statusList """
logger.debug("starting getStatus")
try:
self.getStatusUpdate()
self.checkForCallback()
except Exception as e:
logger.error("error in getStatus Function")
logger.error("error: %s " % e.message)
self.mainLog.addLine(
"error in getStatus Function. Error: %s" % e.message, 4)
def getStatusUpdate(self):
"""Calls get status and updates times """
try:
statusString = self.connection.getStatus()
except socket.error as e:
logger.error(
"failed to get status . message=%s . errno=%s . errstring=%s "
% (e.message, e.errno, e.strerror))
self.mainLog.addLine(
"Failed to get status from Experiment Runner. message=%s . errno=%s . errstring=%s"
% (e.message, e.errno, e.strerror), 3)
self.mainLog.addLine(
"Cannot update timeRunning - callbacks could be wrong this sequence!",
4)
return
self.statusList = statusString.split("\n")
timeFormat = '%d/%m/%Y %H:%M:%S'
timeBegin = datetime.datetime.strptime(self.statusList[2], timeFormat)
timeCurrent = datetime.datetime.strptime(self.statusList[3],
timeFormat)
self.timeRunning = (timeCurrent - timeBegin).total_seconds()
logger.debug("time Running = %s " % self.timeRunning)
def checkForCallback(self):
"""if we've received a sequence, we check through all callback times and
send off a callback on a hardware action if appropriate"""
try:
for hdwAct in [
hdwA for hdwA in self.hardwareActions if hdwA.enabled
]: #only iterate through enable hardware actions
if hdwAct.awaitingCallback and self.timeRunning >= hdwAct.callbackTime: #callback should be started!
try:
logger.debug("attempting to callback %s " %
hdwAct.hardwareActionName)
hdwAct.setVariablesDictionary(self.variables)
logger.debug("vars dictionary set to %s " %
self.variables)
callbackReturnString = hdwAct.callback()
self.mainLog.addLine(
"%s @ %s secs : %s" %
(hdwAct.hardwareActionName, self.timeRunning,
callbackReturnString), 2)
hdwAct.awaitingCallback = False
hdwAct.callbackCounter += 1
except Exception as e:
logger.error(
"error while performing callback on %s. see error message below"
% (hdwAct.hardwareActionName))
logger.error("error: %s " % e.message)
self.mainLog.addLine(
"error while performing callback on %s. Error: %s"
% (hdwAct.hardwareActionName, e.message), 4)
except Exception as e:
logger.error("error in checkForCallbackFunction")
logger.error("error: %s " % e.message)
self.mainLog.addLine(
"error in checkForCallbackFunction. Error: %s" % e.message, 4)
def getCurrent(self):
"""calls the connection objects get status function and updates the variables dictionary """
if self.getCurrentThread and self.getCurrentThread.isAlive():
#logger.debug( "getCurrent - already waiting - will not start new thread")
#removed the above as it fills the log without any useful information
self.sequenceStarted = False
return
else:
logger.info("starting getCurrent Thread")
self.getCurrentThread = SocketThread()
self.getCurrentThread.snakeReference = self # for calling functions of the snake
self.getCurrentThread.start()
def getCurrentBlocking(self):
"""calls getCurrent and won't return until XML parsed. unlike above threaded function
This is useful when starting up the snake so that we don't start looking for hardware events
until a sequence has started and we have received XML"""
self.mainLog.addLine("Waiting for next sequence to start")
self.xmlString = self.connection.getCurrent(
) # only returns at the beginning of a sequence! Experiment runner then returns the entire XML file
logger.debug("length of xml string = %s " % len(self.xmlString))
logger.debug("end of xml file is like [-30:]= %s" %
self.xmlString[-30:])
try:
root = ET.fromstring(self.xmlString)
variables = root.find("variables")
self.variables = {
child[0].text: float(child[1].text)
for child in variables
}
#timing edges dictionary : name--> value
self.timingEdges = {
timingEdge.find("name").text:
float(timingEdge.find("value").text)
for timingEdge in root.find("timing")
}
self.newSequenceStarted()
except ET.ParseError as e:
self.mainLog.addLine("Error. Could not parse XML: %s" % e.message,
3)
self.mainLog.addLine(
"Possible cause is that buffer is full. is XML length %s>= limit %s ????"
