def apply_config(self):
global VALUES
config_reload()
self.cmd = config_get("misc.cmd", str)
self.ip = config_get("misc.ip", str)
self.port = config_get("misc.port", int)
self.values = VALUES[self.cmd]
def work(self):
camera = picamera.PiCamera()
camera.hflip = config_get("raspberry_horizontal_flip")
camera.vflip = config_get("raspberry_vertical_flip")
camera.resolution = (config_get("raspberry_resolution_x"),
config_get("raspberry_resolution_y"))
camera.start_preview()
time.sleep(2)
stream = io.BytesIO()
released = True
try:
for notUsed in camera.capture_continuous(
stream,
format='jpeg',
resize=None,
quality=config_get("raspberry_base_quality")):
self.frame_cd.acquire()
released = False
self.frame = stream.getvalue()
self.frame_cd.notify_all()
self.frame_cd.release()
released = True
stream.seek(0)
stream.truncate()
if not self.keep_working:
break
finally:
camera.close()
if not released: self.frame_cd.release()
def work(self):
camera = picamera.PiCamera()
camera.hflip = config_get("raspberry_horizontal_flip")
camera.vflip = config_get("raspberry_vertical_flip")
camera.resolution = (
config_get("raspberry_resolution_x"),
config_get("raspberry_resolution_y")
)
camera.start_preview()
time.sleep(2)
stream = io.BytesIO()
released = True
try:
for notUsed in camera.capture_continuous(stream, format='jpeg', resize=None, quality=config_get("raspberry_base_quality")):
self.frame_cd.acquire()
released = False
self.frame = stream.getvalue()
self.frame_cd.notify_all()
self.frame_cd.release()
released = True
stream.seek(0)
stream.truncate()
if not self.keep_working:
break
finally:
camera.close()
if not released: self.frame_cd.release()
def getParentArgParse(args=None):
parser = argparse.ArgumentParser(add_help=False)
parser.add_argument('--binSize', '-bs',
help='Size of the bins in bp for the ouput '
'of the bigwig/bedgraph file',
metavar="INT bp",
type=int,
default=50)
parser.add_argument('--region', '-r',
help='Region of the genome to limit the operation '
'to - this is useful when testing parameters to '
'reduce the computing time. The format is '
'chr:start:end, for example --region chr10 or '
'--region chr10:456700:891000',
metavar="CHR:START:END",
required=False,
type=genomicRegion)
parser.add_argument('--numberOfProcessors', '-p',
help='Number of processors to use. Type "max/2" to '
'use half the maximun number of processors or "max" '
'to use all available processors.',
metavar="INT",
type=numberOfProcessors,
default=cfg.config_get('general',
'default_proc_number'),
required=False)
parser.add_argument('--verbose', '-v',
help='Set to see processing messages.',
action='store_true')
return parser
def test_config_get(self):
"""Test the most important function of the config module: config_get"""
# generate and set data
configuration = []
for key, value in self.testconfig.iteritems():
configuration += ["--" + key]
if value:
configuration += [str(value)]
config.set_data(configuration)
# check we can read back the data we set
config.config_get(('server', 'port'))
self.assertEqual(config.config_get(('server', 'port')), 6000,
"can't find argument values set by set_data")
self.assertEqual(
config.config_get("nonexisting", None), None,
"config_get doesn't return None on a nonexisting param")
def test_config_get(self):
"""Test the most important function of the config module: config_get"""
# generate and set data
configuration = []
for key, value in self.testconfig.iteritems():
configuration += ["--" + key]
if value:
configuration += [str(value)]
config.set_data(configuration)
# check we can read back the data we set
config.config_get(('server', 'port'))
self.assertEqual(config.config_get(('server', 'port')),
6000,
"can't find argument values set by set_data")
self.assertEqual(config.config_get("nonexisting", None),
None,
"config_get doesn't return None on a nonexisting param")
def initialize_app(self, argv):
self.LOG.debug('initialize_app')
logging.getLogger("requests").setLevel(logging.WARNING)
self._config = config_get(USER_CONFIG_PATH)
self._session = OxCliSession(self._config['url'],
self._config['user'],
self._config['password'])
self.LOG.debug('config and session ready')
def test_set_data_and_set_conf(self):
"""Test the set_data and set_conf functions"""
# generate and set data
configuration = []
