Python 3 ready on Anaconda

dataman/dataman.py

@@ -6,15 +6,15 @@ import sys
 import cmd
 import logging
 
-from lib.constants import LOG_LEVEL_VERBOSE
-import lib.tools
-from dataman_cli import DataMan
+from dataman.lib.constants import LOG_LEVEL_VERBOSE
+from dataman.dataman_cli import DataMan
 
 __version__ = 0.01
 
 NO_EXIT_CONFIRMATION = True
 LOG_LEVEL = logging.INFO
-if __name__ == "__main__":
+
+def main():
     # Command line parsing
     import argparse
     parser = argparse.ArgumentParser(prog="DataMan")
@@ -68,3 +68,7 @@ if __name__ == "__main__":
     else:
         DataMan().onecmd(' '.join(sys.argv[1:]))
 
+
+if __name__ == "__main__":
+    main()
+

dataman/dataman_cli.py

@@ -5,15 +5,14 @@ from __future__ import print_function
 import sys
 import logging
 import cmd
-import lib.tools
-from lib.constants import LOG_LEVEL_VERBOSE
+from dataman.lib.constants import LOG_LEVEL_VERBOSE
 
 
 class DataMan(cmd.Cmd):
     """Command line tool for quick data documentation."""
 
     prompt = "dm> "
-    intro = "Data Manager\n --Ronny's way of avoiding having to stare at spreadsheets."
+    intro = "Data Manager\n"
 
     def preloop(self):
         self.log = logging.getLogger(__name__)
@@ -32,17 +31,17 @@ class DataMan(cmd.Cmd):
     def do_ls(self, path):
         if not len(path):
             path = '.'
-        import lib.dirstats as ds
+        import dataman.lib.dirstats as ds
         ds.print_table(ds.gather(path))
 
     def do_stats(self, path):
         if not len(path):
             path = '.'
-        import lib.dirstats as ds
+        import dataman.lib.dirstats as ds
         ds.print_table(ds.gather(path))
 
     def do_vis(self, path):
-        from vis import vis
+        from dataman.vis import vis
         vis.run(target=path)
 
     def do_exit(self, line):

dataman/lib/dirstats.py

@@ -2,13 +2,11 @@
 # -*- coding: utf-8 -*-
 
 from __future__ import print_function
-import tools
-from tools import fext, dir_content
 import os
 import sys
 from termcolor import colored
-import open_ephys
-import kwik
+from . import tools, open_ephys, kwik
+from .tools import fext, dir_content
 
 EXT_VIDEO = ['.avi', '.mp4', '.mkv', '.wmv']
 EXT_SOUND = ['.wav', '.mp3', '.snd', '.wma']

dataman/lib/kwik.py

@@ -4,7 +4,7 @@
 from __future__ import print_function
 import os
 import xml.etree.ElementTree as etree
-from tools import fext, dir_content
+from .tools import fext, dir_content
 
 def detect(root, dirs=None, files=None):
     for f in files:

dataman/lib/open_ephys.py

@@ -4,7 +4,7 @@
 from __future__ import print_function
 import os
 import xml.etree.ElementTree as etree
-from tools import fext, dir_content
+from .tools import fext, dir_content
 
 def detect(root=None, dirs=None, files=None):
     """Checks for existence of an open ephys formatted data set in the root directory.

dataman/lib/tools.py

@@ -3,7 +3,6 @@
 
 from __future__ import print_function
 import os
-from os.path import join, getsize
 from termcolor import colored
 import re
 

dataman/vis/Buffer.py

@@ -12,6 +12,7 @@ Inspired by https://github.com/belevtsoff/rdaclient.py
 
 """
 
+from __future__ import print_function
 from multiprocessing import Array
 import ctypes as c
 import logging
@@ -98,7 +99,7 @@ class Buffer(object):
         nptype = datatypes.get_type(hdr.dataType)
 
         bufOffset = c.sizeof(hdr)
-        bufFlatSize = hdr.bufSizeBytes / np.dtype(nptype).itemsize
+        bufFlatSize = hdr.bufSizeBytes // np.dtype(nptype).itemsize
 
         # create numpy view object pointing to the raw array
         self.__raw = raw
@@ -198,8 +199,7 @@ class datatypes():
         ndtype : string
             numpy datatype (e.g. 'float32')
         """
-        idx = cls.types.values().index(ndtype)
-        return cls.types.keys()[idx]
+        return next(key for key, value in cls.types.items() if value == ndtype)
 
     @classmethod
     def get_type(cls, code):
@@ -273,11 +273,11 @@ if __name__ == '__main__':
     buf1.put_data(np.array([[1, 2], [3, 4]]))
     buf2.put_data(np.array([[5, 6], [7, 8]]), start=2)
 
-    print buf1
-    print buf2
+    print(buf1)
+    print(buf2)
 
     dat = buf2.get_data(0, 4)
     dat[0, 0] = 100
 
-    print buf1
-    print buf2
+    print(buf1)
+    print(buf2)

dataman/vis/reader.py

@@ -8,6 +8,7 @@ Created on Sep 23, 2015 18:53
 File reader
 """
 
+from __future__ import print_function
 import numpy as np
 import re
 
@@ -51,7 +52,7 @@ def read_header(filename):
 def read_segment(filename, offset, count, dtype):
     """Read segment of a file from [offset] for [count]x[dtype]"""
     with open(filename, 'rb') as fid:
-        fid.seek(offset)
+        fid.seek(int(offset))
         segment = np.fromfile(fid, dtype=dtype, count=count)
     return segment
 
@@ -80,8 +81,9 @@ def read_record(filename, offset=0, count=30, dtype=DATA_DT):
 
 
 if __name__ == "__main__":
-    print read_header('data/2014-10-30_16-07-29/106_CH1.continuous')
-    print read_segment('data/2014-10-30_16-07-29/106_CH1.continuous', offset=SIZE_HEADER)['samples'].ravel()[0]
+    pass
+    # print(read_header('data/2014-10-30_16-07-29/106_CH1.continuous'))
+    # print(read_segment('data/2014-10-30_16-07-29/106_CH1.continuous', offset=SIZE_HEADER)['samples'].ravel()[0])
 
 
 

dataman/vis/vis.py

@@ -7,7 +7,8 @@
 """
 Multiple real-time digital signals with GLSL-based clipping.
 """
-from __future__ import division
+
+from __future__ import division, print_function
 import logging
 import os
 from vispy import gloo
@@ -16,13 +17,13 @@ from vispy import util
 import numpy as np
 import math
 
-from reader import read_record, read_header
+from .reader import read_record, read_header
 
 # Dimensions of plot segment/signals
 n_rows = 16
 n_cols = 4
 n_signals = n_rows*n_cols
-n_samples = 3e4
+n_samples = int(3e4)
 
 # Buffer to store all the pre-loaded signals
 buf = np.zeros((n_signals, n_samples), dtype=np.float32)

setup.py

@@ -10,9 +10,10 @@ config = {
         'download_url': '',
         'author_email': 'ronny.eichler@gmail.com',
         'version': '0.0.1',
-        'install_requires': ['nose', 'termcolor'],
+        'install_requires': ['nose', 'termcolor', 'vispy'],
         'packages': ['dataman'],
-        'scripts': [],
+        'entry_points': """[console_scripts]
+            dm=dataman.dataman:main""",
         'name': 'dataman'
         }