Merge pull request #18 from sebi06/work_in_progress

Work in progress

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = czitools
-version = 0.1.2
+version = 0.1.3
 author = Sebastian Rhode
 author_email = [email protected]
 url = https://github.com/sebi06/czitools

src/czitools/__init__.py

@@ -1,3 +1,3 @@
 # __init__.py
 # version of the czitools package
-__version__ = "0.1.2"
+__version__ = "0.1.3"

src/czitools/_tests/test_md_general.py

@@ -147,3 +147,27 @@ def test_get_image_dimensions():
     for d, v in zip(dimensions, results):
         print((d, v))
         assert (dim_dict[d] == v)
+
+
+def test_scaling():
+
+    # get the CZI filepath
+    filepath = os.path.join(basedir, r"data/DAPI_GFP.czi")
+    md = czimd.CziMetadata(filepath)
+
+    assert(md.scale.X == 1.0)
+    assert(md.scale.Y == 1.0)
+    assert(md.scale.Z == 1.0)
+    assert(md.scale.ratio == {'xy': 1.0, 'zx': 1.0})
+
+    scaling = czimd.CziScaling(filepath, dim2none=True)
+    assert(scaling.X is None)
+    assert(scaling.Y is None)
+    assert(scaling.Z is None)
+    assert(scaling.ratio == {'xy': None, 'zx': None})
+
+    scaling = czimd.CziScaling(filepath, dim2none=False)
+    assert(scaling.X == 1.0)
+    assert(scaling.Y == 1.0)
+    assert(scaling.Z == 1.0)
+    assert(scaling.ratio == {'xy': 1.0, 'zx': 1.0})

src/czitools/pylibczirw_metadata.py

@@ -562,7 +562,7 @@ def __init__(self, filename: str) -> None:
 
 
 class CziScaling:
-    def __init__(self, filename: str, dim2none: bool = True) -> None:
+    def __init__(self, filename: str, dim2none: bool = False) -> None:
 
         # get metadata dictionary using pylibCZIrw
         self.scalefactorXY = None
@@ -622,8 +622,11 @@ def get_scale_ratio(scalex: float = 1.0,
                         scaley: float = 1.0,
                         scalez: float = 1.0) -> Dict:
 
-        # set default scale factor to 1.0
-        scale_ratio = {"xy": np.round(scalex / scaley, 3), "zx": np.round(scalez / scalex, 3)}
+        if scalex is None or scaley is None or scalez is None:
+            scale_ratio = {"xy": None, "zx": None}
+        else:
+            # set default scale factor to 1.0
+            scale_ratio = {"xy": np.round(scalex / scaley, 3), "zx": np.round(scalez / scalex, 3)}
 
         # get the factor between XY scaling
         # get the scale factor between XZ scaling