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clusterModule.py
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clusterModule.py
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#
# Copyright (c) University of Luxembourg 2019-2020.
# Created by Hazem FAHMY, hazem.fahmy@uni.lu, SNT, 2019.
# Modified by Mojtaba Bagherzadeh, m.bagherzadeh@uottawa.ca, University of Ottawa, 2019.
#
from HeatmapModule import doDistance, collectHeatmaps, calculate_pixel_distance
from imports import shutil, itemgetter, pd, np, time, torch, os, pdist, shc, metrics, sys, normalize, \
AgglomerativeClustering, imageio, math, KMeans, join, exists, isfile, cv2, tqdm, Variable, makedirs, basename
from sklearn.preprocessing import LabelEncoder
import matplotlib.pyplot as plt
#import IEE_V1.ieepredict
import dataSupplier as DS
#import hdbscan
#from scipy import optimize
#from scipy.signal import savgol_filter
#from scipy.interpolate import splprep, splev
#from scipy.interpolate import UnivariateSpline
from kneed import KneeLocator
def run(caseFile):
layers = caseFile["layers"]
outputPath = caseFile["filesPath"]
mode = caseFile["clustMode"]
maxCluster = caseFile["maxCluster"]
start = time.time()
print("Start Clustering Operation")
minAvgICD = [0] * len(layers)
minAvgWICD = [0] * len(layers)
minAvgS = [0] * len(layers)
minAvgD = [0] * len(layers)
clsData = {}
i = 0
layersX = list()
outputPathX = join(outputPath, "ClusterAnalysis_" + str(mode))
if isfile(join(outputPath, "Layer9HMDistance.xlsx")):
if not exists(outputPathX):
os.mkdir(outputPathX)
for layerX in layers:
clsPath = join(outputPath, "ClusterAnalysis_" + str(mode), layerX + ".pt")
if not isfile(clsPath):
layersX.append(layerX)
print("Loading heatmaps' distance matrix \n")
heatMapDistanceExecl = pd.read_excel(join(outputPath, str(layerX) + "HMDistance.xlsx"))
print("Loaded \n")
heatMapDistanceExecl.drop(
heatMapDistanceExecl.columns[heatMapDistanceExecl.columns.str.contains('unnamed', case=False)],
axis=1, inplace=True)
print("clustering based on Layer " + str(layerX))
# maxCluster = int(len(heatMapDistanceExecl)/2)
clsData, minAvgICD[i], minAvgWICD[i] = doClustering(mode, heatMapDistanceExecl, outputPathX, str(layerX)
+ ".xlsx", maxCluster, layerX, "KG")
minAvgICD[0] = 1e9
minAvgWICD[0] = 1e9
torch.save(clsData, join(outputPathX, str(layerX) + ".pt"))
sys.stderr.write("Cluster of " + str(layerX) + " saved \n")
minAvgCluster = pd.DataFrame.from_dict(data=clsData, orient='index')
writer = pd.ExcelWriter(join(outputPathX, str(layerX) + ".xlsx"), engine='xlsxwriter')
minAvgCluster.to_excel(writer, sheet_name="ClustersSummary")
minAvgCluster = pd.DataFrame.from_dict(data=clsData['clusters'], orient='index')
minAvgCluster.to_excel(writer, sheet_name="ClustersDetails")
writer.close()
sys.stderr.write("Cluster of all layers saved \n")
end = time.time()
print("Total time consumption of operation Clustering is " + str((end - start) / 60.0) + " minutes.")
return caseFile
def exportImages_2P(clsData, clsData2, outPathX, caseFile, concepts, layerX):
imgsPath = []
for clusterID2 in clsData2['clusters']:
if len(clsData2['clusters'][clusterID2]['members']) == 1:
continue
clusterPath = join(outPathX, str(clusterID2))
#print("Exists")
DS.cleanMake(clusterPath, True)
clusterImages = []
clusterImages2 = []
clusterImages2List = []
for clusterID in clsData2['clusters'][clusterID2]['members']:
for img in clsData['clusters'][clusterID]['members']:
if concepts:
fileName = img.split(".")[0] + caseFile["imgExt"]
srcPath = join(caseFile["DataSetsPath"], str(caseFile["faceSubset"]) + "_Concepts", str(layerX), fileName)
dirPath = join(clusterPath, fileName)
if caseFile["datasetName"] == "HPD":
#origFile = join(caseFile["DataSetsPath"], "TestSet_Backup", str(int(img.split("_")[1])-1) + caseFile["imgExt"])
origFile = str(join(caseFile["DataSetsPath"], "TestSet_Backup_M", str((img.split("_")[1])) + caseFile["imgExt"])) #HPD-M
else:
origFile = join(caseFile["DataSetsPath"], "TestSet_Backup", str(img.split("_")[1]) + caseFile["imgExt"])
if origFile not in clusterImages2List:
clusterImages2.append(imageio.imread(origFile))
clusterImages2List.append(origFile)
else:
fileName = img.split("_")[1] + caseFile["imgExt"]
fileClass = img.split("_")[2]