% (len(self.xmlString), self.connection.BUFFER_SIZE_XML), 3)
logger.error("could not parse XML: %s " % self.xmlString)
logger.error(e.message)
def updateStatusString(self):
"""update the status string with first element of return of GETSTATUS.
similiar to experiment control and camera control. It also does the analysis
of progress that doesn't need to be as accurate (e.g. progress bar)"""
logger.info("starting update status string")
self.statusString = self.statusList[
0] + "- Time Running = %s " % self.timeRunning
self.queue = int(self.statusList[1])
timeFormat = '%d/%m/%Y %H:%M:%S'
timeBegin = datetime.datetime.strptime(self.statusList[2], timeFormat)
timeEnd = datetime.datetime.strptime(self.statusList[4], timeFormat)
self.timeTotal = (timeEnd - timeBegin).total_seconds()
if self.timeRunning > self.timeTotal:
self.haltedCount += 1
self.runnerHalted = True
if self.haltedCount == 0:
logger.critical("runner was stopped.")
self.mainLog.addLine("Runner stopped!", 3)
self.closeHardwareActions()
else:
if self.haltedCount > 0:
self.initialiseHardwareActions()
self.haltedCount = 0
self.runnerHalted = False
self.progress = 100.0 * self.timeRunning / self.timeTotal
def _examineVariablesDictionary_default(self):
if len(self.hardwareActions) > 0:
logger.debug(
"returning first hardware action %s for examineVariablesDictionary default"
% self.hardwareActions[0].hardwareActionName)
return variableDictionary.ExamineVariablesDictionary(
hdwA=self.hardwareActions[0]
) #default is the first in the list
else:
logger.warning(
"hardwareActions list was empty. how should I populate variable examiner...?!."
)
return None
def updateExamineVariablesDictionary(self, hdwA):
"""Populates the examineVariablesDictionary Pane appropriately. It is passed the
hdwA so that it can find the necessary variables"""
self.examineVariablesDictionary.hdwA = hdwA
self.examineVariablesDictionary.hardwareActionName = hdwA.hardwareActionName
self.examineVariablesDictionary.updateDisplayList()
logger.critical("examineVariablesDictionary changed")
def refreshExamineVariablesDictionary(self):
"""calls the updateDisplayList function of examineVariables Dictionary
this updates the values in the display list to the latest values in variables
dictionary. useful for refereshing at the beginning of a sequence"""
self.examineVariablesDictionary.updateDisplayList()
logger.info("refreshed examine variables dictionary")
def refreshVariableDependentCallbackTimes(self):
"""if a HWA is variable dependent call back time, we refresh the value
using this function. THis should be called in each sequence"""
[
hdwA.parseCallbackTime() for hdwA in self.hardwareActions
if hdwA.callbackTimeVariableDependent
]
def _changeLoggingLevelDebug(self):
"""Menu action function to change logger level """
logger.setLevel(logging.DEBUG)
def _changeLoggingLevelInfo(self):
"""Menu action function to change logger level """
logger.setLevel(logging.INFO)
def _changeLoggingLevelWarning(self):
"""Menu action function to change logger level """
logger.setLevel(logging.WARNING)
def _changeLoggingLevelError(self):
"""Menu action function to change logger level """
logger.setLevel(logging.ERROR)
class HCFT(tr.HasStrictTraits):
'''High-Cycle Fatigue Tool
'''
#=========================================================================
# Traits definitions
#=========================================================================
decimal = tr.Enum(',', '.')
delimiter = tr.Str(';')
records_per_second = tr.Float(100)
take_time_from_time_column = tr.Bool(True)
file_csv = tr.File
open_file_csv = tr.Button('Input file')
skip_first_rows = tr.Range(low=1, high=10**9, mode='spinner')
columns_headers_list = tr.List([])
x_axis = tr.Enum(values='columns_headers_list')
y_axis = tr.Enum(values='columns_headers_list')
force_column = tr.Enum(values='columns_headers_list')
time_column = tr.Enum(values='columns_headers_list')
x_axis_multiplier = tr.Enum(1, -1)
y_axis_multiplier = tr.Enum(-1, 1)
npy_folder_path = tr.Str
file_name = tr.Str
apply_filters = tr.Bool
plot_settings_btn = tr.Button
plot_settings = PlotSettings()
plot_settings_active = tr.Bool
normalize_cycles = tr.Bool
smooth = tr.Bool
plot_every_nth_point = tr.Range(low=1, high=1000000, mode='spinner')
old_peak_force_before_cycles = tr.Float
peak_force_before_cycles = tr.Float
window_length = tr.Range(low=1, high=10**9 - 1, value=31, mode='spinner')
polynomial_order = tr.Range(low=1, high=10**9, value=2, mode='spinner')
activate = tr.Bool(False)
add_plot = tr.Button
add_creep_plot = tr.Button(desc='Creep plot of X axis array')
clear_plot = tr.Button
parse_csv_to_npy = tr.Button
generate_filtered_and_creep_npy = tr.Button
add_columns_average = tr.Button
force_max = tr.Float(100)
force_min = tr.Float(40)
min_cycle_force_range = tr.Float(50)
cutting_method = tr.Enum(
'Define min cycle range(force difference)', 'Define Max, Min')
columns_to_be_averaged = tr.List
figure = tr.Instance(mpl.figure.Figure)
log = tr.Str('')
clear_log = tr.Button
def _figure_default(self):
figure = mpl.figure.Figure(facecolor='white')
figure.set_tight_layout(True)
return figure
#=========================================================================
# File management
#=========================================================================
def _open_file_csv_fired(self):
try:
self.reset()
""" Handles the user clicking the 'Open...' button.
