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tariqdaouda/pyGeno | pyGeno/tools/BinarySequence.py | BinarySequence.decode | def decode(self, binSequence):
"""decodes a binary sequence to return a string"""
try:
binSeq = iter(binSequence[0])
except TypeError, te:
binSeq = binSequence
ret = ''
for b in binSeq :
ch = ''
for c in self.charToBin :
if b & self.forma[self.charToBin[c]] > 0 :
ch += c +'/'
if ch == '' :
raise KeyError('Key %d unkowom, bad format' % b)
ret += ch[:-1]
return ret | python | def decode(self, binSequence):
"""decodes a binary sequence to return a string"""
try:
binSeq = iter(binSequence[0])
except TypeError, te:
binSeq = binSequence
ret = ''
for b in binSeq :
ch = ''
for c in self.charToBin :
if b & self.forma[self.charToBin[c]] > 0 :
ch += c +'/'
if ch == '' :
raise KeyError('Key %d unkowom, bad format' % b)
ret += ch[:-1]
return ret | [
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tariqdaouda/pyGeno | pyGeno/tools/parsers/VCFTools.py | VCFFile.parse | def parse(self, filename, gziped = False, stream = False) :
"""opens a file"""
self.stream = stream
if gziped :
self.f = gzip.open(filename)
else :
self.f = open(filename)
self.filename = filename
self.gziped = gziped
lineId = 0
inLegend = True
while inLegend :
ll = self.f.readline()
l = ll.replace('\r', '\n').replace('\n', '')
if l[:2] == '##' :
eqPos = l.find('=')
key = l[2:eqPos]
values = l[eqPos+1:].strip()
if l[eqPos+1] != '<' :
self.meta[key] = values
else :
if key not in self.meta :
self.meta[key] = {}
svalues = l[eqPos+2:-1].split(',') #remove the < and > that surounf the string
idKey = svalues[0].split('=')[1]
self.meta[key][idKey] = {}
i = 1
for v in svalues[1:] :
sv = v.split("=")
field = sv[0]
value = sv[1]
if field.lower() == 'description' :
self.meta[key][idKey][field] = ','.join(svalues[i:])[len(field)+2:-1]
break
self.meta[key][idKey][field] = value
i += 1
elif l[:6] == '#CHROM': #we are in legend
sl = l.split('\t')
for i in range(len(sl)) :
self.legend[sl[i]] = i
self.dnegel[i] = sl[i]
break
lineId += 1
if not stream :
self.lines = self.f.readlines()
self.f.close() | python | def parse(self, filename, gziped = False, stream = False) :
"""opens a file"""
self.stream = stream
if gziped :
self.f = gzip.open(filename)
else :
self.f = open(filename)
self.filename = filename
self.gziped = gziped
lineId = 0
inLegend = True
while inLegend :
ll = self.f.readline()
l = ll.replace('\r', '\n').replace('\n', '')
if l[:2] == '##' :
eqPos = l.find('=')
key = l[2:eqPos]
values = l[eqPos+1:].strip()
if l[eqPos+1] != '<' :
self.meta[key] = values
else :
if key not in self.meta :
self.meta[key] = {}
svalues = l[eqPos+2:-1].split(',') #remove the < and > that surounf the string
idKey = svalues[0].split('=')[1]
self.meta[key][idKey] = {}
i = 1
for v in svalues[1:] :
sv = v.split("=")
field = sv[0]
value = sv[1]
if field.lower() == 'description' :
self.meta[key][idKey][field] = ','.join(svalues[i:])[len(field)+2:-1]
break
self.meta[key][idKey][field] = value
i += 1
elif l[:6] == '#CHROM': #we are in legend
sl = l.split('\t')
for i in range(len(sl)) :
self.legend[sl[i]] = i
self.dnegel[i] = sl[i]
break
lineId += 1
if not stream :
self.lines = self.f.readlines()
self.f.close() | [
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appknox/pyaxmlparser | pyaxmlparser/stringblock.py | StringBlock._decode8 | def _decode8(self, offset):
"""
Decode an UTF-8 String at the given offset
:param offset: offset of the string inside the data
:return: str
"""
# UTF-8 Strings contain two lengths, as they might differ:
# 1) the UTF-16 length
str_len, skip = self._decode_length(offset, 1)
offset += skip
# 2) the utf-8 string length
encoded_bytes, skip = self._decode_length(offset, 1)
offset += skip
data = self.m_charbuff[offset: offset + encoded_bytes]
assert self.m_charbuff[offset + encoded_bytes] == 0, \
"UTF-8 String is not null terminated! At offset={}".format(offset)
return self._decode_bytes(data, 'utf-8', str_len) | python | def _decode8(self, offset):
"""
Decode an UTF-8 String at the given offset
:param offset: offset of the string inside the data
:return: str
"""
# UTF-8 Strings contain two lengths, as they might differ:
# 1) the UTF-16 length
str_len, skip = self._decode_length(offset, 1)
offset += skip
# 2) the utf-8 string length
encoded_bytes, skip = self._decode_length(offset, 1)
offset += skip
data = self.m_charbuff[offset: offset + encoded_bytes]
assert self.m_charbuff[offset + encoded_bytes] == 0, \
"UTF-8 String is not null terminated! At offset={}".format(offset)
return self._decode_bytes(data, 'utf-8', str_len) | [
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appknox/pyaxmlparser | pyaxmlparser/stringblock.py | StringBlock._decode16 | def _decode16(self, offset):
"""
Decode an UTF-16 String at the given offset
:param offset: offset of the string inside the data
:return: str
"""
str_len, skip = self._decode_length(offset, 2)
offset += skip
# The len is the string len in utf-16 units
encoded_bytes = str_len * 2
data = self.m_charbuff[offset: offset + encoded_bytes]
assert self.m_charbuff[offset + encoded_bytes:offset + encoded_bytes + 2] == b"\x00\x00", \
"UTF-16 String is not null terminated! At offset={}".format(offset)
return self._decode_bytes(data, 'utf-16', str_len) | python | def _decode16(self, offset):
"""
Decode an UTF-16 String at the given offset
:param offset: offset of the string inside the data
:return: str
"""
str_len, skip = self._decode_length(offset, 2)
offset += skip
# The len is the string len in utf-16 units
encoded_bytes = str_len * 2
data = self.m_charbuff[offset: offset + encoded_bytes]
assert self.m_charbuff[offset + encoded_bytes:offset + encoded_bytes + 2] == b"\x00\x00", \
"UTF-16 String is not null terminated! At offset={}".format(offset)
return self._decode_bytes(data, 'utf-16', str_len) | [
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appknox/pyaxmlparser | pyaxmlparser/stringblock.py | StringBlock._decode_length | def _decode_length(self, offset, sizeof_char):
"""
Generic Length Decoding at offset of string
The method works for both 8 and 16 bit Strings.
Length checks are enforced:
* 8 bit strings: maximum of 0x7FFF bytes (See
http://androidxref.com/9.0.0_r3/xref/frameworks/base/libs/androidfw/ResourceTypes.cpp#692)
* 16 bit strings: maximum of 0x7FFFFFF bytes (See
http://androidxref.com/9.0.0_r3/xref/frameworks/base/libs/androidfw/ResourceTypes.cpp#670)
:param offset: offset into the string data section of the beginning of
the string
:param sizeof_char: number of bytes per char (1 = 8bit, 2 = 16bit)
:returns: tuple of (length, read bytes)
"""
sizeof_2chars = sizeof_char << 1
fmt = "<2{}".format('B' if sizeof_char == 1 else 'H')
highbit = 0x80 << (8 * (sizeof_char - 1))
length1, length2 = unpack(fmt, self.m_charbuff[offset:(offset + sizeof_2chars)])
if (length1 & highbit) != 0:
length = ((length1 & ~highbit) << (8 * sizeof_char)) | length2
size = sizeof_2chars
else:
length = length1
size = sizeof_char
if sizeof_char == 1:
assert length <= 0x7FFF, "length of UTF-8 string is too large! At offset={}".format(offset)
else:
assert length <= 0x7FFFFFFF, "length of UTF-16 string is too large! At offset={}".format(offset)
return length, size | python | def _decode_length(self, offset, sizeof_char):
"""
Generic Length Decoding at offset of string
The method works for both 8 and 16 bit Strings.
Length checks are enforced:
* 8 bit strings: maximum of 0x7FFF bytes (See
http://androidxref.com/9.0.0_r3/xref/frameworks/base/libs/androidfw/ResourceTypes.cpp#692)
* 16 bit strings: maximum of 0x7FFFFFF bytes (See
http://androidxref.com/9.0.0_r3/xref/frameworks/base/libs/androidfw/ResourceTypes.cpp#670)
:param offset: offset into the string data section of the beginning of
the string
:param sizeof_char: number of bytes per char (1 = 8bit, 2 = 16bit)
:returns: tuple of (length, read bytes)
"""
sizeof_2chars = sizeof_char << 1
fmt = "<2{}".format('B' if sizeof_char == 1 else 'H')
highbit = 0x80 << (8 * (sizeof_char - 1))
length1, length2 = unpack(fmt, self.m_charbuff[offset:(offset + sizeof_2chars)])
if (length1 & highbit) != 0:
length = ((length1 & ~highbit) << (8 * sizeof_char)) | length2
size = sizeof_2chars
else:
length = length1
size = sizeof_char
if sizeof_char == 1:
assert length <= 0x7FFF, "length of UTF-8 string is too large! At offset={}".format(offset)
else:
assert length <= 0x7FFFFFFF, "length of UTF-16 string is too large! At offset={}".format(offset)
return length, size | [
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* 16 bit strings: maximum of 0x7FFFFFF bytes (See
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appknox/pyaxmlparser | pyaxmlparser/core.py | APK._apk_analysis | def _apk_analysis(self):
"""
Run analysis on the APK file.
This method is usually called by __init__ except if skip_analysis is False.
It will then parse the AndroidManifest.xml and set all fields in the APK class which can be
extracted from the Manifest.
"""
i = "AndroidManifest.xml"
try:
manifest_data = self.zip.read(i)
except KeyError:
log.warning("Missing AndroidManifest.xml. Is this an APK file?")
else:
ap = AXMLPrinter(manifest_data)
if not ap.is_valid():
log.error("Error while parsing AndroidManifest.xml - is the file valid?")
return
self.axml[i] = ap
self.xml[i] = self.axml[i].get_xml_obj()
if self.axml[i].is_packed():
log.warning("XML Seems to be packed, operations on the AndroidManifest.xml might fail.")
if self.xml[i] is not None:
if self.xml[i].tag != "manifest":
log.error("AndroidManifest.xml does not start with a <manifest> tag! Is this a valid APK?")
return
self.package = self.get_attribute_value("manifest", "package")
self.androidversion["Code"] = self.get_attribute_value("manifest", "versionCode")
self.androidversion["Name"] = self.get_attribute_value("manifest", "versionName")
permission = list(self.get_all_attribute_value("uses-permission", "name"))
self.permissions = list(set(self.permissions + permission))
for uses_permission in self.find_tags("uses-permission"):
self.uses_permissions.append([
self.get_value_from_tag(uses_permission, "name"),
self._get_permission_maxsdk(uses_permission)
])
# getting details of the declared permissions
for d_perm_item in self.find_tags('permission'):
d_perm_name = self._get_res_string_value(
str(self.get_value_from_tag(d_perm_item, "name")))
d_perm_label = self._get_res_string_value(
str(self.get_value_from_tag(d_perm_item, "label")))
d_perm_description = self._get_res_string_value(
str(self.get_value_from_tag(d_perm_item, "description")))
d_perm_permissionGroup = self._get_res_string_value(
str(self.get_value_from_tag(d_perm_item, "permissionGroup")))
d_perm_protectionLevel = self._get_res_string_value(
str(self.get_value_from_tag(d_perm_item, "protectionLevel")))
d_perm_details = {
"label": d_perm_label,
"description": d_perm_description,
"permissionGroup": d_perm_permissionGroup,
"protectionLevel": d_perm_protectionLevel,
}
self.declared_permissions[d_perm_name] = d_perm_details
self.valid_apk = True | python | def _apk_analysis(self):
"""
Run analysis on the APK file.
This method is usually called by __init__ except if skip_analysis is False.
It will then parse the AndroidManifest.xml and set all fields in the APK class which can be
extracted from the Manifest.
