def command_mpd(self, args):
args = shell_split(args)
c = mpd.MPDClient()
c.connect(
host=self.config.get('host', 'localhost'),
port=self.config.get('port', '6600'))
password = self.config.get('password', '')
if password:
c.password(password) #pylint: disable=no-member
current = c.currentsong() #pylint: disable=no-member
artist = current.get('artist', 'Unknown artist')
album = current.get('album', 'Unknown album')
title = current.get('title', base(
current.get('file', 'Unknown title')))
s = '%s - %s (%s)' % (artist, title, album)
if 'full' in args:
if 'elapsed' in current and 'time' in current:
current_time = float(c.status()['elapsed']) #pylint: disable=no-member
percents = int(current_time / float(current['time']) * 10)
s += ' \x192}[\x191}' + '-' * (
percents - 1) + '\x193}+' + '\x191}' + '-' * (
10 - percents - 1) + '\x192}]\x19o'
if not self.api.send_message('%s' % (s, )):
self.api.information('Cannot send result (%s)' % s, 'Error')
def command_mpd(self, args):
args = shell_split(args)
c = mpd.MPDClient()
c.connect(
host=self.config.get('host', 'localhost'),
port=self.config.get('port', '6600'))
password = self.config.get('password', '')
if password:
c.password(password) #pylint: disable=no-member
current = c.currentsong() #pylint: disable=no-member
artist = current.get('artist', 'Unknown artist')
album = current.get('album', 'Unknown album')
title = current.get('title', base(
current.get('file', 'Unknown title')))
s = '%s - %s (%s)' % (artist, title, album)
if 'full' in args:
if 'elapsed' in current and 'time' in current:
current_time = float(c.status()['elapsed']) #pylint: disable=no-member
percents = int(current_time / float(current['time']) * 10)
s += ' \x192}[\x191}' + '-' * (
percents - 1) + '\x193}+' + '\x191}' + '-' * (
10 - percents - 1) + '\x192}]\x19o'
if not self.api.send_message('%s' % (s, )):
self.api.information('Cannot send result (%s)' % s, 'Error')
def move(src, dst, copy_function=shutil.copy2):
"""Recursively move a file or directory to another location. This is
similar to the Unix "mv" command. Return the file or directory's
destination.
If the destination is a directory or a symlink to a directory, the source
is moved inside the directory. The destination path must not already
exist.
If the destination already exists but is not a directory, it may be
overwritten depending on os.rename() semantics.
If the destination is on our current filesystem, then rename() is used.
Otherwise, src is copied to the destination and then removed. Symlinks are
recreated under the new name if os.rename() fails because of cross
filesystem renames.
The optional `copy_function` argument is a callable that will be used
to copy the source or it will be delegated to `copytree`.
By default, copy2() is used, but any function that supports the same
signature (like copy()) can be used.
A lot more could be done here... A look at a mv.c shows a lot of
the issues this implementation glosses over.
"""
real_dst = dst
if isdir(dst):
if samefile(src, dst):
# We might be on a case insensitive filesystem,
# perform the rename anyway.
os.rename(src, dst)
return
real_dst = join(dst, base(src))
if exists(real_dst):
raise Error("Destination path '%s' already exists" % real_dst)
try:
os.rename(src, real_dst)
except OSError:
if os.path.islink(src):
linkto = os.readlink(src)
os.symlink(linkto, real_dst)
os.unlink(src)
elif os.path.isdir(src):
if ischild(src, dst):
raise Error("Cannot move a directory '%s' into itself"
" '%s'." % (src, dst))
shutil.copytree(src,
real_dst,
copy_function=copy_function,
symlinks=True)
shutil.rmtree(src)
else:
copy_function(src, real_dst)
os.unlink(src)
return real_dst
def __init__(self, transcriptome_fn, database_fn, output_fn=None,
cutoff=.00001, n_threads=1, n_nodes=None, use_existing_db=None):
self.transcriptome_fn = transcriptome_fn
self.renamed_fn = self.transcriptome_fn + '.renamed'
self.name_map_fn = self.transcriptome_fn + '.names.csv'
self.translated_fn = self.renamed_fn + '.pep'
self.database_fn = database_fn
self.renamed_database_fn = self.database_fn + '.renamed'
self.database_name_map_fn = self.database_fn + '.names.csv'
self.n_threads = n_threads
self.cutoff = cutoff
self.use_existing_db = use_existing_db
self.db_x_translated_fn = '{0}.x.{1}.maf'.format(base(self.renamed_database_fn),
base(self.translated_fn))
self.translated_x_db_fn = '{0}.x.{1}.maf'.format(base(self.translated_fn),
base(self.renamed_database_fn))
self.output_fn = output_fn
if self.output_fn is None:
self.output_prefix = '{0}.x.{1}.rbl'.format(base(self.transcriptome_fn),
base(self.database_fn))
self.unmapped_output_fn = self.output_prefix + '.unmapped.csv'
self.output_fn = self.output_prefix + '.csv'
self.bh = BestHits(comparison_cols=['E', 'EG2'])
def Automatic_Tracking(self):
"""
function takes (the trimmed in time) videofiles and launches flytracker to track them.
