High-level dataset library (#165)

* only log downsampling for each MB ob precessed data

* log every gigabyte instead of every megabyte

* implement PR feedback

* WIP: implement high level dataset api

* WIP: implement TiffMag

* implement test for dataset api

* refactor high level dataset api

* add test data for WKDataset

* improve high level dataset api and add more tests

* use seed in tests to achieve deterministic behaviour

* implement a test for writing out of bounds with a wk_slice

* improve quality of dataset tests

* make naming schema of test files consistent

* implement PR feedback

* rename tiffs in testdata

* Improve error message and reformat code

* add type annotation

* rename Slice to View

* remove comments and reformat code

* add scikit-image (which is needed for skimage) as dependency

* update version of scikit-image

* fix relative paths in tests

* reformat code

pyproject.toml

@@ -17,6 +17,7 @@ cluster_tools = "1.46"
 natsort = "^6.2.0"
 psutil = "^5.6.7"
 nibabel = "^2.5.1"
+scikit-image = "^0.16.2"
 
 [tool.poetry.dev-dependencies]
 pylint = "2.3.1"

testdata/simple_tiff_dataset/datasource-properties.json

@@ -0,0 +1,40 @@
+{
+    "id": {
+        "name": "tiff_dataset_1",
+        "team": ""
+    },
+    "scale": [
+        1
+    ],
+    "dataLayers": [
+        {
+            "name": "color",
+            "category": "color",
+            "elementClass": "uint8",
+            "num_channels": 1,
+            "boundingBox": {
+                "topLeft": [
+                    0,
+                    0,
+                    0
+                ],
+                "width": 265,
+                "height": 265,
+                "depth": 10
+            },
+            "wkwResolutions": [
+                {
+                    "resolution": [
+                        1,
+                        1,
+                        1
+                    ]
+                }
+            ]
+        }
+    ],
+    "grid_shape": [
+        0,
+        0
+    ]
+}

testdata/simple_wk_dataset/datasource-properties.json

@@ -0,0 +1,38 @@
+{
+    "id": {
+        "name": "simple_wk_dataset",
+        "team": ""
+    },
+    "scale": [
+        1
+    ],
+    "dataLayers": [
+        {
+            "dataFormat": "wkw",
+            "name": "color",
+            "category": "color",
+            "elementClass": "uint8",
+            "num_channels": 3,
+            "boundingBox": {
+                "topLeft": [
+                    0,
+                    0,
+                    0
+                ],
+                "width": 24,
+                "height": 24,
+                "depth": 24
+            },
+            "wkwResolutions": [
+                {
+                    "resolution": [
+                        1,
+                        1,
+                        1
+                    ],
+                    "cube_length": 32
+                }
+            ]
+        }
+    ]
+}