fileSource = img.split("_")[0]
if fileSource == "Train":
srcPath = join(caseFile["trainDataPath"], fileClass, fileName)
elif fileSource == "Test":
srcPath = join(caseFile["testDataPath"], fileClass, fileName)
else:
srcPath = join(caseFile["improveDataPath"], fileClass, fileName)
dirPath = join(clusterPath, img + caseFile["imgExt"])
shutil.copy(srcPath, dirPath)
clusterImages.append(imageio.imread(srcPath))
imgsPath.append(join(outPathX, str(clusterID2) + '_' + str(len(clusterImages)) + '.gif'))
imageio.mimsave(join(outPathX, str(clusterID2) + '_' + str(len(clusterImages)) + '.gif'),
clusterImages)
if concepts:
if (len(clusterImages) / len(clusterImages2List)) > 1.5:
gifPath = join(outPathX, str(clusterID2) + '_' + str(len(clusterImages2List)) + 'imgsR.gif')
else:
gifPath = join(outPathX, str(clusterID2) + '_' + str(len(clusterImages2List)) + 'imgs.gif')
imgsPath.append(gifPath)
imageio.mimsave(gifPath, clusterImages2)
return imgsPath
def getCentroidDists(singleClusters, outputPathX, outputPathY, fileName):
if not exists(join(outputPathX, fileName)):
centroidDists = pd.DataFrame()
for clusterID in singleClusters:
diffList = []
centroidHMpath = join(outputPathY, str(clusterID), "centroidHM.pt")
if not exists(centroidHMpath):
continue
hm1 = (torch.load(centroidHMpath)).detach().cpu().numpy()
for clusterID2 in singleClusters:
centroidHMpath2 = join(outputPathY, str(clusterID2), "centroidHM.pt")
if not exists(centroidHMpath2):
continue
hm2 = (torch.load(centroidHMpath2)).detach().cpu().numpy()
diffList.append(math.sqrt(np.sum(np.power(np.subtract(hm1, hm2), 2))))
centroidDists[clusterID] = diffList
if not exists(outputPathX):
makedirs(outputPathX)
writer = pd.ExcelWriter(join(outputPathX, fileName), engine='xlsxwriter')
writer.book.use_zip64()
centroidDists.to_excel(writer)
writer.close()
centroidDists = pd.read_excel(join(outputPathX, fileName))
centroidDists.drop(centroidDists.columns[centroidDists.columns.str.contains('unnamed', case=False, na=False)],
axis=1,
inplace=True)
return centroidDists
def doPass2(outputPathX, layerX, centroidDists):
if not exists(join(outputPathX, str(layerX) + ".pt")):
clsData, _, _ = doClustering("AVG", centroidDists, outputPathX, str(layerX) + ".xlsx", 150, layerX, "R")
else:
clsData = torch.load(join(outputPathX, str(layerX) + ".pt"))
singleClusters = []
for clusterID in clsData['clusters']:
if len(clsData['clusters'][clusterID]['members']) == 1:
singleClusters.append(clsData['clusters'][clusterID]['members'][0])
continue
return clsData, singleClusters
def saveCentroidHMs(caseFile, concepts, outputPathY, layerX, outPath, clsData):
for clusterID in clsData['clusters']:
if len(clsData['clusters'][clusterID]['members']) == 1:
continue
clusterImages = []
clusterImages2 = []
clusterImages2List = []
clusterPath = join(outputPathY, str(clusterID))
if exists(clusterPath):
continue
DS.cleanMake(clusterPath, True)
centroidHM = 0.0
n = 0
for img in clsData['clusters'][clusterID]['members']:
if concepts:
fileName = img.split(".")[0] + caseFile["imgExt"]
srcPath = join(caseFile["DataSetsPath"], caseFile["faceSubset"] + "_Concepts", str(layerX), fileName)
dirPath = join(clusterPath, fileName)
outDir = join(caseFile["outputPathOriginal"], str(caseFile["faceSubset"]), "ConceptsData")
outPathX = join(outDir, "ConceptsHM", str(layerX), img.split(".")[0] + ".pt")
if caseFile["datasetName"] == "HPD":
#origFile = join(caseFile["DataSetsPath"], "TestSet_Backup", str(int(img.split("_")[1])-1) + caseFile["imgExt"])
origFile = str(join(caseFile["DataSetsPath"], "TestSet_Backup_M", str((img.split("_")[1])) + caseFile["imgExt"])) #HPD-M
else:
origFile = join(caseFile["DataSetsPath"], "TestSet_Backup", str((img.split("_")[1])) + caseFile["imgExt"])
if origFile not in clusterImages2List:
clusterImages2.append(imageio.imread(origFile))
clusterImages2List.append(origFile)
else:
fileName = img.split("_")[1] + caseFile["imgExt"]
fileClass = img.split("_")[2]
fileSource = img.split("_")[0]
if fileSource == "Train":
srcPath = join(caseFile["trainDataPath"], fileClass, fileName)
elif fileSource == "Test":
srcPath = join(caseFile["testDataPath"], fileClass, fileName)
else:
srcPath = join(caseFile["improveDataPath"], fileClass, fileName)
