def main():
c = input('Enter manually or read from a csv file?')
if (c == "Y"):
size = int(input("Enter the size of X attribute:"))
x = []
y = []
print("Enter the X Elements:")
for i in range(size):
element = int(input())
x.append(element)
print("Enter the Y Elements:")
for i in range(size):
element = int(input())
y.append(element)
x = np.array(x)
y = np.array(y)
else:
data = gft('test_file.csv', delimiter=',')
X = []
Y = []
for major in data:
X.append(major[0])
Y.append(major[1])
x = np.array(X)
y = np.array(Y)
print("Estimated coefficients of linear regression are: ")
print(estimate_coefficients(x, y))
print("Graph:")
graph_of_regression(x, y, estimate_coefficients(x, y))
def retValid():
image_list, Y_all = read_image_list()
label = ["MEL", "NV", "BCC", "AKIEC", "BKL", "DF", "VASC"]
TASK3_PRED_FILE = '/home/grads/k/kaihe/Documents/ISIC/models/deepModels/resnet_50/valid_results.csv'
predLab = gft(TASK3_PRED_FILE, delimiter=' ')
valid_list = image_list[Y_all.shape[0] - predLab.shape[0]:]
Y_valid = Y_all[Y_all.shape[0] - predLab.shape[0]:, :]
wrongPred = open(
'/home/grads/k/kaihe/Documents/ISIC/models/deepModels/resnet_50/wrongPred.csv',
'w')
wrongPred.write("Image,Correct Label,Predicted Label\n")
for i in range(0, predLab.shape[0] - 1):
if np.argmax(predLab[i, :]) != np.argmax(Y_valid[i, :]):
wrongPred.write("%s," % valid_list[i])
wrongPred.write("%s," % label[np.argmax(Y_valid[i, :])])
wrongPred.write("%s\n" % label[np.argmax(predLab[i, :])])
def read_image_list():
DATA_DIR = '/home/grads/k/kaihe/Documents/ISIC/Task3/'
TASK3_DATA_DIR = DATA_DIR + 'ISIC2018_Task3_Training_Input/Image/'
TASK3_TRUTH_FILE = DATA_DIR + 'ISIC2018_Task3_Training_GroundTruth/ISIC2018_Task3_Training_GroundTruth.csv'
pattern = re.compile(r"\w+\.jpg")
image_files = []
truth_file = open(TASK3_TRUTH_FILE)
csv_reader = csv.reader(truth_file)
for row in csv_reader:
image_files.append(TASK3_DATA_DIR + row[0] + '.jpg')
image_files = image_files[1:]
labels = gft(TASK3_TRUTH_FILE, delimiter=',')
labels = labels[1:, 1:]
return image_files, labels
# -*- coding: utf-8 -*-
"""
Created on Mon Sep 11 08:33:48 2017
PSU-Phys_296: Idependent Study
Purpous:
Read and convert data set
Plot data
@author: Aardvark
"""
## Reading data as .dat
from numpy import genfromtxt as gft # Import package
from pandas import DataFrame as df # Import package
L=open('all_hminus_compass2007.dat').readlines() # read each line
L=[l.strip() for l in L] # remove white space between values in each line
H=L[0].split() # save the second line as H and delete the hashtag
dat = gft('all_hminus_compass2007.dat') # Read file from working dir as numpi array
data = df(dat, columns = H) # save data as a panda data frame with headers
# saving as csv
data.to_csv("all_hminus_compass2007.csv",index=False) # save as csv with out index vaues
def run_Cell_BLAST(DataPath,
LabelsPath,
CV_RDataPath,
OutputDir,
GeneOrderPath="",
NumGenes=0,
aligned="F"):
'''
run Cell_BLAST
Wrapper script to run Cell_BLAST on a benchmark dataset with 5-fold cross validation,
outputs lists of true and predicted cell labels as csv files, as well as computation time.
Parameters
----------
DataPath : Data file path (.csv), cells-genes matrix with cell unique barcodes
as row names and gene names as column names.
LabelsPath : Cell population annotations file path (.csv).
