INSTRUCTION stringlengths 1 46.3k | RESPONSE stringlengths 75 80.2k |
|---|---|
Yield all unions of start with other in shortlex order.
>>> ['{:03b}'.format(s) for s in shortlex(0, [0b100, 0b010, 0b001])]
['000', '100', '010', '001', '110', '101', '011', '111']
>>> ', '.join(''.join(sorted(s))
... for s in shortlex(set(), [{'a'}, {'b'}, {'c'}, {'d'}]))
', a, b, c, d, ab, ac, ... | def shortlex(start, other, excludestart=False):
"""Yield all unions of start with other in shortlex order.
>>> ['{:03b}'.format(s) for s in shortlex(0, [0b100, 0b010, 0b001])]
['000', '100', '010', '001', '110', '101', '011', '111']
>>> ', '.join(''.join(sorted(s))
... for s in shortlex(set(), [{'... |
Yield all intersections of end with other in reverse shortlex order.
>>> ['{:03b}'.format(s) for s in reverse_shortlex(0b111, [0b011, 0b101, 0b110])]
['111', '011', '101', '110', '001', '010', '100', '000']
>>> ', '.join(''.join(sorted(s))
... for s in reverse_shortlex({'a', 'b', 'c', 'd'},
... [{... | def reverse_shortlex(end, other, excludeend=False):
"""Yield all intersections of end with other in reverse shortlex order.
>>> ['{:03b}'.format(s) for s in reverse_shortlex(0b111, [0b011, 0b101, 0b110])]
['111', '011', '101', '110', '001', '010', '100', '000']
>>> ', '.join(''.join(sorted(s))
...... |
Get a representative text of a time (in s). | def time_to_text(time):
"""Get a representative text of a time (in s)."""
if time < 0.001:
return str(round(time * 1000000)) + " µs"
elif time < 1:
return str(round(time * 1000)) + " ms"
elif time < 60:
return str(round(time, 1)) + " s"
else:
return str(round(tim... |
Pass this function to upload_to argument of FileField to store the file on an unguessable path.
The format of the path is class_name/hash/original_filename. | def generate_random_upload_path(instance, filename):
"""
Pass this function to upload_to argument of FileField to store the file on an unguessable path.
The format of the path is class_name/hash/original_filename.
"""
return os.path.join(instance.__class__.__name__.lower(), uuid().hex, filename) |
removes UTF chars from filename | def generate_filename(self, instance, filename):
"""
removes UTF chars from filename
"""
from unidecode import unidecode
return super().generate_filename(instance, unidecode(force_text(filename))) |
Retrieve the next item in the queue.
Returns deserialized value, or None if there were no entries
in the Queue. | def next(self):
""" Retrieve the next item in the queue.
Returns deserialized value, or None if there were no entries
in the Queue.
"""
if self.blocking >= 0:
# returns queue name and item, we just need item
res = self.redis.blpop([self.name], timeout=sel... |
Send a value to this LIFO Queue.
Provided argument is serialized and pushed out. Don't send None. | def send(self, *args):
""" Send a value to this LIFO Queue.
Provided argument is serialized and pushed out. Don't send None.
"""
# this and the serializer could use some streamlining
if None in args:
raise TypeError('None is not a valid queue item.')
serializ... |
Clear any existing values from this queue. | def clear(self):
""" Clear any existing values from this queue. """
logger.debug('Clearing queue: "%s"', self.name)
return self.redis.delete(self.name) |
Converts a 32 bit unsigned number to signed.
uint32:= an unsigned 32 bit number
...
print(u2i(4294967272))
-24
print(u2i(37))
37
... | def u2i(uint32):
"""
Converts a 32 bit unsigned number to signed.
uint32:= an unsigned 32 bit number
...
print(u2i(4294967272))
-24
print(u2i(37))
37
...
"""
mask = (2 ** 32) - 1
if uint32 & (1 << 31):
v = uint32 | ~mask
else:
v = uint32 & mask
r... |
Converts a 32 bit unsigned number to signed. If the number
is negative it indicates an error. On error a pigpio
exception will be raised if exceptions is True. | def _u2i(uint32):
"""
Converts a 32 bit unsigned number to signed. If the number
is negative it indicates an error. On error a pigpio
exception will be raised if exceptions is True.
"""
v = u2i(uint32)
if v < 0:
if exceptions:
raise ApigpioError(error_text(v))
retur... |
Adds a callback. | def append(self, cb):
"""Adds a callback."""
self.callbacks.append(cb.callb)
self.monitor = self.monitor | cb.callb.bit
yield from self.pi._pigpio_aio_command(_PI_CMD_NB, self.handle,
self.monitor) |
Removes a callback. | def remove(self, cb):
"""Removes a callback."""
if cb in self.callbacks:
self.callbacks.remove(cb)
new_monitor = 0
for c in self.callbacks:
new_monitor |= c.bit
if new_monitor != self.monitor:
self.monitor = new_monitor
... |
Runs a pigpio socket command.
sl:= command socket and lock.
cmd:= the command to be executed.
p1:= command parameter 1 (if applicable).
p2:= command parameter 2 (if applicable). | def _pigpio_aio_command(self, cmd, p1, p2,):
"""
Runs a pigpio socket command.
sl:= command socket and lock.
cmd:= the command to be executed.
p1:= command parameter 1 (if applicable).
p2:= command parameter 2 (if applicable).