dirPath = join(clusterPath, img + caseFile["imgExt"])
outPathX = join(outPath, "Heatmaps", str(layerX), img.split(".")[0] + ".pt")
shutil.copy(srcPath, dirPath)
clusterImages.append(imageio.imread(srcPath))
AN = torch.load(outPathX)
if n == 0:
centroidHM = torch.add(AN, 0)
else:
centroidHM = torch.add(centroidHM, AN)
n += 1
centroidHM = centroidHM / n
torch.save(centroidHM, join(clusterPath, "centroidHM.pt"))
imageio.mimsave(join(outputPathY, str(clusterID) + '_' + str(len(clusterImages)) + '.gif'), clusterImages)
if concepts:
if (len(clusterImages)/len(clusterImages2List)) > 1.5:
gifPath = join(outputPathY, str(clusterID) + '_' + str(len(clusterImages2List)) + 'imgsR.gif')
else:
gifPath = join(outputPathY, str(clusterID) + '_' + str(len(clusterImages2List)) + 'imgs.gif')
imageio.mimsave(gifPath, clusterImages2)
def twoPass(caseFile, layerX, concepts, HMDistFile, outPath):
outputPathY = join(outPath, "2P_FC")
outputPathZ = join(outPath, "2P_Final")
if not exists(outputPathZ):
makedirs(outputPathZ)
if not exists(join(outputPathY, str(layerX) + ".pt")):
HMDist1 = pd.read_excel(HMDistFile)
HMDist1.drop(HMDist1.columns[HMDist1.columns.str.contains('unnamed', case=False)], axis=1, inplace=True)
clsData, _, _ = doClustering("WICDWard", HMDist1, outputPathY, str(layerX) + ".xlsx", 150, layerX, "R")
else:
clsData = torch.load(join(outputPathY, str(layerX) + ".pt"))
saveCentroidHMs(caseFile, concepts, outputPathY, layerX, outPath, clsData)
centroidClusters = []
for clusterID in clsData['clusters']:
centroidClusters.append(clusterID)
singleClusters = centroidClusters
i = 1
clsDataList = []
newImgsPath = []
while len(singleClusters) > 1:
outputPathX = join(outPath, "2P_RCC", str(i))
centroidDists = getCentroidDists(singleClusters, outputPathX, outputPathY, "centroidDists.xlsx")
clsData2, singleClusters = doPass2(outputPathX, layerX, centroidDists)
clsDataList.append(clsData2)
imgsPath = exportImages_2P(clsData, clsData2, outputPathX, caseFile, concepts, layerX)
print("SingleClusters:", len(singleClusters))
for img in imgsPath:
fileName = str(i) + "_" + str(basename(img)).split("_")[0] + "_" + str(basename(img)).split("_")[1]
shutil.copy(img, join(outputPathZ, fileName))
newImgsPath.append(join(outputPathZ, fileName))
i += 1
break
return clsData2
def saveIEE_KPs(caseFile, dst, model):
def forward_hook(self, input, output):
# print("forward hook..")
self.X = input[0]
self.Y = output
def update(img, x_p, y_p, x_t=0, y_t=0, gt=False):
height, width = img.shape[0], img.shape[1]
for idx in [-1, 0, 1]:
px = max(min(x_p + idx, width - 1), 0)
if x_t > 0 and y_t > 0:
tx = max(min(x_t + idx, width - 1), 0)
for jdx in [-1, 0, 1]:
py = max(min(y_p + jdx, height - 1), 0)
if x_t > 0 and y_t > 0:
ty = max(min(y_t + jdx, height - 1), 0)
if width > py > 0 and height > px > 0:
if gt: #red
img[py, px, 0] = 0
img[py, px, 1] = 0
img[py, px, 2] = 255
else: #blue
img[py, px, 0] = 0
img[py, px, 1] = 255
img[py, px, 2] = 0
if x_t > 0 and y_t > 0:
if width > ty > 0 and height > tx > 0:
if gt: #red
img[ty, tx, 0] = 0
img[ty, tx, 1] = 0
img[ty, tx, 2] = 255
else: #blue
img[ty, tx, 0] = 255
img[ty, tx, 1] = 0
img[ty, tx, 2] = 0
return img
trainPredict = predict.IEEPredictor(caseFile["trainDataNpy"], caseFile["modelPath"], 0)
trainDataSet, mainCounter = trainPredict.load_data(caseFile["trainDataNpy"])
totalInputs = 0
testPredict = predict.IEEPredictor(caseFile["testDataNpy"], caseFile["modelPath"], 0)
testDataSet, _ = testPredict.load_data(caseFile["testDataNpy"])
for (inputs, cp_labels) in tqdm(testDataSet):
totalInputs += len(inputs)
labels = cp_labels["gm"]
labels_gt = cp_labels["kps"]
labels_msk = np.ones(labels_gt.numpy().shape)
labels_msk[labels_gt.numpy() <= 1e-5] = 0
if torch.cuda.is_available():
model = model.cuda()
inputs = Variable(inputs.cuda())
else:
inputs = Variable(inputs)
model.conv2d_1.register_forward_hook(forward_hook)
predictA = model(inputs.float())
predict_cpu = predictA.cpu()
predict_cpu = predict_cpu.detach().numpy()
predict_xy1 = DS.transfer_target(predict_cpu, n_points=DS.n_points)
predict_xy = np.multiply(predict_xy1, labels_msk)
inputs_cpu = inputs.cpu()
inputs_cpu = inputs_cpu.detach().numpy()
num_sample = inputs_cpu.shape[0]
for idx in range(num_sample):
img = inputs_cpu[idx] * 255.