for key, value in self.testconfig.iteritems():
configuration += ["--" + key]
if value:
configuration += [str(value)]
config.set_data(configuration)
# check we can read back the data we set
self.assertEqual(config.config_get(("server", "port")), 6000,
"can't find argument values set by set_data")
self.assertEqual(config.config_get(("logging", "verbose")), True,
"can't find argument values set by set_data")
# check that the system exits when we give unrecognized arguments
config.set_data("--some values --that --dont --exist".split())
self.assertRaises(SystemExit, config._set_conf)
def test():
from data_load.sql import HubbleBase
from config import config_parser, config_get
config = config_parser()
uri = config_get(config, 'HubbleConnection', 'uri')
session = start_session(uri, HubbleBase)
qm = QueryManager(session, datetime.now() - timedelta(days=7), datetime.now())
o = qm.query_parts()
print('done')
def test_set_data_and_set_conf(self):
"""Test the set_data and set_conf functions"""
# generate and set data
configuration = []
for key, value in self.testconfig.iteritems():
configuration += ["--" + key]
if value:
configuration += [str(value)]
config.set_data(configuration)
# check we can read back the data we set
self.assertEqual(config.config_get(("server","port")),
6000,
"can't find argument values set by set_data")
self.assertEqual(config.config_get(("logging", "verbose")),
True,
"can't find argument values set by set_data")
# check that the system exits when we give unrecognized arguments
config.set_data("--some values --that --dont --exist".split())
self.assertRaises(SystemExit, config._set_conf)
def mask(self, stft):
f1 = config_get("preprocess.mask_f1", float)
f2 = config_get("preprocess.mask_f2", float)
t1 = config_get("preprocess.mask_t1", float)
t2 = config_get("preprocess.mask_t2", float)
s = stft.shape
mask = np.ones(s)
for i in xrange(s[0]):
if i < float(t1) * s[0] or s[0] - i < float(t2) * s[0]:
mask[i] = 0
for i in xrange(s[1]):
if np.abs(i - (s[1] / 2)) < float(f1) * s[1]:
mask[:, i] = 0
if i < float(f2) * s[1] or s[1] - i < float(f2) * s[1]:
mask[:, i] = 0
return mask * stft
def preprocess(self, trace, debug=False):
s = trace
if self.stft:
s = stft(s, self.fft_len, self.fft_step, log=self.stft_log)
if config_get("preprocess.static_alignmet", bool):
s = self.static_alignment_stft(s)
if debug:
plot(s,
f0=cap.frequency,
samp_rate=cap.samp_rate,
fft_step=pre.fft_step,
title="Aligned Trace",
png="/tmp/aligned.png")
if config_get("preprocess.mask", bool):
s = self.mask(s)
return s
def mask(self, stft):
f1 = config_get("preprocess.mask_f1", float)
f2 = config_get("preprocess.mask_f2", float)
t1 = config_get("preprocess.mask_t1", float)
t2 = config_get("preprocess.mask_t2", float)
s = stft.shape
mask = np.ones(s)
for i in xrange(s[0]):
if i < float(t1)*s[0] or s[0]-i < float(t2)*s[0]:
mask[i] = 0
for i in xrange(s[1]):
if np.abs(i - (s[1] / 2)) < float(f1)*s[1]:
mask[:,i] = 0
if i < float(f2)*s[1] or s[1]-i < float(f2)*s[1]:
mask[:,i] = 0
return mask*stft
def __init__(self):
self.i = 0
self.tb = None
self.reference = None
self.do_read = False
self.config_reload()
self.demod_decimation = 1
self.trig_decimation = 100
if self.offline:
self.files = glob.glob(self.tracedir + "/*.cfile")
shuffle(self.files)
else:
self.trig_fifo = "/tmp/trig.fifo"
self.demod_fifo = "/tmp/demod.fifo"
log.debug("creating fifo")
self.bufflen = 1024
try:
os.unlink(self.trig_fifo)
os.unlink(self.demod_fifo)
except:
pass
os.mkfifo(self.trig_fifo)
os.mkfifo(self.demod_fifo)
#start recv_thread
self.queue = Queue(maxsize=1024)
self.recv_t = threading.Thread(target=self.read,
args=(self.queue, ))
self.recv_t.start()
#create top_block
top_block = imp.load_source("top_block", "grc/top_block.py")
self.tb = top_block.top_block()
self.tb.Start(True)
print "started"
self.tb_t = threading.Thread(target=self.tb.Wait)
self.tb_t.start()
log.debug("top_block created")
self.tb_configure()
log.debug("top_bilock configured")
dut = imp.load_source("dut", config_get("dut"))
self.dut = dut.dut()
if self.dump:
try:
os.makedirs(self.tracedir)
except:
pass
def bedGraphToBigWig(chromSizes, bedGraphPath, bigWigPath, sort=True):
"""
takes a bedgraph file, orders it and converts it to
a bigwig file using command line tools.