"""
extns = ['*.csv', ] # seems to handle only one extension...
wildcard = '|'.join(extns)
dialog = FileDialog(title='Select text file',
action='open', wildcard=wildcard,
default_path=self.file_csv)
result = dialog.open()
""" Test if the user opened a file to avoid throwing an exception if he
doesn't """
if result == OK:
self.file_csv = dialog.path
else:
return
""" Filling x_axis and y_axis with values """
headers_array = np.array(
pd.read_csv(
self.file_csv, delimiter=self.delimiter, decimal=self.decimal,
nrows=1, header=None
)
)[0]
for i in range(len(headers_array)):
headers_array[i] = self.get_valid_file_name(headers_array[i])
self.columns_headers_list = list(headers_array)
""" Saving file name and path and creating NPY folder """
dir_path = os.path.dirname(self.file_csv)
self.npy_folder_path = os.path.join(dir_path, 'NPY')
if os.path.exists(self.npy_folder_path) == False:
os.makedirs(self.npy_folder_path)
self.file_name = os.path.splitext(
os.path.basename(self.file_csv))[0]
except Exception as e:
self.deal_with_exception(e)
def _parse_csv_to_npy_fired(self):
# Run method on different thread so GUI doesn't freeze
#thread = Thread(target = threaded_function, function_args = (10,))
thread = Thread(target=self.parse_csv_to_npy_fired)
thread.start()
def parse_csv_to_npy_fired(self):
try:
self.print_custom('Parsing csv into npy files...')
for i in range(len(self.columns_headers_list) -
len(self.columns_to_be_averaged)):
current_column_name = self.columns_headers_list[i]
column_array = np.array(pd.read_csv(
self.file_csv, delimiter=self.delimiter, decimal=self.decimal,
skiprows=self.skip_first_rows, usecols=[i]))
if current_column_name == self.time_column and \
self.take_time_from_time_column == False:
column_array = np.arange(start=0.0,
stop=len(column_array) /
self.records_per_second,
step=1.0 / self.records_per_second)
np.save(os.path.join(self.npy_folder_path, self.file_name +
'_' + current_column_name + '.npy'),
column_array)
""" Exporting npy arrays of averaged columns """
for columns_names in self.columns_to_be_averaged:
temp = np.zeros((1))
for column_name in columns_names:
temp = temp + np.load(os.path.join(self.npy_folder_path,
self.file_name +
'_' + column_name +
'.npy')).flatten()
avg = temp / len(columns_names)
avg_file_suffex = self.get_suffex_for_columns_to_be_averaged(
columns_names)
np.save(os.path.join(self.npy_folder_path, self.file_name +
'_' + avg_file_suffex + '.npy'), avg)
self.print_custom('Finsihed parsing csv into npy files.')
except Exception as e:
self.deal_with_exception(e)
def get_suffex_for_columns_to_be_averaged(self, columns_names):
suffex_for_saved_file_name = 'avg_' + '_'.join(columns_names)
return suffex_for_saved_file_name
def get_valid_file_name(self, original_file_name):
valid_chars = "-_.() %s%s" % (string.ascii_letters, string.digits)
new_valid_file_name = ''.join(
c for c in original_file_name if c in valid_chars)
return new_valid_file_name
def _clear_plot_fired(self):
self.figure.clear()
self.data_changed = True
def _add_columns_average_fired(self):
try:
columns_average = ColumnsAverage()
for name in self.columns_headers_list:
columns_average.columns.append(Column(column_name=name))
# kind='modal' pauses the implementation until the window is closed
columns_average.configure_traits(kind='modal')
columns_to_be_averaged_temp = []
for i in columns_average.columns:
if i.selected:
columns_to_be_averaged_temp.append(i.column_name)
if columns_to_be_averaged_temp: # If it's not empty
self.columns_to_be_averaged.append(columns_to_be_averaged_temp)
avg_file_suffex = self.get_suffex_for_columns_to_be_averaged(
columns_to_be_averaged_temp)
self.columns_headers_list.append(avg_file_suffex)
except Exception as e:
self.deal_with_exception(e)
def _generate_filtered_and_creep_npy_fired(self):
# Run method on different thread so GUI doesn't freeze
#thread = Thread(target = threaded_function, function_args = (10,))
thread = Thread(target=self.generate_filtered_and_creep_npy_fired)
thread.start()
def generate_filtered_and_creep_npy_fired(self):
try:
if self.npy_files_exist(os.path.join(
self.npy_folder_path, self.file_name + '_' + self.force_column
+ '.npy')) == False:
return
self.print_custom('Generating filtered and creep files...')