"""
with (yield from self... |
Runs an extended pigpio socket command.
sl:= command socket and lock.
cmd:= the command to be executed.
p1:= command parameter 1 (if applicable).
p2:= command parameter 2 (if applicable).
p3:= total size in bytes of following extents
extents:= addition... | def _pigpio_aio_command_ext(self, cmd, p1, p2, p3, extents, rl=True):
"""
Runs an extended pigpio socket command.
sl:= command socket and lock.
cmd:= the command to be executed.
p1:= command parameter 1 (if applicable).
p2:= command parameter 2 (if applica... |
Connect to a remote or local gpiod daemon.
:param address: a pair (address, port), the address must be already
resolved (for example an ip address)
:return: | def connect(self, address):
"""
Connect to a remote or local gpiod daemon.
:param address: a pair (address, port), the address must be already
resolved (for example an ip address)
:return:
"""
self.s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
self... |
Store a script for later execution.
script:= the script text as a series of bytes.
Returns a >=0 script id if OK.
...
sid = pi.store_script(
b'tag 0 w 22 1 mils 100 w 22 0 mils 100 dcr p0 jp 0')
... | def store_script(self, script):
"""
Store a script for later execution.
script:= the script text as a series of bytes.
Returns a >=0 script id if OK.
...
sid = pi.store_script(
b'tag 0 w 22 1 mils 100 w 22 0 mils 100 dcr p0 jp 0')
...
"""
... |
Runs a stored script.
script_id:= id of stored script.
params:= up to 10 parameters required by the script.
...
s = pi.run_script(sid, [par1, par2])
s = pi.run_script(sid)
s = pi.run_script(sid, [1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
... | def run_script(self, script_id, params=None):
"""
Runs a stored script.
script_id:= id of stored script.
params:= up to 10 parameters required by the script.
...
s = pi.run_script(sid, [par1, par2])
s = pi.run_script(sid)
s = pi.run_script(sid, [1, 2,... |
Returns the run status of a stored script as well as the
current values of parameters 0 to 9.
script_id:= id of stored script.
The run status may be
. .
PI_SCRIPT_INITING
PI_SCRIPT_HALTED
PI_SCRIPT_RUNNING
PI_SCRIPT_WAITING
PI_SCRIPT_FAILED
... | def script_status(self, script_id):
"""
Returns the run status of a stored script as well as the
current values of parameters 0 to 9.
script_id:= id of stored script.
The run status may be
. .
PI_SCRIPT_INITING
PI_SCRIPT_HALTED
PI_SCRIPT_RUNNING... |
Stops a running script.
script_id:= id of stored script.
...
status = pi.stop_script(sid)
... | def stop_script(self, script_id):
"""
Stops a running script.
script_id:= id of stored script.
...
status = pi.stop_script(sid)
...
"""
res = yield from self._pigpio_aio_command(_PI_CMD_PROCS, script_id, 0)
return _u2i(res) |
Deletes a stored script.
script_id:= id of stored script.
...
status = pi.delete_script(sid)
... | def delete_script(self, script_id):
"""
Deletes a stored script.
script_id:= id of stored script.
...
status = pi.delete_script(sid)
...
"""
res = yield from self._pigpio_aio_command(_PI_CMD_PROCD, script_id, 0)
return _u2i(res) |
Clears gpios 0-31 if the corresponding bit in bits is set.
bits:= a 32 bit mask with 1 set if the corresponding gpio is
to be cleared.
A returned status of PI_SOME_PERMITTED indicates that the user
is not allowed to write to one or more of the gpios.
...
pi.clear_... | def clear_bank_1(self, bits):
"""
Clears gpios 0-31 if the corresponding bit in bits is set.
bits:= a 32 bit mask with 1 set if the corresponding gpio is
to be cleared.
A returned status of PI_SOME_PERMITTED indicates that the user
is not allowed to write to one or... |
Sets gpios 0-31 if the corresponding bit in bits is set.
bits:= a 32 bit mask with 1 set if the corresponding gpio is
to be set.
A returned status of PI_SOME_PERMITTED indicates that the user
is not allowed to write to one or more of the gpios.
...
pi.set_bank_1(i... | def set_bank_1(self, bits):
"""
Sets gpios 0-31 if the corresponding bit in bits is set.
bits:= a 32 bit mask with 1 set if the corresponding gpio is
to be set.
A returned status of PI_SOME_PERMITTED indicates that the user
is not allowed to write to one or more of... |
Sets the gpio mode.
gpio:= 0-53.
mode:= INPUT, OUTPUT, ALT0, ALT1, ALT2, ALT3, ALT4, ALT5.
...
pi.set_mode( 4, apigpio.INPUT) # gpio 4 as input
pi.set_mode(17, apigpio.OUTPUT) # gpio 17 as output
pi.set_mode(24, apigpio.ALT2) # gpio 24 as ALT2
... | def set_mode(self, gpio, mode):
"""
Sets the gpio mode.
gpio:= 0-53.
mode:= INPUT, OUTPUT, ALT0, ALT1, ALT2, ALT3, ALT4, ALT5.
