Merge 4de6d99 into 7b55a25

.travis.yml

@@ -47,6 +47,7 @@ jobs:
 install:
   - pip3 install -e .[testing]
   - pip3 install flake8
+  - pip3 install pooch
 
 services:
   - xvfb

src/histolab/filters/util.py

@@ -1,5 +1,4 @@
 import numpy as np
-from PIL import Image
 
 
 def mask_percent(mask: np.ndarray) -> float:
@@ -18,19 +17,3 @@ def mask_percent(mask: np.ndarray) -> float:
 
     mask_percentage = 100 - np.count_nonzero(mask) / mask.size * 100
     return mask_percentage
-
-
-def tissue_percent(img: Image.Image) -> float:
-    """Compute percentage of tissue in an image.
-
-    Parameters
-    ----------
-    img : Image.Image
-        Input image
-
-    Returns
-    -------
-    float
-        Percentage of image that is not masked
-    """
-    return 100 - mask_percent(img)

src/histolab/tiler.py

@@ -192,16 +192,13 @@ def _grid_coordinates_from_bbox_coordinates(
         n_tiles_row = self._n_tiles_row(bbox_coordinates)
         n_tiles_column = self._n_tiles_column(bbox_coordinates)
 
-        x_ul_lvl_offset = bbox_coordinates.x_ul
-        y_ul_lvl_offset = bbox_coordinates.y_ul
-
         for i in range(n_tiles_row):
             for j in range(n_tiles_column):
-                x_ul_lvl = x_ul_lvl_offset + tile_w_lvl * j - self.pixel_overlap
-                y_ul_lvl = y_ul_lvl_offset + tile_h_lvl * i - self.pixel_overlap
+                x_ul_lvl = bbox_coordinates.x_ul + tile_w_lvl * j - self.pixel_overlap
+                y_ul_lvl = bbox_coordinates.y_ul + tile_h_lvl * i - self.pixel_overlap
 
-                x_ul_lvl = np.clip(x_ul_lvl, x_ul_lvl_offset, None)
-                y_ul_lvl = np.clip(y_ul_lvl, y_ul_lvl_offset, None)
+                x_ul_lvl = np.clip(x_ul_lvl, bbox_coordinates.x_ul, None)
+                y_ul_lvl = np.clip(y_ul_lvl, bbox_coordinates.y_ul, None)
 
                 x_br_lvl = x_ul_lvl + tile_w_lvl
                 y_br_lvl = y_ul_lvl + tile_h_lvl
@@ -232,7 +229,8 @@ def _grid_coordinates_generator(self, slide: Slide) -> CoordinatePair:
         box_mask = self.box_mask(slide)
 
         regions = regions_from_binary_mask(box_mask)
-        for region in regions:  # at the moment there is only one region
+        # ----at the moment there is only one region----
+        for region in regions:
             bbox_coordinates_thumb = region_coordinates(region)
             bbox_coordinates = scale_coordinates(
                 bbox_coordinates_thumb,
@@ -431,12 +429,12 @@ def _random_tile_coordinates(self, slide: Slide) -> CoordinatePair:
         tile_w_thumb = (
             tile_w_lvl * box_mask.shape[1] / slide.level_dimensions(self.level)[0]
         )
-        tile_h_thumn = (
+        tile_h_thumb = (
             tile_h_lvl * box_mask.shape[0] / slide.level_dimensions(self.level)[1]
         )
 
         x_br_lvl = x_ul_lvl + tile_w_thumb
-        y_br_lvl = y_ul_lvl + tile_h_thumn
+        y_br_lvl = y_ul_lvl + tile_h_thumb
 
         tile_wsi_coords = scale_coordinates(
             reference_coords=CoordinatePair(x_ul_lvl, y_ul_lvl, x_br_lvl, y_br_lvl),

tests/unit/data/test_data.py

@@ -1,15 +1,26 @@
 # coding: utf-8
 
+import copy
 
 import os
+import sys
+from unittest.mock import patch
+from importlib import reload
 
 import pytest
 
 import openslide
-from histolab.data import _has_hash, _load_svs, cmu_small_region, data_dir
+from histolab.data import (
+    _fetch,
+    _has_hash,
+    _load_svs,
+    cmu_small_region,
+    data_dir,
+    registry,
+)
 
 from ...fixtures import SVS
-from ...unitutil import function_mock
+from ...unitutil import function_mock, ANY
 
 
 def test_data_dir():
@@ -47,3 +58,63 @@ def it_knows_its_hash(request, file, hash, expected_value):
     has_hash = _has_hash(file, hash)
 
     assert has_hash is expected_value
+
+
+@patch.dict(registry, {"data/cmu_small_region.svs": "bar"}, clear=True)
+@patch("histolab.data.image_fetcher", None)
+def it_raises_error_on_fetch_if_image_fetcher_is_None():
+    with pytest.raises(ModuleNotFoundError) as err:
+        _fetch("data/cmu_small_region.svs")
+
+    assert (
+        str(err.value)
+        == "The requested file is part of the histolab distribution, but requires the "
+        "installation of an optional dependency, pooch. To install pooch, use your "
+        "preferred python package manager. Follow installation instruction found at "
+        "https://www.fatiando.org/pooch/latest/install.html"
+    )
+
+
+def test_pooch_missing(monkeypatch):
+    from histolab import data
+
+    fakesysmodules = copy.copy(sys.modules)
+    fakesysmodules["pooch.utils"] = None
+    monkeypatch.delitem(sys.modules, "pooch.utils")
+    monkeypatch.setattr("sys.modules", fakesysmodules)
+    file = SVS.CMU_1_SMALL_REGION
+    reload(data)
+
+    data.file_hash(file)
+
+    assert data.file_hash.__module__ == "histolab.data"
+
+
+def test_file_hash_with_wrong_algorithm(monkeypatch):
+    from histolab import data
+
+    fakesysmodules = copy.copy(sys.modules)
+    fakesysmodules["pooch.utils"] = None
+    monkeypatch.delitem(sys.modules, "pooch.utils")
+    monkeypatch.setattr("sys.modules", fakesysmodules)
+    file = SVS.CMU_1_SMALL_REGION
+    reload(data)
+
+    with pytest.raises(ValueError) as err:
+        data.file_hash(file, "fakesha")
+    assert str(err.value) == "Algorithm 'fakesha' not available in hashlib"
+    assert data.file_hash.__module__ == "histolab.data"
+
+
+def test_create_image_fetcher_without_pooch(monkeypatch):
+    from histolab import data
+
+    fakesysmodules = copy.copy(sys.modules)
+    fakesysmodules["pooch"] = None
+    monkeypatch.delitem(sys.modules, "pooch")
+    monkeypatch.setattr("sys.modules", fakesysmodules)
+    reload(data)
+
+    create_image_fetcher = data._create_image_fetcher()
+
+    assert create_image_fetcher == (None, ANY)