# 1- Export filtered force
force = np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.force_column
+ '.npy')).flatten()
peak_force_before_cycles_index = np.where(
abs((force)) > abs(self.peak_force_before_cycles))[0][0]
force_ascending = force[0:peak_force_before_cycles_index]
force_rest = force[peak_force_before_cycles_index:]
force_max_indices, force_min_indices = self.get_array_max_and_min_indices(
force_rest)
force_max_min_indices = np.concatenate(
(force_min_indices, force_max_indices))
force_max_min_indices.sort()
force_rest_filtered = force_rest[force_max_min_indices]
force_filtered = np.concatenate(
(force_ascending, force_rest_filtered))
np.save(os.path.join(self.npy_folder_path, self.file_name +
'_' + self.force_column + '_filtered.npy'),
force_filtered)
# 2- Export filtered displacements
for i in range(0, len(self.columns_headers_list)):
if self.columns_headers_list[i] != self.force_column and \
self.columns_headers_list[i] != self.time_column:
disp = np.load(os.path.join(self.npy_folder_path, self.file_name
+ '_' +
self.columns_headers_list[i]
+ '.npy')).flatten()
disp_ascending = disp[0:peak_force_before_cycles_index]
disp_rest = disp[peak_force_before_cycles_index:]
if self.activate == True:
disp_ascending = savgol_filter(
disp_ascending, window_length=self.window_length,
polyorder=self.polynomial_order)
disp_rest_filtered = disp_rest[force_max_min_indices]
filtered_disp = np.concatenate(
(disp_ascending, disp_rest_filtered))
np.save(os.path.join(self.npy_folder_path, self.file_name + '_'
+ self.columns_headers_list[i] +
'_filtered.npy'), filtered_disp)
# 3- Export creep for displacements
# Cutting unwanted max min values to get correct full cycles and remove
# false min/max values caused by noise
if self.cutting_method == "Define Max, Min":
force_max_indices_cutted, force_min_indices_cutted = \
self.cut_indices_of_min_max_range(force_rest,
force_max_indices,
force_min_indices,
self.force_max,
self.force_min)
elif self.cutting_method == "Define min cycle range(force difference)":
force_max_indices_cutted, force_min_indices_cutted = \
self.cut_indices_of_defined_range(force_rest,
force_max_indices,
force_min_indices,
self.min_cycle_force_range)
self.print_custom("Cycles number= ", len(force_min_indices))
self.print_custom("Cycles number after cutting fake cycles = ",
len(force_min_indices_cutted))
for i in range(0, len(self.columns_headers_list)):
if self.columns_headers_list[i] != self.time_column:
array = np.load(os.path.join(self.npy_folder_path, self.file_name +
'_' +
self.columns_headers_list[i]
+ '.npy')).flatten()
array_rest = array[peak_force_before_cycles_index:]
array_rest_maxima = array_rest[force_max_indices_cutted]
array_rest_minima = array_rest[force_min_indices_cutted]
np.save(os.path.join(self.npy_folder_path, self.file_name + '_' +
self.columns_headers_list[i] + '_max.npy'), array_rest_maxima)
np.save(os.path.join(self.npy_folder_path, self.file_name + '_' +
self.columns_headers_list[i] + '_min.npy'), array_rest_minima)
self.print_custom('Filtered and creep npy files are generated.')
except Exception as e:
self.deal_with_exception(e)
def cut_indices_of_min_max_range(self, array, max_indices, min_indices,
range_upper_value, range_lower_value):
cutted_max_indices = []
cutted_min_indices = []
for max_index in max_indices:
if abs(array[max_index]) > abs(range_upper_value):
cutted_max_indices.append(max_index)
for min_index in min_indices:
if abs(array[min_index]) < abs(range_lower_value):
cutted_min_indices.append(min_index)
return cutted_max_indices, cutted_min_indices
def cut_indices_of_defined_range(self, array, max_indices, min_indices, range_):
cutted_max_indices = []
cutted_min_indices = []
for max_index, min_index in zip(max_indices, min_indices):
if abs(array[max_index] - array[min_index]) > range_:
cutted_max_indices.append(max_index)
cutted_min_indices.append(min_index)
if max_indices.size > min_indices.size:
cutted_max_indices.append(max_indices[-1])
elif min_indices.size > max_indices.size:
cutted_min_indices.append(min_indices[-1])
return cutted_max_indices, cutted_min_indices
def get_array_max_and_min_indices(self, input_array):
# Checking dominant sign
positive_values_count = np.sum(np.array(input_array) >= 0)
negative_values_count = input_array.size - positive_values_count
# Getting max and min indices
if (positive_values_count > negative_values_count):
force_max_indices = self.get_max_indices(input_array)
force_min_indices = self.get_min_indices(input_array)
else:
force_max_indices = self.get_min_indices(input_array)
force_min_indices = self.get_max_indices(input_array)
return force_max_indices, force_min_indices
def get_max_indices(self, a):
# This method doesn't qualify first and last elements as max
max_indices = []