Will fail if the bedGraphToBigWig path changes.
"""
from tempfile import NamedTemporaryFile
from os import remove, system
# destination to save chromosome names and sizes
_file2 = NamedTemporaryFile(delete=False)
# bedGraph to bigwig requires the chromosome sizes to be
# saved into a file
for chrom, size in chromSizes:
_file2.write("{}\t{}\n".format(chrom, size))
_file2.close()
chrSizesFileName = _file2.name
if sort:
sort_cmd = cfg.config_get('external_tools', 'sort')
# temporary file to store sorted bedgraph file
_file = NamedTemporaryFile(delete=False)
tempFileName1 = _file.name
system("{} -k1,1 -k2,2n {} > {}".format(sort_cmd,
bedGraphPath, tempFileName1))
bedGraphPath = tempFileName1
bedgraph_to_bigwig = cfg.config_get('external_tools', 'bedgraph_to_bigwig')
system("{} {} {} {}".format(bedgraph_to_bigwig,
bedGraphPath, chrSizesFileName, bigWigPath))
if sort:
remove(tempFileName1)
remove(chrSizesFileName)
def preprocess(self, trace, debug=False):
s = trace
if self.stft:
s = stft(s, self.fft_len, self.fft_step, log=self.stft_log)
if debug:
plot(s, f0=cap.frequency, samp_rate=cap.samp_rate, fft_step=pre.fft_step, title="Aligned Trace")
if config_get("preprocess.mask", bool):
s = self.mask(s)
else:
s = np.abs(s)
return s
def getlogger():
log_path = config_get("logdir")
if not log_path:
print "log path can't find in config file'"
exit(1)
if not os.path.exists(os.path.dirname(log_path)):
os.makedirs(os.path.dirname(log_path))
logger = logging.getLogger()
logger.setLevel(logging.DEBUG)
if not logger.handlers:
handler = logging.handlers.TimedRotatingFileHandler(log_path, 'D')
# fmt = logging.Formatter(“%(asctime)s – %(pathname)s – %(filename)s – %(funcName)s – %(lineno)s – %(levelname)s – %(message)s”, “%Y-%m-%d %H:%M:%S”)
fmt = logging.Formatter(
"%(asctime)s – %(pathname)s – %(filename)s – %(funcName)s – %(lineno)s – %(levelname)s – %(message)s"
)
handler.setFormatter(fmt)
logger.addHandler(handler)
return logger
def center(self):
self.servo_write(self.panServoId, config_get("pan_center"))
self.servo_write(self.tiltServoId, config_get("tilt_center"))
# this block should be first if We want
# has section 'Main' on top of config file
from config import config_get
# config format: float, minutes
INTERVAL = int(float(config_get("Main", "break_interval", 15.0)) * 60)
# config format: int, seconds
PREPARING_TIME = int(config_get("Main", "preparing_time", 3))
if(PREPARING_TIME > INTERVAL):
exit("[ERROR] preparing_time can't be greater than break_interval")
if(PREPARING_TIME < 0):
exit("[ERROR] preparing_time can't be negative number")
from time import sleep
from ui.gtk.gtk_break_screen import GtkBreakScreen
from core.core import UsefulB
ui = GtkBreakScreen()
cor = UsefulB(ui)
while True:
sleep(INTERVAL - PREPARING_TIME)
if(PREPARING_TIME != 0):
ui.sendNotify("Get ready for a break after " +
str(PREPARING_TIME) + " seconds", PREPARING_TIME)
sleep(PREPARING_TIME)
# it will wait until problem is solved
cor.start()
def check_auth(username, password):
return username == config_get("auth_login") and password == config_get("auth_password")
def apply_config(self):
self.outdir = config_get("misc.outdir", str)
self.samp_rate = config_get("capture.samp_rate", int)
def left(self):
self.servo_write(self.panServoId, "+" + config_get("pan_step"))