"""
i = "AndroidManifest.xml"
try:
manifest_data = self.zip.read(i)
except KeyError:
log.warning("Missing AndroidManifest.xml. Is this an APK file?")
else:
ap = AXMLPrinter(manifest_data)
if not ap.is_valid():
log.error("Error while parsing AndroidManifest.xml - is the file valid?")
return
self.axml[i] = ap
self.xml[i] = self.axml[i].get_xml_obj()
if self.axml[i].is_packed():
log.warning("XML Seems to be packed, operations on the AndroidManifest.xml might fail.")
if self.xml[i] is not None:
if self.xml[i].tag != "manifest":
log.error("AndroidManifest.xml does not start with a <manifest> tag! Is this a valid APK?")
return
self.package = self.get_attribute_value("manifest", "package")
self.androidversion["Code"] = self.get_attribute_value("manifest", "versionCode")
self.androidversion["Name"] = self.get_attribute_value("manifest", "versionName")
permission = list(self.get_all_attribute_value("uses-permission", "name"))
self.permissions = list(set(self.permissions + permission))
for uses_permission in self.find_tags("uses-permission"):
self.uses_permissions.append([
self.get_value_from_tag(uses_permission, "name"),
self._get_permission_maxsdk(uses_permission)
])
# getting details of the declared permissions
for d_perm_item in self.find_tags('permission'):
d_perm_name = self._get_res_string_value(
str(self.get_value_from_tag(d_perm_item, "name")))
d_perm_label = self._get_res_string_value(
str(self.get_value_from_tag(d_perm_item, "label")))
d_perm_description = self._get_res_string_value(
str(self.get_value_from_tag(d_perm_item, "description")))
d_perm_permissionGroup = self._get_res_string_value(
str(self.get_value_from_tag(d_perm_item, "permissionGroup")))
d_perm_protectionLevel = self._get_res_string_value(
str(self.get_value_from_tag(d_perm_item, "protectionLevel")))
d_perm_details = {
"label": d_perm_label,
"description": d_perm_description,
"permissionGroup": d_perm_permissionGroup,
"protectionLevel": d_perm_protectionLevel,
}
self.declared_permissions[d_perm_name] = d_perm_details
self.valid_apk = True | [
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appknox/pyaxmlparser | pyaxmlparser/core.py | APK.is_multidex | def is_multidex(self):
"""
Test if the APK has multiple DEX files
:return: True if multiple dex found, otherwise False
"""
dexre = re.compile("^classes(\d+)?.dex$")
return len([instance for instance in self.get_files() if dexre.search(instance)]) > 1 | python | def is_multidex(self):
"""
Test if the APK has multiple DEX files
:return: True if multiple dex found, otherwise False
"""
dexre = re.compile("^classes(\d+)?.dex$")
return len([instance for instance in self.get_files() if dexre.search(instance)]) > 1 | [
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appknox/pyaxmlparser | pyaxmlparser/core.py | APK._format_value | def _format_value(self, value):
"""
Format a value with packagename, if not already set
:param value:
:return:
"""
if len(value) > 0:
if value[0] == ".":
value = self.package + value
else:
v_dot = value.find(".")
if v_dot == 0:
value = self.package + "." + value
elif v_dot == -1:
value = self.package + "." + value
return value | python | def _format_value(self, value):
"""
Format a value with packagename, if not already set
:param value:
:return:
"""
if len(value) > 0:
if value[0] == ".":
value = self.package + value
else:
v_dot = value.find(".")
if v_dot == 0:
value = self.package + "." + value
elif v_dot == -1:
value = self.package + "." + value
return value | [
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] | 8ffe43e81a534f42c3620f3c1e3c6c0181a066bd | https://github.com/appknox/pyaxmlparser/blob/8ffe43e81a534f42c3620f3c1e3c6c0181a066bd/pyaxmlparser/core.py#L633-L649 | train | 54,307 |
appknox/pyaxmlparser | pyaxmlparser/axmlparser.py | AXMLParser.getAttributeName | def getAttributeName(self, index):
"""
Returns the String which represents the attribute name
"""
offset = self._get_attribute_offset(index)
name = self.m_attributes[offset + const.ATTRIBUTE_IX_NAME]
res = self.sb[name]
# If the result is a (null) string, we need to look it up.
if not res:
attr = self.m_resourceIDs[name]
if attr in public.SYSTEM_RESOURCES['attributes']['inverse']:
res = 'android:' + public.SYSTEM_RESOURCES['attributes']['inverse'][attr]
else:
# Attach the HEX Number, so for multiple missing attributes we do not run
# into problems.
res = 'android:UNKNOWN_SYSTEM_ATTRIBUTE_{:08x}'.format(attr)
return res | python | def getAttributeName(self, index):
"""
Returns the String which represents the attribute name
"""
offset = self._get_attribute_offset(index)
name = self.m_attributes[offset + const.ATTRIBUTE_IX_NAME]
res = self.sb[name]
# If the result is a (null) string, we need to look it up.
if not res:
attr = self.m_resourceIDs[name]
if attr in public.SYSTEM_RESOURCES['attributes']['inverse']:
res = 'android:' + public.SYSTEM_RESOURCES['attributes']['inverse'][attr]
else:
# Attach the HEX Number, so for multiple missing attributes we do not run
# into problems.
res = 'android:UNKNOWN_SYSTEM_ATTRIBUTE_{:08x}'.format(attr)
return res | [
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appknox/pyaxmlparser | pyaxmlparser/axmlparser.py | AXMLParser.getAttributeValueType | def getAttributeValueType(self, index):
"""
Return the type of the attribute at the given index
:param index: index of the attribute
"""
offset = self._get_attribute_offset(index)
return self.m_attributes[offset + const.ATTRIBUTE_IX_VALUE_TYPE] | python | def getAttributeValueType(self, index):
"""
Return the type of the attribute at the given index
:param index: index of the attribute
"""
offset = self._get_attribute_offset(index)
return self.m_attributes[offset + const.ATTRIBUTE_IX_VALUE_TYPE] | [
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appknox/pyaxmlparser | pyaxmlparser/axmlparser.py | AXMLParser.getAttributeValueData | def getAttributeValueData(self, index):
"""
Return the data of the attribute at the given index
:param index: index of the attribute
"""
offset = self._get_attribute_offset(index)
return self.m_attributes[offset + const.ATTRIBUTE_IX_VALUE_DATA] | python | def getAttributeValueData(self, index):
"""
Return the data of the attribute at the given index
:param index: index of the attribute
"""
offset = self._get_attribute_offset(index)
return self.m_attributes[offset + const.ATTRIBUTE_IX_VALUE_DATA] | [
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Kyria/EsiPy | esipy/utils.py | make_cache_key | def make_cache_key(request):
""" Generate a cache key from request object data """
headers = frozenset(request._p['header'].items())
path = frozenset(request._p['path'].items())
query = frozenset(request._p['query'])
return (request.url, headers, path, query) | python | def make_cache_key(request):
""" Generate a cache key from request object data """
headers = frozenset(request._p['header'].items())
path = frozenset(request._p['path'].items())
query = frozenset(request._p['query'])
return (request.url, headers, path, query) | [
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Kyria/EsiPy | esipy/utils.py | check_cache | def check_cache(cache):
""" check if a cache fits esipy needs or not """
if isinstance(cache, BaseCache):
return cache
elif cache is False:
return DictCache()
elif cache is None:
return DummyCache()
else:
raise ValueError('Provided cache must implement BaseCache') | python | def check_cache(cache):
""" check if a cache fits esipy needs or not """
if isinstance(cache, BaseCache):
return cache
elif cache is False:
return DictCache()
elif cache is None:
return DummyCache()
else:
raise ValueError('Provided cache must implement BaseCache') | [
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Kyria/EsiPy | esipy/utils.py | get_cache_time_left | def get_cache_time_left(expires_header):
""" return the time left in second for an expires header """
epoch = datetime(1970, 1, 1)
# this date is ALWAYS in UTC (RFC 7231)
expire = (
datetime(
*parsedate(expires_header)[:6]
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now = (datetime.utcnow() - epoch).total_seconds()
return int(expire) - int(now) | python | def get_cache_time_left(expires_header):
""" return the time left in second for an expires header """
epoch = datetime(1970, 1, 1)
# this date is ALWAYS in UTC (RFC 7231)
expire = (
datetime(
*parsedate(expires_header)[:6]
) - epoch
).total_seconds()
now = (datetime.utcnow() - epoch).total_seconds()
return int(expire) - int(now) | [
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Kyria/EsiPy | esipy/app.py | EsiApp.__get_or_create_app | def __get_or_create_app(self, url, cache_key):
""" Get the app from cache or generate a new one if required
Because app object doesn't have etag/expiry, we have to make
a head() call before, to have these informations first... """
headers = {"Accept": "application/json"}
app_url = '%s?datasource=%s' % (url, self.datasource)
cached = self.cache.get(cache_key, (None, None, 0))
if cached is None or len(cached) != 3:
self.cache.invalidate(cache_key)
cached_app, cached_headers, cached_expiry = (cached, None, 0)
else:
cached_app, cached_headers, cached_expiry = cached
if cached_app is not None and cached_headers is not None:
# we didn't set custom expire, use header expiry
expires = cached_headers.get('expires', None)
cache_timeout = -1
if self.expire is None and expires is not None:
cache_timeout = get_cache_time_left(
cached_headers['expires']
)
if cache_timeout >= 0:
return cached_app
# we set custom expire, check this instead
else:
if self.expire == 0 or cached_expiry >= time.time():
return cached_app
# if we have etags, add the header to use them
etag = cached_headers.get('etag', None)
if etag is not None:
headers['If-None-Match'] = etag
# if nothing makes us use the cache, invalidate it
if ((expires is None or cache_timeout < 0 or
cached_expiry < time.time()) and etag is None):
self.cache.invalidate(cache_key)
# set timeout value in case we have to cache it later
timeout = 0
if self.expire is not None and self.expire > 0:
timeout = time.time() + self.expire
# we are here, we know we have to make a head call...
res = requests.head(app_url, headers=headers)
if res.status_code == 304 and cached_app is not None:
self.cache.set(
cache_key,
(cached_app, res.headers, timeout)
)
return cached_app
# ok, cache is not accurate, make the full stuff
app = App.create(app_url)
if self.caching:
self.cache.set(cache_key, (app, res.headers, timeout))
return app | python | def __get_or_create_app(self, url, cache_key):
""" Get the app from cache or generate a new one if required
Because app object doesn't have etag/expiry, we have to make
a head() call before, to have these informations first... """
headers = {"Accept": "application/json"}
app_url = '%s?datasource=%s' % (url, self.datasource)
cached = self.cache.get(cache_key, (None, None, 0))
if cached is None or len(cached) != 3:
self.cache.invalidate(cache_key)
cached_app, cached_headers, cached_expiry = (cached, None, 0)
else:
cached_app, cached_headers, cached_expiry = cached
if cached_app is not None and cached_headers is not None:
# we didn't set custom expire, use header expiry
expires = cached_headers.get('expires', None)
cache_timeout = -1
if self.expire is None and expires is not None:
cache_timeout = get_cache_time_left(
cached_headers['expires']
)
if cache_timeout >= 0:
return cached_app
# we set custom expire, check this instead
else:
if self.expire == 0 or cached_expiry >= time.time():
return cached_app
# if we have etags, add the header to use them
etag = cached_headers.get('etag', None)
if etag is not None:
headers['If-None-Match'] = etag
# if nothing makes us use the cache, invalidate it
if ((expires is None or cache_timeout < 0 or
cached_expiry < time.time()) and etag is None):
self.cache.invalidate(cache_key)
# set timeout value in case we have to cache it later
timeout = 0
if self.expire is not None and self.expire > 0:
timeout = time.time() + self.expire
# we are here, we know we have to make a head call...
res = requests.head(app_url, headers=headers)
if res.status_code == 304 and cached_app is not None:
self.cache.set(
cache_key,
(cached_app, res.headers, timeout)
)
return cached_app
# ok, cache is not accurate, make the full stuff
app = App.create(app_url)
if self.caching:
self.cache.set(cache_key, (app, res.headers, timeout))
return app | [
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Kyria/EsiPy | esipy/app.py | EsiApp.clear_cached_endpoints | def clear_cached_endpoints(self, prefix=None):
""" Invalidate all cached endpoints, meta included
Loop over all meta endpoints to generate all cache key the
invalidate each of them. Doing it this way will prevent the
app not finding keys as the user may change its prefixes
Meta endpoint will be updated upon next call.
:param: prefix the prefix for the cache key (default is cache_prefix)
"""
prefix = prefix if prefix is not None else self.cache_prefix
for endpoint in self.app.op.values():
cache_key = '%s:app:%s' % (prefix, endpoint.url)
self.cache.invalidate(cache_key)
self.cache.invalidate('%s:app:meta_swagger_url' % self.cache_prefix)
self.app = None | python | def clear_cached_endpoints(self, prefix=None):
""" Invalidate all cached endpoints, meta included
Loop over all meta endpoints to generate all cache key the
invalidate each of them. Doing it this way will prevent the
app not finding keys as the user may change its prefixes
Meta endpoint will be updated upon next call.
