def create_resource(path, name, r, c, field):
files = []
for t in T:
for z in Z:
for ch in CH:
if ch in CH_Z:
filename = '%s%s%st%.3d%s%.2df%.2dd%sz%s.%s'%(path, dir_z, name, t, r, c, field, ch, z, ext_z)
else:
filename = '%s%s%st%.3d%s%.2df%.2dd%s.%s'%(path, dir_p, name, t, r, c, field, ch, ext_p)
files.append(filename)
resource = etree.Element ('image', name='%s_%s_%s_%s'%(name, r, c, field))
meta = etree.SubElement (resource, 'tag', name='image_meta', type='image_meta')
etree.SubElement (meta, 'tag', name='image_num_c', value=str(len(CH)), type='number')
etree.SubElement (meta, 'tag', name='image_num_z', value=str(len(Z)), type='number')
etree.SubElement (meta, 'tag', name='image_num_t', value=str(len(T)), type='number')
etree.SubElement (meta, 'tag', name='dimensions', value='XYCZT')
etree.SubElement (meta, 'tag', name='channel_0_name', value='Hoechst')
etree.SubElement (meta, 'tag', name='channel_1_name', value='cmfda')
etree.SubElement (meta, 'tag', name='channel_2_name', value='LysoTrackerRed')
etree.SubElement (meta, 'tag', name='channel_color_0', value='0,0,255')
etree.SubElement (meta, 'tag', name='channel_color_1', value='0,255,0')
etree.SubElement (meta, 'tag', name='channel_color_2', value='255,0,0')
etree.SubElement (resource, 'tag', name='row', value='%s'%r)
etree.SubElement (resource, 'tag', name='column', value='%s'%c, type='number')
etree.SubElement (resource, 'tag', name='field', value='%s'%field, type='number')
for f in files:
v = etree.SubElement (resource, 'value')
v.text = localpath2url(f)
return resource
##################################################################
# Upload
##################################################################
config = ConfigParser.ConfigParser()
config.read('config.cfg')
root = config.get('Host', 'root') or 'localhost:8080'
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')
# Upload
##################################################################
config = ConfigParser.ConfigParser()
config.read('config.cfg')
root = config.get('Host', 'root') or 'localhost:8080'
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)
url = urlparse.urljoin(root, url_import)
request = request_xml.replace('{NAME}', 'cx-11.sld#3')
request = request.replace(
'{PATH}',
localpath2url(
'f:/dima/develop/python/bq5irods/data/imagedir/admin/tests/multi_image/Slidebook/cx-11.sld'
))
request = request.replace('{SERIES}', '3')
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 teardown(self):
self.bq.update_mex('Collecting result...')
# Post all submex for files and return xml list of results
#gobjects = self._read_results()
#tags = [{ 'name': 'outputs',
# 'tag' : [{'name': 'rootimage', 'type':'image', 'value':self.resource_url,
# 'gobject' : [{ 'name': 'root_tips', 'type': 'root_tips', 'gobject' : gobjects }] }]
# }]
#self.bq.finish_mex(tags = tags)
# mex_outputs = self.bq.mex.xmltree.xpath('tag[@name="outputs"]')
# logging.debug('Outputs mex:' + str(mex_outputs))
# if mex_outputs:
# logging.debug('Outputs mex:' + str(mex_outputs))
#
# for tag in mex_outputs[0]:
# if tag.tag == 'tag' and tag.attrib['name'] == 'TipDetection':
# tag.attrib['value'] = "390"
# # if tag.tag == 'tag' and tag.attrib['type'] != 'system-input':
# # logging.debug('Set options with %s as %s'%(tag.attrib['name'],tag.attrib['value']))
# setattr(options,tag.attrib['name'],tag.attrib['value'])
# else:
# logging.debug('No Outputs Found on MEX!')
#load result data from the xml file. For testing, just use the fix xml i.e. will be changed later time
#resultfile = os.path.join(self.options.stagingPath, '0002.jpg_result.xml')
#reload parameters
self.mex_parameter_parser(self.options, self.bq.mex.xmltree)
#get the image downloaded
image = self.bq.load(self.options.image_url)
imageDownloaded = image.name + ".tif"
resultfile = os.path.join(self.options.stagingPath, imageDownloaded + '_result.xml')
logging.debug('Result file: ' + resultfile)
#load the result file and display info.