img = img[0, :]
img = np.repeat(img[:, :, np.newaxis], 3, axis=2)
xy = predict_xy[idx]
lab_xy = labels_gt[idx]
diff = np.square(np.array(lab_xy) - np.array(xy))
sum_diff = np.sqrt(diff[:,0] + diff[:,1])
rightbrow = [2, 3]
leftbrow = [0, 1]
mouth = [23, 24, 25, 26]
righteye = [16, 17, 18, 19, 20, 21, 22]
lefteye = [9, 10, 11, 12, 13, 14, 15]
noseridge = [4, 5]
nose = [6, 7, 8]
KParray = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]
area = caseFile["faceSubset"]
if area == "rightbrow":
KParray = rightbrow
elif area == "leftbrow":
KParray = leftbrow
elif area == "righteye":
KParray = righteye
elif area == "lefteye":
KParray = lefteye
elif area == "nose":
KParray = nose
elif area == "noseridge":
KParray = noseridge
elif area == "mouth":
KParray = mouth
label = 0
worst_label = 0
worst_KP = 0
for KP in sum_diff:
if KParray.count(label) > 0:
if KP > worst_KP:
worst_KP = KP
worst_label = label
label += 1
for coidx in KParray:
x_p = int(xy[coidx, 0] + 0.5)
y_p = int(xy[coidx, 1] + 0.5)
x_t = int(lab_xy[coidx][0] + 0.5)
y_t = int(lab_xy[coidx][1] + 0.5)
if coidx == worst_label:
img = update(img, x_p, y_p, x_t, y_t, True)
else:
img = update(img, x_p, y_p, x_t, y_t)
file_name = join(dst, str(mainCounter)+".png")
mainCounter += 1
if not exists(dst):
os.makedirs(dst)
if not isfile(file_name):
cv2.imwrite(file_name, img)
def drawClusters(caseFile, dst, model):
datasetName = caseFile["datasetName"]
layers = caseFile["layers"]
mode = caseFile["clustMode"]
DataSetsPath = caseFile["DataSetsPath"]
imgExt = caseFile["imgExt"]
outputPath = join(caseFile["filesPath"], "ClusterAnalysis_" + str(mode))
#if datasetName == "IEEKP":
#if drawKP:
#saveIEE_KPs(caseFile, dst, model)
for layerX in layers:
if torch.cuda.is_available():
clsData = torch.load(join(outputPath, str(layerX)) + ".pt")
else:
clsData = torch.load(join(outputPath, str(layerX)) + ".pt", map_location = torch.device('cpu'))
layerPath = join(outputPath, str(layerX))
if not exists(layerPath):
os.mkdir(layerPath)
else:
shutil.rmtree(layerPath)
os.mkdir(layerPath)
allImagesPath = join(layerPath, "AllClusters")
if not exists(allImagesPath):
os.mkdir(allImagesPath)
else:
shutil.rmtree(allImagesPath)
os.mkdir(allImagesPath)
for clusterID in clsData['clusters']:
clusterImages = []
clusterCounter = 0
clusterPath = join(layerPath, str(clusterID))
if not exists(clusterPath):
os.mkdir(clusterPath)
for img in clsData['clusters'][clusterID]['members']:
clusterCounter += 1
fileSource = img.split("_")[0]
if datasetName == "FLD":
fileName = img.split("_")[1] + imgExt
shutil.copy(join(dst, fileName), join(clusterPath, fileName))
else:
fileName = img.split("_")[1] + imgExt
fileClass = img.split("_")[2]
if fileSource == "Train":
shutil.copy(join(DataSetsPath, "TrainingSet", fileClass, fileName)
, join(clusterPath, fileName))
elif fileSource == "Test":
shutil.copy(join(DataSetsPath, "TestSet", fileClass, fileName),
join(clusterPath, fileName))
else:
shutil.copy(join(DataSetsPath, "ImprovementSet", "ImprovementSet", fileClass, fileName),
join(clusterPath, fileName))
if len(clsData['clusters'][clusterID]['members'])>1:
if len(clusterImages) < 140:
clusterImages.append(imageio.imread(join(clusterPath, fileName)))
clusterImages.append(imageio.imread(join(clusterPath, fileName)))
clusterImages.append(imageio.imread(join(clusterPath, fileName)))
if len(clusterImages)>3:
imageio.mimsave(join(allImagesPath, 'Cluster' + str(clusterID) + '_' + str(clusterCounter) + '.gif'),
clusterImages)
print("Exported " + str(layerX))
def plotFig(x_axis, y_axis, y_axis2, x_label, y_label, outputPath, layer, pointOne, pointTwo):
plt.plot(x_axis, y_axis)
if y_axis2 is not None:
plt.plot(x_axis, y_axis2)
if pointOne is not None:
plt.plot(x_axis[pointOne], y_axis[pointOne], 'ro', ms=5)
if pointTwo is not None:
if y_axis2 is not None:
plt.plot(x_axis[pointTwo], y_axis2[pointTwo], 'go', ms=5)
else:
plt.plot(x_axis[pointTwo], y_axis[pointTwo], 'go', ms=5)
plt.ylabel(y_label)
plt.xlabel(x_label)
plt.savefig(join(outputPath, layer + "_" + y_label + ".png"))
plt.cla()
plt.clf()
def KCluster(data, NumClusters):
print("Kmeans Clustering")
data_scaled = normalize(data, norm='max')
print("Distances are normalized")
kmeans = KMeans(n_clusters=NumClusters, random_state=0).fit(data_scaled)
label_array = kmeans.labels_
for i in range(0, len(label_array)):
label_array[i] = label_array[i] + 1
return label_array
def HACluster(data, maxCluster, library, linkage, metric, outputPath, layer, selection):
