def find_plugins():
"""
return (list of str): list of the filenames of the plugins available
"""
hf = get_home_folder()
# Order of paths matters, so that the user can override a system plugin
if os.name == "nt":
paths = (os.path.join(odemis.__path__[0], u"plugins/"),
# There is no official place for putting per-user system
# overriding file, so just put with the config file.
os.path.join(hf, u".config/odemis/plugins/")
)
else: # hopefully this is Linux
paths = (u"/usr/share/odemis/plugins/",
u"/usr/share/local/odemis/plugins/",
os.path.join(hf, u".local/share/odemis/plugins/"),
)
plugins = {} # script name -> full path
for p in paths:
for fn in glob.glob(p + u"*.py"):
if os.path.isfile(fn):
# Discard previous plugin with same name
sn = os.path.basename(fn)
plugins[sn] = fn
return sorted(plugins.values())
def find_plugins():
"""
return (list of str): list of the filenames of the plugins available
"""
hf = get_home_folder()
# Order of paths matters, so that the user can override a system plugin
if os.name == "nt":
# Typically, on Windows, the odemis package is a single file located into
# a dedicated OdemisViewer folder which contains also all the dependencies
# => search inside this folder
paths = (
os.path.join(odemis.__path__[0], u"..", u"plugins"),
# There is no official place for putting per-user system
# overriding file, so just put with the config file.
os.path.join(hf, u".config", u"odemis", u"plugins"))
else: # hopefully this is Linux
paths = (
u"/usr/lib/odemis/plugins",
u"/usr/local/lib/odemis/plugins",
os.path.join(hf, u".local/share/odemis/plugins"),
)
plugins = {} # script name -> full path
for p in paths:
for fn in glob.glob(os.path.join(p, u"*.py")):
if os.path.isfile(fn):
# Discard previous plugin with same name
sn = os.path.basename(fn)
plugins[sn] = fn
return sorted(plugins.values())
def find_plugins():
"""
return (list of str): list of the filenames of the plugins available
"""
hf = get_home_folder()
# Order of paths matters, so that the user can override a system plugin
if os.name == "nt":
paths = (
os.path.join(odemis.__path__[0], u"plugins/"),
# There is no official place for putting per-user system
# overriding file, so just put with the config file.
os.path.join(hf, u".config/odemis/plugins/"))
else: # hopefully this is Linux
paths = (
u"/usr/share/odemis/plugins/",
u"/usr/share/local/odemis/plugins/",
os.path.join(hf, u".local/share/odemis/plugins/"),
)
plugins = {} # script name -> full path
for p in paths:
for fn in glob.glob(p + u"*.py"):
if os.path.isfile(fn):
# Discard previous plugin with same name
sn = os.path.basename(fn)
plugins[sn] = fn
return sorted(plugins.values())
def find_plugins():
"""
return (list of str): list of the filenames of the plugins available
"""
hf = get_home_folder()
# Order of paths matters, so that the user can override a system plugin
if os.name == "nt":
# Typically, on Windows, the odemis package is a single file located into
# a dedicated OdemisViewer folder which contains also all the dependencies
# => search inside this folder
paths = (os.path.join(odemis.__path__[0], u"..", u"plugins"),
# There is no official place for putting per-user system
# overriding file, so just put with the config file.
os.path.join(hf, u".config", u"odemis", u"plugins")
)
else: # hopefully this is Linux
paths = (u"/usr/lib/odemis/plugins",
u"/usr/local/lib/odemis/plugins",
os.path.join(hf, u".local/share/odemis/plugins"),
)
plugins = {} # script name -> full path
for p in paths:
for fn in glob.glob(os.path.join(p, u"*.py")):
if os.path.isfile(fn):
# Discard previous plugin with same name
sn = os.path.basename(fn)
plugins[sn] = fn
return sorted(plugins.values())
def init_logger(level=logging.DEBUG, log_file=None):
"""
Initializes the logger to some nice defaults
To be called only once, at the initialisation
"""
if level <= logging.INFO:
pyrolog = logging.getLogger("Pyro4")
pyrolog.setLevel(min(pyrolog.getEffectiveLevel(), level))
logging.basicConfig(format=" - %(levelname)s \t%(message)s")
l = logging.getLogger()
l.setLevel(level)
frm = "%(asctime)s\t%(levelname)s\t%(module)s:%(lineno)d:\t%(message)s"
l.handlers[0].setFormatter(logging.Formatter(frm))
# Create file handler
# Path to the log file
logfile_path = log_file or os.path.join(get_home_folder(), LOG_FILE)
file_format = logging.Formatter(frm)
# Max 5 log files of 10Mb
file_handler = RotatingFileHandler(logfile_path,
maxBytes=10 * (2**20),
backupCount=5)
file_handler.setFormatter(file_format)
log.addHandler(file_handler)
def init_logger(level=logging.DEBUG, log_file=None):
"""
Initializes the logger to some nice defaults
To be called only once, at the initialisation
"""
if level <= logging.INFO:
