[edfscan] fix get_refs_urls when contains ref* and refHST*

- insure that no keys are overwrite when returns the refs_urls
- close partially the nxtomomill issue nxtomomill#1

tomoscan/esrf/edfscan.py

@@ -469,6 +469,16 @@ class EDFTomoScan(TomoScanBase):
             _logger.error(scan_path + ' is not a directory. Cannot extract '
                                       'RefHST files')
             return res
+        def get_next_free_index(key, keys):
+            """return next free key from keys by converting it to a string
+            with `key_value (n)` after it
+            """
+            new_key = key
+            index = 2
+            while new_key in keys:
+                new_key = '%s (%s)' % (key, index)
+                index += 1
+            return new_key
 
         for file_ in os.listdir(scan_path):
             if file_.startswith(prefix) and file_.endswith(file_ext):
@@ -476,7 +486,12 @@ class EDFTomoScan(TomoScanBase):
                                                               basename=os.path.basename(scan_path))
                 file_fp = os.path.join(scan_path, file_)
                 urls = extract_urls_from_edf(start_index=index, file_=file_fp)
-                res.update(urls)
+                for key in urls:
+                    if key in res:
+                        key_ = get_next_free_index(key, res.keys())
+                    else:
+                        key_ = key
+                    res[key_] = urls[key]
         return res
 
     @staticmethod

tomoscan/esrf/test/test_edfscan.py

@@ -159,13 +159,21 @@ class TestOriDarksFlats(unittest.TestCase):
         self.det_height = 10
 
         self.folder = tempfile.mkdtemp()
-        # create 2 series of ref with 20 frames each
+        # create 2 series of ref with 20 frames each and 2 refHST file
         for ref_index in ('0000', '1500'):
+            # ref files
             for ref_sub_index in range(20):
                 file_desc = fabio.edfimage.EdfImage(data=numpy.random.random((self.det_height,self.det_width)))
                 file_name = '_'.join(('ref', str(ref_sub_index).zfill(4), str(ref_index).zfill(4) + '.edf'))
                 file_name = os.path.join(self.folder, file_name)
                 file_desc.write(file_name)
+            # simulate two refHST generated by tomwer
+            file_desc = fabio.edfimage.EdfImage(
+                data=numpy.random.random((self.det_height, self.det_width)))
+            file_name = 'refHST' + str(ref_index).zfill(4) + '.edf'
+            file_name = os.path.join(self.folder, file_name)
+            file_desc.write(file_name)
+
         # create one dark with 10 frames
         file_desc = fabio.edfimage.EdfImage(
             data=numpy.random.random((self.det_height, self.det_width)))
@@ -206,12 +214,14 @@ class TestOriDarksFlats(unittest.TestCase):
 
     def testFlatsOri(self):
         ref_urls = (self.scan.get_refs_url(prefix='ref', scan_path=self.scan.path))
-        self.assertEqual(len(ref_urls), 40)
+        self.assertEqual(len(ref_urls), 42)
         # checks some random files
         file_paths = [url.file_path() for url in ref_urls.values()]
         for ref_file in ('ref_0000_1500.edf', 'ref_0004_0000.edf', 'ref_0019_1500.edf'):
             ref_full_path = os.path.join(self.scan.path, ref_file)
             self.assertTrue(ref_full_path in file_paths)
+        ref_urls = (self.scan.get_refs_url(prefix='refHST', scan_path=self.scan.path))
+        self.assertEqual(len(ref_urls), 2)
 
     def testDarksOri(self):
         darks = self.scan.get_darks_url(prefix='darkend',