i = 1
while i < a.size - 1:
previous_element = a[i - 1]
# Skip repeated elements and record previous element value
first_repeated_element = True
while a[i] == a[i + 1] and i < a.size - 1:
if first_repeated_element:
previous_element = a[i - 1]
first_repeated_element = False
if i < a.size - 2:
i += 1
else:
break
if a[i] > a[i + 1] and a[i] > previous_element:
max_indices.append(i)
i += 1
return np.array(max_indices)
def get_min_indices(self, a):
# This method doesn't qualify first and last elements as min
min_indices = []
i = 1
while i < a.size - 1:
previous_element = a[i - 1]
# Skip repeated elements and record previous element value
first_repeated_element = True
while a[i] == a[i + 1]:
if first_repeated_element:
previous_element = a[i - 1]
first_repeated_element = False
if i < a.size - 2:
i += 1
else:
break
if a[i] < a[i + 1] and a[i] < previous_element:
min_indices.append(i)
i += 1
return np.array(min_indices)
def _activate_changed(self):
if self.activate == False:
self.old_peak_force_before_cycles = self.peak_force_before_cycles
self.peak_force_before_cycles = 0
else:
self.peak_force_before_cycles = self.old_peak_force_before_cycles
def _window_length_changed(self, new):
if new <= self.polynomial_order:
dialog = MessageDialog(
title='Attention!',
message='Window length must be bigger than polynomial order.')
dialog.open()
if new % 2 == 0 or new <= 0:
dialog = MessageDialog(
title='Attention!',
message='Window length must be odd positive integer.')
dialog.open()
def _polynomial_order_changed(self, new):
if new >= self.window_length:
dialog = MessageDialog(
title='Attention!',
message='Polynomial order must be smaller than window length.')
dialog.open()
#=========================================================================
# Plotting
#=========================================================================
def _plot_settings_btn_fired(self):
try:
self.plot_settings.configure_traits(kind='modal')
except Exception as e:
self.deal_with_exception(e)
def npy_files_exist(self, path):
if os.path.exists(path) == True:
return True
else:
# TODO fix this
self.print_custom(
'Please parse csv file to generate npy files first.')
# dialog = MessageDialog(
# title='Attention!',
# message='Please parse csv file to generate npy files first.')
# dialog.open()
return False
def filtered_and_creep_npy_files_exist(self, path):
if os.path.exists(path) == True:
return True
else:
# TODO fix this
self.print_custom(
'Please generate filtered and creep npy files first.')
# dialog = MessageDialog(
# title='Attention!',
# message='Please generate filtered and creep npy files first.')
# dialog.open()
return False
data_changed = tr.Event
def _add_plot_fired(self):
# Run method on different thread so GUI doesn't freeze
#thread = Thread(target = threaded_function, function_args = (10,))
thread = Thread(target=self.add_plot_fired)
thread.start()
def add_plot_fired(self):
try:
if self.apply_filters:
if self.filtered_and_creep_npy_files_exist(os.path.join(
self.npy_folder_path, self.file_name + '_' + self.x_axis
+ '_filtered.npy')) == False:
return
x_axis_name = self.x_axis + '_filtered'
y_axis_name = self.y_axis + '_filtered'
self.print_custom('Loading npy files...')
# when mmap_mode!=None, the array will be loaded as 'numpy.memmap'
# object which doesn't load the array to memory until it's
# indexed
x_axis_array = np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.x_axis
+ '_filtered.npy'), mmap_mode='r')
y_axis_array = np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.y_axis
+ '_filtered.npy'), mmap_mode='r')
else:
if self.npy_files_exist(os.path.join(
self.npy_folder_path, self.file_name + '_' + self.x_axis
+ '.npy')) == False:
return
x_axis_name = self.x_axis
y_axis_name = self.y_axis
self.print_custom('Loading npy files...')
# when mmap_mode!=None, the array will be loaded as 'numpy.memmap'
# object which doesn't load the array to memory until it's
# indexed
x_axis_array = np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.x_axis
+ '.npy'), mmap_mode='r')
y_axis_array = np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.y_axis
+ '.npy'), mmap_mode='r')
if self.plot_settings_active:
print(self.plot_settings.first_rows)
print(self.plot_settings.distance)
print(self.plot_settings.num_of_rows_after_each_distance)
print(np.size(x_axis_array))
indices = self.get_indices_array(np.size(x_axis_array),
self.plot_settings.first_rows,
self.plot_settings.distance,
self.plot_settings.num_of_rows_after_each_distance)
x_axis_array = self.x_axis_multiplier * x_axis_array[indices]
y_axis_array = self.y_axis_multiplier * y_axis_array[indices]
else:
x_axis_array = self.x_axis_multiplier * x_axis_array
y_axis_array = self.y_axis_multiplier * y_axis_array
self.print_custom('Adding Plot...')
