API tools faq
paste
Advertisement
Guest User

Untitled

a guest
Nov 12th, 2019
108
0
Never
Add comment
Not a member of Pastebin yet? Sign Up, it unlocks many cool features!
text 13.25 KB | None | 0 0
raw download clone embed print report
  1.  
  2. import pandas as pd
  3. import numpy as np
  4. import os.path
  5. import matplotlib.pyplot as plt
  6.  
  7. class Interface:
  8. def __init__(self):
  9. print("Welcome to Bacteria'R'us™\nTo return to main menu enter 'quit'")
  10. self.data = pd.DataFrame([])
  11. self.filename = None
  12. self.filterchosen = False
  13. self.bactchosen = False
  14. self.growchosen = False
  15. self.bactfilterList = []
  16. self.growfilterlist = []
  17. self.l = pd.DataFrame([])
  18.  
  19. def mainprompt(self):
  20. while True:
  21. print('Main menu\nYou have the following options:')
  22. print('1. Load data')
  23. print('2. Filter data')
  24. print('3. Display statistics')
  25. print('4. Generate plots')
  26. print('5. Quit')
  27. choice = input(">> Choose option\n")
  28.  
  29. if choice in ['5', '5.', 'Quit', 'quit', 'q', 'Q']:
  30. print("This instance of Bacteria'R'us™ has terminated.")
  31. print('The team behind wishes you a nice day')
  32. return (0)
  33. elif os.path.exists(choice) == True:
  34. self.data = self.dataLoad(choice)
  35. elif choice in ['1', '1.', 'Load data', 'Load Data', 'load data']:
  36. global filename
  37. filename = input(">>Enter datafile\n")
  38. if os.path.exists(filename) == True:
  39. self.data = self.dataLoad(filename)
  40. else:
  41. print('Invalid file path\n')
  42. elif choice in ['2', '2.', 'Filter data', 'Filter Data', 'filter data']:
  43. if self.data.empty == True:
  44. print('no data')
  45. else:
  46. self.filterchosen = True
  47. self.dataFilter()
  48. elif choice in ['3', '3.', 'Display statistics', 'Display Statistics', 'display statistics']:
  49. if self.data.empty == True:
  50. print('no data')
  51. else:
  52. self.dataStatistics()
  53. elif choice in ['4', '4.', 'Generate plots', 'Generate Plots', 'generate plots']:
  54. if self.data.empty == True:
  55. print('no data')
  56. else:
  57. self.plots()
  58. # make plot function
  59. else:
  60. print('Invalid option')
  61.  
  62. def dataLoad(self, filename):
  63. self.data = pd.read_csv(filename, sep=' ', names=['Temperature', 'Growth rate', 'Bacteria'])
  64. # the columns are named to evaluate conditions below
  65. Temp = np.array(self.data.iloc[:, 0])
  66. Growthrate = np.array(self.data.iloc[:, 1])
  67. Bact = np.array(self.data.iloc[:, 2])
  68. # a new matrix
  69. self.l = pd.DataFrame([])
  70. for i in range(len(Temp)):
  71. if Temp[i] < 10 or Temp[i] > 60:
  72. print('Data on line ' + str(
  73. i) + ' of file was omitted \nReason: temperature must be between 10 and 60 degrees')
  74. elif Growthrate[i] < 0:
  75. print('Data on line ' + str(i) + ' of file was omitted \nReason: Growth rate must be positive')
  76. elif Bact[i] not in [1, 2, 3, 4]:
  77. print('Data on line ' + str(i) + ' of file was omitted \nReason: Bacteria must be one of no. 1-4')
  78. else:
  79. self.l = self.l.append(self.data.iloc[i, :])
  80.  
  81. self.data = self.l
  82. print(self.data)
  83. print('\nThese are the data\n')
  84. return self.data
  85. #return self.l
  86.  
  87. def dataFilter(self):
  88. while True:
  89. if self.bactchosen:
  90. self.bactFilter()
  91. if self.growchosen:
  92. self.growFilter()
  93.  
  94. if not self.filterchosen:
  95. return
  96. afilter = input('Filter bacteria type or growth rate? ')
  97. if afilter in ['Bacteria', 'B', 'b']:
  98. self.bactchosen = True
  99. elif afilter in ['Growth', 'G', 'g']:
  100. self.growchosen = True
  101. elif afilter in ['Q', 'q', 'Quit', 'quit', 'r', 'R', 'Return', 'return']:
  102. self.bactchosen = False
  103. return
  104. else:
  105. print('incorrect option')
  106.  
