tifffile plugin: Various fixes (#567)

* tiffile plugin: Don't assume metadata is the same for all frames

* FEI SEM plugin: Fix after changes to tifffile plugin

* tiffile plugin: Write global metadata only to first frame

and only if no metadata was given for first frame.

* tifffile plugin: Set `contiguous=False` when writing frames

This has been tifffile's default since version 2020.9.3 and allows for
e.g. per-frame metadata.

* tiffile plugin: Use TiffWriter.write instead of .save

if available. `save` was deprecated in tifffile version 2020.9.30.

Co-authored-by: Lukas Schrangl <schrangl@iap.tuwien.ac.at>

imageio/plugins/feisem.py

@@ -52,6 +52,9 @@ def _get_meta_data(self, index=None):
             metadata : dict
                 Dictionary of metadata.
             """
+            if hasattr(self, "_fei_meta"):
+                return self._fei_meta
+
             md = {"root": {}}
             current_tag = "root"
             reading_metadata = False
@@ -80,7 +83,8 @@ def _get_meta_data(self, index=None):
                             md[current_tag][key] = val
             if not md["root"] and len(md) == 1:
                 raise ValueError("Input file %s contains no FEI metadata." % filename)
-            self._meta.update(md)
+
+            self._fei_meta = md
             return md
 
 

imageio/plugins/tifffile.py

@@ -69,6 +69,11 @@ class TiffFormat(Format):
     to read the individual pages, or ``imageio.volread()`` to obtain a
     single (higher dimensional) array.
 
+    Note that global metadata is stored with the first frame in a TIFF file.
+    Thus calling :py:meth:`Format.Writer.set_meta_data` after the first frame
+    was written has no effect. Also, global metadata is ignored if metadata is
+    provided via the `meta` argument of :py:meth:`Format.Writer.append_data`.
+
     Parameters for reading
     ----------------------
     offset : int
@@ -225,9 +230,6 @@ def _open(self, **kwargs):
                 f = self.request.get_file()
             self._tf = _tifffile.TiffFile(f, **kwargs)
 
-            # metadata is the same for all images
-            self._meta = {}
-
         def _close(self):
             self._tf.close()
             if self._f is not None:
@@ -257,35 +259,36 @@ def _get_data(self, index):
                     im = np.stack(ims, 0)
                 else:
                     im = self._tf.asarray()
-                meta = self._meta
+                meta = self._get_meta_data(0)
             else:
                 # Read as 2D image
                 if index < 0 or index >= self._get_length():
                     raise IndexError("Index out of range while reading from tiff file")
                 im = self._tf.pages[index].asarray()
-                meta = self._meta or self._get_meta_data(index)
+                meta = self._get_meta_data(index)
             # Return array and empty meta data
             return im, meta
 
         def _get_meta_data(self, index):
+            meta = {}
             page = self._tf.pages[index or 0]
             for key in READ_METADATA_KEYS:
                 try:
-                    self._meta[key] = getattr(page, key)
+                    meta[key] = getattr(page, key)
                 except Exception:
                     pass
 
             # tifffile <= 0.12.1 use datetime, newer use DateTime
             for key in ("datetime", "DateTime"):
                 try:
-                    self._meta["datetime"] = datetime.datetime.strptime(
+                    meta["datetime"] = datetime.datetime.strptime(
                         page.tags[key].value, "%Y:%m:%d %H:%M:%S"
                     )
                     break
                 except Exception:
                     pass
 
-            return self._meta
+            return meta
 
     # -- writer
     class Writer(Format.Writer):
@@ -307,31 +310,44 @@ def _open(self, bigtiff=None, byteorder=None, software=None):
                 self._software = software
 
             self._meta = {}
+            self._frames_written = 0
 
         def _close(self):
             self._tf.close()
 
