bug with tic

Author: carsen-stringer

jupyter/test_tiff_loader.ipynb

@@ -2061,7 +2061,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="suite2p",
-    version="1.0.2",
+    version="1.0.3",
     author="Marius Pachitariu and Carsen Stringer",
     author_email="[email protected]",
     description="Pipeline for calcium imaging",

suite2p/run_s2p.py

@@ -147,7 +147,6 @@ def run_s2p(ops={},db={}):
         ops0 = default_ops()
         # combine with user options
         ops = {**ops0, **ops}
-        ops['t0'] = t0
         # copy tiff to a binary
         if len(ops['h5py']):
             ops1 = utils.h5py_to_binary(ops)
@@ -183,7 +182,6 @@ def run_s2p(ops={},db={}):
 
     while ipl<len(ops1):
         print('>>>>>>>>>>>>>>>>>>>>> PLANE %d <<<<<<<<<<<<<<<<<<<<<<'%ipl)
-        ops1[ipl]['t0'] = t0
         t1 = tic()
         if not flag_binreg:
             ######### REGISTRATION #########

suite2p/utils.py

@@ -303,7 +303,7 @@ def tiff_to_binary(ops):
     ''' converts tiff to *.bin file '''
     ''' requires ops keys: nplanes, nchannels, data_path, look_one_level_down, reg_file '''
     ''' assigns ops keys: tiffreader, first_tiffs, frames_per_folder, nframes, meanImg, meanImg_chan2'''
-    t0=ops['t0']
+    t0=tic()
     # copy ops to list where each element is ops for each plane
     ops1 = init_ops(ops)
     nplanes = ops1[0]['nplanes']
@@ -413,6 +413,7 @@ def split_multiops(ops1):
 def mesoscan_to_binary(ops):
     # copy ops to list where each element is ops for each plane
     # load json file with line start stops
+    t0 = tic()
     if 'lines' not in ops:
         fpath = os.path.join(ops['data_path'][0], '*json')
         fs = glob.glob(fpath)