print("Hirearchial Agglomerative Clustering")
data_scaled = normalize(data, norm='max')
print("Distances are normalized")
#data_scaled = normalize(data)
if library is None:
if linkage == "Ward":
Z = shc.linkage(pdist(data_scaled), metric='euclidean', optimal_ordering=True, method="ward")
elif linkage == "Avg":
Z = shc.linkage(pdist(data_scaled), metric='euclidean', optimal_ordering=True, method="average")
elif linkage == "Complete":
Z = shc.linkage(pdist(data_scaled), metric='euclidean', optimal_ordering=True, method="complete")
elif linkage == "Single":
Z = shc.linkage(pdist(data_scaled), metric='euclidean', optimal_ordering=True, method="single")
elif linkage == "Centroid":
Z = shc.linkage(pdist(data_scaled), metric='euclidean', optimal_ordering=True, method="centroid")
elif linkage == "Median":
Z = shc.linkage(pdist(data_scaled), metric='euclidean', optimal_ordering=True, method="median")
elif linkage == "Weighted":
Z = shc.linkage(pdist(data_scaled), metric='euclidean', optimal_ordering=True, method="weighted")
print("Linkage", linkage, "data is computed")
start = 2
end = maxCluster + 1
cc_array = [0] * (end - start)
label_array = [0] * (end - start)
x_axis = list()
x_axis2 = list()
y_axis = list()
for i in range(start, end):
print("Clustering:", str(int(100.00*(i/(end-start))))+"%", end="\r")
labels = shc.fcluster(Z, t=i, criterion='maxclust')
#labels = (hdbscan.HDBSCAN(min_cluster_size=10)).fit_predict(data_scaled)
if metric == "Dunn":
aa = dunn(labels, data_scaled, "farthest", "nearest")
identifier = 'max'
if metric == "DunnICD":
aa = dunnICD(data_scaled, labels)
identifier = 'max'
if metric == "ICD":
aa = getAvgLayer_ICD(data_scaled, labels)
identifier = 'min'
if metric == "WICD":
aa = getAvgLayer_WICD(data_scaled, labels)
identifier = 'min'
if metric == "S":
aa = metrics.silhouette_score(data_scaled, labels, metric='euclidean')
identifier = 'max'
if metric == "DBI":
aa = metrics.davies_bouldin_score(data_scaled, labels)
identifier = 'min'
if metric == "AVG":
aa = getAVG(data_scaled, labels)
identifier = 'max'
clustCount = 0
for x in range(1, i + 1):
if ((list(labels)).count(x) > 1):
clustCount += 1
x_axis2.append(clustCount)
x_axis.append(i)
y_axis.append(aa)
cc_array[i - start] = aa
label_array[i - start] = labels
if identifier == 'min':
c = min(cc_array)
elif identifier == 'max':
c = max(cc_array)
index = [i for i, j in enumerate(cc_array) if j == c]
index = index[0]
aa = cc_array[index]
clusters = index + start
print("Clustering is done with " + str(metric) + ": " + str(aa) + " and " + str(clusters) + " clusters \n")
lenX = len(x_axis)
if lenX % 2 <= 0:
lenX = lenX - 1
#smoothY = savgol_filter(y_axis, lenX, 3)
if len(y_axis) == 1:
plotFig(x_axis, y_axis, None, "# Clusters", metric, outputPath, layer, None, None)
#plotFig(x_axis, None, None, "# Clusters", "GradientOfRaw", outputPath, layer, None, None)
return label_array[0]
gradient = gradientO4(np.array(y_axis), 4)
#gradientFit = savgol_filter(gradient, lenX, 3)
if selection == "KR":
kn_raw = KneeLocator(x_axis, y_axis, curve='convex', direction='decreasing')
kneeRaw = kn_raw.knee-start
plotFig(x_axis, y_axis, None, "# Clusters", metric, outputPath, layer, kneeRaw, None)
return label_array[kneeRaw]
elif selection == "KG":
kn_gradient = KneeLocator(x_axis, gradient, curve='concave', direction='increasing')
kneeGrad = kn_gradient.knee-start
plotFig(x_axis, gradient, None, "# Clusters", "GradientOfRaw", outputPath, layer, kneeGrad, None)
return label_array[kneeGrad]
elif selection == "R":
return label_array[index]
def HACluster_SklearnAvg(data: np.array, maxCluster=100): # data is a obseravation matrix of pair distances
data_scaled = normalize(data)
cc_array = [0] * maxCluster
for i in range(2, maxCluster):
cluster = AgglomerativeClustering(n_clusters=i, affinity='precomputed', linkage='average').fit(data_scaled)
# cluster = AgglomerativeClustering(n_clusters=i, affinity='euclidean', linkage='ward').fit(data_scaled)
cc = cluster.fit_predict(data_scaled)
aa = metrics.silhouette_score(data_scaled, cc, metric='euclidean')
cc_array[i - 2] = aa
c = max(cc_array)
index = [i for i, j in enumerate(cc_array) if j == c]
index = index[0]
aa = cc_array[index]
clusters = index + 2
cluster = AgglomerativeClustering(n_clusters=clusters, affinity='precomputed', linkage='average').fit(data_scaled)
# cluster = AgglomerativeClustering(n_clusters=clusters, affinity='euclidean', linkage='ward').fit(data_scaled)
cc = cluster.fit_predict(data_scaled)