...
pi.set_mode( 4, apigpio.INPUT) # gpio 4 as input
pi.set_mode(17, apigpio.OUTPUT) # gpio 17 as output
pi.set_mode(24, apig... |
Sets or clears the internal GPIO pull-up/down resistor.
gpio:= 0-53.
pud:= PUD_UP, PUD_DOWN, PUD_OFF.
...
yield from pi.set_pull_up_down(17, apigpio.PUD_OFF)
yield from pi.set_pull_up_down(23, apigpio.PUD_UP)
yield from pi.set_pull_up_down(24, apigpio.PUD_DOWN)
.... | def set_pull_up_down(self, gpio, pud):
"""
Sets or clears the internal GPIO pull-up/down resistor.
gpio:= 0-53.
pud:= PUD_UP, PUD_DOWN, PUD_OFF.
...
yield from pi.set_pull_up_down(17, apigpio.PUD_OFF)
yield from pi.set_pull_up_down(23, apigpio.PUD_UP)
yie... |
Returns the gpio mode.
gpio:= 0-53.
Returns a value as follows
. .
0 = INPUT
1 = OUTPUT
2 = ALT5
3 = ALT4
4 = ALT0
5 = ALT1
6 = ALT2
7 = ALT3
. .
...
print(pi.get_mode(0))
4
... | def get_mode(self, gpio):
"""
Returns the gpio mode.
gpio:= 0-53.
Returns a value as follows
. .
0 = INPUT
1 = OUTPUT
2 = ALT5
3 = ALT4
4 = ALT0
5 = ALT1
6 = ALT2
7 = ALT3
. .
...
print(pi... |
Sets the gpio level.
gpio:= 0-53.
level:= 0, 1.
If PWM or servo pulses are active on the gpio they are
switched off.
...
pi.set_mode(17, pigpio.OUTPUT)
pi.write(17,0)
print(pi.read(17))
0
pi.write(17,1)
print(pi.read(17))
... | def write(self, gpio, level):
"""
Sets the gpio level.
gpio:= 0-53.
level:= 0, 1.
If PWM or servo pulses are active on the gpio they are
switched off.
...
pi.set_mode(17, pigpio.OUTPUT)
pi.write(17,0)
print(pi.read(17))
0
... |
Returns the GPIO level.
gpio:= 0-53.
...
yield from pi.set_mode(23, pigpio.INPUT)
yield from pi.set_pull_up_down(23, pigpio.PUD_DOWN)
print(yield from pi.read(23))
0
yield from pi.set_pull_up_down(23, pigpio.PUD_UP)
print(yield from pi.read(23))
1
... | def read(self, gpio):
"""
Returns the GPIO level.
gpio:= 0-53.
...
yield from pi.set_mode(23, pigpio.INPUT)
yield from pi.set_pull_up_down(23, pigpio.PUD_DOWN)
print(yield from pi.read(23))
0
yield from pi.set_pull_up_down(23, pigpio.PUD_UP)
... |
Send a trigger pulse to a GPIO. The GPIO is set to
level for pulse_len microseconds and then reset to not level.
user_gpio:= 0-31
pulse_len:= 1-100
level:= 0-1
...
pi.gpio_trigger(23, 10, 1)
... | def gpio_trigger(self, user_gpio, pulse_len=10, level=1):
"""
Send a trigger pulse to a GPIO. The GPIO is set to
level for pulse_len microseconds and then reset to not level.
user_gpio:= 0-31
pulse_len:= 1-100
level:= 0-1
...
pi.gpio_trigger(23, 10, 1... |
Sets a glitch filter on a GPIO.
Level changes on the GPIO are not reported unless the level
has been stable for at least [*steady*] microseconds. The
level is then reported. Level changes of less than [*steady*]
microseconds are ignored.
user_gpio:= 0-31
steady:= 0-3... | def set_glitch_filter(self, user_gpio, steady):
"""
Sets a glitch filter on a GPIO.
Level changes on the GPIO are not reported unless the level
has been stable for at least [*steady*] microseconds. The
level is then reported. Level changes of less than [*steady*]
micros... |
Sets a noise filter on a GPIO.
Level changes on the GPIO are ignored until a level which has
been stable for [*steady*] microseconds is detected. Level
changes on the GPIO are then reported for [*active*]
microseconds after which the process repeats.
user_gpio:= 0-31
... | def set_noise_filter(self, user_gpio, steady, active):
"""
Sets a noise filter on a GPIO.
Level changes on the GPIO are ignored until a level which has
been stable for [*steady*] microseconds is detected. Level
changes on the GPIO are then reported for [*active*]
microse... |
Starts (non-zero dutycycle) or stops (0) PWM pulses on the GPIO.
user_gpio:= 0-31.
dutycycle:= 0-range (range defaults to 255).
The [*set_PWM_range*] function can change the default range of 255.
...
pi.set_PWM_dutycycle(4, 0) # PWM off
pi.set_PWM_dutycycle(4, 64) # PW... | def set_PWM_dutycycle(self, user_gpio, dutycycle):
"""
Starts (non-zero dutycycle) or stops (0) PWM pulses on the GPIO.
user_gpio:= 0-31.
dutycycle:= 0-range (range defaults to 255).
