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Made openmp switch in only dependent on potion in rbf.py and linear.py

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This commit is contained in:
Neil Lawrence 2014-05-13 05:23:36 +01:00
parent 169e81702d
commit 2256127130
7 changed files with 122 additions and 48 deletions
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38
GPy/util/datasets.py
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@ -112,7 +112,7 @@ def download_url(url, store_directory, save_name = None, messages = True, suffix
if content_length_str:
file_size = int(content_length_str[0])
else:
file_size = 1e10
file_size = None
status = ""
file_size_dl = 0
block_sz = 8192
@ -124,9 +124,15 @@ def download_url(url, store_directory, save_name = None, messages = True, suffix
file_size_dl += len(buff)
f.write(buff)
sys.stdout.write(" "*(len(status)) + "\r")
status = r"[{perc: <{ll}}] {dl:7.3f}/{full:.3f}MB".format(dl=file_size_dl/(1.*1e6),
full=file_size/(1.*1e6), ll=line_length,
if file_size:
status = r"[{perc: <{ll}}] {dl:7.3f}/{full:.3f}MB".format(dl=file_size_dl/(1048576.),
full=file_size/(1048576.), ll=line_length,
perc="="*int(line_length*float(file_size_dl)/file_size))
else:
status = r"[{perc: <{ll}}] {dl:7.3f}MB".format(dl=file_size_dl/(1048576.),
ll=line_length,
perc="."*int(line_length*float(file_size_dl/(10*1048576.))))
sys.stdout.write(status)
sys.stdout.flush()
sys.stdout.write(" "*(len(status)) + "\r")
@ -357,8 +363,15 @@ def football_data(season='1314', data_set='football_data'):
def fruitfly_tomancak(data_set='fruitfly_tomancak', gene_number=None):
if not data_available(data_set):
download_data(data_set)
X = None
Y = None
from pandas import read_csv
filename = os.path.join(data_path, 'tomancak_expr.csv')
Y = read_csv(filename, header=0, index_col=0).T
num_repeats = 3
num_time = 12
xt = np.linspace(0, num_time-1, num_time)
xr = np.linspace(0, num_repeats-1, num_repeats)
xtime, xrepeat = np.meshgrid(xt, xr)
X = np.vstack((xtime.flatten(), xrepeat.flatten())).T
return data_details_return({'X': X, 'Y': Y, 'gene_number' : gene_number}, data_set)
# This will be for downloading google trends data.
@ -732,13 +745,16 @@ def hapmap3(data_set='hapmap3'):
def singlecell(data_set='singlecell'):
if not data_available(data_set):
download_data(data_set)
from pandas import read_csv
dirpath = os.path.join(data_path, data_set)
data = np.loadtxt(os.path.join(dirpath, 'singlecell.csv'), delimiter=",", dtype=str)
genes = data[0, 1:]
labels = data[1:, 0]
Y = np.array(data[1:, 1:], dtype=float)
return data_details_return({'Y': Y, 'info' : "qPCR Singlecell experiment in Mouse, measuring 48 gene expressions in 1-64 cell states. The labels have been created as in Guo et al. [2010]",
'genes':genes, 'labels':labels,
filename = os.path.join(dirpath, 'singlecell.csv')
Y = read_csv(filename, header=0, index_col=0)
genes = Y.columns
labels = Y.index
# data = np.loadtxt(os.path.join(dirpath, 'singlecell.csv'), delimiter=",", dtype=str)
return data_details_return({'Y': Y, 'info' : "qPCR singlecell experiment in Mouse, measuring 48 gene expressions in 1-64 cell states. The labels have been created as in Guo et al. [2010]",
'genes': genes, 'labels':labels,
}, data_set)
def swiss_roll_1000():