:param: prefix the prefix for the cache key (default is cache_prefix)
"""
prefix = prefix if prefix is not None else self.cache_prefix
for endpoint in self.app.op.values():
cache_key = '%s:app:%s' % (prefix, endpoint.url)
self.cache.invalidate(cache_key)
self.cache.invalidate('%s:app:meta_swagger_url' % self.cache_prefix)
self.app = None | [
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Kyria/EsiPy | esipy/cache.py | _hash | def _hash(data):
""" generate a hash from data object to be used as cache key """
hash_algo = hashlib.new('md5')
hash_algo.update(pickle.dumps(data))
# prefix allows possibility of multiple applications
# sharing same keyspace
return 'esi_' + hash_algo.hexdigest() | python | def _hash(data):
""" generate a hash from data object to be used as cache key """
hash_algo = hashlib.new('md5')
hash_algo.update(pickle.dumps(data))
# prefix allows possibility of multiple applications
# sharing same keyspace
return 'esi_' + hash_algo.hexdigest() | [
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mjirik/imcut | imcut/models.py | Model3D.fit_from_image | def fit_from_image(self, data, voxelsize, seeds, unique_cls):
"""
This Method allows computes feature vector and train model.
:cls: list of index number of requested classes in seeds
"""
fvs, clsselected = self.features_from_image(data, voxelsize, seeds, unique_cls)
self.fit(fvs, clsselected) | python | def fit_from_image(self, data, voxelsize, seeds, unique_cls):
"""
This Method allows computes feature vector and train model.
:cls: list of index number of requested classes in seeds
"""
fvs, clsselected = self.features_from_image(data, voxelsize, seeds, unique_cls)
self.fit(fvs, clsselected) | [
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mjirik/imcut | imcut/models.py | Model3D.save | def save(self, filename):
"""
Save model to pickle file. External feature function is not stored
"""
import dill
tmpmodelparams = self.modelparams.copy()
# fv_extern_src = None
fv_extern_name = None
# try:
# fv_extern_src = dill.source.getsource(tmpmodelparams['fv_extern'])
# tmpmodelparams.pop('fv_extern')
# except:
# pass
# fv_extern_name = dill.source.getname(tmpmodelparams['fv_extern'])
if "fv_extern" in tmpmodelparams:
tmpmodelparams.pop("fv_extern")
sv = {
"modelparams": tmpmodelparams,
"mdl": self.mdl,
# 'fv_extern_src': fv_extern_src,
# 'fv_extern_src_name': fv_extern_src_name,
# 'fv_extern_name': fv_extern_src_name,
#
}
sss = dill.dumps(self.modelparams)
logger.debug("pickled " + str(sss))
dill.dump(sv, open(filename, "wb")) | python | def save(self, filename):
"""
Save model to pickle file. External feature function is not stored
"""
import dill
tmpmodelparams = self.modelparams.copy()
# fv_extern_src = None
fv_extern_name = None
# try:
# fv_extern_src = dill.source.getsource(tmpmodelparams['fv_extern'])
# tmpmodelparams.pop('fv_extern')
# except:
# pass
# fv_extern_name = dill.source.getname(tmpmodelparams['fv_extern'])
if "fv_extern" in tmpmodelparams:
tmpmodelparams.pop("fv_extern")
sv = {
"modelparams": tmpmodelparams,
"mdl": self.mdl,
# 'fv_extern_src': fv_extern_src,
# 'fv_extern_src_name': fv_extern_src_name,
# 'fv_extern_name': fv_extern_src_name,
#
}
sss = dill.dumps(self.modelparams)
logger.debug("pickled " + str(sss))
dill.dump(sv, open(filename, "wb")) | [
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mjirik/imcut | imcut/models.py | Model3D.load | def load(self, mdl_file):
"""
load model from file. fv_type is not set with this function. It is expected to set it before.
"""
import dill as pickle
mdl_file_e = op.expanduser(mdl_file)
sv = pickle.load(open(mdl_file_e, "rb"))
self.mdl = sv["mdl"]
# self.mdl[2] = self.mdl[0]
# try:
# eval(sv['fv_extern_src'])
# eval("fv_extern_temp_name = " + sv['fv_extern_src_name'])
# sv['fv_extern'] = fv_extern_temp_name
# except:
# print "pomoc,necoje blbe"
# pass
self.modelparams.update(sv["modelparams"])
logger.debug("loaded model from path: " + mdl_file_e) | python | def load(self, mdl_file):
"""
load model from file. fv_type is not set with this function. It is expected to set it before.
"""
import dill as pickle
mdl_file_e = op.expanduser(mdl_file)
sv = pickle.load(open(mdl_file_e, "rb"))
self.mdl = sv["mdl"]
# self.mdl[2] = self.mdl[0]
# try:
# eval(sv['fv_extern_src'])
# eval("fv_extern_temp_name = " + sv['fv_extern_src_name'])
# sv['fv_extern'] = fv_extern_temp_name
# except:
# print "pomoc,necoje blbe"
# pass
self.modelparams.update(sv["modelparams"])
logger.debug("loaded model from path: " + mdl_file_e) | [
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mjirik/imcut | imcut/models.py | Model.features_from_image | def features_from_image(
self, data, voxelsize, seeds=None, unique_cls=None
): # , voxels=None):
"""
Input data is 3d image
:param data: is 3d image
:param seeds: ndimage with same shape as data, nonzero values means seeds.
:param unique_cls: can select only fv for seeds from specific class.
f.e. unique_cls = [1, 2] ignores label 0
funcion is called twice in graph cut
first call is with all params, second is only with data.
based on self.modelparams['fv_type'] the feature vector is computed
keywords "intensity", "voxels", "fv001", "fv_extern" can be used.
modelparams['fv_type'] = 'fv_extern' allows to use external fv function
Example of exter feature function. For easier implementation of return values use function return_fv_by_seeds().
def fv_function(data, voxelsize, seeds=None, cl=None):
data2 = scipy.ndimage.filters.gaussian_filter(data, sigma=5)
arrs = [data.reshape(-1, 1), data2.reshape(-1, 1)]
fv = np.concatenate(arrs, axis=1)
return imcut.features.return_fv_by_seeds(fv, seeds, unique_cls)
modelparams['fv_extern'] = fv_function
"""
fv_type = self.modelparams["fv_type"]
logger.debug("fv_type " + fv_type)
fv = []
if fv_type == "intensity":
fv = data.reshape(-1, 1)
if seeds is not None:
logger.debug("seeds: %s", scipy.stats.describe(seeds, axis=None))
sd = seeds.reshape(-1, 1)
selection = np.in1d(sd, unique_cls)
fv = fv[selection]
sd = sd[selection]
# sd = sd[]
return fv, sd
return fv
# elif fv_type in ("voxels"):
# if seeds is not None:
# fv = np.asarray(voxels).reshape(-1, 1)
# else:
# fv = data
# fv = fv.reshape(-1, 1)
elif fv_type in ("fv001", "FV001", "intensity_and_blur"):
# intensity in pixel, gaussian blur intensity
return features.fv_function_intensity_and_smoothing(
data, voxelsize, seeds, unique_cls
)
# from PyQt4.QtCore import pyqtRemoveInputHook
# pyqtRemoveInputHook()
# print fv1.shape
# print fv2.shape
# print fv.shape
elif fv_type == "fv_extern":
fv_function = self.modelparams["fv_extern"]
return fv_function(data, voxelsize, seeds, unique_cls)
else:
logger.error("Unknown feature vector type: " + self.modelparams["fv_type"])
return fv | python | def features_from_image(
self, data, voxelsize, seeds=None, unique_cls=None
): # , voxels=None):
"""
Input data is 3d image
:param data: is 3d image
:param seeds: ndimage with same shape as data, nonzero values means seeds.
:param unique_cls: can select only fv for seeds from specific class.
f.e. unique_cls = [1, 2] ignores label 0
funcion is called twice in graph cut
first call is with all params, second is only with data.
based on self.modelparams['fv_type'] the feature vector is computed
keywords "intensity", "voxels", "fv001", "fv_extern" can be used.
modelparams['fv_type'] = 'fv_extern' allows to use external fv function
Example of exter feature function. For easier implementation of return values use function return_fv_by_seeds().
def fv_function(data, voxelsize, seeds=None, cl=None):
data2 = scipy.ndimage.filters.gaussian_filter(data, sigma=5)
arrs = [data.reshape(-1, 1), data2.reshape(-1, 1)]
fv = np.concatenate(arrs, axis=1)
return imcut.features.return_fv_by_seeds(fv, seeds, unique_cls)
modelparams['fv_extern'] = fv_function
"""
fv_type = self.modelparams["fv_type"]
logger.debug("fv_type " + fv_type)
fv = []
if fv_type == "intensity":
fv = data.reshape(-1, 1)
if seeds is not None:
logger.debug("seeds: %s", scipy.stats.describe(seeds, axis=None))
sd = seeds.reshape(-1, 1)
selection = np.in1d(sd, unique_cls)
fv = fv[selection]
sd = sd[selection]
# sd = sd[]
return fv, sd
return fv
# elif fv_type in ("voxels"):
# if seeds is not None:
# fv = np.asarray(voxels).reshape(-1, 1)
# else:
# fv = data
# fv = fv.reshape(-1, 1)
elif fv_type in ("fv001", "FV001", "intensity_and_blur"):
# intensity in pixel, gaussian blur intensity
return features.fv_function_intensity_and_smoothing(
data, voxelsize, seeds, unique_cls
)
# from PyQt4.QtCore import pyqtRemoveInputHook
# pyqtRemoveInputHook()
# print fv1.shape
# print fv2.shape
# print fv.shape
elif fv_type == "fv_extern":
fv_function = self.modelparams["fv_extern"]
return fv_function(data, voxelsize, seeds, unique_cls)
else:
logger.error("Unknown feature vector type: " + self.modelparams["fv_type"])
return fv | [
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:param seeds: ndimage with same shape as data, nonzero values means seeds.
:param unique_cls: can select only fv for seeds from specific class.
f.e. unique_cls = [1, 2] ignores label 0
funcion is called twice in graph cut
first call is with all params, second is only with data.
based on self.modelparams['fv_type'] the feature vector is computed
keywords "intensity", "voxels", "fv001", "fv_extern" can be used.
modelparams['fv_type'] = 'fv_extern' allows to use external fv function
Example of exter feature function. For easier implementation of return values use function return_fv_by_seeds().
def fv_function(data, voxelsize, seeds=None, cl=None):
data2 = scipy.ndimage.filters.gaussian_filter(data, sigma=5)
arrs = [data.reshape(-1, 1), data2.reshape(-1, 1)]
fv = np.concatenate(arrs, axis=1)
return imcut.features.return_fv_by_seeds(fv, seeds, unique_cls)
modelparams['fv_extern'] = fv_function | [
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mjirik/imcut | imcut/models.py | Model._fit_one_class | def _fit_one_class(self, clx, cl):
""" Train clas number cl with data clx.
Use trainFromImageAndSeeds() function if you want to use 3D image data
as an input.
clx: data, 2d matrix
cl: label, integer
label: gmmsame, gaussian_kde, dpgmm, stored
"""
logger.debug("clx " + str(clx[:10, :]))
logger.debug("clx type" + str(clx.dtype))
# name = 'clx' + str(cl) + '.npy'
# print name
# np.save(name, clx)
logger.debug("_fit()")
if self.modelparams["adaptation"] == "original_data":
if cl in self.mdl.keys():
return
# if True:
# return
logger.debug("training continues")
if self.modelparams["type"] == "gmmsame":
if len(clx.shape) == 1:
logger.warning(
"reshaping in train will be removed. Use \
\ntrainFromImageAndSeeds() function"
)
print("Warning deprecated feature in train() function")
# je to jen jednorozměrný vektor, tak je potřeba to
# převést na 2d matici
clx = clx.reshape(-1, 1)
gmmparams = self.modelparams["params"]
self.mdl[cl] = sklearn.mixture.GaussianMixture(**gmmparams)
self.mdl[cl].fit(clx)
elif self.modelparams["type"] == "kernel":
# Not working (probably) in old versions of scikits
# from sklearn.neighbors.kde import KernelDensity
from sklearn.neighbors import KernelDensity
# kernelmodelparams = {'kernel': 'gaussian', 'bandwidth': 0.2}
kernelmodelparams = self.modelparams["params"]
self.mdl[cl] = KernelDensity(**kernelmodelparams).fit(clx)
elif self.modelparams["type"] == "gaussian_kde":
# print clx
import scipy.stats
# from PyQt4.QtCore import pyqtRemoveInputHook
# pyqtRemoveInputHook()
# gaussian_kde works only with floating point types
self.mdl[cl] = scipy.stats.gaussian_kde(clx.astype(np.float))
elif self.modelparams["type"] == "dpgmm":
# print 'clx.shape ', clx.shape
# print 'cl ', cl
gmmparams = self.modelparams["params"]
self.mdl[cl] = sklearn.mixture.DPGMM(**gmmparams)
# todo here is a hack
# dpgmm z nějakého důvodu nefunguje pro naše data
# vždy natrénuje jednu složku v blízkosti nuly
# patrně to bude mít něco společného s parametrem alpha
# přenásobí-li se to malým číslem, zázračně to chodí
self.mdl[cl].fit(clx * 0.001)
elif self.modelparams["type"] == "stored":
# Classifer is trained before segmentation and stored to pickle
import pickle
print("stored")
logger.warning("deprecated use of stored parameters")
mdl_file = self.modelparams["params"]["mdl_file"]
self.mdl = pickle.load(open(mdl_file, "rb"))
else:
raise NameError("Unknown model type") | python | def _fit_one_class(self, clx, cl):
""" Train clas number cl with data clx.