The [*set_PWM_range*] function can change the default range of 255.
...
pi.set_PW... |
Calls a user supplied function (a callback) whenever the
specified gpio edge is detected.
user_gpio:= 0-31.
edge:= EITHER_EDGE, RISING_EDGE (default), or FALLING_EDGE.
func:= user supplied callback function.
The user supplied callback receives three parameters, the gpio,
... | def add_callback(self, user_gpio, edge=RISING_EDGE, func=None):
"""
Calls a user supplied function (a callback) whenever the
specified gpio edge is detected.
user_gpio:= 0-31.
edge:= EITHER_EDGE, RISING_EDGE (default), or FALLING_EDGE.
func:= user supplied callback... |
Starts (500-2500) or stops (0) servo pulses on the GPIO.
user_gpio:= 0-31.
pulsewidth:= 0 (off),
500 (most anti-clockwise) - 2500 (most clockwise).
The selected pulsewidth will continue to be transmitted until
changed by a subsequent call to set_servo_pulsewidth.
... | def set_servo_pulsewidth(self, user_gpio, pulsewidth):
"""
Starts (500-2500) or stops (0) servo pulses on the GPIO.
user_gpio:= 0-31.
pulsewidth:= 0 (off),
500 (most anti-clockwise) - 2500 (most clockwise).
The selected pulsewidth will continue to be transmi... |
Converts a camelcase string to a list. | def camelcase2list(s, lower=False):
"""Converts a camelcase string to a list."""
s = re.findall(r'([A-Z][a-z0-9]+)', s)
return [w.lower() for w in s] if lower else s |
Returns parameter names from the route. | def get_route_param_names(endpoint):
"""Returns parameter names from the route."""
try:
g = current_app.url_map.iter_rules(endpoint)
return next(g).arguments
except KeyError:
return {} |
Run the shadowing computation with the values stored in
``self.arg_``. Precomputed information is stored in:
* **.diff_t** (*ndarray*): ``np.diff(t)``
* **.integral** (*ndarray*): Trapezoidal data integration
over time.
The steps are:
... | def run(self):
"""
Run the shadowing computation with the values stored in
``self.arg_``. Precomputed information is stored in:
* **.diff_t** (*ndarray*): ``np.diff(t)``
* **.integral** (*ndarray*): Trapezoidal data integration
over time.
... |
Generates a equally spaced mesh on the Solar Horizont (SH).
Computes the Voronoi diagram from a set of points given by pairs
of (azimuth, zenit) values. This discretization completely
covers all the Sun positions.
The smaller mesh size, the better resolution obtai... | def Vonoroi_SH(self, mesh_size=0.1):
"""
Generates a equally spaced mesh on the Solar Horizont (SH).
Computes the Voronoi diagram from a set of points given by pairs
of (azimuth, zenit) values. This discretization completely
covers all the Sun positions.
... |
Computes the Sun positions for the *t* time vector.
*t* have to be in absolute minutes (0 at 00:00 01 Jan). The and
in Sun positions calculated are in solar time, that is, maximun
solar zenit exactly at midday.
The generated information is stored in:
... | def get_sunpos(self, t, true_time=False):
"""
Computes the Sun positions for the *t* time vector.
*t* have to be in absolute minutes (0 at 00:00 01 Jan). The and
in Sun positions calculated are in solar time, that is, maximun
solar zenit exactly at midday.
... |
Computes the shadoing for the ``pyny.Space`` stored in
``.space`` for the time intervals and Sun positions stored in
``.arg_t`` and ``.sun_pos``, respectively.
The generated information is stored in:
* **.light_vor** (*ndarray (dtype=bool)*): Array with the
... | def compute_shadows(self):
"""
Computes the shadoing for the ``pyny.Space`` stored in
``.space`` for the time intervals and Sun positions stored in
``.arg_t`` and ``.sun_pos``, respectively.
The generated information is stored in:
* **.light_vor** (*... |
Assign the sum of ``.integral``\* to each sensible point in the
``pyny.Space`` for the intervals that the points are visible to
the Sun.
The generated information is stored in:
* **.proj_vor** (*ndarray*): ``.integral`` projected to the
Voronoi diagram.
... | def project_data(self):
'''
Assign the sum of ``.integral``\* to each sensible point in the
``pyny.Space`` for the intervals that the points are visible to
the Sun.
The generated information is stored in:
* **.proj_vor** (*ndarray*): ``.integral`` projected t... |
Voronoi diagram visualizations. There are three types:
1. **vor**: Voronoi diagram of the Solar Horizont.
2. **freq**: Frequency of Sun positions in t in the Voronoi
diagram of the Solar Horizont.
3. **data**: Accumulated time integral of the data projec... | def vor_plot(self, which='vor'):
"""
Voronoi diagram visualizations. There are three types:
1. **vor**: Voronoi diagram of the Solar Horizont.
2. **freq**: Frequency of Sun positions in t in the Voronoi
diagram of the Solar Horizont.
3.... |
Converts ``datetime`` objects lists into absolute minutes
vectors. It also can be used to generate absolute minutes vector
from a time interval (in minutes).
:param time_obj: ``datetime`` objects to convert into absolute
minutes.