CV_RDataPath : Cross validation RData file path (.RData), obtained from Cross_Validation.R function.
OutputDir : Output directory defining the path of the exported file.
GeneOrderPath : Gene order file path (.csv) obtained from feature selection,
defining the genes order for each cross validation fold, default is NULL.
NumGenes : Number of genes used in case of feature selection (integer), default is 0.
'''
# read the Rdata file
robjects.r['load'](CV_RDataPath)
nfolds = np.array(robjects.r['n_folds'], dtype='int')
tokeep = np.array(robjects.r['Cells_to_Keep'], dtype='bool')
col = np.array(robjects.r['col_Index'], dtype='int')
col = col - 1
test_ind = np.array(robjects.r['Test_Idx'])
train_ind = np.array(robjects.r['Train_Idx'])
# read the feature file
# if (NumGenes > 0):
features = pd.read_csv(GeneOrderPath, header=0, index_col=None, sep=',')
# read the data and labels
data_old = cb.data.ExprDataSet.read_table(DataPath,
orientation="cg",
sep=",",
index_col=0,
header=0,
sparsify=True)
labels = pd.read_csv(LabelsPath,
header=0,
index_col=None,
sep=',',
usecols=col)
data = cb.data.ExprDataSet(data_old.exprs[tokeep],
data_old.obs.iloc[tokeep], data_old.var,
data_old.uns)
labels = gft(LabelsPath,
dtype="str",
skip_header=1,
delimiter=",",
usecols=col)
labels = labels[tokeep]
truelab = []
pred = []
tr_time = []
ts_time = []
for i in range(np.squeeze(nfolds)):
train_ind_i = np.array(train_ind[i], dtype='int') - 1
train = data[train_ind_i, :]
y_train = labels[train_ind_i]
if (NumGenes > 0):
feat_to_use = features.iloc[0:NumGenes, i].dropna()
else:
feat_to_use = features.iloc[:, i].dropna()
# train = train[:,feat_to_use]
# test = test[:,feat_to_use]
train.obs['cell_type'] = y_train
start = tm.time()
# reduce dimensions
models = []
for j in range(4):
models.append(
cb.directi.fit_DIRECTi(train,
feat_to_use,
cat_dim=20,
epoch=500,
patience=20,
random_seed=j))
# train model
blast = cb.blast.BLAST(models, train)
tr_time.append(tm.time() - start)
if test_ind.shape[0] != train_ind.shape[
0]: # Make Inter-dataset work correctly
assert train_ind.shape[0] == np.squeeze(
nfolds) == 1 and test_ind.shape[0] > train_ind.shape[0]
test_folds = list(range(test_ind.shape[0]))
else:
test_folds = [i]
for j in test_folds:
test_ind_i = np.array(test_ind[j], dtype='int') - 1
test = data[test_ind_i, :]
y_test = labels[test_ind_i]
# predict labels
start = tm.time()
blast_use = blast.align(test) if aligned == "T" else blast
test_hits = blast_use.query(test)
test_pred = test_hits.reconcile_models().filter().annotate(
'cell_type')
ts_time.append(tm.time() - start)
truelab.extend(y_test)
pred.extend(test_pred.values)
#write results
truelab = pd.DataFrame(truelab)
pred = pd.DataFrame(pred)
tr_time = pd.DataFrame(tr_time)
ts_time = pd.DataFrame(ts_time)
method_name = "Cell_BLAST"
if "seurat_gene" in GeneOrderPath:
method_name += "_seurat"
if aligned == "T":
method_name += "_aligned"
truelab.to_csv(str(Path(OutputDir + f"/{method_name}_true.csv")),
index=False)
pred.to_csv(str(Path(OutputDir + f"/{method_name}_pred.csv")), index=False)
tr_time.to_csv(str(Path(OutputDir + f"/{method_name}_training_time.csv")),
index=False)
ts_time.to_csv(str(Path(OutputDir + f"/{method_name}_test_time.csv")),
index=False)
def run_Cell_BLAST(DataPath,
LabelsPath,
CV_RDataPath,
OutputDir,
GeneOrderPath="",
NumGenes=0):
'''
run Cell_BLAST
Wrapper script to run Cell_BLAST on a benchmark dataset with 5-fold cross validation,
outputs lists of true and predicted cell labels as csv files, as well as computation time.
