readme update with examples

README.md

@@ -16,6 +16,71 @@ pip install pyometiff
 `pyometiff` exposes two main classes: `OMETIFFReader` and `OMETIFFWriter` which
 you can use to read and write OME TIFF files.
 
+
+To open a OME-TIFF image you can create an `OMETIFFReader`object and call its `.read()` method.
+
+
+```python
+import pathlib
+from pyometiff import OMETIFFReader
+img_fpath = pathlib.Path("/path/to/img.ome.tiff")
+
+reader = OMETIFFReader(fpath=img_fpath)
+
+img_array, metadata, xml_metadata = reader.read()
+```
+
+similarly, to write an OME-TIFF file, we use the `OMETIFFWriter` class and its `.write()` method as in the example.
+
+```python
+import pathlib
+from pyometiff import OMETIFFWriter
+output_fpath = pathlib.Path.cwd().joinpath("test_out.ome.tiff")
+
+# a template metadata dict is available at OMETIFFReader._get_metadata_template()
+
+metadata_dict = {
+    "PhysicalSizeX" : "0.88",
+    "PhysicalSizeXUnit" : "µm",
+    "PhysicalSizeY" : "0.88",
+    "PhysicalSizeYUnit" : "µm",
+    "PhysicalSizeZ" : "3.3",
+    "PhysicalSizeZUnit" : "µm",
+    "Channels" : {
+        "405" : {
+            "Name" : "405nm",
+            "SamplesPerPixel": 1,
+            "ExcitationWavelength": 405.,
+            "ExcitationWavelengthUnit": "nm"
+        },
+        "488" : {
+            "Name" : "488nm",
+            "SamplesPerPixel": 1,
+            "ExcitationWavelength": 488.,
+            "ExcitationWavelengthUnit": "nm"
+        },
+        "638" : {
+            "Name" : "638nm",
+            "SamplesPerPixel": 1,
+            "ExcitationWavelength": 638.,
+            "ExcitationWavelengthUnit": "nm"
+        },
+    }
+
+# our data in npy format
+npy_array_data = np.array(shape=(2, 10, 3, 256, 256))
+# a string describing the dimension ordering
+dimension_order = "ZTCYX"
+
+writer = OMETIFFWriter(
+    fpath=output_fpath,
+    dimension_order=dimension_order,
+    array=npy_array_data,
+    metadata=metadata)
+
+writer.write()
+```
+
 ## Contacts
 
 **Author:**
@@ -24,4 +89,4 @@ Filippo Maria Castelli
 castelli@lens.unifi.it  
 LENS, European Laboratory for Non-linear Spectroscopy  
 Via Nello Carrara 1  
-50019 Sesto Fiorentino (FI), Italy
+50019 Sesto Fiorentino (FI), Italy