:type time_obj: list of ``dat... | def to_minutes(time_obj = None, dt = None):
'''
Converts ``datetime`` objects lists into absolute minutes
vectors. It also can be used to generate absolute minutes vector
from a time interval (in minutes).
:param time_obj: ``datetime`` objects to convert into abso... |
Plots the exposure of the sensible points in a space to the data
and the Sun positions. It is required to previously compute the
shadowing.
If the computation has been made with a data timeseries, the plot
will have a colorbar. Units are accumulated kilounits*hour (for
... | def exposure_plot(self, places=-1, c_poly='default', c_holes='default',
s_sop=25, extra_height=0.1):
"""
Plots the exposure of the sensible points in a space to the data
and the Sun positions. It is required to previously compute the
shadowing.
... |
name: str or file or file-like or pathlib.Path
File to be opened | def open(name):
""""
name: str or file or file-like or pathlib.Path
File to be opened
"""
with builtins.open(name, mode='r') as fd:
data = json.load(fd)
return loads(data) |
Extract metadata from serialized file | def extract_db_info(self, obj, keys):
"""Extract metadata from serialized file"""
objl = self.convert_in(obj)
# FIXME: this is too complex
if isinstance(objl, self.__class__):
return objl.update_meta_info()
try:
with builtins.open(objl, mode='r') as fd:... |
Extract metadata from myself | def update_meta_info(self):
"""Extract metadata from myself"""
result = super(BaseStructuredCalibration, self).update_meta_info()
result['instrument'] = self.instrument
result['uuid'] = self.uuid
result['tags'] = self.tags
result['type'] = self.name()
minfo = se... |
Call a Gnuplot script, passing it arguments and
datasets.
Args:
scipt_name(str): The name of the Gnuplot script.
args_dict(dict): A dictionary of parameters to pass
to the script. The `key` is the name of the variable
that the `item` will be passed to the Gnuplot script... | def gnuplot(script_name, args_dict={}, data=[], silent=True):
'''
Call a Gnuplot script, passing it arguments and
datasets.
Args:
scipt_name(str): The name of the Gnuplot script.
args_dict(dict): A dictionary of parameters to pass
to the script. The `key` is the name of the... |
Function to produce a general 2D plot.
Args:
x (list): x points.
y (list): y points.
filename (str): Filename of the output image.
title (str): Title of the plot. Default is '' (no title).
x_label (str): x-axis label.
y_label (str): y-axis label. | def gnuplot_2d(x, y, filename, title='', x_label='', y_label=''):
'''
Function to produce a general 2D plot.
Args:
x (list): x points.
y (list): y points.
filename (str): Filename of the output image.
title (str): Title of the plot. Default is '' (no title).
x_label... |
Function to produce a general 3D plot from a 2D matrix.
Args:
z_matrix (list): 2D matrix.
filename (str): Filename of the output image.
title (str): Title of the plot. Default is '' (no title).
x_label (str): x-axis label.
y_label (str): y-axis label. | def gnuplot_3d_matrix(z_matrix, filename, title='', x_label='', y_label=''):
'''
Function to produce a general 3D plot from a 2D matrix.
Args:
z_matrix (list): 2D matrix.
filename (str): Filename of the output image.
title (str): Title of the plot. Default is '' (no title).
... |
Get reactions from folders.
Parameters
----------
skip: list of str
list of folders not to read
goto_reaction: str
Skip ahead to this metal
goto_reaction:
Skip ahead to this reacion | def read(self, skip=[], goto_metal=None, goto_reaction=None):
"""
Get reactions from folders.
Parameters
----------
skip: list of str
list of folders not to read
goto_reaction: str
Skip ahead to this metal
goto_reaction:
Skip a... |
Create empty dictionaries | def read_reaction(self, root):
folder_name = os.path.basename(root)
self.reaction, self.sites = ase_tools.get_reaction_from_folder(
folder_name) # reaction dict
self.stdout.write(
'----------- REACTION: {} --> {} --------------\n'
.format('+'.join(self.rea... |
Match adsorbate structures with reaction entries | def read_energies(self, root):
self.key_value_pairs_reaction = None
slab_structures = collect_structures(root)
if len(slab_structures) == 0:
self.raise_warning('No structure files in {root}: Skipping this folder'
.format(root=root))
return... |
Return an slice with a symmetric region around center. | def slice_create(center, block, start=0, stop=None):
'''Return an slice with a symmetric region around center.'''
do = coor_to_pix_1d(center - block)
up = coor_to_pix_1d(center + block)
l = max(start, do)
if stop is not None:
h = min(up + 1, stop)
else:
h = up + 1
return ... |
Create a region of size box, around a center in a image of shape. | def image_box(center, shape, box):
'''Create a region of size box, around a center in a image of shape.'''