def writeBedGraph(
bamOrBwFileList, outputFileName, fragmentLength,
func, funcArgs, tileSize=25, region=None, numberOfProcessors=None,
format="bedgraph", extendPairedEnds=True, zerosToNans=True,
smoothLength=0, fixed_step=False):
r"""
Given a list of bamfiles, a function and a function arguments,
this method writes a bedgraph file (or bigwig) file
for a partition of the genome into tiles of given size
and a value for each tile that corresponds to the given function
and that is related to the coverage underlying the tile.
>>> test = Tester()
>>> outFile = tempfile.NamedTemporaryFile()
>>> funcArgs = {'scaleFactor': 1.0}
>>> writeBedGraph([(test.bamFile1, 'bam')], outFile.name,
... 0, scaleCoverage, funcArgs, region='3R:0:200')
>>> open(outFile.name, 'r').readlines()
['3R\t100\t200\t1.0\n']
>>> outFile.close()
"""
bigwig_info = cfg.config_get('external_tools', 'bigwig_info')
bamHandlers = [openBam(indexedFile) for
indexedFile,
fileFormat in bamOrBwFileList if fileFormat == 'bam']
if len(bamHandlers):
genomeChunkLength = getGenomeChunkLength(bamHandlers, tileSize)
# check if both bam files correspond to the same species
# by comparing the chromosome names:
chromNamesAndSize = getCommonChrNames(bamHandlers, verbose=False)
else:
genomeChunkLength = int(10e6)
bigwigs = [fileName for fileName,
fileFormat in bamOrBwFileList if fileFormat == 'bigwig']
cCommon = []
chromNamesAndSize = {}
for bw in bigwigs:
inBlock = False
for line in os.popen(
"{} -chroms {}".format(bigwig_info, bw)).readlines():
if line[0:10] == "chromCount":
inBlock = True
continue
if line[0:5] == "bases":
break
if inBlock:
chromName, id, size = line.strip().split(" ")
size = int(size)
if chromName in chromNamesAndSize:
cCommon.append(chromName)
if chromNamesAndSize[chromName] != size:
print "\nWARNING\n" \
"Chromosome {} length reported in the " \
"bigwig files differ.\n{} for {}\n" \
"{} for {}.\n\nThe smallest " \
"length will be used".format(
chromName, chromNamesAndSize[chromName],
bigwigs[0], size, bigwigs[1])
chromNamesAndSize[chromName] = min(
chromNamesAndSize[chromName], size)
else:
chromNamesAndSize[chromName] = size
# get the list of common chromosome names and sizes
chromNamesAndSize = [(k, v) for k, v in chromNamesAndSize.iteritems()
if k in cCommon]
if region:
# in case a region is used, append the tilesize
region += ":{}".format(tileSize)
res = mapReduce.mapReduce((tileSize, fragmentLength, bamOrBwFileList,
func, funcArgs, extendPairedEnds, smoothLength,
zerosToNans, fixed_step),
writeBedGraph_wrapper,
chromNamesAndSize,
genomeChunkLength=genomeChunkLength,
region=region,
numberOfProcessors=numberOfProcessors)
# concatenate intermediary bedgraph files
outFile = open(outputFileName + ".bg", 'wb')
for tempFileName in res:
if tempFileName:
# concatenate all intermediate tempfiles into one
# bedgraph file
shutil.copyfileobj(open(tempFileName, 'rb'), outFile)
os.remove(tempFileName)
bedGraphFile = outFile.name
outFile.close()
if format == 'bedgraph':
os.rename(bedGraphFile, outputFileName)
if debug:
print "output file: %s" % (outputFileName)
else:
bedGraphToBigWig(
chromNamesAndSize, bedGraphFile, outputFileName, False)
if debug:
print "output file: %s" % (outputFileName)
os.remove(bedGraphFile)
def left(self):