Use trainFromImageAndSeeds() function if you want to use 3D image data
as an input.
clx: data, 2d matrix
cl: label, integer
label: gmmsame, gaussian_kde, dpgmm, stored
"""
logger.debug("clx " + str(clx[:10, :]))
logger.debug("clx type" + str(clx.dtype))
# name = 'clx' + str(cl) + '.npy'
# print name
# np.save(name, clx)
logger.debug("_fit()")
if self.modelparams["adaptation"] == "original_data":
if cl in self.mdl.keys():
return
# if True:
# return
logger.debug("training continues")
if self.modelparams["type"] == "gmmsame":
if len(clx.shape) == 1:
logger.warning(
"reshaping in train will be removed. Use \
\ntrainFromImageAndSeeds() function"
)
print("Warning deprecated feature in train() function")
# je to jen jednorozměrný vektor, tak je potřeba to
# převést na 2d matici
clx = clx.reshape(-1, 1)
gmmparams = self.modelparams["params"]
self.mdl[cl] = sklearn.mixture.GaussianMixture(**gmmparams)
self.mdl[cl].fit(clx)
elif self.modelparams["type"] == "kernel":
# Not working (probably) in old versions of scikits
# from sklearn.neighbors.kde import KernelDensity
from sklearn.neighbors import KernelDensity
# kernelmodelparams = {'kernel': 'gaussian', 'bandwidth': 0.2}
kernelmodelparams = self.modelparams["params"]
self.mdl[cl] = KernelDensity(**kernelmodelparams).fit(clx)
elif self.modelparams["type"] == "gaussian_kde":
# print clx
import scipy.stats
# from PyQt4.QtCore import pyqtRemoveInputHook
# pyqtRemoveInputHook()
# gaussian_kde works only with floating point types
self.mdl[cl] = scipy.stats.gaussian_kde(clx.astype(np.float))
elif self.modelparams["type"] == "dpgmm":
# print 'clx.shape ', clx.shape
# print 'cl ', cl
gmmparams = self.modelparams["params"]
self.mdl[cl] = sklearn.mixture.DPGMM(**gmmparams)
# todo here is a hack
# dpgmm z nějakého důvodu nefunguje pro naše data
# vždy natrénuje jednu složku v blízkosti nuly
# patrně to bude mít něco společného s parametrem alpha
# přenásobí-li se to malým číslem, zázračně to chodí
self.mdl[cl].fit(clx * 0.001)
elif self.modelparams["type"] == "stored":
# Classifer is trained before segmentation and stored to pickle
import pickle
print("stored")
logger.warning("deprecated use of stored parameters")
mdl_file = self.modelparams["params"]["mdl_file"]
self.mdl = pickle.load(open(mdl_file, "rb"))
else:
raise NameError("Unknown model type") | [
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mjirik/imcut | imcut/pycut.py | relabel_squeeze | def relabel_squeeze(data):
""" Makes relabeling of data if there are unused values. """
palette, index = np.unique(data, return_inverse=True)
data = index.reshape(data.shape)
# realy slow solution
# unq = np.unique(data)
# actual_label = 0
# for lab in unq:
# data[data == lab] = actual_label
# actual_label += 1
# one another solution probably slower
# arr = data
# data = (np.digitize(arr.reshape(-1,),np.unique(arr))-1).reshape(arr.shape)
return data | python | def relabel_squeeze(data):
""" Makes relabeling of data if there are unused values. """
palette, index = np.unique(data, return_inverse=True)
data = index.reshape(data.shape)
# realy slow solution
# unq = np.unique(data)
# actual_label = 0
# for lab in unq:
# data[data == lab] = actual_label
# actual_label += 1
# one another solution probably slower
# arr = data
# data = (np.digitize(arr.reshape(-1,),np.unique(arr))-1).reshape(arr.shape)
return data | [
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mjirik/imcut | imcut/pycut.py | ImageGraphCut.load | def load(self, filename, fv_extern=None):
"""
Read model stored in the file.
:param filename: Path to file with model
:param fv_extern: external feature vector function is passed here
:return:
"""
self.modelparams["mdl_stored_file"] = filename
if fv_extern is not None:
self.modelparams["fv_extern"] = fv_extern
# segparams['modelparams'] = {
# 'mdl_stored_file': mdl_stored_file,
# # 'fv_extern': fv_function
# }
self.mdl = Model(modelparams=self.modelparams) | python | def load(self, filename, fv_extern=None):
"""
Read model stored in the file.
:param filename: Path to file with model
:param fv_extern: external feature vector function is passed here
:return:
"""
self.modelparams["mdl_stored_file"] = filename
if fv_extern is not None:
self.modelparams["fv_extern"] = fv_extern
# segparams['modelparams'] = {
# 'mdl_stored_file': mdl_stored_file,
# # 'fv_extern': fv_function
# }
self.mdl = Model(modelparams=self.modelparams) | [
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ArabellaTech/django-basic-cms | basic_cms/templatetags/pages_tags.py | show_slug_with_level | def show_slug_with_level(context, page, lang=None, fallback=True):
"""Display slug with level by language."""
if not lang:
lang = context.get('lang', pages_settings.PAGE_DEFAULT_LANGUAGE)
page = get_page_from_string_or_id(page, lang)
if not page:
return ''
return {'content': page.slug_with_level(lang)} | python | def show_slug_with_level(context, page, lang=None, fallback=True):
"""Display slug with level by language."""
if not lang:
lang = context.get('lang', pages_settings.PAGE_DEFAULT_LANGUAGE)
page = get_page_from_string_or_id(page, lang)
if not page:
return ''
return {'content': page.slug_with_level(lang)} | [
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ArabellaTech/django-basic-cms | basic_cms/templatetags/pages_tags.py | do_get_pages_with_tag | def do_get_pages_with_tag(parser, token):
"""
Return Pages with given tag
Syntax::
{% get_pages_with_tag <tag name> as <varname> %}
Example use:
{% get_pages_with_tag "footer" as pages %}
"""
bits = token.split_contents()
if 4 != len(bits):
raise TemplateSyntaxError('%r expects 2 arguments' % bits[0])
if bits[-2] != 'as':
raise TemplateSyntaxError(
'%r expects "as" as the second last argument' % bits[0])
varname = bits[-1]
tag = parser.compile_filter(bits[1])
varname = bits[-1]
return GetPagesWithTagNode(tag, varname) | python | def do_get_pages_with_tag(parser, token):
"""
Return Pages with given tag
Syntax::
{% get_pages_with_tag <tag name> as <varname> %}
Example use:
{% get_pages_with_tag "footer" as pages %}
"""
bits = token.split_contents()
if 4 != len(bits):
raise TemplateSyntaxError('%r expects 2 arguments' % bits[0])
if bits[-2] != 'as':
raise TemplateSyntaxError(
'%r expects "as" as the second last argument' % bits[0])
varname = bits[-1]
tag = parser.compile_filter(bits[1])
varname = bits[-1]
return GetPagesWithTagNode(tag, varname) | [
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sirfoga/pyhal | hal/files/models/system.py | remove_year | def remove_year(name):
"""Removes year from input
:param name: path to edit
:return: inputs with no years
"""
for i in range(len(
name) - 3): # last index is length - 3 - 1 = length - 4
if name[i: i + 4].isdigit():
name = name[:i] + name[i + 4:]
return remove_year(
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return name | python | def remove_year(name):
"""Removes year from input
:param name: path to edit
:return: inputs with no years
"""
for i in range(len(
name) - 3): # last index is length - 3 - 1 = length - 4
if name[i: i + 4].isdigit():
name = name[:i] + name[i + 4:]
return remove_year(
name) # if there is a removal, start again
return name | [
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sirfoga/pyhal | hal/files/models/system.py | remove_brackets | def remove_brackets(name):
"""Removes brackets form input
:param name: path to fix
:return: inputs with no brackets
"""
name = re.sub(
r"([(\[]).*?([)\]])",
r"\g<1>\g<2>",
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brackets = "()[]{}" # list of brackets
for bracket in brackets:
name = name.replace(bracket, "")
return name | python | def remove_brackets(name):
"""Removes brackets form input
:param name: path to fix
:return: inputs with no brackets
"""
name = re.sub(
r"([(\[]).*?([)\]])",
r"\g<1>\g<2>",
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sirfoga/pyhal | hal/files/models/system.py | extract_name_max_chars | def extract_name_max_chars(name, max_chars=64, blank=" "):
"""Extracts max chars in name truncated to nearest word
:param name: path to edit
:param max_chars: max chars of new name
:param blank: char that represents the blank between words
:return: Name edited to contain at most max_chars
"""
new_name = name.strip()
if len(new_name) > max_chars:
new_name = new_name[:max_chars] # get at most 64 chars
if new_name.rfind(blank) > 0:
new_name = new_name[:new_name.rfind(blank)] # nearest word
return new_name | python | def extract_name_max_chars(name, max_chars=64, blank=" "):
"""Extracts max chars in name truncated to nearest word
:param name: path to edit
:param max_chars: max chars of new name
:param blank: char that represents the blank between words
:return: Name edited to contain at most max_chars
"""
new_name = name.strip()
if len(new_name) > max_chars:
new_name = new_name[:max_chars] # get at most 64 chars
if new_name.rfind(blank) > 0:
new_name = new_name[:new_name.rfind(blank)] # nearest word
return new_name | [
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sirfoga/pyhal | hal/files/models/system.py | get_parent_folder_name | def get_parent_folder_name(file_path):
"""Finds parent folder of file
:param file_path: path
:return: Name of folder container
"""
return os.path.split(os.path.split(os.path.abspath(file_path))[0])[-1] | python | def get_parent_folder_name(file_path):
"""Finds parent folder of file
:param file_path: path
:return: Name of folder container
"""
return os.path.split(os.path.split(os.path.abspath(file_path))[0])[-1] | [
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sirfoga/pyhal | hal/files/models/system.py | ls_dir | def ls_dir(path, include_hidden=False):
"""Finds content of folder
:param path: directory to get list of files and folders
:param include_hidden: True iff include hidden files in list
:return: List of paths in given directory
"""
lst = []
for file in os.listdir(path):
hidden_file = FileSystem(file).is_hidden()
if (hidden_file and include_hidden) or (not hidden_file):
lst.append(os.path.join(path, file))
return list(set(lst)) | python | def ls_dir(path, include_hidden=False):
"""Finds content of folder
:param path: directory to get list of files and folders
:param include_hidden: True iff include hidden files in list
:return: List of paths in given directory
"""
lst = []
for file in os.listdir(path):
hidden_file = FileSystem(file).is_hidden()
if (hidden_file and include_hidden) or (not hidden_file):
lst.append(os.path.join(path, file))
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sirfoga/pyhal | hal/files/models/system.py | ls_recurse | def ls_recurse(path, include_hidden=False):
"""Finds content of folder recursively
:param path: directory to get list of files and folders
:param include_hidden: True iff include hidden files in list
:return: List of paths in given directory recursively
"""
lst = []
for file in os.listdir(path):
hidden_file = FileSystem(file).is_hidden()
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if is_folder(os.path.join(path, file)):
lst += ls_recurse(
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return list(set(lst)) | python | def ls_recurse(path, include_hidden=False):
"""Finds content of folder recursively
:param path: directory to get list of files and folders
:param include_hidden: True iff include hidden files in list
:return: List of paths in given directory recursively
"""
lst = []
for file in os.listdir(path):
hidden_file = FileSystem(file).is_hidden()
if (hidden_file and include_hidden) or (not hidden_file):
lst.append(os.path.join(path, file))
if is_folder(os.path.join(path, file)):
lst += ls_recurse(
os.path.join(path, file),
include_hidden=include_hidden
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return list(set(lst)) | [
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sirfoga/pyhal | hal/files/models/system.py | FileSystem.is_russian | def is_russian(self):
"""Checks if file path is russian
:return: True iff document has a russian name
"""
russian_chars = 0
for char in RUSSIAN_CHARS:
if char in self.name:
russian_chars += 1 # found a russian char
return russian_chars > len(RUSSIAN_CHARS) / 2.0 | python | def is_russian(self):
"""Checks if file path is russian
:return: True iff document has a russian name
"""
russian_chars = 0
for char in RUSSIAN_CHARS:
if char in self.name:
russian_chars += 1 # found a russian char
return russian_chars > len(RUSSIAN_CHARS) / 2.0 | [
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sirfoga/pyhal | hal/files/models/system.py | FileSystem.rename | def rename(self, new_path):
"""Renames to new path
:param new_path: new path to use
"""
rename_path = fix_raw_path(new_path)
if is_folder(self.path):
os.rename(self.path, rename_path)
else:
os.renames(self.path, rename_path) | python | def rename(self, new_path):
"""Renames to new path
:param new_path: new path to use
"""
rename_path = fix_raw_path(new_path)
if is_folder(self.path):
os.rename(self.path, rename_path)
else:
os.renames(self.path, rename_path) | [
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portfors-lab/sparkle | sparkle/gui/drag_label.py | DragLabel.setClass | def setClass(self, factoryclass):
"""Sets the constructor for the component type this label is to
represent
:param factoryclass: a class that, when called, results in an instance of the desired class
:type factoryclass: callable
"""
self.factoryclass = factoryclass
self.setText(str(factoryclass.name)) | python | def setClass(self, factoryclass):
"""Sets the constructor for the component type this label is to
represent
:param factoryclass: a class that, when called, results in an instance of the desired class
:type factoryclass: callable
"""
self.factoryclass = factoryclass
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | BasePlot.getLabel | def getLabel(self, key):
"""Gets the label assigned to an axes
:param key:???