return tuple(slice_create(c, b, stop=s)
for c, s, b in zip(center, shape, box)) |
Expand a slice on the start/stop limits | def expand_slice(s, a, b, start=0, stop=None):
'''Expand a slice on the start/stop limits'''
n1 = max(s.start - a, start)
n2 = s.stop + b
if stop is not None:
n2 = min(n2, stop)
return slice(n1, n2, 1) |
Apply expend_slice on a tuple of slices | def expand_region(tuple_of_s, a, b, start=0, stop=None):
'''Apply expend_slice on a tuple of slices'''
return tuple(expand_slice(s, a, b, start=start, stop=stop)
for s in tuple_of_s) |
Adapt obsres after file copy | def adapt_obsres(self, obsres):
"""Adapt obsres after file copy"""
_logger.debug('adapt observation result for work dir')
for f in obsres.images:
# Remove path components
f.filename = os.path.basename(f.filename)
return obsres |
Store the values of the completed task. | def store(self, completed_task, resultsdir):
"""Store the values of the completed task."""
with working_directory(resultsdir):
_logger.info('storing result')
return completed_task.store(self) |
Validate convertibility to internal representation
Returns
-------
bool
True if 'obj' matches the data type
Raises
-------
ValidationError
If the validation fails | def validate(self, obj):
"""Validate convertibility to internal representation
Returns
-------
bool
True if 'obj' matches the data type
Raises
-------
ValidationError
If the validation fails
"""
if not isinstance(obj, self.... |
Grant SELECT on public schema | def create_user(self, user, table_privileges=['ALL PRIVILEGES'],
schema_privileges=['ALL PRIVILEGES'],
row_limit=50000):
con = self.connection or self._connect()
cur = con.cursor()
cur.execute('CREATE SCHEMA {0};'.format(user))
# self._initialize(... |
Delete user and all data | def delete_user(self, user):
""" Delete user and all data"""
assert self.user == 'catroot' or self.user == 'postgres'
assert not user == 'public'
con = self.connection or self._connect()
cur = con.cursor()
cur.execute('DROP SCHEMA {user} CASCADE;'.format(user=user))
... |
Transfer dataset from one schema to another | def release(self, pub_ids=None, email=None, from_schema='upload',
to_schema='public'):
""" Transfer dataset from one schema to another"""
assert pub_ids or email,\
"Specify either pub_ids or email"
assert not (pub_ids and email),\
"Specify either pub_ids ... |
Check if a user owns a publication | def get_pub_id_owner(self, pub_id):
"""Check if a user owns a publication"""
con = self.connection or self._connect()
cur = con.cursor()
cur.execute(
"""SELECT distinct username from upload.reaction
WHERE pub_id = '{pub_id}'"""
.format(pub_id=pub_id))... |
Delete dataset from upload schema | def delete_publication(self, pub_id, schema='upload'):
""" Delete dataset from upload schema"""
if schema == 'upload':
user = 'upload_admin'
elif schema == 'public':
user = 'catroot'
if not self.user == 'catroot':
assert self.user == user, \
... |
Write to reaction_system tables | def write_reaction(self, value_dict):
con = self.connection or self._connect()
self._initialize(con)
cur = con.cursor()
ase_ids = value_dict['ase_ids']
energy_corrections = value_dict.get('energy_corrections', {})
key_list = get_key_list(start_index=1)
values = ... |
Will delete all data in schema. Only for test use! | def truncate_schema(self):
""" Will delete all data in schema. Only for test use!"""
assert self.server == 'localhost'
con = self.connection or self._connect()
self._initialize(con)
cur = con.cursor()
cur.execute('DELETE FROM publication;')
cur.execute('TRUNCATE... |
Transfer data from local sqlite3 .db file to the
catalysis-hub postgreSQL server
Parameters:
filename_sqlite: str
name of .db file
block_size: int (default 1000)
Number of atomic structures and reactions to write together
in each block.
start_... | def transfer(self, filename_sqlite, block_size=1000,
start_block=0, write_ase=True,
write_publication=True, write_reaction=True,
write_reaction_system=True, check=False):
""" Transfer data from local sqlite3 .db file to the
catalysis-hub postgreSQL serv... |
Call the stream's write method without linebreaks at line endings. | def write(self, *args, **kwargs):
"""
Call the stream's write method without linebreaks at line endings.
"""
return self.stream.write(ending="", *args, **kwargs) |
Initialize the 1D interpolation. | def _update(self):
"""Initialize the 1D interpolation."""
if self.strains.size and self.strains.size == self.values.size:
x = np.log(self.strains)
y = self.values
if x.size < 4:
self._interpolater = interp1d(
x,
... |
If nonlinear properties are specified. | def is_nonlinear(self):
"""If nonlinear properties are specified."""
return any(
isinstance(p, NonlinearProperty)
for p in [self.mod_reduc, self.damping]) |
minimum damping [decimal] | def _calc_damping_min(self):
"""minimum damping [decimal]"""
return ((0.8005 + 0.0129 * self._plas_index * self._ocr ** -0.1069) *
(self._stress_mean * KPA_TO_ATM)
** -0.2889 * (1 + 0.2919 * np.log(self._freq))) / 100 |
Compute the reference strain using Equation (6). | def _calc_strain_ref(x_3, x_3_mean):
"""Compute the reference strain using Equation (6)."""
b_9 = -1.41
b_10 = -0.950
return np.exp(b_9 + b_10 * (x_3 - x_3_mean)) / 100 |
Compute the shear modulus reduction using Equation (1). | def _calc_mod_reduc(self, strains, strain_ref, x_1, x_1_mean, x_2,
x_2_mean, x_3, x_3_mean):
"""Compute the shear modulus reduction using Equation (1)."""
ones = np.ones_like(strains)
# Predictor
x_4 = np.log(self._lab_consol_ratio) * ones
x = np.c_[ones,... |
Compute the damping ratio using Equation (16). | def _calc_damping(mod_reducs, x_2, x_2_mean, x_3, x_3_mean):
"""Compute the damping ratio using Equation (16)."""