self.servo_write(self.panServoId, "+" + config_get("pan_step"))
from datetime import datetime
from config import config_get, CONFIG_FOLDER_PATH
# config format: path
STAT_PATH = config_get("Stats", "file_path", str(CONFIG_FOLDER_PATH / "stats"))
class Stats:
def __init__(self):
time = datetime.now().strftime('%Y-%m-%d %H:%M:%S')
from os.path import isfile
newline = "\n" if isfile(STAT_PATH) else ""
self.write(newline + "--- Started at " + time + " ---", False)
def log_solving(self, task):
txt = self.construct_task_name(task)
# tag 'processing'
txt += "[~] "
txt += task.getTextSolving()
self.write(txt)
def log_wrong(self, task, ans):
txt = self.construct_task_name(task)
# tag 'wrong'
txt += "[-] "
txt += task.getTextWrong(ans)
self.write(txt)
def log_good(self, task):
txt = self.construct_task_name(task)
# tag 'good'
def config_reload(self):
config_reload()
#config
self.capture_frequency = config_get("capture.frequency", int)
self.capture_samp_rate = config_get("capture.samp_rate", int)
self.capture_gain = config_get("capture.gain", int)
self.offline = False
self.dump = False
#trigger
self.trigger_low_pass = config_get("trigger.low_pass", int)
self.trigger_frequency = config_get("trigger.frequency", int)
self.trigger_delay = config_get("trigger.delay", float)
self.trigger_pre = config_get("trigger.pre", float)
self.trigger_post = config_get("trigger.post", float)
#demod
self.demod_select = config_get("demod.select", list)
self.demod_frequency = config_get("demod.frequency", int)
self.demod_bandpass_low = config_get("demod.bandpass_low", int)
self.demod_bandpass_high = config_get("demod.bandpass_high", int)
self.demod_decimation = config_get("demod.decimation", int)
#stft
self.stft = config_get("preprocess.stft", bool)
self.stft_log = config_get("preprocess.stft_log", bool)
self.fft_len = config_get("preprocess.fft_len", int)
self.fft_step = config_get("preprocess.fft_step", int)
self.samp_rate = self.capture_samp_rate / self.demod_decimation
self.demod_bandpass_high = min(self.samp_rate / 2, self.demod_bandpass_high)
if self.demod_select[0] == 0:
self.demod_decimation = 1
self.frequency = self.capture_frequency
elif self.demod_select[0] == 1:
self.demod_decimation = 1
self.frequency = self.trigger_frequency
elif self.demod_select[0] == 2:
self.frequency = self.trigger_frequency
elif self.demod_select[0] == 3:
self.frequency = 0
def center(self):
self.servo_write(self.panServoId, config_get("pan_center"))
self.servo_write(self.tiltServoId, config_get("tilt_center"))
def apply_config(self):
config_reload()
self.port = config_get("misc.port", int)
def up(self):
self.servo_write(self.tiltServoId, "-" + config_get("tilt_step"))
def down(self):
self.servo_write(self.tiltServoId, "+" + config_get("tilt_step"))
def up(self):
self.servo_write(self.tiltServoId, "-" + config_get("tilt_step"))
def down(self):
self.servo_write(self.tiltServoId, "+" + config_get("tilt_step"))
def computeMatrixOptArgs(case=['scale-regions', 'reference-point'][0]):
parser = argparse.ArgumentParser(add_help=False)
optional = parser.add_argument_group('Optional arguments')
if case == 'scale-regions':
optional.add_argument('--regionBodyLength', '-m',
default=1000,
type=int,
help='Distance in bp to which all regions are '
'going to be fitted.')
