Merge pull request #313 from boazmohar/readTiffPage

tiffs with npages not dividing by pageCount will give a warning instead an error

Author: freeman-lab

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

@@ -1,4 +1,5 @@
 import itertools
+import logging
 from io import BytesIO
 from numpy import frombuffer, prod, random, asarray, expand_dims
 
@@ -283,8 +284,8 @@ def frombinary(path, shape=None, dtype=None, ext='bin', start=None, stop=None, r
             raise ValueError("Last dimension '%d' must be divisible by nplanes '%d'" %
                              (shape[-1], nplanes))
 
-    def getarray(idxAndBuf):
-        idx, buf = idxAndBuf
+    def getarray(idx_buffer_filename):
+        idx, buf, _ = idx_buffer_filename
         ary = frombuffer(buf, dtype=dtype, count=int(prod(shape))).reshape(shape, order=order)
         if nplanes is None:
             yield (idx,), ary
@@ -294,17 +295,17 @@ def getarray(idxAndBuf):
             if shape[-1] % nplanes:
                 npoints += 1
             timepoint = 0
-            lastPlane = 0
-            curPlane = 1
-            while curPlane < ary.shape[-1]:
-                if curPlane % nplanes == 0:
-                    slices = [slice(None)] * (ary.ndim - 1) + [slice(lastPlane, curPlane)]
+            last_plane = 0
+            current_plane = 1
+            while current_plane < ary.shape[-1]:
+                if current_plane % nplanes == 0:
+                    slices = [slice(None)] * (ary.ndim - 1) + [slice(last_plane, current_plane)]
                     yield idx*npoints + timepoint, ary[slices].squeeze()
                     timepoint += 1
-                    lastPlane = curPlane
-                curPlane += 1
+                    last_plane = current_plane
+                current_plane += 1
             # yield remaining planes
-            slices = [slice(None)] * (ary.ndim - 1) + [slice(lastPlane, ary.shape[-1])]
+            slices = [slice(None)] * (ary.ndim - 1) + [slice(last_plane, ary.shape[-1])]
             yield (idx*npoints + timepoint,), ary[slices].squeeze()
 
     recount = False if nplanes is None else True
@@ -315,7 +316,7 @@ def getarray(idxAndBuf):
                     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.
 
@@ -346,29 +347,38 @@ 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
 
     if nplanes is not None and nplanes <= 0:
         raise ValueError('nplanes must be positive if passed, got %d' % nplanes)
 
-    def getarray(idxAndBuf):
-        idx, buf = idxAndBuf
+    def getarray(idx_buffer_filename):
+        idx, buf, fname = idx_buffer_filename
         fbuf = BytesIO(buf)
         tfh = tifffile.TiffFile(fbuf)
         ary = tfh.asarray()
         pageCount = ary.shape[0]
         if nplanes is not None:
-            values = [ary[i:(i+nplanes)] for i in range(0, ary.shape[0], nplanes)]
+            extra = pageCount % nplanes
+            if extra:
+                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]
         tfh.close()
 
         if ary.ndim == 3:
             values = [val.squeeze() for val in values]
 
-        if nplanes and (pageCount % nplanes):
-            raise ValueError("nplanes '%d' does not evenly divide '%d'" % (nplanes, pageCount))
         nvals = len(values)
         keys = [(idx*nvals + timepoint,) for timepoint in range(nvals)]
         return zip(keys, values)
@@ -408,8 +418,8 @@ def frompng(path, ext='png', start=None, stop=None, recursive=False, npartitions
     """
     from scipy.misc import imread
 
-    def getarray(idxAndBuf):
-        idx, buf = idxAndBuf
+    def getarray(idx_buffer_filename):
+        idx, buf, _ = idx_buffer_filename
         fbuf = BytesIO(buf)
         yield (idx,), imread(fbuf)
 

thunder/readers.py

@@ -149,9 +149,9 @@ def read(self, path, ext=None, start=None, stop=None, recursive=False, npartitio
         if spark and isinstance(self.engine, spark):
             npartitions = min(npartitions, nfiles) if npartitions else nfiles
             rdd = self.engine.parallelize(enumerate(files), npartitions)
-            return rdd.map(lambda kv: (kv[0], readlocal(kv[1])))
+            return rdd.map(lambda kv: (kv[0], readlocal(kv[1]), kv[1]))
         else:
-            return [(k, readlocal(v)) for k, v in enumerate(files)]
+            return [(k, readlocal(v), v) for k, v in enumerate(files)]
 
 
 class LocalFileReader(object):