Merge pull request #580 from kif/578_edf_fast

Fix `fast_read_data` when reading the last line

src/fabio/edfimage.py

@@ -49,7 +49,7 @@
 __contact__ = "[email protected]"
 __license__ = "MIT"
 __copyright__ = "ESRF"
-__date__ = "01/06/2022"
+__date__ = "20/08/2024"
 
 import os
 import re
@@ -1339,6 +1339,8 @@ def fast_read_roi(self, filename, coords=None):
         Method reading Region of Interest of another file  based on metadata available in current EdfImage.
         The aim is performances, ... but only supports uncompressed files.
 
+        :param filename: name of another file with the same structure.
+        :paran coords: 2 tuple of slices (RECOMMANDED) or a 4 tuple (NOT RECOMMANDED, cryptic fabian convention) 
         :return: ROI-data from another file using positions from current EdfImage
         :rtype: numpy 2darray
         """
@@ -1365,6 +1367,9 @@ def fast_read_roi(self, filename, coords=None):
         with open(filename, "rb")as f:
             f.seek(start)
             raw = f.read(size)
+        if len(raw)<size:
+            # Pad with zero until the right size
+            raw+=b"\x00"*(size-len(raw))
         try:
             data = numpy.frombuffer(raw, dtype=self.bytecode).copy()
             data.shape = -1, d1

src/fabio/fabioimage.py

@@ -42,7 +42,7 @@
 __contact__ = "[email protected]"
 __license__ = "MIT"
 __copyright__ = "ESRF"
-__date__ = "04/05/2021"
+__date__ = "20/08/2024"
 
 import os
 import logging
@@ -169,6 +169,7 @@ def make_slice(self, coords):
         the latter are immutable, meaning the roi can be cached
         """
         assert len(coords) == 4
+        coords = list(coords)
         if len(coords) == 4:
             # fabian edfimage preference
             if coords[0] > coords[2]:

src/fabio/test/codecs/test_edfimage.py

@@ -305,6 +305,29 @@ def test_fastread(self):
         obt = ref.fast_read_data(self.fastFilename)
         self.assertEqual(abs(obt - refdata).max(), 0, "testedffastread: Same data")
 
+    def test_578(self):
+        "Non regression for issue 578: EDFImage.fast_read_data: cannot read a line"
+
+        file_name = os.path.join(UtilsTest.tempdir, "test_578.edf")
+        # create some dummy data
+        edf_writer = fabio.edfimage.EdfImage(
+            data=numpy.arange(0, 99).reshape(9, 11),
+        )
+        edf_writer.write(file_name)
+
+        edf_reader = fabio.open(file_name)
+
+        # if I want to read it line by line
+        line_index_to_read = 4
+        line_data = edf_reader.fast_read_roi(
+            file_name,coords=(
+                slice(3, 9),
+                slice(line_index_to_read, line_index_to_read+1),
+            ),
+        )
+        self.assertTrue(numpy.allclose(edf_writer.data[3:9,line_index_to_read:line_index_to_read+1],
+                                       line_data))
+
 
 class TestEdfWrite(unittest.TestCase):
     """

src/fabio/test/codecs/test_edfimage_expg.py

@@ -433,7 +433,6 @@ def test_special(self):
 
     # test files 10 and 11 for testing with to be copied and added later
 
-
 def suite():
     loadTests = unittest.defaultTestLoader.loadTestsFromTestCase
     testsuite = unittest.TestSuite()