clusterNumber = max(cc) + 1
aa = metrics.silhouette_score(data_scaled, cc, metric='euclidean')
print("Clustering is done with silhouette - Sklearn " + str(aa) + " and " + str(clusterNumber) + " clusters \n")
print(aa)
for i in range(0, len(cc)):
cc[i] = cc[i] + 1
return cc, aa
def HACluster_SklearnSingle(data: np.array, maxCluster=100): # data is a obseravation matrix of pair distances
data_scaled = normalize(data)
cc_array = [0] * maxCluster
for i in range(2, maxCluster):
cluster = AgglomerativeClustering(n_clusters=i, affinity='precomputed', linkage='single').fit(data_scaled)
# cluster = AgglomerativeClustering(n_clusters=i, affinity='euclidean', linkage='ward').fit(data_scaled)
cc = cluster.fit_predict(data_scaled)
aa = metrics.silhouette_score(data_scaled, cc, metric='euclidean')
cc_array[i - 2] = aa
c = max(cc_array)
index = [i for i, j in enumerate(cc_array) if j == c]
index = index[0]
aa = cc_array[index]
clusters = index + 2
cluster = AgglomerativeClustering(n_clusters=clusters, affinity='precomputed', linkage='single').fit(data_scaled)
# cluster = AgglomerativeClustering(n_clusters=clusters, affinity='euclidean', linkage='ward').fit(data_scaled)
cc = cluster.fit_predict(data_scaled)
clusterNumber = max(cc) + 1
aa = metrics.silhouette_score(data_scaled, cc, metric='euclidean')
print("Clustering is done with silhouette - Sklearn " + str(aa) + " and " + str(clusterNumber) + " clusters \n")
print(aa)
for i in range(0, len(cc)):
cc[i] = cc[i] + 1
return cc, aa
def HACluster_SklearnComplete(data: np.array, maxCluster=100): # data is a obseravation matrix of pair distances
data_scaled = normalize(data)
cc_array = [0] * maxCluster
for i in range(2, maxCluster):
cluster = AgglomerativeClustering(n_clusters=i, affinity='precomputed', linkage='complete').fit(data_scaled)
# cluster = AgglomerativeClustering(n_clusters=i, affinity='euclidean', linkage='ward').fit(data_scaled)
cc = cluster.fit_predict(data_scaled)
aa = metrics.silhouette_score(data_scaled, cc, metric='euclidean')
cc_array[i - 2] = aa
c = max(cc_array)
index = [i for i, j in enumerate(cc_array) if j == c]
index = index[0]
aa = cc_array[index]
clusters = index + 2
cluster = AgglomerativeClustering(n_clusters=clusters, affinity='precomputed', linkage='complete').fit(data_scaled)
# cluster = AgglomerativeClustering(n_clusters=clusters, affinity='euclidean', linkage='ward').fit(data_scaled)
cc = cluster.fit_predict(data_scaled)
clusterNumber = max(cc) + 1
aa = metrics.silhouette_score(data_scaled, cc, metric='euclidean')
print("Clustering is done with silhouette - Sklearn " + str(aa) + " and " + str(clusterNumber) + " clusters \n")
print(aa)
for i in range(0, len(cc)):
cc[i] = cc[i] + 1
return cc, aa
def getVarCluster(distance: np.array, clusterMember: list, clusterMembersName):
variance = 0
for m1 in range(0, len(clusterMember)):
for m2 in range(m1 + 1, len(clusterMember)):
indexM1 = clusterMembersName.get_loc(clusterMember[m1])
indexM2 = clusterMembersName.get_loc(clusterMember[m2])
variance += distance[indexM1][indexM2] ** 2
return variance
def getSumDistanceCluster(distance: np.array, clusterMember: list, clusterMembersName):
sumDistance = 0
for m1 in range(0, len(clusterMember)):
for m2 in range(m1 + 1, len(clusterMember)):
indexM1 = clusterMembersName.get_loc(clusterMember[m1])
indexM2 = clusterMembersName.get_loc(clusterMember[m2])
sumDistance += distance[indexM1][indexM2]
return sumDistance
def getVarClusterWithAddition(clusterMember: list, currentVar: int, newMember: str, heatMapTestSet,
heatmapTraningSet, metric):
variance = currentVar
for m1 in range(0, len(clusterMember)):
variance += doDistance(heatMapTestSet[m1], heatmapTraningSet[newMember], metric)
return variance
def dunnICD(distance, cc):
#return getAvgCluster_ICD(distance, cc)/getAvgLayer_ICD(distance, cc)
return getAvgCluster_ICD(distance, cc)/getFarthestLayer_ICD(distance, cc)
#return getAvgCluster_ICD(distance, cc)/getAvgLayer_WICD(distance, cc)
def getAvgCluster_ICD(distance: np.array, cc):
ClosestPairDists = list()
for label1 in range(1, max(cc)+ 1):
groupLen1 = list(cc).count(label1)
PairDists = list()
if groupLen1 > 1:
groupIndex1 = [0] * groupLen1
j = 0
for i in range(0, len(cc)):
if (cc[i] == label1):
groupIndex1[j] = i
j = j + 1
for label2 in range(1, max(cc)+1):
if label1 != label2:
groupLen2 = list(cc).count(label2)
if groupLen2 > 1:
