Update dimensions and add test for 3D image

tests/test_write.py

@@ -52,8 +52,8 @@ def tearDownModule():
 
 class TestZarrWrite(unittest.TestCase):
 
-    def test_write_zarr_2d(self):
-        """test_write_zarr_2d - Write zarr using TSWriter"""
+    def test_write_zarr_5d(self):
+        """test_write_zarr_5d - Write zarr using TSWriter"""
 
         br = TSReader(
             str(TEST_DIR.joinpath("5025551.zarr/0")),
@@ -84,7 +84,7 @@ def test_write_zarr_2d(self):
             channels = Seq(0, 0, 1)
             tsteps = Seq(0, 0, 1)
 
-            bw = TSWriter(test_file_path, tmp.shape, tmp.shape, str(tmp.dtype), "ZCTYX")
+            bw = TSWriter(test_file_path, tmp.shape, tmp.shape, str(tmp.dtype), "TCZYX")
             bw.write_image_data(tmp, rows, cols, layers, channels, tsteps)
             bw.close()
 
@@ -100,8 +100,56 @@ def test_write_zarr_2d(self):
             assert tmp.sum() == 183750394
             assert tmp.shape == (1, 1, 1, 2700, 2702)
 
-    def test_write_zarr_chunk_2d(self):
-        """test_write_zarr_2d - Write zarr using TsWriter"""
+    def test_write_zarr_3d(self):
+        """test_write_zarr_5d - Write zarr using TSWriter"""
+
+        br = TSReader(
+            str(TEST_DIR.joinpath("5025551.zarr/0")),
+            FileType.OmeZarr,
+            "",
+        )
+
+        assert br._X == 2702
+        assert br._Y == 2700
+        assert br._Z == 1
+        assert br._C == 27
+        assert br._T == 1
+
+        rows = Seq(0, br._Y - 1, 1)
+        cols = Seq(0, br._X - 1, 1)
+        layers = Seq(0, 0, 1)
+        channels = Seq(0, 0, 1)
+        tsteps = Seq(0, 0, 1)
+        tmp = br.data(rows, cols, layers, channels, tsteps)
+
+        with tempfile.TemporaryDirectory() as dir:
+            # Use the temporary directory
+            test_file_path = os.path.join(dir, 'out/test.ome.zarr')
+
+            rows = Seq(0, br._Y - 1, 1)
+            cols = Seq(0, br._X - 1, 1)
+            layers = Seq(0, 0, 1)
+
+            tmp =  np.expand_dims(np.squeeze(tmp), axis=0) # modify image to be 3D instead of 5D
+
+            bw = TSWriter(test_file_path, tmp.shape, tmp.shape, str(tmp.dtype), "ZYX")
+            bw.write_image_data(tmp, rows, cols, layers)
+            bw.close()
+
+            br = TSReader(
+                str(test_file_path),
+                FileType.OmeZarr,
+                "",
+            )
+
+            tmp = br.data(rows, cols, layers)
+
+            assert tmp.dtype == np.uint8
+            assert tmp.sum() == 183750394
+            assert tmp.shape == (1, 1, 1, 2700, 2702)
+
+    def test_write_zarr_chunk_5d(self):
+        """test_write_zarr_5d - Write zarr using TsWriter"""
 
         br = TSReader(
             str(TEST_DIR.joinpath("5025551.zarr/0")),
@@ -130,7 +178,7 @@ def test_write_zarr_chunk_2d(self):
             chunk_shape = [1, 1, 1, 1350, 1351]
             #chunk_shape = tmp.shape
             print("dtype: " + str(tmp.dtype))
-            bw = TSWriter(test_file_path, tmp.shape, chunk_shape, str(tmp.dtype), "ZCTYX")
+            bw = TSWriter(test_file_path, tmp.shape, chunk_shape, str(tmp.dtype), "TCZYX")
 
             rows = Seq(0, br._Y//2, 1)
             cols = Seq(0, br._X - 1, 1)
@@ -171,7 +219,7 @@ def test_write_zarr_chunk_2d(self):
             assert tmp.sum() == 183750394
 
     def test_write_zarr_3d(self):
-        """test_write_zarr_2d - Write zarr using TsWriter"""
+        """test_write_zarr_5d - Write zarr using TsWriter"""
 
         br = TSReader(
             str(TEST_DIR.joinpath("5025551.zarr/0")),
@@ -204,7 +252,7 @@ def test_write_zarr_3d(self):
             channels = Seq(0, 2, 1)
             tsteps = Seq(0, 0, 1)
 
-            bw = TSWriter(test_file_path, tmp.shape, tmp.shape, str(tmp.dtype), "ZCTYX")
+            bw = TSWriter(test_file_path, tmp.shape, tmp.shape, str(tmp.dtype), "TCZYX")
             bw.write_image_data(tmp, rows, cols, layers, channels, tsteps)
             bw.close()
 
@@ -222,7 +270,7 @@ def test_write_zarr_3d(self):
 
 
     def test_write_zarr_chunk_3d(self):
-        """test_write_zarr_2d - Write zarr using TsWriter"""
+        """test_write_zarr_5d - Write zarr using TsWriter"""
 
         br = TSReader(
             str(TEST_DIR.joinpath("5025551.zarr/0")),
@@ -251,7 +299,7 @@ def test_write_zarr_chunk_3d(self):
 
             chunk_size = (1,1,1,2700,2702)
 
-            bw = TSWriter(test_file_path, tmp.shape, chunk_size, str(tmp.dtype), "ZCTYX")
+            bw = TSWriter(test_file_path, tmp.shape, chunk_size, str(tmp.dtype), "TCZYX")
 
             # write first channel
             rows = Seq(0, br._Y - 1, 1)