def vicvb_to_jbrowse(self,
genome_name,
annot_inp_fasta,
annot_out,
index_html,
data_dir_out
):
annot_out = util.abspath(annot_out)
index_html = util.abspath(index_html)
data_dir_out = util.abspath(data_dir_out)
if annot_inp_fasta:
annot_inp_fasta = util.abspath(annot_inp_fasta)
res_gb = self.vicvb_to_genbank(
genome_name=genome_name,
annot_out=annot_out,
annot_inp_fasta=annot_inp_fasta
)
res_gff = self.genbank_to_gff(genbank_file=res_gb["genbank_file"])
self.gff_to_jbrowse(
gff_file=res_gff["gff_file"],
index_html=index_html,
data_dir_out=data_dir_out
)
def install_jbrowse(install_dir,
root_url,
rename_to=None,
conf_file=None):
if not conf_file:
conf_file = config.get_default_conf_file()
install_dir = util.abspath(install_dir)
pkg_data_dir = config.get_pkg_data_dir()
jbrowse_zip = glob(pjoin(pkg_data_dir,"JBrowse*"))
assert len(jbrowse_zip) == 1, "Expected a single JBrowse archive "+\
"stored within the package data dir: %s" % (pkg_data_dir,)
jbrowse_zip = jbrowse_zip[0]
util.makedir(install_dir)
#context manager only works for zipfile in Python 2.7
f = zipfile.ZipFile(jbrowse_zip, 'r')
try:
install_name = os.path.dirname(f.namelist()[0])
assert (install_name not in (".","..")) and \
os.path.dirname(install_name) == "",\
"Unsafe path detected in JBrowse archive: {}".format(f.namelist()[0])
install_home = pjoin(install_dir,install_name)
#JBrowse setup script will not install Pelr modules
#if it is executed in a directory where it was ran before,
#even unsuccessfuly.
#Wack the existing directory:
if os.path.exists(install_home):
shutil.rmtree(install_home)
#somehow zipfile module wacks executable bits
#f.extractall(path=install_dir)
#unsafe:
check_call(["unzip","-q","-o",jbrowse_zip],cwd=install_dir)
finally:
f.close()
if rename_to:
install_home_new = pjoin(install_dir,rename_to)
if os.path.exists(install_home_new):
shutil.rmtree(install_home_new)
os.rename(install_home,install_home_new)
install_home = install_home_new
check_call(["./setup.sh"],cwd=install_home)
for line in fileinput.input(pjoin(install_home,"index.html"),inplace=True):
#Galaxy Web server intercepts 'data' in URL params, we need to use another name
print line.replace('queryParams.data','queryParams.jbrowse_data'),
conf = util.load_config_json(conf_file)
conf["jbrowse_bin_dir"] = util.abspath(pjoin(install_home,"bin"))
conf["jbrowse_url"] = util.urljoin_path(root_url,
os.path.basename(install_home))
util.save_config_json(conf,conf_file)
return conf_file
def export_handler(command):
def path_ok(path):
return os.path.isdir(path) and not os.path.exists(os.path.join(path, csv_filename(use_id=True)))
path = os.path.expanduser(request.args.get("path", get_export_path()))
if command == "info":
return flask.jsonify(
filename=csv_filename(use_id=True),
path=path,
default_path=get_export_path(),
ok=path_ok(path),
stats=stats(callback=dict),
)
elif command == "check_path":
ok = path_ok(path)
if ok:
conf.set("export_path", path)
conf.save()
return flask.jsonify(ok=ok)
elif command == "do_export":
if not path_ok(path):
return flask.jsonify(ok=False, error="Invalid path: %s" % path)
try:
shutil.copyfile(csv_path(), os.path.join(path, csv_filename(use_id=True)))
shutil.move(
csv_path(), util.abspath("backups", "%s-%s" % (csv_filename(), time.strftime("%d-%b-%Y-%H-%M-%S-%p")))
)
conf.set("export_id", conf.get("export_id", "1", type=int) + 1)
return flask.jsonify(ok=True)
except Exception as e:
return flask.jsonify(ok=False, error=str(e))
else:
flask.abort(404)
def load_grammar(base_structures, tag_dicts):
grammar_dir = util.abspath('grammar')
# with Timer('Loading grammar'):
with open(os.path.join(grammar_dir, 'rules.txt')) as f:
#regex = '\(([^()]+)\)'
for line in f:
fields = line.split()
# tags = tuple(re.findall(regex, fields[0])) # extracts the tags
tags = fields[0]
base_structures[tags] = float(fields[1]) # maps grammar rule (tags) to probability
tagdicts_dir = os.path.join(grammar_dir, 'seg_dist')
# with Timer('Loading tag dictionaries'):
for fname in os.listdir(tagdicts_dir):
if not fname.endswith('.txt'): continue
with open(os.path.join(tagdicts_dir, fname)) as f:
tag = fname.replace('.txt', '')
words = []
for line in f:
fields = line.split('\t')
try:
words.append((fields[0], float(fields[1])))