groupIndex2 = [0] * groupLen2
j = 0
for i in range(0, len(cc)):
if (cc[i] == label2):
groupIndex2[j] = i
j = j + 1
for index in groupIndex1:
for index2 in groupIndex2:
PairDists.append(distance[index][index2])
if not len(PairDists) == 0:
ClosestPairDists.append(min(PairDists))
return sum(ClosestPairDists)/len(ClosestPairDists)
def getFarthestLayer_ICD(distance: np.array, cc):
Clusters_ICD = list()
for label in range(1, max(cc) + 1):
groupLen = list(cc).count(label)
# weight = groupLen / len(cc)
numPairs = int((groupLen * (groupLen - 1)) / 2)
Dists = [0] * numPairs
groupIndex = [0] * groupLen
j = 0
for i in range(0, len(cc)):
if (cc[i] == label):
groupIndex[j] = i
j = j + 1
k = 0
for index in groupIndex:
for index2 in groupIndex:
if (index2 > index):
Dists[k] = distance[index][index2]
k = k + 1
if (groupLen > 1):
Clusters_ICD.append(max(Dists))
return sum(Clusters_ICD)/len(Clusters_ICD)
def getAvgLayer_ICD(distance: np.array, cc):
Clusters_ICD = list()
for label in range(1, max(cc) + 1):
groupLen = list(cc).count(label)
# weight = groupLen / len(cc)
numPairs = int((groupLen * (groupLen - 1)) / 2)
Dists = [0] * numPairs
groupIndex = [0] * groupLen
j = 0
for i in range(0, len(cc)):
if (cc[i] == label):
groupIndex[j] = i
j = j + 1
k = 0
for index in groupIndex:
for index2 in groupIndex:
if (index2 > index):
Dists[k] = distance[index][index2]
k = k + 1
if (groupLen > 1):
Clusters_ICD.append(sum(Dists)/numPairs)
return sum(Clusters_ICD)/len(Clusters_ICD)
def getAVG(distance: np.array, cc):
Clusters_ICD = list()
Clusters_Indices = list()
for label in range(1, max(cc) + 1):
groupIndex = list()
for i in range(0, len(cc)):
if (cc[i] == label):
groupIndex.append(i)
Clusters_Indices.append(groupIndex)
k = 0
for cluster_indices1 in Clusters_Indices:
j = 0
for cluster_indices2 in Clusters_Indices:
if (j > k):
dist = list()
for index1 in cluster_indices1:
for index2 in cluster_indices2:
dist.append(distance[index1][index2])
Clusters_ICD.append(min(dist))
j += 1
k += 1
return sum(Clusters_ICD)/len(Clusters_ICD)
def getAvgLayer_NewICD(distance: np.array, cc):
n_clusters = 0
ICDlayer = 0
for label in range(1, max(cc) + 1):
groupLen = list(cc).count(label)
# weight = groupLen / len(cc)
numPairs = int((groupLen * (groupLen - 1)) / 2)
Dists = [0] * numPairs
groupIndex = [0] * groupLen
j = 0
for i in range(0, len(cc)):
if (cc[i] == label):
groupIndex[j] = i
j = j + 1
k = 0
for index in groupIndex:
for index2 in groupIndex:
if (index2 > index):
Dists[k] = distance[index][index2]
k = k + 1
if (groupLen > 1):
Avglabel = sum(Dists) / numPairs
ICDc = Avglabel * groupLen
# ICDc = Avglabel * weight
ICDlayer = ICDlayer + ICDc
n_clusters += 1
return ICDlayer / n_clusters
def getAvgLayer_WICD(distance: np.array, cc):
n_clusters = max(cc)
ICDlayer = 0
for label in range(1, n_clusters + 1):
groupLen = list(cc).count(label)
weight = groupLen / len(cc)
numPairs = int((groupLen * (groupLen - 1)) / 2)
Dists = [0] * numPairs
groupIndex = [0] * groupLen
j = 0
for i in range(0, len(cc)):
if (cc[i] == label):
groupIndex[j] = i
j = j + 1
k = 0
for index in groupIndex:
for index2 in groupIndex:
if (index2 > index):
Dists[k] = distance[index][index2]
k = k + 1
if (groupLen > 1):
Avglabel = sum(Dists) / numPairs
# ICDc = Avglabel
ICDc = Avglabel * weight
ICDlayer = ICDlayer + ICDc
return ICDlayer / n_clusters
def doClustering(mode, heatmapsDistance: dict, outPutPath: str, outputFile: str, maxCluster: int, layer, selection):
if not exists(outPutPath):
makedirs(outPutPath)
sys.stderr.write("Clustering ... \n")
clusters = {}
clusters['selected_ICD'] = False
clusters['selected_WICD'] = False
clusters['selected_S'] = False
clusters['selected_Dunn'] = False
if mode.startswith('AVG'):
metric = 'AVG'
linkage = 'Ward'
if mode.startswith('ICD'):
metric = 'ICD'
if mode == 'ICDWard':
linkage = 'Ward'
if mode == 'ICDAvg':
linkage = 'Avg'
if mode == 'ICDSingle':
linkage = 'Single'
if mode.startswith('WICD'):
metric = 'WICD'
if mode == 'WICDWard':
linkage = 'Ward'
if mode == 'WICDAvg':
linkage = 'Avg'
if mode.startswith('Dunn'):
metric = 'Dunn'
if mode == 'DunnWard':
linkage = 'Ward'
if mode == 'DunnAvg':
linkage = 'Avg'
if mode.startswith('DunnICD'):
metric = 'DunnICD'
if mode == 'DunnICDWard':
linkage = 'Ward'
if mode == 'DunnICDAvg':
linkage = 'Avg'
if mode.startswith('DBI'):
metric = 'DBI'
if mode == 'DBIWard':
linkage = 'Ward'
if mode == 'DBIAvg':
linkage = 'Avg'
if mode.startswith('S'):
metric = 'S'
if mode == 'SWard':