:type key: str
"""
axisItem = self.getPlotItem().axes[key]['item']
return axisItem.label.toPlainText() | python | def getLabel(self, key):
"""Gets the label assigned to an axes
:param key:???
:type key: str
"""
axisItem = self.getPlotItem().axes[key]['item']
return axisItem.label.toPlainText() | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | TraceWidget.updateData | def updateData(self, axeskey, x, y):
"""Replaces the currently displayed data
:param axeskey: name of data plot to update. Valid options are 'stim' or 'response'
:type axeskey: str
:param x: index values associated with y to plot
:type x: numpy.ndarray
:param y: values to plot at x
:type y: numpy.ndarray
"""
if axeskey == 'stim':
self.stimPlot.setData(x,y)
# call manually to ajust placement of signal
ranges = self.viewRange()
self.rangeChange(self, ranges)
if axeskey == 'response':
self.clearTraces()
if self._traceUnit == 'A':
y = y * self._ampScalar
if self.zeroAction.isChecked():
start_avg = np.mean(y[5:25])
y = y - start_avg
self.tracePlot.setData(x,y*self._polarity) | python | def updateData(self, axeskey, x, y):
"""Replaces the currently displayed data
:param axeskey: name of data plot to update. Valid options are 'stim' or 'response'
:type axeskey: str
:param x: index values associated with y to plot
:type x: numpy.ndarray
:param y: values to plot at x
:type y: numpy.ndarray
"""
if axeskey == 'stim':
self.stimPlot.setData(x,y)
# call manually to ajust placement of signal
ranges = self.viewRange()
self.rangeChange(self, ranges)
if axeskey == 'response':
self.clearTraces()
if self._traceUnit == 'A':
y = y * self._ampScalar
if self.zeroAction.isChecked():
start_avg = np.mean(y[5:25])
y = y - start_avg
self.tracePlot.setData(x,y*self._polarity) | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | TraceWidget.appendData | def appendData(self, axeskey, bins, ypoints):
"""Appends data to existing plotted data
:param axeskey: name of data plot to update. Valid options are 'stim' or 'response'
:type axeskey: str
:param bins: bins to plot a point for
:type bin: numpy.ndarray
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:type ypoints: numpy.ndarray
"""
if axeskey == 'raster' and len(bins) > 0:
x, y = self.rasterPlot.getData()
# don't plot overlapping points
bins = np.unique(bins)
# adjust repetition number to response scale
ypoints = np.ones_like(bins)*self.rasterYslots[ypoints[0]]
x = np.append(x, bins)
y = np.append(y, ypoints)
self.rasterPlot.setData(x, y) | python | def appendData(self, axeskey, bins, ypoints):
"""Appends data to existing plotted data
:param axeskey: name of data plot to update. Valid options are 'stim' or 'response'
:type axeskey: str
:param bins: bins to plot a point for
:type bin: numpy.ndarray
:param ypoints: iteration number of raster, *should* match bins dimension, but really takes the first value in array for iteration number and plot row at proper place for included bins
:type ypoints: numpy.ndarray
"""
if axeskey == 'raster' and len(bins) > 0:
x, y = self.rasterPlot.getData()
# don't plot overlapping points
bins = np.unique(bins)
# adjust repetition number to response scale
ypoints = np.ones_like(bins)*self.rasterYslots[ypoints[0]]
x = np.append(x, bins)
y = np.append(y, ypoints)
self.rasterPlot.setData(x, y) | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | TraceWidget.setThreshold | def setThreshold(self, threshold):
"""Sets the current threshold
:param threshold: the y value to set the threshold line at
:type threshold: float
"""
self.threshLine.setValue(threshold)
self.threshold_field.setValue(threshold) | python | def setThreshold(self, threshold):
"""Sets the current threshold
:param threshold: the y value to set the threshold line at
:type threshold: float
"""
self.threshLine.setValue(threshold)
self.threshold_field.setValue(threshold) | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | TraceWidget.setRasterBounds | def setRasterBounds(self, lims):
"""Sets the raster plot y-axis bounds, where in the plot the raster will appear between
:param lims: the (min, max) y-values for the raster plot to be placed between
:type lims: (float, float)
"""
self.rasterBottom = lims[0]
self.rasterTop = lims[1]
self.updateRasterBounds() | python | def setRasterBounds(self, lims):
"""Sets the raster plot y-axis bounds, where in the plot the raster will appear between
:param lims: the (min, max) y-values for the raster plot to be placed between
:type lims: (float, float)
"""
self.rasterBottom = lims[0]
self.rasterTop = lims[1]
self.updateRasterBounds() | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | TraceWidget.updateRasterBounds | def updateRasterBounds(self):
"""Updates the y-coordinate slots where the raster points
are plotted, according to the current limits of the y-axis"""
yrange = self.viewRange()[1]
yrange_size = yrange[1] - yrange[0]
rmax = self.rasterTop*yrange_size + yrange[0]
rmin = self.rasterBottom*yrange_size + yrange[0]
self.rasterYslots = np.linspace(rmin, rmax, self.nreps)
self.rasterBoundsUpdated.emit((self.rasterBottom, self.rasterTop), self.getTitle()) | python | def updateRasterBounds(self):
"""Updates the y-coordinate slots where the raster points
are plotted, according to the current limits of the y-axis"""
yrange = self.viewRange()[1]
yrange_size = yrange[1] - yrange[0]
rmax = self.rasterTop*yrange_size + yrange[0]
rmin = self.rasterBottom*yrange_size + yrange[0]
self.rasterYslots = np.linspace(rmin, rmax, self.nreps)
self.rasterBoundsUpdated.emit((self.rasterBottom, self.rasterTop), self.getTitle()) | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | TraceWidget.askRasterBounds | def askRasterBounds(self):
"""Prompts the user to provide the raster bounds with a dialog.
Saves the bounds to be applied to the plot"""
dlg = RasterBoundsDialog(bounds= (self.rasterBottom, self.rasterTop))
if dlg.exec_():
bounds = dlg.values()
self.setRasterBounds(bounds) | python | def askRasterBounds(self):
"""Prompts the user to provide the raster bounds with a dialog.
Saves the bounds to be applied to the plot"""
dlg = RasterBoundsDialog(bounds= (self.rasterBottom, self.rasterTop))
if dlg.exec_():
bounds = dlg.values()
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | TraceWidget.rangeChange | def rangeChange(self, pw, ranges):
"""Adjusts the stimulus signal to keep it at the top of a plot,
after any ajustment to the axes ranges takes place.
This is a slot for the undocumented pyqtgraph signal sigRangeChanged.
From what I can tell the arguments are:
:param pw: reference to the emitting object (plot widget in my case)
:type pw: object
:param ranges: I am only interested when this turns out to be a nested list of axis bounds
:type ranges: object
"""
if hasattr(ranges, '__iter__'):
# adjust the stim signal so that it falls in the correct range
yrange_size = ranges[1][1] - ranges[1][0]
stim_x, stim_y = self.stimPlot.getData()
if stim_y is not None:
stim_height = yrange_size*STIM_HEIGHT
# take it to 0
stim_y = stim_y - np.amin(stim_y)
# normalize
if np.amax(stim_y) != 0:
stim_y = stim_y/np.amax(stim_y)
# scale for new size
stim_y = stim_y*stim_height
# raise to right place in plot
stim_y = stim_y + (ranges[1][1] - (stim_height*1.1 + (stim_height*0.2)))
self.stimPlot.setData(stim_x, stim_y)
# rmax = self.rasterTop*yrange_size + ranges[1][0]
# rmin = self.rasterBottom*yrange_size + ranges[1][0]
self.updateRasterBounds() | python | def rangeChange(self, pw, ranges):
"""Adjusts the stimulus signal to keep it at the top of a plot,
after any ajustment to the axes ranges takes place.
This is a slot for the undocumented pyqtgraph signal sigRangeChanged.
From what I can tell the arguments are:
:param pw: reference to the emitting object (plot widget in my case)
:type pw: object
:param ranges: I am only interested when this turns out to be a nested list of axis bounds
:type ranges: object
"""
if hasattr(ranges, '__iter__'):
# adjust the stim signal so that it falls in the correct range
yrange_size = ranges[1][1] - ranges[1][0]
stim_x, stim_y = self.stimPlot.getData()
if stim_y is not None:
stim_height = yrange_size*STIM_HEIGHT
# take it to 0
stim_y = stim_y - np.amin(stim_y)
# normalize
if np.amax(stim_y) != 0:
stim_y = stim_y/np.amax(stim_y)
# scale for new size
stim_y = stim_y*stim_height
# raise to right place in plot
stim_y = stim_y + (ranges[1][1] - (stim_height*1.1 + (stim_height*0.2)))
self.stimPlot.setData(stim_x, stim_y)
# rmax = self.rasterTop*yrange_size + ranges[1][0]
# rmin = self.rasterBottom*yrange_size + ranges[1][0]
self.updateRasterBounds() | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | TraceWidget.update_thresh | def update_thresh(self):
"""Emits a Qt signal thresholdUpdated with the current threshold value"""
thresh_val = self.threshLine.value()
self.threshold_field.setValue(thresh_val)
self.thresholdUpdated.emit(thresh_val, self.getTitle()) | python | def update_thresh(self):
"""Emits a Qt signal thresholdUpdated with the current threshold value"""
thresh_val = self.threshLine.value()
self.threshold_field.setValue(thresh_val)
self.thresholdUpdated.emit(thresh_val, self.getTitle()) | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | SpecWidget.updateImage | def updateImage(self, imgdata, xaxis=None, yaxis=None):
"""Updates the Widget image directly.
:type imgdata: numpy.ndarray, see :meth:`pyqtgraph:pyqtgraph.ImageItem.setImage`
:param xaxis: x-axis values, length should match dimension 1 of imgdata
:param yaxis: y-axis values, length should match dimension 0 of imgdata
"""
imgdata = imgdata.T
self.img.setImage(imgdata)
if xaxis is not None and yaxis is not None:
xscale = 1.0/(imgdata.shape[0]/xaxis[-1])
yscale = 1.0/(imgdata.shape[1]/yaxis[-1])
self.resetScale()
self.img.scale(xscale, yscale)
self.imgScale = (xscale, yscale)
self.imageArray = np.fliplr(imgdata)
self.updateColormap() | python | def updateImage(self, imgdata, xaxis=None, yaxis=None):
"""Updates the Widget image directly.