except:
sys.stderr.write("error inserting {} in the tag dictionary {}\n".format(fields, tag))
tag_dicts[tag] = words
def consistencyCheck(ref_csv,
outputBshellFile=None,
outPutResolutionFile=None):
try:
ref_imgs, _ = read_imgs_masks(ref_csv)
except:
ref_imgs = read_imgs(ref_csv)
if isfile(outputBshellFile) and isfile(outPutResolutionFile):
ref_bvals = read_bvals(outputBshellFile)
ref_res = np.load(outPutResolutionFile)
else:
ref_bshell_img = ref_imgs[0]
print(f'Using {ref_bshell_img} to determine b-shells')
inPrefix = abspath(ref_bshell_img).split('.nii')[0]
ref_bvals = findBShells(inPrefix + '.bval', outputBshellFile)
ref_res = load(ref_bshell_img).header['pixdim'][1:4]
np.save(outPutResolutionFile, ref_res)
print('b-shells are', ref_bvals)
print('\nSite', ref_csv, '\n')
print('Checking consistency of b-shells among subjects')
check_bshells(ref_imgs, ref_bvals)
print('spatial resolution is', ref_res)
print('Checking consistency of spatial resolution among subjects')
check_resolution(ref_imgs, ref_res)
def check_bshells(ref_imgs, ref_bvals):
unmatched = []
for imgPath in ref_imgs:
imgPath = local.path(imgPath)
if not imgPath.exists():
FileNotFoundError(imgPath)
inPrefix = abspath(imgPath).split('.nii')[0]
bvals = findBShells(inPrefix + '.bval')
if (bvals == ref_bvals).all():
print('b-shells matched for', imgPath.name)
else:
print(f'\nUnmatched b-shells for {imgPath.name}')
print(bvals)
print(f'ref_bvals {ref_bvals}\n')
unmatched.append(imgPath._path)
print('')
if len(unmatched):
print('Unmatched cases:')
print(unmatched)
raise ValueError(
'Leave out the unmatched cases or change the reference case for determining b-shell to run multi-shell-dMRIharmonization'
)
else:
print(
'All cases have same b-shells. Data is good for running multi-shell-dMRIharmonization'
)
print('')
def rename(folder, format):
"""
This function renames all images in a given
directory according to the pattern given in
the format given, init.
Format:
use NUM for the number of the image.
imgNUM -> img1, img2, .., img100,..
"""
# Get list of all files then rename images
path = util.abspath(folder)
names_lis = os.listdir(path)
os.chdir(path) # cwd to work with OS commands
# Scan for images and rename them
for i in range(0, len(names_lis)):
f = names_lis[i]
extension = get_extension(f)
location = "".join([path, "/", f])
# Need absolute location
#print("checking location %s. Is file? %s " % (location, is_image(location)))
if util.is_image(location):
new_f = "".join([format.replace("NUM", str(i)), ".", extension])
util.update_line("Renaming file %s to %s." % (f, new_f))
os.rename(f, new_f) #Tada, done
def save_frame(capture, num, path, w=100, h=100):
"""
This function will save the current
frame in the video capture to an image
file.
"""
# Video's dimensions
width = int(capture.get(3))
height = int(capture.get(4))
# Get number of images (rows*cols) in each frame
cols = int(width/w)
rows = int(height/h)
# Read specific frame
capture.set(1, num) # set to nth frame
ret, frame = capture.read()
# Loop to split image into many window_size images
for row in range(rows):
for col in range(cols):
# Gets the cropped image
img = frame[h*row:(row+1)*h, w*col:(col+1)*w]
name = "img%s-%s-%s.jpg" % (str(num), row, col)
cv2.imwrite(util.abspath(path) + "/" + name, img)
def install_jbrowse(install_dir, root_url, rename_to=None, conf_file=None):
if not conf_file:
conf_file = config.get_default_conf_file()
install_dir = util.abspath(install_dir)
pkg_data_dir = config.get_pkg_data_dir()
jbrowse_zip = glob(pjoin(pkg_data_dir, "JBrowse*"))
assert len(jbrowse_zip) == 1, "Expected a single JBrowse archive "+\
"stored within the package data dir: %s" % (pkg_data_dir,)
jbrowse_zip = jbrowse_zip[0]
util.makedir(install_dir)
#context manager only works for zipfile in Python 2.7
f = zipfile.ZipFile(jbrowse_zip, 'r')
try:
install_name = os.path.dirname(f.namelist()[0])
assert (install_name not in (".","..")) and \
os.path.dirname(install_name) == "",\
"Unsafe path detected in JBrowse archive: {}".format(f.namelist()[0])
install_home = pjoin(install_dir, install_name)
#JBrowse setup script will not install Pelr modules
#if it is executed in a directory where it was ran before,
#even unsuccessfuly.