# tree.parse('/home/tuan/bisque/modules/RootNavLinuxModuleV3/0002.jpg_result.xml')
tree = etree.ElementTree()
tree.parse(resultfile)
rootNode = tree.getroot()
#
logging.debug('Root node: ' + rootNode.tag)
#
# # look for the Tips Output tag
tipDetectionNode = rootNode.findall("./Output/TipsDetected")
outputTag = etree.Element('tag', name='outputs')
outputSubTag = etree.SubElement(outputTag, 'tag', name='summary')
if len(tipDetectionNode) > 0:
totalAttrib = tipDetectionNode[0].get('total')
logging.debug('tipDetectionNode : ' + totalAttrib)
##etree.SubElement(outputTag, 'tag', name='TipDetection', value=str(23))
#etree.SubElement( outputSubTag, 'tag', name='Tip(s) detected', value=str(23))
etree.SubElement( outputSubTag, 'tag', name='Tip(s) detected', value=totalAttrib)
#using testing image: /home/tuan/bisque/modules/RootNavLinuxModuleV3/FeatureMapInMain.png
#filepath = '/home/tuan/bisque/modules/RootNavLinuxModuleV3/FeatureMapInMain.png'
#filepath = '/home/tuan/bisque/modules/RootNavLinuxModuleV3/0002_copy.jpg'
#just for testing
outputImgTag = etree.SubElement(outputTag, 'tag', name='OutputImage', value=self.options.image_url)
#outputImgTag = etree.SubElement(outputTag, 'tag', name='OutputImage', value=localpath2url(filepath))
#gObjectValue = ""
#gObjectTag = etree.SubElement(outputImgTag, 'gobject', name='PointsDetected')
logging.debug('appending children to the output image tag')
gObjectTag = rootNode.findall("./Output/TipsDetected/gobject")[0]
outputImgTag.append(gObjectTag)
#test colour (this works for one point, change colour from red to yello)
#etree.SubElement(gObjectTag[0], 'tag', name='color', value="#ffff00")
#for tip in tipDetectionNode[0]:
# gPoint = etree.SubElement(gObjectTag, 'point', name=tip.attrib['id'])
# etree.SubElement(gPoint, 'vertex', x=tip.attrib['x'], y=tip.attrib['y'])
#display root info
#rootsTopMostNodes = rootNode.findall("./Output/RootTree/Root")
rootsTopMostNodes = rootNode.xpath('./Output/RootTree/Root[@order="-1"]')
for root in rootsTopMostNodes:
etree.SubElement( outputSubTag, 'tag', name='Root length', value=root.get('length'))
etree.SubElement( outputSubTag, 'tag', name='Root area', value=root.get('area'))
etree.SubElement( outputSubTag, 'tag', name='Primary root', value=root.get('primaryRoots'))
#outputExtraImgTag = etree.SubElement(outputTag, 'tag', name='OutputExtraImage', value=self.options.image_url)
#resource = etree.Element ('image', name=os.path.basename(filepath), value=localpath2url(filepath))
#meta = etree.SubElement (resource, 'tag', name='Experimental')
#etree.SubElement (meta, 'tag', name='numberpoints', value="12")
#resource = etree.Element ('image', name='new file %s'%(os.path.basename(filepath)))
#logging.debug('resource: ' + str(resource))
#self.uploadFileToServer(filepath)
logging.debug('self.bq.service_map in teardown: ' + str(self.bq.service_map))
#url = self.bq.service_url('data_service', 'image')
#url = self.bq.service_url('blob_service')
#url = self.bq.service_url('image_service', 'image') ##couldnt use for upload
#url = self.bq.service_url('/import/transfer') #not a service
#url = self.bq.service_url('import', 'transfer') #not a service
#url = self.bq.service_url('import', path='transfer') #not a service
#url = self.bq.service_url('http://127.0.0.1:8080/', '/import/transfer') #not a service
#response = save_blob(self.bq, resource=resource)
#logging.debug('url : ' + str(url))
#response_xml = self.bq.postblob(localpath2url(filepath), xml=resource) #post image to bisque and get the response
#logging.debug('response_xml: ' + str(response_xml))
#r = self.bq.postxml(url, resource, method='POST')
#logging.debug('Response: ' + str(r))
#response = self.bq.postblob(filepath, xml=resource)
#response = self.bq.postblob(filepath, xml=resource)
#blob = etree.XML(response).find('./')
# if blob is None or blob.get('uri') is None:
# logging.debug('Could not insert the Histogram file into the system')
# self.bq.fail_mex('Could not insert the Histogram file into the system')
# else:
# outputExtraImgTag = etree.SubElement(outputTag, 'tag', name='/home/tuan/bisque/modules/RootNavLinuxModuleV3/FeatureMapInMain.png')
# outputExtraImgTag = etree.SubElement(outputTag, 'tag', name='OutputExtraImage', value=blob.get('uri'), type='image')
# if r is None or r.get('uri') is None:
# logging.debug('Could not insert the Histogram file into the system')
# self.bq.fail_mex('Could not insert the Histogram file into the system')
# else:
# outputExtraImgTag = etree.SubElement(outputTag, 'tag', name='/home/tuan/bisque/modules/RootNavLinuxModuleV3/FeatureMapInMain.png')
# logging.debug('resource id: %s' %r.get('resource_uniq'))
# logging.debug('url: %s' %r.get('uri'))
# outputExtraImgTag = etree.SubElement(outputTag, 'tag', name='OutputExtraImage', value=r.get('uri'), type='image')
# outputExtraImgTag = etree.SubElement(outputImgTag, 'tag', name='OutputExtraImage', value=r.get('value'), type='image')
#etree.SubElement(outputTag, 'tag', name='OutputImage', value='/home/tuan/bisque/modules/RootNavLinuxModuleV3/FeatureMapInMain.png')
#etree.SubElement(outputTag, 'tag', name='OutputImage', value='file:///home/tuan/bisque/modules/RootNavLinuxModuleV3/FeatureMapInMain.png')
