def anchor(self, drifting_t, anchored_t):
"""
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
o -- [ D ] -- o ==> o -- [ A ] -- o
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Anchor `drifting_t` at `anchored_t`
Parameters
----------
drifting_t :
Drifting time to anchor
anchored_t :
When to anchor `drifting_t`
"""
drifting_t = T(drifting_t)
anchored_t = T(anchored_t)
assert (drifting_t in self) and (drifting_t.drifting)
assert anchored_t.anchored
if anchored_t not in self:
self.add_node(anchored_t)
self._merge(drifting_t, anchored_t)
def _outfFieldsValue(self, field_names, outdir):
#Inital 2d array for PCA input, with all elements equal to 0
#Rows = number of features, Cols = fields used for PCA analysis
print "Start collecting attributes' values from the table of " + self._featureName
stTime = T()
num_of_PCA_vars = len(field_names)
AllData = [[0 for i in range(num_of_PCA_vars)]
for i in range(self.num_of_features)]
#Get fields value from the feature dataset
with arcpy.da.SearchCursor(self.dataPath,
field_names) as cursor: #@UndefinedVariable
rowNum = 0
for row in cursor:
for colNum in xrange(num_of_PCA_vars):
AllData[rowNum][colNum] = row[colNum]
rowNum += 1
outfPath = os.path.join(outdir, "Attribute_Table.txt")
outf = open(outfPath, 'w')
# -----output format-----
# Number of features: XX
# Fields: field1 field2 field3 field4 ...
# feature1_field1_value feature1_field2_value feature1_field3_value feature1_field4_value ...
# feature2_field1_value feature2_field2_value feature2_field3_value feature2_field4_value ...
# ...
outString = "Number of features: " + str(self.num_of_features) + "\n"
outString += "Fields: " + '\t'.join(field_names) + '\n'
outString += '\n'.join('\t'.join(str(x) for x in y) for y in AllData)
outf.write(outString)
outf.close()
print "All required attributes' values are written to " + outfPath + ". Elapsed Time: " + timer(
stTime, T()) + "\n"
return outfPath
def add_edge(self, t1, t2, key=None, attr_dict=None, **attrs):
"""Add annotation to the graph between times t1 and t2
Parameters
----------
t1, t2: float, str or None
data : dict, optional
{annotation_type: annotation_value} dictionary
Example
-------
>>> G = Transcription()
>>> G.add_edge(T(1.), T(), speaker='John', 'speech'='Hello world!')
"""
t1 = T(t1)
t2 = T(t2)
# make sure Ts are connected in correct chronological order
if t1.anchored and t2.anchored:
assert t1 <= t2
super(Transcription, self).add_edge(t1,
t2,
key=key,
attr_dict=attr_dict,
**attrs)
def omm2osm(inputfile, outputfile):
import xml.etree.cElementTree as ET # for xml
import os # for detecting if file is empty
from time import time as T # for elapsed time
# start timer
start = T()
#create output file if not exists
try:
tempfile = open(outputfile, 'r')
except FileNotFoundError:
tempfile = open(outputfile, 'w')
tempfile.write('')
tempfile.close()
#create root xml root if not exists
output = open(outputfile, 'ab+')
if os.path.getsize(outputfile) == 0:
temproot = ET.Element('osm')
temproot.attrib['version'] = '0.6'
temproot.attrib['generator'] = 'omconvert 0.1'
temproot.attrib['copyright'] = 'OpenStreetMap and contributors'
temproot.attrib[
'attribution'] = 'http://www.openstreetmap.org/copyright'
temproot.attrib[
'license'] = 'http://opendatacommons.org/licenses/odbl/1-0/'
temptree = ET.ElementTree(temproot)
temptree.write(outputfile,
encoding='utf-8',
method='xml',
short_empty_elements=False)
output.write(b'\n')
output.seek(-7, 2)
output.truncate()
input = open(inputfile, 'r')
for line in input:
stringoutput = m2s(line)
if line.split('>')[0] == '0':
stringoutput = b'\n' + stringoutput + b'\n'
elif line.split('>')[0] == '2':
stringoutput = stringoutput[:-1]
output.write(stringoutput.replace(b' "', b'"'))
output.write(b'\n</osm>')
output.close()
print('Elapsed Time: ' + str(T() - start) + 's')
def pre_align(self, t1, t2, t):
"""
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p -- [ t1 ] p [ t1 ]
⟍ ⟋
==> [ t ]
⟋ ⟍
p' -- [ t2 ] p' [ t2 ]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"""
t1 = T(t1)
t2 = T(t2)
t = T(t)
# make sure --[t1] incoming edges are empty
# because they're going to be removed afterwards,
# and we don't want to loose data
pred1 = self.predecessors(t1)
for p in pred1:
for key, data in self[p][t1].iteritems():
assert not data
# make sure --[t2] incoming edges are empty
# (for the same reason...)
pred2 = self.predecessors(t2)
for p in pred2:
for key, data in self[p][t2].iteritems():
assert not data
# let's get started (remove all incoming edges)
for p in pred1:
for key in list(self[p][t1]):
self.remove_edge(p, t1, key=key)
for p in pred2:
for key in list(self[p][t2]):
self.remove_edge(p, t2, key=key)
for p in set(pred1) | set(pred2):
self.add_edge(p, t)
self.add_edge(t, t1)
self.add_edge(t, t2)
def post_align(self, t1, t2, t):
"""
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ t1 ] -- s [ t1 ] s
⟍ ⟋
==> [ t ]
⟋ ⟍
[ t2 ] -- s' [ t2 ] s'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"""
t1 = T(t1)
t2 = T(t2)
t = T(t)
# make sure [t1]-- outgoing edges are empty
# because they're going to be removed afterwards,
# and we don't want to loose data
succ1 = self.successors(t1)
for s in succ1:
for key, data in self[t1][s].iteritems():
assert not data
# make sure --[t2] outgoing edges are empty
# (for the same reason...)
succ2 = self.successors(t2)
for s in succ2:
for key, data in self[t2][s].iteritems():
assert not data
# let's get started (remove all outgoing edges)
for s in succ1:
for key in list(self[t1][s]):
self.remove_edge(t1, s, key=key)
for s in succ2:
for key in list(self[t2][s]):
self.remove_edge(t2, s, key=key)
for s in set(succ1) | set(succ2):
self.add_edge(t, s)
self.add_edge(t1, t)
self.add_edge(t2, t)
def align(self, one_t, another_t):
"""
Align two (potentially drifting) times
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
o -- [ F ] -- o o o
⟍ ⟋
==> [ F ]
⟋ ⟍
o -- [ f ] -- o o o
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Parameters
----------
one_t, another_t
Two times to be aligned.
Notes
-----
* If both `one_t` and `another_t` are drifting, the resulting graph
will no longer contain `one_t`.
* In case `another_t` is anchored, `align` is equivalent to `anchor`.
* `one_t` and `another_t` cannot be both anchored.
"""
one_t = T(one_t)
another_t = T(another_t)
assert one_t in self
assert another_t in self
# first time is drifting
if one_t.drifting:
self._merge(one_t, another_t)
# second time is drifting
elif another_t.drifting:
self._merge(another_t, one_t)
# both times are anchored --> FAIL
else:
raise ValueError('Cannot align two anchored times')
def grow(self, num=0, layer=0):
if (num != 0):
layer = 9999
elif (num == 0 and layer == 0):
layer = 9999
num = self._featureAmount
else:
num = sys.maxsize
pass
print "\nStart Organic Growth from current layer " + str(
self.currentLayer) + " (Number of features: " + str(
self.featureCount) + ")."