#Wack the existing directory:
if os.path.exists(install_home):
shutil.rmtree(install_home)
#somehow zipfile module wacks executable bits
#f.extractall(path=install_dir)
#unsafe:
check_call(["unzip", "-q", "-o", jbrowse_zip], cwd=install_dir)
finally:
f.close()
if rename_to:
install_home_new = pjoin(install_dir, rename_to)
if os.path.exists(install_home_new):
shutil.rmtree(install_home_new)
os.rename(install_home, install_home_new)
install_home = install_home_new
check_call(["./setup.sh"], cwd=install_home)
for line in fileinput.input(pjoin(install_home, "index.html"),
inplace=True):
#Galaxy Web server intercepts 'data' in URL params, we need to use another name
print line.replace('queryParams.data', 'queryParams.jbrowse_data'),
conf = util.load_config_json(conf_file)
conf["jbrowse_bin_dir"] = util.abspath(pjoin(install_home, "bin"))
conf["jbrowse_url"] = util.urljoin_path(root_url,
os.path.basename(install_home))
util.save_config_json(conf, conf_file)
return conf_file
def __init__(self, *args, **kwargs):
super(ConfigForm, self).__init__(*args, **kwargs)
event_names = [('', '')]
for f in os.listdir(util.abspath('match_schedules')):
name, ext = os.path.splitext(f)
if ext == '.json':
event_names.append((name, name))
self.event_name.choices = event_names
def __init__(self, *args, **kwargs):
super(ConfigForm, self).__init__(*args, **kwargs)
event_names = [('', '')]
for f in os.listdir(util.abspath('match_schedules')):
name, ext = os.path.splitext(f)
if ext == '.json':
event_names.append((name, name))
self.event_name.choices = event_names
def separateAllBshells(ref_csv, ref_bvals_file, ncpu=4, outPrefix=None):
ref_bvals = read_bvals(ref_bvals_file)
try:
imgs, masks = read_imgs_masks(ref_csv)
except:
imgs = read_imgs(ref_csv)
masks = None
pool = Pool(int(ncpu))
for imgPath in imgs:
pool.apply_async(separateBshells,
kwds={
'imgPath': imgPath,
'ref_bvals': ref_bvals
},
error_callback=RAISE)
pool.close()
pool.join()
if outPrefix:
outPrefix = abspath(outPrefix)
else:
return
for bval in ref_bvals:
f = open(f'{outPrefix}_b{int(bval)}.csv', 'w')
if masks:
for imgPath, maskPath in zip(imgs, masks):
inPrefix = abspath(imgPath).split('.nii')[0]
bPrefix = inPrefix + f'_b{int(bval)}'
f.write(f'{bPrefix}.nii.gz,{maskPath}\n')
else:
for imgPath in imgs:
inPrefix = abspath(imgPath).split('.nii')[0]
bPrefix = inPrefix + f'_b{int(bval)}'
f.write(f'{bPrefix}.nii.gz\n')
f.close()
def joinBshells(imgPath, ref_bvals_file=None, ref_bvals=None, sep_prefix=None):
if ref_bvals_file:
print('Reading reference b-shell file ...')