mpl.rcParams['agg.path.chunksize'] = 10000
ax = self.figure.add_subplot(1, 1, 1)
ax.set_xlabel(x_axis_name)
ax.set_ylabel(y_axis_name)
ax.plot(x_axis_array, y_axis_array, 'k',
linewidth=1.2, color=np.random.rand(3), label=self.file_name +
', ' + x_axis_name)
ax.legend()
self.data_changed = True
self.print_custom('Finished adding plot.')
except Exception as e:
self.deal_with_exception(e)
def _add_creep_plot_fired(self):
# Run method on different thread so GUI doesn't freeze
#thread = Thread(target = threaded_function, function_args = (10,))
thread = Thread(target=self.add_creep_plot_fired)
thread.start()
def add_creep_plot_fired(self):
try:
if self.filtered_and_creep_npy_files_exist(os.path.join(
self.npy_folder_path, self.file_name + '_' + self.x_axis
+ '_max.npy')) == False:
return
self.print_custom('Loading npy files...')
disp_max = self.x_axis_multiplier * \
np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.x_axis + '_max.npy'))
disp_min = self.x_axis_multiplier * \
np.load(os.path.join(self.npy_folder_path,
self.file_name + '_' + self.x_axis + '_min.npy'))
complete_cycles_number = disp_max.size
self.print_custom('Adding creep-fatigue plot...')
mpl.rcParams['agg.path.chunksize'] = 10000
ax = self.figure.add_subplot(1, 1, 1)
ax.set_xlabel('Cycles number')
ax.set_ylabel(self.x_axis)
if self.plot_every_nth_point > 1:
disp_max = disp_max[0::self.plot_every_nth_point]
disp_min = disp_min[0::self.plot_every_nth_point]
if self.smooth:
# Keeping the first item of the array and filtering the rest
disp_max = np.concatenate((
np.array([disp_max[0]]),
savgol_filter(disp_max[1:],
window_length=self.window_length,
polyorder=self.polynomial_order)
))
disp_min = np.concatenate((
np.array([disp_min[0]]),
savgol_filter(disp_min[1:],
window_length=self.window_length,
polyorder=self.polynomial_order)
))
if self.normalize_cycles:
ax.plot(np.linspace(0, 1., disp_max.size), disp_max,
'k', linewidth=1.2, color=np.random.rand(3), label='Max'
+ ', ' + self.file_name + ', ' + self.x_axis)
ax.plot(np.linspace(0, 1., disp_min.size), disp_min,
'k', linewidth=1.2, color=np.random.rand(3), label='Min'
+ ', ' + self.file_name + ', ' + self.x_axis)
else:
ax.plot(np.linspace(0, complete_cycles_number,
disp_max.size), disp_max,
'k', linewidth=1.2, color=np.random.rand(3), label='Max'
+ ', ' + self.file_name + ', ' + self.x_axis)
ax.plot(np.linspace(0, complete_cycles_number,
disp_min.size), disp_min,
'k', linewidth=1.2, color=np.random.rand(3), label='Min'
+ ', ' + self.file_name + ', ' + self.x_axis)
ax.legend()
self.data_changed = True
self.print_custom('Finished adding creep-fatigue plot.')
except Exception as e:
self.deal_with_exception(e)
def get_indices_array(self,
array_size,
first_rows,
distance,
num_of_rows_after_each_distance):
result_1 = np.arange(first_rows)
result_2 = np.arange(start=first_rows, stop=array_size,
step=distance + num_of_rows_after_each_distance)
result_2_updated = np.array([], dtype=np.int_)
for result_2_value in result_2:
data_slice = np.arange(result_2_value, result_2_value +
num_of_rows_after_each_distance)
result_2_updated = np.concatenate((result_2_updated, data_slice))
result = np.concatenate((result_1, result_2_updated))
return result
def reset(self):
self.columns_to_be_averaged = []
self.log = ''
def print_custom(self, *input_args):
print(*input_args)
if self.log == '':
self.log = ''.join(str(e) for e in list(input_args))
else:
self.log = self.log + '\n' + \
''.join(str(e) for e in list(input_args))
def deal_with_exception(self, e):
self.print_custom('SOMETHING WENT WRONG!')