Parameters
----------
DataPath : Data file path (.csv), cells-genes matrix with cell unique barcodes
as row names and gene names as column names.
LabelsPath : Cell population annotations file path (.csv).
CV_RDataPath : Cross validation RData file path (.RData), obtained from Cross_Validation.R function.
OutputDir : Output directory defining the path of the exported file.
GeneOrderPath : Gene order file path (.csv) obtained from feature selection,
defining the genes order for each cross validation fold, default is NULL.
NumGenes : Number of genes used in case of feature selection (integer), default is 0.
'''
# read the Rdata file
robjects.r['load'](CV_RDataPath)
nfolds = np.array(robjects.r['n_folds'], dtype='int')
tokeep = np.array(robjects.r['Cells_to_Keep'], dtype='bool')
col = np.array(robjects.r['col_Index'], dtype='int')
col = col - 1
test_ind = np.array(robjects.r['Test_Idx'])
train_ind = np.array(robjects.r['Train_Idx'])
# read the feature file
if (NumGenes > 0):
features = pd.read_csv(GeneOrderPath,
header=0,
index_col=None,
sep=',')
# read the data and labels
data_old = cb.data.ExprDataSet.read_table(DataPath,
orientation="cg",
sep=",",
index_col=0,
header=0,
sparsify=True).normalize()
labels = pd.read_csv(LabelsPath,
header=0,
index_col=None,
sep=',',
usecols=col)
data = cb.data.ExprDataSet(data_old.exprs[tokeep],
data_old.obs.iloc[tokeep], data_old.var,
data_old.uns)
labels = gft(LabelsPath,
dtype="str",
skip_header=1,
delimiter=",",
usecols=col)
labels = labels[tokeep]
truelab = []
pred = []
tr_time = []
ts_time = []
for i in range(np.squeeze(nfolds)):
test_ind_i = np.array(test_ind[i], dtype='int') - 1
train_ind_i = np.array(train_ind[i], dtype='int') - 1
train = data[train_ind_i, :]
test = data[test_ind_i, :]
y_train = labels[train_ind_i]
y_test = labels[test_ind_i]
if (NumGenes > 0):
feat_to_use = features.iloc[0:NumGenes, i]
train = train[:, feat_to_use]
test = test[:, feat_to_use]
train.obs['cell_type'] = y_train
start = tm.time()
# reduce dimensions
num_epoch = 50
models = []
for j in range(4):
models.append(
cb.directi.fit_DIRECTi(train,
epoch=num_epoch,
patience=10,
random_seed=j,
path="%d" % j))
# train model
blast = cb.blast.BLAST(models, train).build_empirical()
tr_time.append(tm.time() - start)
# predict labels
start = tm.time()
test_pred = blast.query(test).annotate('cell_type')
ts_time.append(tm.time() - start)
truelab.extend(y_test)
pred.extend(test_pred.values)
#write results
truelab = pd.DataFrame(truelab)
pred = pd.DataFrame(pred)
tr_time = pd.DataFrame(tr_time)
ts_time = pd.DataFrame(ts_time)
truelab.to_csv(str(Path(OutputDir + "/Cell_BLAST_true.csv")), index=False)
pred.to_csv(str(Path(OutputDir + "/Cell_BLAST_pred.csv")), index=False)
tr_time.to_csv(str(Path(OutputDir + "/Cell_BLAST_training_time.csv")),
index=False)
ts_time.to_csv(str(Path(OutputDir + "/Cell_BLAST_test_time.csv")),
index=False)
import numpy as np
from numpy import genfromtxt as gft
import matplotlib.pyplot as plt
import pickle
from sklearn.cluster import KMeans
from sklearn.svm import SVC
file = open("classifier.pkl","rb")
clf = pickle.load(file)
file.close()
data = gft("./Dataset.csv", delimiter = ',')
mydata = data[2:,1:9]
time = []
value1 = []
value2 = []
value3 = []
value4 = []
value5 = []
value6 = []
value7 = []
value8 = []
fig = plt.figure()
for f in range(len(data)):
time.append(f)
value1.append(mydata[f,0])
# -*- coding: utf-8 -*-
"""
Created on Mon Sep 11 08:33:48 2017
PSU-Phys_296: Idependent Study
Purpous:
Read and convert data set
Plot data
@author: Aardvark
"""
# Reading data as .dat
from numpy import genfromtxt as gft # Import package
dat = gft('clas_data.dat') # Read file from working dir
# saving as csv
from pandas import DataFrame as df # Import package
data = df(dat) # data as a panda data frame
data.to_csv("clas_data.csv", index=False) # save as csv with out index vaues
# plot Pht with random and systimatic error
import matplotlib.pyplot as plt # Import package
plt.figure() # this seems to be usless
plt.errorbar(dat[:, 0], dat[:, 1], dat[:, 2], dat[:, 3],
fmt='o') # bild scatter with error bars
plt.title('Figure 1') # add title
plt.show() # seems to be usless
plt.clf(
) # should be clearing the figure but it is only ploting in my console so, usless?