         def _append_data(self, im, meta):
-            if meta:
-                self.set_meta_data(meta)
+            if meta is not None:
+                meta = self._sanitize_meta(meta)
+            else:
+                # Use global metadata for first frame
+                meta = self._meta if self._frames_written == 0 else {}
+            if self._software is not None and self._frames_written == 0:
+                meta["software"] = self._software
             # No need to check self.request.mode; tifffile figures out whether
             # this is a single page, or all page data at once.
-            if self._software is None:
-                self._tf.save(np.asanyarray(im), **self._meta)
-            else:
-                # tifffile >= 0.15
-                self._tf.save(np.asanyarray(im), software=self._software, **self._meta)
-
-        def set_meta_data(self, meta):
-            self._meta = {}
+            try:
+                # TiffWriter.save has been deprecated in version 2020.9.30
+                write_meth = self._tf.write
+            except AttributeError:
+                write_meth = self._tf.save
+            write_meth(np.asanyarray(im), contiguous=False, **meta)
+            self._frames_written += 1
+
+        @staticmethod
+        def _sanitize_meta(meta):
+            ret = {}
             for (key, value) in meta.items():
                 if key in WRITE_METADATA_KEYS:
                     # Special case of previously read `predictor` int value
                     # 1(=NONE) translation to False expected by TiffWriter.save
                     if key == "predictor" and not isinstance(value, bool):
-                        self._meta[key] = value > 1
+                        ret[key] = value > 1
                     else:
-                        self._meta[key] = value
+                        ret[key] = value
+            return ret
+
+        def set_meta_data(self, meta):
+            self._meta = self._sanitize_meta(meta)
 
 
 # Register

tests/test_tifffile.py

@@ -24,9 +24,9 @@ def test_tifffile_format():
 
 def test_tifffile_reading_writing():
     """ Test reading and saving tiff """
-    
+
     need_internet()  # We keep a test image in the imageio-binary repo
-    
+
     im2 = np.ones((10, 10, 3), np.uint8) * 2
 
     filename1 = os.path.join(test_dir, 'test_tiff.tiff')
@@ -38,7 +38,7 @@ def test_tifffile_reading_writing():
     assert im.shape == im2.shape
     assert (im == im2).all()
     assert len(ims) == 1
-    
+
     # Multiple images
     imageio.mimsave(filename1, [im2, im2, im2])
     im = imageio.imread(filename1)
@@ -57,7 +57,7 @@ def test_tifffile_reading_writing():
     assert len(vols) == 1 and vol.shape == vols[0].shape
     for i in range(3):
         assert (vol[i] == im2).all()
-    
+
     # remote multipage rgb file
     filename2 = get_remote_file('images/multipage_rgb.tif')
     img = imageio.mimread(filename2)
@@ -81,7 +81,7 @@ def test_tifffile_reading_writing():
     # Fail
     raises(IndexError, R.get_data, -1)
     raises(IndexError, R.get_data, 3)
-    
+
     # Ensure imread + imwrite works round trip
     filename3 = os.path.join(test_dir, 'test_tiff2.tiff')
     im1 = imageio.imread(filename1)
@@ -90,7 +90,7 @@ def test_tifffile_reading_writing():
     assert im1.ndim == 3
     assert im1.shape == im3.shape
     assert (im1 == im3).all()
-    
+
     # Ensure imread + imwrite works round trip - volume like
     filename3 = os.path.join(test_dir, 'test_tiff2.tiff')
     im1 = imageio.volread(filename1)
@@ -110,18 +110,22 @@ def test_tifffile_reading_writing():
 
     # Write metadata
     dt = datetime.datetime(2018, 8, 6, 15, 35, 5)
-    w = imageio.get_writer(filename1, software='testsoftware')
-    w.append_data(np.zeros((10, 10)), meta={'description': 'test desc',
-                                            'datetime': dt})
-    w.close()
-    r = imageio.get_reader(filename1)
-    md = r.get_meta_data()
-    assert 'datetime' in md
-    assert md['datetime'] == dt
-    assert 'software' in md
-    assert md['software'] == 'testsoftware'
-    assert 'description' in md
-    assert md['description'] == 'test desc'
+    with imageio.get_writer(filename1, software='testsoftware') as w:
+        w.append_data(np.zeros((10, 10)), meta={'description': 'test desc',
+                                                'datetime': dt})
+        w.append_data(np.zeros((10, 10)), meta={'description': 'another desc'})
+    with imageio.get_reader(filename1) as r:
+        for md in r.get_meta_data(), r.get_meta_data(0):
+            assert 'datetime' in md
+            assert md['datetime'] == dt
+            assert 'software' in md
+            assert md['software'] == 'testsoftware'
+            assert 'description' in md
+            assert md['description'] == 'test desc'
+
+        md = r.get_meta_data(1)
+        assert 'description' in md
+        assert md['description'] == 'another desc'
 
 
 run_tests_if_main()