##########################
#upload the probability image
outputFileNode = rootNode.findall("./Output/File")
probabilityimagepathNode = outputFileNode[0].find("ProbabilityImageFile").text
imagefile = os.path.basename(probabilityimagepathNode)
#get mexid
parts = self.options.stagingPath.split('/')
mexid = parts[len(parts) - 1]
resource = etree.Element ('image', name=os.path.join(UPLOADED_FOLDER, mexid, imagefile))
response = self.postblobbytxn(self.bq, (probabilityimagepathNode), xml=resource)
blob = etree.XML(response).find('./')
if blob is None or blob.get('uri') is None:
logging.debug('Could not upload the probability image file into the system')
self.bq.fail_mex('Could not upload the probability image file into the system')
else:
##create node for mex
linkprobabilityimgupload = blob.get('uri')
probabilityImageTag = etree.SubElement(outputTag, 'tag', name='ProbabilityImage', value=linkprobabilityimgupload, type='image')
#######################################################
#output shortest paths
outputPathImgTag = etree.SubElement(outputTag, 'tag', name='OutputPathImage', value=self.options.image_url)
#get primary paths
primaryPathsNode = rootNode.findall("./Output/PrimaryPaths")
if (primaryPathsNode is not None) and (len(primaryPathsNode) > 0):
for path in primaryPathsNode[0]:
outputPathImgTag.append(path)
#get lateral paths
lateralPathsNode = rootNode.findall("./Output/LateralPaths")
if (lateralPathsNode is not None) and (len(lateralPathsNode) > 0):
for path in lateralPathsNode[0]:
outputPathImgTag.append(path)
#node to display the root and convex hull
outputRootImgTag = etree.SubElement(outputTag, 'tag', name='OutputRootsImage', value=self.options.image_url)
gObjectRootNode = etree.SubElement(outputRootImgTag, 'gobject', name='Roots')
splineInOtherRootsNodes = rootNode.xpath('./Output/RootTree/Root[@order!="-1"]/Spline')
for spline in splineInOtherRootsNodes:
#outputRootImgTag.append(spline[0])
gObjectRootNode.append(spline[0])
for root in rootsTopMostNodes:
convexNodes = root.findall('ConvexHull')
for cx in convexNodes:
#outputRootImgTag.append(cx[0])
gObjectRootNode.append(cx[0])
#get data for measurement table
measurementTablesNode = rootNode.xpath('./Output/Measurement/Tables')
if (measurementTablesNode is not None and len (measurementTablesNode) > 0):
#outputRootImgTag.append(measurementTablesNode[0])
gObjectRootNode.append(measurementTablesNode[0])
#get data for curvature profile
curvNode = etree.SubElement(gObjectRootNode, 'tag', name='CurvatureProfile')
curvatureProfileDataNode = rootNode.xpath('./Output/Measurement/CurvatureProfile')
if (curvatureProfileDataNode is not None and len (curvatureProfileDataNode) > 0):
for rowDataNode in curvatureProfileDataNode[0]:
#gObjectRootNode.append()
gObjectCurv = etree.SubElement(curvNode, 'gobject', type='row')
etree.SubElement(gObjectCurv, 'tag', name='col0', value=rowDataNode.attrib['col0'])
etree.SubElement(gObjectCurv, 'tag', name='col1', value=rowDataNode.attrib['col1'])
#get data for travel map
mapNode = etree.SubElement(gObjectRootNode, 'tag', name='MapProfile')
mapProfileDataNode = rootNode.xpath('./Output/Measurement/MapProfile')
if (mapProfileDataNode is not None and len (mapProfileDataNode) > 0):
#gObjectRootNode.append(mapProfileDataNode[0])
for rowDataNode in mapProfileDataNode[0]:
gObjectMap = etree.SubElement(mapNode, 'gobject', type='row')
etree.SubElement(gObjectMap, 'tag', name='col0', value=rowDataNode.attrib['col0'])
etree.SubElement(gObjectMap, 'tag', name='col1', value=rowDataNode.attrib['col1'])
etree.SubElement(gObjectMap, 'tag', name='col2', value=rowDataNode.attrib['col2'])
#get data for RSML file for downloading
#extract rsml file from xml data
inputFileNode = rootNode.findall("./Input/File")
rsmlFileNode = inputFileNode[0].find("RSMLFile").text
rsmlPathNode = inputFileNode[0].find("RSMLPath").text
#upload rsml file
parts = self.options.stagingPath.split('/')
mexid = parts[len(parts) - 1]
resultrsmlfile = os.path.join(rsmlPathNode, rsmlFileNode)
#resource = etree.Element ('image', name="\'" + os.path.join(mexid, rsmlFileNode) + "\'")
resource = etree.Element ('resource', name=os.path.join(mexid, rsmlFileNode))
#resource = etree.Element ('resource', name='new file %s'%rsmlFileNode )
#resource = etree.Element ('image', name='new file P.rsml')
logging.debug('name resource: ' + os.path.join(mexid, rsmlFileNode))
logging.debug('resultrsmlfile: ' + resultrsmlfile)
logging.debug('localpath: ' + localpath2url(resultrsmlfile))
logging.debug('resource: ' + str(resource))
#self.uploadFileToServer(resultrsmlfile);
#response = self.bq.postblob(localpath2url(resultrsmlfile), xml=resource)
#response = self.bq.postblob((resultrsmlfile), xml=resource)
response = self.postblobbytxn(self.bq, (resultrsmlfile), xml=resource)
blob = etree.XML(response).find('./')
if blob is None or blob.get('uri') is None:
logging.debug('Could not upload the rsml file into the system')
self.bq.fail_mex('Could not upload the rsml file into the system')
else:
##create node for mex
linkdataservice = blob.get('uri')