:type imgdata: numpy.ndarray, see :meth:`pyqtgraph:pyqtgraph.ImageItem.setImage`
:param xaxis: x-axis values, length should match dimension 1 of imgdata
:param yaxis: y-axis values, length should match dimension 0 of imgdata
"""
imgdata = imgdata.T
self.img.setImage(imgdata)
if xaxis is not None and yaxis is not None:
xscale = 1.0/(imgdata.shape[0]/xaxis[-1])
yscale = 1.0/(imgdata.shape[1]/yaxis[-1])
self.resetScale()
self.img.scale(xscale, yscale)
self.imgScale = (xscale, yscale)
self.imageArray = np.fliplr(imgdata)
self.updateColormap() | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | SpecWidget.resetScale | def resetScale(self):
"""Resets the scale on this image. Correctly aligns time scale, undoes manual scaling"""
self.img.scale(1./self.imgScale[0], 1./self.imgScale[1])
self.imgScale = (1.,1.) | python | def resetScale(self):
"""Resets the scale on this image. Correctly aligns time scale, undoes manual scaling"""
self.img.scale(1./self.imgScale[0], 1./self.imgScale[1])
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | SpecWidget.updateData | def updateData(self, signal, fs):
"""Displays a spectrogram of the provided signal
:param signal: 1-D signal of audio
:type signal: numpy.ndarray
:param fs: samplerate of signal
:type fs: int
"""
# use a separate thread to calculate spectrogram so UI doesn't lag
t = threading.Thread(target=_doSpectrogram, args=(self.spec_done, (fs, signal),), kwargs=self.specgramArgs)
t.start() | python | def updateData(self, signal, fs):
"""Displays a spectrogram of the provided signal
:param signal: 1-D signal of audio
:type signal: numpy.ndarray
:param fs: samplerate of signal
:type fs: int
"""
# use a separate thread to calculate spectrogram so UI doesn't lag
t = threading.Thread(target=_doSpectrogram, args=(self.spec_done, (fs, signal),), kwargs=self.specgramArgs)
t.start() | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | SpecWidget.setSpecArgs | def setSpecArgs(**kwargs):
"""Sets optional arguments for the spectrogram appearance.
Available options:
:param nfft: size of FFT window to use
:type nfft: int
:param overlap: percent overlap of window
:type overlap: number
:param window: Type of window to use, choices are hanning, hamming, blackman, bartlett or none (rectangular)
:type window: string
:param colormap: Gets set by colormap editor. Holds the information to generate the colormap. Items: :meth:`lut<pyqtgraph:pyqtgraph.ImageItem.setLookupTable>`, :meth:`levels<pyqtgraph:pyqtgraph.ImageItem.setLevels>`, state (info for editor)
:type colormap: dict
"""
for key, value in kwargs.items():
if key == 'colormap':
SpecWidget.imgArgs['lut'] = value['lut']
SpecWidget.imgArgs['levels'] = value['levels']
SpecWidget.imgArgs['state'] = value['state']
for w in SpecWidget.instances:
w.updateColormap()
else:
SpecWidget.specgramArgs[key] = value | python | def setSpecArgs(**kwargs):
"""Sets optional arguments for the spectrogram appearance.
Available options:
:param nfft: size of FFT window to use
:type nfft: int
:param overlap: percent overlap of window
:type overlap: number
:param window: Type of window to use, choices are hanning, hamming, blackman, bartlett or none (rectangular)
:type window: string
:param colormap: Gets set by colormap editor. Holds the information to generate the colormap. Items: :meth:`lut<pyqtgraph:pyqtgraph.ImageItem.setLookupTable>`, :meth:`levels<pyqtgraph:pyqtgraph.ImageItem.setLevels>`, state (info for editor)
:type colormap: dict
"""
for key, value in kwargs.items():
if key == 'colormap':
SpecWidget.imgArgs['lut'] = value['lut']
SpecWidget.imgArgs['levels'] = value['levels']
SpecWidget.imgArgs['state'] = value['state']
for w in SpecWidget.instances:
w.updateColormap()
else:
SpecWidget.specgramArgs[key] = value | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | SpecWidget.clearImg | def clearImg(self):
"""Clears the current image"""
self.img.setImage(np.array([[0]]))
self.img.image = None | python | def clearImg(self):
"""Clears the current image"""
self.img.setImage(np.array([[0]]))
self.img.image = None | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | SpecWidget.editColormap | def editColormap(self):
"""Prompts the user with a dialog to change colormap"""
self.editor = pg.ImageView()
# remove the ROI and Norm buttons
self.editor.ui.roiBtn.setVisible(False)
self.editor.ui.menuBtn.setVisible(False)
self.editor.setImage(self.imageArray)
if self.imgArgs['state'] is not None:
self.editor.getHistogramWidget().item.gradient.restoreState(self.imgArgs['state'])
self.editor.getHistogramWidget().item.setLevels(*self.imgArgs['levels'])
self.editor.closeEvent = self._editor_close
self.editor.setWindowModality(QtCore.Qt.ApplicationModal)
self.editor.show() | python | def editColormap(self):
"""Prompts the user with a dialog to change colormap"""
self.editor = pg.ImageView()
# remove the ROI and Norm buttons
self.editor.ui.roiBtn.setVisible(False)
self.editor.ui.menuBtn.setVisible(False)
self.editor.setImage(self.imageArray)
if self.imgArgs['state'] is not None:
self.editor.getHistogramWidget().item.gradient.restoreState(self.imgArgs['state'])
self.editor.getHistogramWidget().item.setLevels(*self.imgArgs['levels'])
self.editor.closeEvent = self._editor_close
self.editor.setWindowModality(QtCore.Qt.ApplicationModal)
self.editor.show() | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | SpecWidget.updateColormap | def updateColormap(self):
"""Updates the currently colormap accoring to stored settings"""
if self.imgArgs['lut'] is not None:
self.img.setLookupTable(self.imgArgs['lut'])
self.img.setLevels(self.imgArgs['levels']) | python | def updateColormap(self):
"""Updates the currently colormap accoring to stored settings"""
if self.imgArgs['lut'] is not None:
self.img.setLookupTable(self.imgArgs['lut'])
self.img.setLevels(self.imgArgs['levels']) | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | SimplePlotWidget.appendData | def appendData(self, xdata, ydata, color='b', legendstr=None):
"""Adds the data to the plot
:param xdata: index values for data, plotted on x-axis
:type xdata: numpy.ndarray
:param ydata: value data to plot, dimension must match xdata
:type ydata: numpy.ndarray
"""
item = self.plot(xdata, ydata, pen=color)
if legendstr is not None:
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return item | python | def appendData(self, xdata, ydata, color='b', legendstr=None):
"""Adds the data to the plot
:param xdata: index values for data, plotted on x-axis
:type xdata: numpy.ndarray
:param ydata: value data to plot, dimension must match xdata
:type ydata: numpy.ndarray
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item = self.plot(xdata, ydata, pen=color)
if legendstr is not None:
self.legend.addItem(item, legendstr)
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | SimplePlotWidget.setLabels | def setLabels(self, xlabel=None, ylabel=None, title=None, xunits=None, yunits=None):
"""Sets the plot labels
:param xlabel: X-axis label (do not include units)
:type xlabel: str
:param ylabel: Y-axis label (do not include units)
:type ylabel: str
:param title: Plot title
:type title: str
:param xunit: SI units for the x-axis. An appropriate label will be appended according to scale
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:param yunit: SI units for the y-axis. An appropriate label will be appended according to scale
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if xlabel is not None:
self.setLabel('bottom', xlabel, units=xunits)
if ylabel is not None:
self.setLabel('left', ylabel, units=yunits)
if title is not None:
self.setTitle(title) | python | def setLabels(self, xlabel=None, ylabel=None, title=None, xunits=None, yunits=None):
"""Sets the plot labels
:param xlabel: X-axis label (do not include units)
:type xlabel: str
:param ylabel: Y-axis label (do not include units)
:type ylabel: str
:param title: Plot title
:type title: str
:param xunit: SI units for the x-axis. An appropriate label will be appended according to scale
:type xunit: str
:param yunit: SI units for the y-axis. An appropriate label will be appended according to scale
:type yunit: str
"""
if xlabel is not None:
self.setLabel('bottom', xlabel, units=xunits)
if ylabel is not None:
self.setLabel('left', ylabel, units=yunits)
if title is not None:
self.setTitle(title) | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | ProgressWidget.setPoint | def setPoint(self, x, group, y):
"""Sets the given point, connects line to previous point in group
:param x: x value of point
:type x: float
:param group: group which plot point for
:type group: float
:param y: y value of point
:type y: float
"""
if x == -1:
# silence window
self.plot([0],[y], symbol='o')
else:
yindex = self.groups.index(group)
xdata, ydata = self.lines[yindex].getData()
if ydata is None:
xdata = [x]
ydata = [y]
else:
xdata = np.append(xdata, x)
ydata = np.append(ydata, y)
self.lines[yindex].setData(xdata, ydata) | python | def setPoint(self, x, group, y):
"""Sets the given point, connects line to previous point in group
:param x: x value of point
:type x: float
:param group: group which plot point for
:type group: float
:param y: y value of point
:type y: float
"""
if x == -1:
# silence window
self.plot([0],[y], symbol='o')
else:
yindex = self.groups.index(group)
xdata, ydata = self.lines[yindex].getData()
if ydata is None:
xdata = [x]
ydata = [y]
else:
xdata = np.append(xdata, x)
ydata = np.append(ydata, y)
self.lines[yindex].setData(xdata, ydata) | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | ProgressWidget.setLabels | def setLabels(self, name):
"""Sets plot labels, according to predefined options
:param name: The type of plot to create labels for. Options: calibration, tuning, anything else labels for spike counts
:type name: str
"""
if name == "calibration":
self.setWindowTitle("Calibration Curve")
self.setTitle("Calibration Curve")
self.setLabel('bottom', "Frequency", units='Hz')
self.setLabel('left', 'Recorded Intensity (dB SPL)')
elif name == "tuning":
self.setWindowTitle("Tuning Curve")
self.setTitle("Tuning Curve")
self.setLabel('bottom', "Frequency", units="Hz")
self.setLabel('left', "Spike Count (mean)")
else:
self.setWindowTitle("Spike Counts")
self.setTitle("Spike Counts")
self.setLabel('bottom', "Test Number", units='')
self.setLabel('left', "Spike Count (mean)", units='') | python | def setLabels(self, name):
"""Sets plot labels, according to predefined options
:param name: The type of plot to create labels for. Options: calibration, tuning, anything else labels for spike counts
:type name: str
"""
if name == "calibration":
self.setWindowTitle("Calibration Curve")
self.setTitle("Calibration Curve")
self.setLabel('bottom', "Frequency", units='Hz')
self.setLabel('left', 'Recorded Intensity (dB SPL)')
elif name == "tuning":
self.setWindowTitle("Tuning Curve")
self.setTitle("Tuning Curve")
self.setLabel('bottom', "Frequency", units="Hz")
self.setLabel('left', "Spike Count (mean)")
else:
self.setWindowTitle("Spike Counts")
self.setTitle("Spike Counts")
self.setLabel('bottom', "Test Number", units='')
self.setLabel('left', "Spike Count (mean)", units='') | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | ProgressWidget.loadCurve | def loadCurve(data, groups, thresholds, absvals, fs, xlabels):
"""Accepts a data set from a whole test, averages reps and re-creates the
progress plot as the same as it was during live plotting. Number of thresholds
must match the size of the channel dimension"""
xlims = (xlabels[0], xlabels[-1])
pw = ProgressWidget(groups, xlims)
spike_counts = []
# skip control
for itrace in range(data.shape[0]):
count = 0
for ichan in range(data.shape[2]):
flat_reps = data[itrace,:,ichan,:].flatten()
count += len(spikestats.spike_times(flat_reps, thresholds[ichan], fs, absvals[ichan]))
spike_counts.append(count/(data.shape[1]*data.shape[2])) #mean spikes per rep
i = 0
for g in groups:
for x in xlabels:
pw.setPoint(x, g, spike_counts[i])
i +=1
return pw | python | def loadCurve(data, groups, thresholds, absvals, fs, xlabels):
"""Accepts a data set from a whole test, averages reps and re-creates the
progress plot as the same as it was during live plotting. Number of thresholds
must match the size of the channel dimension"""
xlims = (xlabels[0], xlabels[-1])
pw = ProgressWidget(groups, xlims)
spike_counts = []
# skip control
for itrace in range(data.shape[0]):
count = 0
for ichan in range(data.shape[2]):
flat_reps = data[itrace,:,ichan,:].flatten()
count += len(spikestats.spike_times(flat_reps, thresholds[ichan], fs, absvals[ichan]))
spike_counts.append(count/(data.shape[1]*data.shape[2])) #mean spikes per rep
i = 0
for g in groups:
for x in xlabels:
pw.setPoint(x, g, spike_counts[i])
i +=1
return pw | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | PSTHWidget.processData | def processData(self, times, response, test_num, trace_num, rep_num):
"""Calulate spike times from raw response data"""
# invert polarity affects spike counting
response = response * self._polarity
if rep_num == 0:
# reset
self.spike_counts = []
self.spike_latencies = []
self.spike_rates = []
fs = 1./(times[1] - times[0])
# process response; calculate spike times
spike_times = spikestats.spike_times(response, self._threshold, fs)
self.spike_counts.append(len(spike_times))
if len(spike_times) > 0:
self.spike_latencies.append(spike_times[0])
else:
self.spike_latencies.append(np.nan)
self.spike_rates.append(spikestats.firing_rate(spike_times, times))
binsz = self._bins[1] - self._bins[0]
response_bins = spikestats.bin_spikes(spike_times, binsz)
# self.putnotify('spikes_found', (response_bins, rep_num))
self.appendData(response_bins, rep_num) | python | def processData(self, times, response, test_num, trace_num, rep_num):
"""Calulate spike times from raw response data"""
# invert polarity affects spike counting
response = response * self._polarity
if rep_num == 0:
# reset
self.spike_counts = []
self.spike_latencies = []
self.spike_rates = []
fs = 1./(times[1] - times[0])
# process response; calculate spike times
spike_times = spikestats.spike_times(response, self._threshold, fs)
self.spike_counts.append(len(spike_times))
if len(spike_times) > 0:
self.spike_latencies.append(spike_times[0])
else:
self.spike_latencies.append(np.nan)
self.spike_rates.append(spikestats.firing_rate(spike_times, times))
binsz = self._bins[1] - self._bins[0]
response_bins = spikestats.bin_spikes(spike_times, binsz)
# self.putnotify('spikes_found', (response_bins, rep_num))
self.appendData(response_bins, rep_num) | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | ChartWidget.setSr | def setSr(self, fs):
"""Sets the samplerate of the input operation being plotted"""
self.tracePlot.setSr(fs)
self.stimPlot.setSr(fs) | python | def setSr(self, fs):
"""Sets the samplerate of the input operation being plotted"""
self.tracePlot.setSr(fs)
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | ChartWidget.setWindowSize | def setWindowSize(self, winsz):
"""Sets the size of scroll window"""
self.tracePlot.setWindowSize(winsz)
self.stimPlot.setWindowSize(winsz) | python | def setWindowSize(self, winsz):
"""Sets the size of scroll window"""
self.tracePlot.setWindowSize(winsz)
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | StackedPlot.addSpectrogram | def addSpectrogram(self, ydata, fs, title=None):
"""Adds a new spectorgram plot for the given image. Generates a SpecWidget
:param ydata: 2-D array of the image to display
:type ydata: numpy.ndarray
:param fs: the samplerate of the signal in the image, used to set time/ frequency scale
:type fs: int
:param title: Plot title
:type title: str
"""
p = SpecWidget()
p.updateData(ydata, fs)
if title is not None:
p.setTitle(title)
self.stacker.addWidget(p) | python | def addSpectrogram(self, ydata, fs, title=None):
"""Adds a new spectorgram plot for the given image. Generates a SpecWidget
:param ydata: 2-D array of the image to display
:type ydata: numpy.ndarray
:param fs: the samplerate of the signal in the image, used to set time/ frequency scale
:type fs: int
:param title: Plot title
:type title: str
"""
p = SpecWidget()
p.updateData(ydata, fs)
if title is not None:
p.setTitle(title)
self.stacker.addWidget(p) | [
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | StackedPlot.nextPlot | def nextPlot(self):
"""Moves the displayed plot to the next one"""
if self.stacker.currentIndex() < self.stacker.count():
self.stacker.setCurrentIndex(self.stacker.currentIndex()+1) | python | def nextPlot(self):
"""Moves the displayed plot to the next one"""
if self.stacker.currentIndex() < self.stacker.count():
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portfors-lab/sparkle | sparkle/gui/plotting/pyqtgraph_widgets.py | StackedPlot.prevPlot | def prevPlot(self):
"""Moves the displayed plot to the previous one"""
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NoviceLive/pat | pat/utils.py | most_even_chunk | def most_even_chunk(string, group):
"""Divide a string into a list of strings as even as possible."""
