Python calculate Examples

Example #1

File: jorgeStats.py Project: cjgrady/pamRandomization

PATH_FOR_LM_COMPUTE = '/home/cjgrady/computeTest/'

sys.path.append(PATH_FOR_LM_COMPUTE)

from LmCompute.plugins.rad.calculate.calculate import calculate

INPUT_DIR = "/home/cjgrady/jorge/"
PAM_NAME = "pam_present"
NUM_PAMS = 6000
PHI_KEY = 'Per-siteRangeSizeofaLocality'
PSI_KEY = 'Range-richnessofaSpecies'

fn = '/home/cjgrady/pams/npys/pam_present.npy'
mat = numpy.load(fn)
status, summaryData = calculate(mat)
phiCmp = summaryData['sites'][PHI_KEY]
psiCmp = summaryData['species'][PSI_KEY]



phis = numpy.zeros((14904, NUM_PAMS))
psis = numpy.zeros((2255, NUM_PAMS))

for i in xrange(0, NUM_PAMS):
   try:
      numRnd = (i+1) * 1000
      subDir = "%04d" % (numRnd / 100000, )
      phiFn = os.path.join(INPUT_DIR, 'phi', subDir, '%s-%s-%s-phi.npy' % (PAM_NAME, i, numRnd))
      psiFn = os.path.join(INPUT_DIR, 'psi', subDir, '%s-%s-%s-psi.npy' % (PAM_NAME, i, numRnd))
      

Example #2

File: cmpCJrandWithJorge.py Project: cjgrady/pamRandomization

PAM_FN = "/home/cjgrady/ecosim/observed.npy"
IN_CSV_FN = "/home/cjgrady/ecosim/cjEcoDiversity.csv"
OUT_CSV = "/home/cjgrady/ecosim/cjEcoScores.csv"
# PAM_FN = "/home/cjgrady/pams/npys/pam_present.npy"
# IN_CSV_FN = "/home/cjgrady/pams/cjDiversity.csv"
# OUT_CSV = "/home/cjgrady/pams/cjScores.csv"

zScores = []
absZscores = []
avgDifs = []

# Load PAM
mtx = numpy.load(PAM_FN)

status, sData = calculate(mtx)

phis = sData['sites']['Per-siteRangeSizeofaLocality']

# Load CSV with sites
f = open(IN_CSV_FN)
reader = csv.reader(f)
i = 0
for row in reader:
   val = phis[i]
   
   a = numpy.array(row, dtype=numpy.float)
   
   mean = numpy.average(a)
   stdDev = numpy.std(a)