ref_bvals = read_bvals(ref_bvals_file)
print('Joining b-shells for', imgPath)
imgPath = local.path(imgPath)
img = load(imgPath._path)
dim = img.header['dim'][1:5]
inPrefix = abspath(imgPath).split('.nii')[0]
directory = dirname(inPrefix)
prefix = basename(inPrefix)
bvalFile = inPrefix + '.bval'
bvecFile = inPrefix + '.bvec'
if sep_prefix:
harmPrefix = pjoin(directory, sep_prefix + prefix)
else:
harmPrefix = inPrefix
if not isfile(harmPrefix + '.bval'):
copyfile(bvalFile, harmPrefix + '.bval')
if not isfile(harmPrefix + '.bvec'):
copyfile(bvecFile, harmPrefix + '.bvec')
bvals = np.array(read_bvals(inPrefix + '.bval'))
joinedDwi = np.zeros((dim[0], dim[1], dim[2], dim[3]), dtype='float32')
for bval in ref_bvals:
# ind= np.where(bval==bvals)[0]
ind = np.where(abs(bval - bvals) <= BSHELL_MIN_DIST)[0]
if bval == 0.:
b0Img = load(inPrefix + '_b0.nii.gz')
b0 = b0Img.get_data()
for i in ind:
joinedDwi[:, :, :, i] = b0
else:
b0_bshell = load(harmPrefix + f'_b{int(bval)}.nii.gz').get_data()
joinedDwi[:, :, :, ind] = b0_bshell[:, :, :, 1:]
if not isfile(harmPrefix + '.nii.gz'):
save_nifti(harmPrefix + '.nii.gz', joinedDwi, b0Img.affine,
b0Img.header)
else:
print(harmPrefix + '.nii.gz', 'already exists, not overwritten.')
def __init__(self,
jbrowse_url,
jbrowse_bin_dir,
jbrowse_galaxy_index_html_tpl=None,
jbrowse_data_subdir="data",
tbl_to_asn_tpl=None,
tbl_to_asn_exe=None):
#the line below should be the first in
#order to get all parameters into a dict
self.opt = locals().copy()
self.opt.pop("self")
self.opt["jbrowse_bin_dir"] = util.abspath(self.opt["jbrowse_bin_dir"])
def render(theme, item, context=None):
feed = item.feed
reldir = 'themes/%s' % theme
absdir = util.abspath(reldir)
if feed.has_favicon:
icon = util.abspath(feed.favicon_path)
else:
icon = util.abspath('icons/feed.png')
context = context or {}
context['item'] = item
context['feed'] = feed
context['icon'] = icon
context['reldir'] = reldir
context['absdir'] = absdir
try:
template = 'themes/%s/index.html' % theme
template = env.get_template(template)
return template.render(context)
except Exception:
if theme == DEFAULT_THEME:
raise
return render(DEFAULT_THEME, item, context)
def install_to_galaxy(galaxy_home,galaxy_root_url="/",conf_file=None):
galaxy_home = util.abspath(galaxy_home)
jb_rel_dir = pjoin("static","vicvb")
jb_install_dir = pjoin(galaxy_home,jb_rel_dir)
jb_root_url = util.urljoin_path(galaxy_root_url,jb_rel_dir)
#tool_install_dir = pjoin(galaxy_home,"tools","vicvb")
#util.makedir(tool_install_dir)
conf_file = install_jbrowse(jb_install_dir,
jb_root_url,
#rename_to="jbrowse",
conf_file=conf_file)
#shutil.copy(config.get_pkg_data_file("galaxy_vicvb_browser.xml"),
# pjoin(tool_install_dir,"vicvb_browser.xml"))
return conf_file
def install_to_galaxy(galaxy_home, galaxy_root_url="/", conf_file=None):
galaxy_home = util.abspath(galaxy_home)
jb_rel_dir = pjoin("static", "vicvb")
jb_install_dir = pjoin(galaxy_home, jb_rel_dir)
jb_root_url = util.urljoin_path(galaxy_root_url, jb_rel_dir)
#tool_install_dir = pjoin(galaxy_home,"tools","vicvb")
#util.makedir(tool_install_dir)
conf_file = install_jbrowse(
jb_install_dir,
jb_root_url,
#rename_to="jbrowse",
conf_file=conf_file)
#shutil.copy(config.get_pkg_data_file("galaxy_vicvb_browser.xml"),
# pjoin(tool_install_dir,"vicvb_browser.xml"))
return conf_file
def separateBshells(imgPath, ref_bvals_file=None, ref_bvals=None):
if ref_bvals_file:
print('Reading reference b-shell file ...')