optional.add_argument('--startLabel',
default='TSS',
help='Label shown in the plot for the start of '
'the region. Default is TSS (transcription '
'start site), but could be changed to anything, '
'e.g. "peak start".'
'Same for the --endLabel option. See below')
optional.add_argument('--endLabel',
default='TES',
help='Label shown in the plot for the region '
'end. Default is TES (transcription end site).')
optional.add_argument('--beforeRegionStartLength', '-b', '--upstream',
default=0,
type=int,
help='Distance upstream of the start site of '
'the regions defined in the region file. If the '
'regions are genes, this would be the distance '
'upstream of the transcription start site.')
optional.add_argument('--afterRegionStartLength', '-a', '--downstream',
default=0,
type=int,
help='Distance downstream of the end site '
'of the given regions. If the '
'regions are genes, this would be the distance '
'downstream of the transcription end site.')
elif case == 'reference-point':
optional.add_argument('--referencePoint',
default='TSS',
choices=['TSS', 'TES', 'center'],
help='The reference point for the plotting '
'could be either the region start (TSS), the '
'region end (TES) or the center of the region. ')
# set region body length to zero for reference point mode
optional.add_argument('--regionBodyLength', help=argparse.SUPPRESS,
default=0, type=int)
optional.add_argument('--beforeRegionStartLength', '-b', '--upstream',
default=500,
type=int,
metavar='INT bp',
help='Distance upstream of the reference-point '
'selected ',
required=True)
optional.add_argument('--afterRegionStartLength', '-a', '--downstream',
default=1500,
metavar='INT bp',
type=int,
help='Distance downstream of the '
'reference-point selected',
required=True)
optional.add_argument('--nanAfterEnd',
action='store_true',
help='If set, any values after the region end '
'are discarted. This is useful to visualize '
'the region end when not using the '
'scale-regions mode and when the reference-'
'point is set to the TSS')
optional.add_argument('--binSize', '-bs',
help='Length, in base pairs, of the non-overlapping '
'bin for averaging the score over the '
'regions length',
type=int,
default=10)
optional.add_argument('--sortRegions',
help='Whether the output file should present the '
'regions sorted. The default is to sort in '
'descending order based on '
'the mean value per region.',
choices=["descend", "ascend", "no"],
default='no')
optional.add_argument('--sortUsing',
help='Indicate which method should be used for '
'sorting. The value is computed for each row.',
choices=["mean", "median", "max", "min", "sum",
"region_length"],
default='mean')
optional.add_argument('--averageTypeBins',
default='mean',
choices=["mean", "median", "min",
"max", "std", "sum"],
help='Define the type of statistic that should be '
'used over the bin size range. The '
'options are: "mean", "median", "min", "max" and '
'"std". The default is "mean"')
optional.add_argument('--missingDataAsZero',
help='[only for bigwig input] Set to "yes", if '
'missing data should be indicated as zeros. Default '
'is to ignore such cases which will be depicted as '
'black areas in the heatmap. (see '
'--missingDataColor argument of the heatmapper '
'for additional options)',
action='store_true')
optional.add_argument('--skipZeros',
help='Whether regions with only scores of zero '
'should be included or not. Default is to include '
'them. ',
action='store_true')
optional.add_argument('--minThreshold',
default=None,
type=float,
help='Numeric value. Any region containing a '
'value that is equal or less than this numeric '
'value will be skipped. This is useful to skip, '
'for example, genes where the read count is zero '
'for any of the bins. This could be the result of '
'unmappable areas and can bias the overall results.')