"""
from os.path import basename as base # see function get_fname for clarification on base
eng = matlab.engine.start_matlab() # import matlab engine
# for each of the videos, launch Logans auto_track.m matlab script which inputs these
# variables into the Flytracker matlab script tracker.m
for f_vid in self.matlab_vid_paths:
# define matlab inputs
self.f_vid = f_vid
self.f_calib = self.f_vid[:-4] + '_calibration.mat'
"""
THE LINE BELOW IS THE PROBLEM CHILD
"""
self.root = os.path.dirname(self.f_vid) + '\\'
# Launch Fly Tracker Tracking
eng.auto_track(
{self.root}, base(self.f_vid), self.f_calib, nargout=0
) # no matlab argument outputs, else code drowns in a sea of errors
"""
THIS IS WHAT LOGAN THINKS THE LINE SHOULD BE!!!!!
# Launch Fly Tracker Tracking
eng.auto_track({os.path.dirname(self.f_vid) + '\\'},
base(self.f_vid),
self.f_calib,
nargout=0) # no matlab argument outputs, else code drowns in a sea of errors
"""
# Move the video file once you're done tracking it into the folder JAABA needs it to be in
os.rename(
self.f_vid,
self.root + base(self.f_vid)[:-4] + '\\' + base(self.f_vid))
# Add the renamed path above to a list for later use by JAABA
self.output_list.append(self.root + base(self.f_vid)[:-4] + '\\' +
base(self.f_vid))
try: # exit matlab
eng.quit()
except: # weak error exception = bad programming logan
pass
def __init__(self, transcriptome_fn, database_fn, output_fn=None,
model_fn=None, cutoff=.00001, n_threads=1, use_existing_db=True):
self.crbl_output_fn = output_fn
self.crbl_output_prefix = output_fn
if output_fn is None:
self.crbl_output_prefix = '{0}.x.{1}.crbl'.format(base(transcriptome_fn),
base(database_fn))
self.crbl_output_fn = self.crbl_output_prefix + '.csv'
self.unmapped_crbl_output_fn = self.crbl_output_prefix + '.unmapped.csv'
self.model_fn = model_fn
if model_fn is None:
self.model_fn = self.crbl_output_prefix + '.model.csv'
self.model_plot_fn = self.model_fn + '.plot.pdf'
super(CRBL, self).__init__(transcriptome_fn,
database_fn,
output_fn=None,
cutoff=cutoff,
n_threads=n_threads,
use_existing_db=use_existing_db)
def image_intercept(bbox_geojson,
image_folder,
out_folder,
image_id_field,
create_subset=False):
gdf = gpd.read_file(bbox_geojson)
unique = gdf[image_id_field].unique()
if create_subset == True:
for i in image_id_field:
src = op(image_folder, i)
dst = op(subset_folder, i)
copyfile(src, dst)
with open(op(out_folder,
sp(base(bbox_geojson))[0] + "_images.csv"), 'w') as f:
writer = csv.writer(f)
writer.writerows(zip(unique))
def __init__(self, image_name=None, user_id=None):
self.image_name = image_name
self.path_to_img_translation = create_path(split(base(image_name))[0]+"_translation")
self.langs = {'es':'spanish','fr':'french','en':'english','du':'dutch'}
def __init__(self, image_name=None, user_id=None):
self.image_name = image_name
self.path_to_img_translation = create_path(split(base(image_name))[0] + "_translation")
self.langs = {"es": "spanish", "fr": "french", "en": "english", "du": "dutch"}