ref_bvals = read_bvals(ref_bvals_file)
print('Separating b-shells for', imgPath)
imgPath = local.path(imgPath)
img = load(imgPath._path)
dwi = img.get_data()
inPrefix = abspath(imgPath).split('.nii')[0]
bvals = np.array(read_bvals(inPrefix + '.bval'))
bvecs = np.array(read_bvecs(inPrefix + '.bvec'))
for bval in ref_bvals:
# ind= np.where(bval==bvals)[0]
ind = np.where(abs(bval - bvals) <= BSHELL_MIN_DIST)[0]
N_b = len(ind)
bPrefix = inPrefix + f'_b{int(bval)}'
if bval == 0.:
b0 = find_b0(dwi, ind)
else:
b0_bshell = np.zeros(
(dwi.shape[0], dwi.shape[1], dwi.shape[2], N_b + 1),
dtype='float32')
b0_bshell[:, :, :, 0] = b0
b0_bshell[:, :, :, 1:] = dwi[:, :, :, ind]
b0_bvals = [0.] + [bval] * N_b
b0_bvecs = np.zeros((N_b + 1, 3), dtype='float32')
b0_bvecs[1:, ] = bvecs[ind, :]
bshell_written = load(bPrefix + '.nii.gz').get_fdata()
bvals_written = read_bvals(bPrefix + '.bval')
bvecs_written = read_bvecs(bPrefix + '.bvec')
print('bshell difference', abs(b0_bshell - bshell_written).sum())
print('bvals difference',
(np.array(b0_bvals) - np.array(bvals_written)).sum())
print('bvecs difference',
(np.array(b0_bvecs) - np.array(bvecs_written)).sum())
def separateBshells(imgPath, ref_bvals_file=None, ref_bvals=None):
if ref_bvals_file:
print('Reading reference b-shell file ...')
ref_bvals = read_bvals(ref_bvals_file)
print('Separating b-shells for', imgPath)
imgPath = local.path(imgPath)
img = load(imgPath._path)
dwi = img.get_data()
inPrefix = abspath(imgPath).split('.nii')[0]
bvals = np.array(read_bvals(inPrefix + '.bval'))
bvecs = np.array(read_bvecs(inPrefix + '.bvec'))
for bval in ref_bvals:
# ind= np.where(bval==bvals)[0]
ind = np.where(abs(bval - bvals) <= BSHELL_MIN_DIST)[0]
N_b = len(ind)
bPrefix = inPrefix + f'_b{int(bval)}'
if bval == 0.:
b0 = find_b0(dwi, ind)
if isfile(bPrefix + '.nii.gz'):
continue
if bval == 0.:
save_nifti(bPrefix + '.nii.gz', b0, img.affine, img.header)
else:
b0_bshell = np.zeros(
(dwi.shape[0], dwi.shape[1], dwi.shape[2], N_b + 1),
dtype='float32')
b0_bshell[:, :, :, 0] = b0
b0_bshell[:, :, :, 1:] = dwi[:, :, :, ind]
b0_bvals = [0.] + [bval] * N_b
b0_bvecs = np.zeros((N_b + 1, 3), dtype='float32')
b0_bvecs[1:, ] = bvecs[ind, :]
save_nifti(bPrefix + '.nii.gz', b0_bshell, img.affine, img.header)
write_bvals(bPrefix + '.bval', b0_bvals)
write_bvecs(bPrefix + '.bvec', b0_bvecs)
def select_folder_sample(root, features, output, test=False, test_num=0, test_out=""):
"""
This method will select samples from a
directory-sample structure. This means
structure where each directory is a sample
under different conditions (i.e each
directory is a person's face).
root - the path of the root folder.
features - list with numbered features to get.
"""
# Holds the images
data = []
# Get all the directories (i.e samples)
dirs = util.get_directories(root)
# Now go through every directory and
# pick the desired features from each folder
for d in dirs:
# use numpy to get the partial samples
images = np.array(util.get_images(d))
samples = images[features]
data.extend(list(samples)) # adds to the list
util.update_line("Getting imgs in folder: %s." % d)
# Get the testing stuff if chosen
if test: select_test(data, test_num, test_out)
# Save all remaining images to the output dir
print(Fore.GREEN) # Change colour to RED
for i in range(len(data)):
sample = data[i]
percent = ((i+1)/len(data))*100
util.update_line("Copying samples progess: %.1f%%" % percent)
dts = "/".join([util.abspath(output), os.path.basename(sample)])
util.copy_image(sample, dts)
print(Style.RESET_ALL)
def match_data():
if conf.get("station", "none") == "none":
return flask.jsonify(error="No station specified")
event_name = conf.get("event_name", "")
if not event_name:
return flask.jsonify(error="No match specified")
path = util.abspath("match_schedules", event_name + ".json")
try:
with open(path) as f:
raw_data = json.load(f)
except (IOError, ValueError) as e:
return flask.jsonify(error="Could not load match data: %s" % e)
data = {}
station = conf.get("station")
for k, v in raw_data.items():
if not isinstance(v, dict):