linkblobservice = linkdataservice.replace('data_service', 'blob_service');
outputRSMLFileTag = etree.SubElement(outputTag, 'tag', name='RSMLFile', value=linkblobservice, type='file')
outputRSMLNameTag = etree.SubElement(outputTag, 'tag', name='RSMLName', value=rsmlFileNode, type='name')
#response = save_blob(self.bq, localpath2url(resultrsmlfile), resource=resource)
# response = save_blob(self.bq, resultrsmlfile, resource=resource)
#
# if response is None or response.get('uri') is None:
# logging.debug('Could not upload the rsml file into the system')
# self.bq.fail_mex('Could not upload the rsml file into the system')
# else:
# #create node for mex
# outputRSMLFileTag = etree.SubElement(outputTag, 'tag', name='RSMLFile', value=response.get('uri'), type='file')
#or using # self.bq.addTag()
#self.bq.finish_mex(tags = [outputTag], gobjects = [gObjectRootNode])
self.bq.finish_mex(tags = [outputTag])
#self.bq.finish_mex('Finished')
self.bq.close()
return;
root = config.get('Host', 'root') or 'localhost:8080'
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)
start = datetime.now()
url = urlparse.urljoin(root, url_import)
members = []
for f in files:
resource = etree.Element('resource',
name=os.path.basename(f),
value=localpath2url(f))
print etree.tostring(resource)
r = save_blob(session, resource=resource)
#r = session.postblob(xml=resource)
if r is None or r.get('uri') is None:
print 'Upload failed for %s' % f
else:
members.append(r.get('uri'))
print "Inserted all in: %s" % (datetime.now() - start)
dataset = etree.Element('dataset',
name=os.path.basename(os.path.dirname(files[0])))
for m in members:
n = etree.SubElement(dataset, 'value')
n.text = m
# model document
##################################################################
resource = etree.Element('connoisseur',
name="Watersipora: aiBrandon",
resource_uniq="00-4Eq9rrT6SuWoApxPUNDgUf")
files = [
'/XYZ/network_weights.caffemodel',
'/XYZ/mean.binaryproto',
'/XYZ/deploy.prototxt',
'/XYZ/solver.prototxt',
]
for f in files:
v = etree.SubElement(resource, 'value')
v.text = localpath2url(f)
etree.SubElement(resource, 'tag', name="author", value="dima")
etree.SubElement(resource,
'tag',
name="license",
type="license",
value="unrestricted")
etree.SubElement(resource,
'tag',
name="copyright",
type="copyright",
value="CBI, UCSB")
etree.SubElement(
resource,
'tag',
def teardown(self):
self.bq.update_mex('Collecting result...')
# Post all submex for files and return xml list of results
#gobjects = self._read_results()
#tags = [{ 'name': 'outputs',
# 'tag' : [{'name': 'rootimage', 'type':'image', 'value':self.resource_url,
# 'gobject' : [{ 'name': 'root_tips', 'type': 'root_tips', 'gobject' : gobjects }] }]
# }]
#self.bq.finish_mex(tags = tags)
# mex_outputs = self.bq.mex.xmltree.xpath('tag[@name="outputs"]')
# logging.debug('Outputs mex:' + str(mex_outputs))
# if mex_outputs:
# logging.debug('Outputs mex:' + str(mex_outputs))
#
# for tag in mex_outputs[0]:
# if tag.tag == 'tag' and tag.attrib['name'] == 'TipDetection':
# tag.attrib['value'] = "390"
# # if tag.tag == 'tag' and tag.attrib['type'] != 'system-input':
# # logging.debug('Set options with %s as %s'%(tag.attrib['name'],tag.attrib['value']))
# setattr(options,tag.attrib['name'],tag.attrib['value'])
# else:
# logging.debug('No Outputs Found on MEX!')
#load result data from the xml file. For testing, just use the fix xml i.e. will be changed later time
#resultfile = os.path.join(self.options.stagingPath, '0002.jpg_result.xml')
#reload parameters
self.mex_parameter_parser(self.options, self.bq.mex.xmltree)
#get the image downloaded
image = self.bq.load(self.options.image_url)
imageDownloaded = image.name + ".tif"
resultfile = os.path.join(self.options.stagingPath, imageDownloaded + '_result.xml')
logging.debug('Result file: ' + resultfile)
#load the result file and display info.
# tree.parse('/home/tuan/bisque/modules/RootNavLinuxModuleV3/0002.jpg_result.xml')
tree = etree.ElementTree()
tree.parse(resultfile)
rootNode = tree.getroot()
#
logging.debug('Root node: ' + rootNode.tag)
#
# # look for the Tips Output tag
tipDetectionNode = rootNode.findall("./Output/TipsDetected")
outputTag = etree.Element('tag', name='outputs')
outputSubTag = etree.SubElement(outputTag, 'tag', name='summary')
if len(tipDetectionNode) > 0:
totalAttrib = tipDetectionNode[0].get('total')
logging.debug('tipDetectionNode : ' + totalAttrib)
##etree.SubElement(outputTag, 'tag', name='TipDetection', value=str(23))
#etree.SubElement( outputSubTag, 'tag', name='Tip(s) detected', value=str(23))
etree.SubElement( outputSubTag, 'tag', name='Tip(s) detected', value=totalAttrib)
#using testing image: /home/tuan/bisque/modules/RootNavLinuxModuleV3/FeatureMapInMain.png
#filepath = '/home/tuan/bisque/modules/RootNavLinuxModuleV3/FeatureMapInMain.png'
filepath = '/home/tuan/bisque/modules/RootNavLinuxModuleV3/0002_copy.jpg'
#just for testing
outputImgTag = etree.SubElement(outputTag, 'tag', name='OutputImage', value=self.options.image_url)
#outputImgTag = etree.SubElement(outputTag, 'tag', name='OutputImage', value=localpath2url(filepath))
#gObjectValue = ""
#gObjectTag = etree.SubElement(outputImgTag, 'gobject', name='PointsDetected')
logging.debug('appending children to the output image tag')
gObjectTag = rootNode.findall("./Output/TipsDetected/gobject")[0]
outputImgTag.append(gObjectTag)
#test colour (this works for one point, change colour from red to yello)
#etree.SubElement(gObjectTag[0], 'tag', name='color', value="#ffff00")
#for tip in tipDetectionNode[0]:
# gPoint = etree.SubElement(gObjectTag, 'point', name=tip.attrib['id'])
# etree.SubElement(gPoint, 'vertex', x=tip.attrib['x'], y=tip.attrib['y'])
#outputExtraImgTag = etree.SubElement(outputTag, 'tag', name='OutputExtraImage', value=self.options.image_url)
resource = etree.Element ('image', name=os.path.basename(filepath), value=localpath2url(filepath))
meta = etree.SubElement (resource, 'tag', name='Experimental')
etree.SubElement (meta, 'tag', name='numberpoints', value="12")
#resource = etree.Element ('image', name='new file %s'%(os.path.basename(filepath)))
logging.debug('resource: ' + str(resource))
#self.uploadFileToServer(filepath)
logging.debug('self.bq.service_map in teardown: ' + str(self.bq.service_map))
#url = self.bq.service_url('data_service', 'image')
#url = self.bq.service_url('blob_service')
#url = self.bq.service_url('image_service', 'image') ##couldnt use for upload
#url = self.bq.service_url('/import/transfer') #not a service
#url = self.bq.service_url('import', 'transfer') #not a service
#url = self.bq.service_url('import', path='transfer') #not a service
#url = self.bq.service_url('http://127.0.0.1:8080/', '/import/transfer') #not a service
#response = save_blob(self.bq, resource=resource)
#logging.debug('url : ' + str(url))
#response_xml = self.bq.postblob(localpath2url(filepath), xml=resource) #post image to bisque and get the response
#logging.debug('response_xml: ' + str(response_xml))
#r = self.bq.postxml(url, resource, method='POST')
#logging.debug('Response: ' + str(r))
#response = self.bq.postblob(filepath, xml=resource)
#response = self.bq.postblob(filepath, xml=resource)
#blob = etree.XML(response).find('./')
# if blob is None or blob.get('uri') is None:
# logging.debug('Could not insert the Histogram file into the system')
# self.bq.fail_mex('Could not insert the Histogram file into the system')
# else:
# outputExtraImgTag = etree.SubElement(outputTag, 'tag', name='/home/tuan/bisque/modules/RootNavLinuxModuleV3/FeatureMapInMain.png')
# outputExtraImgTag = etree.SubElement(outputTag, 'tag', name='OutputExtraImage', value=blob.get('uri'), type='image')
# if r is None or r.get('uri') is None:
# logging.debug('Could not insert the Histogram file into the system')
# self.bq.fail_mex('Could not insert the Histogram file into the system')
# else:
# outputExtraImgTag = etree.SubElement(outputTag, 'tag', name='/home/tuan/bisque/modules/RootNavLinuxModuleV3/FeatureMapInMain.png')
# logging.debug('resource id: %s' %r.get('resource_uniq'))
# logging.debug('url: %s' %r.get('uri'))
# outputExtraImgTag = etree.SubElement(outputTag, 'tag', name='OutputExtraImage', value=r.get('uri'), type='image')
# outputExtraImgTag = etree.SubElement(outputImgTag, 'tag', name='OutputExtraImage', value=r.get('value'), type='image')
#etree.SubElement(outputTag, 'tag', name='OutputImage', value='/home/tuan/bisque/modules/RootNavLinuxModuleV3/FeatureMapInMain.png')
#etree.SubElement(outputTag, 'tag', name='OutputImage', value='file:///home/tuan/bisque/modules/RootNavLinuxModuleV3/FeatureMapInMain.png')
#output shortest paths
outputPathImgTag = etree.SubElement(outputTag, 'tag', name='OutputPathImage', value=self.options.image_url)
#get primary paths
primaryPathsNode = rootNode.findall("./Output/PrimaryPaths")
if (primaryPathsNode is not None) and (len(primaryPathsNode) > 0):
for path in primaryPathsNode[0]:
outputPathImgTag.append(path)
#get lateral paths
lateralPathsNode = rootNode.findall("./Output/LateralPaths")
if (lateralPathsNode is not None) and (len(lateralPathsNode) > 0):
for path in lateralPathsNode[0]:
outputPathImgTag.append(path)
#or using # self.bq.addTag()
self.bq.finish_mex(tags = [outputTag])
#self.bq.finish_mex('Finished')
self.bq.close()
return;
config.read('config.cfg')
root = config.get('Host', 'root') or 'localhost:8080'
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)
url = session.service_url('data_service', 'image')
request = '<image name="%s">' % 'kif5b 8102010.mvd2#0'
request = '%s<value>%s</value>' % (request, '%s#0' % localpath2url(
'f:/dima/develop/python/bq5irods/data/imagedir/admin/tests/multi_file/8102010-kif5b_control/kif5b 8102010.mvd2'
))
request = '%s<value>%s</value>' % (
request,
localpath2url(
'f:/dima/develop/python/bq5irods/data/imagedir/admin/tests/multi_file/8102010-kif5b_control/Data/119.aiix'
))
request = '%s<value>%s</value>' % (
request,
localpath2url(
'f:/dima/develop/python/bq5irods/data/imagedir/admin/tests/multi_file/8102010-kif5b_control/Data/151.aiix'
))
request = '%s<value>%s</value>' % (
request,
localpath2url(
'f:/dima/develop/python/bq5irods/data/imagedir/admin/tests/multi_file/8102010-kif5b_control/Data/157.aiix'
def teardown(self):
self.bq.update_mex('Collecting result...')