# Mean values of the predictors
x_1_mean = -1.0
x_1 = np.log(np.log(1 / mod_reducs) + 0.103)
ones = np.ones_like(mod_reducs)
x = np.c_[ones, x_1, x_2, x_3, (... |
The relative error, in percent, between the two iterations. | def relative_error(self):
"""The relative error, in percent, between the two iterations.
"""
if self.previous is not None:
# FIXME
# Use the maximum strain value -- this is important for error
# calculation with frequency dependent properties
# pr... |
Create a copy of the layer. | def duplicate(cls, other):
"""Create a copy of the layer."""
return cls(other.soil_type, other.thickness, other.shear_vel) |
Strain-compatible damping. | def damping(self):
"""Strain-compatible damping."""
try:
value = self._damping.value
except AttributeError:
value = self._damping
return value |
Strain-compatible complex shear modulus [kN/m²]. | def comp_shear_mod(self):
"""Strain-compatible complex shear modulus [kN/m²].
"""
damping = self.damping
if COMP_MODULUS_MODEL == 'seed':
# Frequency independent model (Seed et al., 1970)
# Correct dissipated energy
# Incorrect shear modulus: G * \sqrt... |
Strain-compatible shear modulus [kN//m²]. | def shear_mod(self):
"""Strain-compatible shear modulus [kN//m²]."""
try:
value = self._shear_mod.value
except AttributeError:
value = self._shear_mod
return value |
Vertical stress from the top of the layer [kN//m²]. | def stress_vert(self, depth_within=0, effective=False):
"""Vertical stress from the top of the layer [kN//m²]."""
assert depth_within <= self.thickness
stress_vert = self._stress_vert + depth_within * self.unit_wt
if effective:
pore_pressure = self._profile.pore_pressure(self... |
Subdivide the layers to capture strain variation.
Parameters
----------
max_freq: float
Maximum frequency of interest [Hz].
wave_frac: float
Fraction of wavelength required. Typically 1/3 to 1/5.
Returns
-------
profile: Profile
... | def auto_discretize(self, max_freq=50., wave_frac=0.2):
"""Subdivide the layers to capture strain variation.
Parameters
----------
max_freq: float
Maximum frequency of interest [Hz].
wave_frac: float
Fraction of wavelength required. Typically 1/3 to 1/5.
... |
Create a Location for a specific depth.
Parameters
----------
wave_field: str
Wave field. See :class:`Location` for possible values.
depth: float, optional
Depth corresponding to the :class`Location` of interest. If
provided, then index is ignored.
... | def location(self, wave_field, depth=None, index=None):
"""Create a Location for a specific depth.
Parameters
----------
wave_field: str
Wave field. See :class:`Location` for possible values.
depth: float, optional
Depth corresponding to the :class`Locati... |
Calculate the time-average velocity.
Parameters
----------
depth: float
Depth over which the average velocity is computed.
Returns
-------
avg_vel: float
Time averaged velocity. | def time_average_vel(self, depth):
"""Calculate the time-average velocity.
Parameters
----------
depth: float
Depth over which the average velocity is computed.
Returns
-------
avg_vel: float
Time averaged velocity.
"""
de... |
Simplified Rayliegh velocity of the site.
This follows the simplifications proposed by Urzua et al. (2017)
Returns
-------
rayleigh_vel : float
Equivalent shear-wave velocity. | def simplified_rayliegh_vel(self):
"""Simplified Rayliegh velocity of the site.
This follows the simplifications proposed by Urzua et al. (2017)
Returns
-------
rayleigh_vel : float
Equivalent shear-wave velocity.
"""
# FIXME: What if last layer has ... |
Iterate over the varied thicknesses.
The layering is generated using a non-homogenous Poisson process. The
following routine is used to generate the layering. The rate
function, :math:`\lambda(t)`, is integrated from 0 to t to generate
cumulative rate function, :math:`\Lambda(t)`. This ... | def iter_thickness(self, depth_total):
"""Iterate over the varied thicknesses.
The layering is generated using a non-homogenous Poisson process. The
following routine is used to generate the layering. The rate
function, :math:`\lambda(t)`, is integrated from 0 to t to generate
c... |
Calculate the covariance matrix.
Parameters
----------
profile : site.Profile
Input site profile
Yields
------
covar : `class`:numpy.array
Covariance matrix | def _calc_covar_matrix(self, profile):
"""Calculate the covariance matrix.
Parameters
----------
profile : site.Profile
Input site profile
Yields
------
covar : `class`:numpy.array
Covariance matrix
"""
corr = self._calc_c... |
Compute the adjacent-layer correlations
Parameters
----------
profile : :class:`site.Profile`
Input site profile
Yields
------
corr : :class:`numpy.array`
Adjacent-layer correlations | def _calc_corr(self, profile):
"""Compute the adjacent-layer correlations
Parameters
----------
profile : :class:`site.Profile`
Input site profile
Yields
------
corr : :class:`numpy.array`
Adjacent-layer correlations
"""
d... |
Use generic model parameters based on site class.
