Add Subimage Reading and unit tests

Author: XericZephyr

bioformats/formatreader.py

@@ -725,9 +725,9 @@ def init_reader(self):
 
 
     def read(self, c = None, z = 0, t = 0, series = None, index = None,
-             rescale = True, wants_max_intensity = False, channel_names = None):
+             rescale = True, wants_max_intensity = False, channel_names = None, XYWH=None):
         '''Read a single plane from the image reader file.
-        
+        :param XYWH: a (x, y, w, h) tuple
         :param c: read from this channel. `None` = read color image if multichannel
             or interleaved RGB.
         :param z: z-stack index
@@ -740,14 +740,20 @@ def read(self, c = None, z = 0, t = 0, series = None, index = None,
                   return a tuple of image and max intensity
         :param channel_names: provide the channel names for the OME metadata
         '''
+        if XYWH is not None:
+            assert isinstance(XYWH, tuple) and len(XYWH) == 4, "Invalid XYWH tuple"
+            openBytes_func = lambda x: self.rdr.openBytesXYWH(x, XYWH[0], XYWH[1], XYWH[2], XYWH[3])
+            width, height = XYWH[2], XYWH[3]
+        else:
+            openBytes_func = self.rdr.openBytes
+            width, height = self.rdr.getSizeX(), self.rdr.getSizeY()
         FormatTools = make_format_tools_class()
         ChannelSeparator = make_reader_wrapper_class(
             "loci/formats/ChannelSeparator")
         env = jutil.get_env()
         if series is not None:
             self.rdr.setSeries(series)
-        width = self.rdr.getSizeX()
-        height = self.rdr.getSizeY()
+
         pixel_type = self.rdr.getPixelType()
         little_endian = self.rdr.isLittleEndian()
         if pixel_type == FormatTools.INT8:
@@ -781,7 +787,7 @@ def read(self, c = None, z = 0, t = 0, series = None, index = None,
             except:
                 logger.warning("WARNING: failed to get MaxSampleValue for image. Intensities may be improperly scaled.")
         if index is not None:
-            image = np.frombuffer(self.rdr.openBytes(index), dtype)
+            image = np.frombuffer(openBytes_func(index), dtype)
             if len(image) / height / width in (3,4):
                 n_channels = int(len(image) / height / width)
                 if self.rdr.isInterleaved():
@@ -793,13 +799,13 @@ def read(self, c = None, z = 0, t = 0, series = None, index = None,
                 image.shape = (height, width)
         elif self.rdr.isRGB() and self.rdr.isInterleaved():
             index = self.rdr.getIndex(z,0,t)
-            image = np.frombuffer(self.rdr.openBytes(index), dtype)
+            image = np.frombuffer(openBytes_func(index), dtype)
             image.shape = (height, width, self.rdr.getSizeC())
             if image.shape[2] > 3:
                 image = image[:, :, :3]
         elif c is not None and self.rdr.getRGBChannelCount() == 1:
             index = self.rdr.getIndex(z,c,t)
-            image = np.frombuffer(self.rdr.openBytes(index), dtype)
+            image = np.frombuffer(openBytes_func(index), dtype)
             image.shape = (height, width)
         elif self.rdr.getRGBChannelCount() > 1:
             n_planes = self.rdr.getRGBChannelCount()
@@ -818,7 +824,7 @@ def read(self, c = None, z = 0, t = 0, series = None, index = None,
             del rdr
         elif self.rdr.getSizeC() > 1:
             images = [
-                np.frombuffer(self.rdr.openBytes(self.rdr.getIndex(z,i,t)), dtype)
+                np.frombuffer(openBytes_func(self.rdr.getIndex(z,i,t)), dtype)
                       for i in range(self.rdr.getSizeC())]   
             image = np.dstack(images)
             image.shape = (height, width, self.rdr.getSizeC())
@@ -837,7 +843,7 @@ def read(self, c = None, z = 0, t = 0, series = None, index = None,
             # a monochrome RGB image
             #
             index = self.rdr.getIndex(z,0,t)
-            image = np.frombuffer(self.rdr.openBytes(index),dtype)
+            image = np.frombuffer(openBytes_func(index),dtype)
             if pixel_type in (FormatTools.INT16, FormatTools.UINT16):
                 lut = self.rdr.get16BitLookupTable()
                 if lut is not None:
@@ -858,7 +864,7 @@ def read(self, c = None, z = 0, t = 0, series = None, index = None,
                 image = lut[image, :]
         else:
             index = self.rdr.getIndex(z,0,t)
-            image = np.frombuffer(self.rdr.openBytes(index),dtype)
+            image = np.frombuffer(openBytes_func(index),dtype)
             image.shape = (height,width)
 
         if rescale:

bioformats/tests/test_formatreader.py

@@ -121,6 +121,39 @@ def test_03_02_load_using_bioformats(self):
              [5, 2, 3, 3, 2, 2, 2, 3, 2, 2]], dtype=np.uint8)
         self.assertTrue(np.all(expected_0_10_0_10 == data[:10,:10]))
         self.assertTrue(np.all(expected_n10_n10 == data[-10:,-10:]))
+
+    def test_03_03_read_subimage_tif(self):
+        path = os.path.join(os.path.dirname(__file__), 'Channel1-01-A-01.tif')
+        with bioformats.ImageReader(path) as f:
+            data_0_10_0_10 = f.read(XYWH=(0, 0, 10, 10), rescale=False)
+
+        #
+        # Data as read by cellprofiler.modules.loadimages.load_using_PIL
+        #
+        expected_0_10_0_10 = np.array(
+            [[ 0,  7,  7,  6,  5,  8,  4,  2,  1,  2],
+             [ 0,  8,  8,  7,  6, 10,  4,  2,  2,  2],
+             [ 0,  9,  9,  7,  8,  8,  2,  1,  3,  2],
+             [ 0, 10,  9,  8, 10,  6,  2,  2,  3,  2],
+             [ 0, 10, 10, 10,  9,  4,  2,  2,  2,  2],
+             [ 0,  9,  9, 10,  8,  3,  2,  4,  2,  2],
+             [ 0,  9,  9, 10,  8,  2,  2,  4,  3,  2],
+             [ 0,  9,  8,  9,  7,  4,  2,  2,  2,  2],
+             [ 0, 10, 11,  9,  9,  4,  2,  2,  2,  2],
+             [ 0, 12, 13, 12,  9,  4,  2,  2,  2,  2]], dtype=np.uint8)
+        expected_n10_n10 = np.array(
+            [[2, 1, 1, 1, 2, 2, 1, 2, 1, 2],
+             [1, 2, 2, 2, 2, 1, 1, 1, 2, 1],
+             [1, 1, 1, 2, 1, 2, 2, 2, 2, 1],
+             [2, 2, 2, 2, 3, 2, 2, 2, 2, 1],
+             [1, 2, 2, 1, 1, 1, 1, 1, 2, 2],
+             [2, 1, 2, 2, 2, 1, 1, 2, 2, 2],
+             [2, 2, 3, 2, 2, 1, 2, 2, 2, 1],
+             [3, 3, 1, 2, 2, 2, 2, 3, 2, 2],
+             [3, 2, 2, 2, 2, 2, 2, 2, 3, 3],
+             [5, 2, 3, 3, 2, 2, 2, 3, 2, 2]], dtype=np.uint8)
+        self.assertTrue(np.all(expected_0_10_0_10 == data_0_10_0_10))
+        # self.assertTrue(np.all(expected_n10_n10 == data[-10:,-10:]))
 
     # def test_03_03_load_using_bioformats_url(self):
     #     data = F.load_using_bioformats_url(