linkage = 'Ward'
if mode == 'SAvg':
linkage = 'Avg'
if mode.startswith('K'):
metric = 'K'
linkage = None
data = heatmapsDistance.values
print(metric)
print(linkage)
if metric == 'K':
cc = KCluster(data, maxCluster)
else:
cc = HACluster(data, maxCluster, None, linkage, metric, outPutPath, layer, selection)
data_scaled = normalize(data, norm='max')
numAC = 0
for label in range(1, max(cc) + 1):
if list(cc).count(label) > 1:
numAC += 1
if numAC == 0:
WICD = 1e9
ICD = 1e9
S = -1e9
DunnIndex = -1e9
DBI = 1e9
else:
WICD = getAvgLayer_WICD(data, cc)
ICD = getAvgLayer_ICD(data, cc)
S = metrics.silhouette_score(data_scaled, cc, metric='euclidean')
DunnIndex = dunn(cc, data_scaled, "farthest", "nearest")
DBI = metrics.davies_bouldin_score(data_scaled, cc)
clusters['WeightedavgLayer'] = WICD
clusters['avgLayer'] = ICD
# clusters['avgLayer'] = getAvgLayer_NewICD(heatmapsDistance.values, cc)
clusters['silhouette'] = S
clusters['dunn'] = DunnIndex
clusters['DBI'] = DBI
clusters['label list'] = cc
index = 0
for clusterID in cc:
if not 'clusters' in clusters:
clusters['clusters'] = {}
if not clusterID in clusters['clusters']:
clusters['clusters'][clusterID] = {}
if not 'members' in clusters['clusters'][clusterID]:
clusters['clusters'][clusterID]['members'] = []
clusters['clusters'][clusterID]['members'].append(heatmapsDistance.columns[index])
index = index + 1
avgDistLayers = []
nonSingleClusters = 0
for clusterID in clusters['clusters']:
clusters['clusters'][clusterID]['variance'] = getVarCluster(heatmapsDistance.values,
clusters['clusters'][clusterID][
'members'],
heatmapsDistance.columns)
clusters['clusters'][clusterID]['length'] = len(clusters['clusters'][clusterID]['members'])
if len(clusters['clusters'][clusterID]['members']) > 1:
nonSingleClusters += 1
clusters['clusters'][clusterID]['sumDistance'] = getSumDistanceCluster(
heatmapsDistance.values, clusters['clusters'][clusterID]['members'],
heatmapsDistance.columns)
clusters['clusters'][clusterID]['errorSum'] = clusters['clusters'][clusterID]['variance'] / \
clusters['clusters'][clusterID]['length']
avgDistLayers.append(
clusters['clusters'][clusterID]['sumDistance'] / clusters['clusters'][clusterID][
'length'])
print("Number of non-single clusters:", nonSingleClusters)
minAvgCluster = pd.DataFrame.from_dict(data=clusters, orient='index')
writer = pd.ExcelWriter(outPutPath + "/" + outputFile, engine='xlsxwriter')
minAvgCluster.to_excel(writer, sheet_name="ClustersSummary")
minAvgCluster = pd.DataFrame.from_dict(data=clusters['clusters'], orient='index')
minAvgCluster.to_excel(writer, sheet_name="ClustersDetails")
writer.close()
torch.save(clusters, outPutPath + "/" + outputFile.split(".")[0] + ".pt")
return clusters, ICD, WICD
def inter_cluster_distances(labels, distances, method='nearest'):
"""Calculates the distances between the two nearest points of each cluster.
:param labels: a list containing cluster labels for each of the n elements
:param distances: an n x n numpy.array containing the pairwise distances between elements
:param method: `nearest` for the distances between the two nearest points in each cluster, or `farthest`
"""
if method == 'nearest':
return __cluster_distances_by_points(labels, distances)
elif method == 'farthest':
return __cluster_distances_by_points(labels, distances, farthest=True)
def __cluster_distances_by_points(labels, distances, farthest=False):
n_unique_labels = len(np.unique(labels))
cluster_distances = np.full((n_unique_labels, n_unique_labels),
float('inf') if not farthest else 0)
np.fill_diagonal(cluster_distances, 0)
for i in np.arange(0, len(labels) - 1):
for ii in np.arange(i, len(labels)):
if labels[i] != labels[ii] and (
(not farthest and
distances[i, ii] < cluster_distances[labels[i], labels[ii]])
or
(farthest and
distances[i, ii] > cluster_distances[labels[i], labels[ii]])):
cluster_distances[labels[i], labels[ii]] = cluster_distances[
labels[ii], labels[i]] = distances[i, ii]
return cluster_distances
def diameter(labels, distances, method='farthest'):
"""Calculates cluster diameters
:param labels: a list containing cluster labels for each of the n elements
:param distances: an n x n numpy.array containing the pairwise distances between elements
:param method: either `mean_cluster` for the mean distance between all elements in each cluster, or `farthest` for the distance between the two points furthest from each other
"""
n_clusters = len(np.unique(labels))