pyrolog = logging.getLogger("Pyro4")
pyrolog.setLevel(min(pyrolog.getEffectiveLevel(), level))
logging.basicConfig(format=" - %(levelname)s \t%(message)s")
l = logging.getLogger()
l.setLevel(level)
frm = "%(asctime)s %(levelname)-7s %(module)-15s: %(message)s"
l.handlers[0].setFormatter(logging.Formatter(frm))
# Create file handler
# Path to the log file
logfile_path = log_file or os.path.join(get_home_folder(), LOG_FILE)
# Formatting string for logging messages to file
frm = "%(asctime)s %(levelname)-7s %(module)s:%(lineno)d: %(message)s"
file_format = logging.Formatter(frm)
# Max 5 log files of 10Mb
file_handler = RotatingFileHandler(logfile_path, maxBytes=10 * (2 ** 20), backupCount=5)
file_handler.setFormatter(file_format)
log.addHandler(file_handler)
def test_find_plugins(self):
""" Test that find_plugins can find plugin modules"""
paths = plugin.find_plugins()
if not paths:
# A typical reason for this to fail is that no plugin are installed
hf = get_home_folder()
upath = os.path.join(hf, u".local/share/odemis/plugins")
if not os.path.isdir(upath) or not os.listdir(upath):
self.fail(
"Please install at least one plugin in ~/.local/share/odemis/plugins"
)
self.assertGreater(len(paths), 0)
daterev = time.strftime("%d%m%Y")
timeshrt = time.strftime("%H%M")
timeshrt_colon = time.strftime("%H:%M")
timelng = time.strftime("%H%M%S")
# date_sl = time.strftime("%Y/%m/%d")
# timelng_sl = time.strftime("%H/%M/%S")
current_year = time.strftime("%Y")
dshrtrev = time.strftime("%d%m%y")
# Note: dateshrt cannot be used in tests, as on days similar to the year, such as 20-10-20,
# it's not clear what is the day and what is the year, but the code convention is to
# guess DDMMYY (aka dshrtrev).
# dateshrt = time.strftime("%y%m%d")
dshrtrev_hyphen = time.strftime("%d-%m-%y")
EXTS = ('.tiff', '.ome.tiff', '.0.ome.tiff', '.h5', '.hdf5')
PATH = get_home_folder()
class TestFilenameSuggestions(unittest.TestCase):
"""
Tests the util-acquisition functions for filename suggestions.
"""
def test_guess_pattern(self):
fn_ptns = {
'test-123': ('test-{cnt}', '123'),
'%stest-123' % date: ('{datelng}test-{cnt}', '123'),
'123-test-%s' % date: ('{cnt}-test-{datelng}', '123'),
'test-123-%s' % timeshrt: ('test-{cnt}-{timeshrt}', '123'),
'test-123-%s' % timeshrt_colon:
('test-{cnt}-{timeshrt_colon}', '123'),
'%s%s-acquisition' % (date, timelng):
import ConfigParser
from ConfigParser import NoOptionError
except ImportError: # Python 3 naming
import configparser as ConfigParser
from configparser import NoOptionError
import logging
import math
import os.path
from odemis.dataio import tiff
from odemis.acq.align import delphi
from odemis.gui.util import get_picture_folder, get_home_folder
import sys
from past.builtins import unicode
CONF_PATH = os.path.join(get_home_folder(), u".config/odemis")
ACQUI_PATH = get_picture_folder()
class Config(with_metaclass(ABCMeta, object)):
""" Abstract configuration super class
Configurations are built around the :py:class:`ConfigParser.SafeConfigParser` class.
The main difference is that the filename is fixed, and changes are automatically saved.
"""
@abstractproperty
def file_name(self):
"""Name of the configuration file"""
from abc import ABCMeta, abstractproperty
try:
import ConfigParser
from ConfigParser import NoOptionError
except ImportError: # Python 3 naming
import configparser as ConfigParser
from configparser import NoOptionError
import logging
import math
import os.path
from odemis.dataio import tiff
from odemis.acq.align import delphi
from odemis.gui.util import get_picture_folder, get_home_folder
CONF_PATH = os.path.join(get_home_folder(), u".config/odemis")
ACQUI_PATH = get_picture_folder()
class Config(object):
""" Abstract configuration super class
Configurations are built around the :py:class:`ConfigParser.SafeConfigParser` class.
The main difference is that the filename is fixed, and changes are automatically saved.
"""
__metaclass__ = ABCMeta
@abstractproperty
from odemis.dataio import get_available_formats
import odemis.gui
from odemis.gui.conf import get_acqui_conf
from odemis.gui.conf import util
from odemis.gui.plugin import Plugin, AcquisitionDialog
from odemis.gui.util import formats_to_wildcards, get_home_folder
import os.path
import time
import wx
try:
import configparser
except ImportError: # Python 2
import ConfigParser as configparser
CONF_FILE = os.path.join(get_home_folder(), ".config", "odemis", "cli_rgb.ini")
class RGBCLIntensity(Plugin):
name = "RGB CL-intensity"
__version__ = "1.2"
__author__ = u"Toon Coenen & Éric Piel"
__license__ = "GNU General Public License 2"
vaconf = OrderedDict((
("filter1", {
"label": "Blue",
"choices": util.format_band_choices,
}),
("filter2", {
"label": "Green",
