- added some type aliases

- an overridden compress_frame in a class subclassing IJTiffWrite can now write multiple frames

.github/workflows/pytest.yml

@@ -8,12 +8,12 @@ jobs:
     strategy:
       matrix:
         python-version: ["3.10", "3.12"]
-        os: [ubuntu-20.04, windows-2019, macOS-11]
+        os: [ubuntu-latest, windows-latest, macOS-latest]
 
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install

README.md

@@ -64,7 +64,6 @@ or
     tiffwrite('file.tif', image, 'TCXY')
 
 ## Write one frame at a time
-    from itertools import product
     from tiffwrite import IJTiffFile
     import numpy as np
 
@@ -76,7 +75,6 @@ or
                     tif.save(np.random.randint(0, 10, (32, 32)), c, z, t)
 
 ## Saving multiple tiffs simultaneously
-    from itertools import product
     from tiffwrite import IJTiffFile
     import numpy as np
     
@@ -89,7 +87,7 @@ or
                     tif_b.save(np.random.randint(0, 10, (32, 32)), c, z, t)
 
 ## Tricks & tips
-- The order of feeding frames to IJTiffFile is unimportant, IJTiffFile will order de ifd's such that the file will
+- The order of feeding frames to IJTiffFile is unimportant, IJTiffFile will order the ifd's such that the file will
 be opened as a correctly ordered hyperstack.
 - Using the colormap parameter you can make ImageJ open the file and apply the colormap. colormap='glasbey' is very
 useful.

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "tiffwrite"
-version = "2024.4.0"
+version = "2024.10.0"
 description = "Parallel tiff writer compatible with ImageJ."
 authors = ["Wim Pomp, Lenstra lab NKI <w.pomp@nki.nl>"]
 license = "GPL-3.0-or-later"
@@ -16,7 +16,7 @@ numpy = "*"
 tqdm = "*"
 colorcet = "*"
 matplotlib = "*"
-parfor = ">=2024.3.0"
+parfor = ">=2024.9.2"
 pytest = { version = "*", optional = true }
 mypy = { version = "*", optional = true }
 

tiffwrite/__init__.py

@@ -31,6 +31,11 @@ except Exception:  # noqa
     __version__ = "unknown"
 
 
+type Strip = tuple[list[int], list[int]]
+type CZT = tuple[int, int, int]
+type FrameInfo = tuple[IFD, Strip, CZT]
+
+
 def tiffwrite(file: str | Path, data: np.ndarray, axes: str = 'TZCXY', dtype: DTypeLike = None, bar: bool = False,
               *args: Any, **kwargs: Any) -> None:
     """ file:       string; filename of the new tiff file
@@ -389,8 +394,8 @@ class IJTiffFile:
         self.nframes = np.prod(self.shape[1:]) if self.colormap is None and self.colors is None else np.prod(self.shape)
         self.frame_extra_tags: dict[tuple[int, int, int], dict[int, Tag]] = {}
         self.fh = FileHandle(self.path)
+        self.pool = ParPool(self.compress_frame)  # type: ignore
         self.hashes = PoolSingleton().manager.dict()
-        self.pool = ParPool(self.compress_frame)
         self.main_process = True
 
         with self.fh.lock() as fh:  # noqa
@@ -477,13 +482,14 @@ class IJTiffFile:
         if self.main_process:
             ifds, strips = {}, {}
             for n in list(self.pool.tasks):
-                framenr, channel = self.get_frame_number(n)
+                for ifd, strip, delta in self.pool[n]:
-                ifds[framenr], strips[(framenr, channel)] = self.pool[n]
+                    framenr, channel = self.get_frame_number(tuple(i + j for i, j in zip(n, delta)))  # type: ignore
+                    ifds[framenr], strips[(framenr, channel)] = ifd, strip
 
             self.pool.close()
             with self.fh.lock() as fh:  # noqa
                 for n, tags in self.frame_extra_tags.items():
-                    framenr, channel = self.get_frame_number(n)
+                    framenr, _ = self.get_frame_number(n)
                     ifds[framenr].update(tags)
                 if 0 in ifds and self.colormap is not None:
                     ifds[0][320] = Tag('SHORT', self.colormap_bytes)
@@ -547,14 +553,17 @@ class IJTiffFile:
             fh.write(bvalue)
             return offset
 
-    def compress_frame(self, frame: np.ndarray) -> tuple[IFD, tuple[list[int], list[int]]]:
+    def compress_frame(self, frame: np.ndarray) -> Sequence[FrameInfo]:
-        """ This is run in a different process"""
+        """ This is run in a different process. Turns an image into bytes, writes them and returns the ifd, strip info
+             and czt delta. When subclassing IJTiffWrite this can be overridden to write one or more (using czt delta)
+             frames.
+        """
         stripbytecounts, ifd, chunks = self.get_chunks(self.ij_tiff_frame(frame))
         stripbyteoffsets = []
         with self.fh.lock() as fh:  # noqa
             for chunk in chunks:
                 stripbyteoffsets.append(self.write(fh, chunk))
-        return ifd, (stripbyteoffsets, stripbytecounts)
+        return (ifd, (stripbyteoffsets, stripbytecounts), (0, 0, 0)),
 
     @staticmethod
     def get_chunks(frame: bytes) -> tuple[list[int], IFD, list[bytes]]: