Merge pull request #19 from DaniGodin/master

Update 1.7.2

apeer_ometiff_library/io.py

@@ -1,6 +1,6 @@
 import tifffile
 import numpy as np
-from apeer_ometiff_library import omexmlClass
+from apeer_ometiff_library import omexmlClass 
 
 
 def read_ometiff(input_path):
@@ -27,6 +27,28 @@ def read_ometiff(input_path):
     if size_t == 1:
         array = np.expand_dims(array, axis=-5)
 
+    # Makes sure to return the array in (T, Z, C, X, Y) order
+
+    dim_format = pixels.DimensionOrder
+
+    if dim_format == "XYCZT":
+        pass
+    elif dim_format == "XYZCT":
+        array = np.moveaxis(array, 1, 2)
+    elif dim_format == "XYCTZ":
+        array = np.moveaxis(array, 0, 1)
+    elif dim_format == "XYZTC":
+        array = np.moveaxis(array, 0, 2)
+    elif dim_format == "XYTZC":
+        array = np.moveaxis(array, 0, 2)
+        array = np.moveaxis(array, 0, 1)
+    elif dim_format == "XYTCZ":
+        array = np.moveaxis(array, 1, 2)
+        array = np.moveaxis(array, 0, 1)
+    else:
+        print(array.shape)
+        raise Exception("Unknow dimension format") 
+
     return array, omexml_string
 
 def update_xml(omexml, Image_ID=None, Image_Name=None, Image_AcquisitionDate=None,

requirements.txt

@@ -1,3 +1,2 @@
 numpy==1.16.5
-xmltodict==0.12.0
 tifffile==2020.2.16

setup.py

@@ -2,12 +2,12 @@
 from setuptools import setup
 
 setup(name='apeer-ometiff-library',
-      version='1.7.1',
+      version='1.7.2',
       description='Library to read and write ometiff images',
       url='https://github.com/apeer-micro/apeer-ometiff-library',
       author='apeer-micro',
       packages=setuptools.find_packages(),
-      install_requires=['numpy', 'scikit-image'],
+      install_requires=['numpy','tifffile'],
       license='MIT',
       classifiers=[
           "Programming Language :: Python :: 3",