return flask.jsonify(error="Bad match entry (%s)" % k)
elif station not in raw_data[k]:
return flask.jsonify(error="Match %s missing team ID for %s" % (k, station))
else:
data[k] = raw_data[k][station]
return flask.jsonify(data)
def match_data():
if conf.get('station', 'none') == 'none':
return flask.jsonify(error='No station specified')
event_name = conf.get('event_name', '')
if not event_name:
return flask.jsonify(error='No match specified')
path = util.abspath('match_schedules', event_name + '.json')
try:
with open(path) as f:
raw_data = json.load(f)
except (IOError, ValueError) as e:
return flask.jsonify(error='Could not load match data: %s' % e)
data = {}
station = conf.get('station')
for k, v in raw_data.items():
if not isinstance(v, dict):
return flask.jsonify(error='Bad match entry (%s)' % k)
elif station not in raw_data[k]:
return flask.jsonify(error='Match %s missing team ID for %s' % (k, station))
else:
data[k] = raw_data[k][station]
return flask.jsonify(data)
def read(self, path):
grammar_dir = util.abspath(path)
with open(os.path.join(grammar_dir, 'rules.txt')) as f:
for line in f:
fields = line.split()
tags = fields[0]
# map grammar rule (tags) to probability
self.base_structures[tags] = float(fields[1])
tagdicts_dir = os.path.join(grammar_dir, 'nonterminals')
for fname in os.listdir(tagdicts_dir):
if not fname.endswith('.txt'): continue
with open(os.path.join(tagdicts_dir, fname)) as f:
tag = fname.replace('.txt', '')
words = []
for line in f:
fields = line.split('\t')
try:
word, prob = fields
words.append(word)
self.probabilities[(tag, word)] = float(prob)
except:
sys.stderr.write(
"error inserting {} in the tag dictionary {}\n".
format(fields, tag))
self.tag_dicts[tag] = words
with open(os.path.join(grammar_dir, 'verb-treecut.pickle'), 'rb') as f:
self.verb_treecut = pickle.load(f)
with open(os.path.join(grammar_dir, 'noun-treecut.pickle'), 'rb') as f:
self.noun_treecut = pickle.load(f)
with open(os.path.join(grammar_dir, 'params.pickle'), 'rb') as f:
opts = pickle.load(f)
self.lowres = opts.lowres
self.tagtype = opts.tags
def match_data():
if conf.get('station', 'none') == 'none':
return flask.jsonify(error='No station specified')
event_name = conf.get('event_name', '')
if not event_name:
return flask.jsonify(error='No match specified')
path = util.abspath('match_schedules', event_name + '.json')
try:
with open(path) as f:
raw_data = json.load(f)
except (IOError, ValueError) as e:
return flask.jsonify(error='Could not load match data: %s' % e)
data = {}
station = conf.get('station')
for k, v in raw_data.items():
if not isinstance(v, dict):
return flask.jsonify(error='Bad match entry (%s)' % k)
elif station not in raw_data[k]:
return flask.jsonify(error='Match %s missing team ID for %s' %
(k, station))
else:
data[k] = raw_data[k][station]
return flask.jsonify(data)
def export_handler(command):
def path_ok(path):
return os.path.isdir(path) and not os.path.exists(
os.path.join(path, csv_filename(use_id=True)))
path = os.path.expanduser(request.args.get('path', get_export_path()))
if command == 'info':
return flask.jsonify(
filename=csv_filename(use_id=True),
path=path,
default_path=get_export_path(),
ok=path_ok(path),
stats=stats(callback=dict),
)
elif command == 'check_path':
ok = path_ok(path)
if ok:
conf.set('export_path', path)
conf.save()
return flask.jsonify(ok=ok)
elif command == 'do_export':
if not path_ok(path):
return flask.jsonify(ok=False, error="Invalid path: %s" % path)
try:
shutil.copyfile(csv_path(),
os.path.join(path, csv_filename(use_id=True)))
shutil.move(
csv_path(),
util.abspath(
'backups', '%s-%s' %
(csv_filename(), time.strftime('%d-%b-%Y-%H-%M-%S-%p'))))
conf.set('export_id', conf.get('export_id', '1', type=int) + 1)
return flask.jsonify(ok=True)
except Exception as e:
return flask.jsonify(ok=False, error=str(e))
else:
flask.abort(404)
def schedule_select():
return flask.jsonify(file=subprocess.check_output([sys.executable, util.abspath("filedialog.py")]).decode().strip())
def csv_path():
return util.abspath('..', csv_filename())
