z5py lacks a pypi package, so make imports conditional constantinpape…

…/z5#146

caiman/base/movies.py

@@ -38,7 +38,8 @@
 from tqdm import tqdm
 from typing import Any, Dict, List, Tuple, Union
 import warnings
-import z5py
+# Flip to normal import if this is ever resolved: https://github.com/constantinpape/z5/issues/146
+# import z5py
 from zipfile import ZipFile
 
 import caiman as cm
@@ -1288,7 +1289,7 @@ def play(self,
             im.axes.figure.canvas.draw()
             pl.pause(1)
 
-        if backend == 'notebook':
+        elif backend == 'notebook':
             # First set up the figure, the axis, and the plot element we want to animate
             fig = pl.figure()
             im = pl.imshow(self[0], interpolation='None', cmap=pl.cm.gray)
@@ -1685,6 +1686,10 @@ def rgb2gray(rgb):
                     raise Exception('Key not found in hdf5 file')
 
         elif extension in ('.n5', '.zarr'):
+           try:
+               import z5py
+           except ImportError:
+               raise Exception("z5py library not available; if you need this functionality use the conda package")
            with z5py.File(file_name, "r") as f:
                 fkeys = list(f.keys())
                 if len(fkeys) == 1: # If the n5/zarr file we're parsing has only one dataset inside it, ignore the arg and pick that dataset

caiman/source_extraction/cnmf/utilities.py

@@ -35,7 +35,8 @@
 import scipy.ndimage.morphology as morph
 import tifffile
 from typing import List
-import z5py
+# https://github.com/constantinpape/z5/issues/146
+#import z5py
 
 from .initialization import greedyROI
 from ...base.rois import com
@@ -1029,6 +1030,11 @@ def get_file_size(file_name, var_name_hdf5='mov'):
                         raise Exception('Variable not found. Use one of the above')
                 T, dims = siz[0], siz[1:]
             elif extension in ('.n5', '.zarr'):
+                try:
+                    import z5py
+                except:
+                    raise Exception("z5py not available; if you need this use the conda-based setup")
+
                 with z5py.File(file_name, "r") as f:
                     kk = list(f.keys())
                     if len(kk) == 1:

requirements.txt

@@ -27,4 +27,3 @@ tifffile
 tk
 tqdm
 yapf
-z5py

requirements_gpu.txt

@@ -25,4 +25,3 @@ tifffile
 tk
 tqdm
 yapf
-z5py