# Post all submex for files and return xml list of results
#gobjects = self._read_results()
#tags = [{ 'name': 'outputs',
# 'tag' : [{'name': 'rootimage', 'type':'image', 'value':self.resource_url,
# 'gobject' : [{ 'name': 'root_tips', 'type': 'root_tips', 'gobject' : gobjects }] }]
# }]
#self.bq.finish_mex(tags = tags)
# mex_outputs = self.bq.mex.xmltree.xpath('tag[@name="outputs"]')
# logging.debug('Outputs mex:' + str(mex_outputs))
# if mex_outputs:
# logging.debug('Outputs mex:' + str(mex_outputs))
#
# for tag in mex_outputs[0]:
# if tag.tag == 'tag' and tag.attrib['name'] == 'TipDetection':
# tag.attrib['value'] = "390"
# # if tag.tag == 'tag' and tag.attrib['type'] != 'system-input':
# # logging.debug('Set options with %s as %s'%(tag.attrib['name'],tag.attrib['value']))
# setattr(options,tag.attrib['name'],tag.attrib['value'])
# else:
# logging.debug('No Outputs Found on MEX!')
#load result data from the xml file. For testing, just use the fix xml i.e. will be changed later time
#resultfile = os.path.join(self.options.stagingPath, '0002.jpg_result.xml')
#reload parameters
self.mex_parameter_parser(self.options, self.bq.mex.xmltree)
#get the image downloaded
image = self.bq.load(self.options.image_url)
imageDownloaded = image.name + ".tif"
resultfile = os.path.join(self.options.stagingPath,
imageDownloaded + '_result.xml')
logging.debug('Result file: ' + resultfile)
#load the result file and display info.
# tree.parse('/home/tuan/bisque/modules/RootNavLinuxModuleV3/0002.jpg_result.xml')
tree = etree.ElementTree()
tree.parse(resultfile)
rootNode = tree.getroot()
#
logging.debug('Root node: ' + rootNode.tag)
#
# # look for the Tips Output tag
tipDetectionNode = rootNode.findall("./Output/TipsDetected")
outputTag = etree.Element('tag', name='outputs')
outputSubTag = etree.SubElement(outputTag, 'tag', name='summary')
if len(tipDetectionNode) > 0:
totalAttrib = tipDetectionNode[0].get('total')
logging.debug('tipDetectionNode : ' + totalAttrib)
##etree.SubElement(outputTag, 'tag', name='TipDetection', value=str(23))
#etree.SubElement( outputSubTag, 'tag', name='Tip(s) detected', value=str(23))
etree.SubElement(outputSubTag,
'tag',
name='Tip(s) detected',
value=totalAttrib)
#using testing image: /home/tuan/bisque/modules/RootNavLinuxModuleV3/FeatureMapInMain.png
#filepath = '/home/tuan/bisque/modules/RootNavLinuxModuleV3/FeatureMapInMain.png'
#filepath = '/home/tuan/bisque/modules/RootNavLinuxModuleV3/0002_copy.jpg'
#just for testing
outputImgTag = etree.SubElement(outputTag,
'tag',
name='OutputImage',
value=self.options.image_url)
#outputImgTag = etree.SubElement(outputTag, 'tag', name='OutputImage', value=localpath2url(filepath))
#gObjectValue = ""
#gObjectTag = etree.SubElement(outputImgTag, 'gobject', name='PointsDetected')
logging.debug('appending children to the output image tag')
gObjectTag = rootNode.findall("./Output/TipsDetected/gobject")[0]
outputImgTag.append(gObjectTag)
#test colour (this works for one point, change colour from red to yello)
#etree.SubElement(gObjectTag[0], 'tag', name='color', value="#ffff00")
#for tip in tipDetectionNode[0]:
# gPoint = etree.SubElement(gObjectTag, 'point', name=tip.attrib['id'])
# etree.SubElement(gPoint, 'vertex', x=tip.attrib['x'], y=tip.attrib['y'])
#display root info
#rootsTopMostNodes = rootNode.findall("./Output/RootTree/Root")
rootsTopMostNodes = rootNode.xpath(
'./Output/RootTree/Root[@order="-1"]')
for root in rootsTopMostNodes:
etree.SubElement(outputSubTag,
'tag',
name='Root length',
value=root.get('length'))
etree.SubElement(outputSubTag,
'tag',
name='Root area',
value=root.get('area'))
etree.SubElement(outputSubTag,
'tag',
name='Primary root',
value=root.get('primaryRoots'))
#outputExtraImgTag = etree.SubElement(outputTag, 'tag', name='OutputExtraImage', value=self.options.image_url)
#resource = etree.Element ('image', name=os.path.basename(filepath), value=localpath2url(filepath))
#meta = etree.SubElement (resource, 'tag', name='Experimental')
#etree.SubElement (meta, 'tag', name='numberpoints', value="12")
#resource = etree.Element ('image', name='new file %s'%(os.path.basename(filepath)))
#logging.debug('resource: ' + str(resource))
#self.uploadFileToServer(filepath)
logging.debug('self.bq.service_map in teardown: ' +
str(self.bq.service_map))
#url = self.bq.service_url('data_service', 'image')
#url = self.bq.service_url('blob_service')
#url = self.bq.service_url('image_service', 'image') ##couldnt use for upload
#url = self.bq.service_url('/import/transfer') #not a service
#url = self.bq.service_url('import', 'transfer') #not a service
#url = self.bq.service_url('import', path='transfer') #not a service
#url = self.bq.service_url('http://127.0.0.1:8080/', '/import/transfer') #not a service
#response = save_blob(self.bq, resource=resource)
#logging.debug('url : ' + str(url))
#response_xml = self.bq.postblob(localpath2url(filepath), xml=resource) #post image to bisque and get the response