counts = [0] + most_even(len(string), group)
indices = accumulate(counts)
slices = window(indices, 2)
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"""Divide a string into a list of strings as even as possible."""
counts = [0] + most_even(len(string), group)
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sirfoga/pyhal | hal/meta/attributes.py | _get_modules | def _get_modules(path):
"""Finds modules in folder recursively
:param path: directory
:return: list of modules
"""
lst = []
folder_contents = os.listdir(path)
is_python_module = "__init__.py" in folder_contents
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full_path = os.path.join(path, file)
if is_file(full_path):
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lst += _get_modules(full_path) # recurse in folder
return list(set(lst)) | python | def _get_modules(path):
"""Finds modules in folder recursively
:param path: directory
:return: list of modules
"""
lst = []
folder_contents = os.listdir(path)
is_python_module = "__init__.py" in folder_contents
if is_python_module:
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full_path = os.path.join(path, file)
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sirfoga/pyhal | hal/meta/attributes.py | ModuleFile._find_package | def _find_package(self, root_package):
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package = root_package + package # add root
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package = self.path.replace(root_package, "")
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sirfoga/pyhal | hal/meta/attributes.py | ModuleTree._get_instances | def _get_instances(self, instance):
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sirfoga/pyhal | hal/meta/attributes.py | ModuleTree.get_classes | def get_classes(self):
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"""Finds classes in file
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lowandrew/OLCTools | spadespipeline/skesa.py | Skesa.best_assemblyfile | def best_assemblyfile(self):
"""
Determine whether the contigs.fasta output file from the assembler is present. If not, set the .bestassembly
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"""
for sample in self.metadata:
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sample.general.bestassemblyfile = 'NA'
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sample.general.bestassemblyfile = sample.general.assemblyfile
shutil.copyfile(sample.general.bestassemblyfile, filtered_outputfile)
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sample.general.bestassemblyfile = 'NA'
# Add the name and path of the filtered file to the metadata
sample.general.filteredfile = filtered_outputfile
except AttributeError:
sample.general.assemblyfile = 'NA'
sample.general.bestassemblyfile = 'NA' | python | def best_assemblyfile(self):
"""
Determine whether the contigs.fasta output file from the assembler is present. If not, set the .bestassembly
attribute to 'NA'
"""
for sample in self.metadata:
try:
# Set the name of the filtered assembly file
filtered_outputfile = os.path.join(self.path, 'raw_assemblies', '{}.fasta'.format(sample.name))
# Set the name of the unfiltered spades assembly output file
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if size == 0:
sample.general.bestassemblyfile = 'NA'
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sample.general.bestassemblyfile = sample.general.assemblyfile
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sample.general.bestassemblyfile = 'NA'
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sample.general.filteredfile = filtered_outputfile
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sample.general.assemblyfile = 'NA'
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outini/python-pylls | pylls/cachet.py | ComponentGroups.get | def get(self, group_id=None, **kwargs):
"""Get component groups
:param group_id: Component group ID (optional)
:return: Component groups data (:class:`dict`)
Additional named arguments may be passed and are directly transmitted
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.. seealso:: https://docs.cachethq.io/reference#get-componentgroups
.. seealso:: https://docs.cachethq.io/docs/advanced-api-usage
"""
path = 'components/groups'
if group_id is not None:
path += '/%s' % group_id
return self.paginate_get(path, data=kwargs) | python | def get(self, group_id=None, **kwargs):
"""Get component groups
:param group_id: Component group ID (optional)
:return: Component groups data (:class:`dict`)
Additional named arguments may be passed and are directly transmitted
to API. It is useful to use the API search features.
.. seealso:: https://docs.cachethq.io/reference#get-componentgroups
.. seealso:: https://docs.cachethq.io/docs/advanced-api-usage
"""
path = 'components/groups'
if group_id is not None:
path += '/%s' % group_id
return self.paginate_get(path, data=kwargs) | [
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outini/python-pylls | pylls/cachet.py | ComponentGroups.create | def create(self, name, order=None, collapsed=None):
"""Create a new Component Group
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:param int order: Order of the component group
:param int collapsed: Collapse the group? 0-2
:return: Created component group data (:class:`dict`)
.. seealso:: https://docs.cachethq.io/reference#post-componentgroups
"""
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return self._post('components/groups', data=data)['data'] | python | def create(self, name, order=None, collapsed=None):
"""Create a new Component Group
:param str name: Name of the component group
:param int order: Order of the component group
:param int collapsed: Collapse the group? 0-2
:return: Created component group data (:class:`dict`)
.. seealso:: https://docs.cachethq.io/reference#post-componentgroups
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data = ApiParams()
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outini/python-pylls | pylls/cachet.py | ComponentGroups.update | def update(self, group_id, name=None, order=None, collapsed=None):
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"""Update a Component Group
:param int group_id: Component Group ID
:param str name: Name of the component group
:param int order: Order of the group
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"""
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outini/python-pylls | pylls/cachet.py | Incidents.create | def create(self, name, message, status, visible, component_id=None,
component_status=None, notify=None, created_at=None,
template=None, tplvars=None):
"""Create a new Incident
:param str name: Name of the incident
:param str message: Incident explanation message
:param int status: Status of the incident
:param int visible: Whether the incident is publicly visible
:param int component_id: Component to update
:param int component_status: The status to update the given component
:param bool notify: Whether to notify subscribers
:param str created_at: When the incident was created
:param str template: The template slug to use
:param list tplvars: The variables to pass to the template
:return: Created incident data (:class:`dict`)
.. seealso:: https://docs.cachethq.io/reference#incidents
"""
data = ApiParams()
data['name'] = name
data['message'] = message
data['status'] = status
data['visible'] = visible
data['component_id'] = component_id
data['component_status'] = component_status
data['notify'] = notify
data['created_at'] = created_at
data['template'] = template
data['vars'] = tplvars
return self._post('incidents', data=data)['data'] | python | def create(self, name, message, status, visible, component_id=None,
component_status=None, notify=None, created_at=None,
template=None, tplvars=None):
"""Create a new Incident
:param str name: Name of the incident
:param str message: Incident explanation message
:param int status: Status of the incident
:param int visible: Whether the incident is publicly visible
:param int component_id: Component to update
:param int component_status: The status to update the given component
:param bool notify: Whether to notify subscribers
:param str created_at: When the incident was created
:param str template: The template slug to use
:param list tplvars: The variables to pass to the template
:return: Created incident data (:class:`dict`)
.. seealso:: https://docs.cachethq.io/reference#incidents
"""
data = ApiParams()
data['name'] = name
data['message'] = message
data['status'] = status
data['visible'] = visible
data['component_id'] = component_id
data['component_status'] = component_status
data['notify'] = notify
data['created_at'] = created_at
data['template'] = template
data['vars'] = tplvars
return self._post('incidents', data=data)['data'] | [
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outini/python-pylls | pylls/cachet.py | Incidents.update | def update(self, incident_id, name=None, message=None, status=None,
visible=None, component_id=None, component_status=None,
notify=None, created_at=None, template=None, tpl_vars=None):
"""Update an Incident
:param int incident_id: Incident ID
:param str name: Name of the incident
:param str message: Incident explanation message
:param int status: Status of the incident
:param int visible: Whether the incident is publicly visible
:param int component_id: Component to update
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:param bool notify: Whether to notify subscribers
:param str created_at: When the incident was created
:param str template: The template slug to use
:param list tpl_vars: The variables to pass to the template
:return: Created incident data (:class:`dict`)
.. seealso:: https://docs.cachethq.io/reference#update-an-incident
"""
data = ApiParams()
data['name'] = name
data['message'] = message
data['status'] = status
data['visible'] = visible
data['component_id'] = component_id
data['component_status'] = component_status
data['notify'] = notify
data['created_at'] = created_at
data['template'] = template
data['vars'] = tpl_vars
return self._put('incidents/%s' % incident_id, data=data)['data'] | python | def update(self, incident_id, name=None, message=None, status=None,
visible=None, component_id=None, component_status=None,
notify=None, created_at=None, template=None, tpl_vars=None):
"""Update an Incident
:param int incident_id: Incident ID
:param str name: Name of the incident
:param str message: Incident explanation message
:param int status: Status of the incident
:param int visible: Whether the incident is publicly visible
:param int component_id: Component to update
:param int component_status: The status to update the given component
:param bool notify: Whether to notify subscribers
:param str created_at: When the incident was created
:param str template: The template slug to use
:param list tpl_vars: The variables to pass to the template
:return: Created incident data (:class:`dict`)
.. seealso:: https://docs.cachethq.io/reference#update-an-incident
"""
data = ApiParams()
data['name'] = name
data['message'] = message
data['status'] = status
data['visible'] = visible
data['component_id'] = component_id
data['component_status'] = component_status
data['notify'] = notify
data['created_at'] = created_at
data['template'] = template
data['vars'] = tpl_vars
return self._put('incidents/%s' % incident_id, data=data)['data'] | [
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outini/python-pylls | pylls/cachet.py | Metrics.create | def create(self, name, suffix, description, default_value, display=None):
"""Create a new Metric
:param str name: Name of metric
:param str suffix: Metric unit
:param str description: Description of what the metric is measuring
:param int default_value: Default value to use when a point is added
:param int display: Display the chart on the status page
:return: Created metric data (:class:`dict`)
.. seealso:: https://docs.cachethq.io/reference#metrics
"""
data = ApiParams()
data['name'] = name
data['suffix'] = suffix
data['description'] = description
data['default_value'] = default_value
data['display'] = display
return self._post('metrics', data=data)['data'] | python | def create(self, name, suffix, description, default_value, display=None):
"""Create a new Metric
:param str name: Name of metric
:param str suffix: Metric unit
:param str description: Description of what the metric is measuring
:param int default_value: Default value to use when a point is added
:param int display: Display the chart on the status page
:return: Created metric data (:class:`dict`)
.. seealso:: https://docs.cachethq.io/reference#metrics
"""
data = ApiParams()
data['name'] = name
data['suffix'] = suffix
data['description'] = description
data['default_value'] = default_value
data['display'] = display
return self._post('metrics', data=data)['data'] | [
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outini/python-pylls | pylls/cachet.py | MetricPoints.create | def create(self, metric_id, value, timestamp=None):
"""Add a Metric Point to a Metric
:param int metric_id: Metric ID
:param int value: Value to plot on the metric graph
:param str timestamp: Unix timestamp of the point was measured
:return: Created metric point data (:class:`dict`)
.. seealso:: https://docs.cachethq.io/reference#post-metric-points
"""
data = ApiParams()
data['value'] = value
data['timestamp'] = timestamp
return self._post('metrics/%s/points' % metric_id, data=data)['data'] | python | def create(self, metric_id, value, timestamp=None):
"""Add a Metric Point to a Metric
:param int metric_id: Metric ID
:param int value: Value to plot on the metric graph
:param str timestamp: Unix timestamp of the point was measured