import numpy as np
from numpy import *
from google.colab import drive
drive.mount('/content/gdrive')
from numpy import genfromtxt as gft
!pip install scipy
#https://riptutorial.com/numpy/example/22990/reading-csv-files
X_train= gft("/content/gdrive/My Drive/P2/Prob2_Xtrain.csv", delimiter=",")
Y_train= gft("/content/gdrive/My Drive/P2/Prob2_ytrain.csv", delimiter=",")
X_train
Y_train
X_test = gft("/content/gdrive/My Drive/P2/Prob2_Xtest.csv", delimiter=",")
Y_test = gft("/content/gdrive/My Drive/P2/Prob2_ytest.csv", delimiter=",")
#Splitting X_train into its two associated output classes based on Y_train
X_train_class0=[]
def run_Cell_BLAST(input_dir,output_dir,datafile,labfile,Rfile):
'''
Run CellBlast
Parameters
----------
input_dir : directory of the input files
output_dir : directory of the output files
datafile : name of the data file
labfile : name of the label file
Rfile : file to read the cross validation indices from
'''
os.chdir(input_dir)
# read the Rdata file
robjects.r['load'](Rfile)
nfolds = np.array(robjects.r['n_folds'], dtype = 'int')
tokeep = np.array(robjects.r['Cells_to_Keep'], dtype = 'bool')
col = np.array(robjects.r['col_Index'], dtype = 'int')
col = col - 1
test_ind = np.array(robjects.r['Test_Idx'])
train_ind = np.array(robjects.r['Train_Idx'])
# read the data and labels
os.chdir(input_dir)
data_old = cb.data.ExprDataSet.read_table(input_dir + datafile,orientation="cg", sep=",", index_col = 0, header = 0)
labels = pd.read_csv(labfile, header=0,index_col=None, sep=',', usecols = col)
data = cb.data.ExprDataSet(data_old.exprs[tokeep],data_old.obs.iloc[tokeep],data_old.var,data_old.uns)
labels = gft(input_dir + labfile, dtype = "str", skip_header = 1, delimiter = ",", usecols = col)
labels = labels[tokeep]
os.chdir(output_dir)
truelab = []
pred = []
tr_time = []
ts_time = []
for i in range(np.squeeze(nfolds)):
test_ind_i = np.array(test_ind[i], dtype = 'int') - 1
train_ind_i = np.array(train_ind[i], dtype = 'int') - 1
train=data[train_ind_i,:]
test=data[test_ind_i,:]
y_train = labels[train_ind_i]
y_test = labels[test_ind_i]
train.obs['cell_type'] = y_train
start = tm.time()
train = train.normalize()
# reduce dimensions
num_epoch = 50
models = []
for j in range(4):
models.append(cb.directi.fit_DIRECTi(train, latent_dim = 10, cat_dim=20, epoch=num_epoch, patience=10, random_seed = j, path="%d" % j))
# train model
blast = cb.blast.BLAST(models, train).build_empirical()
tr_time.append(tm.time()-start)
# predict labels
start = tm.time()
test_pred = blast.query(test).annotate('cell_type')
ts_time.append(tm.time()-start)
truelab.extend(y_test)
pred.extend(test_pred.values)
#write results
os.chdir(output_dir)
truelab = pd.DataFrame(truelab)
pred = pd.DataFrame(pred)
tr_time = pd.DataFrame(tr_time)