#logging.debug('response_xml: ' + str(response_xml))
#r = self.bq.postxml(url, resource, method='POST')
#logging.debug('Response: ' + str(r))
#response = self.bq.postblob(filepath, xml=resource)
#response = self.bq.postblob(filepath, xml=resource)
#blob = etree.XML(response).find('./')
# if blob is None or blob.get('uri') is None:
# logging.debug('Could not insert the Histogram file into the system')
# self.bq.fail_mex('Could not insert the Histogram file into the system')
# else:
# outputExtraImgTag = etree.SubElement(outputTag, 'tag', name='/home/tuan/bisque/modules/RootNavLinuxModuleV3/FeatureMapInMain.png')
# outputExtraImgTag = etree.SubElement(outputTag, 'tag', name='OutputExtraImage', value=blob.get('uri'), type='image')
# if r is None or r.get('uri') is None:
# logging.debug('Could not insert the Histogram file into the system')
# self.bq.fail_mex('Could not insert the Histogram file into the system')
# else:
# outputExtraImgTag = etree.SubElement(outputTag, 'tag', name='/home/tuan/bisque/modules/RootNavLinuxModuleV3/FeatureMapInMain.png')
# logging.debug('resource id: %s' %r.get('resource_uniq'))
# logging.debug('url: %s' %r.get('uri'))
# outputExtraImgTag = etree.SubElement(outputTag, 'tag', name='OutputExtraImage', value=r.get('uri'), type='image')
# outputExtraImgTag = etree.SubElement(outputImgTag, 'tag', name='OutputExtraImage', value=r.get('value'), type='image')
#etree.SubElement(outputTag, 'tag', name='OutputImage', value='/home/tuan/bisque/modules/RootNavLinuxModuleV3/FeatureMapInMain.png')
#etree.SubElement(outputTag, 'tag', name='OutputImage', value='file:///home/tuan/bisque/modules/RootNavLinuxModuleV3/FeatureMapInMain.png')
##########################
#upload the probability image
outputFileNode = rootNode.findall("./Output/File")
probabilityimagepathNode = outputFileNode[0].find(
"ProbabilityImageFile").text
imagefile = os.path.basename(probabilityimagepathNode)
#get mexid
parts = self.options.stagingPath.split('/')
mexid = parts[len(parts) - 1]
resource = etree.Element('image',
name=os.path.join(UPLOADED_FOLDER, mexid,
imagefile))
response = self.postblobbytxn(self.bq, (probabilityimagepathNode),
xml=resource)
blob = etree.XML(response).find('./')
if blob is None or blob.get('uri') is None:
logging.debug(
'Could not upload the probability image file into the system')
self.bq.fail_mex(
'Could not upload the probability image file into the system')
else:
##create node for mex
linkprobabilityimgupload = blob.get('uri')
probabilityImageTag = etree.SubElement(
outputTag,
'tag',
name='ProbabilityImage',
value=linkprobabilityimgupload,
type='image')
#######################################################
#output shortest paths
outputPathImgTag = etree.SubElement(outputTag,
'tag',
name='OutputPathImage',
value=self.options.image_url)
#get primary paths
primaryPathsNode = rootNode.findall("./Output/PrimaryPaths")
if (primaryPathsNode is not None) and (len(primaryPathsNode) > 0):
for path in primaryPathsNode[0]:
outputPathImgTag.append(path)
#get lateral paths
lateralPathsNode = rootNode.findall("./Output/LateralPaths")
if (lateralPathsNode is not None) and (len(lateralPathsNode) > 0):
for path in lateralPathsNode[0]:
outputPathImgTag.append(path)
#node to display the root and convex hull
outputRootImgTag = etree.SubElement(outputTag,
'tag',
name='OutputRootsImage',
value=self.options.image_url)
gObjectRootNode = etree.SubElement(outputRootImgTag,
'gobject',
name='Roots')
splineInOtherRootsNodes = rootNode.xpath(
'./Output/RootTree/Root[@order!="-1"]/Spline')
for spline in splineInOtherRootsNodes:
#outputRootImgTag.append(spline[0])
gObjectRootNode.append(spline[0])
for root in rootsTopMostNodes:
convexNodes = root.findall('ConvexHull')
for cx in convexNodes:
#outputRootImgTag.append(cx[0])
gObjectRootNode.append(cx[0])
#get data for measurement table
measurementTablesNode = rootNode.xpath('./Output/Measurement/Tables')
if (measurementTablesNode is not None
and len(measurementTablesNode) > 0):
#outputRootImgTag.append(measurementTablesNode[0])
gObjectRootNode.append(measurementTablesNode[0])
#get data for curvature profile
curvNode = etree.SubElement(gObjectRootNode,
'tag',
name='CurvatureProfile')
curvatureProfileDataNode = rootNode.xpath(
'./Output/Measurement/CurvatureProfile')
if (curvatureProfileDataNode is not None
and len(curvatureProfileDataNode) > 0):
for rowDataNode in curvatureProfileDataNode[0]:
#gObjectRootNode.append()
gObjectCurv = etree.SubElement(curvNode, 'gobject', type='row')
etree.SubElement(gObjectCurv,
'tag',
name='col0',
value=rowDataNode.attrib['col0'])
etree.SubElement(gObjectCurv,
'tag',
name='col1',
value=rowDataNode.attrib['col1'])
#get data for travel map
mapNode = etree.SubElement(gObjectRootNode, 'tag', name='MapProfile')
mapProfileDataNode = rootNode.xpath('./Output/Measurement/MapProfile')