:return: Created metric point data (:class:`dict`)
.. seealso:: https://docs.cachethq.io/reference#post-metric-points
"""
data = ApiParams()
data['value'] = value
data['timestamp'] = timestamp
return self._post('metrics/%s/points' % metric_id, data=data)['data'] | [
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outini/python-pylls | pylls/cachet.py | Subscribers.create | def create(self, email, verify=None, components=None):
"""Create a new subscriber
:param str email: Email address to subscribe
:param bool verify: Whether to send verification email
:param list components: Components ID list, defaults to all
:return: Created subscriber data (:class:`dict`)
.. seealso:: https://docs.cachethq.io/reference#subscribers
"""
data = ApiParams()
data['email'] = email
data['verify'] = verify
data['components'] = components
return self._post('subscribers', data=data)['data'] | python | def create(self, email, verify=None, components=None):
"""Create a new subscriber
:param str email: Email address to subscribe
:param bool verify: Whether to send verification email
:param list components: Components ID list, defaults to all
:return: Created subscriber data (:class:`dict`)
.. seealso:: https://docs.cachethq.io/reference#subscribers
"""
data = ApiParams()
data['email'] = email
data['verify'] = verify
data['components'] = components
return self._post('subscribers', data=data)['data'] | [
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lowandrew/OLCTools | coreGenome/core.py | AnnotatedCore.annotatedcore | def annotatedcore(self):
"""
Calculates the core genome of organisms using custom databases
"""
logging.info('Calculating annotated core')
# Determine the total number of core genes
self.total_core()
# Iterate through all the samples, and process all Escherichia
for sample in self.metadata:
if sample.general.bestassemblyfile != 'NA':
# Create a set to store the names of all the core genes in this strain
sample[self.analysistype].coreset = set()
if sample.general.referencegenus == 'Escherichia':
# Add the Escherichia sample to the runmetadata
self.runmetadata.samples.append(sample)
# Parse the BLAST report
try:
report = sample[self.analysistype].report
self.blastparser(report=report,
sample=sample,
fieldnames=self.fieldnames)
except KeyError:
sample[self.analysistype].coreset = list()
# Create the report
self.reporter() | python | def annotatedcore(self):
"""
Calculates the core genome of organisms using custom databases
"""
logging.info('Calculating annotated core')
# Determine the total number of core genes
self.total_core()
# Iterate through all the samples, and process all Escherichia
for sample in self.metadata:
if sample.general.bestassemblyfile != 'NA':
# Create a set to store the names of all the core genes in this strain
sample[self.analysistype].coreset = set()
if sample.general.referencegenus == 'Escherichia':
# Add the Escherichia sample to the runmetadata
self.runmetadata.samples.append(sample)
# Parse the BLAST report
try:
report = sample[self.analysistype].report
self.blastparser(report=report,
sample=sample,
fieldnames=self.fieldnames)
except KeyError:
sample[self.analysistype].coreset = list()
# Create the report
self.reporter() | [
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lowandrew/OLCTools | coreGenome/core.py | AnnotatedCore.total_core | def total_core(self):
"""
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corefile = os.path.join(self.reffilepath, self.analysistype, 'Escherichia', 'core_combined.fasta')
for record in SeqIO.parse(corefile, 'fasta'):
gene_name = record.id.split('-')[0]
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"""
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sirfoga/pyhal | hal/system/process.py | Process.get_simple_output | def get_simple_output(self, stderr=STDOUT):
"""Executes a simple external command and get its output
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:param stderr: where to put stderr
:return: output of command
"""
args = shlex.split(self.cmd)
proc = Popen(args, stdout=PIPE, stderr=stderr)
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"""Executes a simple external command and get its output
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:param stderr: where to put stderr
:return: output of command
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sirfoga/pyhal | hal/system/process.py | Process.get_complex_output | def get_complex_output(self, stderr=STDOUT):
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:param stderr: where to put stderr
:return: output of command
"""
proc = Popen(self.cmd, shell=True, stdout=PIPE, stderr=stderr)
return proc.stdout.readlines() | python | def get_complex_output(self, stderr=STDOUT):
"""Executes a piped command and get the lines of the output in a list
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:return: output of command
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sirfoga/pyhal | hal/system/process.py | Process.keep_alive | def keep_alive(self):
"""Keeps a process alive. If the process terminates, it will restart it
The terminated processes become zombies. They die when their parent
terminates
"""
while True:
pid = self.execute_in_background()
p = psutil.Process(pid)
while p.is_running() and str(p.status) != 'zombie':
os.system('sleep 5') | python | def keep_alive(self):
"""Keeps a process alive. If the process terminates, it will restart it
The terminated processes become zombies. They die when their parent
terminates
"""
while True:
pid = self.execute_in_background()
p = psutil.Process(pid)
while p.is_running() and str(p.status) != 'zombie':
os.system('sleep 5') | [
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portfors-lab/sparkle | sparkle/tools/util.py | increment_title | def increment_title(title):
"""
Increments a string that ends in a number
"""
count = re.search('\d+$', title).group(0)
new_title = title[:-(len(count))] + str(int(count)+1)
return new_title | python | def increment_title(title):
"""
Increments a string that ends in a number
"""
count = re.search('\d+$', title).group(0)
new_title = title[:-(len(count))] + str(int(count)+1)
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Frzk/Ellis | ellis/rule.py | Rule.check_limit | def check_limit(self, limit):
"""
Checks if the given limit is valid.
A limit must be > 0 to be considered valid.
Raises ValueError when the *limit* is not > 0.
"""
if limit > 0:
self.limit = limit
else:
raise ValueError("Rule limit must be strictly > 0 ({0} given)"
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return self | python | def check_limit(self, limit):
"""
Checks if the given limit is valid.
A limit must be > 0 to be considered valid.
Raises ValueError when the *limit* is not > 0.
"""
if limit > 0:
self.limit = limit
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jmbhughes/suvi-trainer | scripts/make_movie_frames.py | get_args | def get_args():
"""
request the arguments for running
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ap.add_argument("start", help="date string as start time")
ap.add_argument("end", help="date string as end time")
ap.add_argument("step", type=float, help="fraction of a day to step by")
ap.add_argument("--config", help="path to a config file", default="config.json")
return ap.parse_args() | python | def get_args():
"""
request the arguments for running
"""
ap = argparse.ArgumentParser(description="Create frames for a movie that can be compiled using ffmpeg")
ap.add_argument("start", help="date string as start time")
ap.add_argument("end", help="date string as end time")
ap.add_argument("step", type=float, help="fraction of a day to step by")
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jmbhughes/suvi-trainer | scripts/make_movie_frames.py | main | def main():
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args.end = date_parser.parse(args.end)
args.step = timedelta(args.step)
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times = [args.start + i * args.step for i in range(int((args.end - args.start) / args.step))]
for i, time in enumerate(times):
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"""
process the main task
"""
args = get_args()
args.start = date_parser.parse(args.start)
args.end = date_parser.parse(args.end)
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yamcs/yamcs-python | yamcs-client/examples/events.py | listen_to_event_updates | def listen_to_event_updates():
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sleep(5) | python | def listen_to_event_updates():
"""Subscribe to events."""
def callback(event):
print('Event:', event)
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JukeboxPipeline/jukeboxmaya | src/jukeboxmaya/mayaplugins/jbscene.py | get_current_scene_node | def get_current_scene_node():
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:rtype: str | None
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"""Return the name of the jb_sceneNode, that describes the current scene or None if there is no scene node.
:returns: the full name of the node or none, if there is no scene node
:rtype: str | None
:raises: None
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portfors-lab/sparkle | sparkle/gui/plotting/protocoldisplay.py | ProtocolDisplay.updateSpec | def updateSpec(self, *args, **kwargs):
"""Updates the spectrogram. First argument can be a filename,
or a data array. If no arguments are given, clears the spectrograms.
For other arguments, see: :meth:`SpecWidget.updateData<sparkle.gui.plotting.pyqtgraph_widgets.SpecWidget.updateData>`
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"""Updates the spectrogram. First argument can be a filename,
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For other arguments, see: :meth:`SpecWidget.updateData<sparkle.gui.plotting.pyqtgraph_widgets.SpecWidget.updateData>`
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portfors-lab/sparkle | sparkle/gui/plotting/protocoldisplay.py | ProtocolDisplay.showSpec | def showSpec(self, fname):
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portfors-lab/sparkle | sparkle/gui/plotting/protocoldisplay.py | ProtocolDisplay.updateSpiketrace | def updateSpiketrace(self, xdata, ydata, plotname=None):
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:param xdata: index values
:type xdata: numpy.ndarray
:param ydata: values to plot
:type ydata: numpy.ndarray
"""
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plotname = self.responsePlots.keys()[0]
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self.responsePlots[plotname].addTraces(xdata, ydata) | python | def updateSpiketrace(self, xdata, ydata, plotname=None):
"""Updates the spike trace
:param xdata: index values
:type xdata: numpy.ndarray
:param ydata: values to plot
:type ydata: numpy.ndarray
"""
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portfors-lab/sparkle | sparkle/gui/plotting/protocoldisplay.py | ProtocolDisplay.updateSignal | def updateSignal(self, xdata, ydata, plotname=None):
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:param ydata: brain potential at time points
"""
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portfors-lab/sparkle | sparkle/gui/plotting/protocoldisplay.py | ProtocolDisplay.setXlimits | def setXlimits(self, lims):
"""Sets the X axis limits of the trace plot
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:type lims: (float, float)
"""
# update all "linked", plots
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sizes[1] +=1
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self._ignore_range_signal = False | python | def setXlimits(self, lims):
"""Sets the X axis limits of the trace plot
:param lims: (min, max) of x axis, in same units as data
:type lims: (float, float)
"""
# update all "linked", plots
self.specPlot.setXlim(lims)
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plot.setXlim(lims)
# ridiculous...
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portfors-lab/sparkle | sparkle/gui/plotting/protocoldisplay.py | ProtocolDisplay.setNreps | def setNreps(self, nreps):
"""Sets the number of reps before the raster plot resets"""
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plot.setNreps(nreps) | python | def setNreps(self, nreps):
"""Sets the number of reps before the raster plot resets"""
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portfors-lab/sparkle | sparkle/gui/plotting/protocoldisplay.py | ProtocolDisplay.specAutoRange | def specAutoRange(self):
"""Auto adjusts the visible range of the spectrogram"""
trace_range = self.responsePlots.values()[0].viewRange()[0]
vb = self.specPlot.getViewBox()
vb.autoRange(padding=0)
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"""Auto adjusts the visible range of the spectrogram"""
trace_range = self.responsePlots.values()[0].viewRange()[0]
vb = self.specPlot.getViewBox()
vb.autoRange(padding=0)
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] | 5fad1cf2bec58ec6b15d91da20f6236a74826110 | https://github.com/portfors-lab/sparkle/blob/5fad1cf2bec58ec6b15d91da20f6236a74826110/sparkle/gui/plotting/protocoldisplay.py#L209-L214 | train | 54,398 |
jmbhughes/suvi-trainer | suvitrainer/gui.py | App.save | def save(self):
""" Save as a FITS file and attempt an upload if designated in the configuration file """
out = Outgest(self.output, self.selection_array.astype('uint8'), self.headers, self.config_path)
out.save()
out.upload() | python | def save(self):
""" Save as a FITS file and attempt an upload if designated in the configuration file """
out = Outgest(self.output, self.selection_array.astype('uint8'), self.headers, self.config_path)
out.save()
out.upload() | [
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