Parameters
----------
site_class: str
Site classification. Possible options are:
* Geomatrix AB
* Geomatrix CD
* USGS AB
* USGS CD
* USGS A
* USGS B
... | def generic_model(cls, site_class, **kwds):
"""Use generic model parameters based on site class.
Parameters
----------
site_class: str
Site classification. Possible options are:
* Geomatrix AB
* Geomatrix CD
* USGS AB
* USG... |
Calculate the standard deviation as a function of G/G_max.
Equation 7.29 from Darendeli (2001).
Parameters
----------
mod_reduc : array_like
Modulus reduction values.
Returns
-------
std : :class:`numpy.ndarray`
Standard deviation. | def calc_std_mod_reduc(mod_reduc):
"""Calculate the standard deviation as a function of G/G_max.
Equation 7.29 from Darendeli (2001).
Parameters
----------
mod_reduc : array_like
Modulus reduction values.
Returns
-------
std : :class:`numpy.... |
Calculate the standard deviation as a function of damping in decimal.
Equation 7.30 from Darendeli (2001).
Parameters
----------
damping : array_like
Material damping values in decimal.
Returns
-------
std : :class:`numpy.ndarray`
Standa... | def calc_std_damping(damping):
"""Calculate the standard deviation as a function of damping in decimal.
Equation 7.30 from Darendeli (2001).
Parameters
----------
damping : array_like
Material damping values in decimal.
Returns
-------
std :... |
Append the ``element`` to the ``field`` of the record.
This method is smart: it does nothing if ``element`` is empty and
creates ``field`` if it does not exit yet.
Args:
:param field: the name of the field of the record to append to
:type field: string
:para... | def _append_to(self, field, element):
"""Append the ``element`` to the ``field`` of the record.
This method is smart: it does nothing if ``element`` is empty and
creates ``field`` if it does not exit yet.
Args:
:param field: the name of the field of the record to append to
... |
Add name variant.
Args:
:param name: name variant for the current author.
:type name: string | def add_name_variant(self, name):
"""Add name variant.
Args:
:param name: name variant for the current author.
:type name: string
"""
self._ensure_field('name', {})
self.obj['name'].setdefault('name_variants', []).append(name) |
Add native name.
Args:
:param name: native name for the current author.
:type name: string | def add_native_name(self, name):
"""Add native name.
Args:
:param name: native name for the current author.
:type name: string
"""
self._ensure_field('name', {})
self.obj['name'].setdefault('native_names', []).append(name) |
Add previous name.
Args:
:param name: previous name for the current author.
:type name: string | def add_previous_name(self, name):
"""Add previous name.
Args:
:param name: previous name for the current author.
:type name: string
"""
self._ensure_field('name', {})
self.obj['name'].setdefault('previous_names', []).append(name) |
Add email address.
Args:
:param email: email of the author.
:type email: string
:param hidden: if email is public or not.
:type hidden: boolean | def add_email_address(self, email, hidden=None):
"""Add email address.
Args:
:param email: email of the author.
:type email: string
:param hidden: if email is public or not.
:type hidden: boolean
"""
existing_emails = get_value(self.obj, ... |
Add a personal website.
Args:
:param url: url to the person's website.
:type url: string
:param description: short description of the website.
:type description: string | def add_url(self, url, description=None):
"""Add a personal website.
Args:
:param url: url to the person's website.
:type url: string
:param description: short description of the website.
:type description: string
"""
url = {
... |
Add an institution where the person works/worked.
Args:
:param institution: name of the institution.
:type institution: string
:param start_date: the date when the person joined the institution, in any format.
:type start_date: string
:param end_dat... | def add_institution(self, institution, start_date=None, end_date=None, rank=None, record=None, curated=False, current=False):
"""Add an institution where the person works/worked.
Args:
:param institution: name of the institution.
:type institution: string
:param sta... |
Add an experiment that the person worked on.
Args:
:param name: name of the experiment.
:type name: string
:param start_date: the date when the person started working on the experiment.
:type start_date: string
:param end_date: the date when the per... | def add_project(self, name, record=None, start_date=None, end_date=None, curated=False, current=False):
"""Add an experiment that the person worked on.
Args:
:param name: name of the experiment.
:type name: string
:param start_date: the date when the person started ... |
Add an advisor.
Args:
:param name: full name of the advisor.
:type name: string
:param ids: list with the IDs of the advisor.
:type ids: list
:param degree_type: one of the allowed types of degree the advisor helped with.
:type degree_ty... | def add_advisor(self, name, ids=None, degree_type=None, record=None, curated=False):
"""Add an advisor.
Args:
:param name: full name of the advisor.
:type name: string
:param ids: list with the IDs of the advisor.
:type ids: list
:param degr... |
Add a private note.
Args:
:param comment: comment about the author.
:type comment: string
:param source: the source of the comment.
:type source: string | def add_private_note(self, note, source=None):
"""Add a private note.
Args:
:param comment: comment about the author.
:type comment: string
:param source: the source of the comment.
:type source: string
"""
note = {
'value': n... |
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