optional.add_argument('--maxThreshold',
default=None,
type=float,
help='Numeric value. Any region containing a value '
'that is equal or higher that this numeric value '
'will be skipped. The maxThreshold is useful to '
'skip those few regions with very high read counts '
'(e.g. major satellites) that may bias the average '
'values.')
optional.add_argument('--verbose',
help='set to yes, to see Warning messages and '
'other information',
action='store_true')
optional.add_argument('--scale',
help='If set, all values are multiplied by '
'this number',
type=float,
default=1)
optional.add_argument('--numberOfProcessors', '-p',
help='Number of processors to use. Type "max/2" to '
'use half the maximun number of processors or "max" '
'to use all available processors.',
metavar="INT",
type=numberOfProcessors,
default=cfg.config_get('general',
'default_proc_number'),
required=False)
return parser
def right(self):
self.servo_write(self.panServoId, "-" + config_get("pan_step"))
def apply_config(self):
self.outdir = config_get("misc.outdir", str)
self.samp_rate = config_get("capture.samp_rate", int)
def config_reload(self):
config_reload()
#config
self.center_frequency = config_get("capture.center_frequency", int)
self.capture_samp_rate = config_get("capture.samp_rate", int)
self.capture_gain = config_get("capture.gain", int)
self.offline = False
self.dump = False
#trigger
self.trigger_frequency = config_get("capture.trigger_frequency", int)
self.trigger_delay = config_get("capture.delay", float)
self.trigger_execution_time = config_get("capture.execution_time",
float)
#demod
self.demod_select = config_get("capture.demod", int)
self.demod_frequency = config_get("capture.demod_frequency", int)
self.demod_lowpass = config_get("capture.demod_lowpass", int)
self.demod_bandpass_low = config_get("capture.demod_bandpass_low", int)
self.demod_bandpass_high = config_get("capture.demod_bandpass_high",
int)
#stft
self.stft = config_get("preprocess.stft", bool)
self.stft_log = config_get("preprocess.stft_log", bool)
self.fft_len = config_get("preprocess.fft_len", int)
self.fft_step = config_get("preprocess.fft_step", int)
def right(self):
self.servo_write(self.panServoId, "-" + config_get("pan_step"))
def apply_config(self):
config_reload()
self.cmd = config_get("misc.cmd", str)
self.ip = config_get("misc.ip", str)
self.port = config_get("misc.port", int)
self.test_value = n2hex(2**2048 - 1)
from pathlib import Path
BUILTIN_TASKS_FOLDER_PATH = str(
(Path(__file__).parent / "../../tasks").resolve())
from config import config_get
from ast import literal_eval
# config format: list of paths to folders with .py files that contains class 'Task'
TASKS_FOLDERS_PATHS = literal_eval(
config_get("Core", "tasks_folders_paths", [BUILTIN_TASKS_FOLDER_PATH]))
# check all elements in list is str
if not all(isinstance(x, str) for x in TASKS_FOLDERS_PATHS):
exit(
"'tasks_folders_paths' is list ONLY with strings\n(try wrap all elements to quotes)"
)
from glob import glob
py_files = []
for p in TASKS_FOLDERS_PATHS:
py_files += glob(p + "/*.py")
module_by_name_dict = {}
from importlib import util as import_util
for m in py_files:
# this is module file name (as file.py), not task name
m_name = m.split("/")[-1]
spec = import_util.spec_from_file_location(m_name, m)
m_exe = import_util.module_from_spec(spec)
spec.loader.exec_module(m_exe)
task_name = m_exe.TASK_NAME
import discord
import sqlalchemy
import re
from config import config_get
from db import Session, reset_db, Message
reset_db()
s = Session()
config = config_get()
def all(iterable, func):
for x in iterable:
if not func(x):
return False
return True
def strip(iterable):
for x in iterable:
yield x.strip()
class R9kBot(discord.Client):
async def on_ready(self):
print('Logged on as', self.user)
async def on_message(self, message):
if message.author == self.user:
def apply_config(self):
config_reload()
self.port = config_get("misc.port", int)