def schedule_select():
return flask.jsonify(file=subprocess.check_output(
[sys.executable, util.abspath('filedialog.py')]).strip())
def csv_path():
return util.abspath('..',csv_filename())
def gff_to_jbrowse(self,
gff_file,
index_html,
data_dir_out,
jbrowse_url=None
):
opt = self.opt
if jbrowse_url is None:
jbrowse_url = opt["jbrowse_url"]
env = None
if self.opt.get("jbrowse_bin_dir",None):
env = os.environ.copy()
util.add_to_path(opt["jbrowse_bin_dir"],
prepend=True,
env=env)
if not os.path.exists(data_dir_out):
os.makedirs(data_dir_out)
gff_file = util.abspath(gff_file)
#fasta_file = util.abspath(fasta_file)
jbrowse_out_dir = os.path.join(data_dir_out,opt["jbrowse_data_subdir"])
#can use os.devnull to discard all output
jbrowse_conv_log_base = os.path.join(os.getcwd(),"jbrowse_conv_log")
with nested( open(jbrowse_conv_log_base+".out","w"),\
open(jbrowse_conv_log_base+".err","w") ) as ( stdout, stderr ):
check_call(["prepare-refseqs.pl","--gff",gff_file,"--out",jbrowse_out_dir],
env=env,
stdout=stdout,
stderr=stderr)
#@todo use biodb-to-json instead with flat file input, and accept config
#file as a parameter (provide a default one too). See volvox.json config
#in the distribution. Also add dropped_features param to load everything
#unique in field 3 of GFF and check that only dropped_features are missing
#from the config
check_call(["flatfile-to-json.pl","--gff",gff_file,"--out",jbrowse_out_dir,
"--trackLabel","Genes",
"--cssClass","feature5",
"--type","gene",
"--autocomplete","all"
"--getLabel",
"--getType"
],
env=env,
stdout=stdout,
stderr=stderr)
check_call(["flatfile-to-json.pl","--gff",gff_file,"--out",jbrowse_out_dir,
"--trackLabel","CDS",
"--cssClass","generic_parent",
"--subfeatureClasses",'{ "exon" : "exon" }',
"--type","CDS",
"--type","exon",
"--autocomplete","all"
"--getLabel",
"--getType",
"--getSubs",
"--getPhase"
],
env=env,
stdout=stdout,
stderr=stderr)
check_call(["flatfile-to-json.pl","--gff",gff_file,"--out",jbrowse_out_dir,
"--trackLabel","Peptides",
"--cssClass","est",
"--subfeatureClasses",'{ "mat_peptide" : "transcript-CDS" }',
"--type","mat_peptide",
"--autocomplete","all"
"--getLabel",
"--getType",
"--getSubs",
"--getPhase"
],
env=env,
stdout=stdout,
stderr=stderr)
check_call(["flatfile-to-json.pl","--gff",gff_file,"--out",jbrowse_out_dir,
"--trackLabel","Misc",
"--cssClass","feature3",
"--type","misc_feature",
"--autocomplete","all"
"--getLabel",
"--getType",
"--getSubs",
"--getPhase"
],
env=env,
stdout=stdout,
stderr=stderr)
check_call(["generate-names.pl","--out",jbrowse_out_dir],
env=env,
stdout=stdout,
stderr=stderr)
tracks_conf_file = os.path.join(jbrowse_out_dir,"trackList.json")
tracks_conf = util.load_config_json(tracks_conf_file)
tracks_conf["refSeqDropdown"] = True #show pull-down even for very many sequences
util.save_config_json(tracks_conf,tracks_conf_file)
#create index.html that redirects to JBrowse index.html with correct data param etc
_jbrowse_dataset_index_html = \
config.get_data_string(self.opt["jbrowse_galaxy_index_html_tpl"],
"galaxy.index.html")
jbrowse_url_params = util.to_url_params(dict(
tracks=",".join(("DNA","Genes","CDS","Peptides","Misc")),
tracklist=0
))
with open(index_html,"w") as f:
f.write(_jbrowse_dataset_index_html.\
format(jbrowse_url=jbrowse_url.rstrip("/"),
jbrowse_data_subdir=opt["jbrowse_data_subdir"],
jbrowse_url_params=jbrowse_url_params))
# Print erlcome text
print(Fore.BLUE)
print("Negative Annotation... Settings passed:")
print("Background file path: %s" % bg_info_path)
print("Background images sample %s" % images_path)
print("Use relative path: %s" % arguments['--relative'])
print(Style.RESET_ALL)
# Open/create background file
open(bg_info_path, "w").close()
bg_file = open(bg_info_path, "a")
print("file opened successfully, retrieving imags (might take a while)")
# Go through all images and save them
images = get_images(abspath(images_path))
print("Starting to save images")
print(Fore.GREEN)
for i in range(len(images)):
# Print progress here
percent = ((i + 1) / len(images)) * 100
update_line("Progress: %.2f" % percent)
