def upload_new_file(bqsession, path):
"""
uploads files to bisque server
"""
r = save_blob(bqsession, path)
print 'Uploaded id: %s url: %s'%(r.get('resource_uniq'), r.get('uri'))
return r
def process_full_set(session, start_path):
'''
This function will upload files (including non-images) and add annotations to the image
get relevant file paths
'''
file_list = []
uri_list = []
file_names = []
for dirname, dirnames, filenames in os.walk(start_path):
for filename in filenames:
# find relevant images
# TODO: Add a check for the file types / avoid certain types
file_names.append(filename.split('.')[0])
path = os.path.join(dirname, filename)
path = path.replace('\\', '/')
file_list.append(path)
if notFsFile(path):
if isValidFile(path):
r = save_blob(session, path)
if r is None:
print('Error uploading')
# r is a created metadata document in etree form
else:
uri = r.get('uri')
#this line adds all the tags (by passing into createtags to get the tags, then passing the return into addtags)
addTag(uri, path)
uri_list.append(uri)
print(uri)
return uri_list
def main():
parser = argparse.ArgumentParser(
description='Set Basic auth credentials on CAS protected Bisque')
parser.add_argument('-u',
'--credentials',
default=None,
help="CAS credentials in form of user:password")
parser.add_argument("bisque_host", nargs=1)
args = parser.parse_args()
session = setbasicauth(args.bisque_host[0], *args.credentials.split(':'))
resource = etree.Element('image', name="IMG_2014-10-01_18-55-17.png")
etree.SubElement(resource, 'tag', name="experiment", value="RPi test")
etree.SubElement(resource,
'tag',
name="timestamp",
value="2014-10-01_18-55-17")
r = save_blob(session, LOCAL_FILE_PATH, resource=resource)
#r = save_image_pixels(session, LOCAL_FILE_PATH)
if r is None:
print("Error uploading")
else:
uri = r.get('uri')
print(uri)
def upload_file(self, path, resource=None):
#if resource is not None:
# print etree.tostring(resource)
r = save_blob(self.session, path, resource=resource)
if r is None or r.get('uri') is None:
print 'Error uploading: %s' % path.encode('ascii', 'replace')
return None
print 'Uploaded id: %s url: %s' % (r.get('resource_uniq'),
r.get('uri'))
return r
def take_photo(filename):
app_settings = DBSession.query(Settings).first()
if app_settings.image_ISO == 'auto':
iso_call = ''
else:
iso_call = ' -ISO ' + str(app_settings.image_ISO)
call([
'raspistill -t 500' + ' -n ' + ' -w ' + str(app_settings.image_width) +
' -h ' + str(app_settings.image_height) + ' -e ' +
app_settings.encoding_mode + ' -ex ' + app_settings.exposure_mode +
' -awb ' + app_settings.awb_mode + ' -rot ' +
str(app_settings.image_rotation) + ' -ifx ' +
app_settings.image_effect + iso_call + ' -o ' + RASPISTILL_DIRECTORY +
filename
],
stdout=PIPE,
shell=True)
# if not (RASPISTILL_DIRECTORY == 'raspistillweb/pictures/'):
# call (
# ['ln -s ' + RASPISTILL_DIRECTORY + filename
# + ' raspistillweb/pictures/' + filename], shell=True
# )
#generate_thumbnail(filename)
if app_settings.bisque_enabled == 'Yes':
resource = etree.Element('image', name=filename)
etree.SubElement(resource, 'tag', name="experiment", value="Phenotiki")
etree.SubElement(resource,
'tag',
name="timestamp",
value=os.path.splitext(filename)[0])
bqsession = setbasicauth(bisque_root_url, bisque_user, bisque_pswd)
print 'Uploading \'' + filename + '\' to Bisque...'
start_time = time()
r = save_blob(bqsession,
localfile=RASPISTILL_DIRECTORY + filename,
resource=resource)
elapsed_time = time() - start_time
if r is None:
print 'Error uploading!'
preferences_fail_alert.append('Error uploading \'' + filename +
'\' to Bisque!')