self.print_custom('--------- Error message: ---------')
self.print_custom(traceback.format_exc())
self.print_custom('----------------------------------')
def _clear_log_fired(self):
self.log = ''
#=========================================================================
# Configuration of the view
#=========================================================================
traits_view = ui.View(
ui.HSplit(
ui.VSplit(
ui.VGroup(
ui.VGroup(
ui.Item('decimal'),
ui.Item('delimiter'),
ui.HGroup(
ui.UItem('open_file_csv', has_focus=True),
ui.UItem('file_csv', style='readonly', width=0.1)),
label='Importing csv file',
show_border=True)),
ui.VGroup(
ui.VGroup(
ui.VGroup(
ui.Item('take_time_from_time_column'),
ui.Item('time_column',
enabled_when='take_time_from_time_column == True'),
ui.Item('records_per_second',
enabled_when='take_time_from_time_column == False'),
label='Time calculation',
show_border=True),
ui.UItem('add_columns_average'),
ui.Item('skip_first_rows'),
ui.UItem('parse_csv_to_npy', resizable=True),
label='Processing csv file',
show_border=True)),
ui.VGroup(
ui.VGroup(
ui.HGroup(ui.Item('x_axis'), ui.Item(
'x_axis_multiplier')),
ui.HGroup(ui.Item('y_axis'), ui.Item(
'y_axis_multiplier')),
ui.VGroup(
ui.HGroup(ui.UItem('add_plot'),
ui.Item('apply_filters'),
ui.Item('plot_settings_btn',
label='Settings',
show_label=False,
enabled_when='plot_settings_active == True'),
ui.Item('plot_settings_active',
show_label=False)
),
show_border=True,
label='Plotting X axis with Y axis'
),
ui.VGroup(
ui.HGroup(ui.UItem('add_creep_plot'),
ui.VGroup(
ui.Item('normalize_cycles'),
ui.Item('smooth'),
ui.Item('plot_every_nth_point'))
),
show_border=True,
label='Plotting Creep-fatigue of X axis variable'
),
ui.UItem('clear_plot', resizable=True),
show_border=True,
label='Plotting'))
),
ui.VGroup(
ui.Item('force_column'),
ui.VGroup(ui.VGroup(
ui.Item('window_length'),
ui.Item('polynomial_order'),
enabled_when='activate == True or smooth == True'),
show_border=True,
label='Smoothing parameters (Savitzky-Golay filter):'
),
ui.VGroup(ui.VGroup(
ui.Item('activate'),
ui.Item('peak_force_before_cycles',
enabled_when='activate == True')
),
show_border=True,
label='Smooth ascending branch for all displacements:'
),
ui.VGroup(ui.Item('cutting_method'),
ui.VGroup(ui.Item('force_max'),
ui.Item('force_min'),
label='Max, Min:',
show_border=True,
enabled_when='cutting_method == "Define Max, Min"'),
ui.VGroup(ui.Item('min_cycle_force_range'),
label='Min cycle force range:',
show_border=True,
enabled_when='cutting_method == "Define min cycle range(force difference)"'),
show_border=True,
label='Cut fake cycles for creep:'),
ui.VSplit(
ui.UItem('generate_filtered_and_creep_npy'),
ui.VGroup(
ui.Item('log',
width=0.1, style='custom'),
ui.UItem('clear_log'))),
show_border=True,
label='Filters'
),
ui.UItem('figure', editor=MPLFigureEditor(),
resizable=True,
springy=True,
width=0.8,
label='2d plots')
),
title='High-cycle fatigue tool',
resizable=True,
width=0.85,
height=0.7
)
class HCFF(tr.HasStrictTraits):
'''High-Cycle Fatigue Filter
'''
something = tr.Instance(Something)
decimal = tr.Enum(',', '.')
delimiter = tr.Str(';')
path_hdf5 = tr.Str('')
def _something_default(self):
return Something()
#=========================================================================
# File management
#=========================================================================
file_csv = tr.File
open_file_csv = tr.Button('Input file')
def _open_file_csv_fired(self):
""" Handles the user clicking the 'Open...' button.
"""
extns = [
'*.csv',
] # seems to handle only one extension...
wildcard = '|'.join(extns)
dialog = FileDialog(title='Select text file',
action='open',
wildcard=wildcard,
default_path=self.file_csv)
dialog.open()
self.file_csv = dialog.path
""" Filling x_axis and y_axis with values """
headers_array = np.array(
pd.read_csv(self.file_csv,
delimiter=self.delimiter,
decimal=self.decimal,
nrows=1,
header=None))[0]
for i in range(len(headers_array)):
headers_array[i] = self.get_valid_file_name(headers_array[i])
self.columns_headers_list = list(headers_array)
#=========================================================================
# Parameters of the filter algorithm
#=========================================================================
chunk_size = tr.Int(10000, auto_set=False, enter_set=True)
skip_rows = tr.Int(4, auto_set=False, enter_set=True)
# 1) use the decorator
@tr.on_trait_change('chunk_size, skip_rows')
def whatever_name_size_changed(self):
print('chunk-size changed')
# 2) use the _changed or _fired extension
def _chunk_size_changed(self):
print('chunk_size changed - calling the named function')
data = tr.Array(dtype=np.float_)
read_loadtxt_button = tr.Button()
def _read_loadtxt_button_fired(self):
self.data = np.loadtxt(self.file_csv,
skiprows=self.skip_rows,
delimiter=self.delimiter)
print(self.data.shape)
read_csv_button = tr.Button
read_hdf5_button = tr.Button
def _read_csv_button_fired(self):
self.read_csv()
def _read_hdf5_button_fired(self):
self.read_hdf5_no_filter()
def read_csv(self):
'''Read the csv file and transform it to the hdf5 format.
