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-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/gn2.py24
1 files changed, 18 insertions, 6 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/gn2.py b/wqflask/wqflask/my_pylmm/pyLMM/gn2.py
index 7bceb089..40b2021d 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/gn2.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/gn2.py
@@ -1,7 +1,10 @@
-# Genenetwork2 specific methods and callback handler
+# Standalone specific methods and callback handler
#
# Copyright (C) 2015 Pjotr Prins (pjotr.prins@thebird.nl)
#
+# Set the log level with
+#
+# logging.basicConfig(level=logging.DEBUG)
from __future__ import absolute_import, print_function, division
@@ -9,8 +12,10 @@ import numpy as np
import sys
import logging
-# logging.basicConfig(level=logging.DEBUG)
-# np.set_printoptions()
+# logger = logging.getLogger(__name__)
+logger = logging.getLogger('lmm2')
+logging.basicConfig(level=logging.DEBUG)
+np.set_printoptions(precision=3,suppress=True)
progress_location = None
progress_current = None
@@ -37,13 +42,20 @@ def progress(location, count, total):
logger.info("Progress: %s %d%%" % (location,perc))
progress_location = location
progress_prev_perc = perc
-
+
def mprint(msg,data):
"""
Array/matrix print function
"""
m = np.array(data)
- print(msg,m.shape,"=\n",m)
+ if m.ndim == 1:
+ print(msg,m.shape,"=\n",m[0:3]," ... ",m[-3:])
+ if m.ndim == 2:
+ print(msg,m.shape,"=\n[",
+ m[0][0:3]," ... ",m[0][-3:],"\n ",
+ m[1][0:3]," ... ",m[1][-3:],"\n ...\n ",
+ m[-2][0:3]," ... ",m[-2][-3:],"\n ",
+ m[-1][0:3]," ... ",m[-1][-3:],"]")
def fatal(msg):
logger.critical(msg)
@@ -68,7 +80,7 @@ def uses(*funcs):
Some sugar
"""
return [callbacks()[func] for func in funcs]
-
+
# ----- Minor test cases:
if __name__ == '__main__':