if (mapProfileDataNode is not None and len(mapProfileDataNode) > 0):
#gObjectRootNode.append(mapProfileDataNode[0])
for rowDataNode in mapProfileDataNode[0]:
gObjectMap = etree.SubElement(mapNode, 'gobject', type='row')
etree.SubElement(gObjectMap,
'tag',
name='col0',
value=rowDataNode.attrib['col0'])
etree.SubElement(gObjectMap,
'tag',
name='col1',
value=rowDataNode.attrib['col1'])
etree.SubElement(gObjectMap,
'tag',
name='col2',
value=rowDataNode.attrib['col2'])
#get data for RSML file for downloading
#extract rsml file from xml data
inputFileNode = rootNode.findall("./Input/File")
rsmlFileNode = inputFileNode[0].find("RSMLFile").text
rsmlPathNode = inputFileNode[0].find("RSMLPath").text
#upload rsml file
parts = self.options.stagingPath.split('/')
mexid = parts[len(parts) - 1]
resultrsmlfile = os.path.join(rsmlPathNode, rsmlFileNode)
#resource = etree.Element ('image', name="\'" + os.path.join(mexid, rsmlFileNode) + "\'")
resource = etree.Element('resource',
name=os.path.join(mexid, rsmlFileNode))
#resource = etree.Element ('resource', name='new file %s'%rsmlFileNode )
#resource = etree.Element ('image', name='new file P.rsml')
logging.debug('name resource: ' + os.path.join(mexid, rsmlFileNode))
logging.debug('resultrsmlfile: ' + resultrsmlfile)
logging.debug('localpath: ' + localpath2url(resultrsmlfile))
logging.debug('resource: ' + str(resource))
#self.uploadFileToServer(resultrsmlfile);
#response = self.bq.postblob(localpath2url(resultrsmlfile), xml=resource)
#response = self.bq.postblob((resultrsmlfile), xml=resource)
response = self.postblobbytxn(self.bq, (resultrsmlfile), xml=resource)
blob = etree.XML(response).find('./')
if blob is None or blob.get('uri') is None:
logging.debug('Could not upload the rsml file into the system')
self.bq.fail_mex('Could not upload the rsml file into the system')
else:
##create node for mex
linkdataservice = blob.get('uri')
linkblobservice = linkdataservice.replace('data_service',
'blob_service')
outputRSMLFileTag = etree.SubElement(outputTag,
'tag',
name='RSMLFile',
value=linkblobservice,
type='file')
outputRSMLNameTag = etree.SubElement(outputTag,
'tag',
name='RSMLName',
value=rsmlFileNode,
type='name')
#response = save_blob(self.bq, localpath2url(resultrsmlfile), resource=resource)
# response = save_blob(self.bq, resultrsmlfile, resource=resource)
#
# if response is None or response.get('uri') is None:
# logging.debug('Could not upload the rsml file into the system')
# self.bq.fail_mex('Could not upload the rsml file into the system')
# else:
# #create node for mex
# outputRSMLFileTag = etree.SubElement(outputTag, 'tag', name='RSMLFile', value=response.get('uri'), type='file')
#or using # self.bq.addTag()
#self.bq.finish_mex(tags = [outputTag], gobjects = [gObjectRootNode])
self.bq.finish_mex(tags=[outputTag])
#self.bq.finish_mex('Finished')
self.bq.close()
return
config.read('config.cfg')
root = config.get('Host', 'root') or 'localhost:8080'
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_z_tiff'
request = '%s<value>%s</value>' % (
request,
localpath2url(
'f:/dima/develop/python/bq5irods/data/imagedir/admin/tests/multi_file/series_z_tiff/z_000001.tiff'
))
request = '%s<value>%s</value>' % (
request,
localpath2url(
'f:/dima/develop/python/bq5irods/data/imagedir/admin/tests/multi_file/series_z_tiff'
))
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', '30')
request = '%s<tag name="%s" value="%s" type="number" />' % (request,
'image_num_t', '1')
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" />' % (
config = ConfigParser.ConfigParser()
config.read('config.cfg')
root = config.get('Host', 'root') or 'localhost:8080'
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)
#url = session.service_url('data_service', 'image')
request = '<image name="%s">'%'AndorMM#0'
request = '%s<value>%s</value>'%(request, '%s#0'%localpath2url('f:/dima/develop/python/bq5irods/data/imagedir/admin/tests/multi_file/AndorMM/DiskInfo5.kinetic'))
request = '%s<value>%s</value>'%(request, localpath2url('f:/dima/develop/python/bq5irods/data/imagedir/admin/tests/multi_file/AndorMM'))
request = '%s</image>'%request
#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')
request = '<image name="%s">'%'AndorMM#1'
request = '%s<value>%s</value>'%(request, '%s#1'%localpath2url('f:/dima/develop/python/bq5irods/data/imagedir/admin/tests/multi_file/AndorMM/DiskInfo5.kinetic'))
config.read('config.cfg')
root = config.get('Host', 'root') or 'localhost:8080'
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">' % 'IM-0001-0001.dcm'
request = '%s<value>%s</value>' % (
request,
localpath2url(
'f:/dima/develop/python/bq5irods/data/imagedir/admin/tests/multi_file/dicom/IM-0001-0001.dcm'
))
request = '%s<value>%s</value>' % (
request,
localpath2url(
'f:/dima/develop/python/bq5irods/data/imagedir/admin/tests/multi_file/dicom'
))
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')