The output file has the same name as the input csv file
with an extension hdf5
'''
path_csv = self.file_csv
# Following splitext splits the path into a pair (root, extension)
self.path_hdf5 = os.path.splitext(path_csv)[0] + '.hdf5'
for i, chunk in enumerate(
pd.read_csv(path_csv,
delimiter=self.delimiter,
decimal=self.decimal,
skiprows=self.skip_rows,
chunksize=self.chunk_size)):
chunk_array = np.array(chunk)
chunk_data_frame = pd.DataFrame(
chunk_array, columns=['a', 'b', 'c', 'd', 'e', 'f'])
if i == 0:
chunk_data_frame.to_hdf(self.path_hdf5,
'all_data',
mode='w',
format='table')
else:
chunk_data_frame.to_hdf(self.path_hdf5,
'all_data',
append=True)
def read_hdf5_no_filter(self):
# reading hdf files is really memory-expensive!
force = np.array(pd.read_hdf(self.path_hdf5, columns=['b']))
weg = np.array(pd.read_hdf(self.path_hdf5, columns=['c']))
disp1 = np.array(pd.read_hdf(self.path_hdf5, columns=['d']))
disp2 = np.array(pd.read_hdf(self.path_hdf5, columns=['e']))
disp3 = np.array(pd.read_hdf(self.path_hdf5, columns=['f']))
force = np.concatenate((np.zeros((1, 1)), force))
weg = np.concatenate((np.zeros((1, 1)), weg))
disp1 = np.concatenate((np.zeros((1, 1)), disp1))
disp2 = np.concatenate((np.zeros((1, 1)), disp2))
disp3 = np.concatenate((np.zeros((1, 1)), disp3))
dir_path = os.path.dirname(self.file_csv)
npy_folder_path = os.path.join(dir_path, 'NPY')
if os.path.exists(npy_folder_path) == False:
os.makedirs(npy_folder_path)
file_name = os.path.splitext(os.path.basename(self.file_csv))[0]
np.save(
os.path.join(npy_folder_path, file_name + '_Force_nofilter.npy'),
force)
np.save(
os.path.join(npy_folder_path,
file_name + '_Displacement_machine_nofilter.npy'),
weg)
np.save(
os.path.join(npy_folder_path,
file_name + '_Displacement_sliding1_nofilter.npy'),
disp1)
np.save(
os.path.join(npy_folder_path,
file_name + '_Displacement_sliding2_nofilter.npy'),
disp2)
np.save(
os.path.join(npy_folder_path,
file_name + '_Displacement_crack1_nofilter.npy'),
disp3)
# Defining chunk size for matplotlib points visualization
mpl.rcParams['agg.path.chunksize'] = 50000
plt.subplot(111)
plt.xlabel('Displacement [mm]')
plt.ylabel('kN')
plt.title('original data', fontsize=20)
plt.plot(disp2, force, 'k')
plt.show()
figure = tr.Instance(Figure)
def _figure_default(self):
figure = Figure(facecolor='white')
figure.set_tight_layout(True)
return figure
columns_headers_list = tr.List([])
x_axis = tr.Enum(values='columns_headers_list')
y_axis = tr.Enum(values='columns_headers_list')
npy_folder_path = tr.Str
file_name = tr.Str
plot = tr.Button
def _plot_fired(self):
ax = self.figure.add_subplot(111)
print('plotting figure')
print(type(self.x_axis), type(self.y_axis))
print(self.data[:, 1])
print(self.data[:, self.x_axis])
print(self.data[:, self.y_axis])
ax.plot(self.data[:, self.x_axis], self.data[:, self.y_axis])
traits_view = ui.View(ui.HSplit(
ui.VSplit(
ui.HGroup(ui.UItem('open_file_csv'),
ui.UItem('file_csv', style='readonly'),
label='Input data'),
ui.VGroup(ui.Item('chunk_size'),
ui.Item('skip_rows'),
ui.Item('decimal'),
ui.Item('delimiter'),
label='Filter parameters'),
ui.VGroup(
ui.HGroup(ui.Item('read_loadtxt_button', show_label=False),
ui.Item('plot', show_label=False),
show_border=True),
ui.HGroup(ui.Item('read_csv_button', show_label=False),
ui.Item('read_hdf5_button', show_label=False),
show_border=True))),
ui.UItem('figure',
editor=MPLFigureEditor(),
resizable=True,
springy=True,
label='2d plots'),
),
resizable=True,
width=0.8,
height=0.6)