# Save the info to the file
save_bg_info(images[i], bg_file, func)
print(Style.RESET_ALL)
# Finally close the file
bg_file.close()
low = int(arguments['LOW'])
high = int(arguments['HIGH'])
size = int(arguments['SIZE'])
features = func(list(range(low, high)), size)
else: # Here use default function to select (random)
low = int(arguments['LOW'])
high = int(arguments['HIGH'])
size = int(arguments['SIZE'])
features = get_random(list(range(low, high)), size)
# Get the mandatory arguments
root_path = arguments['ROOT']
out_path = arguments['OUTPUT']
# Print out info to user
print(Fore.BLUE + "Setting passed: ")
print("Root directory..... %s." % root_path)
print("Output directory... %s." % out_path)
print("Features passed.... %s." % list(features))
print(Style.RESET_ALL)
# Finally save the data
if arguments['--test']:
num = int(arguments['--test'])
test_out = util.abspath(os.path.join(out_path, "test"))
select_folder_sample(root_path, features, out_path, True, num, test_out)
else:
select_folder_sample(root_path, features, out_path)
def get_path(self, item):
return abspath(join(self.dir, item))
# Print welcome and setting:
print(Fore.BLUE)
print("Generating Negatives script... Settings are:\n")
print("Video path: %s"% vid_path)
print("Output folder path: %s" % output_path)
print("Starting frame: %s" % start)
print("Time interval: %s" % interval)
print("Number of frames: %s" % n_frames)
print("Width of samples: %s" % width)
print("Height of samples: %s" % height)
print(Style.RESET_ALL) # BAck to normal color
# Open video here
video_cap = cv2.VideoCapture(util.abspath(vid_path))
# Calculate video stuff
video_fps = video_cap.get(cv2.CAP_PROP_FPS)
video_frames = video_cap.get(cv2.CAP_PROP_FRAME_COUNT)
frame_gap = int(interval*video_fps)
# Make sure there are sufficient frames in the video
if (start + n_frames*frame_gap) > video_frames:
print(Fore.RED, end='')
print("Interval or #frames to save too large for video duration.")
print(Style.RESET_ALL)
sys.exit(1) # Exit
# Do the saving here
print(Fore.GREEN) # change output to green
# Create the obj
face_cascade = cv2.CascadeClassifier(xml_file)
# Now open/create the file
if not os.path.isfile(positive_info_file):
# Doesn't exist so create file beforehand
open(positive_info_file, "w").close()
# Now open in append mode for writing the lines
info_file = open(positive_info_file, "w").close()
info_file = open(positive_info_file, "a") # append mode
# Get relative path of img folders to info file
#os.chdir(os.path.dirname(positive_info_file))
#img_rel_path = get_relative_dir(positive_info_file, img_path)
img_path = abspath(img_path)
# Not just save faces for every image
printf(Fore.GREEN) # Change colour
for path in images:
save_func(path, info_file, face_cascade)
# Use ansi to update line (FIX FOR WINDOWS)
update_line("Image processed: %s " % path)
# Set things back to normal (colors and style)
print(Style.RESET_ALL)
info_file.close() # Close as function doesnt'do it
print(Fore.GREEN + "Finished" + Style.RESET_ALL)
print('\nSite', ref_csv, '\n')
print('Checking consistency of b-shells among subjects')
check_bshells(ref_imgs, ref_bvals)
print('spatial resolution is', ref_res)
print('Checking consistency of spatial resolution among subjects')
check_resolution(ref_imgs, ref_res)
if __name__ == '__main__':
if len(sys.argv) == 1 or sys.argv[1] == '-h' or sys.argv[1] == '--help':
print(
'''Check consistency of b-shells and spatial resolution among subjects
Usage:
consistencyCheck list.csv/txt ref_bshell_bvalues.txt ref_res_file.npy
Provide a csv/txt file with first column for dwi and 2nd column for mask: dwi1,mask1\\ndwi2,mask2\\n...
or just one column for dwi1\\ndwi2\\n...
In addition, provide ref_bshell_bvalues and ref_res_file.''')
exit()
ref_csv = abspath(sys.argv[1])
outputBshellFile = abspath(sys.argv[2])
outPutResolutionFile = abspath(sys.argv[3])
if isfile(ref_csv):
consistencyCheck(ref_csv, outputBshellFile, outPutResolutionFile)
else:
raise FileNotFoundError(f'{ref_csv} does not exists.')
def csv_path():
return util.abspath("..", csv_filename())