enh: support .ome.tif files (no stacks supported yet)

CHANGELOG

@@ -1,3 +1,5 @@
+0.4.7
+ - enh: support .ome.tif files (no stacks supported yet)
 0.4.6
  - maintenance release
 0.4.5

impose/formats/__init__.py

@@ -15,6 +15,7 @@
 from .fmt_fl_zeiss import load_czi
 from .fmt_bm_bmlab import load_h5
 from .fmt_bf_generic import load_img
+from .fmt_fl_ometif import load_ometif
 
 
 def load(path):
@@ -72,7 +73,8 @@ def get_signature(path):
 
 suffix_dict = {
     ".czi": load_czi,
-    ".png": load_img,
     ".h5": load_h5,
     ".jpg": load_img,
+    ".png": load_img,
+    ".tif": load_ometif,
 }

impose/formats/fmt_fl_ometif.py

@@ -0,0 +1,46 @@
+from collections import OrderedDict
+from xml.dom.minidom import parseString
+
+import numpy as np
+import tifffile
+
+
+def load_ometif(path):
+    """Load .ome.tif files
+
+    Please see :func:`impose.formats.load` for more information.
+    """
+    with tifffile.TiffFile(path) as tif:
+        if not tif.is_ome:
+            raise NotImplementedError(
+                f"Could not load ome_metadata from file {path}. Please ask "
+                f"for implementing support for your file format.")
+        ome_meta = parseString(tif.ome_metadata)
+        data = tif.asarray()
+
+    channels = OrderedDict()
+    name = ome_meta.getElementsByTagName("Image")[0].attributes["Name"].value
+    channels[name] = data
+
+    # Initial Metadata
+    px = ome_meta.getElementsByTagName("Pixels")[0]
+    xs = float(px.attributes["PhysicalSizeX"].value)
+    ys = float(px.attributes["PhysicalSizeY"].value)
+
+    # sanity checks
+    assert px.attributes["PhysicalSizeXUnit"].value == "µm"
+    assert px.attributes["PhysicalSizeYUnit"].value == "µm"
+
+    # Channel names
+    data_uuid = ome_meta.getElementsByTagName(
+        "UUID")[0].childNodes[0].data.split(":")[-1]
+
+    meta = {
+        "pixel size x": xs,
+        "pixel size y": ys,
+        "pixel size z": np.nan,
+        "shape": data.shape,
+        "signature": data_uuid,
+    }
+
+    return channels, meta

tests/test_fmt_czi.py

@@ -34,11 +34,3 @@ def test_load_czi():
     assert data["mCher"][10, 10, 0] == 1
     assert data["mCher"][205, 227, 0] == 255
     assert data["mCher"][113, 206, 0] == 123
-
-
-if __name__ == "__main__":
-    # Run all tests
-    loc = locals()
-    for key in list(loc.keys()):
-        if key.startswith("test_") and hasattr(loc[key], "__call__"):
-            loc[key]()

tests/test_fmt_fl_ometif.py

@@ -0,0 +1,34 @@
+import pathlib
+import tempfile
+import zipfile
+
+import numpy as np
+
+from impose import formats
+
+
+data_path = pathlib.Path(__file__).parent / "data"
+
+
+def get_ometif():
+    td = pathlib.Path(tempfile.mkdtemp(prefix="impose_ometif_"))
+    with zipfile.ZipFile(data_path / "fmt_fl_ometif.zip") as arc:
+        arc.extractall(path=td)
+    return list(td.glob("*.ome.tif"))[0]
+
+
+def test_load_ometif():
+    path = get_ometif()
+    data, meta = formats.load(path)
+
+    # check metadata
+    assert np.allclose(meta["pixel size x"], 0.2136)
+    assert np.allclose(meta["pixel size y"], 0.2136)
+    assert np.isnan(meta["pixel size z"])
+    assert meta["shape"] == (512, 512)
+    assert meta["signature"] == "a704111f-8e8d-40b0-9f55-4d649ef49167"
+    chan = "Brillouin-2_MMStack_Default"
+    assert data[chan].shape == (512, 512)
+    assert data[chan][10, 10] == 246
+    assert data[chan][205, 227] == 217
+    assert data[chan][113, 206] == 280