stTime = T()
for layerIndex in xrange(self.currentLayer + 1, layer + 1):
# Look for all first order neighbors of current grown region
currentSet = self.layers[layerIndex - 1]
if (currentSet == 0):
baseLayerSet = currentSet
excludedNeighborSet = currentSet
newLayerSet = self._findNextFirstOrderNeighborLayer(
baseLayerSet, excludedNeighborSet, self._adjDict)
else:
prevSet = self.layers[layerIndex - 2]
baseLayerSet = currentSet
excludedNeighborSet = currentSet | prevSet
newLayerSet = self._findNextFirstOrderNeighborLayer(
baseLayerSet, excludedNeighborSet, self._adjDict)
# Update current layer number and total included features
self.currentLayer += 1
self.totalSet = self.totalSet | newLayerSet
# Look for all feature that are not classified as first order neighbors of previous grown region but surrounded by the new grown regions
enclosedFeatures = self._findWithinFeatures(self.totalSet)
if (len(enclosedFeatures) > 0):
self.totalSet = self.totalSet | enclosedFeatures
newLayerSet = newLayerSet | enclosedFeatures
# Add the newly found layer to the original region to grow it
self.layers.append(newLayerSet)
self.featureCount += len(newLayerSet)
self.increasedLayerNumberList.append(len(newLayerSet))
if (self.featureCount >= num):
break
print "\nOrganic Growth analysis has completed. " + "\nCurrent layer: " + str(
self.currentLayer) + "\nNumber of features: " + str(
self.featureCount) + "\nElapsed time: " + timer(stTime, T())
def _outfSpatialContiguityMatrix(self, spatialContRel, outdir):
print "Start producing spatial contiguity matrix for " + self._featureName + ".\nTotally " + str(
self.num_of_features) + " number of features."
stTimeEntireOp = T()
baselyr = os.path.join(self._scratchFolder, "BaseLayer.lyr")
arcpy.MakeFeatureLayer_management(self.dataPath, baselyr)
outString = ""
for i in xrange(self.num_of_features):
if (i % 100 == 0):
stTime1Feature = T()
selectedlyr = os.path.join(self._scratchFolder,
"SelectedLayer_" + str(i) + ".lyr")
arcpy.MakeFeatureLayer_management(
self.dataPath, selectedlyr, '\"' + self.ObjIDField + '\" = ' +
str(i + self.ObjIDInitialValue))
arcpy.SelectLayerByLocation_management(baselyr, spatialContRel,
selectedlyr)
outString += str(i) + ": "
neighborFeatureList = []
with arcpy.da.SearchCursor(
baselyr, ("OID@")) as cursor: #@UndefinedVariable
for row in cursor:
# row only contain 1 element, ObjectID
cKey = row[0] - self.ObjIDInitialValue
if (i != cKey):
neighborFeatureList.append(cKey)
outString += ', '.join(str(x)
for x in neighborFeatureList) + '\n'
if (i % 100 == 99):
print "100 features' neighbors are identified (total: " + str(
i + 1) + "). Elapsed Time: " + timer(stTime1Feature, T())
arcpy.SelectLayerByAttribute_management(baselyr, "CLEAR_SELECTION")
outfPath = os.path.join(
outdir, "Spatial_Contiguity_" + spatialContRel + ".txt")
outf = open(outfPath, 'w')
# -----Output format------
# 0 (feature id, defaultly starting from 0): neighbor1_id, neighbor2_id, ...
# 1: neighbor1_id, neighbor2_id, ...
# ...
outf.write(outString)
outf.close()
print "Spatial Contiguity matrix has been written into " + outfPath + ". Elapsed time: " + timer(
stTimeEntireOp, T()) + "\n"
return outfPath
def osc2omc(inputfile, outputfile):
import xml.etree.cElementTree as ET # xml processing
from time import time as T # timer
# start timer
start = T()
output = open(outputfile, 'a')
# parse xml
context = ET.iterparse(inputfile, events=("start", "end"))
context = iter(context)
event, root = next(context)
for event, elem in context:
if event == "start" and (elem.tag == "create" or elem.tag == "modify"
or elem.tag == "delete"):
# determine modification action
if elem.tag == 'create':
output.write('3: \n')
root.clear()
continue
elif elem.tag == 'modify':
output.write('4: \n')
root.clear()
continue
elif elem.tag == 'delete':
output.write('5: \n')
root.clear()
continue
else:
print('Modification method not identified.')
quit()
if event == "end" and (elem.tag == "node" or elem.tag == "way"
or elem.tag == "relation"):
# write to file
output.write(m2s(elem))
root.clear()
# close file
output.close()
print('Elapsed Time: ' + str(T() - start) + 's')
def run(self):
proc_name = self.name
while True:
next_task = self.task_queue.get()
if next_task is None:
# Poison pill means shutdown
print '%s: Exiting' % proc_name
self.task_queue.task_done()
break
start = T()
answer = next_task()
end = T()
print '%s : %s : %s' % (proc_name, next_task, end-start)
self.task_queue.task_done()
if next_task.task_type == 'train':
self.result_queue_tr.put(answer)
elif next_task.task_type == 'test':
self.result_queue_te.put(answer)
else:
raise ValueError('Incorrect task type: {}'.format(next_task.task_type))
return
def osm2omm(inputfile, outputfile):
import xml.etree.cElementTree as ET # xml processing
from time import time as T # timer
# start timer
start = T()
output = open(outputfile, 'a')
# parse xml
context = ET.iterparse(inputfile, events=("start", "end"))
context = iter(context)
event, root = next(context)
for event, elem in context:
if event == "end" and (elem.tag == "node" or elem.tag == "way"
or elem.tag == "relation"):
output.write(s2m(elem))
root.clear()
# close file
output.close()
print('Elapsed time: ' + str(T() - start) + 's')
def parallel_video_cropping(self):
"""
Launches four cpus to paralizes the video cropping
INPUTS
------
self: an instance of the class VideoPipelineNew
IMPORTANT
---------
Code assumes you want a five minute long subclip but if instead want a different length,
just change the variable subclip_length below to whatever one you used, make sure to change
all subclip_length variables in other functions (see five_min_subclips)
"""
from time import time as T
subclip_length = self.subclip_length
n_cpus = 4 # if computer has more than 4 cpus, change this
p = Pool(n_cpus)
func_in = zip([self] * int(self.clip_duration / subclip_length),
xrange(int(self.clip_duration / subclip_length)))
s1 = T()
p.map(crop_vid, func_in)
s2 = T()
print 'parallel time', (s2 - s1)
def relabel_drifting_nodes(self, mapping=None):
"""Relabel drifting nodes
Parameters
----------
mapping : dict, optional
A dictionary with the old labels as keys and new labels as values.
Returns
-------
g : Transcription
New annotation graph
mapping : dict
A dictionary with the new labels as keys and old labels as values.
Can be used to get back to the version before relabelling.
"""
if mapping is None:
old2new = {n: T() for n in self.drifting()}
else:
old2new = dict(mapping)
new2old = {new: old for old, new in old2new.iteritems()}
return nx.relabel_nodes(self, old2new, copy=True), new2old
def timerange(self, t1, t2, inside=True, sort=None):
"""Infer edge timerange from graph structure
a -- ... -- [ t1 ] -- A -- ... -- B -- [ t2 ] -- ... -- b
==> [a, b] (inside=False) or [A, B] (inside=True)
Parameters
----------
t1, t2 : anchored or drifting times
inside : boolean, optional
Returns
-------
segment : Segment
"""
t1 = T(t1)
t2 = T(t2)
# in case it is not provided, compute temporal sort
if sort is None:
sort = self.temporal_sort()
# if edge start is anchored, use it as start time
if t1.anchored:
start = t1
# otherwise, look for the closest anchored time in temporal order:
# - just after if inside is True
# - just before otherwise
else:
start = None
# find time index in temporal sort
istart = sort.index(t1)
# search just before or just after depending on 'inside' value
search = sort[istart + 1:] if inside else sort[istart - 1::-1]
for t in search:
if t.anchored:
start = t
break
# if we could not find any anchored time
# use document end of start depending on 'inside' value
if start is None:
start = TEnd if inside else TStart
# same treatment for the other end of edge
if t2.anchored:
end = t2
else:
end = None
iend = sort.index(t2)
search = sort[iend - 1::-1] if inside else sort[iend + 1:]
for t in search:
if t.anchored:
end = t
break
if end is None:
end = TStart if inside else TEnd
