Merge pull request #455 from flatironinstitute/dev

Dev

Dockerfile

@@ -1,41 +1,9 @@
-FROM ubuntu
+FROM continuumio/anaconda3
 
-RUN apt-get update
-RUN apt-get install -y libglib2.0-0
-RUN apt-get install -y git wget
-RUN apt-get install bzip2
-RUN apt-get install -y gcc
-RUN apt-get install -y g++
-RUN apt-get install -y libgtk2.0-0
-RUN apt-get install -y xvfb
-RUN export MINICONDA=$HOME/miniconda
-RUN export PATH="$MINICONDA/bin:$PATH"
-RUN hash -r
-RUN wget -q https://3230d63b5fc54e62148e-c95ac804525aac4b6dba79b00b39d1d3.ssl.cf1.rackcdn.com/Anaconda2-2.5.0-Linux-x86_64.sh -O anaconda.sh
-# RUN bash anaconda.sh -b -p $ANACONDA
-RUN bash anaconda.sh -p /anaconda -b
-ENV PATH=/anaconda/bin:${PATH}
 RUN conda config --set always_yes yes
 RUN conda update --yes conda
-RUN conda info -a
-RUN CONDA_SSL_VERIFY=false conda update pyopenssl
-# RUN conda install -c menpo opencv3=3.1.0
-# RUN conda install -c cvxgrp cvxpy
-# RUN conda install -c https://conda.anaconda.org/conda-forge tifffile
-# RUN git clone --recursive -b agiovann-master https://github.com/valentina-s/Constrained_NMF.git
-# RUN git clone --recursive https://github.com/agiovann/Constrained_NMF.git
-# RUN git clone --recursive -b dev https://github.com/agiovann/Constrained_NMF.git
-ADD . /CaImAn
-WORKDIR /CaImAn/
-RUN conda env update -f environment.yml -n root
-#RUN conda install --file requirements_conda.txt
-#RUN pip install -r requirements_pip.txt
-RUN apt-get install libc6-i386
-RUN apt-get install -y libsm6 libxrender1
-RUN conda install pyqt=4.11.4
-RUN python setup.py install
-RUN python setup.py build_ext -i
+RUN apt-get install -y gcc g++ libgl1
+RUN mkdir src && cd src && git clone -b dev https://github.com/flatironinstitute/CaImAn.git && cd CaImAn && conda env create -n caiman -f environment.yml && conda install --override-channels -c conda-forge -n caiman pip
+RUN /bin/bash -c "cd src/CaImAn && source activate caiman && /opt/conda/envs/caiman/bin/pip install ."
+RUN /bin/bash -c "source activate caiman && caimanmanager.py install"
 
-# RUN nosetests
-
-EXPOSE 8080

caiman/mmapping.py

@@ -270,13 +270,14 @@ def save_portion(pars):
         del big_mov
     else:
         with open(big_mov, 'r+b') as f:
-            f.seek(idx_start * Yr_tot.dtype.itemsize * tot_frames)
+            f.seek(idx_start * int(Yr_tot.dtype.itemsize) * tot_frames)
             f.write(Yr_tot)
-            if f.tell() != idx_end * Yr_tot.dtype.itemsize * tot_frames:
-                    logging.debug(f.tell())
-                    logging.debug(idx_end * Yr_tot.dtype.itemsize * tot_frames)
+            computed_position = idx_end * int(Yr_tot.dtype.itemsize) * tot_frames
+            if f.tell() != computed_position:
+                    logging.critical(f"Error in mmap portion write: at position {f.tell()}")
+                    logging.critical(f"But should be at position {idx_end} * {Yr_tot.dtype.itemsize} * {tot_frames} = {computed_position}")
                     f.close()
-                    raise Exception('Writing at the wrong location!')
+                    raise Exception('Internal error in mmapping: Actual position does not match computed position')
 
     del Yr_tot
     logging.debug('done')

caiman/source_extraction/cnmf/utilities.py

@@ -911,7 +911,7 @@ def get_file_size(file_name, var_name_hdf5=None):
                 T, dims = siz[0], siz[1:]
             elif extension == '.avi':
                 cap = cv2.VideoCapture(file_name)
-                dims = (0, 0)
+                dims = [0, 0]
                 try:
                     T = int(cap.get(cv2.CAP_PROP_FRAME_COUNT))
                     dims[0] = int(cap.get(cv2.CAP_PROP_FRAME_WIDTH))

caiman/utils/utils.py

@@ -6,7 +6,7 @@
 
 See Also
 ------------
-https://docs.python.org/2/library/urllib.html
+https://docs.python.org/3/library/urllib.request.htm
 
 """
 
@@ -36,11 +36,7 @@
 except:
     pass
 
-# TODO: Simplify conditional imports below
-try:
-    from urllib2 import urlopen
-except ImportError:
-    from urllib.request import urlopen
+from urllib.request import urlopen
 from ..external.cell_magic_wand import cell_magic_wand
 from ..source_extraction.cnmf.spatial import threshold_components
 
@@ -84,7 +80,8 @@ def download_demo(name='Sue_2x_3000_40_-46.tif', save_folder=''):
         path_movie = os.path.join(base_folder, save_folder, name)
         if not os.path.exists(path_movie):
             url = file_dict[name]
-            logging.info("downloading " + str(name) + " with urllib")
+            logging.info(f"downloading {name} with urllib")
+            logging.info(f"GET {url} HTTP/1.1")
             f = urlopen(url)
             data = f.read()
             with open(path_movie, "wb") as code:
@@ -410,8 +407,8 @@ def recursively_save_dict_contents_to_group(h5file, path, dic):
             item = np.array(item)
         if not isinstance(key, str):
             raise ValueError("dict keys must be strings to save to hdf5")
-        # save strings, numpy.int64, and numpy.float64 types
-        if isinstance(item, (np.int64, np.float64, str, np.float, float, np.float32,int)):
+        # save strings, numpy.int64, numpy.int32, and numpy.float64 types
+        if isinstance(item, (np.int64, np.int32, np.float64, str, np.float, float, np.float32,int)):
             h5file[path + key] = item
             if not h5file[path + key].value == item:
                 raise ValueError('The data representation in the HDF5 file does not match the original dict.')
@@ -442,7 +439,7 @@ def recursively_save_dict_contents_to_group(h5file, path, dic):
         elif type(item).__name__ in ['CNMFParams', 'Estimates']: # parameter object
             recursively_save_dict_contents_to_group(h5file, path + key + '/', item.__dict__)
         else:
-            raise ValueError('Cannot save %s type.' % type(item))
+            raise ValueError("Cannot save %s type for key '%s'." % (type(item), key))
 
 
 def recursively_load_dict_contents_from_group( h5file, path):

environment.yml

@@ -7,6 +7,7 @@ dependencies:
 - cython
 - future
 - h5py
+- ipykernel=4.10
 - ipython
 - ipyparallel
 - jupyter