  107. def bactFilter(self):
  108. while True:
  109. print("Bacteria filtered:", str(self.bactfilterList),
  110. "\nenter 'Return' for other filters or 'Quit' to exit to main")
  111. n = input('toggle bacterium number:(1-4)')
  112. if n in ['Q', 'q', 'Quit', 'quit', 'r', 'R', 'Return', 'return']:
  113. self.bactchosen = False
  114. if n in ['Q', 'q', 'Quit', 'quit']:
  115. self.filterchosen = False
  116. return
  117. elif n in []:
  118. self.bactchosen = False
  119. return
  120. elif n in ['1', '2', '3', '4', '1.0', '2.0', '3.0', '4.0']:
  121. if float(n) in self.bactfilterList:
  122. self.bactfilterList.remove(float(n))
  123. else:
  124. self.bactfilterList += [float(n)]
  125. self.l = pd.DataFrame([])
  126. length = len(np.array(self.data.iloc[:, 0]))
  127. for i in range(length):
  128. if self.data.iloc[i, 0] in self.bactfilterList:
  129. pass
  130. else:
  131. self.l = self.l.append(self.data.iloc[i, :])
  132. print(self.l)
  133. else:
  134. print('invalid number')
  135.  
  136. def growFilter(self):
  137. while True:
  138. print('growth rate filters:', str(self.growfilterlist))
  139. length = len(np.array(self.data.iloc[:, 0]))
  140. lower = input('enter lower bound(float)')
  141. if lower in ['Q', 'q', 'Quit', 'quit', 'r', 'R', 'Return', 'return']:
  142. self.growchosen = False
  143. if lower in ['Q', 'q', 'Quit', 'quit']:
  144. self.filterchosen = False
  145. return
  146. upper = input('enter upper bound(float)')
  147. if upper in ['Q', 'q', 'Quit', 'quit', 'r', 'R', 'Return', 'return']:
  148. self.growchosen = False
  149. if upper in ['Q', 'q', 'Quit', 'quit']:
  150. self.filterchosen = False
  151. print('quitted')
  152. return
  153. elif (lower == float) and (upper == float):
  154. # elif float(u) not float: #or (float(l) is not float):
  155. # print('range must be entered as float values')
  156. self.growfilterlist.append(lower)
  157. self.l=pd.DataFrame([])
  158. for i in range(length):
  159. if float(l) > float(self.data.iloc[i, 0]) or float(self.data.iloc[i, 1]) > float(u):
  160. pass
  161. else:
  162. self.l = self.l.append(self.data.iloc[i, :])
  163. print(self.l)
  164.  
  165. def dataStatistics(self):
  166. while True:
  167. print('Options:')
  168. print('1.’Mean Temperature’:\nMean (average) Temperature.')
  169. print('\n2.’Std Temperature’:\nStandard deviation of Temperature.')
  170. print('\n3.’Std Growth rate’:\nStandard deviation of Growth rate.')
  171. print('\n4.’Rows’:\nThe total number of rows in the data.')
  172. print('\n5.’Mean Cold Growth rate’:\nAverage Growth rate for Temperature below 20 degrees.')
  173. print('\n6.’Mean Hot Growth rate’:\nAverage Growth rate for Temperature above 50 degrees.')
  174. statistics = input("choose statistic:")
  175. result = 0
  176. if self.l.empty == True:
  177. print('Statistics can not be computed when all data is filtered')
  178. return
  179. if statistics in ['1', 'Mean Temperature', 'mean temperature', 'mean Temperature', 'mt', 'MT']:
  180. result = np.mean(np.array(self.l.iloc[:, 2]))
  181. print(result)
  182. elif statistics in ['2', 'Mean Growth rate', 'MGR', 'mgr']:
  183. result = np.mean(np.array(self.l.iloc[:, 1]))
  184. print(result)
  185. elif statistics in ['3', 'Std Temperature', 'ST', 'st']:
  186. result = np.std(np.array(self.l.iloc[:, 2]))
  187. print(result)
  188. elif statistics in ['4', 'Rows', 'rows', 'rs']:
  189. result = len(np.array(self.l.iloc[:, 0]))
  190. print(result)
  191. elif statistics in ['5', 'Mean Cold Growth Rate', 'mean cold growth rate', 'mcgr', 'MCGR']:
  192. Sum = 0
  193. n = 0
  194. for i in range(len(self.l.iloc[:, 1])):
  195. if self.l.iloc[i, 2] < 20:
  196. n += 1
  197. Sum += self.l.iloc[i, 1]
  198. if n <= 0:
  199. print('no data below 20 degrees found')
  200. else:
  201. result = Sum / n
  202. print(result)
  203. elif statistics in ['6', 'Mean Hot Growth Rate', 'mean hot growth rate', 'mhgr', 'MHGR']:
  204. Sum = 0
  205. n = 0
  206. for i in range(len(self.l.iloc[:, 1])):
  207. if self.l.iloc[i, 2] > 50:
  208. n += 1
  209. Sum += self.l.iloc[i, 1]
  210. if n <= 0:
  211. print('no data above 50 degrees found')
  212. else:
  213. result = Sum / n
  214. print(result)
  215. elif statistics in ['Q', 'q', 'Quit', 'quit', 'r', 'R', 'Return', 'return']:
  216. return
  217.  
  218. # enter rest
  219. else:
  220. print("not valid, retry or quit?")
  221.  
  222. def plots(self):
  223. plotchoice=input("What plots do you want to see? \nYou have the following options: \n1.Frequency of the Bacteria \n2.Growth Rate by Temperature")
  224. if plotchoice in ['1', 'Bacteria', 'bacteria','b','B']:
  225. measurements = [0,0,0,0]
  226. for i in range (len(self.l.iloc[:,0])):
  227. if self.l.iloc[i,0] == 1.0:
  228. measurements[0]+=1
  229. elif self.l.iloc[i,0] == 2.0:
  230. measurements[1]+=1
  231. elif self.l.iloc[i,0] == 3.0:
  232. measurements[2]+=1
  233. elif self.l.iloc[i,0] == 4.0:
  234. measurements[3]+=1
  235. objects = ('Salmonella \nenterica', 'Bacillus \ncereus', 'Listeria', 'Brochothrix \nthermosphacta')
  236. y_pos=np.arange(len(objects))
  237. plt.bar(y_pos, measurements, width=0.7, align='center', alpha=0.7)
  238. plt.xticks(y_pos, objects)
  239. plt.ylabel('Amount')
  240. plt.xlabel('Bacteria',fontdict=None, labelpad=None)
  241. plt.title('Frequency of the Bacteria')
  242. plt.show()
  243.  
  244. elif plotchoice in ['2','GT','gt','Gt','gT','G','g','Growth','growth','Temperature','temperature','Growth Temperature','Growth temperature','growth temperature']:
  245. bacttemp1=[]
  246. bacttemp2=[]
  247. bacttemp3=[]
  248. bacttemp4=[]
  249. bactgrowth1=[]
  250. bactgrowth2=[]
  251. bactgrowth3=[]
  252. bactgrowth4=[]
  253. length=len(self.l.iloc[:,0])
  254. for i in range(length):
  255. if self.l.iloc[i,0] == [1.0]:
  256. bacttemp1.append(self.l.iloc[i,2])
  257. bactgrowth1.append(self.l.iloc[i,1])
  258. elif self.l.iloc[i,0] == 2.0:
  259. bacttemp2.append(int(self.l.iloc[i,2]))
  260. bactgrowth2.append(self.l.iloc[i,1])
  261. elif self.l.iloc[i,0] == 3.0:
  262. bacttemp3.append(int(self.l.iloc[i,2]))
  263. bactgrowth3.append(self.l.iloc[i,1])
  264. elif self.l.iloc[i,0] == 4.0:
  265. bacttemp4.append(self.l.iloc[i,2])
  266. bactgrowth4.append(self.l.iloc[i,1])
  267. z1 = sorted(zip(bacttemp1,bactgrowth1))
  268. bacttemp1=[i[0] for i in z1]
  269. bactgrowth1=[i[1] for i in z1]
  270. z2 = sorted(zip(bacttemp2,bactgrowth2))
  271. bacttemp2=[i[0] for i in z2]
  272. bactgrowth2=[i[1] for i in z2]
  273. z3 = sorted(zip(bacttemp3,bactgrowth3))
  274. bacttemp3=[i[0] for i in z3]
  275. bactgrowth3=[i[1] for i in z3]
  276. z4 = sorted(zip(bacttemp4,bactgrowth4))
  277. bacttemp4=[i[0] for i in z4]
  278. bactgrowth4=[i[1] for i in z4]
  279. # setting up a graph showing the relation of the growth rate to the temperature for each type of bacteria
  280. plt.plot(bacttemp1, bactgrowth1, 'b-', label='Salmonella enterica')
  281. plt.plot(bacttemp2, bactgrowth2, 'r-', label='Bacillus cereus')
  282. plt.plot(bacttemp3, bactgrowth3, 'g-', label='Listeria')
  283. plt.plot(bacttemp4, bactgrowth4, 'm-', label='Brochothrix thermosphacta')
  284. plt.legend(loc='best') #'best' localisation makes sure that the legend won't cover the data
  285. plt.ylabel('Growth rate')
  286. plt.xlabel('Temperature')
  287. plt.title('Growth Rate by Temperature for different bacteria')
  288. plt.xlim(xmin=10.0, xmax=60.0)
  289. plt.ylim(ymin=0.0, ymax=1.0)
  290. plt.grid(True)
  291. plt.show()
  292.  
  293. if __name__ == '__main__':
  294. interface = Interface()
  295. interface.mainprompt()
Advertisement
Add Comment
Please, Sign In to add comment
Advertisement
Public Pastes
Advertisement
We use cookies for various purposes including analytics. By continuing to use Pastebin, you agree to our use of cookies as described in the Cookies Policy.  OK, I Understand
Not a member of Pastebin yet?
Sign Up, it unlocks many cool features!