# return a 'Segment'
return Segment(start=start, end=end)
def omc2osc(inputfile, outputfile):
import xml.etree.cElementTree as ET # xml process
import os # check if file is empty
from time import time as T # timer
# start timer
start = T()
input = open(inputfile, 'r')
# create file if not exists
try:
tempfile = open(outputfile, 'r')
except FileNotFoundError:
tempfile = open(outputfile, 'w')
tempfile.write('')
tempfile.close()
# create root for xml
output = open(outputfile, 'ab+')
if os.stat(outputfile).st_size == 0:
temproot = ET.Element('osmChange')
temproot.attrib['version'] = '0.6'
temproot.attrib['generator'] = 'omconvert 0.1'
treetemp = ET.ElementTree(temproot)
treetemp.write(outputfile, method='xml', short_empty_elements=False)
output.write(b'\n')
output.seek(-13, 2)
output.truncate()
# parse xml
input = open(inputfile, 'r')
mfindex = []
mfindex.append('')
mfindex.append('')
for line in input:
# determine modification action
if line.find('3: ') != -1:
mfindex[1] = 3
output.write(endlast(mfindex[0]).encode('utf-8'))
mfindex[0] = mfindex[1]
output.write(b'\n<create>\n')
elif line.find('4: ') != -1:
mfindex[1] = 4
output.write(endlast(mfindex[0]).encode('utf-8'))
mfindex[0] = mfindex[1]
output.write(b'\n<modify>\n')
elif line.find('5: ') != -1:
mfindex[1] = 5
output.write(endlast(mfindex[0]).encode('utf-8'))
mfindex[0] = mfindex[1]
output.write(b'\n<delete>\n')
else:
stringoutput = m2s(line)
output.write(stringoutput.replace(b' "', b'"'))
if mfindex[0] == 3:
output.write(b'</create>')
if mfindex[0] == 4:
output.write(b'</modify>')
if mfindex[0] == 5:
output.write(b'</modify>')
output.write(b'\n</osmChange>')
output.close()
print('Elapsed Time: ' + str(T() - start) + 's')
X = SS().fit_transform(X)
# ## Train the Support Vector Classifier
# In[10]:
from sklearn.svm import SVC
# Hyperparameters
kernel = 'rbf'
C = 13
gamma = 0.325
from time import time as T
start = T()
model = SVC(kernel=kernel, C=C, gamma=gamma)
clf = model.fit(X_train, Y_train)
end = T()
pred = clf.predict(X_test)
mScore = clf.score(X_test, Y_test)
print(f'Score against Testing Data: {mScore * 100:.3f}%')
print(f'Model took {(end-start)*1000:.3f}ms to train')
# ### Generate Classification Report
# In[11]:
from sklearn.metrics import classification_report as CR
def crop(self, source, target=None):
"""Get minimum subgraph between source time and target time
Parameters
----------
source : Segment
target : float or str, optional
Returns
-------
g : Transcription
Sub-graph between source and target
"""
if isinstance(source, Segment):
source, target = source.start, source.end
source = T(source)
target = T(target)
# sorted list of anchored times will be needed later
# make sure it is computed only once
if source.anchored or target.anchored:
anchored = sorted(self.anchored())
# ~~~ from_source = set of nodes reachable from source ~~~~~~~~~~~~~~~~
# source is drifting
if source.drifting:
if source not in self:
raise ValueError(
'Drifting time %s is not in the transcription.' % source)
else:
from_source = {source} | nx.algorithms.descendants(
self, source)
# source is anchored
else:
# if source is in graph, then it is easy
if source in self:
from_source = {source} | nx.algorithms.descendants(
self, source)
# if source is not in graph,
# find anchored time just before source
else:
if source < anchored[0]:
from_source = set(self) # take no risk!
else:
before = [n for n in anchored if n <= source][-1]
from_source = {before} | nx.algorithms.descendants(
self, before)
# ~~~ to_target = set of nodes from which target is reachable ~~~~~~~~~
# target is drifting
if target.drifting:
if target not in self:
raise ValueError(
'Drifting time %s is not in the transcription.' % target)
else:
to_target = {target} | nx.algorithms.ancestors(self, target)
else:
# if target is in graph, then it is easy
if target in self:
to_target = {target} | nx.algorithms.ancestors(self, target)
# if target is not in graph,
# find anchored time just after target
else:
if target > anchored[-1]:
to_target = set(self) # take no risk!