else:
print 'Image uploaded in %.2f seconds' % elapsed_time
print r.items()
print 'Image URI:', r.get('uri')
#call(['cp raspistillweb/pictures/preview.jpg raspistillweb/pictures/'+filename],shell=True)
#generate_thumbnail(filename)
return
def main():
parser = argparse.ArgumentParser(description='Set Basic auth credentials on CAS protected Bisque')
parser.add_argument ('-u', '--credentials', default=None, help="CAS credentials in form of user:password")
parser.add_argument ("bisque_host", nargs=1)
args = parser.parse_args()
session = setbasicauth(args.bisque_host[0], *args.credentials.split(':'))
resource = etree.Element('image', name="IMG_2014-10-01_18-55-17.png")
etree.SubElement(resource, 'tag', name="experiment", value="RPi test")
etree.SubElement(resource, 'tag', name="timestamp", value="2014-10-01_18-55-17")
r = save_blob(session, LOCAL_FILE_PATH, resource=resource)
#r = save_image_pixels(session, LOCAL_FILE_PATH)
if r is None:
print("Error uploading")
else:
uri = r.get('uri')
print(uri)
user = config.get('Host', 'user') or 'test'
pswd = config.get('Host', 'password') or 'test'
session = BQSession().init_local(user, pswd, bisque_root=root, create_mex=False)
request = '<image name="%s">'%'series_t_jpeg'
request = '%s<value>%s</value>'%(request, localpath2url('f:/dima/develop/python/bq5irods/data/imagedir/admin/tests/multi_file/series_t_jpeg/t_000241.jpg'))
request = '%s<value>%s</value>'%(request, localpath2url('f:/dima/develop/python/bq5irods/data/imagedir/admin/tests/multi_file/series_t_jpeg'))
request = '%s<tag name="%s" type="%s">'%(request, 'image_meta', 'image_meta')
request = '%s<tag name="%s" value="%s" type="number" />'%(request, 'image_num_z', '1')
request = '%s<tag name="%s" value="%s" type="number" />'%(request, 'image_num_t', '80')
request = '%s<tag name="%s" value="%s" />'%(request, 'dimensions', 'XYCZT')
request = '%s<tag name="%s" value="%s" type="number" />'%(request, 'pixel_resolution_x', '0.4')
request = '%s<tag name="%s" value="%s" type="number" />'%(request, 'pixel_resolution_y', '0.4')
request = '%s<tag name="%s" value="%s" type="number" />'%(request, 'pixel_resolution_t', '2.0')
request = '%s<tag name="%s" value="%s" />'%(request, 'pixel_resolution_unit_x', 'micron')
request = '%s<tag name="%s" value="%s" />'%(request, 'pixel_resolution_unit_y', 'micron')
request = '%s<tag name="%s" value="%s" />'%(request, 'pixel_resolution_unit_t', 'seconds')
request = '%s</tag>'%(request)
request = '%s</image>'%request
#url = session.service_url('data_service', 'image')
#r = session.postxml(url, etree.fromstring(request), method='POST')
r = save_blob(session, resource=request)
if r is None or r.get('uri') is None:
print 'Upload failed'
else:
print 'id: %s'%r.get('resource_uniq')
print 'url: %s'%r.get('uri')
def take_photo(filename):
app_settings = DBSession.query(Settings).first()
if app_settings.image_ISO == 'auto':
iso_call = ''
else:
iso_call = ' -ISO ' + str(app_settings.image_ISO)
# ----- TEST CODE -----#
#print PiCamera.AWB_MODES
#with picamera.PiCamera() as camera:
# camera.resolution = (app_settings.image_width,app_settings.image_height)
# # Camera warm-up time
# time.sleep(2)
# camera.shutter_speed = camera.exposure_speed
# camera.exposure_mode = app_settings.exposure_mode
# camera.awb_mode = app_settings.awb_mode
# camera.image_rotation = app_settings.image_rotation
# camera.image_effect = app_settings.image_effect
# camera.iso = 0 if app_settings.image_ISO == 'auto' else app_settings.image_ISO
# camera.capture(RASPISTILL_DIRECTORY + filename + '_test', format=app_settings.encoding_mode)
# ----- TEST CODE -----#
call (
['raspistill -t 500'
+ ' -n '
+ ' -w ' + str(app_settings.image_width)
+ ' -h ' + str(app_settings.image_height)
+ ' -e ' + app_settings.encoding_mode
+ ' -ex ' + app_settings.exposure_mode
+ ' -awb ' + app_settings.awb_mode
+ ' -rot ' + str(app_settings.image_rotation)
+ ' -ifx ' + app_settings.image_effect
+ iso_call
+ ' -o ' + RASPISTILL_DIRECTORY + filename],
stdout=PIPE, shell=True
)
# if not (RASPISTILL_DIRECTORY == 'raspistillweb/pictures/'):
# call (
# ['ln -s ' + RASPISTILL_DIRECTORY + filename
# + ' raspistillweb/pictures/' + filename], shell=True
# )
#generate_thumbnail(filename)
if app_settings.bisque_enabled == 'Yes':
resource = etree.Element('image', name=filename)
etree.SubElement(resource, 'tag', name="experiment", value="Phenotiki")
etree.SubElement(resource, 'tag', name="timestamp", value=os.path.splitext(filename)[0])
bqsession = setbasicauth(app_settings.bisque_root_url, app_settings.bisque_user, app_settings.bisque_pswd)
print 'Uploading \'' + filename + '\' to Bisque...'