ts_time = pd.DataFrame(ts_time)
truelab.to_csv("Cell_BLAST_" + str(col) +"_true.csv", index = False)
pred.to_csv("Cell_BLAST_" + str(col) +"_pred.csv", index = False)
tr_time.to_csv("Cell_BLAST_" + str(col) +"_training_time.csv", index = False)
ts_time.to_csv("Cell_BLAST_" + str(col) +"_test_time.csv", index = False)
def run_Cell_BLAST(DataPath, LabelsPath, CV_RDataPath, OutputDir, GeneOrderPath = "", NumGenes = 0):
# read the Rdata file
robjects.r['load'](CV_RDataPath)
nfolds = np.array(robjects.r['n_folds'], dtype = 'int')
tokeep = np.array(robjects.r['Cells_to_Keep'], dtype = 'bool')
col = np.array(robjects.r['col_Index'], dtype = 'int')
col = col - 1
test_ind = np.array(robjects.r['Test_Idx'])
train_ind = np.array(robjects.r['Train_Idx'])
# read the feature file
if (NumGenes > 0):
features = pd.read_csv(GeneOrderPath,header=0,index_col=None, sep=',')
# read the data and labels
data_old = cb.data.ExprDataSet.read_table(DataPath,orientation="cg", sep=",", index_col = 0, header = 0, sparsify = True).normalize()
labels = pd.read_csv(LabelsPath, header=0,index_col=None, sep=',', usecols = col)
data = cb.data.ExprDataSet(data_old.exprs[tokeep],data_old.obs.iloc[tokeep],data_old.var,data_old.uns)
labels = gft(LabelsPath, dtype = "str", skip_header = 1, delimiter = ",", usecols = col)
labels = labels[tokeep]
truelab = []
pred = []
tr_time = []
ts_time = []
for i in range(np.squeeze(nfolds)):
test_ind_i = np.array(test_ind[i], dtype = 'int') - 1
train_ind_i = np.array(train_ind[i], dtype = 'int') - 1
train=data[train_ind_i,:]
test=data[test_ind_i,:]
y_train = labels[train_ind_i]
y_test = labels[test_ind_i]
if (NumGenes > 0):
feat_to_use = features.iloc[0:NumGenes,i]
train = train[:,feat_to_use]
test = test[:,feat_to_use]
train.obs['cell_type'] = y_train
start = tm.time()
# reduce dimensions
num_epoch = 50
models = []
for j in range(4):
models.append(cb.directi.fit_DIRECTi(train, epoch=num_epoch, patience=10, random_seed = j, path="%d" % j))
# train model
blast = cb.blast.BLAST(models, train)#.build_empirical()
tr_time.append(tm.time()-start)
# predict labels
start = tm.time()
test_pred = blast.query(test).annotate('cell_type')
ts_time.append(tm.time()-start)
truelab.extend(y_test)
pred.extend(test_pred.values)
#write results
truelab = pd.DataFrame(truelab)
pred = pd.DataFrame(pred)
tr_time = pd.DataFrame(tr_time)
ts_time = pd.DataFrame(ts_time)
if not os.path.exists(OutputDir):
os.mkdir(OutputDir)
truelab.to_csv(str(Path(OutputDir+"/Cell_BLAST_true.csv")),index = False)
pred.to_csv(str(Path(OutputDir+"/Cell_BLAST_pred.csv")),index = False)
tr_time.to_csv(str(Path(OutputDir+"/Cell_BLAST_training_time.csv")), index = False)
ts_time.to_csv(str(Path(OutputDir+"/Cell_BLAST_test_time.csv")),index = False)