else:
after = [n for n in anchored if n >= target][0]
to_target = {after} | nx.algorithms.ancestors(self, after)
# union of source, target and source-to-target paths
nbunch = from_source & to_target
return self.subgraph(nbunch)
default='unet',
help='checkpoint prefix')
parser.add_argument('--out_dir',
type=str,
default='out',
help='dir to restore results')
args = parser.parse_args()
step = args.step
sym, arg_params, aux_params = mx.model.load_checkpoint(
args.prefix, args.restore_step)
# print(sym.list_outputs())
mod = mx.mod.Module(symbol=sym, label_names=None, context=mx.gpu())
mod.bind(for_training=False,
data_shapes=[('data', (1, 3, step, step))],
label_shapes=mod._label_shapes)
mod.set_params(arg_params, aux_params, allow_missing=True)
Batch = namedtuple('Batch', ['data'])
imgns = [i for i in os.listdir(args.test_path) if i[-4:] == '.jpg']
dic = {}
for img_name in imgns[:]:
start = T()
name = img_name[:-9]
print('test {}'.format(img_name))
filename = os.path.join(args.test_path, img_name)
label = predict(filename, dic)
imsave(os.path.join(args.out_dir, img_name[:-4] + '_class.png'), label)
# print('save to {}.tif, using {}s'.format(img_name[:-4]+'_class.tif', T() - start))
def from_json(cls, data):
graph = node_link_graph(data[PYANNOTE_JSON_TRANSCRIPTION])
mapping = {node: T(node) for node in graph}
graph = nx.relabel_nodes(graph, mapping)
return cls(graph=graph, **graph.graph)
df = pd.read_csv('../data/featuressimple.csv')
X = df.drop('vehicle_list_price',axis =1)
y = df.vehicle_list_price
### Train test splits
X_train, X_test, y_train, y_test = train_test_split(
X, y, test_size=0.2, random_state=42)
#For regressors that needs standarlization
scaler = StandardScaler()
X_train_scaled = scaler.fit_transform(X_train)
X_test_scaled = scaler.transform(X_test)
print("-"*100)
print("Linear regression...")
start = T()
reg_linear.fit(X_train,y_train)
y_pred = reg_linear.predict(X_test)
print(f"R2: {r2_score(y_test,y_pred): .2f}")
print(f"RMSE: {np.sqrt(mean_squared_error(y_test,y_pred)):.2f}")
print(f"Finished in {T()- start: .2f} seconds")
print("-"*100)
print("Ridge regression...")
start = T()
reg_ridge.fit(X_train_scaled,y_train)
y_pred = reg_ridge.predict(X_test_scaled)
print(f"R2: {r2_score(y_test,y_pred): .2f}")
print(f"RMSE: {np.sqrt(mean_squared_error(y_test,y_pred)):.2f}")
print(f"Finished in {T()- start: .2f} seconds")
# Make it into a dataframe
df = pd.concat(lunge_per_well, axis=1)
# Make a file if its not there
excel_root = os.path.join(root, name) + '\\lunge_excel_output.xlsx'
if not os.path.exists(excel_root):
writer = pd.ExcelWriter(excel_root) # +'output.xlsx')
df.to_excel(writer, name)
writer.save()
writer.close()
# DO NOT OVER WRITE DATA, CHECK IF FILE IS THERE ALREADY!!!
elif os.path.exists(excel_root):
book = load_workbook(excel_root)
writer = pd.ExcelWriter(excel_root, engine='openpyxl')
writer.book = book
df.to_excel(writer, sheet_name=name)
writer.save()
writer.close()
# Basically means, run this if you're not import functions from this script e.g. you hit run
# instead of in another script typing from VideoPipelineFinal import parallel_video_cropping etc.
if __name__ == '__main__':
from time import time as T
s = T()
self = VideoPipelineNew()
print 'Program took this long to run: ' + str(time() - s)
parallel_video_cropping(self)
self.matlab_stuff()