start_time = time()
r = save_blob(bqsession, localfile=RASPISTILL_DIRECTORY+filename, resource=resource)
elapsed_time = time() - start_time
if r is None:
print 'Error uploading!'
preferences_fail_alert.append('Error uploading \'' + filename + '\' to Bisque!')
else:
print 'Image uploaded in %.2f seconds' % elapsed_time
print r.items()
print 'Image URI:', r.get('uri')
#call(['cp raspistillweb/pictures/preview.jpg raspistillweb/pictures/'+filename],shell=True)
#generate_thumbnail(filename)
return
def take_photo(filename):
app_settings = DBSession.query(Settings).first()
if app_settings.image_ISO == 'auto':
iso_call = ''
else:
iso_call = ' -ISO ' + str(app_settings.image_ISO)
# ----- TEST CODE -----#
#print PiCamera.AWB_MODES
#with picamera.PiCamera() as camera:
# camera.resolution = (app_settings.image_width,app_settings.image_height)
# # Camera warm-up time
# time.sleep(2)
# camera.shutter_speed = camera.exposure_speed
# camera.exposure_mode = app_settings.exposure_mode
# camera.awb_mode = app_settings.awb_mode
# camera.image_rotation = app_settings.image_rotation
# camera.image_effect = app_settings.image_effect
# camera.iso = 0 if app_settings.image_ISO == 'auto' else app_settings.image_ISO
# camera.capture(RASPISTILL_DIRECTORY + filename + '_test', format=app_settings.encoding_mode)
# ----- TEST CODE -----#
call (
['raspistill -t 500'
+ ' -n '
+ ' -w ' + str(app_settings.image_width)
+ ' -h ' + str(app_settings.image_height)
+ ' -e ' + app_settings.encoding_mode
+ ' -ex ' + app_settings.exposure_mode
+ ' -awb ' + app_settings.awb_mode
+ ' -rot ' + str(app_settings.image_rotation)
+ ' -ifx ' + app_settings.image_effect
+ iso_call
+ ' -o ' + RASPISTILL_DIRECTORY + filename],
stdout=PIPE, shell=True
)
# if not (RASPISTILL_DIRECTORY == 'raspistillweb/pictures/'):
# call (
# ['ln -s ' + RASPISTILL_DIRECTORY + filename
# + ' raspistillweb/pictures/' + filename], shell=True
# )
#generate_thumbnail(filename)
if app_settings.bisque_enabled == 'Yes' and internet_on():
resource = etree.Element('image', name=filename)
etree.SubElement(resource, 'tag', name="experiment", value="Phenotiki")
etree.SubElement(resource, 'tag', name="timestamp", value=os.path.splitext(filename)[0])
bqsession = setbasicauth(app_settings.bisque_root_url, app_settings.bisque_user, app_settings.bisque_pswd)
print 'Uploading \'' + filename + '\' to Bisque...'
start_time = time()
r = save_blob(bqsession, localfile=RASPISTILL_DIRECTORY+filename, resource=resource)
elapsed_time = time() - start_time
if r is None:
print 'Error uploading!'
preferences_fail_alert.append('Error uploading \'' + filename + '\' to Bisque!')
else:
print 'Image uploaded in %.2f seconds' % elapsed_time
print r.items()
print 'Image URI:', r.get('uri')
#call(['cp raspistillweb/pictures/preview.jpg raspistillweb/pictures/'+filename],shell=True)
#generate_thumbnail(filename)
return