- added a flag discard_extra

- added a test

Author: boazmohar

test/test_images_io.py

@@ -114,6 +114,16 @@ def test_from_tif_multi_planes(eng):
     assert [x.sum() for x in data.toarray()] == [1140006, 1119161, 1098917]
 
 
+def test_from_tif_multi_planes_discard_extra(eng):
+    path = os.path.join(resources, 'multilayer_tif', 'dotdotdot_lzw.tif')
+    data = fromtif(path, nplanes=2, engine=eng, discard_extra=True)
+    assert data.shape[0] == 1
+    assert data.shape[1] == 2
+    with pytest.raises(BaseException) as error_msg:
+        data = fromtif(path, nplanes=2, engine=eng, discard_extra=False)
+    assert 'nplanes' in str(error_msg.value)
+
+
 def test_from_tif_multi_planes_many(eng):
     path = os.path.join(resources, 'multilayer_tif', 'dotdotdot_lzw*.tif')
     data = fromtif(path, nplanes=3, engine=eng)

thunder/images/readers.py

@@ -1,5 +1,5 @@
 import itertools
-import warnings
+import logging
 from io import BytesIO
 from numpy import frombuffer, prod, random, asarray, expand_dims
 
@@ -316,7 +316,7 @@ def getarray(idx_buffer_filename):
                     dims=newdims, dtype=dtype, labels=labels, recount=recount,
                     engine=engine, credentials=credentials)
 
-def fromtif(path, ext='tif', start=None, stop=None, recursive=False, nplanes=None, npartitions=None, labels=None, engine=None, credentials=None):
+def fromtif(path, ext='tif', start=None, stop=None, recursive=False, nplanes=None, npartitions=None, labels=None, engine=None, credentials=None, discard_extra=False):
     """
     Loads images from single or multi-page TIF files.
 
@@ -347,6 +347,10 @@ def fromtif(path, ext='tif', start=None, stop=None, recursive=False, nplanes=Non
 
     labels : array, optional, default = None
         Labels for records. If provided, should be one-dimensional.
+
+    discard_extra : boolean, optional, default = False
+        If True and nplanes doesn't divide by the number of pages in a multi-page tiff, the reminder will
+        be discarded and a warning will be shown. If False, it will raise an error
     """
     import skimage.external.tifffile as tifffile
 
@@ -362,8 +366,11 @@ def getarray(idx_buffer_filename):
         if nplanes is not None:
             extra = pageCount % nplanes
             if extra:
-                pageCount = pageCount - extra
-                warnings.warn('Ignored %d pages in file %s' % (extra, fname), RuntimeWarning)
+                if discard_extra:
+                    pageCount = pageCount - extra
+                    logging.getLogger('thunder').warn('Ignored %d pages in file %s' % (extra, fname))
+                else:
+                    raise ValueError("nplanes '%d' does not evenly divide '%d'" % (nplanes, pageCount))
             values = [ary[i:(i+nplanes)] for i in range(0, pageCount, nplanes)]
         else:
             values = [ary]